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https://www.readbyqxmd.com/read/28340301/ten-years-of-barcoding-at-the-african-centre-for-dna-barcoding
#1
Simeon Bezeng Bezeng, T Jonathan Davies, Barnabas H Daru, Ronny Mukala Kabongo, Olivier Maurin, Kowiyou Yessoufou, Herman van der Bank, Michelle Van der Bank
The African Centre for DNA Barcoding (ACDB) was established in 2005 as part of a global initiative to accurately and rapidly survey biodiversity using short DNA sequences. The mitochondrial cytochrome c oxidase 1 gene (CO1) was rapidly adopted as the de facto barcode for animals. Following the evaluation of several candidate loci for plants, the Plant Working Group of the Consortium for the Barcoding of Life in 2009 recommended that the two plastid genes, rbcLa and matK, be adopted as core DNA barcodes for terrestrial plants...
March 24, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28338988/phylogenetics-of-lophotrochozoan-bhlh-genes-and-the-evolution-of-lineage-specific-gene-duplicates
#2
Yongbo Bao, Fei Xu, Sebastian M Shimeld
The gain and loss of genes encoding transcription factors is of importance to understanding the evolution of gene regulatory complexity. The basic helix-loop-helix (bHLH) genes encode a large superfamily of transcription factors. We systematically classify the bHLH genes from five mollusc, two annelid and one brachiopod genomes, tracing the pattern of bHLH gene evolution across these poorly-studied Phyla. 56 to 88 bHLH genes were identified in each genome, with most identifiable as members of previously described bilaterian families, or of new families we define...
March 11, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338931/evolutionary-dynamics-of-pathoadaptation-revealed-by-three-independent-acquisitions-of-the-virb-d4-type-iv-secretion-system-in-bartonella
#3
Alexander Harms, Francisca H I D Segers, Maxime Quebatte, Claudia Mistl, Pablo Manfredi, Jonas Körner, Bruno B Chomel, Michael Kosoy, Soichi Maruyama, Philipp Engel, Christoph Dehio
The α-proteobacterial genus Bartonella comprises a group of ubiquitous mammalian pathogens that are studied as a model for the evolution of bacterial pathogenesis. Vast abundance of two particular phylogenetic lineages of Bartonella had been linked to enhanced host adaptability enabled by lineage-specific acquisition of a VirB/D4 type IV secretion system (T4SS) and parallel evolution of complex effector repertoires. However, the limited availability of genome sequences from one of those lineages as well as other, remote branches of Bartonella has so far hampered comprehensive understanding of how the VirB/D4 T4SS and its effectors called Beps have shaped Bartonella evolution...
March 7, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338679/entomopathogenic-bacteria-use-multiple-mechanisms-for-bioactive-peptide-library-design
#4
Xiaofeng Cai, Sarah Nowak, Frank Wesche, Iris Bischoff, Marcel Kaiser, Robert Fürst, Helge B Bode
The production of natural product compound libraries has been observed in nature for different organisms such as bacteria, fungi and plants; however, little is known about the mechanisms generating such chemically diverse libraries. Here we report mechanisms leading to the biosynthesis of the chemically diverse rhabdopeptide/xenortide peptides (RXPs). They are exclusively present in entomopathogenic bacteria of the genera Photorhabdus and Xenorhabdus that live in symbiosis with nematodes delivering them to insect prey, which is killed and utilized for nutrition by both nematodes and bacteria...
April 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28338049/breeding-system-and-spatial-isolation-from-congeners-strongly-constrain-seed-set-in-an-insect-pollinated-apomictic-tree-sorbus-subcuneata-rosaceae
#5
Tracey J Hamston, Robert J Wilson, Natasha de Vere, Tim C G Rich, Jamie R Stevens, James E Cresswell
In plants, apomixis results in the production of clonal offspring via seed and can provide reproductive assurance for isolated individuals. However, many apomicts require pollination to develop functional endosperm for successful seed set (pseudogamy) and therefore risk pollination-limitation, particularly in self-incompatible species that require heterospecific pollen. We used microsatellite paternity analysis and hand pollinations to investigate pollen-limitation in Sorbus subcuneata, a threatened endemic tree that co-occurs with its congener, S...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28337178/glucose-uptake-in-prochlorococcus-diversity-of-kinetics-and-effects-on-the-metabolism
#6
María Del Carmen Muñoz-Marín, Guadalupe Gómez-Baena, Jesús Díez, Robert J Beynon, David González-Ballester, Mikhail V Zubkov, José M García-Fernández
We have previously shown that Prochlorococcus sp. SS120 strain takes up glucose by using a multiphasic transporter encoded by the Pro1404 gene. Here, we studied the glucose uptake kinetics in multiple Prochlorococcus strains from different ecotypes, observing diverse values for the Ks constants (15-126.60 nM) and the uptake rates (0.48-6.36 pmol min(-1) mg prot(-1)). Multiphasic kinetics was observed in all studied strains, except for TAK9803-2. Pro1404 gene expression studies during the 21st Atlantic Meridional Transect cruise showed positive correlation with glucose concentrations in the ocean...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28336178/symbiont-acquisition-and-replacement-as-a-source-of-ecological-innovation
#7
REVIEW
Sailendharan Sudakaran, Christian Kost, Martin Kaltenpoth
Nutritional symbionts play a major role in the ecology and evolution of insects. The recent accumulation of knowledge on the identity, function, genomics, and phylogenetic relationships of insect-bacteria symbioses provides the opportunity to assess the effects of symbiont acquisitions and replacements on the shift into novel ecological niches and subsequent lineage diversification. The megadiverse insect order Hemiptera presents a particularly large diversity of symbiotic associations that has frequently undergone shifts in symbiont localization and identity, which have contributed to the exploitation of nutritionally imbalanced diets such as plant saps or vertebrate blood...
March 20, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28335721/transcriptomic-insights-into-the-genetic-basis-of-mammalian-limb-diversity
#8
Jennifer A Maier, Marcelo Rivas-Astroza, Jenny Deng, Anna Dowling, Paige Oboikovitz, Xiaoyi Cao, Richard R Behringer, Chris J Cretekos, John J Rasweiler, Sheng Zhong, Karen E Sears
BACKGROUND: From bat wings to whale flippers, limb diversification has been crucial to the evolutionary success of mammals. We performed the first transcriptome-wide study of limb development in multiple species to explore the hypothesis that mammalian limb diversification has proceeded through the differential expression of conserved shared genes, rather than by major changes to limb patterning. Specifically, we investigated the manner in which the expression of shared genes has evolved within and among mammalian species...
March 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28334262/discriminating-the-reaction-types-of-plant-type-iii-polyketide-synthases
#9
Yugo Shimizu, Hiroyuki Ogata, Susumu Goto
Motivation: Functional prediction of paralogs is challenging in bioinformatics because of rapid functional diversification after gene duplication events combined with parallel acquisitions of similar functions by different paralogs. Plant type III polyketide synthases (PKSs), producing various secondary metabolites, represent a paralogous family that has undergone gene duplication and functional alteration. Currently, there is no computational method available for the functional prediction of type III PKSs...
March 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334223/is-bamm-flawed-theoretical-and-practical-concerns-in-the-analysis-of-multi-rate-diversification-models
#10
Daniel L Rabosky, Jonathan S Mitchell, Jonathan Chang
BAMM (Bayesian Analysis of Macroevolutionary Mixtures) is a statistical framework that uses reversible jump MCMC to infer complex macroevolutionary dynamics of diversification and phenotypic evolution on phylogenetic trees. A recent article by Moore and coauthors (MEA) reported a number of theoretical and practical concerns with BAMM. Major claims from MEA are that (1) BAMM's likelihood function is incorrect, because it does not account for unobserved rate shifts; (2) the posterior distribution on the number of rate shifts is overly sensitive to the prior; and (3) diversification rate estimates from BAMM are unreliable...
February 21, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28334206/polyploid-species-rely-on-vegetative-reproduction-more-than-diploids-a-re-examination-of-the-old-hypothesis
#11
Tomáš Herben, Jan Suda, Jitka Klimešová
Background and Aims: Polyploidy is arguably the single most important genetic mechanism in plant speciation and diversification. It has been repeatedly suggested that polyploids show higher vegetative reproduction than diploids (to by-pass low fertility after the polyploidization), but there are no rigorous tests of it. Methods: Data were analysed by phylogenetic regressions of clonal growth parameters, and vegetative reproduction in culture on the ploidy status of a large set of species (approx...
February 27, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28334085/environmental-niche-divergence-among-three-dune-shrub-sister-species-with-parapatric-distributions
#12
Sergio Chozas, Rosa M Chefaoui, Otília Correia, Raúl Bonal, Joaquín Hortal
Background and Aims: The geographical distributions of species are constrained by their ecological requirements. The aim of this work was to analyse the effects of environmental conditions, historical events and biogeographical constraints on the diversification of the three species of the western Mediterranean shrub genus Stauracanthus , which have a parapatric distribution in the Iberian Peninsula. Methods: Ecological niche factor analysis and generalized linear models were used to measure the response of all Stauracanthus species to the environmental gradients and map their potential distributions in the Iberian Peninsula...
February 20, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28333396/conflicting-phylogenomic-signals-reveal-a-pattern-of-reticulate-evolution-in-a-recent-high-andean-diversification-asteraceae-astereae-diplostephium
#13
Oscar M Vargas, Edgardo M Ortiz, Beryl B Simpson
High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods...
March 23, 2017: New Phytologist
https://www.readbyqxmd.com/read/28333336/comparative-sperm-proteomics-in-mouse-species-with-divergent-mating-systems
#14
Alberto Vicens, Kirill Borziak, Timothy L Karr, Eduardo R S Roldan, Steve Dorus
Sexual selection is the pervasive force underlying the dramatic divergence of sperm form and function. Although it has been demonstrated that testis gene expression evolves rapidly, exploration of the proteomic basis of sperm diversity is in its infancy. We have employed a whole-cell proteomics approach to characterize sperm divergence among closely related Mus species that experience different sperm competition regimes and exhibit pronounced variation in sperm energetics, motility and fertilization capacity...
February 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28331386/phylogenetic-analysis-of-the-genus-laparocerus-with-comments-on-colonisation-and-diversification-in-macaronesia-coleoptera-curculionidae-entiminae
#15
Antonio Machado, Eduardo Rodríguez-Expósito, Mercedes López, Mariano Hernández
The flightless Entiminae weevil genus Laparocerus is the species-richest genus, with 237 species and subspecies, inhabiting Macaronesia (Madeira archipelago, Selvagens, Canary Islands) and the continental 'Macaronesian enclave' in Morocco (one single polytypic species). This is the second contribution to gain insight of the genus and assist in its systematic revision with a mitochondrial phylogenetic analysis. It centres on the Canarian clade, adding the 12S rRNA gene to the combined set of COII and 16S rRNA used in our first contribution on the Madeiran clade (here re-analysed)...
2017: ZooKeys
https://www.readbyqxmd.com/read/28330989/form-function-relationships-in-dragonfly-mandibles-under-an-evolutionary-perspective
#16
Alexander Blanke, Helmut Schmitz, Alessandra Patera, Hugo Dutel, Michael J Fagan
Functional requirements may constrain phenotypic diversification or foster it. For insect mouthparts, the quantification of the relationship between shape and function in an evolutionary framework remained largely unexplored. Here, the question of a functional influence on phenotypic diversification for dragonfly mandibles is assessed with a large-scale biomechanical analysis covering nearly all anisopteran families, using finite element analysis in combination with geometric morphometrics. A constraining effect of phylogeny could be found for shape, the mandibular mechanical advantage (MA), and certain mechanical joint parameters, while stresses and strains, the majority of joint parameters and size are influenced by shared ancestry...
March 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28330866/response-to-comment-on-diversification-of-the-antigen-specific-t-cell-receptor-repertoire-after-varicella-zoster-vaccination
#17
Jorg Goronzy, Qian Qi, Cornelia Weyand
In our repertoire studies of varicella zoster virus-specific T cells, we used very stringent computational criteria to keep contamination with T cell receptor sequences from bystander-activated T cells to a minimum.
March 22, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28330864/comment-on-diversification-of-the-antigen-specific-t-cell-receptor-repertoire-after-varicella-zoster-vaccination
#18
Christophe Parizot, Hélène Brisson, Jehane Fadlallah, Delphine Sterlin, Guy Gorochov
Analysis of antigen-specific T cells can be confounded by T cell activation in vitro.
March 22, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28330170/an-efficient-and-cost-effective-method-of-rna-extraction-from-mucilage-phenol-and-secondary-metabolite-rich-bark-tissue-of-tossa-jute-c-olitorius-l-actively-developing-phloem-fiber
#19
S B Choudhary, M Kumar, I Chowdhury, R K Singh, S P Pandey, H K Sharma, P G Karmakar
Tossa jute is an important natural fiber crop of Southeast Asian countries including India, Bangladesh, China, Thailand, Myanmar etc. Traditional industrial application of jute fiber is limited to the packaging products like hessians, sacks, etc. and the fiber found unsuitable for textile industries largely due to significantly high lignin content. Therefore, understanding genetic factors underlying lignin biosynthesis in tossa jute holds promise for jute based product diversification. The major limiting factor in undertaking such study is unavailability of efficient protocol for RNA extraction at secondary growth active stage of tossa jute...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329560/patient-provider-communication-concordance-and-ratings-of-care-in-dermatology-results-of-a-cross-sectional-study
#20
Valerie M Harvey, Uchechukwu Ozoemena, Joan Paul, Hind A Beydoun, Nashay N Clemetson, Ginette A Okoye
ObjectiveTo determine the impact of race concordance on patient perception of quality of dermatologic care.Study designCross-sectional study.SettingAcademic outpatient practices in the Departments of Dermatology of Eastern Virginia Medical School and the Johns Hopkins University School of Medicine.ParticipantsThe study cohort comprised 124 participants including 6 providers and 118 established patients.Main Outcome MeasuresWe hypothesized, a priori, that patients in race-discordant dyads would report lower ratings of participatory decision-making (PDM), satisfaction, trust in the provider, and similarities with providers...
November 15, 2016: Dermatology Online Journal
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