Biochemical and structural characterization of the apicoplast dihydrolipoamide dehydrogenase of Plasmodium falciparum

PDC (pyruvate dehydrogenase complex) is a multi-enzyme complex comprising an E1 (pyruvate decarboxylase), an E2 (dihydrolipomide acetyltransferase) and an E3 (dihydrolipoamide dehydrogenase). PDC catalyses the decarboxylation of pyruvate and forms acetyl-CoA and NADH. In the human malaria parasite Plasmodium falciparum, the single PDC is located exclusively in the apicoplast. Plasmodium PDC is essential for parasite survival in the mosquito vector and for late liver stage development in the human host, suggesting its suitability as a target for intervention strategies against malaria. Here, PfaE3 (P. falciparum apicoplast E3) was recombinantly expressed and characterized. Biochemical parameters were comparable with those determined for E3 from other organisms. A homology model for PfaE3 reveals an extra anti-parallel β-strand at the position where human E3BP (E3-binding protein) interacts with E3; a parasite-specific feature that may be exploitable for drug discovery against PDC. To assess the biological role of Pfae3, it was deleted from P. falciparum and although the mutants are viable, they displayed a highly synchronous growth phenotype during intra-erythrocytic development. The mutants also showed changes in the expression of some mitochondrial and antioxidant proteins suggesting that deletion of Pfae3 impacts on the parasite''s metabolic function with downstream effects on the parasite''s redox homoeostasis and cell cycle.     

Detection and Identification of Salmonella enterica,Escherichia coli,and Shigella spp. via PCR-Electrospray Ionization Mass Spectrometry: Isolate Testing and Analysis of Food Samples

An assay to identify the common food-borne pathogens Salmonella, Escherichia coli, Shigella, and Listeria monocytogenes was developed in collaboration with Ibis Biosciences (a division of Abbott Molecular) for the Plex-ID biosensor system, a platform that uses electrospray ionization mass spectroscopy (ESI-MS) to detect the base composition of short PCR amplicons. The new food-borne pathogen (FBP) plate has been experimentally designed using four gene segments for a total of eight amplicon targets. Initial work built a DNA base count database that contains more than 140 Salmonella enterica, 139 E. coli, 11 Shigella, and 36 Listeria patterns and 18 other Enterobacteriaceae organisms. This assay was tested to determine the scope of the assay''s ability to detect and differentiate the enteric pathogens and to improve the reference database associated with the assay. More than 800 bacterial isolates of S. enterica, E. coli, and Shigella species were analyzed. Overall, 100% of S. enterica, 99% of E. coli, and 73% of Shigella spp. were detected using this assay. The assay was also able to identify 30% of the S. enterica serovars to the serovar level. To further characterize the assay, spiked food matrices and food samples collected during regulatory field work were also studied. While analysis of preenrichment media was inconsistent, identification of S. enterica from selective enrichment media resulted in serovar-level identifications for 8 of 10 regulatory samples. The results of this study suggest that this high-throughput method may be useful in clinical and regulatory laboratories testing for these pathogens.     

Microarray Analysis of Microbial Virulence Factors

Hybridization with oligonucleotide microchips (microarrays) was used for discrimination among strains of Escherichia coli and other pathogenic enteric bacteria harboring various virulence factors. Oligonucleotide microchips are miniature arrays of gene-specific oligonucleotide probes immobilized on a glass surface. The combination of this technique with the amplification of genetic material by PCR is a powerful tool for the detection of and simultaneous discrimination among food-borne human pathogens. The presence of six genes (eaeA, slt-I, slt-II, fliC, rfbE, and ipaH) encoding bacterial antigenic determinants and virulence factors of bacterial strains was monitored by multiplex PCR followed by hybridization of the denatured PCR product to the gene-specific oligonucleotides on the microchip. The assay was able to detect these virulence factors in 15 Salmonella, Shigella, and E. coli strains. The results of the chip analysis were confirmed by hybridization of radiolabeled gene-specific probes to genomic DNA from bacterial colonies. In contrast, gel electrophoretic analysis of the multiplex PCR products used for the microarray analysis produced ambiguous results due to the presence of unexpected and uncharacterized bands. Our results suggest that microarray analysis of microbial virulence factors might be very useful for automated identification and characterization of bacterial pathogens.     

Development of hyperspectral imaging as a bio-optical taxonomic tool for pigmented marine organisms

Reflection spectra obtained from hyperspectral imaging can be used as a bio-optical taxonomic identification tool if the pigment composition and the corresponding optical absorption signatures of an organism are known. In this study we elucidate species-specific absorption and corresponding reflection signatures of marine organisms and discuss optical fingerprints from underwater hyperspectral imaging (UHI) for future automated identification of organisms on the seafloor. When mounted on underwater robots, UHI has the potential to be a time- and cost-efficient identification and mapping method covering large areas over a short time. Hyperspectral imaging in vivo and in situ were used to obtain species-specific reflection signatures (optical fingerprints). High performance liquid chromatography, liquid chromatography–mass spectroscopy and nuclear magnetic resonance were used for pigment identification and to obtain species-specific absorption signatures of four marine benthic species; the spoonworm Bonellia viridis, and the sponges Isodictya palmata, Hymedesmia paupertas and Hymedesima sp. Species-specific optical fingerprints based on a UHI-based reflectance signature were verified successfully in the organisms investigated.     

Genetic studies to re-affiliate Edwardsiella tarda fish isolates to Edwardsiella piscicida and Edwardsiella anguillarum species

Until 2012, the genus Edwardsiella was composed by three species Edwardsiella tarda, Edwardsiella hoshinae and Edwardsiella ictaluri. In 2013, Edwardsiella piscicida, compiling fish pathogenic strains previously identified as E. tarda was described, and more recently a new species isolated from diseased eel was reported, namely Edwardsiella anguillarum.The incorporation of these species into the genus makes necessary a revision of the taxonomic position of the isolates previously identified as E. tarda. Using AFLP technique, MLSA studies and in silico DNA–DNA hybridization, 46 of 49 E. tarda isolates were re-assigned as E. piscicida and 2 as E. anguillarum, whereas it was confirmed previous classification of the Edwardsiella types and reference strains used. The study of the taxonomic resolution of the genes 16S rRNA, adk, atpD, dnaJ, glnA, hsp60, tuf as well as the possible combinations among housekeeping genes, showed that the gene dnaJ was the more resolutive. In conclusion, the use of molecular techniques is necessary to accurately identify Edwardsiella isolates, especially when differentiating new species from E. tarda.     

Identification of Single Meloidogyne Juveniles by Polymerase Chain Reaction Amplification of Mitochondrial DNA

Polymerase chain reaction (PCR) was used to amplify a specific 1.8-kb sequence of mitochondrial DNA from single juveniles and eggs from 17 populations of Meloidogyne incognita, M. hapla, M. javanica, and M. arenaria. Approximately 2 μg amplified product were produced per reaction. Restriction digestion of the amplified product with HinfI permitted discrimination of clonal lineages of the four species. Meloidogyne javanica, however, could not be separated from M. hapla by the enzymes used in these experiments. Various amplification conditions and nematode lysis procedures were examined in order to optimize the speed and quality of identifications.     

Metabolic flux balance analysis and the in silicoanalysis of Escherichia coliK-12 gene deletions

Background

Genome sequencing and bioinformatics are producing detailed lists of the molecular components contained in many prokaryotic organisms. From this 'parts catalogue' of a microbial cell, in silicorepresentations of integrated metabolic functions can be constructed and analyzed using flux balance analysis (FBA). FBA is particularly well-suited to study metabolic networks based on genomic, biochemical, and strain specific information.

Results

Herein, we have utilized FBA to interpret and analyze the metabolic capabilities of Escherichia coli. We have computationally mapped the metabolic capabilities of E. coliusing FBA and examined the optimal utilization of the E. colimetabolic pathways as a function of environmental variables. We have used an in silicoanalysis to identify seven gene products of central metabolism (glycolysis, pentose phosphate pathway, TCA cycle, electron transport system) essential for aerobic growth of E. colion glucose minimal media, and 15 gene products essential for anaerobic growth on glucose minimal media. The in silico tpi ^-, zwf, and pta ^-mutant strains were examined in more detail by mapping the capabilities of these in silicoisogenic strains.

Conclusions

We found that computational models of E. colimetabolism based on physicochemical constraints can be used to interpret mutant behavior. These in silicaresults lead to a further understanding of the complex genotype-phenotype relation. Supplementary information: 10.1186/1471-2105-1-1     

Natural variation in the genes responsible for maturity loci E1, E2, E3 and E4 in soybean

Background and Aims

The timing of flowering has a direct impact on successful seed production in plants. Flowering of soybean (Glycine max) is controlled by several E loci, and previous studies identified the genes responsible for the flowering loci E1, E2, E3 and E4. However, natural variation in these genes has not been fully elucidated. The aims of this study were the identification of new alleles, establishment of allele diagnoses, examination of allelic combinations for adaptability, and analysis of the integrated effect of these loci on flowering.

Methods

The sequences of these genes and their flanking regions were determined for 39 accessions by primer walking. Systematic discrimination among alleles was performed using DNA markers. Genotypes at the E1–E4 loci were determined for 63 accessions covering several ecological types using DNA markers and sequencing, and flowering times of these accessions at three sowing times were recorded.

Key Results

A new allele with an insertion of a long interspersed nuclear element (LINE) at the promoter of the E1 locus (e1-re) was identified. Insertion and deletion of 36 bases in the eighth intron (E2-in and E2-dl) were observed at the E2 locus. Systematic discrimination among the alleles at the E1–E3 loci was achieved using PCR-based markers. Allelic combinations at the E1–E4 loci were found to be associated with ecological types, and about 62–66 % of variation of flowering time could be attributed to these loci.

Conclusions

The study advances understanding of the combined roles of the E1–E4 loci in flowering and geographic adaptation, and suggests the existence of unidentified genes for flowering in soybean,     

Chemical cues involved in the attraction of the oligolectic bee Hoplitis adunca to its host plant Echium vulgare

Host recognition is a key process in oligolectic bees but the mechanisms through which they find and recognize appropriate pollen host plant are not entirely clear. Hoplitis adunca is a monolectic bee collecting pollen only from Echium spp. (Boraginaceae). We aimed to test whether Echium vulgare floral scent plays a major role in the attraction of H. adunca females, and to identify components of E. vulgare scent that may be involved in this specific attraction. We used a combination of behavioral and chemical (GC/GC–MS, PTR-MS) analyses. In order to identify the chemical cues likely to be involved in the specific attraction of H. adunca, we compared the scent of fresh flowers, nectar, pollen, and whole plants of E. vulgare and Anchusa officinalis, another Boraginaceae, which does not attract H. adunca. H. adunca females were attracted to the scent of E. vulgare flowers when offered against a blank or against the scent of A. officinalis flowers. However, H. adunca females were not attracted to the scent of A. officinalis flowers when offered against a blank. The emission spectra of the two plant species differed markedly, as did the emission spectra of various flower components (pollen, nectar and whole flowers) within a species. Pollen presented a low volatile release, but emitted significantly higher amounts of mass 55 (butanal, 1,3-butadiene, or other volatiles of molecular mass 54), and mass 83 (hexanal, hexenols, hexenyl acetate, or other volatiles of molecular mass 82) in E. vulgare than in A. officinalis. Nectar produced a particular emission spectrum with high emission rates of masses 109 and 123. Mass 109 may likely correspond to 1,4-benzoquinone, a volatile specifically measured in E. vulgare in parallel studies to this one. The flower emission spectrum was mainly a combination of the pollen and the nectar scents, although it also contained additional volatile compounds such as those of mass 63 or mass 81. As for terpenes, E. vulgare emitted limonene, longicyclene, junipene, trans-caryophyllene and α-humulene, that were not detected in A. officinalis, and the most emitted monoterpenes were α-pinene, junipene and limonene whereas the most emitted terpenoid by A. officinalis was α-pinene. After identifying these chemical cues, olfactory/behavioural assays with specific volatiles and combinations of volatiles are necessary to understand the chemical interactions of the H. adunca-E. vulgare system.     

Distribution patterns of pelagic euphausiids in the East China Sea

Distribution patterns and abundance of the euphausiids were examined in the East China Sea (23°30′ –33°00′N, 118°30′ –128°00′ E) in relation to temperature and salinity. The data were collected in 4 surveys from 1997 to 2000. The density or yield density model was used to predict optimum temperature and salinity of water for euphausiid distribution, and thereafter distribution patterns of euphausiids were determined based on the predicted parameters. Of 23 species, Euphausia pacifica, E. nana, Pseudeuphausia sinica and P. latifrons were numerically dominant. The analyses indicate that Euphausia pacifica is an offshore temperate water species, E. nana is an offshore temperate warm water species, P. sinica is a coastal subtropical water species and P. latifrons is an oceanic tropical water species. The 4 species occupied 4 different water masses, respectively, namely, cold water mass, cold and warm water mixed masses in winter and spring, cold and warm water mixed masses in summer and autumn, and warm water mass, which could be the good designators of individual water masses, respectively. The predicated optimal temperatures for E. tenera, S. carinatum, E. diomedeae, Stylocheiron affine, Nematoscelis sp., N. gracilis, N. atlantica, Stylocheiron sp. and S. suhmii are all > 25°. These species are mainly distributed in southern Kuroshio in winter and spring, Kuroshio, the Taiwan Warm Current and Tsushima Current in summer and autumn, the equatorial waters of Pacific Ocean and the eastern waters of the Taiwan Strait. They are called as oceanic tropical water species. Nematoscelis tenella and T. tricuspidata are referred to as offshore subtropical water species according to their geographic distributions even if they are halobionts. Euphausia sanzoi is considered as a typical offshore subtropical water species, which inhabited waters below 25°. Stylocheiron microphthalma, occupying warm current waters where temperature and salinity are nearly 25° and 34 in summer and autumn, belongs to oceanic tropical water species. In the same way, E. similes, E. mutica, Euphausia sp., E. brevis and E. recurva are classified into offshore subtropical water species in accordance with the optimum temperature and salinity of waters as well as locations and seasons of their occurrence. Optimum temperature, rather than salinity, is a better parameter in determining the distribution patterns of euphausiids.     

Identification of Olfactory Volatiles using Gas Chromatography-Multi-unit Recordings (GCMR) in the Insect Antennal Lobe

All organisms inhabit a world full of sensory stimuli that determine their behavioral and physiological response to their environment. Olfaction is especially important in insects, which use their olfactory systems to respond to, and discriminate amongst, complex odor stimuli. These odors elicit behaviors that mediate processes such as reproduction and habitat selection^1-3. Additionally, chemical sensing by insects mediates behaviors that are highly significant for agriculture and human health, including pollination^4-6, herbivory of food crops⁷, and transmission of disease^8,9. Identification of olfactory signals and their role in insect behavior is thus important for understanding both ecological processes and human food resources and well-being.To date, the identification of volatiles that drive insect behavior has been difficult and often tedious. Current techniques include gas chromatography-coupled electroantennogram recording (GC-EAG), and gas chromatography-coupled single sensillum recordings (GC-SSR)^10-12. These techniques proved to be vital in the identification of bioactive compounds. We have developed a method that uses gas chromatography coupled to multi-channel electrophysiological recordings (termed ''GCMR'') from neurons in the antennal lobe (AL; the insect''s primary olfactory center)^13,14. This state-of-the-art technique allows us to probe how odor information is represented in the insect brain. Moreover, because neural responses to odors at this level of olfactory processing are highly sensitive owing to the degree of convergence of the antenna''s receptor neurons into AL neurons, AL recordings will allow the detection of active constituents of natural odors efficiently and with high sensitivity. Here we describe GCMR and give an example of its use.Several general steps are involved in the detection of bioactive volatiles and insect response. Volatiles first need to be collected from sources of interest (in this example we use flowers from the genus Mimulus (Phyrmaceae)) and characterized as needed using standard GC-MS techniques^14-16. Insects are prepared for study using minimal dissection, after which a recording electrode is inserted into the antennal lobe and multi-channel neural recording begins. Post-processing of the neural data then reveals which particular odorants cause significant neural responses by the insect nervous system.Although the example we present here is specific to pollination studies, GCMR can be expanded to a wide range of study organisms and volatile sources. For instance, this method can be used in the identification of odorants attracting or repelling vector insects and crop pests. Moreover, GCMR can also be used to identify attractants for beneficial insects, such as pollinators. The technique may be expanded to non-insect subjects as well.     

Human Plasma and the Antibacterial Effect of Peritoneal Dialysis Solutions

The influence of human plasma on the antibacterial effect of solutions for peritoneal dialysis was studied. The solutions contained 43 mEq per litre of either acetate or lactate as the source of base. Enough pooled human plasma was added to half of each solution to give a total concentration of a gramme of protein per litre. The numbers of viable organisms from 15 clinical isolates each of Staphylococcus aureus, Escherichia coli, and Pseudomonas species were counted before and after incubation in the four solutions. Numbers of viable Staph. aureus and E. coli diminished consistently after incubation in all four solutions, but the greatest decreases occurred in the acetate solution which contained no plasma. Plasma abolished the greater antibacterial effect of acetate on these organisms. Differences between numbers of viable Pseudomonas sp. after incubation in the four solutions were not significant. The diffusion of substances from plasma into dialysis fluids during peritoneal dialysis, therefore, may abolish the greater antibacterial effect of solutions made with acetate rather than lactate.     

Progress in developing a new detection method for the harmful algal bloom species,Karenia brevis,through multiwavelength spectroscopy

Multiwavelength spectroscopy is a rapid analytical technique that can be applied to detect, identify, and quantify microorganisms such as Karenia brevis, the species known for frequent red-tide blooms in Florida's coastal waters. This research will report on a model-based interpretation of UV–vis spectra of K. brevis. The spectroscopy models are based on light scattering and absorption theories, and the approximation of the frequency-dependant optical properties of the basic constituents of living organisms. Absorption and scattering properties of K. brevis, such as cell size/shape, internal structure, and chemical composition, are shown to predict the spectral features observed in the measured spectra. The parameters for the interpretation model were based upon both reported literature values, and experimental values obtained from live cultures and pigment standards. Measured and mathematically derived spectra were compared to determine the adequacy of the model, contribute new spectral information, and to establish the proposed spectral interpretation approach as a new detection method for K. brevis.     

Survival Times of Selected Enteropathogenic Bacteria in Frozen Passionfruit Nectar Base

Five test organisms were used: Escherichia coli, Salmonella typhosa, Salmonella schottmuelleri, Salmonella enteritidis, and Shigella paradysenteriae. Even when large inocula of these test cultures were introduced into fresh passionfruit nectar base, all test organisms were killed within 1 to 2 hr, provided the nectar base was held at room temperature for more than 1 hr before freezing. If the nectar base was frozen immediately after inoculation, four of the five test organisms were eliminated almost as quickly. But the fifth, Salmonella enteritidis, proved to be exceptional: it was being recovered after 90 days of storage at -20 C, when the last available sample was analyzed.     

Resistant Germplasm in Gossypium Species and Related Plants to Rotylenchulus reniformis

Gossypium hirsutum, G. herbaceum, G. arboreum, G. barbadense, wild Gossypium spp., Hibiscus spp, and other Malvaceae were tested in the greenhouse to identify germplasm resistant to Rotylenchulus reniformis (Rr). Host resistance was based on Rr egg production per gram of root compared with known G. hirsutum susceptible ''Deltapine 16'' as check. G. longicalyx and Sida rhombifolia were nonhosts. High levels of resistance were found in G. stocksii, G. somalense, and G. barbadense ''Texas 110.'' Other cotton lines with potential value in breeding for Rr resistance were G. herbaceum P.I. 408775; G. arboreum P.I. 41895, P.I, 417891, CB 3839; and G. hirsutum 893. All these supported less than 20% of the egg production on the check. Seventy-three percent of the Hibiscus spp. tested were resistant. Female development and egg production reflected host resistance; healthy females and large egg masses were observed on susceptible plants, and degenerated females and small egg masses on resistant plants. Females penetrating nonhost G. longicalyx never matured to kidney shape.     

Porins from marine bacteria of the genus Pseudoalteromonas (Gammaproteobacteria: Pseudoalteromonadaceae)

Outer membrane (OM) fractions were isolated from marine bacteria of the genus Pseudoalteromonas (P. haloplanktis, P. tetraodonis, and Pseudoalteromonas sp. KMM 223). The purity of OM fractions was confirmed by ultracentrifugation in a sucrose gradient. Using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and the bilayer lipid membrane (BLM) technique, heat-modifiable porin-like proteins were identified among the OM proteins of marine pseudomonads. The pore-forming P-1 and P-2 proteins with molecular masses of 43 and 39 kDa, respectively, were obtained from the marine bacterium P. haloplanktis. The nature of current fluctuations in the BLM and the conductivity of pores formed by these proteins suggest that these isolated porins are not identical in their functional properties. A nonlinear dependence of channel conductivity on salt concentration in the aqueous phase was found for the P-2 protein, which is typical of marine bacterial porins.     

Mutations that permit residual CFTR function delay acquisition of multiple respiratory pathogens in CF patients

Background

Lung infection by various organisms is a characteristic feature of cystic fibrosis (CF). CFTR genotype effects acquisition of Pseudomonas aeruginosa (Pa), however the effect on acquisition of other infectious organisms that frequently precede Pa is relatively unknown. Understanding the role of CFTR in the acquisition of organisms first detected in patients may help guide symptomatic and molecular-based treatment for CF.

Methods

Lung infection, defined as a single positive respiratory tract culture, was assessed for 13 organisms in 1,381 individuals with CF. Subjects were divided by predicted CFTR function: ''Residual'': carrying at least one partial function CFTR mutation (class IV or V) and ''Minimal'' those who do not carry a partial function mutation. Kaplan-Meier estimates were created to assess CFTR effect on age of acquisition for each organism. Cox proportional hazard models were performed to control for possible cofactors. A separate Cox regression was used to determine whether defining infection with Pa, mucoid Pa or Aspergillus (Asp) using alternative criteria affected the results. The influence of severity of lung disease at the time of acquisition was evaluated using stratified Cox regression methods by lung disease categories.

Results

Subjects with ''Minimal'' CFTR function had a higher hazard than patients with ''Residual'' function for acquisition of 9 of 13 organisms studied (HR ranging from 1.7 to 3.78 based on the organism studied). Subjects with minimal CFTR function acquired infection at a younger age than those with residual function for 12 of 13 organisms (p-values ranging: < 0.001 to 0.017). Minimal CFTR function also associated with younger age of infection when 3 alternative definitions of infection with Pa, mucoid Pa or Asp were employed. Risk of infection is correlated with CFTR function for 8 of 9 organisms in patients with good lung function (>90%ile) but only 1 of 9 organisms in those with poorer lung function (<50%ile).

Conclusions

Residual CFTR function correlates with later onset of respiratory tract infection by a wide spectrum of organisms frequently cultured from CF patients. The protective effect conferred by residual CFTR function is diminished in CF patients with more advanced lung disease.     

Systematic investigation of interactions between papain and MPA-capped CdTe quantum dots

Fluorescent quantum dots (QDs) have been widely applied in biological and biomedical areas, but relatively little is known about the interaction of QDs with some natural enzymes. Herein, the interactions between 3-mercaptopropionic acid-capped CdTe QDs (MPA-QDs) and papain were systematically investigated by UV–Vis absorption spectra, fluorescence spectra and circular dichroism (CD) spectra under the physiological conditions. The fluorescence spectra results indicated that MPA-QDs quenched the fluorescence intensity of papain. The modified Stern–Volmer quenching constant K _a at different temperatures and the corresponding thermodynamic parameters ΔH, ΔG and ΔS were also calculated. The binding of MPA-QDs and papain is a result of the formation of QDs-papain complex and the electrostatic interactions play a major role in stabilizing the complex. The CD technique was further used to analyze the conformational changes of papain induced by MPA-QDs and the results indicated that the biological activity of papain was affected by MPA-QDs dramatically.     

Evidence of taxa-, clone-, and kin-discrimination in protists: ecological and evolutionary implications

Unicellular eukaryotes, or protists, are among the most ancient organisms on Earth. Protists belong to multiple taxonomic groups; they are widely distributed geographically and in all environments. Their ability to discriminate among con- and heterospecifics has been documented during the past decade. Here we discuss exemplar cases of taxa-, clone-, and possible kin-discrimination in five major lineages: Mycetozoa (Dictyostelium, Polysphondylium), Dikarya (Saccharomyces), Ciliophora (Tetrahymena), Apicomplexa (Plasmodium) and Archamoebae (Entamoeba). We summarize the proposed genetic mechanisms involved in discrimination-mediated aggregation (self vs. different), including the csA, FLO and trg (formerly lag) genes, and the Proliferation Activation Factors, which facilitate clustering in some protistan taxa. We caution about the experimental challenges intrinsic to studying recognition in protists, and highlight the opportunities for exploring the ecology and evolution of complex forms of cell–cell communication, including social behavior, in a polyphyletic, still superficially understood group of organisms. Because unicellular eukaryotes are the evolutionary precursors of multicellular life, we infer that their mechanisms of taxa-, clone-, and possible kin-discrimination gave origin to the complex diversification and sophistication of traits associated with species and kin recognition in plants, fungi, invertebrates and vertebrates.     

Major Soybean Maturity Gene Haplotypes Revealed by SNPViz Analysis of 72 Sequenced Soybean Genomes

In this Genomics Era, vast amounts of next-generation sequencing data have become publicly available for multiple genomes across hundreds of species. Analyses of these large-scale datasets can become cumbersome, especially when comparing nucleotide polymorphisms across many samples within a dataset and among different datasets or organisms. To facilitate the exploration of allelic variation and diversity, we have developed and deployed an in-house computer software to categorize and visualize these haplotypes. The SNPViz software enables users to analyze region-specific haplotypes from single nucleotide polymorphism (SNP) datasets for different sequenced genomes. The examination of allelic variation and diversity of important soybean [Glycine max (L.) Merr.] flowering time and maturity genes may provide additional insight into flowering time regulation and enhance researchers'' ability to target soybean breeding for particular environments. For this study, we utilized two available soybean genomic datasets for a total of 72 soybean genotypes encompassing cultivars, landraces, and the wild species Glycine soja. The major soybean maturity genes E1, E2, E3, and E4 along with the Dt1 gene for plant growth architecture were analyzed in an effort to determine the number of major haplotypes for each gene, to evaluate the consistency of the haplotypes with characterized variant alleles, and to identify evidence of artificial selection. The results indicated classification of a small number of predominant haplogroups for each gene and important insights into possible allelic diversity for each gene within the context of known causative mutations. The software has both a stand-alone and web-based version and can be used to analyze other genes, examine additional soybean datasets, and view similar genome sequence and SNP datasets from other species.