Lateral Acquisition Research Articles

Growth Models for Top Indian Software Firms

Indian software service providers are in an enviable position due to unprecedented market growth, overseas shortage of manpower, and access to high quality, low cost manpower within the country. We describe two alternate models for future growth of top Indian firms: manpower based growth (MBG) and knowledge based growth (KBG). In the first model, revenue growth is fuelled largely by growth in manpower. In the second model, the firm penetrates value added market segments, and growth is foelled by increasing the revenue per person. We evaluate these options in detail, after examining the current markets, the recent changes and trends, entry barriers to value added segments, client and market perceptions of Indian service providers, and changes needed within the firm.We argue that knowledge based growth needs significant improvement on three different dimensions: technical, consulting and project management capabilities. We propose a mentor model where these capabilities are largely built in house rather than by lateral recruitment or acquisition. This type of growth also requires several changes in the organization, including building a culture of knowledge, a reward and recognition system for it, and the willingness to differentiate people based on their abilities. A key change would be the ability of its people to take more decisions, whether it is about technology, consulting or project management.Unfortunately, decision making has not yet been delegated to the rank and file in these firms. The KBG model generates much higher revenues, limits recruitment to reasonable levels, and positions the company to resist onslaught from low cost competitors. Manpower based growth on the other hand does not require so much effort, change, or capability building but is difficult to sustain since the number of people needed would perhaps be excessive. We argue that the recent spectacular success could be an obstacle to future growth. That is because past success has been based on low cost delivery of relatively low end work. The natural tendency to continue on this path ignores several more lucrative market opportunities. We also describe how a firm following this model fells into the so called low value trap. Such a firm could also face price based competition from new and upcoming Indian firms, and perhaps those from China, Philippines or other countries.We also examine whether it is feasible for an Indian firm to follow the KBG model and become a truly world class company. On balance, the MBG model is easier to implement, but does not take the best advantage of market opportunities. The KBG model is difficult to implement, but builds a truly world class company. It seems to be a trade off between what can easily be done and what seems desirable for achieving full potential.

Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae

BackgroundGeobacter lovleyi is a unique member of the Geobacteraceae because strains of this species share the ability to couple tetrachloroethene (PCE) reductive dechlorination to cis-1,2-dichloroethene (cis-DCE) with energy conservation and growth (i.e., organohalide respiration). Strain SZ also reduces U(VI) to U(IV) and contributes to uranium immobilization, making G. lovleyi relevant for bioremediation at sites impacted with chlorinated ethenes and radionuclides. G. lovleyi is the only fully sequenced representative of this distinct Geobacter clade, and comparative genome analyses identified genetic elements associated with organohalide respiration and elucidated genome features that distinguish strain SZ from other members of the Geobacteraceae.ResultsSequencing the G. lovleyi strain SZ genome revealed a 3.9 Mbp chromosome with 54.7% GC content (i.e., the percent of the total guanines (Gs) and cytosines (Cs) among the four bases within the genome), and average amino acid identities of 53–56% compared to other sequenced Geobacter spp. Sequencing also revealed the presence of a 77 kbp plasmid, pSZ77 (53.0% GC), with nearly half of its encoded genes corresponding to chromosomal homologs in other Geobacteraceae genomes. Among these chromosome-derived features, pSZ77 encodes 15 out of the 24 genes required for de novo cobalamin biosynthesis, a required cofactor for organohalide respiration. A plasmid with 99% sequence identity to pSZ77 was subsequently detected in the PCE-dechlorinating G. lovleyi strain KB-1 present in the PCE-to-ethene-dechlorinating consortium KB-1. Additional PCE-to-cis-DCE-dechlorinating G. lovleyi strains obtained from the PCE-contaminated Fort Lewis, WA, site did not carry a plasmid indicating that pSZ77 is not a requirement (marker) for PCE respiration within this species. Chromosomal genomic islands found within the G. lovleyi strain SZ genome encode two reductive dehalogenase (RDase) homologs and a putative conjugative pilus system. Despite the loss of many c-type cytochrome and oxidative-stress-responsive genes, strain SZ retained the majority of Geobacter core metabolic capabilities, including U(VI) respiration.ConclusionsGene acquisitions have expanded strain SZ’s respiratory capabilities to include PCE and TCE as electron acceptors. Respiratory processes core to the Geobacter genus, such as metal reduction, were retained despite a substantially reduced number of c-type cytochrome genes. pSZ77 is stably maintained within its host strains SZ and KB-1, likely because the replicon carries essential genes including genes involved in cobalamin biosynthesis and possibly corrinoid transport. Lateral acquisition of the plasmid replicon and the RDase genomic island represent unique genome features of the PCE-respiring G. lovleyi strains SZ and KB-1, and at least the latter signifies adaptation to PCE contamination.

Novel plasmids and resistance phenotypes in Yersinia pestis: unique plasmid inventory of strain Java 9 mediates high levels of arsenic resistance.

Growing evidence suggests that the plasmid repertoire of Yersinia pestis is not restricted to the three classical virulence plasmids. The Java 9 strain of Y. pestis is a biovar Orientalis isolate obtained from a rat in Indonesia. Although it lacks the Y. pestis-specific plasmid pMT, which encodes the F1 capsule, it retains virulence in mouse and non-human primate animal models. While comparing diverse Y. pestis strains using subtractive hybridization, we identified sequences in Java 9 that were homologous to a Y. enterocolitica strain carrying the transposon Tn2502, which is known to encode arsenic resistance. Here we demonstrate that Java 9 exhibits high levels of arsenic and arsenite resistance mediated by a novel promiscuous class II transposon, named Tn2503. Arsenic resistance was self-transmissible from Java 9 to other Y. pestis strains via conjugation. Genomic analysis of the atypical plasmid inventory of Java 9 identified pCD and pPCP plasmids of atypical size and two previously uncharacterized cryptic plasmids. Unlike the Tn2502-mediated arsenic resistance encoded on the Y. enterocolitica virulence plasmid; the resistance loci in Java 9 are found on all four indigenous plasmids, including the two novel cryptic plasmids. This unique mobilome introduces more than 105 genes into the species gene pool. The majority of these are encoded by the two entirely novel self-transmissible plasmids, which show partial homology and synteny to other enterics. In contrast to the reductive evolution in Y. pestis, this study underlines the major impact of a dynamic mobilome and lateral acquisition in the genome evolution of the plague bacterium.

Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen

Methanobrevibacter smithii is the most abundant archaeon in the human colon. As most of its neighbors are bacterial species, it is expected that lateral gene acquisition from bacteria might have contributed to the evolution and adaptation of this archaeon. We performed a tree-based genome-wide survey of putative lateral gene transfer products in M. smithii, using a phylogenetic pipeline. Over 15% of the coding genes of M. smithii are inferred to be bacterial in origin, based on this analysis. Laterally acquired genes have had the largest contribution to surface functions, and encode glycosyl-transferases and adhesin-like proteins. In addition, several important ABC transporters, especially metal transporters are of bacterial origin. Thus, bacterial genes contributed to the host-adaptation by allowing a larger variety of surface structures and increasing the efficiency of metal ion uptake in the competitive gut niche.

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in Two Corynebacterium pseudotuberculosis Strains

Background Corynebacterium pseudotuberculosis, a Gram-positive, facultative intracellular pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL mainly affects small ruminants, such as goats and sheep; it also causes infections in humans, though rarely. This species is distributed worldwide, but it has the most serious economic impact in Oceania, Africa and South America. Although C. pseudotuberculosis causes major health and productivity problems for livestock, little is known about the molecular basis of its pathogenicity.Methodology and FindingsWe characterized two C. pseudotuberculosis genomes (Cp1002, isolated from goats; and CpC231, isolated from sheep). Analysis of the predicted genomes showed high similarity in genomic architecture, gene content and genetic order. When C. pseudotuberculosis was compared with other Corynebacterium species, it became evident that this pathogenic species has lost numerous genes, resulting in one of the smallest genomes in the genus. Other differences that could be part of the adaptation to pathogenicity include a lower GC content, of about 52%, and a reduced gene repertoire. The C. pseudotuberculosis genome also includes seven putative pathogenicity islands, which contain several classical virulence factors, including genes for fimbrial subunits, adhesion factors, iron uptake and secreted toxins. Additionally, all of the virulence factors in the islands have characteristics that indicate horizontal transfer.ConclusionsThese particular genome characteristics of C. pseudotuberculosis, as well as its acquired virulence factors in pathogenicity islands, provide evidence of its lifestyle and of the pathogenicity pathways used by this pathogen in the infection process. All genomes cited in this study are available in the NCBI Genbank database (http://www.ncbi.nlm.nih.gov/genbank/) under accession numbers CP001809 and CP001829.

Lateral acquisition of genes is affected by the friendliness of their products

A major factor in the evolution of microbial genomes is the lateral acquisition of genes that evolved under the functional constraints of other species. Integration of foreign genes into a genome that has different components and circuits poses an evolutionary challenge. Moreover, genes belonging to complex modules in the pretransfer species are unlikely to maintain their functionality when transferred alone to new species. Thus, it is widely accepted that lateral gene transfer favors proteins with only a few protein-protein interactions. The propensity of proteins to participate in protein-protein interactions can be assessed using computational methods that identify putative interaction sites on the protein. Here we report that laterally acquired proteins contain significantly more putative interaction sites than native proteins. Thus, genes encoding proteins with multiple protein-protein interactions may in fact be more prone to transfer than genes with fewer interactions. We suggest that these proteins have a greater chance of forming new interactions in new species, thus integrating into existing modules. These results reveal basic principles for the incorporation of novel genes into existing systems.

Cross structured illumination for high speed high resolution line scanning confocal microscopy

Previous research presented the structured illumination confocal scanning microscope (SICSM) so as to improve the lateral resolution of the confocal microscope. However, the image acquisition speed of the SICSM is very slow and also an alignment error due to the mechanical rotation of a grating and a slit can easily occur. As a theoretical study, in this paper we propose a new SI method, the cross SI method, which improves lateral resolution and image acquisition speed. Performances of the conventional SI and the proposed SI methods are compared by analysis of the modulation transfer function. The proposed SI method shows similar lateral resolution and can shorten the image acquisition time compared to the conventional SI method. The cross structured illumination confocal microscope (CSICM) is combined with the cross SI pattern optics and the line scanning confocal microscope. We have introduced a 2-D diffractive grating, four linear polarizers and four cylindrical lenses in order to create the cross SI pattern. The effects of the cross SI pattern, intensity and visibility, on the system performance are analyzed. The CSICM has double the lateral resolution of the conventional microscope, an optical sectioning ability and a fast image acquisition speed.

Extended MLST-based population genetics and phylogeny of Vibrio parahaemolyticus with high levels of recombination

A collection of 174 global isolates of Vibrio parahaemolyticus were analyzed by multilocus sequence typing (MLST) on the basis of ten conserved genes. The results showed a high level of nucleotide and allelic diversity with the evidence of purifying selection and of frequent recombination. Recombination played a much greater role than mutation in generating genetic heterogeneity. The 174 strains could be assigned into 89 different sequence types, which could be further separated into six clonal complexes (CCs; CC1 to CC6) plus 71 singletons. The three major CCs, namely CC1 to CC3, corresponded to the groups of pre-1996 clinical old-O3:K6 strains ( trh + , T3SS2β + , tdh − , T3SS2α − , and GS-PCR − ), post-1996 pandemic strains ( trh − , T3SS2β − , tdh + , T3SS2α + , and GS-PCR + ) and non-clinical isolates ( trh − , T3SS2β − , tdh − , T3SS2α − , and GS-PCR − ), respectively. The MLST data enable the construction of a phylogenetic structure from the allelic profiles rather the nucleotide sequences, so as to reduce the affect of frequent recombination. The six CCs arose on a background of mutation and recombination, and according to the previously reported data, this bacterium could be evolved fast due to lateral acquisition of foreign genes especially including those encoding virulence determinants. V. parahaemolyticus had a typical epidemic population structure that is driven by mutation, recombination and lateral gene transfer.

Microbial evolution of sulphate reduction when lateral gene transfer is geographically restricted

Lateral gene transfer (LGT) is an important mechanism by which micro-organisms acquire new functions. This process has been suggested to be central to prokaryotic evolution in various environments. However, the influence of geographical constraints on the evolution of laterally acquired genes in microbial metabolic evolution is not yet well understood. In this study, the influence of geographical isolation on the evolution of laterally acquired dissimilatory sulphite reductase (dsr) gene sequences in the sulphate-reducing micro-organisms (SRM) was investigated. Sequences on four continental blocks related to SRM known to have received dsr by LGT were analysed using standard phylogenetic and multidimensional statistical methods. Sequences related to lineages with large genetic diversity correlated positively with habitat divergence. Those affiliated to Thermodesulfobacterium indicated strong biogeographical delineation; hydrothermal-vent sequences clustered independently from hot-spring sequences. Some of the hydrothermal-vent and hot-spring sequences suggested to have been acquired from a common ancestral source may have diverged upon isolation within distinct habitats. In contrast, analysis of some Desulfotomaculum sequences indicated they could have been transferred from different ancestral sources but converged upon isolation within the same niche. These results hint that, after lateral acquisition of dsr genes, barriers to gene flow probably play a strong role in their subsequent evolution.

Phylogenetic evidence for extensive horizontal gene transfer of type III secretion system genes among enterobacterial plant pathogens

This study uses sequences from four genes, which are involved in the formation of the type III secretion apparatus, to determine the role of horizontal gene transfer in the evolution of virulence genes for the enterobacterial plant pathogens. Sequences of Erwinia, Brenneria, Pectobacterium, Dickeya and Pantoea were compared (a) with one another, (b) with sequences of enterobacterial animal pathogens, and (c) with sequences of plant pathogenic gamma and beta proteobacteria, to evaluate probable paths of lateral exchange leading to the current distribution of virulence determinants among these micro-organisms. Phylogenies were reconstructed based on hrcC, hrcR, hrcJ and hrcV gene sequences using parsimony and maximum-likelihood algorithms. Virulence gene phylogenies were also compared with several housekeeping gene loci in order to evaluate patterns of lateral versus vertical acquisition. The resulting phylogenies suggest that multiple horizontal gene transfer events have occurred both within and among the enterobacterial plant pathogens and plant pathogenic gamma and beta proteobacteria. hrcJ sequences are the most similar, exhibiting anywhere from 2 to 50 % variation at the nucleotide level, with the highest degree of variation present between plant and animal pathogen sequences. hrcV sequences are conserved among plant and animal pathogens at the N terminus. The C-terminal domain is conserved only among the enterobacterial plant pathogens, as are the hrcC and hrcR sequences. Additionally, hrcJ and hrcV sequence phylogenies suggest that at least some type III secretion system virulence genes from enterobacterial plant pathogens are related more closely to those of the genus Pseudomonas, a conclusion neither supported nor refuted by hrcC or hrcR.

Which Lateral Radiographic Positioning Technique Provides the Most Reliable and Functional Representation of a Patient’s Sagittal Balance?

Prospective nonscoliotic cohort evaluation of the effects of various positions for obtaining standing lateral thoracolumbar radiographs. The purpose of this study was to compare the effects of various upper extremity positions on thoracolumbar sagittal spinal alignment. The standing position used to capture a lateral plane radiograph can have marked effects on measurements of sagittal spinal alignment and may compound the variability between measurements from successive radiographs. Twenty-two healthy female adolescents performed 3 repeated trials of 4 standing positions in a motion analysis laboratory. The positions included: (1) relaxed standing with arms at sides (CONTROL), (2) standing with fists overlying ipsilateral clavicles (CLAVICLE), (3) active shoulder flexion to 30 degrees with elbows extended (30 ACTIVE), and (4) passive shoulder flexion to 30 degrees with hand supports (30 PASSIVE). Sagittal alignment of the spine was described by kyphosis, lordosis, and the sagittal vertical axis (SVA), all of which were measured from the positions of reflective markers attached to the surface of the back and pelvis. Differences between alignment measures obtained for each of the 3 radiographic positions relative to the functional position (CONTROL) were calculated. Mean differences were then compared between positions using repeated measures ANOVAs (alpha = 0.05). Relative to the CONTROL position, all other positions resulted in negative shifts in SVA (range = -1.1 cm- -4.6 cm), decreased kyphosis (range = -1 degrees- -3 degrees), and increased lordosis (4 degrees for all positions). The shift in the SVA with the 30 PASSIVE position was significantly less than the other 2 positions (P < 0.05) and demonstrated the least variability. Standing with the hands supported while flexing the shoulders 30 degrees during positioning for lateral spinopelvic radiographic acquisition resulted in an SVA and measures of sagittal plane curvature that were comparable with a functional standing position with arms at the side. This seems to be the best way to move the arms anterior to the spine with the least effect on overall sagittal balance.

A computer aided method for closed reduction of diaphyseal tibial fracture using projection images: A feasibility study

A computer aided method for closed tibial shaft fracture reduction based on measurements of 12 projection parameters (6 angulations and 6 translations) from an anteroposterior radiograph, a lateral radiograph, and a transverse projection photograph is examined. The development, validation and reliability of the computer aided method are presented. A custom-made unilateral external fixation device consisting of 7 calibrated one-degree-of-freedom joints was employed to execute the reduction. Five tibial fracture phantoms with initial deformities that covered a wide range of misalignments were tested. The mean (standard deviation) resultant rotational and translational errors after the reduction were 3.32° (0.96°) and 1.65 (0.86) mm, respectively, which indicates good reduction accuracy. Three independent raters made the measurements of the projection parameters to test inter-rater reliability. The intra-class correlation coefficients were found to range between 0.935 and 1, indicating good reliability. Since ideal patient positioning for AP, lateral and transverse image acquisition is not easily attainable, the effect of patient positioning errors on the measurement of projection parameters was explored using a tibial phantom. The preliminary results revealed that 10° deviations in positioning do not greatly affect the measurement of AP and lateral angulation parameters (<1.7°). However, a 10° positioning error about the long bone axis may result in a change of as much as 10.7° in the measurements of transverse projection angulation parameters. In addition, a 10° positioning error about an arbitrary anatomical axis may result in translational projection parameter changes of up to 6.8 mm. For these reasons, a previously validated method that allows for accurate positioning of the tibia about its long axis and a two-step reduction strategy to achieve the best possible deformity reduction are proposed. Procedures to facilitate reliable measurement of tibial torsion are also discussed. It appears that the projection-based reduction method exposes the patient to less radiation and allows for simple, quick and accurate reductions, making it an attractive choice for acute clinical applications.

Automatic exposure control in pediatric and adult multidetector CT examinations: A phantom study on dose reduction and image quality

The aim of this study was to assess the potential of a modern x,y,z modulation-based automatic exposure control system (AEC) for dose reduction in pediatric and adult multidetector CT (MDCT) imaging and evaluate the quality of the images obtained. Five physical anthropomorphic phantoms that simulate the average individual as neonate, 1-, 5-, 10-year old child, and adult were scanned with a MDCT scanner, equipped with a modern AEC system. Dose reduction (%DR) was calculated as the percentage difference of the mean modulated and the preset tube current-time product that is prescribed for standard head and body scan protocols. The effect of the tube potential and the orientation of the topogram acquisition on dose reduction were assessed. Image quality was evaluated on the basis of image noise and signal to noise ratio (SNR). The dose reduction values achieved in pediatric phantoms were remarkably lower than those achieved for the adult. The efficiency of the AEC is decreased at 80 kVp compared to higher tube potentials and for helical scans following an anterior posterior (AP-AEC) compared to a lateral (LAT-AEC) topogram acquisition. In AP-AEC scans, the dose reduction ranged between 4.7 and 34.7% for neonate, 15.4 and 30.9% for 1 year old, 3.1 and 26.7% for 5 years old, 1.2 and 58.7% for 10 years old, and 15.5 and 57.4% for adult. In LAT-AEC scans, the corresponding dose reduction ranged between 11.0 and 36.5%, 27.2 and 35.7%, 11.3 and 35.6%, 0.3 and 67.0%, and 15.0 and 61.7%, respectively. AP-AEC scans resulted in a 17.1% and 19.7% dose increase in the thorax of neonate and the pelvis of the 10-year old phantom, respectively. The variation in the measured noise among images obtained along the scanning z axis was lower in AEC activated compared to fixed milliamperes scans. However, image noise was significantly increased (P<.001) and SNR significantly decreased (P<.001) in most AEC activated compared to fixed milliamperes scans. In conclusion, AEC resulted in a (i) substantial dose reduction, which is less pronounced in children compared to adult, (ii) higher dose reduction in scans following a lateral compared to scans following an anterior-posterior topogram acquisition, (iii) increase of image noise and degradation of SNR in the obtained images compared to the fixed milliamperes technique.

Novel homologs of the multiple resistance regulator marA in antibiotic-contaminated environments

Antibiotics are commonly detected in the environment as contaminants. Exposure to antibiotics may induce antimicrobial-resistance, as well as the horizontal transfer of resistance genes in bacterial populations. We selected the resistance gene marA, mediating resistance to multiple antibiotics, and explored its distribution in sediment and water samples from surface and sewage treatment waters. Ciprofloxacin and ofloxacin (fluoroquinolones), sulphamethoxazole (sulphonamide), erythromycin, clarythromycin, and spiramycin (macrolides), lincomycin (lincosamide), and oxytetracycline (tetracycline) were measured in the same samples to determine antibiotic contamination. Bacterial populations from environmental samples were challenged with antibiotics to identify resistant isolates. The gene marA was found in almost all environmental samples and was confirmed by PCR amplification in antibiotic-resistant colonies. 16S rDNA sequencing revealed that the majority of resistant isolates belonged to the Gram-positive genus Bacillus, not previously known to possess the regulator marA. We assayed the incidence of marA in environmental bacterial populations of Escherichia coli and Bacillus by quantitative real-time PCR in correlation with the levels of antibiotics. Phylogenetic analysis indicated the possible lateral acquisition of marA by Bacillus from Gram-negative Enterobacteriaceae revealing a novel marA homolog in Bacillus. Quantitative PCR assays indicate that the frequency of this gene in antropised environments seems to be related to bacterial exposure to water-borne antibiotics.

Raman and FTIR microscopic imaging of colon tissue: a comparative study

Colon tissue constitutes a valid model for the comparative analysis of soft tissue by Raman and Fourier transform infrared (FTIR) imaging because it contains four major tissue types such as muscle tissue, connective tissue, epithelium and nerve cells. Raman microscopic images were recorded in the mapping mode using 785 nm laser excitation and a step size of 10 microm from three regions within a thin section that encompassed mucus, mucosa, submucosa, and longitudinal and circular muscle layers. FTIR microscopic images that were composed of 4, 8 and 9 individual images of 4096 spectra each were recorded from the same regions using a FTIR spectrometer coupled to a microscope with a focal plane array detector. Furthermore, Raman microscopic images were recorded at a step size of 2.5 microm from three ganglia that belong to the myenteric plexus. The results are discussed with respect to lateral resolution, spectral resolution, acquisition time and sensitivity of both modalities.

Lateral Symbiont Acquisition in a Maternally Transmitted Chemosynthetic Clam Endosymbiosis

Deep-sea clams of the family Vesicomyidae live in symbiosis with intracellular chemosynthetic bacteria. These symbionts are transmitted maternally (vertically) between host generations and should therefore show a pattern of genetic variation paralleling that of the cotransmitted host mitochondrion. However, instances of lateral (nonvertical) symbiont acquisition could still occur, thereby decoupling symbiont and mitochondrial phylogenies. Here, we provide the first evidence against strict maternal cotransmission of symbiont and mitochondrial genomes in vesicomyids. Analysis of Vesicomya sp. mt-II clams from hydrothermal vents on the Juan de Fuca Ridge (northeastern Pacific) revealed a symbiont phylotype (designated symB(VII)) highly divergent from previously described symbionts of the same host lineage. SymB(VII)-hosting clams occurred at low frequency (0.02) relative to individuals hosting the dominant symbiont phylotype. Phylogenetic analysis of 16S rRNA genes from a wide range of symbionts and free-living bacteria clustered symB(VII) within the monophyletic clade of vesicomyid symbionts. Further analysis of 3 symbiont loci (23S, dnaK, and soxA) across 11 vesicomyid taxa unambiguously placed symB(VII) as sister to the symbiont of a distantly related host lineage, Vesicomya sp. from the Mid-Atlantic Ridge (98.9% median nucleotide identity across protein-coding loci). Using likelihood and Bayesian model discrimination methods, we rejected the strict maternal cotransmission hypothesis by showing a significant decoupling of symbiont and host mitochondrial (COI and mt16S genes) phylogenies. Indeed, decoupling occurred even when symB(VII) was excluded from phylogenetic reconstructions, suggesting a history of host switching in this group. Together, the data indicate a history of lateral symbiont transfer in vesicomyids, with symB(VII) being the most conspicuous example. Interpreted alongside previous studies of the vesicomyid symbiosis, these results suggest a mixed mode of symbiont transmission characterized by predominantly vertical transmission punctuated with instances of lateral symbiont acquisition. Lateral acquisition may facilitate the exchange of genetic material (recombination) among divergent symbiont lineages, rendering the evolutionary history of vesicomyid symbiont genomes much more complex than previously thought.

Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic large DNA viruses

BackgroundNucleo-Cytoplasmic Large DNA viruses (NCLDV), a diverse group that infects a wide range of eukaryotic hosts, exhibit a large heterogeneity in genome size (between 100 kb and 1.2 Mb) but have been suggested to form a monophyletic group on the basis of a small subset of approximately 30 conserved genes. NCLDV were proposed to have evolved by simplification from cellular organism although some of the giant NCLDV have clearly grown by gene accretion from a bacterial origin.ResultsWe demonstrate here that many NCLDV lineages appear to have undergone frequent gene exchange in two different ways. Viruses which infect protists directly (Mimivirus) or algae which exist as intracellular protists symbionts (Phycodnaviruses) acquire genes from a bacterial source. Metazoan viruses such as the Poxviruses show a predominant acquisition of host genes. In both cases, the laterally acquired genes show a strong tendency to be positioned at the tip of the genome. Surprisingly, several core genes believed to be ancestral in the family appear to have undergone lateral gene transfers, suggesting that the NCLDV ancestor might have had a smaller genome than previously believed. Moreover, our data show that the larger the genome, the higher is the number of laterally acquired genes. This pattern is incompatible with a genome reduction from a cellular ancestor.ConclusionWe propose that the NCLDV viruses have evolved by significant growth of a simple DNA virus by gene acquisition from cellular sources.

Treeness Triangles: Visualizing the Loss of Phylogenetic Signal

It is well known that molecular data "saturates" with increasing sequence divergence (thereby losing phylogenetic information) and that in addition the accumulation of misleading information due to chance similarities or to systematic bias may accompany saturation as well. Exploratory data analysis methods that can quantify the extent of signal loss or convergence for a given data set are scarce. Such methods are needed because genomics delivers very long sequence alignments spanning substantial phylogenetic depth, where site saturation may be compounded by systematic biases or other alternative signals. Here we introduce the Treeness Triangle (TT) graph, in which signals detectable by Hadamard (spectral) analysis are summed into 3 categories--those supporting 1) external and 2) internal branches in the optimal tree, in addition to 3) the residuals (potential internal branches not present in the optimal tree). These 3 values are plotted in a standard ternary coordinate system. The approach is illustrated with simulated and real data sets, the latter from complete chloroplast genomes, where potential problems of paralogy or lateral gene acquisition can be excluded. The TT uncovers the divergence-dependent loss of phylogenetic signal as subsets of chloroplast genomes are investigated that span increasingly deeper evolutionary timescales. The rate of signal loss (or signal retention) varies with the gene and/or the method of analysis.

Evidence for increased horizontal gene transfers among streptococci from group A streptococcal endemic regions

Streptococcus dysgalactiae subsp. equisimilis (group G streptococcus, GGS) is generally regarded as a commensal organism but can cause a similar spectrum of diseases as Streptococcus pyogenes (group A streptococcus, GAS). While the lateral acquisition of genes between these two phylogenetically closely related species is well documented, the extent and mechanisms of lateral transfers are yet to be elucidated. We have recently demonstrated that cross-species genetic transfers are common between GGS and two closely related human pathogens, group A streptococcus and the group B streptococcus. Furthermore, we suggested that phage mediated lateral gene transfers may occur more frequently in populations with a high burden of GAS infection. To further substantiate this, we examined the dissemination of a functional prophage in selected GGS and GAS isolates belonging to distinct genotypes from GAS-endemic and non-endemic regions. Our results confirm that phage mediated lateral transfers between GAS and GGS are common in GAS endemic regions. This observation further impacts on the epidemiology of GAS diseases in endemic regions and future vaccine stratagies.

Identification of the Acidobacterium capsulatum LexA box reveals a lateral acquisition of the Alphaproteobacteria lexA gene

Acidobacterium capsulatum is the most thoroughly studied species of a new bacterial phylogenetic group designated the phylum Acidobacteria. Through a tblastn search, the A. capsulatum lexA gene has been identified, and its product purified. Electrophoretic mobility shift assays have shown that A. capsulatum LexA protein binds specifically to the direct repeat GTTCN(7)GTTC motif. Strikingly, this is also the LexA box of the Alphaproteobacteria, but had not previously been described outside this subclass of the Proteobacteria. In addition, a phylogenetic analysis of the LexA protein clusters together Acidobacterium and the Alphaproteobacteria, moving the latter away from their established phylogenetic position as a subclass of the Proteobacteria, and pointing to a lateral gene transfer of the lexA gene from the phylum Acidobacteria, or an immediate ancestor, to the Alphaproteobacteria. Lastly, in vivo experiments demonstrate that the A. capsulatum recA gene is DNA-damage inducible, despite the fact that a LexA-binding sequence is not present in its promoter region.