bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential probiotic activity of Lactobacillus
brevis SCML 504 isolated from traditional Korean fermented food
and the preparation of ‘Sikhye’ with brown rice
Authors: Seo Ji Won , Yang Hee-Jong , Jeong Su-Ji , Ryu Myeong Seon , Jeong Do-Youn
Published: March 2020

We attempted to screen lactic acid bacteria having probable safety, antibacterial
and antioxidant activities and potential probiotic activity from
‘Meju’, and to improve the functionality of lactic acid-fermented
‘Sikhye’ by producing it using brown rice. We first selected six
strains by measuring safety-related indicators such as their antibacterial
activity against Bacillus cereus, biogenic amine production,
hemolytic properties, and production of harmful substances and enzymes. The
antioxidant activity, β-glucosidase activity, and probiotic
characteristics of the six selected lactic acid bacteria were measured, and SCML
504 was selected as the final strain to act as a potential starter for
manufacturing ‘Sikhye’. SCML 504 was identified as
Lactobacillus brevis by 16S rRNA sequencing, and named
L. brevis SCML 504 (KCCM 12526P). Finally, we manufactured
the lactic acid-fermented ‘Sikhye’ from brown rice using SCML 504,
and confirmed the fermentation properties. Functional characterization of the
manufactured ‘Sikhye’ indicated that its DPPH radical scavenging
and SOD activities were 66.42 and 69.25%, respectively. Free amino acid
analysis revealed that the content of γ-aminobutyric acid was increased
about two-fold compared to the pre-fermentation level. These findings are
expected to be useful for the development of traditional Korean beverages with
various functional properties via lactic acid fermentation.
Nanopore-based long-read transcriptome data ofNosema ceranae-infected and un-infected western honeybee workers’ midguts
Authors: Chen Huazhi , Fan Xiaoxue , Du Yu , Fan Yuanchan , Wang Jie , Jiang Haibin , Xiong Cuiling , Zheng Yanzhen , Chen Dafu , Guo Rui
Published: March 2020

Apis mellifera ligusticais a subspecies of western honeybee,Apis mellifera. Nosema ceranaeis known to cause bee microspodiosis, which seriously affects bee survival and colony productivity. In this article, Nanopore long-read sequencing was used to sequenceN. ceranae-infected and un-infected midguts ofA. m. ligusticaworkers at 7 d and 10 d post inoculation (dpi). In total, 5942745, 6664923, 7100161 and 6506665 raw reads were respectively yielded from AmT1, AmT2, AmCK1 and AmCK2, with average lengths of 1148, 1196, 1178 and 1201 bp, and N50 of 1328, 1394, 1347 and 1388 bp. The length distribution of raw reads from AmT1, AmT2, AmCK1 and AmCK2 was ranged from 1 kb to more than 10 kb. Additionally, the distribution of quality score of raw reads from AmT1 and AmT2 was among Q6∼Q12, while that from AmCK1 and AmCK2 was among Q6∼Q16. Further, 5745048, 6416987, 6928170, 6353066 clean reads were respectively gained from AmT1, AmT2, AmCK1 and AmCK2, and among them 4172542, 4638289, 5068270 and 4857960 were identified as being full-length. After removing redundant reads, the length distribution of remaining full-length transcripts was among 1 kb∼8 kb, with the most abundant length of 2 kb. The long-read transcriptome data reported here contributes to a deeper understanding of the molecular regulatingN. ceranae-response ofA. m. ligusticaand host-fungal parasite interaction during microsporidiosis.
Potent human neutralizing antibodies elicited by SARS-CoV-2 infection
Authors: Ju Bin , Zhang Qi , Ge Xiangyang , Wang Ruoke , Yu Jiazhen , Shan Sisi , Zhou Bing , Song Shuo , Tang Xian , Yu Jinfang , Ge Jiwan , Lan Jun , Yuan Jing , Wang Haiyan , Zhao Juanjuan , Zhang Shuye , Wang Youchun , Shi Xuanling , Liu Lei , Wang Xinquan , Zhang Zheng , Zhang Linqi
Published: March 2020

The pandemic caused by emerging coronavirus SARS-CoV-2 presents a serious global public health emergency in urgent need of prophylactic and therapeutic interventions. SARS-CoV-2 cellular entry depends on binding between the viral Spike protein receptor-binding domain (RBD) and the angiotensin converting enzyme 2 (ACE2) target cell receptor. Here, we report on the isolation and characterization of 206 RBD-specific monoclonal antibodies (mAbs) derived from single B cells of eight SARS-CoV-2 infected individuals. These mAbs come from diverse families of antibody heavy and light chains without apparent enrichment for particular families in the repertoire. In samples from one patient selected for further analyses, we found coexistence of germline and germline divergent clones. Both clone types demonstrated impressive binding and neutralizing activity against pseudovirus and live SARS-CoV-2. However, the antibody neutralizing potency is determined by competition with ACE2 receptor for RBD binding. Surprisingly, none of the SARS-CoV-2 antibodies nor the infected plasma cross-reacted with RBDs from either SARS-CoV or MERS-CoV although substantial plasma cross-reactivity to the trimeric Spike proteins from SARS-CoV and MERS-CoV was found. These results suggest that antibody response to RBDs is viral species-specific while that cross-recognition target regions outside the RBD. The specificity and neutralizing characteristics of this plasma cross-reactivity requires further investigation. Nevertheless, the diverse and potent neutralizing antibodies identified here are promising candidates for prophylactic and therapeutic SARS-CoV-2 interventions.
Characterization Of Hydrocarbon Utilizing Bacteria In Waste Engine Oil-Impacted Sites
Authors: Jones A. M. , James I. I. , Akpan P. S. , Eka I.I. , Oruk A. E. , Ibuot A. A.
Published: March 2020

The present work was aimed at isolating and identifying hydrocarbon utilizing bacteria from waste engine oil polluted soil, and assessing their hydrocarbon-utilizing ability. Materials and method: Eight bacterial species;Corynebacterium kutscheri, Pseudomonas aeruginosa, Flavobacterium aquatile, Serratia odorifera, Micrococcus agilis, Staphylococcus aureus, Micrococcus luteusandBacillus substiliswere isolated by selective enrichment technique and screened for hydrocarbon utilization capability in mineral salt media with waste engine oil as a sole carbon and energy source. Bacterial species showed varied hydrocarbon utilization during the 15 days of incubation. All isolates also showed variable emulsification ability. These results demonstrate the presence of indigenous bacteria in hydrocarbon polluted soils and the potential towards remediation of hydrocarbons.
Contrasting responses of protistan plant parasites and phagotrophs to ecosystems, land management and soil properties
Authors: Fiore-Donno Anna Maria , Richter-Heitmann Tim , Bonkowski Michael
Published: March 2020

Functional traits are increasingly used in ecology to link the structure of microbial communities to ecosystem processes. We investigated two important protistan lineages, Cercozoa and Endomyxa (Rhizaria) in soil using Illumina sequencing and analysed their diversity and functional traits along with their responses to environmental factors in grassland and forest across Germany. From 600 soil samples, we obtained 2,101 Operational Taxonomy Units representing ~18 million Illumina reads (region V4, 18S rRNA gene). All major taxonomic and functional groups were present, dominated by small bacterivorous flagellates (Glissomonadida). Endomyxan plant parasites were absent from forest. In grassland, they were promoted by more intensive land use management. Grassland and forest strikingly differed in community composition. Relative abundances of bacterivores and eukaryvores were contrastingly influenced by environmental factors, indicating bottom-up regulation by food resources. These patterns provide new insights into the functional organization of soil biota and indications for a more sustainable land-use management.

Highlights

Protistan plant parasites of worldwide importance (Phytomyxea) are absent from forest

Protistan plant parasites are enhanced by land use intensification in grassland

Opposite responses of protistan trophic guilds to environmental conditions in forest

Drastic differences in protistan community composition between grassland and forest
F5N: Nanopore Sequence Analysis Toolkit for Android Smartphones
Authors: Samarakoon Hiruna , Punchihewa Sanoj , Senanayake Anjana , Ragel Roshan , Gamaarachchi Hasindu
Published: March 2020

F5Nis the first ever Android application for nanopore sequence analysis on a mobile phone, comprised of popular tools for read alignment (Minimap2), sequence data manipulation (Samtools) and methylation calling (F5C/Nanopolish). On NA12878 nanopore data,F5Ncan perform a complete methylation calling pipeline on a mobile phone in ∼15 minutes for a batch of 4000 nanopore reads (∼34 megabases).F5Nis not only a toolkit but also a framework for integrating existing C/C++ based command line tools to run on Android.F5Nwill enable performing nanopore sequence analysis on-site when used with an ultra-portable nanopore sequencer (eg: MinION or the anticipated smidgION), consequently reducing the cost for special computers and high-speed Internet.

Availability and implementation

F5NAndroid application is available on Google Play store athttps://play.google.com/store/apps/details?id=com.mobilegenomics.genopo&hl=enand the source code is available on Github athttps://github.com/SanojPunchihewa/f5n.

Contact

hirunas@eng.pdn.ac.lk
Governance networks around grasslands with contrasting management history
Authors: Manolache Steluta , Nita Andreea , Hartel Tibor , Miu Iulia Viorica , Ciocanea Cristiana Maria , Rozylowicz Laurentiu
Published: March 2020

Romanian grasslands have high nature value, being among the most important biodiversity hotspots at the European level. The European Union Common Agricultural Policy (CAP) contradicts the Biodiversity Strategy to 2020 objective by hindering coordinated grassland governance and collaboration among the involved actors. At the European level, few attempts have been made in creating conceptual strategies for implementing conservation measures in a multi-actor and multi-scale governance setting. Our paper focuses on a comparative network analysis of grassland landscape governance of three Romanian regions (Iron Gates Natural Park – SW; Sighisoara - Tarnava Mare – center; and Dobrogea - SE), representatives for grassland management in mountain and lowland settings. We investigated the structural characteristics of one-mode directed grassland governance networks in the three protected areas (standard cohesion and reciprocity metrics and exponential random graph models), the position of institutions participating in networks (node-level centrality metrics), and the perception of CAP influence on grassland governance by farmers benefiting of CAP agri-environmental payments. In Sighisoara, grasslands governance has been centralized but biodiversity-friendly, while in Iron Gates, grasslands were traditionally managed through a decentralized, community-level system, and this type of governance continues to date. Whereas for Dobrogea’s grasslands, the governance was performed in an intensive, centralized state-run management regime during the communist time and by large landowners after the transition period ended. Our findings illustrate the structure of the three governance networks and dissimilar patterns of collaboration, indicating distinct particularities to be considered when exploring barriers to and options for successful governance in traditionally managed grasslands in the context of CAP measures-driven management.
Dynamic Normalization
Authors: Heeger David J. , Zemlianova Klavdia O.
Published: March 2020

The normalization model has been applied to explain neural activity in diverse neural systems including primary visual cortex (V1). The model’s defining characteristic is that the response of each neuron is divided by a factor that includes a weighted sum of activity of a pool of neurons. In spite of the success of the normalization model, there are 3 unresolved issues. 1) Experimental evidence supports the hypothesis that normalization in V1 operates via recurrent amplification, i.e., amplifying weak inputs more than strong inputs. It is unknown how nor-malization arises from recurrent amplification. 2) Experiments have demonstrated that normalization is weighted such that each weight specifies how one neuron contributes to another’s normalization pool. It is unknown how weighted normalization arises from a recurrent circuit. 3) Neural activity in V1 exhibits complex dynamics, including gamma oscillations, linked to normalization. It is unknown how these dynamics emerge from normalization. Here, a new family of recurrent circuit models is reported, each of which comprises coupled neural integrators to implement normalization via recurrent amplification with arbitrary normalization weights, some of which can reca-pitulate key experimental observations of the dynamics of neural activity in V1.

Significance Statement

A family of recurrent circuit models is proposed to explain the dynamics of neural activity in primary visual cortex (V1). Each of the models in this family exhibits steady state output responses that are already known to fit a wide range of experimental data from diverse neural systems. These models can recapitulate the complex dynamics of V1 activity, including oscillations (so-called gamma oscillations, ∼30-80 Hz). This theoretical framework may also be used to explain key aspects of working memory and motor control. Consequently, the same circuit architecture is applicable to a variety of neural systems, and V1 can be used as a model system for understanding the neural computations in many brain areas.
Organized cannabinoid receptor distribution in neurons revealed by super-resolution fluorescence imaging
Authors: Li Hui , Yang Jie , Cuiping Tian , Diao Min , Wang Quan , Zhao Simeng , Li Shanshan , Tan Fangzhi , Hua Tian , Lin Chao-Po , Deska-Gauthier Dylan , Thompson Garth , Zhang Ying , Wang Tong , Shui Wenqing , Liu Zhi-Jie , Zhong Guisheng
Published: March 2020

G-protein-coupled receptors (GPCRs) play important roles in cellular functions. However, their intracellular organization is largely unknown. Through investigation of the cannabinoid receptor 1 (CB1), we discovered periodically repeating clusters of CB1 hotspots within the axons of neurons. We observed these CB1hotspots interact with the membrane-associated periodic skeleton (MPS) forming a complex crucial in the regulation of CB1signaling. Furthermore, we found that CB1hotspot periodicity increased upon CB1agonist application, and these activated CB1 displayed less dynamic movement compared to non-activated CB1. Our results suggest that CB1forms periodic hotspots organized by the MPS as a mechanism to increase signaling efficacy when being activated.
Single-cell RNA-Seq reveals the link betweenCD45isoforms and tumor-infiltrating T cells heterogeneity in liver cancer
Authors: Zhou Biaofeng , Liu Shang , Wu Liang , Sun Yan , Chen Jie , Liu Shiping
Published: March 2020

CD45isoforms play a major role in characterizing T cell function, phenotype, and development. However, there is lacking comprehensive interrogation about the relationship betweenCD45isoforms and T lymphocytes from cancer patients at the single-cell level yet. Here, we investigated the CD45 isoforms component of published 5,063 T cells of hepatocellular carcinoma (HCC), which has been assigned functional states. We found that the distribution ofCD45isoforms in T lymphocytes cells depended on tissue resource, cell type, and functional state. Further, we demonstrated that CD45RO and CD45RA dominate in characterizing the phenotype and function of T cell though multipleCD45isoforms coexist in T cells, through a novel alternative splicing pattern analysis. We identified a novel development trajectory of tumor-infiltrating T cells from Tcm to Temra (effector memory T cells re-expresses CD45RA) after detecting two subpopulations in state of transition, Tcm (central memory T) and Tem (effector memory T). Temra, capable of high cytotoxic characteristics, was discovered to be associated with the stage of HCC and may be a target of immunotherapy. Our study presents a comprehension of the connection betweenCD45isoforms and the function, states, sources of T lymphocytes cells in HCC patients at the single-cell level, providing novel insight for the effect ofCD45isoforms on T cell heterogeneity.
Sex determination through X-Y heterogamety inSalix nigra
Authors: Sanderson Brian J. , Feng Guanqiao , Hu Nan , Carlson Craig H. , Smart Lawrence B. , Keefover-Ring Ken , Yin Tongming , Ma Tao , Liu Jianquan , DiFazio Stephen P. , Olson Matthew S.
Published: March 2020

The development of non-recombining sex chromosomes has radical effects on the evolution of discrete sexes and sexual dimorphism. Although dioecy is rare in plants, sex chromosomes have evolved repeatedly throughout the diversification of angiosperms, and many of these sex chromosomes are relatively young compared to those found in vertebrates. In this study, we designed and used a sequence capture array to identify a novel sex-linked region (SLR) inSalix nigra, a basal species in the willow clade, and demonstrated that this species has XY heterogamety. We did not detect any genetic overlap with the previously characterized ZW SLRs in willows, which map to a different chromosome. TheS. nigraSLR is characterized by strong recombination suppression across a 2 MB region and an excess of low frequency alleles, resulting in a low Tajima’s D compared to the remainder of the genome. We speculate that either a recent bottleneck in population size or factors related to positive or background selection generated this differential pattern of Tajima’s D on the X and autosomes. This discovery provides insights into factors that may influence the evolution of sex chromosomes in plants and contributes to a large number of recent observations that underscore their dynamic nature.
Mechanism of action of HBV capsid assembly modulators predicted from binding to early assembly intermediates
Authors: Pavlova Anna , Bassit Leda , Cox Bryan D. , Korablyov Maksym , Chipot Chris , Verma Kiran , Russell Olivia O. , Schinazi Raymond F. , Gumbart James C.
Published: March 2020

Interfering with the self-assembly of virus nucleocapsids is a promising approach for the development of novel antiviral agents. Applied to hepatitis B virus (HBV), this approach has led to several classes of capsid assembly modulators (CAMs) that target the virus by either accelerating nucleocapsid assembly or misdirecting it into non-capsid-like particles. Here, we have assessed the structures of early nucleocapsid assembly intermediates, with and without bound CAMs, using molecular dynamics simulations. We find that distinct conformations of the intermediates are induced depending on whether the bound CAM accelerates or misdirects assembly; these structures are predictive of the final assembly. We also selected non-capsid-like structures from our simulations for virtual screening, resulting in the discovery of several compounds with moderate anti-viral activity and low toxicity. Cryo-electron microscopy and capsid melting experiments suggest that our compounds possess a novel mechanism for assembly modulation, potentially opening new avenues for HBV inhibition.
Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data with ImmClassifier
Authors: Liu Xuan , Gosline Sara J.C. , Pflieger Lance T. , Wallet Pierre , Iyer Archana , Guinney Justin , Bild Andrea H. , Chang Jeffrey T.
Published: March 2020

Single-cell RNA sequencing is an emerging strategy for characterizing the immune cell population in diverse environments including blood, tumor or healthy tissues. While this has traditionally been done with flow or mass cytometry targeting protein expression, scRNA-Seq has several established and potential advantages in that it can profile immune cells and non-immune cells (e.g. cancer cells) in the same sample, identify cell types that lack precise markers for flow cytometry, or identify a potentially larger number of immune cell types and activation states than is achievable in a single flow assay. However, scRNA-Seq is currently limited due to the need to identify the types of each immune cell from its transcriptional profile, which is not only time-consuming but also requires a significant knowledge of immunology. While recently developed algorithms accurately annotate coarse cell types (e.g. T cells vs macrophages), making fine distinctions has turned out to be a difficult challenge. To address this, we developed a machine learning classifier called ImmClassifier that leverages a hierarchical ontology of cell type. We demonstrate that ImmClassifier outperforms other tools (+20% recall, +14% precision) in distinguishing fine-grained cell types (e.g. CD8+ effector memory T cells) with comparable performance on coarse ones. Thus, ImmClassifier can be used to explore more deeply the heterogeneity of the immune system in scRNA-Seq experiments.
Modality-independent effect of gravity in shaping the internal representation of 3D space
Authors: Theo Morfoisse , Gabriela Herrera Altamira , Leonardo Angelini , Gilles Clément , Mathieu Beraneck , Joseph McIntyre , Michele Tagliabue
Published: March 2020

Human 3D perception of visual objects is flawed by distortions, which are influenced by non-visual factors, such as gravitational vestibular signals. Whether gravity acts specifically on the visual system or at a higher, modality-independent, level of information processing remains unknown. To test these modality-specific vs modality-independent hypotheses, we performed experiments comparing visual versus haptic 3D shape perception in normo-gravity and microgravity. The results obtained for upright and supine posture in 1g show that visual and haptic perceptual anisotropies are systematically in opposing ego-centered, but not gravity-centered, directions suggesting they share a common origin. On the other hand, microgravity significantly modulates both visual and haptic perceptual distortion in the same direction. Overall, our results show a clear link between the visual and haptic perceptual distortions and demonstrate a role of gravity-related signals on a modality-independent internal representation of 3D space used to interpret incoming sensory inputs.
The Presence of Periodontal Pathogens in Gastric Cancer
Authors: de Leeuw Marcel A. , Duval Manuel X.
Published: March 2020

Background

The microbiome is thought to play a role in the development of gastric cancer (GC). Several studies have put forward putatively carcinogenic species in addition toHelicobacter pylori, but are not in perfect alignment, possibly due to variable parameters in the experiments, including downstream processing. Meta-analyses have not been published so far, so there is lack in clinical guidance beyondH. pylorieradication therapy.

Methods

Here, we analysed gastric mucosa samples from nine public data sets, including GC samples. Using both unsupervised and supervised learning, we defined fine grain bacterial networks of gastric mucosa and identified species associated with tumor status of samples.

Results

We found anatomic locations and cohort regions among the possible factors leading to the observation of study specific gastric microbiomes. Despite this variability, the periodontal speciesFusobacterium nucleatum, Parvimonas micraandPeptostreptococcus stomatiswere found in association with tumor status in several datasets. The three species were predicted to be in interaction by ecological network analysis and also formed the intersection of tumor associated species between four GC data sets and five colorectal cancer (CRC) data sets we reanalyzed. We formulated a probiotic composition putatively competing with the GC pathogen spectrum, from correlation analysis in a large superset of gut samples (n=17,800) from clinical- and crowd-sourced studies.

Implications

The overlapping bacterial pathogen spectrum between two gastrointestinal tumor types, GC and CRC, has implications for etiology, treatment and prevention. In vitro testing results reported in literature suggestH. pylorieradication treatment should be efficient against the GC pathogen spectrum, yet the existence of an upstream periodontal reservoir is of concern. To address this, we propose longer term use of the formulated probiotics composition.
The mechanism of coupled folding-upon-binding of an intrinsically disordered protein
Authors: Robustelli Paul , Piana Stefano , Shaw David E.
Published: March 2020

Intrinsically disordered proteins (IDPs), which in isolation do not adopt a well-defined tertiary structure but instead populate a structurally heterogeneous ensemble of interconverting states, play important roles in many biological pathways. IDPs often fold into ordered states upon binding to their physiological interaction partners (a so-called “folding-upon-binding” process), but it has proven difficult to obtain an atomic-level description of the structural mechanisms by which they do so. Here, we describe in atomic detail the folding-upon-binding mechanism of an IDP segment to its binding partner, as observed in unbiased molecular dynamics simulations. In our simulations, we observed over 70 binding and unbinding events between the α-helical molecular recognition element (α-MoRE) of the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (NTAIL) and the X domain (XD) of the measles virus phosphoprotein complex. We found that folding-upon-binding primarily occurred through induced-folding pathways (in which intermolecular contacts form before or concurrently with the secondary structure of the disordered protein)—an observation supported by previous experiments—and that the transition state ensemble was characterized by the formation of just a few key intermolecular contacts, and was otherwise highly structurally heterogeneous. We found that when a large amount of helical content was present early in a transition path, NTAILtypically unfolded, then refolded after additional intermolecular contacts formed. We also found that, among conformations with similar numbers of intermolecular contacts, those with less helical content had a higher probability of ultimately forming the native complex than conformations with more helical content, which were more likely to unbind. These observations suggest that even after intermolecular contacts have formed, disordered regions can have a kinetic advantage over folded regions in the folding-upon-binding process.
A long noncoding RNA, LOC157273, is the effector transcript at the chromosome 8p23.1-PPP1R3B metabolic traits and type 2 diabetes risk locus
Authors: Manning Alisa K. , Goustin Anton Scott , Kleinbrink Erica L. , Thepsuwan Pattaraporn , Cai Juan , Ju Donghong , Leong Aaron , Udler Miriam S. , Brown James Bentley , Goodarzi Mark O. , Rotter Jerome I. , Sladek Robert , Meigs James B. , Lipovich Leonard
Published: March 2020

Aims

Causal transcripts at genomic loci associated with type 2 diabetes are mostly unknown. The chr8p23.1 variant rs4841132, associated with an insulin resistant diabetes risk phenotype, lies in the second exon of a long non-coding RNA (lncRNA) gene, LOC157273, located 175 kilobases from PPP1R3B, which encodes a key protein regulating insulin-mediated hepatic glycogen storage in humans. We hypothesized that LOC157273 regulates expression of PPP1R3B in human hepatocytes.

Methods

We tested our hypothesis using Stellaris fluorescent in-situ hybridization to assess subcellular localization of LOC157273; siRNA knockdown of LOC157273, followed by RT-PCR to quantify LOC157273 and PPP1R3B expression; RNA-seq to quantify the whole-transcriptome gene expression response to LOC157273 knockdown and an insulin-stimulated assay to measure hepatocyte glycogen deposition before and after knockdown.

Results

We found that siRNA knockdown decreased LOC157273 transcript levels by approximately 80%, increased PPP1R3B mRNA levels by 1.7-fold and increased glycogen deposition by >50% in primary human hepatocytes. An A/G heterozygous carrier (vs. three G/G carriers) had reduced LOC157273 abundance due to reduced transcription of the A allele and increased PPP1R3B expression and glycogen deposition.

Conclusion

We show that the lncRNA LOC157273 is a negative regulator of PPP1R3B expression and glycogen deposition in human hepatocytes and the causal transcript at an insulin resistant type 2 diabetes risk locus.
Machine learning pattern recognition and differential network analysis of gastric microbiome in the presence of proton pump inhibitor treatment orHelicobacter pyloriinfection
Authors: Ciucci Sara , Durán Claudio , Palladini Alessandra , Ijaz Umer Z. , Sterbini Francesco Paroni , Masucci Luca , Cammarota Giovanni , Ianiro Gianluca , Spuul Pirjo , Schroeder Michael , Grill Stephan W. , Parsons Bryony N. , Pritchard D. Mark , Posteraro Brunella , Sanguinetti Maurizio , Gasbarrini Giovanni , Gasbarrini Antonio , Cannistraci Carlo Vittorio
Published: March 2020

Although long thought to be a sterile and inhospitable environment, the stomach is inhabited by diverse microbial communities, co-existing in a dynamic balance. Long-term use of orally administered drugs such as Proton Pump Inhibitors (PPIs), or bacterial infection such asHelicobacter pylori, cause significant microbial alterations. Yet, studies revealing how the commensal bacteria re-organize, due to these perturbations of the gastric environment, are in the early phase. They mainly focus on the most prevalent taxa and rely on linear techniques for multivariate analysis.

Here we disclose the importance of complementing linear dimensionality reduction techniques such as Principal Component Analysis and Multidimensional Scaling with nonlinear approaches derived from the physics of complex systems. Then, we show the importance to complete multivariate pattern analysis with differential network analysis, to reveal mechanisms of re-organizations which emerge from combinatorial microbial variations induced by a medical treatment (PPIs) or an infectious state (H. pylori).
In plants distal regulatory sequences overlap with unmethylated rather than low-methylated regions, in contrast to mammals
Authors: Oka Rurika , Bliek Mattijs , Hoefsloot Huub C.J. , Stam Maike
Published: March 2020

Background

DNA methylation is an important factor in the regulation of gene expression and genome stability. High DNA methylation levels are associated with transcriptional repression. In mammalian systems, unmethylated, low methylated and fully methylated regions (UMRs, LMRs, and FMRs, respectively) can be distinguished. UMRs are associated with proximal regulatory regions, while LMRs are associated with distal regulatory regions. Although DNA methylation is mainly limited to the CG context in mammals, while it occurs in CG, CHG and CHH contexts in plants, UMRs and LMRs were expected to occupy similar genomic sequences in both mammals and plants.

Results

This study investigated major model and crop plants such asArabidopsis thaliana, tomato (Solanum lycopersicum), rice (Oryza sativa) and maize (Zea mays), and shows that plant genomes can also be subdivided in UMRs, LMRs and FMRs, but that LMRs are mainly present in the CHG context rather than the CG context. Strikingly, the identified CHG LMRs were enriched in transposable elements rather than regulatory regions. Maize candidate regulatory regions overlapped with UMRs. LMRs were enriched for heterochromatic histone modifications and depleted for DNase accessibility and H3K9 acetylation. CHG LMRs form a distinct, abundant cluster of loci, indicating they have a different role than FMRs.

Conclusions

Both mammalian and plant genomes can be segmented in three distinct classes of loci, UMRs, LMRs and FMRs, indicating similar underlying mechanisms. Unlike in mammals, distal regulatory sequences in plants appear to overlap with UMRs instead of LMRs. Our data indicate that LMRs in plants have a different function than those in mammals.
mir-21 is associated with inactive low molecular weight Argonaute complexes in thyroid cancer cell lines
Authors: Powell Bonita H. , Turchinovich Andrey , Wang Yongchun , Liao Zhaohao , Dar Mohammad Aasif , Rocca Gaspare La , Umanah George Essien , Zeiger Martha A. , Umbricht Christopher B. , Witwer Kenneth W.
Published: March 2020

Thyroid cancer is the most prevalent endocrine malignancy. We and others have shown that several microRNAs, which are post-transcriptional gene regulators, are aberrantly expressed in anaplastic thyroid cancer (ATC) and papillary thyroid cancer (PTC) tissues, as well as cell lines derived from these cancers. In the cell, miRNAs are bound to Argonaute (AGO) proteins as what could be termed low molecular weight RNA-Induced Silencing Complexes (LMW-RISCs) that can assemble with additional proteins, mRNA, and translation machinery into high molecular weight RISCs (HMW-RISCs) that exert regulatory function. In this study, we sought to analyze the association of miRNAs with RISC complexes in ATC and PTC. For ATC and PTC lines, miRNA species were enriched in both HMW-RISC and LMW-RISC cellular fractions, compared with intermediate molecular weight fractions and very low molecular weight (AGO-poor) fractions. Furthermore, 60% of all miRNAs were slightly more abundant in LMW-RISC versus HMW-RISC fractions by ~2-4 fold. Surprisingly, miR-21-5p, one of the most abundant miRNAs in both ATC and PTC lines and one of the most widely studied oncogenic miRNAs in many solid tumors, was consistently one the least abundant miRNAs in HMW-RISC and the most enriched miRNA in LMW-RISC fractions. These findings may suggest that miR-21 has a role or roles distinct from canonical post-transcriptional regulation in cancer. Furthermore, the methodology described here is a useful way to assess the distribution of miR-21 between HMW and LMW-RISCs and may help to reveal the true roles of this miRNA in thyroid cancer development, progression, and treatment.
Open source software tool for the automated detection and characterization of epithelial cells from trace biological samples
Authors: Olsen Anita , Miller Mekhi , Yadavalli Vamsi K. , Ehrhardt Christopher J.
Published: March 2020

This paper presents a strategy for an unsupervised workflow for identifying epithelial cells in microscopic images and characterizing their morphological and/or optical properties. The proposed method can be used on cells that have been stained with fluorescent dyes and imaged using conventional optical microscopes. The workflow was tested on cell populations that were imaged directly on touch/contact surfaces and stained with nucleic acid dyes to visualize genetic content. Our results show that this approach could be a useful strategy for characterizing differences in staining efficiency and/or morphological properties of individual cells or aggregate populations within a biological sample. Further, they can potentially reduce the laborious nature of microscopic analysis and increase throughput and reproducibility of similar studies.
Effects of cell cycle variability on lineage and population measurements of mRNA abundance
Authors: Perez-Carrasco Ruben , Beentjes Casper , Grima Ramon
Published: March 2020

Many models of gene expression do not explicitly incorporate a cell cycle description. Here we derive a theory describing how mRNA fluctuations for constitutive and bursty gene expression are influenced by stochasticity in the duration of the cell cycle and the timing of DNA replication. Analytical expressions for the moments show that omitting cell cycle duration introduces an error in the predicted mean number of mRNAs that is a monotonically decreasing function ofη, which is proportional to the ratio of the mean cell cycle duration and the mRNA lifetime. By contrast, the error in the variance of the mRNA distribution is highest for intermediate values ofηconsistent with genome-wide measurements in many organisms. Using eukaryotic cell data, we estimate the errors in the mean and variance to be at most 3% and 25%, respectively. Furthermore, we derive an accurate negative binomial mixture approximation to the mRNA distribution. This indicates that stochasticity in the cell cycle can introduce fluctuations in mRNA numbers that are similar to the effect of bursty transcription. Finally, we show that for real experimental data, disregarding cell cycle stochasticity can introduce errors in the inference of transcription rates larger than 10%.
Layered Feedback Control Improves Robust Functionality across Heterogeneous Cell Populations
Authors: Ren Xinying , Murray Richard M.
Published: March 2020

Realizing homeostatic control of metabolites or proteins is one of the key goals of synthetic circuits. However, if control is only implemented internally in individual cells, cell-cell heterogeneity may break the homeostasis on population level since cells do not contribute equally to the production or regulation. New control structures are needed to achieve robust functionality in heterogeneous cell populations. Quorum sensing (QS) serves as a collective mechanism by releasing and sensing small and diffusible signaling molecules for group decision-making. We propose a layered feedback control structure that includes a global controller using quorum sensing and a local controller via internal signal-receptor systems. We demonstrate with modeling and simulation that the global controller drives contributing cells to compensate for disturbances while the local controller governs the fail-mode performance in non-contributing cells. The layered controller can tolerate a higher portion of non-contributing cells or longer generations of mutant cells while maintaining metabolites or proteins level within a small error range, compared with only internal feedback control. We further discuss the potential of such layered structures in robust control of cell population size, population fraction and other population-dependent functions.
Structure and mechanism of potent bifunctional β-lactam- and homoserine lactone-degrading enzymes from marine microorganisms
Authors: Selleck Christopher , Pedroso Marcelo Monteiro , Wilson Liam , Krco Stephan , Knaven Esmée Gianna , Miraula Manfredi , Mitić Nataša , Larrabee James A. , Brück Thomas , Clark Alice , Guddat Luke W. , Schenk Gerhard
Published: March 2020

Genes that confer antibiotic resistance can rapidly be disseminated from one microorganism to another by mobile genetic elements, thus transferring resistance to previously susceptible bacterial strains. The misuse of antibiotics in health care and agriculture has provided a powerful evolutionary pressure to accelerate the spread of resistance genes, including those encoding β-lactamases. These are enzymes that are highly efficient in inactivating most of the commonly used β-lactam antibiotics. However, genes that confer antibiotic resistance are not only associated with pathogenic microorganisms, but are also found in non-pathogenic (i.e. environmental) microorganisms. Two recent examples are metal-dependent β-lactamases (MBLs) from the marine organismsNovosphingobium pentaromativoransandSimiduia agarivorans. Previous studies have demonstrated that their β-lactamase activity is comparable to those of well-known MBLs from pathogenic sources (e.g. NDM-1, AIM-1) but that they also possess efficient lactonase activity, an activity associated with quorum sensing. Here, we probed the structure and mechanism of these two enzymes using crystallographic, spectroscopic and fast kinetics techniques. Despite highly conserved active sites both enzymes demonstrate significant variations in their reaction mechanisms, highlighting both the extraordinary ability of MBLs to adapt to changing environmental conditions and the rather promiscuous acceptance of diverse substrates by these enzymes.
Integrated analysis of a compendium of RNA-Seq datasets for splicing factors
Authors: Yu Peng , Li Jin , Deng Su-Ping , Zhang Feiran , Grozdanov Petar N. , Chin Eunice W. M. , Martin Sheree D. , Vergnes Laurent , Islam M. Saharul , Sun Deqiang , LaSalle Janine M. , McGee Sean L. , Goh Eyleen , MacDonald Clinton C. , Jin Peng
Published: March 2020

A vast amount of public RNA-sequencing datasets have been generated and used widely to study transcriptome mechanisms. These data offer precious opportunity for advancing biological research in transcriptome studies such as alternative splicing. We report the first large-scale integrated analysis of RNA-Seq data of splicing factors for systematically identifying key factors in diseases and biological processes. We analyzed 1,321 RNA-Seq libraries of various mouse tissues and cell lines, comprising more than 6.6 TB sequences from 75 independent studies that experimentally manipulated 56 splicing factors. Using these data, RNA splicing signatures and gene expression signatures were computed, and signature comparison analysis identified a list of key splicing factors in Rett syndrome and cold-induced thermogenesis. We show that cold-induced RNA-binding proteins rescue the neurite outgrowth defects in Rett syndrome using neuronal morphology analysis, and we also reveal that SRSF1 and PTBP1 are required for energy expenditure in adipocytes using metabolic flux analysis. Our study provides an integrated analysis for identifying key factors in diseases and biological processes and highlights the importance of public data resources for identifying hypotheses for experimental testing.
Transcriptome-Wide Combinatorial RNA Structure Probing in Living Cells
Authors: Chan Dalen , Feng Chao , England Whitney , Wyman Dana , Flynn Ryan A. , Wang Xiuye , Shi Yongsheng , Mortazavi Ali , Spitale Robert C.
Published: March 2020

RNA molecules can fold into complex structures and interact with trans-acting factors to control their biology. Recent methods have been focused on developing novel tools to measure RNA structure transcriptome-wide, but their utility to study and predict RNA-protein interactions or RNA processing has been limited thus far. Here, we extend these studies with the first transcriptomewide mapping method for cataloging RNA solvent accessibility, icLASER. By combining solvent accessibility (icLASER) with RNA flexibility (icSHAPE) data, we efficiently predict RNA-protein interactions transcriptome-wide and catalog RNA polyadenylation sites by RNA structure alone. These studies showcase the power of designing novel chemical approaches to studying RNA biology. Further, our study exemplifies merging complementary methods to measure RNA structure inside cells and its utility for predicting transcriptome-wide interactions that are critical for control of and regulation by RNA structure. We envision such approaches can be applied to studying different cell types or cells under varying conditions, using RNA structure and footprinting to characterize cellular interactions and processing involving RNA.
Enhancing the Antiviral Efficacy of RNA-Dependent RNA Polymerase Inhibition by Combination with Modulators of Pyrimidine Metabolism
Authors: Liu Qi , Gupta Amita , Okesli-Armlovich Ayse , Qiao Wenjie , Fischer Curt R. , Smith Mark , Carette Jan E. , Bassik Michael C. , Khosla Chaitan
Published: March 2020

Genome-wide analysis of the mode of action of GSK983, a potent antiviral agent, led to the identification of dihydroorotate dehydrogenase (DHODH) as its target, along with the discovery that knockdown of genes in pyrimidine salvage pathways sensitized cells to GSK983. Because GSK983 is an ineffective antiviral in the presence of physiological uridine concentrations, we explored combining GSK983 with pyrimidine salvage inhibitors. We synthesized and evaluated analogs of cyclopentenyl uracil (CPU), an inhibitor of uridine salvage. We found that CPU was efficiently converted into its triphosphates in cells. When combined with GSK983, it led to large drops in cellular UTP and CTP pools. Consequently, CPU-GSK983 suppressed dengue virus replication in the presence of physiological concentrations of uridine. In addition, the CPU-GSK983 combination markedly enhanced the effect of RNA-dependent RNA polymerase (RdRp) inhibition on viral genome infection. Our findings highlight a new host-targeting strategy for potentiating the antiviral activities of RdRp inhibitors.
Exact resolution function for double-disk chopper neutron time-of-flight spectrometers: application to reflectivity
Authors: Lairez Didier , Chennevière Alexis , Ott Frédéric
Published: March 2020

The exact resolution function of the transfer vector for the HERMÈS reflectometer at the Laboratoire Léon Brillouin is calculated as an example of a neutron time-of-flight spectrometer with a double-disk chopper. The calculation accounts for the wavelength distribution of the incident beam, the tilt of the chopper axis, collimation and gravity, without an assumption of Gaussian distributions or the independence of these different contributions. A numerical implementation is provided. It is shown that data fitting using this exact resolution function allows much better results to be reached than with the usual approximation by a Gaussian profile.
In meso crystallogenesis. Compatibility of the lipid cubic phase with the synthetic digitonin analogue, glyco-diosgenin
Authors: van Dalsen Leendert , Weichert Dietmar , Caffrey Martin
Published: March 2020

Digitonin has long been used as a mild detergent for extracting proteins from membranes for structure and function studies. As supplied commercially, digitonin is inhomogeneous and requires lengthy pre-treatment for reliable downstream use. Glyco-diosgenin (GDN) is a recently introduced synthetic surfactant with features that mimic digitonin. It is available in homogeneously pure form. GDN is proving to be a useful detergent, particularly in the area of single-particle cryo-electron microscopic studies of membrane integral proteins. With a view to using it as a detergent for crystallization trials by the in meso or lipid cubic phase method, it was important to establish the carrying capacity of the cubic mesophase for GDN. This was quantified in the current study using small-angle X-ray scattering for mesophase identification and phase microstructure characterization as a function of temperature and GDN concentration. The data show that the lipid cubic phase formed by hydrated monoolein tolerates GDN to concentrations orders of magnitude in excess of those used for membrane protein studies. Thus, having GDN in a typical membrane protein preparation should not deter use of the in meso method for crystallogenesis.
RaDMaX online: a web-based program for the determination of strain and damage profiles in irradiated crystals using X-ray diffraction
Authors: Boulle A. , Mergnac V.
Published: March 2020

RaDMaX online is a major update to the previously published RaDMaX (radiation damage in materials analysed with X-ray diffraction) software [Souilah, Boulle & Debelle (2016). J. Appl. Cryst.
49, 311–316]. This program features a user-friendly interface that allows retrieval of strain and disorder depth profiles in irradiated crystals from the simulation of X-ray diffraction data recorded in symmetrical θ/2θ mode. As compared with its predecessor, RaDMaX online has been entirely rewritten in order to be able to run within a simple web browser, therefore avoiding the necessity to install any programming environment on the users' computers. The RaDMaX online web application is written in Python and developed within a Jupyter notebook implementing graphical widgets and interactive plots. RaDMaX online is free and open source and can be accessed on the internet at https://aboulle.github.io/RaDMaX-online/.