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https://www.readbyqxmd.com/read/27930742/analysis-of-domain-architecture-and-phylogenetics-of-family-2-glycoside-hydrolases-gh2
#1
David Talens-Perales, Anna Górska, Daniel H Huson, Julio Polaina, Julia Marín-Navarro
In this work we report a detailed analysis of the topology and phylogenetics of family 2 glycoside hydrolases (GH2). We distinguish five topologies or domain architectures based on the presence and distribution of protein domains defined in Pfam and Interpro databases. All of them share a central TIM barrel (catalytic module) with two β-sandwich domains (non-catalytic) at the N-terminal end, but differ in the occurrence and nature of additional non-catalytic modules at the C-terminal region. Phylogenetic analysis was based on the sequence of the Pfam Glyco_hydro_2_C catalytic module present in most GH2 proteins...
2016: PloS One
https://www.readbyqxmd.com/read/27930649/multiple-factors-affect-socioeconomics-and-wellbeing-of-artisanal-sea-cucumber-fishers
#2
Steven W Purcell, Poasi Ngaluafe, Simon J Foale, Nicole Cocks, Brian R Cullis, Watisoni Lalavanua
Small-scale fisheries are important to livelihoods and subsistence seafood consumption of millions of fishers. Sea cucumbers are fished worldwide for export to Asia, yet few studies have assessed factors affecting socioeconomics and wellbeing among fishers. We interviewed 476 men and women sea cucumber fishers at multiple villages within multiple locations in Fiji, Kiribati, Tonga and New Caledonia using structured questionnaires. Low rates of subsistence consumption confirmed a primary role of sea cucumbers in income security...
2016: PloS One
https://www.readbyqxmd.com/read/27929718/lotus-japonicus-nf-ya1-plays-an-essential-role-during-nodule-differentiation-and-targets-members-of-the-shi-sty-gene-family
#3
Md Shakhawat Hossain, Arina Shrestha, Sihui Zhong, Mandana Miri, Ryan S Austin, Shusei Sato, Loretta Ross, Terry Huebert, Alexandre Tromas, Ivone Torres-Jerez, Yuhong Tang, Michael Udvardi, Jeremy Dale Murray, Krzysztof Szczyglowski
Legume plants engage in intimate relationships with rhizobial bacteria to form nitrogen-fixing nodules, root-derived organs that accommodate the micro-symbiont. Members of the Nuclear Factor Y (NF-Y) gene family, which have undergone significant expansion and functional diversification during plant evolution, are essential for this symbiotic liaison. Acting in a partially redundant manner, NF-Ys were shown previously to regulate bacterial infection, including selection of a superior rhizobial strain, and to mediate nodule structure formation...
December 8, 2016: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/27929467/an-optimized-protocol-for-electrophoretic-mobility-shift-assay-using-infrared-fluorescent-dye-labeled-oligonucleotides
#4
Yi-Wen Hsieh, Amel Alqadah, Chiou-Fen Chuang
Electrophoretic Mobility Shift Assays (EMSA) are an instrumental tool to characterize the interactions between proteins and their target DNA sequences. Radioactivity has been the predominant method of DNA labeling in EMSAs. However, recent advances in fluorescent dyes and scanning methods have prompted the use of fluorescent tagging of DNA as an alternative to radioactivity for the advantages of easy handling, saving time, reducing cost, and improving safety. We have recently used fluorescent EMSA (fEMSA) to successfully address an important biological question...
November 29, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27929063/a-large-carnivorous-mammal-from-the-late-cretaceous-and-the-north-american-origin-of-marsupials
#5
Gregory P Wilson, Eric G Ekdale, John W Hoganson, Jonathan J Calede, Abby Vander Linden
Marsupial mammal relatives (stem metatherians) from the Mesozoic Era (252-66 million years ago) are mostly known from isolated teeth and fragmentary jaws. Here we report on the first near-complete skull remains of a North American Late Cretaceous metatherian, the stagodontid Didelphodon vorax. Our phylogenetic analysis indicates that marsupials or their closest relatives evolved in North America, as part of a Late Cretaceous diversification of metatherians, and later dispersed to South America. In addition to being the largest known Mesozoic therian mammal (node-based clade of eutherians and metatherians), Didelphodon vorax has a high estimated bite force and other craniomandibular and dental features that suggest it is the earliest known therian to invade a durophagous predator-scavenger niche...
December 8, 2016: Nature Communications
https://www.readbyqxmd.com/read/27928690/from-shoot-to-leaf-step-wise-shifts-in-meristem-and-knox1-activity-correlate-with-the-evolution-of-a-unifoliate-body-plan-in-gesneriaceae
#6
Kanae Nishii, Bing-Hong Huang, Chun-Neng Wang, Michael Möller
Typical dicots possess equal-sized cotyledons and leaf-bearing shoots topped with a shoot apical meristem (SAM), the source of lateral organs, and where KNOX1 homeobox genes act as key regulators. New World Gesneriaceae show typical cotyledons, whereas Old World Gesneriaceae show anisocotyly, the unequal post-germination growth of cotyledons, and include unifoliate (one-leaf) plants. One-leaf plants show an extremely reduced body plan: the adult above-ground photosynthetic tissue consisting of a single cotyledon, a macrocotyledon enlarged by the basal meristem (BM), but lacking a SAM...
December 8, 2016: Development Genes and Evolution
https://www.readbyqxmd.com/read/27927184/ty1-copia-elements-reveal-diverse-insertion-sites-linked-to-polymorphisms-among-flax-linum-usitatissimum-l-accessions
#7
Leonardo Galindo-González, Corinne Mhiri, Marie-Angèle Grandbastien, Michael K Deyholos
BACKGROUND: Initial characterization of the flax genome showed that Ty1-copia retrotransposons are abundant, with several members being recently inserted, and in close association with genes. Recent insertions indicate a potential for ongoing transpositional activity that can create genomic diversity among accessions, cultivars or varieties. The polymorphisms generated constitute a good source of molecular markers that may be associated with phenotype if the insertions alter gene activity...
December 7, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27927169/comparative-phylogeography-in-the-atlantic-forest-and-brazilian-savannas-pleistocene-fluctuations-and-dispersal-shape-spatial-patterns-in-two-bumblebees
#8
Elaine Françoso, Alexandre Rizzo Zuntini, Ana Carolina Carnaval, Maria Cristina Arias
BACKGROUND: Bombus morio and B. pauloensis are sympatric widespread bumblebee species that occupy two major Brazilian biomes, the Atlantic forest and the savannas of the Cerrado. Differences in dispersion capacity, which is greater in B. morio, likely influence their phylogeographic patterns. This study asks which processes best explain the patterns of genetic variation observed in B. morio and B. pauloensis, shedding light on the phenomena that shaped the range of local populations and the spatial distribution of intra-specific lineages...
December 7, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27926804/the-impact-of-racism-and-midwifery-s-lack-of-racial-diversity-a-literature-review
#9
REVIEW
Jyesha Wren Serbin, Elizabeth Donnelly
INTRODUCTION: The United States is increasingly racially diverse. Racial disparities in maternal-child health persist. Despite national calls for workforce diversification, more than 90% of certified nurse-midwives are white. This systematic review examines how racism and midwifery's lack of racial diversity impact both midwives and their patients. METHODS: Databases were searched in January 2016 for studies that explored 1) racially concordant or racially discordant maternity care provided, at least in part, by midwives; 2) women of color's experience of race and discrimination in maternity care provided, at least in part, by midwives; and 3) midwives of color's experience of race and discrimination in clinical, educational, and/or professional settings...
November 2016: Journal of Midwifery & Women's Health
https://www.readbyqxmd.com/read/27925707/natural-mineral-bottled-waters-available-on-the-polish-market-as-a-source-of-minerals-for-the-consumers-part-2-the-intake-of-sodium-and-potassium
#10
Anna Gątarska, Joanna Ciborska, Elżbieta Tońska
Background: Natural mineral waters are purchased and consumed according to consumer preferences and possible recommendations. The choice of appropriate water should take into account not only the general level of mineralization but also the content of individual components, including electrolytes such as sodium and potassium. Sodium is necessary to ensure the proper physiological functions of the body. It is defined as a health risk factor only when its excessive intake occurs. Potassium acts antagonistically towards sodium and calcium ions, contributes to a reduction of the volume of extracellular fluids and at the same time reduces muscle tension and permeability of cell membranes...
2016: Roczniki Państwowego Zakładu Higieny
https://www.readbyqxmd.com/read/27925684/ecological-diversification-associated-with-the-benthic-to-pelagic-transition-by-north-american-minnows
#11
Edward D Burress, Jordan M Holcomb, Milton Tan, Jonathan W Armbruster
Ecological opportunity is often regarded as a key factor that explains why diversity is unevenly distributed across life. Colonization of novel environments or adaptive zones may promote diversification. North American minnows exhibit an ancestral benthic to pelagic habitat shift that coincided with a burst in diversification. Here, we evaluate the phenotypic and ecological implications of this habitat shift by assessing craniofacial and dietary traits among 34 species and testing for morphology-diet covariation, convergence, and adaptive optima...
December 7, 2016: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/27925177/t-cell-diversification-reflects-antigen-selection-in-the-blood-of-patients-on-immune-checkpoint-inhibition-and-may-be-exploited-as-liquid-biopsy-biomarker
#12
Nuray Akyüz, Anna Brandt, Alexander Stein, Simon Schliffke, Thorben Mährle, Julia Quidde, Eray Goekkurt, Sonja Loges, Thomas Haalck, Christopher Ford, Anne Marie Asemissen, Benjamin Thiele, Janina Radloff, Toni Thenhausen, Artus Krohn-Grimberghe, Carsten Bokemeyer, Mascha Binder
Cancer immunotherapy with antibodies targeting immune checkpoints, such as programmed cell death protein 1 (PD-1), shows encouraging results, but reliable biomarkers predicting response to this costly and potentially toxic treatment approach are still lacking. To explore an immune signature predictive for response, we performed liquid biopsy immunoprofiling in 18 cancer patients undergoing PD-1 inhibition before and shortly after initiation of treatment by multicolor flow cytometry and next-generation T- and B-cell immunosequencing (TCRß/IGH)...
December 7, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27925171/matching-habitat-choice-in-nomadic-crossbills-appears-most-pronounced-when-food-is-most-limiting
#13
Craig W Benkman
Of the various forms of non-random dispersal, matching habitat choice, whereby individuals preferentially reside in habitats where they are best adapted, has relatively little empirical support. Here I use mark-recapture data to test for matching habitat choice in two nomadic ecotypes of North American Red Crossbills (Loxia curvirostra complex) that occur in the lodgepole pine (Pinus contorta) forests in the South Hills, Idaho every summer. Crossbills are adapted for foraging on seeds in conifer cones, and in the South Hills the cones are distinctive, favoring a relatively large bill...
December 7, 2016: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27923409/geographical-landscape-and-host-associations-of-trypanosoma-cruzi-dtus-and-lineages
#14
Amaia Izeta-Alberdi, Carlos N Ibarra-Cerdeña, David A Moo-Llanes, Janine M Ramsey
BACKGROUND: The evolutionary history and ecological associations of Trypanosoma cruzi, the need to identify genetic markers that can distinguish parasite subpopulations, and understanding the parasite's evolutionary and selective processes have been the subject of a significant number of publications since 1998, the year when the first DNA sequence analysis for the species was published. METHODS: The current analysis systematizes and re-analyzes this original research, focusing on critical methodological and analytical variables and results that have given rise to interpretations of putative patterns of genetic diversity and diversification of T...
December 7, 2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27921295/digest-sticklebacks-don-t-just-go-with-the-flow-genetic-differentiation-between-lake-and-stream-populations-due-to-more-than-just-geographic-distance1
#15
Emilie Richards, Aaron Comeault, Jelmer Poelstra
Speciation is thought to occur in large part through the gradual accumulation of genetic differences between partly or completely isolated populations. However, many species differ greatly in their ecology, prompting research into ecology's role in driving genetic differentiation and speciation. Ultimately, understanding diversification requires understanding the factors that allow populations to diverge enough to no longer be considered the same species. This article is protected by copyright. All rights reserved...
December 6, 2016: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27920373/human-influences-on-evolution-and-the-ecological-and-societal-consequences
#16
Andrew P Hendry, Kiyoko M Gotanda, Erik I Svensson
Humans have dramatic, diverse and far-reaching influences on the evolution of other organisms. Numerous examples of this human-induced contemporary evolution have been reported in a number of 'contexts', including hunting, harvesting, fishing, agriculture, medicine, climate change, pollution, eutrophication, urbanization, habitat fragmentation, biological invasions and emerging/disappearing diseases. Although numerous papers, journal special issues and books have addressed each of these contexts individually, the time has come to consider them together and thereby seek important similarities and differences...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920231/bayesian-morphological-clock-methods-resurrect-placoderm-monophyly-and-reveal-rapid-early-evolution-in-jawed-vertebrates
#17
Benedict King, Tuo Qiao, Michael S Y Lee, Min Zhu, John A Long
The phylogeny of early gnathostomes provides an important framework for understanding one of the most significant evolutionary events, the origin and diversification of jawed vertebrates. A series of recent cladistic analyses have suggested that the placoderms, an extinct group of armoured fish, form a paraphyletic group basal to all other jawed vertebrates. We revised and expanded this morphological data set, most notably by sampling autapomorphies in a similar way to parsimony-informative traits, thus ensuring this data (unlike most existing morphological data sets) satisfied an important assumption of Bayesian tip-dated morphological clock approaches...
December 5, 2016: Systematic Biology
https://www.readbyqxmd.com/read/27918625/host-shifts-enhance-diversification-of-ectomycorrhizal-fungi-diversification-rate-analysis-of-the-ectomycorrhizal-fungal-genera-strobilomyces-and-afroboletus-with-an-80-gene-phylogeny
#18
Hirotoshi Sato, Akifumi S Tanabe, Hirokazu Toju
Mutualisms with new host lineages can provide symbionts with novel ecological opportunities to expand their geographical distribution, thereby leading to evolutionary diversification. Because ectomycorrhizal (ECM) fungi provide ideal opportunities to test the relationship between host shifts and diversification, we tested whether mutualism with new host lineages could increase the diversification rates of ECM fungi. Using a Bayesian tree inferred from 23 027-base nucleotide sequences of 80 single-copy genes, we tested whether the diversification rate had changed through host-shift events in the monophyletic clade containing the ECM fungal genera Strobilomyces and Afroboletus...
December 5, 2016: New Phytologist
https://www.readbyqxmd.com/read/27918539/rapidly-evolving-homing-crispr-barcodes
#19
Reza Kalhor, Prashant Mali, George M Church
We present an approach for engineering evolving DNA barcodes in living cells. A homing guide RNA (hgRNA) scaffold directs the Cas9-hgRNA complex to the DNA locus of the hgRNA itself. We show that this homing CRISPR-Cas9 system acts as an expressed genetic barcode that diversifies its sequence and that the rate of diversification can be controlled in cultured cells. We further evaluate these barcodes in cell populations and show that they can be used to record lineage history and that the barcode RNA can be amplified in situ, a prerequisite for in situ sequencing...
December 5, 2016: Nature Methods
https://www.readbyqxmd.com/read/27918293/structural-and-theoretical-characterization-of-a-new-twisted-4-substituted-terpyridine-compound-4-isoquinolin-4-yl-2-2-6-2-terpyridine
#20
Juan Granifo, Beatriz Arévalo, Rubén Gaviño, Sebastián Suárez, Ricardo Baggio
4'-Substituted derivatives of 2,2':6',2''-terpyridine with N-containing heteroaromatic substituents, such as pyridyl groups, might be able to coordinate metal centres through the extra N-donor atom, in addition to the chelating terpyridine N atoms. The incorporation of these peripheral N-donor sites would also allow for the diversification of the types of noncovalent interactions present, such as hydrogen bonding and π-π stacking. The title compound, C24H16N4, consists of a 2,2':6',2''-terpyridine nucleus (tpy), with a pendant isoquinoline group (isq) bound at the central pyridine (py) ring...
December 1, 2016: Acta Crystallographica. Section C, Structural Chemistry
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