bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA degradation analysis reveals ribosome dynamics in complex microbiome samples
Authors: Huch Susanne , Nersisyan Lilit , Ropat Maria , Barret Donal , Wang Jing , Huerta-Cepas Jaime , Wei Wu , Steinmetz Lars M , Engstrand Lars , Pelechano Vicent 
Published: April 2021

AbstractPost-transcriptional regulation is essential for life, yet we are currently unable to investigate its role in complex microbiome samples. Here we discover that co-translational mRNA degradation, where the degradation machinery follows the last translating ribosome, is conserved across prokaryotes. By investigating 5’P mRNA decay intermediates, we obtainin vivoribosome protection information that allows the study of codon and gene specific ribosome stalling in response to stress and drug treatment at single nucleotide resolution. We use this approach to investigatein vivospecies-specific ribosome footprints of clinical and environmental microbiomes and show for the first time that ribosome protection patterns can be used to phenotype microbiome perturbations. Our work paves the way for the study of the metatranslatome, and enables the investigation of fast, species-specific, post-transcriptional responses to environmental and chemical perturbations in unculturable microbial communities.
A CENH3 mutation promotes meiotic exit and restores fertility in SMG7-deficient Arabidopsis
Authors: Capitao Claudio , Tanasa Sorin , Fulnecek Jaroslav , Raxwal Vivek K. , Akimcheva Svetlana , Bulankova Petra , Mikulkova Pavlina , Lermontova Inna , Scheid Ortrun Mittelsten , Riha Karel 
Published: April 2021

AbstractMeiosis in angiosperm plants is followed by mitotic divisions to form multicellular haploid gametophytes. Termination of meiosis and transition to gametophytic development is, in Arabidopsis, governed by a dedicated mechanism that involves SMG7 and TDM1 proteins. Mutants carrying thesmg7-6allele are semi-fertile due to reduced pollen production. We found that instead of forming tetrads,smg7-6pollen mother cells undergo multiple rounds of chromosome condensation and spindle assembly at the end of meiosis, resembling aberrant attempts to undergo additional meiotic divisions. A suppressor screen uncovered a mutation in centromeric histone H3 (CENH3) that increased fertility and promoted meiotic exit insmg7-6plants. The mutation led to inefficient splicing of the CENH3 mRNA and a substantial decrease of CENH3, resulting in smaller centromeres. The reduced level of CENH3 delayed formation of the mitotic spindle but did not have an apparent effect on plant growth and development. We suggest that impaired spindle re-assembly at the end of meiosis limits aberrant divisions insmg7-6plants and promotes formation of tetrads and viable pollen. Furthermore, the reduced level of CENH3 did not induce haploid plants in crosses with wild plants, indicating that differences in centromere size is not the key determinant of centromere-mediate genome elimination.
Uhrf1 governs the proliferation and differentiation of muscle satellite cells
Authors: Sakai Hiroshi , Sawada Yuichiro , Tokunaga Naohito , Nakagawa So , Sakakibara Iori , Ono Yusuke , Fukada So-ichiro , Kikugawa Tadahiko , Saika Takashi , Imai Yuuki 
Published: April 2021

SummaryDNA methylation is an essential form of epigenetic regulation responsible for cellular identity. In muscle stem cells, termed satellite cells, DNA methylation patterns are tightly regulated during differentiation. However, it is unclear how these DNA methylation patterns are maintained. We demonstrate that a key epigenetic regulator, ubiquitin like with PHD and RING finger domains 1 (Uhrf1), is activated in proliferating myogenic cells but not expressed in quiescent or differentiated myogenic cells in mice. Ablation of Uhrf1 in mouse satellite cells impairs their proliferation and differentiation, leading to failed muscle regeneration. Loss of Uhrf1 in satellite cells alters transcriptional programs, leading to DNA hypomethylation with activation of Cdkn1a and Notch signaling. Although down-regulation of Cdkn1a rescued proliferation but not differentiation, inhibition of Notch signaling rescued impaired differentiation of Uhrf1-deficient satellite cells. These findings point to Uhrf1 as a regulator of self-renewal and differentiation of satellite cells via genome-wide DNA methylation patterning.
Intergenerational Stress Transmission is Associated with Brain
Metabotranscriptome Remodeling and Mitochondrial Dysfunction
Authors: Alhassen Sammy , Chen Siwei , Alhassen Lamees , Phan Alvin , Khoudari Mohammad , De Silva Angele , Barhoosh Huda , Wang Zitong , Parrocha Chelsea , Shapiro Emily , Henrich Charity , Wang Zicheng , Mutesa Leon , Baldi Pierre , Abbott Geoffrey W. , Alachkar Amal 
Published: April 2021

Abstract
Intergenerational stress increases lifetime susceptibility to depression and
other psychiatric disorders. Whether intergenerational stress transmission is a
consequence of in utero neurodevelopmental
disruptions vs early-life mother-infant interaction is largely unknown. Here, we
demonstrated that exposure to traumatic stress in mice during pregnancy, through
predator scent exposure, induces in the offspring social deficits and
depressive-like behavior. We found, through cross-fostering experiments, that
raising of normal pups by traumatized mothers produced a similar behavioral
phenotype to that induced in pups raised by their biological traumatized
mothers. Good caregiving (by non-traumatized mothers), however, did not
completely protect against the prenatal trauma-induced behavioral deficits.
These findings support a two-hit stress mechanism of both in
utero and early-life parenting (poor caregiving by the
traumatized mothers) environments. Associated with the behavioral deficits, we
found profound changes in brain metabolomics and transcriptomic
(metabotranscriptome). Striking increases in the mitochondrial hypoxia marker
and epigenetic modifier 2-hydroxyglutaric acid, in the brains of neonatal and
adult pups whose mothers were exposed to stress during pregnancy, indicated
mitochondrial metabolism dysfunctions and epigenetic mechanisms. Bioinformatic
analyses revealed mechanisms involving stress- and hypoxia-response metabolic
pathways in the brains of the neonatal mice, which appear to lead to
long-lasting alterations in mitochondrial-energy metabolism, and epigenetic
processes pertaining to DNA and chromatin modifications. Most strikingly, we
demonstrated that an early pharmacological intervention that can correct
mitochondria metabolism - lipid metabolism and epigenetic modifications with
acetyl-L-carnitine (ALCAR) supplementation - produces long-lasting protection
against the behavioral deficits associated with intergenerational transmission
of traumatic stress.
Genetic mechanisms for tissue-specific essential genes
Authors: Dvir Elad , Shohat Shahar , Shifman Sagiv 
Published: April 2021

AbstractGenetic diseases often manifest in specific tissues despite having the genetic risk variants in all cells. The most commonly assumed mechanism is selective expression of the causal gene in the pathogenic tissues, but other mechanisms are less explored. Using CRISPR screens from 789 cell lines and 27 lineages, we identified 1274 lineage-specific essential genes (LSEGs). We show that only a minority of LSEGs are explained by preferential expression (n = 115), and a big proportion of them (n = 509) is explained by lineage-specific gene amplification. Three other mechanisms were identified by genome-wide expression analysis. First, lineage-specific expression of paralogs leads to reduced functional redundancy and can account for 153 LSEGs. Second, for 45 LSEGs, the paralog expression increases vulnerability, implying functional codependency. Third, we suggest that the transfer of small molecules to mutant cells could explain blood-specific essentiality. Overall, LSEGs were more likely to be associated with human diseases than common essential genes, were highly intolerant to mutations and function in developmental pathways. Analysis of diverse human cell types found that the expression specificity of LSEGs and their paralogs is consistent with preferential expression and functional redundancy being a general phenomenon. Our findings offer important insights into genetic mechanisms for tissue specificity of human diseases.
Chromosome-level genome assembly and transcriptome- based annotation of the oleaginous yeastRhodotorula toruloidesCBS 14
Authors: Martín-Hernández Giselle C. , Müller Bettina , Chmielarz Mikołaj , Brandt Christian , Hölzer Martin , Viehweger Adrian , Passoth Volkmar 
Published: April 2021

AbstractRhodotorula toruloidesis an oleaginous yeast with high biotechnological potential. In order to understand the molecular physiology of lipid synthesis inR. toruloidesand to advance metabolic engineering, a high-resolution genome is required. We constructed a genome draft ofR. toruloidesCBS 14, using a hybrid assembly approach, consisting of short and long reads generated by Illumina and Nanopore sequencing, respectively. The genome draft consists of 23 contigs and 3 scaffolds, with a N50 length of 1,529,952 bp, thus largely representing chromosomal organization. The total size is 20,534,857 bp with a GC content of 61.83%. Transcriptomic data from different growth conditions was used to aid species-specific gene annotation. In total we annotated 9,464 genes and identified 11,691 transcripts. Furthermore, we demonstrated the presence of a potential plasmid, an extrachromosomal circular structure of about 11 kb with a copy number about three times as high as the other chromosomes.SignificanceThis obtained high-quality draft genome provides the suitable framework needed for genetic manipulations, and future studies of lipid metabolism and evolution of oleaginous yeasts. The identified extrachromosomal circular DNA may be useful for developing efficient episomal vectors for the manipulation ofRhodotorulayeasts.Data depositionThis project has been deposited at ENA under the accession PRJEB-40807.
An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes
Authors: Wong Thomas K. F. , Li Teng , Ranjard Louis , Wu Steven , Sukumaran Jeet , Rodrigo Allen G. 
Published: April 2021

AbstractA current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new method to recover the phylogeny of haplotypes from short-read sequences obtained using pooled amplicons from a mixture of individuals, without barcoding. The method, AFPhyloMix, accepts an alignment of the mixture of reads against a reference sequence, obtains the single-nucleotide-polymorphisms (SNP) patterns along the alignment, and constructs the phylogenetic tree according to the SNP patterns. AFPhyloMix adopts a Bayesian model of inference to estimates the phylogeny of the haplotypes and their relative frequencies, given that the number of haplotypes is known. In our simulations, AFPhyloMix achieved at least 80% accuracy at recovering the phylogenies and frequencies of the constituent haplotypes, for mixtures with up to 15 haplotypes. AFPhyloMix also worked well on a real data set of kangaroo mitochondrial DNA sequences.
A global phylogenetic regionalisation of vascular plants reveals a deep split between Gondwanan and Laurasian biotas
Authors: Carta Angelino , Peruzzi Lorenzo , Ramírez-Barahona Santiago 
Published: April 2021

AbstractExisting global regionalisation schemes for plants consider the compositional affinities among biotas, but these have not considered phylogenetic information explicitly. Incorporating phylogenetic information may substantially advance our understanding of the relationships among regions and the synopsis of biogeographical schemes, because phylogeny captures information on the evolutionary history of taxa. Here, we present the first phytogeographical delineation of the global vascular flora based on the evolutionary relationships of species.We analysed 8,738,520 geographical occurrence records for vascular plant species together with a time-calibrated phylogenetic tree including 67,420 species. We estimated species composition within 200 × 200 km grid cells across the world, and used a metric of phylogenetic beta diversity to generate a phylogenetic delineation of floristic regions. We contrasted these results with a regionalisation generated using a taxonomic beta diversity metric.We identified 16 phylogenetically distinct phytogeographical units, deeply split into two main clusters that broadly correspond to the Laurasia-Gondwana separation. Our regionalisation broadly matches currently recognized phytogeographical classifications, but also highlights that the Gondwanan area is split into a large Holotropical cluster and an Australian-NeoZelandic-Patagonian cluster. In turn, we found that the northernmost and southernmost units have the most evolutionarily distinct vascular plant assemblages. In contrast, taxonomic dissimilarity returned a regionalisation composed of 23 units with a high degree of shared taxa between Laurasian and Gondwanan areas, with no clear split among their biotas.The integration of phylogenetic information provided new insights into the historical relationships among phytogeographical units, enabling the identification of three large, clearly differentiated biotas, here referred to as kingdoms: Holarctic, Holotropical, and Austral. Our regionalization scheme provides further evidence for delineating transition zones between the Holarctic and Holotropical kingdoms. The latitudinal patterns of evolutionary distinctiveness of vascular plant assemblages are consistent with recent evidence of higher and more recent diversification of flowering plants outside tropical regions.
A trimeric hydrophobic zipper mediates the intramembrane assembly of SARS-CoV-2 spike
Authors: Fu Qingshan , Chou James J. 
Published: April 2021

ABSTRACTThe S protein of the SARS-CoV-2 is a Type I membrane protein that mediates membrane fusion and viral entry. A vast amount of structural information is available for the ectodomain of S, a primary target by the host immune system, but much less is known regarding its transmembrane domain (TMD) and its membrane-proximal regions. Here, we determined the nuclear magnetic resonance (NMR) structure of the S protein TMD in bicelles that closely mimic a lipid bilayer. The TMD structure is a transmembrane α-helix (TMH) trimer that assembles spontaneously in membrane. The trimer structure shows an extensive hydrophobic core along the 3-fold axis that resembles that of a trimeric leucine/isoleucine zipper, but with tetrad, not heptad, repeat. The trimeric core is strong in bicelles, resisting hydrogen-deuterium exchange for weeks. Although highly stable, structural guided mutagenesis identified single mutations that can completely dissociate the TMD trimer. Multiple studies have shown that the membrane anchor of viral fusion protein can form highly specific oligomers, but the exact function of these oligomers remain unclear. Our findings should guide future experiments to address the above question for SARS coronaviruses.
Thyroid hormone regulates abrupt skin morphogenesis during zebrafish postembryonic development
Authors: Aman Andrew J. , Kim Margaret , Saunders Lauren M. , Parichy David M. 
Published: April 2021

ABSTRACTThyroid hormone is a key regulator of post-embryonic vertebrate development. Skin is a biomedically important thyroid hormone target organ, but the cellular and molecular mechanisms underlying skin pathologies associated with thyroid dysfunction remain obscure. The transparent skin of zebrafish is an accessible model system for studying vertebrate skin development. During post-embryonic development of the zebrafish, scales emerge in the skin from a hexagonally patterned array of dermal papillae, like other vertebrate skin appendages such as feathers and hair follicles. We show here that thyroid hormone regulates the rate of post-embryonic dermal development through interaction with nuclear hormone receptors. This couples skin development with body growth to generate a well ordered array of correctly proportioned scales. This work extends our knowledge of thyroid hormone actions on skin by providing in-vivo evidence that thyroid hormone regulates multiple aspects of dermal development.HighlightsThyroid hormone (TH) is necessary for normal squamation patterning in zebrafish.Stratified dermis develops by migration of primary hypodermal cells.Dermis stratifies in an invariant wave.TH regulates the rates of multiple aspects of dermis development.Scale size and density are sensitive to skin size at onset of squamation.
Branding “Halal”: application of a certain religious emotion to attract a specific customer segment
Authors: Hosain Md Sajjad 
Published: April 2021

Purpose
The main purpose of this conceptual paper is to identify and explain the technique of branding “Halal” as a marketing strategy to reach and capture a certain market segment (niche), particularly Muslims.

Design/methodology/approach
The approach of this paper is descriptive based on literature survey as well as the author’s own opinion, experience and judgment.

Findings
In many cases, particularly in food market, the term “Halal” is being used to attract the Muslim customers’ religious feelings rather than providing them cost-effective value products.

Research limitations/implications
The paper is expected to contribute to the theoretical base, as it focuses on the use of religious sentiments in marketing that is worth further research conduction.

Practical implications
The arguments of this paper can be used by the producers of “Halal” products in including certain features that might satisfy the demands of religious Muslims regarding food products.

Social implications
This paper can be contributive for the greater needs regarding societal and Islamic values.

Originality/value
This paper is one of the initial attempts to highlight the religious feelings to attract a specific market segment.
Preparation of a photocurable hydrogel with adjustable mechanical properties for 3D printing
Authors: Xu Yifan , Gu Xiang , Meng Qinghua , Wang Bin , Fan Jun 
Published: April 2021

Purpose
This paper aims to show a series of hydrogels with adjustable mechanical properties, which can be cured quickly with visible light. The hydrogel is prepared conveniently with hydroxyethyl acrylate, cross-linker, gelatin and photoinitiator, and can be printed into certain 3D patterns with the direct ink write (DIW) 3D printer designed and developed by the research group.

Design/methodology/approach
In this paper, the authors designed a composite sensitization initiation system that is suitable for hydrogels. The concentration of photoinitiator, gelatin and cross-linker was studied to optimize the curing efficiency and adjust the mechanical properties. A DIW 3D printer was designed for the printing of hydrogel. Pre-gel solution was loaded into printer for printing into established models. The models were made and sliced with software.

Findings
The hydrogels can be cured efficiently with 405-nm visible light. While adding various content of gelatin and cross-linker, the mechanical properties of hydrogels show from soft and fragile (elastic modulus of 121.18 kPa and work of tension of 218.11 kJ·m−3) to rigid and tough (elastic modulus of 505.15 kPa and work of tension of 969.00 kJ·m−3). The hydrogels have high capacity of water absorption. With the DIW 3D printer, pre-gel hydrogel solution can be printed into objects with certain dimension.

Originality/value
In this work, a composite sensitization initiation system was designed, and fast curing hydrogels with adjustable mechanical properties had been prepared conveniently, which has high equilibrium water content and 3D printability with the DIW 3D printer.
Synthesis of bulk silicon oxynitride glass through nitridation of SiO2 aerogels and determination of Tg
Authors: Osawa Yuta , Iwasaki Kenichiro , Nakanishi Takayuki , Yasumori Atsuo , Matsui Yoshio , Nishimura Toshiyuki , Ohsawa Takeo , Segawa Hiroyo , Ohashi Naoki 
Published: April 2021

AbstractThe development of transparent glass for use in high‐temperature applications is continuing. In this study, we synthesized bulk silicon oxynitride glasses (a‐Si(O,N)x) through the nitridation of SiO2 aerogels containing methyl (CH3‐) groups and evaluated their bulk properties, including their glass transition temperature (Tg). Tetramethyl orthosilicate and methyltrimethoxysilane were added into the precursor gels, and those gels were subjected to a supercritical CO2 drying process. The presence of CH3‐group in the gel avoided cracking during ammonolysis at 750°C–1400°C, and the transparency of the gel was remained even after ammonolysis at 1300°C. The ammonolysis successfully introduced nitrogen into the gels even at relatively low temperatures, for example, 750°C, and the highest nitrogen content (11.7 mass%) was achieved in the gel after ammonolysis at 1300°C. As the nitrogen‐related signals in electron spectroscopy indicated presence of nitride ions (N3−) after ammonolysis and the infrared absorption signals attributed to Si–N bonds were enhanced with the increase of nitrogen concentration, we successfully obtained oxynitride glasses. Those oxynitride glasses showed increase of Tg with their nitrogen concentration.
Trends in hepatitis C virus‐associated mortality rates in Japan, 1998–2017
Authors: Hagiya Hideharu , Koyama Toshihiro , Deguchi Matsuo , Minato Yusuke , Miura Satomi , Funahashi Tomoko , Teratani Yusuke , Zamami Yoshito , Shinomiya Kazuaki , Kitamura Yoshihisa , Sendo Toshiaki , Hinotsu Shiro , Kano Mitsunobu 
Published: April 2021

AbstractBackground and AimThe current prevalence of hepatitis C virus infection and hepatitis C virus‐associated mortality in Japan falls short of the World Health Organization goal of viral hepatitis elimination by 2030. We aimed to evaluate the trends in hepatitis C virus‐associated mortality in Japan.MethodsThis nationwide observational study used the Japanese Vital Statistics from 1998 to 2017 and included all Japanese hepatitis C virus‐associated deaths (84 936) of adults aged ≥ 40 years. We calculated the crude and age‐standardized mortality rates per 100 000 persons by age and sex. Joinpoint regression analysis was used to identify significant changing points in trends and to estimate the annual percentage changes and the average annual percentage changes for the entire study period.ResultsThe crude mortality rate per 100 000 persons (annual death number) increased from 5.5 (3548) in 1998 to 7.0 (4843) in 2005 and decreased to 4.0 (3095) in 2017. By 2017, the crude mortality rates per 100 000 persons among men and women had dropped to 3.6 and 4.3, respectively. The age‐standardized mortality rate was higher in women than in men. The average annual percentage change was −3.8% (95% confidence interval: −5.0 to −2.5). The declining trend was more rapid in men (−4.5%, 95% confidence interval: −5.3 to −3.6) than in women (−2.7%, 95% confidence interval: −3.8 to −1.6).ConclusionsTrends in hepatitis C virus‐associated mortality rates have declined in an accelerating manner in Japan, especially among men.