bluuebunny/crossref_metadata_2025_split huggingface dataset:
Full-length Genome of aOgataea polymorphastrain CBS4732ura3Δ reveals large duplicated segments in subtelomeric regions
Authors: Chang Jia , Bei Jinlong , Shao Qi , Wang Hemu , Fan Huan , Yau Tung On , Bu Wenjun , Ruan Jishou , Wei Dongsheng , Gao Shan 
Published: April 2021

AbstractBackgroundCurrently, methylotrophic yeasts (e.g.,Pichia pastoris, Ogataea polymorpha, andCandida boindii) are subjects of intense genomics studies in basic research and industrial applications. In the genusOgataea, most research is focused on three basicO. polymorphastrains—CBS4732, NCYC495, and DL-1. However, the relationship between CBS4732, NCYC495, and DL-1 remains unclear, as the genomic differences between them have not be exactly determined without their high-quality complete genomes. As a nutritionally deficient mutant derived from CBS4732, theO. polymorphastrain CBS4732ura3Δ (named HU-11) is being used for high-yield production of several important proteins or peptides. HU-11 has the same reference genome as CBS4732 (noted as HU-11/CBS4732), because the only genomic difference between them is a 5-bp insertion.ResultsIn the present study, we have assembled the full-length genome ofO. polymorphaHU-11/CBS4732 using high-depth PacBio and Illumina data. Long terminal repeat (LTR) retrotransposons, rDNA, 5’ and 3’ telomeric, subtelomeric, low complexity and other repeat regions were curated to improve the genome quality. Particularly, we detected large duplicated segments (LDSs) in the subtelomeric regions and exactly determined all the structural variations (SVs) between CBS4732 and NCYC495.New findings mainly include(1) the genomic differences between HU-11/CBS4732 and NCYC495 include single nucleotide polymorphisms, small insertions and deletions, and only three SVs; (2) six genes were incorporated into CBS4732 fromCyberlindnera jadiniiby horizontal gene transfer and may bring HU-11/CBS4732 new biological functions or physiological properties; (3) many recombination events may have occurred on chromosome 4 and 5 of CBS4732 and NCYC495’ ancestors and two large segments were acquired by CBS4732 and NCYC495 from chromosome 6 andC. jadiniiduring recombination, respectively; and (4) the genome expansion in methylotrophic yeasts is mainly driven by large segment duplication in subtelomeric regions.ConclusionsThe present study preliminarily revealed the complex relationship between CBS4732, NCYC495, and DL-1. The new findings provide new opportunities for in-depth understanding of genome evolution in methylotrophic yeasts and lay the foundations for the industrial applications ofO. polymorphaCBS4732, NCYC495, DL-1, and their derivative strains. The full-length genome of theO. polymorphastrain HU-11/CBS4732 should be included into the NCBI RefSeq database for future studies ofOgataeaspp..
A variable-rate quantitative trait evolution model using penalized-likelihood
Authors: Revell Liam J. 
Published: April 2021

ABSTRACTIn recent years it has become increasingly popular to use phylogenetic comparative methods to investigate heterogeneity in the rate or process of quantitative trait evolution across the branches or clades of a phylogenetic tree. Here, I present a new method for modeling variability in the rate of evolution of a continuously-valued character trait on a reconstructed phylogeny. The underlying model of evolution is stochastic diffusion (Brownian motion), but in which the instantaneous diffusion rate (σ2)alsoevolves by Brownian motion on a logarithmic scale. Unfortunately, it’s not possible to simultaneously estimate the rates of evolution along each edge of the treeandthe rate of evolution ofσ2itself using Maximum Likelihood. As such, I propose a penalized-likelihood method in which the penalty term is equal to the log-transformed probability density of the rates under a Brownian model, multiplied by a ‘smoothing’ coefficient,λ, selected by the user.λdetermines the magnitude of penalty that’s applied to rate variation between edges. Lower values ofλpenalize rate variation relatively little; whereas largerλvalues result in minimal rate variation among edges of the tree in the fitted model, eventually converging on a single value ofσ2for all of the branches of the tree. In addition to presenting this model here, I have also implemented it as part of myphytoolsR package in the functionmultirateBM. Using different values of the penalty coefficient,λ, I fit the model to simulated data with: Brownian rate variation among edges (the model assumption); uncorrelated rate variation; rate changes that occur in discrete places on the tree; and no rate variation at all among the branches of the phylogeny. I then compare the estimated values ofσ2to their known true values. In addition, I use the method to analyze a simple empirical dataset of body mass evolution in mammals. Finally, I discuss the relationship between the method of this article and other models from the phylogenetic comparative methods and finance literature, as well as some applications and limitations of the approach.
The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes
Authors: de Santana C. David , Parenti Lynne R. , Dillman Casey B. , Coddington Jonathan A. , Bastos D. A. , Baldwin Carole C. , Zuanon Jansen , Torrente-Vilara Gislene , Covain Raphaël , Menezes Naércio A. , Datovo Aléssio , Sado T. , Miya M. 
Published: April 2021

AbstractIchthyological surveys have traditionally been conducted using whole-specimen, capture-based sampling with varied, but conventional fishing gear. Recently, environmental DNA (eDNA) metabarcoding has emerged as a complementary, and possible alternative, approach to whole-specimen methodologies. In the tropics, where much of the diversity remains undescribed, vast reaches continue unexplored, and anthropogenic activities are constant threats; there have been few eDNA attempts for ichthyological inventories. We tested the discriminatory power of eDNA using MiFish primers with existing public reference libraries and compared this with capture-based methods in two distinct ecosystems in the megadiverse Amazon basin. In our study, eDNA provided an accurate snapshot of the fishes at higher taxonomic levels and corroborated its effectiveness to detect specialized fish assemblages. Some flaws in fish metabarcoding studies are routine issues addressed in natural history museums. Thus, by expanding their archives to include eDNA and adopting a series of initiatives linking collection-based research, training and outreach, natural history museums can enable the effective use of eDNA to survey Earth’s hotspots of biodiversity before taxa go extinct. Our project surveying poorly explored rivers and using DNA vouchered archives to build metabarcoding libraries for Neotropical fishes can serve as a model of this protocol.
Drug metabolic activity is a critical cell-intrinsic determinant for selection of hepatocytes during long-term culture
Authors: Akiyama Saeko , Saku Noriaki , Miyata Shoko , Ite Kenta , Toyoda Masashi , Kimura Tohru , Kuroda Masahiko , Nakazawa Atsuko , Kasahara Mureo , Nonaka Hidenori , Kamiya Akihide , Kiyono Tohru , Kobayshi Toru , Murakami Yasufumi , Umezawa Akihiro 
Published: April 2021

SUMMARYHepatocytes can be used to study the pathogenesis of liver diseases and drug discovery research. Human hepatocytes are, however, hardly expandable in vitro making it difficult to secure large numbers of cells from one donor. In this study, we aimed to establish an in vitro long-term culture system that enables stable proliferation and maintenance of human hepatocytes to ensure a constant supply. We purified human hepatocytes by selection with cytocidal puromycin, and cultured them for more than 60 population doublings over a span of more than 350 days. These results show that this simple culture system with usage of the cytocidal antibiotics enables efficient hepatocyte proliferation and is an effective method for generating a stable supply of hepatocytes for drug discovery research at a significant cost reduction.
A new species of the genusEuphlyctis(Anura: Dicroglossidae) from West Bengal, India
Authors: Bhakat Somnath , Bhakat Soumendranath 
Published: April 2021

AbstractA new species of green frog of the genusEuphlyctisFitzinger, 1843 is described from West Bengal, a state of eastern India. A robust frog, SVL of male 86mm and that of female 132mm. The species is diagnosed by the presence of following characters: green dorsum and female with a greenish white mid-dorsal line, tibiotarsal articulation reaches eye, male with two vocal sac openings at the junction of jaw, female is larger than male though body parameters is proportionately longer in male, nostril snout length 3.45% of SVL, nostril much closer to snout tip than eye, units of hind limb i. e. thigh, shank and foot are almost equal in length, relative length of finger: II < IV < I < III.The new species is compared with existing eight species of the genusEuphlyctis.
Multiview tiling light sheet microscopy for 3D high resolution live imaging
Authors: Aakhte Mostafa , Müller H.-Arno J. 
Published: April 2021

AbstractLight sheet or selective plane illumination microscopy (SPIM) is ideally suited forin totoimaging of living specimens at high temporal-spatial resolution. In SPIM, the light scattering that occurs during imaging of opaque specimens brings about limitations in terms of resolution and the imaging field of view. To ameliorate this shortcoming, the illumination beam can be engineered into a highly confined light sheet over a large field of view and multi-view imaging can be performed by applying multiple lenses combined with mechanical rotation of the sample. Here, we present a Multiview tiling SPIM (MT-SPIM) that combines the Multi-view SPIM (M-SPIM) with a confined, multi-tiled light sheet. The MT-SPIM provides high-resolution, robust and rotation-free imaging of living specimens. We applied the MT-SPIM to image nuclei and Myosin II from the cellular to subcellular spatial scale in earlyDrosophilaembryogenesis. We show that the MT-SPIM improves the axial-resolution relative to the conventional M-SPIM by a factor of two. We further demonstrate that this axial resolution enhancement improves the automated segmentation of Myosin II distribution and of nuclear volumes and shapes.
Eukaryotic ribosome recognizes 3′ context and stimulates stop codon readthrough
Authors: Sokolova Elizaveta , Egorova Tatiana , Shuvalov Alexey , Alkalaeva Elena 
Published: April 2021

ABSTRACTIt is known that the nucleotide context surrounding stop codons significantly affects the efficiency of translation termination. In eukaryotes, various 3′ contexts have been described that are unfavourable for translation termination; however, the exact molecular mechanism that mediates their effect remains unknown. In this study, we used a reconstituted mammalian translation system to examine the efficiency of stop codons in different contexts, including several previously described weak 3′ stop codon contexts. Our results revealed that ribosomes can independently recognize certain contexts and ignore stop codons that are followed by these sequences. Moreover, the efficiency of translation termination at the weak 3′ contexts was almost equal to the one at the standard context. We propose that weak 3′ contexts interact with the 18S rRNA provoking a conformational change in the U-turn-like structure of the stop codon in the A site of ribosome. This change makes incorporation of the near-cognate tRNA more preferable than recognition of the stop codon by the release factors and increases readthrough.
Bacteriophage λ RexA and RexB Functions Assist the Transition from Lysogeny to Lytic Growth
Authors: Thomason Lynn C. , Schiltz Carl J. , Court Carolyn , Hosford Christopher J. , Adams Myfanwy C. , Chappie Joshua S. , Court Donald L. 
Published: April 2021

SummaryThe CI and Cro repressors of bacteriophage λ create a bistable switch between lysogenic and lytic growth. In λ lysogens, CI repressor expressed from thePRMpromoter blocks expression of the lytic promotersPLandPRto allow stable maintenance of the lysogenic state. When lysogens are induced, CI repressor is inactivated and Cro repressor is expressed from the lyticPRpromoter. Cro repressor blocksPRMtranscription and CI repressor synthesis to ensure that the lytic state proceeds. RexA and RexB proteins, like CI, are expressed from thePRMpromoter in λ lysogens; RexB is also expressed from a second promoter,PLIT, embedded inrexA.Here we show that RexA binds CI repressor and assists the transition from lysogenic to lytic growth, using both intact lysogens and defective prophages with reporter genes under control of the lyticPLandPRpromoters. Once lytic growth begins, if the bistable switch does return to the immune state, RexA expression lessens the probability that it will remain there, thus stabilizing the lytic state and activation of the lyticPLandPRpromoters. RexB modulates the effect of RexA and may also help establish phage DNA replication as lytic growth ensues.
Synchronization of iPS-derived cardiomyocytes to visitor heartbeat in an interactive museum exhibit
Authors: Perez-Bermejo Juan A. , Reisman Samuel J. , Ma Joyce , Cerrito Chris , Conklin Bruce R. , Yu Kristina 
Published: April 2021

AbstractScience museums play an important role in science education, both engaging the public with science concepts and building support for scientific research. Designing museum exhibits to meet increasing public interests in the life sciences is particularly important, yet remains challenging. In this report we describeGive Heart Cells a Beat, a permanent interactive science exhibit that allows museum visitors to synchronize the beating of live stem cell-derived cardiomyocytes to their own heart rate in real-time. Evaluation with museum visitors reveals that the exhibit engaged the public with the specimen and prompted curiosity in heart biology and, to a lesser degree, stem cells and electrophysiology.Give Heart Cells a Beatis the product of a close collaboration between a museum and a research laboratory, and, to our knowledge, the first example of the use of live human heart cells in an interactive exhibit. We hope this exhibit will serve as an example for the implementation of stem cell technology in the field of informal science education and encourage others to pursue close working relationships between academia and public science venues such as museums.
Cannabidiol pretreatment attenuates locomotor alterations and cytokine production in an autoimmune hepatitis model
Authors: Mesiakaris Konstantinos , Atsopardi Korina , Margarity Marigoula , Poulas Konstantinos 
Published: April 2021

AbstractCannabidiol (CBD) is a major active component of the Cannabis plant (Cannabis Sativa L.), which unlike tetrahydrocannabinol (THC) is devoid of euphoria-inducing properties. Broadly, CBD has demonstrated anxiolytic-like, anti-inflammatory and immunomodulatory effects. Concanavalin A (ConA) is a lectin found in the jack bean (Canavalia ensiformis) and it has been associated with a variety of toxicological effects (upon them mitogenic, cytotoxic and hepatotoxic). Intravenous administration of ConA is widely used for the induction of a model to study autoimmune hepatitis (AIH) in mice and the injury is mainly driven by activation and uptake of T-cells in liver. The aim of the present study was to investigate the effects of CBD administration (20 mg/kg), on adult mice, on locomotor activity and inflammatory markers, upon induction of AIH by ConA administration (20 mg/kg) on Balb/C mice. Inflammatory analysis was assessed by determining the IL-2, IL-4, IL-10 and INF-γ levels on plasma and sickness-like behavior assessed with open-field test. The results indicate that CBD pretreatment ameliorates impaired locomotor activity. IL-2, IL-4 and INF-γ levels on plasma were increased after ConA intoxication (inflammation index) and were reduced when mice were pre-treated with CBD. The detected IL-10 levels were increased when CBD pretreated, suggesting a protective anti-inflammatory effect.
Development of Small Molecule Inhibitors Targeting PBX1 Transcription Signaling as a Novel Cancer Therapeutic Strategy
Authors: Shen Yao-An , Jung Jin , Shimberg Geoffrey D. , Hsu Fang-Chi , Rahmanto Yohan Suryo , Gaillard Stephanie L , Hong Jiaxin , Bosch Jürgen , Shih Ie-Ming , Chuang Chi-Mu , Wang Tian-Li 
Published: April 2021

AbstractPBX1 (pre-B cell leukemia transcription factor 1) is a transcription factor involved in diverse cellular functions including organ development, stem cell renewal, and tumorigenesis. PBX1 is localized at chr1q23.3, a frequently amplified chromosomal region, and it is overexpressed in many human malignancies including breast, lung, melanoma, and ovarian carcinomas. Cancer cells with elevated PBX1 signaling are particularly vulnerable to PBX1-withdrawal. We designed a series of small molecule compounds capable of docking to the interface between PBX1 and its cognate DNA target sequence and identified a lead compound, T417, which efficiently hindered the formation of the PBX1 transcriptional complex and affected the transcription of PBX1 target genes. In cell-based assays, T417 significantly suppressed long-term self-renewal and proliferation of cancer cells expressing high levels of PBX1 but not of those expressing low levels of PBX1. T417 also re-sensitized platinum-resistant ovarian tumor cells to carboplatin and produced synergistic anti-tumorigenic effectsin vivoin combination with carboplatin. Normal tissues were spared, likely due to the lower PBX1 expression levels. Since PBX1 functions as a molecular hub in developing cancer recurrence and treatment resistance, our data highlight the potential of targeting the PBX-DNA interface as a therapeutic strategy for patients whose tumors rely on PBX1 activation for survival.
A SARS-CoV-2 targeted siRNA-nanoparticle therapy for COVID-19
Authors: Idris Adi , Davis Alicia , Supramaniam Aroon , Acharya Dhruba , Kelly Gabrielle , Tayyar Yaman , West Nic , Zhang Ping , McMillan Christopher L.D. , Soemardy Citradewi , Ray Roslyn , O’Meally Denis , Scott Tristan A. , McMillan Nigel A. J. , Morris Kevin V. 
Published: April 2021

AbstractCoronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in humans. Despite several emerging vaccines, there remains no verifiable therapeutic targeted specifically to the virus. Here we present a highly effective siRNA therapeutic against SARS-CoV-2 infection using a novel lipid nanoparticle delivery system. Multiple small-interfering RNAs (siRNAs) targeting highly conserved regions of the SARS-CoV-2 virus were screened and three candidate siRNAs emerged that effectively inhibit virus by greater than 90% either alone or in combination with one another. We simultaneously developed and screened two novel lipid nanoparticle formulations for the delivery of these candidate siRNA therapeutics to the lungs, an organ that incurs immense damage during SARS-CoV-2 infection. Encapsulation of siRNAs in these LNPs followed byin vivoinjection demonstrated robust repression of virus in the lungs and a pronounced survival advantage to the treated mice. Our LNP-siRNA approaches are scalable and can be administered upon the first sign of SARS-CoV-2 infection in humans. We suggest that an siRNA-LNP therapeutic approach could prove highly useful in treating COVID-19 disease as an adjunctive therapy to current vaccine strategies.
Nanosecond timing and synchronization scheme for holographic pump–probe studies at the MID instrument at European XFEL
Authors: Osterhoff Markus , Vassholz Malte , Hoeppe Hannes Paul , Rosselló Juan Manuel , Mettin Robert , Hagemann Johannes , Möller Johannes , Hallmann Jörg , Scholz Markus , Schaffer Robert , Boesenberg Ulrike , Kim Chan , Zozulya Alexey , Lu Wei , Shayduk Roman , Madsen Anders , Salditt Tim 
Published: April 2021

Single-pulse holographic imaging at XFEL sources with 1012 photons delivered in pulses shorter than 100 fs reveal new quantitative insights into fast phenomena. Here, a timing and synchronization scheme for stroboscopic imaging and quantitative analysis of fast phenomena on time scales (sub-ns) and length-scales (≲100 nm) inaccessible by visible light is reported. A fully electronic delay-and-trigger system has been implemented at the MID station at the European XFEL, and applied to the study of emerging laser-driven cavitation bubbles in water. Synchronization and timing precision have been characterized to be better than 1 ns.
Reduced crop density increases floral resources to pollinators without affecting crop yield in organic and conventional fields
Authors: Sidemo‐Holm William , Carrié Romain , Ekroos Johan , Lindström Sandra A. M. , Smith Henrik G. 
Published: April 2021

Abstract

Effective weed control in agricultural crop fields increases yields, but simultaneously reduces floral resources for pollinators because many weed species provide pollen and nectar. Consequently, efforts to enhance crop yields on organic farms by using effective weed control methods risk compromising positive effects of organic farming on pollinating insects. Thus, it is important to find management strategies that alleviate the trade‐off between crop yields and flowering weeds on organic farms.

We investigated the relationship between cereal yields, flowering weeds and bumblebees on organic and conventional arable land. We also investigated the potential of adjusting crop sowing density to benefit flowering weed species richness and floral resources to bumblebees without affecting crop yield.

Floral resources and species richness of flowering weeds were higher in organic compared to conventional fields and were negatively related to crop yield in organic but not conventional fields (where the variation of floral resources and flowering weed species richness was comparatively low). Bumblebee species richness was higher in organic compared to conventional fields, and abundance was twice as high in organic as in conventional fields, but not significantly so. Yields in organic fields were two thirds of those in conventional fields. When simultaneously testing the effect of farming type (organic vs. conventional), crop yield and floral resources, only floral resources were related significantly to bumblebee abundance and species richness. A lower sowing density of the crop increased floral resources without negatively affecting crop yield.

Synthesis and applications. We show that organic farming practices in cereals benefit bumblebees by allowing more flowering weeds, but at a cost in terms of lower yields. However, adjusting crop sowing density provides an opportunity to attain increased floral resources without negatively affecting crop yields. Thus, by increasing floral resources, adjusting crop sowing density may contribute to supporting high bumblebee densities, which in turn sustain pollination services to wild plants and insect‐pollinated crops, such as oilseed rape and field beans, in agricultural landscapes. We suggest that sowing strategies have the potential to contribute to ecological intensification by supporting organisms that provide ecosystem services to agriculture.