SwePub - search: WFRF:(Evans Jay)

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1.	Beal, Jacob, et al. (author) Robust estimation of bacterial cell count from optical density 2020 In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1 Journal article (peer-reviewed)abstract Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
2.	Werren, John H, et al. (author) Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. 2010 In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 327:5963, s. 343-8 Journal article (peer-reviewed)abstract We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.
3.	Aalto, Susanne, 1964, et al. (author) A precessing molecular jet signaling an obscured, growing supermassive black hole in NGC 1377? 2016 In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 590, s. Art. no. A73- Journal article (peer-reviewed)abstract With high resolution (0."25 × 0."18) ALMA CO 3-2 (345 GHz) observations of the nearby (D = 21 Mpc, 1" = 102 pc), extremely radio-quiet galaxy NGC 1377, we have discovered a high-velocity, very collimated nuclear outflow which we interpret as a molecular jet with a projected length of ± 150 pc. The launch region is unresolved and lies inside a radius r 40% of the flux in NGC 1377 and may be a slower, wide-angle molecular outflow which is partially entrained by the molecular jet. We discuss the driving mechanism of the molecular jet and suggest that it is either powered by a (faint) radio jet or by an accretion disk-wind similar to those found towards protostars. It seems unlikely that a massive jet could have been driven out by the current level of nuclear activity which should then have undergone rapid quenching. The light jet would only have expelled 10% of the inner gas and may facilitate nuclear activity instead of suppressing it. The nucleus of NGC 1377 harbours intense embedded activity and we detect emission from vibrationally excited HCN J = 4-3?2 = 1f which is consistent with hot gas and dust. We find large columns of H2 in the centre of NGC 1377 which may be a sign of a high rate of recent gas infall. The dynamical age ofthe molecular jet is short (
4.	Abbasi, Rasha, et al. (author) IceCube search for neutrinos from GRB 221009A 2023 In: Proceedings of 38th International Cosmic Ray Conference (ICRC 2023). - : Sissa Medialab Srl. Conference paper (peer-reviewed)abstract GRB 221009A is the brightest Gamma Ray Burst (GRB) ever observed. The observed extremelyhigh flux of high and very-high-energy photons provide a unique opportunity to probe the predictedneutrino counterpart to the electromagnetic emission. We have used a variety of methods to searchfor neutrinos in coincidence with the GRB over several time windows during the precursor, promptand afterglow phases of the GRB. MeV scale neutrinos are studied using photo-multiplier ratescalers which are normally used to search for galactic core-collapse supernovae neutrinos. GeVneutrinos are searched starting with DeepCore triggers. These events don’t have directionallocalization, but instead can indicate an excess in the rate of events. 10 GeV - 1 TeV and >TeVneutrinos are searched using traditional neutrino point source methods which take into accountthe direction and time of events with DeepCore and the entire IceCube detector respectively. The>TeV results include both a fast-response analysis conducted by IceCube in real-time with timewindows of T0 − 1 to T0 + 2 hours and T0 ± 1 day around the time of GRB 221009A, as well asan offline analysis with 3 new time windows up to a time window of T0 − 1 to T0 + 14 days, thelongest time period we consider. The combination of observations by IceCube covers 9 ordersof magnitude in neutrino energy, from MeV to PeV, placing upper limits across the range forpredicted neutrino emission.
5.	Bai, Wen Feng, et al. (author) Phylogenetic Analysis of Small Hive Beetles From Native to Introduced Populations 2022 In: Frontiers in Genetics. - : Frontiers Media S.A.. - 1664-8021. ; 13 Journal article (peer-reviewed)abstract The small hive beetle (SHB), a social parasite of beehives, is native to sub-Saharan Africa and has spread to America, Europe, and Australia. Recently, these beetles invaded China, causing widespread colony collapses in the honeybee, Apis cerana. In this study, single nucleotide polymorphisms (SNPs) were identified in the beetle genome from its native range (Africa), a region that was invaded by SHBs nearly 30 years ago (America), and more recent invasions (Asia). The beetles in the United States formed the earliest branch and show signs of two decades of gene flow and local adaptation to differentiate this population from the native ones. The beetles in China were deep branched and showed the highest fixation index when compared to the US populations. The number of SNPs in overexpressed genes was significantly higher than the transcriptome. Gene-expression profiles presented here distinguish the characters between adult and larvae SHBs.
6.	Callejas, Ileana A., et al. (author) Effect of COVID-19 Anthropause on Water Clarity in the Belize Coastal Lagoon 2021 In: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 8 Journal article (peer-reviewed)abstract The Coronavirus disease 2019 (COVID-19) pandemic halted human activities globally in multiple sectors including tourism. As a result, nations with heavy tourism, such as Belize, experienced improvements in water quality. Remote sensing technologies can detect impacts of “anthropauses” on coastal water quality. In this study, moderate resolution imaging spectroradiometer (MODIS) satellite data were employed along the Belizean coast to investigate impacts of the COVID-19 shutdown on water quality. The attenuation coefficient at 490 nm, Kd(490), was used as an indicator of water quality, with a lower Kd(490) indicating increased water clarity. Four Coastal Management Zones were characterized by marine traffic as high traffic areas (HTAs) and two as low traffic areas (LTAs). Monthly composites for two periods, 2002–2019 (baseline) and 2020 were examined for Kd(490). For months prior to the COVID-19 shutdown in Belize, there was generally no significant difference in Kd(490) (p > 0.05) between 2020 and baseline period in HTAs and LTAs. Through the shutdown, Kd was lower in 2020 at HTAs, but not for LTAs. At the LTAs, the Kd(490)s observed in 2020 were similar to previous years through October. In November, an unusually active hurricane season in 2020 was associated with decreased water clarity along the entire coast of Belize. This study provides proof of concept that satellite-based monitoring of water quality can complement in situ data and provide evidence of significant water quality improvements due to the COVID-19 shutdown, likely due to reduced marine traffic. However, these improvements were no longer observed following an active hurricane season.
7.	Clark, Andrew G., et al. (author) Evolution of genes and genomes on the Drosophila phylogeny 2007 In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218 Journal article (peer-reviewed)abstract Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
8.	Engel, Philipp, et al. (author) The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions 2016 In: mBio. - : American Society for Microbiology. - 2161-2129 .- 2150-7511. ; 7:2 Research review (peer-reviewed)abstract As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the micro biome. The bee micro biome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee micro biome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health.
9.	Falstad, Niklas, 1987, et al. (author) Hidden molecular outflow in the LIRG Zw 049.057 2018 In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 609 Journal article (peer-reviewed)abstract Context. Feedback in the form of mass outflows driven by star formation or active galactic nuclei is a key component of galaxy evolution. The luminous infrared galaxy Zw 049.057 harbours a compact obscured nucleus with a possible far-infrared signature of outflowing molecular gas. Due to the high optical depths at far-infrared wavelengths, however, the interpretation of the outflow signature is uncertain. At millimeter and radio wavelengths, the radiation is better able to penetrate the large columns of gas and dust responsible for the obscuration. Aims. We aim to investigate the molecular gas distribution and kinematics in the nucleus of Zw 049.057 in order to confirm and locate the molecular outflow, with the ultimate goal to understand how the nuclear activity affects the host galaxy. Methods. We used high angular resolution observations from the Submillimeter Array (SMA), the Atacama Large Millimeter/submillimeter Array (ALMA), and the Karl G. Jansky Very Large Array (VLA) to image the CO J = 2-1 and J = 6-5 emission, the 690 GHz continuum, the radio centimeter continuum, and absorptions by rotationally excited OH. Results. The CO line profiles exhibit wings extending ~ 300 km s -1 beyond the systemic velocity. At centimeter wavelengths, we find a compact (~ 40 pc) continuum component in the nucleus, with weaker emission extending several 100 pc approximately along the major and minor axes of the galaxy. In the OH absorption lines toward the compact continuum, wings extending to a similar velocity as for the CO are only seen on the blue side of the profile. The weak centimeter continuum emission along the minor axis is aligned with a highly collimated, jet-like dust feature previously seen in near-infrared images of the galaxy. Comparison of the apparent optical depths in the OH lines indicate that the excitation conditions in Zw 049.057 differ from those within other OH megamaser galaxies. Conclusions. We interpret the wings in the spectral lines as signatures of a nuclear molecular outflow. A relation between this outflow and the minor axis radio feature is possible, although further studies are required to investigate this possible association and understand the connection between the outflow and the nuclear activity. Finally, we suggest that the differing OH excitation conditions are further evidence that Zw 049.057 is in a transition phase between megamaser and kilomaser activity.
10.	Gerardo, Nicole M, et al. (author) Immunity and other defenses in pea aphids, Acyrthosiphon pisum. 2010 In: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 11:2 Journal article (peer-reviewed)abstract BACKGROUND: Recent genomic analyses of arthropod defense mechanisms suggest conservation of key elements underlying responses to pathogens, parasites and stresses. At the center of pathogen-induced immune responses are signaling pathways triggered by the recognition of fungal, bacterial and viral signatures. These pathways result in the production of response molecules, such as antimicrobial peptides and lysozymes, which degrade or destroy invaders. Using the recently sequenced genome of the pea aphid (Acyrthosiphon pisum), we conducted the first extensive annotation of the immune and stress gene repertoire of a hemipterous insect, which is phylogenetically distantly related to previously characterized insects models.RESULTS: Strikingly, pea aphids appear to be missing genes present in insect genomes characterized to date and thought critical for recognition, signaling and killing of microbes. In line with results of gene annotation, experimental analyses designed to characterize immune response through the isolation of RNA transcripts and proteins from immune-challenged pea aphids uncovered few immune-related products. Gene expression studies, however, indicated some expression of immune and stress-related genes.CONCLUSIONS: The absence of genes suspected to be essential for the insect immune response suggests that the traditional view of insect immunity may not be as broadly applicable as once thought. The limitations of the aphid immune system may be representative of a broad range of insects, or may be aphid specific. We suggest that several aspects of the aphid life style, such as their association with microbial symbionts, could facilitate survival without strong immune protection.
11.	Richards, Stephen, et al. (author) Genome Sequence of the Pea Aphid Acyrthosiphon pisum 2010 In: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313- Journal article (peer-reviewed)abstract Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
12.	Richards, Stephen, et al. (author) The genome of the model beetle and pest Tribolium castaneum. 2008 In: Nature. - 1476-4687. ; 452:7190, s. 949-55 Journal article (peer-reviewed)abstract Tribolium castaneum is a representative of earth’s most numerous eukaryotic order, a powerful model organism for the study of generalized insect development, and also an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved an ability to interact with a diverse chemical environment as evidenced by large expansions in odorant and gustatory receptors, as well as p450 and other detoxification enzymes. Developmental patterns in Tribolium are more representative of other arthropods than those found in Drosophila, a fact represented in gene content and function. For one, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, and some are expressed in the growth zone crucial for axial elongation in short germ development. Systemic RNAi in T. castaneum appears to use mechanisms distinct from those found in C. elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
13.	Sackton, Timothy B, et al. (author) Dynamic evolution of the innate immune system in Drosophila. 2007 In: Nat Genet. - 1061-4036. ; 39:12, s. 1461-8 Journal article (peer-reviewed)abstract The availability of complete genome sequence from 12 Drosophila species presents the opportunity to examine how natural selection has affected patterns of gene family evolution and sequence divergence among different components of the innate immune system. We have identified orthologs and paralogs of 245 Drosophila melanogaster immune-related genes in these recently sequenced genomes. Genes encoding effector proteins, and to a lesser extent genes encoding recognition proteins, are much more likely to vary in copy number across species than genes encoding signaling proteins. Furthermore, we can trace the apparent recent origination of several evolutionarily novel immune-related genes and gene families. Using codon-based likelihood methods, we show that immune-system genes, and especially those encoding recognition proteins, evolve under positive darwinian selection. Positively selected sites within recognition proteins cluster in domains involved in recognition of microorganisms, suggesting that molecular interactions between hosts and pathogens may drive adaptive evolution in the Drosophila immune system.
14.	Samanta, Sumanta, et al. (author) Interpenetrating gallol functionalized tissue adhesive hyaluronic acid hydrogel polarizes macrophages to an immunosuppressive phenotype 2022 In: Acta Biomaterialia. - : Elsevier. - 1742-7061 .- 1878-7568. ; 142, s. 36-48 Journal article (peer-reviewed)abstract Innovative scaffold designs that modulate the local inflammatory microenvironment through favorable macrophage polarization and suppressing oxidative stress are needed for successful clinical translation of regenerative cell therapies and graft integration. We herein report derivation of a hydrazone-crosslinked gallol functionalized hyaluronic acid (HA-GA)-based hydrogel that displayed outstanding viscoelastic properties and immunomodulatory characteristics. Grafting of 6% gallol (GA) to a HA-backbone formed an interpenetrative network by promoting an additional crosslink between the gallol groups in addition to hydrazone crosslinking. This significantly enhanced the mechanical stability and displayed shear-thinning/self-healing characteristics, facilitated tissue adhesive properties to porcine tissue and also displayed radical scavenging properties, protecting encapsulated fibroblasts from peroxide challenge. The THP-1 human macrophage cell line or primary bone-marrow-derived murine macrophages cultured within HA-GA gels displayed selective polarization to a predominantly anti-inflammatory phenotype by upregulating IL4ra, IL-10, TGF-β, and TGF-βR1 expression when compared with HA-HA gels. Conversely, culturing of pro-inflammatory activated primary murine macrophages in HA-GA gels resulted in a significant reduction of pro-inflammatory TNF-α, IL-1β, SOCS3 and IL-6 marker expression, and upregulated expression of anti-inflammatory cytokines including TGF-β. Finally, when the gels were implanted subcutaneously into healthy mice, we observed infiltration of pro-inflammatory myeloid cells in HA-HA gels, while immunosuppressive phenotypes were observed within the HA-GA gels. Taken together these data suggest that HA-GA gels are an ideal injectable scaffold for viable immunotherapeutic interventions.Statement of significanceHost immune response against the implanted scaffolds that are designed to deliver stem cells or therapeutic proteins in vivo significantly limits the functional outcome. For this reason, we have designed immunomodulatory injectable scaffolds that can favorably polarize the recruited macrophages and impart antioxidant properties to suppress oxidative stress. Specifically, we have tailored a hyaluronic acid-based extracellular matrix mimetic injectable scaffold that is grafted with immunomodulatory gallol moiety. Gallol functionalization of hydrogel not only enhanced the mechanical properties of the scaffold by forming an interpenetrating network but also induced antioxidant properties, tissue adhesive properties, and polarized primary murine macrophages to immunosuppressive phenotype. We believe such immunoresponsive implants will pave the way for developing the next-generation of biomaterials for regenerative medicine applications.
15.	Segal, Eran, et al. (author) Building an international consortium for tracking coronavirus health status 2020 In: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 26:8, s. 1161-1165 Journal article (other academic/artistic)abstract We call upon the research community to standardize efforts to use daily self-reported data about COVID-19 symptoms in the response to the pandemic and to form a collaborative consortium to maximize global gain while protecting participant privacy.
16.	Skirgård, Hedvig, et al. (author) Grambank reveals the importance of genealogical constraints on linguistic diversity and highlights the impact of language loss. Science Advances 2023 In: Science Advances. ; 9:16:eadg6175, s. 1-15 Journal article (peer-reviewed)
17.	Voss, Michael G., et al. (author) Time to Peak Glucose and Peak C-Peptide During the Progression to Type 1 Diabetes in the Diabetes Prevention Trial and TrialNet Cohorts 2021 In: Diabetes Care. - : American Diabetes Association. - 1935-5548 .- 0149-5992. ; 44:10, s. 2329-2336 Journal article (peer-reviewed)abstract OBJECTIVE: To assess the progression of type 1 diabetes using time to peak glucose or C-peptide during oral glucose tolerance tests (OGTTs) in autoantibody-positive relatives of people with type 1 diabetes. RESEARCH DESIGN AND METHODS: We examined 2-h OGTTs of participants in the Diabetes Prevention Trial Type 1 (DPT-1) and TrialNet Pathway to Prevention (PTP) studies. We included 706 DPT-1 participants (mean ± SD age, 13.84 ± 9.53 years; BMI Z-score, 0.33 ± 1.07; 56.1% male) and 3,720 PTP participants (age, 16.01 ± 12.33 years; BMI Z-score, 0.66 ± 1.3; 49.7% male). Log-rank testing and Cox regression analyses with adjustments (age, sex, race, BMI Z-score, HOMA-insulin resistance, and peak glucose/C-peptide levels, respectively) were performed. RESULTS: In each of DPT-1 and PTP, higher 5-year diabetes progression risk was seen in those with time to peak glucose >30 min and time to peak C-peptide >60 min (P < 0.001 for all groups), before and after adjustments. In models examining strength of association with diabetes development, associations were greater for time to peak C-peptide versus peak C-peptide value (DPT-1: χ2 = 25.76 vs. χ2 = 8.62; PTP: χ2 = 149.19 vs. χ2 = 79.98; all P < 0.001). Changes in the percentage of individuals with delayed glucose and/or C-peptide peaks were noted over time. CONCLUSIONS: In two independent at-risk populations, we show that those with delayed OGTT peak times for glucose or C-peptide are at higher risk of diabetes development within 5 years, independent of peak levels. Moreover, time to peak C-peptide appears more predictive than the peak level, suggesting its potential use as a specific biomarker for diabetes progression.
18.	Wallberg, Andreas, et al. (author) A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds 2019 In: BMC Genomics. - : BMC. - 1471-2164. ; 20 Journal article (peer-reviewed)abstract BackgroundThe ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map.ResultsEach of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor >98% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features.ConclusionsThe improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics.
19.	Yabe, Daisuke, et al. (author) Efficacy of lixisenatide in patients with type 2 diabetes : A post hoc analysis of patients with diverse β-cell function in the GetGoal-M and GetGoal-S trials 2016 In: Journal of Diabetes and its Complications. - : Elsevier BV. - 1056-8727. ; 30:7, s. 1385-1392 Journal article (peer-reviewed)abstract Aims: To evaluate the impact of β-cell function on the efficacy of lixisenatide, a once-daily prandial glucagon-like peptide-1 receptor agonist, in patients with type 2 diabetes (T2D). Materials and methods: In this post hoc analysis, patients from the Phase 3 GetGoal-M and GetGoal-S clinical trials randomized to lixisenatide 20. μg once daily were stratified into quartiles by baseline β-cell function, as measured by the secretory units of islet in transplantation (SUIT) index. Results: Patients (N = 437) were distributed evenly among SUIT index quartiles 1 to 4 (lowest to highest β-cell function). Clinical outcomes improved from baseline across all SUIT quartiles; mean changes at week 24 were: glycated hemoglobin (HbA1c; % [mmol/mol]), -0.99 (-10.8), -0.87 (-9.5), -0.86 (-9.4), -0.83 (-9.1); and postprandial plasma glucose (PPG; mmol/L), -7.9, -5.6, -5.5, -4.3 (overall effect . P .
20.	Zou, Zhen, et al. (author) Comparative genomic analysis of the Tribolium immune system. 2007 In: Genome Biol. - 1465-6914. ; 8:8, s. R177.1-16 Journal article (peer-reviewed)abstract BACKGROUND: Tribolium castaneum is a species of Coleoptera, the largest and most diverse order of all eukaryotes. Components of the innate immune system are hardly known in this insect, which is in a key phylogenetic position to inform us about genetic innovations accompanying the evolution of holometabolous insects. We have annotated immunity-related genes and compared them with homologous molecules from other species. RESULTS: Around 300 candidate defense proteins are identified based on sequence similarity to homologs known to participate in immune responses. In most cases, paralog counts are lower than those of Drosophila melanogaster or Anopheles gambiae but are substantially higher than Apis mellifera. The genome contains probable orthologs for nearly all members of the Toll, IMD, and JAK/STAT pathways. While total numbers of the clip-domain serine proteinases are approximately equal in the fly (29), mosquito (32) and beetle (30), lineage-specific expansion of the family is discovered in all three species. Sixteen of the thirty-one serpin genes form a large cluster in a 50 kb region resulted from extensive gene duplications. Among the nine Toll-like proteins, four are orthologous to Drosophila Toll. The presence of scavenger receptors and other related proteins indicates a role of cellular responses in the entire system. The structures of some antimicrobial peptides drastically differ from those in other orders of insects. CONCLUSIONS: A framework of information on Tribolium immunity is established, which may serve as a stepping stone for future genetic analyses of defense responses in a nondrosophiline genetic model insect.

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