Phylogenetic

Molecular Phylogenetics An introduction to computational methods and tools for analyzing evolutionary relationships Karen Dowell Math 500 Fall 2008 Molecular Phylogenetics Karen Dowell 1 Abstract Molecular phylogenetics applies a combination of molecular and statistical techniques to infer evolutionary relationships among organisms or genes.This review paper provides a general introduction to phylogenetics and phylogenetic trees, describes some of the most common computational methods used to infer phylogenetic information from molecular data, and provides an overview of some of the many different online tools available for phylogenetic analysis. In addition, several phylogenetic case studies are summarized to illustrate how researchers in different biological disciplines are applying molecular phylogenetics in their work. Introduction to Molecular PhylogeneticsThe similarity of biological functions and molecular mechanisms in living organisms strongly suggests that species descended from a common ancestor. Molecular phylogenetics uses the structure and function of molecules and how they change over time to infer these evolutionary relationships. This branch of study emerged in the early 20th century but didn’t begin in earnest until the 1960s, with the advent of protein sequencing, PCR, electrophoresis, and other molecular biology techniques.Over the past 30 years, as computers have become more powerful and more generally accessible, and computer algorithms more sophisticated, researchers have been able to tackle the immensely complicated stochastic and probabilistic problems that define evolution at the molecular level more effectively. Within past decade, this field has been further reenergized and redefined as whole genome sequencing for complex organisms has become faster and less expensive. As mounds of genomic data becomes publically available, molecular phylogenetics is continuing to grow and find new applications. 4, 10, 17, 20, 22] The primary objective of molecular phylogenetic studies is to recover the order of evolutionary events and represent them in evolutionary trees that graphically depict relationships among species or genes over time. This is an extremely complex process, further complicated by the fact that there is no one right way to approach all phylogenetic problems. Phylogenetic data sets can consist of hundreds of different species, each of which may have varying mutation rates and patterns that influence evolutionary change.Consequently, there are numerous different evolutionary models and stochastic methods available. The optimal methods for a phylogenetic analysis depend on the nature of the study and data used. [5, 19, 20] Molecular Evolution: Beyond Darwin Evolution is a process by which the traits of a population change from one generation to another. In On the Origin of Species by Means of Natural Selection, Darwin proposed that, given overwhelming evidence from his extensive comparative analysis of living specimens and fossils, all living organisms descended from a common ancestor.The book’s only illustration (see Figure 1) is a tree-like structure that suggests how slow and successive modifications could lead to the extreme variations seen in species today. [11, 27] Molecular Phylogenetics Karen Dowell 2 Figure 1. Evolution Defined Graphically. The sole illustration in Darwin’s Origin of the Species uses a tree-like structure to describe evolution. This drawing shows ancestors at the limbs and branches of the tree, more recent ancestors at its twigs, and contemporary organisms at its buds. [34] Darwin’s theory of evolution is based on three underlying principles: ariation in traits exist among individuals within a population, these variations can be passed from one generation to the next via inheritance, and that some forms of inherited traits provide individuals a higher chance of survival and reproduction than others. [11] Although Darwin developed his theory of evolution without any knowledge of the molecular basis of life, it has since been determined that evolution is actually a molecular process based on genetic information, encoded in DNA, RNA, and proteins. At a molecular level, evolution is driven by the same types of mechanisms Darwin observed at the species level.One molecule undergoes diversification into many variations. One or more of those variants can be selected to be reproduced or amplified throughout a population over many generations. Such variations at the molecular level can be caused by mutations, such as deletions, insertions, inversions, or substitutions at the nucleotide level, which in turn affect protein structure and biological function. [11, 22] What is a Phylogeny? According to modern evolutionary theory, all organisms on earth have descended from a common ancestor, which means that any set of species, extant or extinct, is related.This relationship is called a phylogeny, and is represented by phyloge netic trees, which graphically represent the evolutionary history related to the species of interest (see Figure 2). Phylogenetics infers trees from observations about existing organisms using morphological, physiological, and molecular characteristics. Figure 2. Phylogeny of Mammalia. This phylogenetic tree shows the evolutionary relationships among six orders of Mammalian species (taxa). Taxa listed in grey are extinct. The â€Å"tree of life† represents a phylogeny of all organisms, living and extinct.Other, more specialized species and molecular phylogenies are used to support comparative studies, test biogeographic hypotheses, evaluate mode and timing of speciation, infer amino acid sequence of extinct proteins, track the evolution of diseases, and even provide evidence in criminal cases. [19] Molecular Phylogenetics Karen Dowell 3 Understanding Phylogenetic Trees Before exploring statistical and bioinformatic methods for estimating phylogenetic trees from molecular data , it’s important to have a basic familiarity of the terms and elements common to these types of trees. See Figure 3. ) Figure 3. Basic elements of a phylogenetic tree. Phylogenetic trees are composed of branches, also known as edges, that connect and terminate at nodes. Branches and nodes can be internal or external (terminal). The terminal nodes at the tips of trees represent operational taxonomic units (OTUs). OTUs correspond to the molecular sequences or taxa (species) from which the tree was inferred. Internal nodes represent the last common ancestor (LCA) to all nodes that arise from that point.Trees can be made of a single gene from many taxa (a species tree) or multi-gene families (gene trees). [1, 10] A tree is considered to be â€Å"rooted† if there is a particular node or outgroup (an external point of reference) from which all OTUs in the tree arises. The root is the oldest point in the tree and the common ancestor of all taxa in the analysis. In the absence of a known outgroup, the root can be placed in the middle of the tree or a rootless tree may be generated. Branches of a tree can be grouped together in different ways. (See Figure 4. ) Figure 4.Groups and associations of taxonomical units in trees. A monophyletic group consists of an internal LCA node and all OTUs arising from it. All members within the group are derived from a common ancestor and have inherited a set of unique common traits. A paraphyletic group excludes some of its descendents (for examples all mammals, except the marsupialia Molecular Phylogenetics Karen Dowell 4 taxa). And a polyphyletic group can be a collection of distantly related OTUs that are associated by a similar characteristic or phenotype, but are not directly descended from a common ancestor. 1, 17] Trees and Homology Evolution is shaped by homology, which refers to any similarity due to common ancestry. Similarly, phylogenetic trees are defined by homologous relationships. Paralogs are homologous s equences separated by a gene duplication event. Orthologs are homologous sequences separated by a speciation event (when one species diverges into two). Homologs can be either paralogs or orthologs. [1, 11, 22] Molecular phylogenetic trees are drawn so that branch length corresponds to amount of evolution (the percent difference in molecular sequences) between nodes. 1, 19] Figure 5. Understanding paralogs and orthologs. Paralogs are created by gene duplication events. (See Figure 5. ) Once a gene has been duplicated, all subsequent species in the phylogeny will inherit both copies of the gene, creating orthologs. Interestingly, evolutionary divergence of different species may result in many variations of a protein, all with similar structures and functions, but with very different amino acid sequences. Phylogenetic studies can trace the origin of such proteins to an ancestral protein family or gene. [1, 22] Figure 6. Mirror Phylogenies.Gene A and Gene A1 are paralogs, whereas all i nstances of Gene A are orthologs of each other in different Canid species. One way to ensure that paralogs and orthologs are appropriately referenced in a phylogenetic tree, and guard against misrepresentation due to missing or incomplete taxonomic information is to generate mirror phylogenies (see Figure 6) in which paralogs serve as each other’s outgroup. [1, 4, 19, 22] Estimating Molecular Phylogenetic Trees Molecular phylogenetic trees are generated from character datasets that provides evolutionary content and context.Character data may consist of biomolecular sequence alignments of DNA, RNA, or amino acids, molecular markers, such as single nucleotide polymorphisms (SNPs) or restriction fragment length polymorphisms (RFLPs), morphology data, or information on gene order and content. Evolution is modeled as a process that changes the state of a character, such as the type of nucleotide (AGTC) at a Molecular Phylogenetics Karen Dowell 5 specific location in a DNA sequence ; each character is a function that maps a set of taxa to distinct states. 1, 19] Note that most of the examples in this paper use DNA sequences as character data, but trees can be accurately estimated from many different types of molecular data. Figure 7. Evolution of a DNA Sequence Figure 7 illustrates how a molecular sequence might evolve over time as a result of multiple mutations that results small, but evolutionarily important changes in a nucleotide sequence. At the protein level, these changes may not initially affect protein structure or function, but over time, they may eventually shape a new purpose for a protein within divergent species. 10, 19, 22] OTUs can be used to build an unrooted phylogenetic tree that clearly depicts a path of evolutionary change. Steps in Phylogenetic Analysis Although the nature and scope of phylogenetic studies may vary significantly and require different datasets and computational methods, the basic steps in any phylogenetic analysis remain t he same: assemble and align a dataset, build (estimate) phylogenetic trees from sequences using computational methods and stochastic models, and statistically test and assess the estimated trees. 4, 19, 20] Assemble and Align Datasets The first step is to identify a protein or DNA sequence of interest and assemble a dataset consisting of other related sequences. For example, to explore relationships among different members of the Notch family of proteins, one might select DNA sequences for Notch1 through Notch4, in different species, such as human, dog, rat, and mouse, then perform a multiple sequence alignment to identify homologies. [1, 10, 13, 19, 20] There are a number of free, online tools available to simplify and streamline this process. DNA sequences of interest can be retrieved using NCBI BLAST or similar search tools.When evaluating a set of related sequences retrieved in a BLAST search, pay close attention to the score and E-value. A high score indicates the subject seque nce retrieved with closely related to the sequence used to initiate the query. The smaller the E-value, the higher the probability that the homology reflects a true evolutionary relationship, as opposed to sequence similarity due to chance. As a general rule, sequences with E-values less than 10-5 are homologs of a query sequence. [10] Once sequences are selected and retrieved, multiple sequence alignment is created.This involves arranging a set of sequences in a matrix to identify regions of homology. Typically, gaps (one or more spaces in the alignment) are introduced in one or more sequences to represent insertions or deletions in the molecular code that may have occurred over time. Effective multiple sequence alignment hinged on gap analysis—determining where to insert gaps and how large to make them. There are many websites and software programs, such as ClustalW, MSA, MAFFT, and T-Coffee, designed to perform multiple sequence on a given set of molecular data. ClustalW i s currently the most mature and most widely used. 1, 10. 19] Molecular Phylogenetics Karen Dowell 6 Building Phylogenetic Trees To build phylogenetic trees, statistical methods are applied to determine the tree topology and calculate the branch lengths that best describe the phylogenetic relationships of the aligned sequences in a dataset. Many different methods for building trees exist and no single method performs well for all types of trees and datasets. The most common computational methods applied include distance-matrix methods, and discrete data methods, such as maximum parsimony and maximum likelihood. 4, 17, 20] There are several software packages, such as Paup*, PAML, PHYLIP, that apply most popular methods. [4] Paup* is a commercially available program that implements a wide variety of methods for phylogenetic inference, including maximum likelihood analysis for DNA data using different models. Paup* also includes a set of exact and heuristic methods for searching optimal trees. PAML (Phylogenetic Analysis by Maximum Likelihood) is open-access set of programs for phylogenetic analysis and evolutionary model comparison.PAML includes many advanced models—DNA- and AAbased models as well as codon-based models that can be used to detect positive selection. Many of the programs in PAML can model heterogeneity of evolutionary rates among sequence sites using ? distributions, and evolutionary dynamics of different sequence regions (concatenated gene sequences). PHYLIP is another large suite of open-access programs for phylogenetic inference that estimates trees using numerous methods, including pairwise distance, maximum parsimony, and maximum likelihood.The maximum likelihood programs can handle a few simple stochastic models and have good tree searching capabilities. PHYLIP is generally considered good educational software for novice phylogeneticists. Distance-Matrix Methods Distance matrix methods compute a matrix of pairwise â€Å"distances† between sequences that approximate evolutionary distance. Distance-based methods tend to be in polynomial time and are quite fast in practice. These methods use clustering techniques to compute evolutionary distances, such as the number of nucleotide or amino acid substitutions between sequences, for all pairs of taxa.They then construct phylogenetic trees using algorithms based on functional relationships among distance values. There are several different distance-matrix methods, including the Unweighted Pair-Group Method with Arithmetic Mean (UPGMA), which uses a sequential clustering algorithm; the Transformed Distance Method, which uses an outgroup as a reference, then applies UPGMA; the Neighbor-Relations Method, which applies 4point condition to adjust the distance matrix, then applies UPGMA; and the Neighbor-Joining Method, which arranges OTUs in a star, the finds neighbors sequentially to minimize total length of tree. 4, 17] The following section on the UPGMA method prov ides a more detailed example of how distance-matrix methods work. UPGMA Method UPGMA produces rooted trees for which the edge lengths can be viewed as times measured by a molecular clock with a constant rate. This method uses a sequential clustering algorithm to identify two OTUs that are most similar (meaning they have the shortest evolutionary distance and are most similar in sequence) and treat them as a single new composite OTU. This process is repeated iteratively until only two OTUs remain.The algorithm defines the distance (d) between two clusters Ci and Cj as the average distance between pairs of sequences from each cluster: Molecular Phylogenetics Karen Dowell 7 Where |Ci| and |Cj| are the number of sequences in clusters i and j. This sequential clustering process is visually described in Figure 8. In this example, the two most homologous sequences are 1 and 2. They are clustered into a new composite parent node (6), and the branch lengths (t1 and t2) are defined as 1/2d1,2 . The next step is to search for the closest pair among remaining sequences and node 6.Pair 4 and 5 are identified and clustered into a new parent node (7), and the branch length for t4 and t5 is calculated. [4, 17] Figure 8. Sequential clustering of sequences using the UPGMA method. [17] In this interactive process, parent node 8 is created from pairs 7 and 3, and parent node 9 is created by clustering nodes 6 and 8. [4, 17] Thus, all sequences are clustered into a single evolutionary tree. The total time (t9) can be calculated as: D6,8 = 1/6 (d1,3 + d1,4 + d1,5 + d2,3 + d2,4 +d2,5)Discrete Data Methods Discrete data methods examine each column of a multiple sequence alignment dataset separately and search for the tree that best represents all this information. Although distance-based methods tend to be much faster than discrete data methods, they typically yield little information beyond the basic tree structure. Discrete data analyses, on the other hand, are information rich. The se methods produce a separate tree for each column in the alignment, so it is possible to trace the evolution for specific elements within a given sequence, such as catalytic sites or regulatory regions. 10, 17, 19, 20) Commonly used discrete data methods include maximum parsimony, which searches for the most parsimonious tree that requires the least number of evolutionary changes to explain differences observed, maximum likelihood, which requires a probabilistic model for the process of nucleotide substitution, and Bayesian MCMC, which also requires a stochastic model of evolution, but creates a probability distribution on a set of trees or aspects of evolutionary history. [17, 19, 20] Discrete data methods are generally considered to produce the best estimates of evolutionary history.However, these methods can be computationally expensive, and it can take weeks or months to obtain a reasonable level of accuracy for moderate to large datasets with 100 or more OTUs. [19] Molecular P hylogenetics Maximum Parsimony Karen Dowell 8 Among the most widely used tree-estimation techniques, maximum parsimony applies a set of algorithms to search for the tree that requires the minimum number of evolutionary changes observed among the OTUs in the study. For example, Figure 9 lists four sample sequences from which phylogenetic trees could be inferred using maximum parsimony.Site Seq 1 2 3 4 1 A A A A 2 A G G G 3 G C A A 4 A C T G 5 G G A A 6 T T T T 7 G G C C 8 C C C C 9 A G A G Figure 9. Sample sequences for a maximum parsimony study [17] Maximum parsimony algorithms identify phylogenetically informative sites, meaning the site favors some trees over others. Consider the sequences in Figure 9: Site 1 is not informative, because all sequences at that site (in column 1) are A (Adenine), and no change in state is required to match any one sequence (1-4) to another.Similarly, Site 2 is not informative because all three trees require one change and there is no reason to favor one tree over another. Site 3 is not informative because all three trees require two changes. (See Figure 10). Figure 10. Site 3 trees all require one evolutionary change. [17] Site 4 is not informative because all three trees require three changes. No one tree can be identified as parsimonious. (See Figure 10 Figure 11. Site 4 trees all require three evolutionary changes. [17] Site 5 is informative because one tree requires only one nucleotide change, whereas the other two trees require 2 changes.In Figure 12, the first tree on the left, which requires only one nucleotide change, is identified as the maximum parsimony tree. Figure 12. Site 5 trees vary in the number of evolutionary changes required. [17] Molecular Phylogenetics Maximum Likelihood Karen Dowell 9 The maximum likelihood method requires a probabalistic model of evolution for estimating nucleotide substitution. This method evaluates competing hypotheses (trees and parameters) by selecting those with the highest likeliho od, meaning those that render the observed data most plausible. The ikelihood of a hypothesis is defined as the probability of the data given that hypothesis. In phylogeny reconstruction, the hypotheses are the evolutionary tree (its topology and branch lengths) and any other parameters of the evolutionary model. [17, 20] The likelihood calculations required for evolutionary trees are far from straightforward and usually require complex computations that must allow for all possible unobserved sequences at the LCA nodes of hypothesized trees. This method specifies the transition probability from one nucleotide state to another in a time interval in each branch.For example, for a one-parameter model with rate of substitution ? per site per unit time, the probability that the nucleotide at time t is i is: The probability that the nucleotide at time t is j is: To set up a likelihood function, given x as the ancestral node and y and z as internal nodes, the probability of observing nucle otides i, j, k, l at the tips of the tree is computed as: Pxl(t1+t2+t3)Pxy(t1)Pyk(t2+t3)Pyz(t2)Pzi(t3)Pzj(t3) For the ancestral node (root) x, the probability of having nucleotide l in sequence 4 is calculated as: Pxl(t1+t2+t3)Because x, y, and z can be any one of four nucleotides (ACGT), it is necessary to sum over all possibilities to obtain the probability of observing the configuration of nucleotides i, j, k, l, in sequences 1, 2, 3, 4, for a given hypothetical tree (see Figure 13. ). This likelihood probability is calculated as: h(I,j,k,l)= [? gxPxl(t1+t2+t3)] [? Pxy(t1)Pyk(t2+t3)] [? Pyz(t2)Pzi(t3) Pzj(t3)] The appropriate likelihood function depends on the hypothetical tree and the evolutionary model used. (See Figure 13. ) [17] Figure 13. Different types of model trees for the derivation of the maximum likelihood function. 17] Molecular Phylogenetics Stochastic Models of Evolution Karen Dowell 10 Evolutionary changes in molecular sequences result from mutations, some of whic h occur by chance, others by natural selection. Rates of change can also differ among OTUs, depending on several factors ranging from GC content to genome size. To accurately estimate phylogenetic trees, assumptions must be made about the substitution process and those assumptions must be stated in the form of a stochastic evolutionary model. These probabilistic models are used to rank trees according to likelihood: P(data|tree).From a Bayesian perspective, they rank trees according to a posterior probability: P(tree|data). [17, 20] The objective of probabilistic models is to find likelihood or posterior probability of a particular taxonomic feature, then define and compute: P(x? |T,t ? ) Where x ? is xj for j=1†¦n, T is a tree with n leaves with sequence j at leaf j, and t ? are tree edge lengths. [17] A few popular stochastic models of evolution include the single parameter Jukes-Cantor (JC) method, Kimura 2-parameter (K2P), Hasegawa-Kishino-Yano (HKY), and Equal-Input.Some s oftware programs, such as Paup*, will automatically use a default model for the tree estimation method chosen. The JC method is the easiest one to comprehend, because it assumes that if a site changes its state, it changes with equal probability to the other states. This is not very realistic, however, as some sites are known to evolve more rapidly than others, and some sites may be invariable and not allowed to change at all. Determining how best to select the appropriate model is a topic of another paper (or papers) as there is no one model that incorporates all mutation rules and patterns across different species and macromolecules. 4, 17, 20] Hidden Markov Models Profile hidden Markov models (HMMs) are a form of Bayesian network that provides statistical models of the consensus structure of a sequence family. Gary Churchill at The Jackson Lab was the first evolutionary geneticist to propose using profile HMMs to model rates of evolution. Many software packages and web services n ow apply HMMs to estimate phylogenetic relationships. [8] In the HMM format, each position in the model corresponds to a site in the sequence alignment. For each position, there are a number of possible states, each of which corresponds to a different rate of evolution.In addition, transitions between all possible rate-states at adjacent positions. Transition probabilities capture any tendency for patterns of rates to occur in successive sites. [2, 4] Assessing Trees Tree estimating algorithms generate one or more optimal trees. This set of possible trees is subjected to a series of statistical tests to evaluate whether one tree is better than another – and if the proposed phylogeny is reasonable. Common methods for assessing trees include the Bootstrap and Jackknife Resampling methods, and analytical methods, such as parsimony, distance, and likelihood.To illustrate how these methods are used, consider the steps involved in a bootstrap analysis. Bootstrap Analysis A bootstra p is a statistical method for assessing trees that takes its name from the fact that it can â€Å"pull itself up by its bootstraps† and generate meaningful statistical distributions from almost nothing. Using bootstrap analysis, distributions that would otherwise be difficult to calculate exactly are estimated by repeated creation and analysis of artificial datasets. In a Non-parametric bootstrap, artificial datasets Molecular Phylogenetics Karen Dowell 11 generated by resampling from original data.In a parametric bootstrap, data is simulated according to hypothesis tested. The objective of any bootstrap analysis is to test whether the whole dataset supports the tree. [1, 4, 17] Figure 14 illustrates the basic steps in any bootstrap analysis. Sample datasets are automatically generated from an original dataset. Trees are then estimated from each sample dataset. The results are compiled and compared to determine a bootstrap consensus tree. Figure 14. Steps in a phylogenetic tr ee bootstrap analysis. [1] Phylogenetic Analysis Tools There are several good online tools and databases that can be used for phylogenetic analysis.These include PANTHER, P-Pod, PFam, TreeFam, and the PhyloFacts structural phylogenomic encyclopedia. Each of these databases uses different algorithms and draws on different sources for sequence information, and therefore the trees estimated by PANTHER, for example, may differ significantly from those generated by P-Pod or PFam. As with all bioinformatics tools of this type, it is important to test different methods, compare the results, then determine which database works best (according to consensus results, not researcher bias) for studies involving different types of datasets.In addition, to the phylogenetic programs already mentioned in this paper, a comprehensive list of more than 350 software packages, web-services, and other resources can be found here: http://evolution. genetics. washington. edu/phylip/software. html. PANTHER ( pantherdb. org) Protein ANalysis Through Evolutionary Relationships, known by its acronym PANTHER, is a library of protein families and subfamilies indexed by function. Panther version 6. 1 contains 5547 protein families. Molecular Phylogenetics Karen Dowell 12It categorizes proteins by evolutionary related proteins (families) and related proteins with same function (subfamilies). [8, 21, 26] PANTHER is composed of both a library and index. The library is a collection of â€Å"books† that represent a protein family as a collection of multiple sequence alignments, HMMs, and a family phylogenetic tree. Functional divergence within the tree is represented by dividing the parent tree into child trees and HMMs based on shared functions. These subfamilies enable database curators to more accurately capture functional divergence of protein sequences as inferred from genomic DNA. 25, 26] PANTHER database entries are annotated to molecular function, biological process and pathway with a proprietary PANTHER/X ontology system, which is supposed to be easier to understand than the more global standard Gene Ontology (GO). Database entries in PANTHER are generated through clustering of UniProt database using a BLAST-based similarity score. Trees are automatically generated based on multiple sequence alignments and parameters of the protein family HMMs using the Tree Inferred from Profile Score (TIPS) clustering algorithm.Scientific curators review all family trees, annotate each tree, and determine how best to divide them into subtrees using a tree-attribute viewer that tabulates annotations for sequences in a tree. In addition, trees and subfamilies are manually cross-checked and validated by curators. [25, 26] P-POD (ortholog. princeton. edu) The Princeton Protein Orthology Database (P-POD) combines results from multiple comparative methods with curated information culled from the literature.Designed to be a resource for experimental biologists seeking evolutionary information on genes on interest, P-POD employs a modular architecture, based on their Generic Model Organism Database (GMOD). P-POD can be accessed from their web service or downloaded to run on local computer systems. [12] P-POD accepts FASTA-formatted protein sequences as input, and performs comparative genomic analyses on those sequences using OrthoMCL and Jaccard clustering methods. The P-POD database contains both phylogenetic information and manually curated experimental results.The site also provides many links to sites rich in human disease and gene information. This tool may be particularly helpful for bioinformaticists and statisticians developing comparative genomic database tools and resources. Pfam (pfam. sanger. ac. uk/) PFam is a collection of protein families represented by multiple sequence alignments and HMMs. It contains models of protein clans, families, domains, and motifs, and uses HMMs representing conserved functional and structural domains. It is a large, widely used, actively curated mature database that has been available online since 1995.Pfam can be used to retrieve the domain architectures for a specific protein by conducting a search using a protein sequence against the Pfam library of HMMs. This database is also helpful for proteomes and protein domain architecture analysis. [6, 8, 24] There are two versions of the Pfam database: Pfam–B is generated automatically from ProDom, using PsiBLAST, an open access bioinformatics tool available through NCBI for identifying weak, but biologically relevant sequence similarities. Pfam-A is hand-curated from custom multiple sequence alignments. Pfam protein domain families are clustered with Mkdom2, and aligned with ProDomAlign.ProDom is a comprehensive set of protein domain families automatically generated from the SWISSPROT and TrEMBL sequence databases. Mkdom2 is a ProDom program used to make ProDom family clusters. Protein domain families in ProDom were aligned using an improved parallelized program called Molecular Phylogenetics Karen Dowell 13 ProDomAlign, developed in C++ using OpenMP. ProDomAlign is based on MultAlign, a program well suited for aligning very large sequence families with thousands of associated sequences. As of early 2008, Pfam matched 72 percent of known proteins sequences, and 95 percent of proteins for which there is a known structure.Within the Pfam database, 75 percent of sequences will have one match to Pfam-A, 19 percent to Pfam-B. There are also two versions of Pfam-A and Pfam-B. Pfam-ls handles global alignments, and Pfam-fs is optimized for local alignments. Interestingly, Pfam entries can be classified as â€Å"unknown,† but that doesn’t mean the protein is undocumented. Unknown entries can be proteins for which some information is known, but it has not been fully researched or cannot be adequately annotated. For example, Pfam entry PFO1816 is a LeucineRich Repeat Variant (LRV), which has a known structure (1LRV ) available in the Protein Databank (pdb. rg). LRV repeat regions, which are found in many different proteins, are often involved in cell adhesion, DNA repair, and hormone reception—but identification of an LRV within a sequence encoding a protein doesn’t specifically reveal the protein’s function. For studies involving a large number of protein searches, it may be more convenient to run Pfam locally on a client machine. The standalone Pfam system requires the HMMER2 software, the Pfam HMM libraries and a couple of additional files from the Pfam website to be installed on the client machine. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis. ) Once the initial search is complete, researchers can go to the Pfam website to further analyze select number of sequences using additional features on website. [6, 8, 24] TreeFam (TreeFam. org) TreeFam is a curated database of phylogenetic trees and orthology predictions f or all animal gene families that focuses on gene sets from animals with completely sequenced genomes. Orthologs and paralogs are inferred from phylogenetic tree of gene family.Release 4 contains curated trees for 1314 families and automatically generated trees for another 14351 families. [16, 23] Like Pfam, TreeFam is a two-part database: TreeFam-B contains automatically generated trees, and TreeFam-A consists of manually curated trees. To automatically generate trees, an algorithm selects clusters of genes to create TreeFam-B â€Å"seeds† from core species with high-quality reference genome sequences, first using BLAST to rapidly assemble an initial list of possible matches, then HMMER to expand and filter probable sequence matches for each TreeFam B seed family.The filtered alignment is fed into a neighbor-joining algorithm and a tree is constructed based on amino acid mismatch distances. For TreeFam version 4, the most current release, five â€Å"clean† family trees were built for each TreeFam B seed, two using a maximum likelihood tree generated using PHYML (one based on the protein alignment, the other on codon alignment), three using a neighbor joining tree, using different distance measurements based on codon alignments. 16, 23] Scientific curators then manually any correct errors (based on information in the literature) in automatically generated TreeFam-B trees. Curated TreeFam-B trees then become seeds for TreeFam-A trees. Clean TreeFam-A trees are build using three merging algorithms and bootstrapping to find the consensus tree of seven trees: two constrained maximum likelihood trees based on protein and codon alignment, and five unconstrained neighbor-joining trees generated using different distance measurements based on codon alignments.For both TreeFam-B and TreeFam-A families, orthologs and paralogs are inferred only from clean trees using Duplication/Loss Inference (DLI) algorithm that requires a species tree (NCBI taxonomy tree). [16, 23] Molecular Phylogenetics PhyloFacts (phylogenomics. berkeley. edu/phylofacts) Karen Dowell 14 PhyloFacts is an online phylogenomic encyclopedia for protein functional and structural classification. It contains more than 57,000 â€Å"books† for protein superfamilies and structural domains.Each book contains heterogenous data for protein families, including multiple sequence alignments, one or more phylogenetic trees, predicted 3-D protein structures, predicted functional subfamilies, taxonomic distributions, GO annotations, and PFAM domains. HMMs constructed for each family and subfamily permit novel sequences to be classified to different functional classes. [14] Unlike other databases mentioned in this paper, PhyloFacts seeks to correct and clarify annotation errors associated with computational methods for predicting protein function based on sequence homology.It uses a consensus approach that integrates many different prediction methods and sources of experimental data over an evolutionary tree. By applying evolutionary and structural clustering of proteins, PhyloFacts is able to analyze disparate datasets using multiple methods, identify potential errors in database annotations, and provide a mechanism for improving the accuracy of functional annotation in general. [14] PhyloFacts can be used to search for protein structure prediction or functional classification for a particular protein sequence.Researchers may also browse through protein family books and multiple sequence alignments, phylogenetic trees, HMMs and other pertinent information for proteins of interest. This webservice also provides many links to literature and other information sources. [14] Applied Molecular Phylogenetics Molecular phylogenetic studies have many diverse applications. As the amount of publically available molecular sequence data grows and methods for modeling evolution become more sophisticated and accessible, more and more biologists are incorporating phylog enetic analyses into their research trategy. Here’s a sampling of how molecular phylogenetics might be applied. Tracing the evolution of man In one case study, molecular phylogenetic techniques were used to compare and analyze variation in DNA sequences using modern human and Neanderthal mitochondrial DNA (mtDNA). For this study, 206 modern human mtDNAs and parts of two Neanderthal mtDNAs sequences derived from skeletal remains were used to generate an initial dataset. Genetic distance was first estimated using the Jukes-Cantor single parameter model.Then the Kimura 2-Parameter model was used to distinguish between transition (replacement of one purine with another purine or one pyrimidine with another pyrimidine) and transversion (replacement of one purine with a pyrimidine or vice versa) probabilities with Kimura 2parameter model. A phylogenetic tree representing primate evolution was generated using pairwise genetic distances between primate Hypervariable regions I and II of mtDNA. [3] Chasing an epidemic: SARS Using publically available genomic data, it is possible to reconstruct the progression of the SARS epidemic over time and geographically.To conduct this phylogenetic analysis, researchers used the neighborjoining method to construct a phylogenetic tree of spike proteins in various coronaviruses and identify the viral host (a Himalyan palm civet). They then obtained 13 SARs genome sequences with documented information on the date and location of the sample. The neighbor-joining method and a distance matrix based on Jukes-Cantor model, were used to generate an epidemic tree, from which it was possible to identify the origin (date and location) of the virus by observing progression of mutations over time. 3] Molecular Phylogenetics Barking up the right tree Karen Dowell 15 Phylogenetics is increasingly incorporated into biological and biomedical research papers. When the canine genome was published, researchers used sequence data to estimate a co mprehensive phylogeny of the canid family. Figure 15. Phylogenetic Tree of the Canid family This canid family phylogenetic tree is based on 15 kb of exon and intron sequence. It was constructed using the maximum parsimony method and represents the single most parsimonious tree.A good example of how phylogenies are referenced in the literature, this tree includes bootstrap values and Bayesian posterior probability values listed above and below internodes, respectively. Dashes indicate bootstrap values below 50%. In addition, divergence time in millions of years (Myr) is indicated for three nodes. [18] Seeing the Forest from the Trees Molecular phylogenetics is a broad, diverse field with many applications, supported by multiple computational and statistical methods. The sheer volumes of genomic data currently available (and rapidly growing) render molecular phylogenetics a key component of much biological research.Genome-scale studies on gene content, conserved gene order, gene expre ssion, regulatory networks, metabolic pathways, functional genome annotation can all be enriched by evolutionary studies based on phylogenetic statistical analyses. [19, 25 27] Molecular phylogenies have fast become an integral part of biological research, pharmaceutical drug design, and bioinformatics techniques for protein structure prediction and multiple sequence alignment. Although not all molecular biologists and bioinformaticians may be familiar with the techniques describedMolecular Phylogenetics Karen Dowell 16 in this paper, this is a rapidly growing and expanding field and there is ongoing need for novel algorithms to solve complex phylogeny reconstruction problems. References 1. Baldauf, SL (2003) â€Å"Phylogeny for the faint of heart: a tutorial. † Trends in Genetics, 19(6):345-351. 2. Brown, D, K Sjolander (2006) â€Å"Functional Classification Using Phylogenomic Inference. † PLos Computational Biology, 2(6):0479-0483. 3. Cristianini, N, and M Hahn (2007 ) Introduction to Computational Genomics: A Case Studies Approach.Cambridge University Press: Cambridge. 4. Durbin, R, S Eddy, A Krogh, G Mitchison (1998) Biological Sequence Analysis. Cambridge University Press: Cambridge. 5. Ewens, WJ, R Grant (2005) Statistical Methods in Bioinformatics. Springer Science and Business Media: New York. 6. Finn, RD, J Tate, J Mistry, PC Coggill, SJ Sammut, HR Hotz, G Ceric, K Forslund, SR Eddy, ELL Sonnhammer, A Bateman (2008) â€Å"The Pfam protein families database. † Nucleic Acids Research, 36:D281288. 7. Gabaldon, T (2008) â€Å"Large-scale assignment of orthology: back to phylogenetics? Genome Biology, 9:235. 1-235. 6. 8. Gollery, M. (2008) Handbook of Hidden Markov Models in Bioinformatics. CRC Press, Taylor & Francis Group: London. 9. Goodstadt, L, CP Ponting (2006) â€Å"Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human. † PLoS Computational Biology, 2(9):1134-1150. 10. Hall, BG. (2004 ) Phylogenetic Trees Made Easy: A How-To Manual, 2nd ed. Sinauer Associates, Inc. : Sunderland, MA. 11. Hartwell, LH, L Hood, ML Goldberg, AE Reynolds, LM Silver, RC Veres (2008) Genetics: From Genes to Genomes, 3rd Ed.McGraw-Hill: New York. 12. Heinicke, S, MS Livstone, C Lu, R Oughtred, F Kang, SV Angiuoli, O White, D Botstein, K Dolinski (2007) â€Å"The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists. † PLoS ONE, 8:e766. 1-15. 13. Kortschak, RD, R Tamme (2001) â€Å"Evolutionary analysis of vertebrate Notch genes. † Dev Genes Evol, 211:350-354. 14. Krishnamurthy, N, DP Brown, D Kirshner, K Sjolander (2006) â€Å"PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification. † Genome Biology, 7:R83. -13. 15. Kuzniar, A, RCHJ van Ham, S Pongor, JAM Leunissen (2008) â€Å"The quest for orthologs: finding the corresponding gene across genomes. † Trends in G enetics, 24(11):539-551. Molecular Phylogenetics Karen Dowell 17 16. Li, H, A Coghlan, J Ruan, LJ Coin, JK Heriche, L Osmotherly, R Li, T Liu, Z Zhang, L Bolund, GKS Wong, W Zheng, P Dehal, J Wang, R Durbin (2006) â€Å"TreeFam: a curated database of phylgenetic trees of animal gene families. † Nucleic Acids Research, 34:D573-580. 17. Li, WH (1997) Molecular Evolution. Sinauer Associates: Sunderland, MA. 18.Lindblad-Toh, K, CM Wade, TS Mikkelsen, EK Karlsson, DB Jaffe, M Kamal, M Clamp, JL Chang, EJ Kulbokas III, MC Zody, E Mauceli, X Xie, M Breen, RK Wayne, EA Ostrander, CP Ponting, F Galibert, DR Smith, PJ deJong, E Kirkness, P Alvarez, T Biagi, W Brockman, J Butler, C Chin, A Cook, J Cuff, MJ Daly, D DeCaprio, S Gnerre, M Grabherr, M Kellis, M Kleber, C Bardeleben, L Goodstadt, A Heger, C Hitte, L Kim, KP Koepfli, HG Parker, JP Pollinger, SMJ Searle, NB Sutter, R Thomas, C Webber, ES Lander (2005) â€Å"Genome Sequence, Comparative Analysis and Haplotype Structure of the Domestic Dog.Nature, 438:803-819. 19. Linder, CR, T Warnow (2005) â€Å"An overview of phylogeny reconstruction. † In the Handbook of Computational Molecular Biology, Chapman and Hall/CRC Computer & Information Science. 20. Lio, P, N Goldman (1998) â€Å"Models of Molecular Evolution and Phylogeny. † Genome Research, 8:12331244. 21. Mi, H, N Guo, A Kejariwal, PD Thomas (2007) â€Å"PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Research, 35:D247-252. 22. Patthy, Laszlo. (1999) Protein Evolution. Blackwell Science, Ltd: Malden, MA. 23. Ruan, J, H Li Z Chen, A Coghlan, LJM Coin, Y Guo, JK Heriche, Y Hu, K Kristiansen, R Li, T Liu, A Mose, J Qin, S Vang, AJ Vilella, A Ureta-Vidal, L Bolund, J Wang, R Durbin (2008) â€Å"TreeFam: 2008 Update. † Nucleic Acids Research, 36:D735-740. 24. Sammut, SJ, RD Finn, A Bateman (2008) â€Å"Pfam 10 years on: 10000 families and still growing. â €  Briefings in Bioinformatics, 9(3):210-219. 5. Thomas, PD, A Kejariwal, N Guo, H Mi, MJ Campbell, A Muruganujan, B Lazareva-Ulitsky (2006) â€Å"Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. † Nucleic Acids Research, 34:W645-650. 26. Thomas, PD, MJ Campbell, A Kejariwal, H Mi, B Karlak, R Daverman, K Diemer, A Muruganujan, A Narechania. â€Å"PANTHER: A Library of Protein Families and Subfamilies Indexed by Function. † Genome Research, 13:2129-2141. 27.Warnow, T (2004) â€Å"Computational Methods in Phylogenetics† Computational Systems Biology Conference, Stanford, CA 28. Whelan, S, P Lio, N Goldman (2001) â€Å"Molecular phylogenetics: state of the art methods for looking into the past. † Trends in Genetics, 17(5):262-272. Molecular Phylogenetics Karen Dowell 18 Appendix Website Resources Phylogeny Programs. A University of Washington site formerly supported by the National Science Foundation. http://www. evolution. genetics. washington. edu/phylip/software. tml TreeFam Tree Families Database. http://wwww. treefam. org Protein Analysis Through Evolutionary Relationships (PANTHER) Classification System. http://www. pantherdb. org. 29. Pfam Database of Protein Families. http://pfam. sanger. ac. uk 30. Princeton Protein Orthology Database (P-POD). http://ppod. princeton. edu 31. Wikipedia. http://en. wikipedia. org/wiki/Tree_of_life(science) Cover Page The cover image is from a phylogeny of canid species that appeared in Lindblad-Toh et al, 2005. [18]

Role of Women in Ancient Egypt

Thesis: Women in Ancient Egypt had numerous amounts of roles during Ancient History. What was the Role of a Woman in Ancient Egypt? I. Legal Rights of an Egyptian Woman A. Equal with men 1. Right to possess property and dispose of it 2. Often added threats and curses against people who tried to violate their rights B. Divorce 1. A letter describing how a man announced his intention to divorce his wife. 2. Women kept their own property C. Property 1. Sell, Buy Own. 2. Leave it to whomever she wanted. D.Legal Rights in Open Court 1. Right to bring lawsuits against anyone 2. Won legal cases without gender-bias II. Jobs A. Female Rulers 1. Ahhotep a. Wife of Segnenre-Taa and mother of Kamose and Ahmose b. Presented with the Order of Valor and venerated as the mother of the heroes 2. Ahmose-Nefertari a. Sister and wife of King Ahmose the First b. Presented with patron deities of the villages 3. Queen Tiye a. Wife of Amenhotep the Third and mother of Akhenaten b. Became Royal Wife favored by the King . Nefertiti a. Wife of Akhenaten b. Supported her husband and all his reforms, gave him 6 daughters 5. Nefertari a. Wife of Ramesses the Second b. Had the most beautiful tomb in the Valley of the Queens B. Enslavement 1. Hired themselves 2. Served for royalty C. Medicine III. Role of Women A. Child Care B. Senior Women in Charge if Household shopping C. Servants IV. Marriage A. Right to decide official Marriage B. Becoming Pregnant gained respect C. First duty was to be a good wife and mother

Comparative public sector management Essay Example | Topics and Well Written Essays - 2250 words

Comparative public sector management - Essay Example The elements of public management are tools that maximise efficiency of public management and are applicable to the private and public domains. There are many theories that provide a framework for public policy, and their application is varied depending on the context (Khaleghian & Gupta 2005, pp 1083-1099). Public policy is often characterised by dynamic, complex and interactive systems. It is through these systems that the problems affecting the public are identified and solved. The most basic solutions in this line are usually the formulation of new policies that reform the existing ways of doing things and as such increase the connectedness of the government and other players to the public. Using a theoretic approach to formulation and implementation of public policy prevents the use of fantasy, unreal and phantasm approaches to service to the public (Kapucu 2009, pp 1187-1190). Phallocentric perspective refers to the concept that directs perceptive as predominantly male-oriented of favouring. Some of the public policies in education especially in areas where inequalities in education have been an issue have been seen as inclined towards favouring men. A feministic approach in the opposite of this, it refers to the recognition of women as an important and independent entity in the development. Free primary education in Australia is a public sector policy that has been effective in ensuring a boost to the females who missed education opportunities in the past due to cultural and economic barriers (Kapucu 2009). In is very necessary that public policies are set aside from politics. This is because most of the political activities are designed to provide administrative powers, and rule over people, the public policy, on the other hand, are meant to provide public service and management in a non-profit approach from the government and other stakeholders in the selected issue. The

QUESTION 3 Essay Example | Topics and Well Written Essays - 500 words

QUESTION 3 - Essay Example Companies can adapt the principles into their policies, rules, and regulations to enhance their performance. Handling these obstacles and balancing the risks with the company growth and return goals to avoid facing challenges from uncertainty, â€Å"Enterprise â€Å" (2004) outlines internal environment, objective setting, event identification, risk assessment, information and communication, risk response, control activities, and monitoring as the eight principal factors warranting attention in that order: (1) ERM helps the company to prevent risk by creating a good environment within the firm. The risk will be identified by including risk management philosophy, risk appetite, integrity and will be monitored by the firm’s people. (2) Management should set up the objectives before identifying the risk to ensure that it aligns with the company’s mission and risk appetite is appropriately factored in. (3) A company should identify both internal and external events that have an impact on its success and distinguish between risks and opportunities. (4) A company can deal with and respond to the risks effectively by setting up and implementing policies and procedures. (5) The company should identify, capture, and communicate the relevant information across the organization in a suitable format and timeframe so that its workforce has total clarity and are accountable to their duties. (6) Management can decide a set of actions to respond to risks by avoiding, accepting, reduci ng, or sharing risk along the company’s risk tolerances guideline and risk appetite. (7) In order to manage the risks, the company should analyze the likelihood and impact of them and evaluate on an inherent and a residual basis. (8) Dynamically monitoring the whole process of activities by independent evaluations, and modifying some points when necessary represents the ultimate flexibility of ERM, rendering it complete and effective. While abiding by

UN Resolution on Israel (assigned Country is Nigeria) 1.15 single Essay

UN Resolution on Israel (assigned Country is Nigeria) 1.15 single spacings - Essay Example ons Human Rights Council of 24 January 2008 and of the United Nations  Office for the Coordination of Humanitarian Affairs of 25 May 2010, as well as the statements conveyed by the United Nations Special Rapporteurs present in the Gaza Strip, Fully alarmed that the continuation of the present crisis in the relations between the State of Israel and the Palestinian authorities in the Gaza Strip may undermine the peace process and lead to significant challenges to the regional stability, 1. Calls upon the two Parties concerned to exert all efforts necessary to resolve their differences and to make full use of the instruments of pacific settlement of disputes provided for in Chapter VI of the Charter of the United Nations. Such a settlement shall be conducted under the procedural rules the two Parties find the most beneficial to their common interests, and shall be supervised by the special Commission of the Security Council of the United Nations; 2. Condemns the unjustifiable acts of violence committed by the armed forces of the State of Israel and the paramilitary formations of the Palestinian authorities in the Gaza Strip against the civilians residing both in Israel and Palestine and calls for the objective arraignment of all the persons involved in them; (a) Avoid interfering with independent attempts of international non-governmental organizations to provide humanitarian assistance to the civilian population of the Gaza Strip, invite the States concerned to provide security assistance to the participants in such efforts; 4. Recalls an obligation on both Parties to respect the previous Resolutions of the Security Council with regard to maintenance of the peace and stability in the Middle East and appeals to all Parties concerned to exercise the maximum restraint when faced with mutual disagreements; 5. Welcomes the efforts of the Government of the United Kingdom of Great Britain and Northern Ireland to enable the relaxation of the blockade of the Gaza

Social media as a Method to Drive Acquisition of Customers Assignment

Social media as a Method to Drive Acquisition of Customers - Assignment Example The researcher states that the social media is known as an important means of creating brand awareness and customer acquisition. However, the major question is how companies are supposed to convert users of various social media sites into actual customers. Furthermore, different brands face varying challenges concerning customer acquisition. This owing to the fact that different companies have varying market positions, objectives, target audiences and acquisition techniques. Companies are advised to come up with strategies that are appropriate for their brands. This essay critically assesses social media as a method to drive acquisitions of customers and marketing campaigns for two campaigns. Social media marketing is used to drive customer acquisitions through brand recognition. This is known as one of the most effective tools for using social media as a branding tool. This is because, with social media marketing, companies can decide the kind of information their customers are expo sed to and decide on how they want the company’s position to be. Companies can build brand name using the great content and consistent effort around the company values and benefits. Well- established companies including Wal-Mart, Starbucks, and The Weather Channel Shows Off have developed more attractive advertising initiatives on social media sites including YouTube, Instagram and Vine respectively to develop their brand names in the online market leading to an increase in the number of users. The companies have successfully used social media marketing to reach their customers and make sales. Other small companies are advised to follow suit as the social media has proven to be an effective tool to build a company’s brand name.

Ols 252 Essay Example | Topics and Well Written Essays - 1250 words

Ols 252 - Essay Example What makes me love the profession is my admiration of how pharmacists play a major role in ensuring patients are able to regain their good health. This makes me to have a sight in being the most respected pharmacist of the community (Yukl et al., 76). The type of organization I would like to lead is majorly a retail pharmacy because I would enjoy the direct communication I would be accorded with the patients and also working with my colleagues in completing each task efficiently. One year after graduation, I expect to be a pharmacist in a retail pharmacy. This is useful in me gaining experience by accepting responsibilities as a pharmacist. Five years after graduation, I expect a pharmacy manager in a retail store. This will be achieved through hard work, teamwork and helping new members in adapting to their new environment. Finally, ten years after graduation, I expect to be a regional pharmacist manager or intern coordinator. With experience and proficient in executing my job as a pharmacist, this type of leadership will put me in a position to give back to the profession. As an intern coordinator, I will stand a chance to be able to mentor and lead pharmacy students. Step 2: assessing my leadership qualities There are many assessments that had a greater effect into my life but the six most important assessments to me are self-confidence which entails: generalized self-efficacy, leader-member exchange, motivation to lead, influential tactics, emotional intelligence and participatory leadership attitudes. Generalized self-efficacy is an important attribute which shows the importance of having self-confidence for one to be an effective leader and leader emergence. Self-confidence is important to leaders as they show one’s ability to believe in being successful and be able to influence others to achieve a common desired goal or results. Generalized self-efficacy can be strongly manifested in an individual with high self-confidence which has an end-result of strong and effective leadership. In the assessment, a score of 6 represented a strong sense of generalized self-efficacy and a low score of say 2 shows a weaker sense of generalized self-efficacy. Faced with different situations, I have a capacity to succeed as evidenced by my high score of 5 since it indicates a strong sense of efficacy. I chose this assessment because of the score and I have the belief I have that, I will succeed and whatever am doing will produce a desirable result faced with a situation. Leader-member exchange is another assessment I chose because I it assesses the pros and cons of a follower while being supervised. In this assessment the quality of relationship exchanged between the leader and member is taken into account, a score above 6 shows a high quality and a low-quality relationship is shown by a lower score than 2. I have a score of 5.43 which shows my relationship with a leader was of high-quality. Motivation to lead is the assessment I also valued because it contained dimensions on what motivates one to lead. A high score say above 6 in all the dimensions shows a strong motivation to lead and a weak motivation to lead as indicated by a low score, say below 2. My scores in this assessment were 4.2, 4.11 and 4.7 which were relatively high and indicate that I love the role of a leader and like giving directions to my followers. Since I have a goal of being an intern coordinator, this assessment will be handy since I would like to effective lead my fellow pharmacist students

Global Operation Management Essay Example | Topics and Well Written Essays - 2500 words

Global Operation Management - Essay Example There are also more than 25 training centres distributed throughout the world. The official Huawei report of 2007 revealed that the corporation had realised US$12.6 billion in that financial year. Huawei’s overseas profits had increased by 60.4% from the previous year. Huawei’s evident success in such a competitive industry stems from its ventures in the local market. In 1988, Huawei began with a modest capital of RMB 20,000. It participated in reselling telephone switchboards for a period before it started producing its own products. In 1990, the Huawei Corporation invested its capital in channelling proceeds into a branch of research and development into creating its own telephone switches. In 1992, Huawei introduced its new digital switch product which came from its own design and development facilities. The company proceeds that year exceeded RMB95 million. The Huawei Corporation then made the decision to invest more capital in more research and development, which r esulted in assisting the corporation to corner the telecom market in China. At the start of the 90s, the Chinese telecom market dominated by equipment providers from the Western democracies. When the Huawei Corporation first introduced its products, it had to deal with the business rivals right in its own nation. Most Chinese consumers of electronic products viewed the products manufactured in the West as having more value as than any goods that were manufactured domestically. The Huawei Corporation at first concentrated on reaching the populations in rural China with its products. This is because these areas were not viewed as having many people interested in electronic products by the multinational corporations that dealt in electronic products. In these areas, Huawei slowly acquired a respected brand name, thus generating a faithful clientele. Then, Huawei then began to market its electronic products, as well as software, to average sized municipalities. The move to corner the ma rket in the bigger towns would come later. The Huawei Corporation experienced a considerable measure of success because the Chinese government, then, viewed the growth of the telecommunications industry as an important part of the nation’s economic objectives. The government of China extended a lot of support in terms of financial investments and policy to the Huawei Corporation. The 90s were actually the golden era of the development of the telecom industry in China. Between 1991 and 1999, the proceeds from the telecommunications industry increased by 2050%. With the support of the government, the Huawei Corporation successfully made use of the chance to be the foremost supplier of electronic goods in China. By 1996, Huawei was realising profits of RMB2.6 billion on an annual basis, making it the leading provider of telecom goods in China. The excellent performance of a corporation in its own nation is generally a fact that stimulates it towards internationalisation. The Hua wei Corporation was not contented to dominate the Chinese domestic market, but wished to compete in the international arena against bigger rivals. There were some reasons for this. Even though the telecom industry in China had great potential, fierce competition among corporations that were established in the same decade meant that proceeds would be limited even for the corporation that

Banking and the political situation in Bahrain Essay

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Software Research Paper Example | Topics and Well Written Essays - 1000 words

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Honeywell International Success Essay Example for Free

Honeywell International Success Essay This paper introduces the reader to Honeywell International Inc. Honeywell is a world leader in the application of lean manufacturing and its Six Sigma Plus processes. With the use of carefully monitored cost standards, net present value in investment decisions, and the transparency of the company’s financial statements are all methods that Honeywell has successfully implemented and utilized to reach and maintain their status as a world-wide competitor. The company has continued its growth, despite the market downturn that began in 2007, and continues to prove its resilience and pioneering spirit by continually improving their product lines, globally expanding their market, and, monitoring and maintaining financial stability. Its forward thinking and willingness to take risk will provide Honeywell the capacity to maintain its role as a major competitor and contributor to the growth and recovery of our economy. Table of Contents Page Abstract2 Company Overview4 Six Sigma and Lean Manufacturing8 The Use of Standard Costs11 The Use of Net Present Value14 Summary15 References18 Honeywell International Inc. is an American based advanced-technology company that manufactures aerospace and automotive products; residential, commercial, and industrial control systems; specialty chemicals and plastics; and engineered materials. Its assent into history can be traced back to 1885, spanning 125 years of history. Honeywell International is a $38 billion diversified technology and manufacturing leader, with 132,000 employees in over 100 countries and it a Fortune 75 Company. It is a diverse and global-wide organization and is a leading supplier of avionics and electronics, consumable hardware, engine controls, environmental controls, landing systems, power systems, propulsion engines, aerospace services and space products, and systems for the aerospace industry, as well as Original Equipment Manufacturers (OEMs) of commercial, regional, business and military aircraft and spacecraft. Today, its main competitors in the aerospace defense product and service industry are BorgWarner Inc. , Johnson Controls Inc. and United Technologies Corp. State-of-the-art technology, world known brands and global solutions have placed Honeywell in the unique position as one of the premier worldwide suppliers in the aerospace industry, offering solutions of systems, products and services to the largest aerospace and airline companies in the industry. Throughout their 125 years in business, Honeywell has helped revolutionize the aerospace industry with its dedication to research and development and its enthusiasm to advance technology in their various markets. Honeywells reliable and efficient aerospace services and support programs deliver the right level of engineering expertise, maintenance services and asset availability solutions to simplify operations while keeping systems and equipment at peak operational performance. It has proven to be successful in its quest for growth and global expansion from the time of inception. Their quest to acquire and expand began in 1927; the original company, Minneapolis Heat Regulator Company, and Honeywell Heating Specialty Co. merged to form the Minneapolis-Honeywell Regulator Co. From the merger, the name Honeywell was adopted and has remained the same since. In the course of its acquisitions, Honeywell purchased other businesses whose focus was in the controls area; among those acquisitions, was Brown Instrument Co. who was a wide-reaching leader in the field of industrial controls and indicators. This acquisition further increased their already successful market to a wider range of customers, as Minneapolis-Honeywell Regulator Co. had already established an overseas trading agreement with Japanese distributors such as Yamatake Trading Company. It was no surprise that, in 1934, Honeywell pursued and eventually acquired Time-O-Stat Controls Corporation. With the acquisition of Time-O-Stat, Honeywell further expanded its global presence, establishing offices in Toronto, Canada and The Netherlands; a few years later, they had offices in London and Stockholm. By 1941, Honeywell had expanded into markets in Chile, Panama, Trinidad, New Zealand, Argentina, and South Africa. By 1972, it operated 25 wholly-owned subsidiaries, 142 branch offices, and joint ventures in five countries outside the U. S. True to its reputation as a risk taker, Honeywell ventured into the computer industry. This venture was brief and by 1991 Honeywell was on longer in the computer business. Even though the venture was short lived, it proved to be of great value; Honeywell used the knowledge gained from their digital computer experience and applied it to the traditional field of automation control, integrating sensors, and activators. In 1986, Honeywell purchased Sperry Aerospace, and markedly enhanced its position in the aerospace industry. Edson Spencer, Honeywell chairman and chief executive officer, said the purchase was among the most important his company had made, It is an outstanding opportunity for Honeywell that positions us for the long term in a market that is expected to have significant growth for the next 10 years commercial and military aviation (Arnold, 2012). This purchase made Honeywell the worlds leading integrator of avionics systems, incorporation flight controls, space vehicles, and the first FAA-certified wind shear warning system. It continued to expand, and by 1993, the company continued its world-wide expansion by opening affiliates in Abu Dhabi, China, Oman, Romania, and the Ukraine. In a span of 26 years, Honeywell had operations in 95 countries through 83 wholly-owned subsidiaries and 13 joint ventures. One of the most noted and discussed mergers occurred in 1999 when AlliedSignal, a diverse manufacturer, bought Honeywell for $13. 8 billion in stock. AlliedSignal kept the Honeywell name, merging offices, and closed its Morristown, New Jersey headquarters. The merger resulted in a major restructuring for Honeywell which added to its product line and services. The deal created a company with $25 billion in annual sales and a market capitalization in excess of $45 billion. The merger gave the combined company the marketing edge, providing their airline customers to take advantage of new technology that would boost cost savings for both parties. In an unexpected turn, the early part of 2001 brought difficulties for Honeywell when the European Commission rejected the purchase of Honeywell by General Electric (GE). In October 2001, Honeywell and GE, the largest corporation in the world and the number one producer of jet engines, announced the intent to embark on one of the largest industrial mergers in history. The plan was for GE to acquire Honeywell, the largest worldwide supplier of non-engine aerospace equipment. During negotiations it was anticipated that there would be no antitrust problem; as GE and Honeywell were not competitors and not part of the same supply chain. The merger was intended to bring together complementary products that were component parts of large jet aircraft. The deal would have been the largest industrial merger in history. Instead, it became recognized as the first, and so far only, merger between US companies to be derailed solely by the European anti-trust authorities, while being cleared by the US Department of Justice (DoJ). On July 3, 2001, in an unprecedented act, the EU officially rejected the planned $42 billion acquisition of Honeywell International Inc. , by GE. The merger was denied by the EU after concluding that the merger would create or strengthen dominant positions on several markets and that the remedies proposed by G.E. were insufficient to resolve the competition concerns resulting from the proposed acquisition of Honeywell. The merger between G. E. and Honeywell, as it was notified, would have severely reduced competition in the aerospace industry and resulted ultimately in higher prices for customers, particularly airlines† (Pellegrini, 2001). Despite the fact that the GE buyout failure was a stumbling block, Honeywell used the experience to strengthen its core businesses by continuing to develop and introduce new products. The company started an aggressive acquisition strategy with the goal to increase revenues and decrease cost in a strategy that, â€Å"†¦divested small, underperforming operations, reduced the number of suppliers, and streamlined operations in small ways elsewhere† Honeywell History, n. a. ) The results paid off for Honeywell, as they continued to win a large percentage of their contract bids, sales were ahead of budget, and the rate of turnover in managers did not significantly increase from the same period in the prior year, and customer satisfaction was up. Honeywell faced some challenges after the GE debacle, however, by making changes it displayed that tenacity, hard work and a willingness to take risk, can result in huge payoffs. Honeywell continued to streamline and improve their lean manufacturing processes, i. e. Six Sigma Plus, implement and ensure compliance of the company code of conduct and maintain its dominance as a government contractor. Honeywell began its Six Sigma process and concept of self-managed teams in 1995 to â€Å"drive data-based decision making, ensure quality levels, and improve customer satisfaction† (Crager, 2007). Through training, leadership, and senior management support, Honeywell successfully developed their Six Sigma program. In late 2001 Honeywell combined the concepts of lean manufacturing and Six Sigma in a program called Six Sigma Plus to create a more robust program. The program was designed to align improvement objectives directly with business needs by integrating top talent and generating bottom-line results. Six Sigma Plus is an overall strategy to accelerate improvements in all processes, products and services, and reduce the punitive cost of poor quality through elimination of waste and reduction of defects and variations. One of the ultimate aims documented in the Six Sigma Plus strategy is providing maximum value to customers by applying a logical and structured approach to all business processes. One of the pluses of Six Sigma is that it empowered employees, allowing them to make decisions that impacted how their unit or line was performing. This provided Honeywell an excellent tool that is a highly respected measure of excellence. (M. Calderon, personal communication, May 1, 2012) Honeywell took the basic concept of Six Sigma and created its own version which is known as Six Sigma Plus. It is currently used across all businesses and brands to drive growth and productivity. â€Å"The standard operates by providing a measurement of how effective the organization is in eliminating defects and variations from processes. To meet its requirements, a process must operate at 3. 4 defects or less per million opportunities. This equates to 99. 9997% error free† (Six Sigma Plus, n. d. ). Conscious application of the Six Sigma methodology to all business processes delivers greater value to its customers and makes Honeywell a more desirable business partner. The implementation of lean manufacturing processes has enabled Honeywell to maintain tight controls in all aspects of the managerial accounting processes. With the use of managerial accounting, Honeywell has ensured that their productions and service is well planned and controlled. With the budget cuts facing government, private sector job loss, and tightened markets, it is impressive that Honeywell has continued to maintain its sales growth in the United States. The diversity of Honeywell’s world-wide enterprise, exemplifies the importance of a creative corporate marketing approach. Honeywell consists of unique business units, with each, offering a variety of products and services. Strategies and implementation of those strategies must be developed and executed at the corporate, business unit, and product levels. Overall, strategy and long-term planning are guided by the company’s vision and stated mission. At the business level, planning begins with an examination of the current situation, including technological changes and competitive effects. By using this type of analysis, Honeywell is better equipped to address and identify threats and new business opportunities. Decisions to pursue new opportunities are followed by establishing a set of objectives, often stated in terms of market share, sales volume, or profitability. Subsequently, business and marketing strategies are developed to achieve those objectives. Effective execution of strategy in implementation must then occur for objectives to be realized. Effective financial statement analysis will be a primary indicator that indicates the progress and demonstrates whether company goals are being met. Honeywell has been a leader in their industry in planning and control and have used financial analysis in depth to evaluate and control their growth and profitability. It continues to be effective in identifying opportunities to improve the organization’s efficiency and in developing strategic plans to realize those opportunities. By using a diversity of analytical tools Honeywell is better prepared in making operating decisions, such as how and where products are to be manufactured and serviced, whether insourcing or outsourcing is more equitable, and whether to expand and the area to expand to. Timely and accurate financial statement preparation is critical to the success or failure of a business. The financial officer, owner, partner or members management team of a business must review the business financial statements and have a good understanding of them. Financial statements are critical to Honeywell’s ability to make solid, informed decisions. Such decisions are needed in order for Honeywell to meet one of its primary goals, which is to realize a high rate of return on their investments. The measurement and success of this initiative is arrived at by measuring it against other industry averages. This information helps Honeywell understand that current initiatives do show a market response. In view of the fact that the industry average can be general in nature the industry average should be used as a guide. A failure to use the data appropriately can mislead investors and have a disastrous affect on Honeywell’s reputation and marketability. Achieving their strategic plan will not only involve Honeywell’s internal planning and controlling, but it will also involve the support of creditors and investors. Both are key players in providing capital needs to support new initiatives and milestones; the use of financial statements in this process will no doubt be the backbone of the decision making process. It is difficult to know the health and direction of a company if financial statements are not reviewed in a timely manner. In its pursuit of investors, or the success in the results of an external audit, the financial statements are the ultimate representation of company’s financial position. In general accounting practices, Honeywell uses process costing for its furnace thermostats (home products division) and job costing for customized aerospace contracting products. When thinking in terms of standard costs and whether they would be beneficial, one factor to consider is the fact that Honeywell is a world-wide producer with operations in many countries outside of the United States (US). There are ramifications when doing business overseas as well as doing business in the US and each scenario has its own benefits and consequences that are unique to specified circumstances. Honeywell, like their competitors has migrated to low cost countries because of the labor rate differential. The move to overseas production creates additional concerns and dynamics. World-class manufacturing in today’s competitive environment demands more than a single-minded focus on eliminating defects. Since the introduction of Six Sigma and Lean tools to their operations over a decade ago, Honeywell has delivered significant results for customers in terms of the quality, delivery and value of our products and services. To achieve competitive advantage in today’s environment, Honeywell has continued to build on its Six Sigma and Lean foundation, and identify new ways to differentiate themselves. Benchmark companies such as Toyota and Nissan use Six Sigma and Lean tools. Like Honeywell, they also have a disciplined management system that standardizes work and engage employees in improving work processes. In doing this, organizations have achieved tremendous performance improvements. The Honeywell Operating System is a comprehensive, integrated approach to managing their organization. It is characterized by a consistent focus on results for the benefit of our customers, not on the use of specific tools. The objective is to simplify and standardize processes everywhere, to remove variation across operations, and to drive significant and sustainable improvements in safety, quality, delivery and cost. Employees are encouraged use tools such as Six Sigma, in achieving a common purpose: global wide use of an operating system that consistently yields excellent results for the customers and the company. Implementing standardized cost standards is not an easy task and it will take time. Honeywell maintains that standardization will evolve to fit different business environments and changing customer needs and will become an essential part of the process that will bind their company across business and geographic boundaries. Honeywell’s workforce consists of residents of the country they are in to satisfy requirements imposed by foreign nations. It is almost mandatory to have overseas operations to reduce labor and material costs; however, these operations come with high risk. Foreign workers are not always equipped with the necessary skills to perform the manufacturing duties required by a highly technical company. The expense of employing and developing such a workforce can create additional costs. In determining what the additional costs, standard costs prove beneficial because they would provide Honeywell the ability to budget costs with a great understanding and degree of confidence. A standard cost system allows a company to factor in methods that would absorb the periods in which higher costs are identified due to foreign employment development and when costs are low or minimal due to workforce stabilization. In its foreign production, Honeywell will have to set attainable standards in order maintain its performing baseline. Another factor in foreign operations is the volatile condition of the world. The United States is not always welcomed in other countries. It is not uncommon for a common protest to turn into a major world crisis. Such examples are those of the uprisings in Israel and Libya. Honeywell hosts operations in Israel, where relations between the government and the general population are volatile and unpredictable. In addition, we have seen several instances where regimes have changed power and attitudes toward the US in a matter of days. Standard costing is paramount as an aide for monitoring and managing the risk of unpredictability. It is a healthy practice that can protect Honeywell from severe monetary damage if a foreign tragedy should affect the business. The information obtained from standard costing aides Honeywell against the volatility of today’s markets and the strategy of its competitors. Honeywell is continuously improving its processes, products and management style to maintain their competitive edge. To be competitive, Honeywell will continue to use their standard cost system to help them execute planning and control of their strategic priorities. Tracking costs will also help Honeywell identify weakness and variances in their production system. Undetected problems in the areas of materials and labor can eventually raise variance to a point of hindering Honeywell from maintaining their core competencies. Consequently, today’s market provides no room for error, but every opportunity for a competitor to gain the lead. In many respects, some of the rationale that goes into using standard costs also applies to formulating the right strategy to gain a positive Net Present Value. Honeywell’s reach is global and therefore its investment opportunities are also global. Due to the unique factors involved with global markets, it is necessary for Honeywell to perform critical planning for investment decisions. Honeywell has a reputation as an organization that is willing to take risks to make money. It has done that by acquiring other business or expanding its existing facilities for future business. Such expansions are expensive and these expansions require additional staff which adds to the cost of investment. Large expenditures are a challenge to control the net present value (NPV) and require clear identification of cost and risks in order to be a success. Strategic moves, such as partnering with the national government, can leverage the way to a positive NPV. In this approach, there are tradeoff between the corporation and the government in which both interests can be mutually met. Corporation’s like Honeywell utilize these paths in order to reduce investment costs and have accurate projections for calculating and incorporating NPV baselines. Because of the ongoing activity of many investments occurring at one time, it is critical that Honeywell has complete knowledge of their NPV and ensure profitable investments are achieved. Failing to do this can result in major losses, especially when an unplanned shortfall occurs. Although the investment sounds promising, it is critical that NPV is properly measured. It is also advisable from an NPV and program management position that Honeywell phase its investment into NPV milestones which help determine if they should move forward to the next phase of the investment. This process would provide a safeguard while allowing the innovation to prove itself. While the actual rate of return (IRR) that  a given project ends up generating will often differ from its estimated IRR rate, a project with a substantially higher IRR value than other available options would still provide a much better chance of strong growth. IRRs can also be compared against prevailing rates of return in the securities market. If a firm cant find any projects with IRRs greater than the returns that can be generated in the financial markets, it may simply choose to invest its retained earnings into the market. The need for Honeywell to practice continuous NPV drills in a market with circumstances such as those faced in China by US companies, is critical. While both countries maintain a civil business partnership, there is an unspoken adversarial relationship which creates instability. China is strategically positioning itself as a global power therefore, the relationship between both countries is precarious and any misstep by Honeywell could severely damage the existing business relationship. Another potential concern for Honeywell is that China is currently the largest lender to the US. At the point that China reaches the economic capacity to sustain its prosperity internally, we have to ask ourselves if they will request repayment by the US prior to maturity dates. As we have seen in several European countries, a request of that magnitude could destabilize an already fragile US economy. In consideration of this scenario, and other contributing factors, Honeywell should be careful in investment planning, and phase its activities so that the NPV is not contingent upon results that will take a long period to realize a return. In summary, Honeywell has proven itself as a world leader of technology. This corporation is known world-wide and is a household name. Honeywell leads the way in advanced switching and sensing technology in their home division, and its aerospace division. In spite of the GE failure, it has kept its mark on the global economy through market highs and lows and has maintained its dominant position in an extremely competitive industry. As a long-time survivor and global competitor on the world stage, Honeywell continues to make its mark in history by developing innovative safety products, driving the modernization of global air traffic management, revolutionizing combat technology and their commitment to improving operational efficiencies. Honeywell continues to display their dominance with its diversity and profitable risk taking ventures. Perhaps Honeywell’s greatest strength has been the fact that it has adapted to a world that is ever changing and has embraced the challenge that other companies find daunting. With the continued vision to improve processes for safety, quality and cost, reducing waste, and using integrated strategies Honeywell continues to be a standard for their industry. They continue to be innovative and competitive and have a strong commitment to bringing profitable products that their customers need and want. Due to the diversity and competitive market that Honeywell has chosen to operate in, it is of extreme importance that the company maintains sound financial practices that will support the moral fiber and marketability of the company. As Honeywell moves into the future I believe they will continue to perfect their processes to produce the right financial statements, useful in calculating their position in the market, and providing the best advice for investment decisions. The proper use of standard costs and net present value are an example of the critical tools that ensure Honeywell continues to thrive in today’s unknown global conditions. Also critical to the success of Honeywell is the continued utilization of strong and proper ethical practices as the company is well known, world-wide competitor and a representative of the American business ethics and values. Whether it is in the Middle Eastern or the Far East, Honeywell is known and recognized; such a position makes it important for Honeywell to be transparent in its fiscal disclosures. Sound financial practices are essential to Honeywell in order for the company to continue its success and market dominance. Primary emphasis on these practices will serve to maintain Honeywells status and help them make the most profitable investment decisions for their investors and the company. As recent as April 23, 2012, Honeywell declared a â€Å"regular quarterly dividend of $0. 3725 per share on the companys outstanding common stock. The dividend is payable on June 8, 2012 to shareowners of record at the close of business on May 18, 2012† (Honeywell Declares Quarterly Dividend, 2012). If this is any indication, Honeywell will continue to be a viable global competitor and financial contributor to our financial and job market. Honeywell is an excellent example of an organization that is forward thinking and proactive. It has operated with a strong ethical code of conduct, strong financial discipline and an ever present focus on the future. This methodology and ideology will ensure their continued financial growth and market expansion. It is apparent that their cost standards, lean processes, and disciplined managerial financial management has enabled them to overcome obstacles, secure their position as a global competitor and a viable contender in today’s competitive, technology-oriented world.

The PESTEL Framework Essay Example for Free

The PESTEL Framework Essay The PESTEL framework examines the six main macro environmental influencing factors of companies: political, economic, social, technological, environmental and legal. These influences determine the future success or failure of the corporate strategies. The political influence include the role of the governments; economics embraces the macro economic factors such as growth rate, exchange rates and business cycles; the social component stands for changing cultures and demographics; technological influences include innovations; environment refers to the â€Å"green† issues including pollution and waste; and legal entails legislative changes and constraints. Gerry(2008) argues that identifying the key drivers for change helps to focus on the important PESTEL factors. Based on those managers can make the optimal decision for effective action. Thus, the key drivers for change determine the success or failure of a strategy. For instance the clothing retailers are concerned about the social changes which drive consumer taste and behaviour. When there is a high uncertainty in the business environment due to complexity or rapid change, it is unlikely to build a single vision of how the environment can affect companies’ strategies.

Appraisal of the person centred approach

Appraisal of the person centred approach There are several therapeutic frameworks which can be used within different realms to help an individual with psychological problems they may be experiencing; cognitive-behavioural therapy, person-centred therapy or psychodynamic therapy, to name a few. Each therapy is distinct from each other in terms of methods of intervention and ideas and assumptions about the nature and sources of psychopathology. Each therapy is also, of course, considered by those who practice it, as widely applicable to the problems presented for psychotherapeutic treatment (Gabbard, Beck Holmes 2005; Feltham Horton, 2006). Within mainstream psychology, person centred therapy is often criticised because it lacks a solid theoretical and empirical foundation but in counselling and psychotherapy it remains influential. Definition and Theory The person-centred approach was established by Carl Rogers in the 1940s and 1950s. It offers a dynamic, process-focussed explanation of the development and functioning of personality, vulnerability to psychopathology, and of therapeutic growth toward psychological well being (Rogers, 1959). According to person-centred theory each individual is born with actualising tendency. This is what is described by Rogers (1951) as the built in motivation in every life form to develop to their full potential, within their own individual unique life circumstances and potentialities (Gillon, 2007). Although this is a controversial concept (Ryan, 1995; Levitt, 2008), and hence a main criticism of person-centred theory as a whole, it is a fundamental concept within the therapy; the therapy is rooted in the clients ability for awareness and self-directed change in their attitudes and behaviour (Bradley, 1999). Rogers theory of the person is made up of two concepts, the first being the organismic self. This is the true and real person that we are. Roger suggests that this is innate and consistent throughout our lives; we do not learn this concept of ourselves we just are. He postulates that it is within the organismic self where the actualising tendency exists. The other part or the person, as theorised by Rogers, is the self concept. This is the learned way of being and develops through the messages we receive from others. This begins in childhood with messages we receive from our parents and continues throughout our lives through interactions within other relationships. According to Rogers, a healthy self concept exists when we experience unconditional positive regard from the other people in our lives and are not placed under any conditions of worth. In contrast, an unhealthy self concept occurs when we are effected by interjected values and conditions of worth. In this state we often ex perience denial and distortion which are defence mechanisms which come into play when we do not fit into the conditions of worth. In Rogers theory, psychological distress happens when there is a poor fit between the organismic self and self concept i.e. there is incongruence. There is a disintegration of the self concept and there is often experience of very serious emotions such as fear, depression and anxiety. The goal of psychotherapy is to promote the self-actualization in the client. PCT utilises the presence of the actualizing tendency in the client makes it possible for the client to control and direct the therapy process, with the facilitation of the therapist. The therapist is not guiding the therapy but aiding the client through their own particular path; in person centred therapy, there are no specific interventions made by the therapist, as such. The Seven Stages of Change Through empirical research, Rogers was able to recognise identifiable features that characterise positions on a continuum of personality change effected by the process of psychotherapy. It is the belief that the client goes through the seven stages of change from incongruence to congruence in therapy which, at the end of the therapy allows them to offer themselves unconditional positive regard and trust in their organismic valuing process (Rogers, 1961). Stage 1 At this stage it is unlikely that the individual will present in a clinical or counselling setting. The person does not perceive themselves as having any problems and they have very rigid views of the world based on past experiences. An individual who does attend a therapeutic session at this stage is unlikely to return after the first session as the therapy seems pointless to them (McMillan, 2004) Stage 2 At this stage the individual has some awareness of negative feelings and is a little more able to express this. However, there is little inner reflection and often the problem is perceived to be external to them. (Cooper et al., 2007) Stage 3 This is the point where most clients enter counselling. At this stage, there is a little more inward reflection and a realisation of self-ownership, although this is not yet fully established. Often the self reflection is focussed on the past and there is a tendency to externalise present thoughts and feelings. (Cooper et al., 2007) Stage 4 According to Rogers, this is where the majority of the therapeutic work will begin. The client begins to talk about deep feelings and there is an increased tendency to to experience things in the present, although this is still often uncomfortable for the client. This is when the client begins to question their thoughts and perceptions of the world. (McMillan, 2004) Stage 5 At this stage the client has a true sense of self awareness. They can express present emotions and are critical of their own previous constructs, but often there is an acceptance e.g. That was a silly thing to do, but maybe thats alright because everyone makes mistakes? (McMillan, 2004) Stage 6 T here is now a rapid growth towards congruence and the client begins to develop unconditional positive regard for other. The previous incongruence experienced by the client is now embraced and challenged by the client. (Mearns Thorne, 2000) Stage 7 The client is now a fully functioning, self actualised individual who is empathic and shows unconditional positive regard for others. It is not necessary for the client to reach this stage and very few do. (Mearns Thorne,2000) Rogers (1967) emphasis that the number of stages are not crucial and they are loose terms with much interplay along the continuum. The Core Conditions As previously stated, the therapy is based upon the belief that the client will primarily bring about change, not the therapist, and the clients self healing will be activated as they become empowered (Casemore, 2006). Instead of making interventions, the therapist has belief in the inner resources of the client that creates the therapeutic climate for growth (Seligman, 2006). The client works within their own frame of reference and within the sessions there are six necessary and sufficient conditions which are referred to as the six Core Conditions, which must be present in order for the client to benefit from their time with the therapist and which are referred to by Rogers as necessary and sufficient (Rogers, 1957). The core conditions are not techniques or skills which can be learned but are regarded as personal attitudes or attributes experienced by the therapist, and communicated to the client (Gillon, 2007). Therapist-Client Psychological Contact One of these six core conditions is therapist-client psychological contact. This means a relationship between client and therapist must exist, and it must be a relationship in which each persons perception of the other is important (Casemore, 2006). In other words, a real relationship must be established between the therapist and Margaret, rather than simply just being in a room together. Prouty, Van Werde Porter (2002) have emphasised that such a relationship cannot simply be assumed and must be worked upon or, arguably, the whole therapeutic framework will fail. Establishing a psychological relationship with a client may be initially difficult, particularly for an individual who has previously had a bad experience of therapy, or simply finds it difficult to talk to other people about the issues they may be having, even those close to them. The rejection of help from people in pre-established relationships, such as friends or family members might suggest that there may be hesitatio n by the client, in establishing a relationship where the purpose is to gain help. Conversely, building a relationship which will provide an individual with the ability to help themselves may be appealing for such a person, and particularly when person-centred therapy removes the conditions of worth placed on an individual by their family and friends. (Todd Bohart, 1994) . The relationship between the therapist and the client is crucial to the person-centred approach and it cannot just be assumed but must be worked on (Prouty, 2002). Incongruent Client It is also a core condition that the client is in a state of incongruence, being vulnerable or anxious. It is only when this core condition is present that there is a need for change. This idea of knowledge of need for change is important, because the condition implies that, as a result of the experience of vulnerability or anxiety, the client is aware that they are encountering difficulties. (Singh Tudor, 1997) It is important for the client to be aware of their own difficulties as the therapy is based upon the client helping themselves without obvious intervention from the therapist. Without the knowledge of their problems and difficulties, it becomes impossible for the client to confront their problems and work through them. Often, the fact that an individual has asked for help from a primary care service which has referred them to therapy, or have chosen to privately visit a therapist demonstrates an awareness of their problems. If a client is not in therapy voluntarily, is host ile toward the process and the therapist, and is noncommittal about attending sessions, the likelihood of a positive outcome from the therapy diminishes drastically. Conversely, if a client enters the therapeutic relationship feeling a strong need to obtain help, are open and willing to give therapy a try, attend their sessions and establishes a helpful therapeutic relationship with their therapist, it is much more likely that they will benefit from PCT (Corsini,Wedding Dumont, 2007). Congruent Therapist Conversely, in order for the therapy to be effective the therapist must be congruent or integrated in the relationship. Congruence means that the therapists outward responses match their inner awareness and feelings; that they are genuine, real, open, authentic and transparent (Casemore, 2006). Rogers (1957) stressed that congruence is not a question of the therapist blurting out compulsively every passing feeling; rather it is a state of being. These feelings should only be expressed when they are persistent and of great strength and when communication of them assists the therapeutic process (Rogers, 1966, p185). By building this self-awareness not only does the therapist build trust with the client but it also reduces the likelihood that a therapists own experiences in relation to a client, such as distress or anger, will not be influenced by his/her own incongruence and thus conditions of worth being imposed. (Gillon, 2007) For example, if there is a persistent feeling of irritati on from the therapist in regard to how they perceive their clients behaviour, (such as the client rejecting help from family members being perceived as avoiding taking responsibilities for their own problems) this issue will need to be addressed in order to maintain congruence in the therapist in the relationship, and hence maintain a central core condition, to enable effective therapy sessions. The concept of phenomenology must be taken into account in such a situation. The multiple reality theory is defined as a subjective view of the world, constructed by each individuals collective experiences (Rogers, 1951). As a result, no other human being can possibly determine what is the correct or incorrect behaviour for any other individual. Therefore, the therapist must respect this, remain non-directive and supportive, and allow each individual the freedom to live according to this reality and to make all decisions about their growth and direction. (Kensit, 2000) It is notable that this feeling will have an effect on the core condition of congruence which the therapist must bring to the relationship within therapy. It is important for a therapist to be aware of what inner experiences to expose to the client during therapy and in what manner to do so. (Gillon, 2007) Taking the previous example of a feeling of irritation in the therapist, it can be seen that this feeling the ther apist is experiencing is not only putting the therapeutic relationship at risk but it may be an option, if this feeling persists, for the therapist to disclose this feeling to the client in a tactful way, as it may ultimately aid her in therapy. Congruent therapist self disclosure has been shown to achieve a more favourable perception of the therapist, and a higher attractiveness perception, as well as a greater desire to choose a therapist practicing congruent self disclosure over incongruent self disclosure. (Knox, Hess, Peterson Hill, 1997; Nyman Daugherty, 2001; Audet Everall, 2003) Self disclosure not only allows the therapist to remain in a congruent state in the therapeutic relationship but also a self disclosure by the therapist in relation to an issue which the client may be having difficulties confronting, may encourage the self healing process. However, within this solution lies a further problem, as sharing this information may evoke strong feelings from the therapist which could damage the therapeutic relationship which has been built with the client. It is a decision which the therapist must regard carefully and personally make the decision as to whether or not to share the information, by balancing the benefits and risks of this self-disclosure. Further to this it is important for the therapist to decide how much information is sufficient to share without overwhelming their client, or placing conditions of worth within the relationship. As previously mentioned, studies have shown that congruent therapist self disclosure is often a positive thing and so should not be shied away from (Knox, Hess, Peterson Hill, 1997; Nyman Daugherty, 2001; Audet Everall, 2003). However, it must be emphasised the importance of careful consideration before engaging in this technique, as if the self disclosure is misread by the client the relationship will be jeopardised, and the clients progress halted. Unconditional Positive Regard Another important core condition which must be present during a therapy session is that the therapist should experience unconditional positive regard for the client. This means that the therapist offers the person respect, acceptance (although it does not have to be approval) caring and appreciation regardless of the clients attitude or behaviour (Gillon, 2007). This non-judgemental attitude and acceptance of the client is important because it challenges the clients beliefs that they are only valued if they behave as required by significant others (conditions of worth). There is no longer any need for the client to shy away from aspects of their inner self which may be painful or that they may see as shameful because they learn that it is possible to be truly themselves and still be accepted. This is an important aspect of person centred therapy as it opens up the opportunity for the client to explore their anxieties and accept them within their own frame of reference. This, in turn, allows for the self-healing process which is central to person-centred therapy. Empathic Understanding Another core condition which must be achieved is that the therapist experiences an empathic understanding of the clients internal frame of reference and endeavours to communicate this experience to the client. In other words, the therapist enters into the clients world as if it were their own and has increased awareness of how an event or situation has affected the client. This will show the client that they understand them and that their views, feelings and thoughts have value. This will henceforth reinforce the idea that the client is accepted and will allow the therapeutic relationship to flourish to enable a deeper exploration of the self concept. This empathic understanding is often demonstrated to the client through the use of techniques such as reflection and paraphrasing. It has been demonstrated through meta analyses that empathy is a core component of most therapeutic approaches, despite various definitions and uses (Feller and Coccone , 2003). However, contrary to the idea s of Rogers, empathy appears to be necessary, but, not sufficient, for therapy to produce positive outcomes. An extensive review of research on empathy over the 1950s to the 1990s (Duan Hill, 1997), notes a decline in academic interest in the concept of empathy in therapy, since the 1980s. They found that that this appeared to stem from continuing methodological problems, which generally appeared to arise from difficulty is defining the various aspects of empathy. A further meta-study, which examined commonalities across various therapy types, found further support for the idea of empathy as a core concept throughout therapies (Beutler, 2000). As above, this does not require the therapist to experience the same emotions as the client, but to understand and respect those emotions. Client Perception of UPR and Empathic Understanding Arguably, the most important condition is that the client perceives this unconditional positive regard and empathic understanding of the therapist through the way the therapist is in session. This can be demonstrated through warmth, and techniques such as reflection, paraphrasing and clarifying. Not only will this reassure the client that they are being understood and so do not have to explain themselves, but it may also trigger further realisations about thoughts and feelings, which in turn will help the client to move through the self healing process with the prospect of increasing congruence. Todd and Bohart (1994) studied a group of patients in psychiatric care, suffering from varying degrees of psychopathology. It was found that when a therapist did not put conditions of worth on (i.e., judge) the patient they responded with more confidence and less hostility. This is an important finding when relating this therapeutic approach to practice, particularly for individuals who may b e reluctant to obtain help from friends and family; who are often the source of conditions of worth. By removing these conditions of worth an individual may be more open to getting help for their problems. As these conditions are actively removed in a person-centred therapy session, it is suggested that such an environment will encourage an individual to feel comfortable enough to open up and explore their thoughts and feelings within their own internal framework. The theory and necessary and sufficient core conditions which construct person-centred therapy will allow an individual to increase congruence and ultimately reduce the levels of psychological distress they feel. Through talking to the therapist within a session which incorporates the six necessary and sufficient conditions, it is hoped they will go through the seven stages of change and at the end of the therapy can be regarded as a fully functioning person, as described by Rogers (1961). Criticism and Limitations A frequent criticism of this approach is that the core conditions as outlined by Rogers, is what any good therapist does anyway. Superficially, this criticism reflects a misinterpretation of the real challenges of consistently manifesting unconditional positive regard, empathic understanding and congruence (Malhauser, 2010). This is particularly the case in regard to congruence, to the extent that some therapeutic techniques used in some other approaches are dependent upon the therapists willingness to suppress, mentally formulate hypotheses about the client, or constantly maintain a professional front, hiding their own personal reactions, there is a real challenge in applying these techniques with the openness and honesty which defines congruence. Nevertheless, as previously discussed, much of the meta-analysis research being carried out is showing the common factor of an accepting therapeutic relationship to be the pivotal aspect of any therapeutic approach. A PCT therapist may often run the risk, due to the nature of the role of the therapist in the relationship, to be very supportive of their clients but not challenge them. If a therapist directs the client to discuss contents that the therapist believes to be central to the process, the therapy is not client-centered. If the therapist arranges the ways in which clients relate to their concerns or to how they express those concerns, the therapy is directive and not client-centered. In this respect, client-centered therapy stands alone within the family of person-centered and humanistic therapies (Witty, 2007). Kahn (1999) discusses the concept of nondirectivity in person-centered theory. He argues that, since personal and theoretical biases are unavoidable, it is impossible for a therapist to be consistently nondirective. Furthermore, the concept of nondirectivity, with its focus on the psychology of the client, implies that person-centered therapy is a one-person rather than a two-per son psychology. The article quotes therapists who believe that when a clients autonomy is respected, a wide variety of therapeutic interventions are possible. The argument is made that therapist shortcomings may be a more relevant concept than nondirectivity. With the fallibility of the therapist and a respect for the autonomy of the client, Kahn postulates that therapeutic responses can become more flexible and innovative, increasing the power of the person-centered approach. It has been said that the only limitation to person centred therapy is the limitations of the therapist themselves (Dryden, 2007) and it is postulated that perhaps this is the key to effective person centred therapy. There has been criticism of the nondirective attitude associated with this particular therapeutic approach. There is also research that indicates that the personality of the therapist is a better predictor of success than the techniques used (Boeree, 2006). In saying that the techniques used are just as personal to the therapist and are often effected by their personality. As laid out in the core conditions, the therapist themselves must be congruent and authentic and so therefore must be constantly aware of their role in a session. It is important that self disclosure is considered and evaluated before brought into a session but similarly it is important that to both challenge and reassure the client, that it does occur at some point. It is a difficult balance to get ri ght but is crucial to the outcome of therapy for the client. Cognitive behavioural therapy (CBT) is often regarded as the most effective therapeutic framework practiced by counselling psychologists. This is due to high volumes of research into the effectiveness of CBT to treat a wide range of psychological problems which individuals may have. A recent development has seen NICE (National Institute for Health and Clinical Excellence) recommending computerised cognitive-behavioural therapy as a cost-effective and clinically effective practice (NICE, 2006; Mental Health Foundation, 2006). Although the benefits and effectiveness of cognitive-behavioural therapies are undeniable, and cannot be overlooked, it has, as with any therapy, its limitations and comparative research is showing that very little actually stands between CBT and other therapeutic therapies. The person-centred approach has been successful in treating many different psychological problems including anxiety disorders, alcoholism, psychosomatic problems, agoraphobia, interpersonal d ifficulties, depression, and personality disorders (Bozarth, Zimring Tausch, 2002). It is not, however, a suitable therapy to help someone who is suffering from more severe mental health issues such as severe psychosis, as it is unlikely that they will be able to engage with their own thoughts enough to guide their own therapy. As previously stated, it has also been shown to be as equally effective as CBT when used to help an individual who is suffering from major depression (Osatuke, Glick, Stiles, Greenberg, Shapiro Barkham, 2005); with the client in the aforementioned study being helped using CBT managing her needs better and the client being helped using person-centred therapy, accepting her needs more. The authors concluded that despite the qualitative differences, the success was equal in each case and suggest that there is more than one way of being psychologically healthy. A recent study (Stiles, Barham, Twigg, Mellor-Clark Cooper, 2006) into the effectiveness of cognitive-behavioural, person-centred and psychodynamic therapies as practised in the NHS, took into account over 1300 patients, across 58 NHS care sites over a period of 3 years. They found that each of the therapeutic frameworks, either by itself or in conjunction with another therapy such as art, averaged similar marked improvement in individuals well being. This finding suggests that different approaches tend to have equivalent outcomes, an idea which is also demonstrated in other research in the area. (Shadish, Navarro, Matt Phillips, 2000; Holmes, 2002; Stirman, DeRubeis, Crits-Christoph Brody, 2003). For example, Lambert and Bergin (1994) carried out a meta-analysis of studies on psychotherapeutic efficacy, in which they found that there is only a small amount of evidence which weights one particular therapy above another and that most of a clients improvement is related to factors c ommon to all therapeutic approaches. They also propose that it is not the form of therapeutic style a therapist uses, but the therapist themselves which is the main impacting factor on the outcome of a therapeutic treatment. This finding can be considered to be a result of the Dodo bird verdict; a phrase conceived by Rosenzweig (1936). It is often extensively referred to in literature as a consequence of the common factors theory, which proposes that the specific techniques that are applied in different therapeutic approaches serve a very limited purpose and that most of the positive effect that is gained from psychotherapy is due to factors that the schools have in common. This is often the therapeutic effect of having a relationship with a therapist who is warm, respectful and empathic. Meta-analyses by Luborsky (2002) shows that all therapies are considered equal and all must have prizes. On the other hand, scientists who believe in empirically supported therapies (EST) challenge the concept. Chambless (2002) emphasises the importance of remembering that specific therapies are there for specific people in specific situations with specific problems and postulates that grouping problems and therapies, d etracts from the overall importance and individuality of therapy as a whole. Whilst there is much agreement about this, the Dodo bird verdict is still very much accepted within research and is especially important because policymakers have to decide on the usefulness of investing in the diversity of psychotherapies that exist, as demonstrated by the rise of CBT as the therapy of choice in the NHS. Cooper, Elliot, Stiles and Bohart (2008) released a joint statement at the Conference of the World Association for Person-Centred Psychotherapies and Counselling in which they stated that they believe it is scientifically irresponsible to continue to imply and act as though CBTs are more effective than other therapies. They base this opinion on the fact that more academic researchers subscribe to a CBT approach than any other therapy and these researchers get more research grants and publish more studies on the effectiveness of CBT, in comparison to researchers in other areas of psychother apeutic practice. They also take into consideration the previously mentioned research in which scientifically valid studies demonstrate that when established therapies are compared to one another the most common result is that both therapies are equally effective. In conclusion, the person-centred approach is an effective and well researched therapeutic method. It has been shown to have no less standing or effectiveness than cognitive behavioural therapy, despite being pushed to one side within the NHS. It is suggested that an increased scientific research evidence base may increase the likelihood of it being propelled to the same stature within health services as CBT, however as the therapy does not use standardised assessment, measures or clearly defined goals, it would be difficult to measure the effectiveness to the same degree. It is also argued that by researching the approach in such a scientific way it is deviating away from the core principles of the approach itself, which are humanistic. The principles of person-centred therapy are applicable out with the therapeutic relationship and the core conditions which Rogers defines as being necessary for effective treatment, are a valuable tool in allowing an individual to gain self awarenes s and aid their own recovery. It is successful in numerous settings such as family and couples counselling, as well as teaching and management and has been shown to be effective in conflict resolution. The person-centred approach is continuing to develop e.g. relational depth and configurations as outlined by Mearns and Thorne (2000), and will undoubtedly continue to do so with the continued work of key psychologists in the field. Word Count: 4897