bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lipid droplets disrupt mechanosensing in human hepatocytes
Authors: Chin LiKang , Theise Neil D. , Loneker Abigail E. , Janmey Paul A. , Wells Rebecca G. 
Published: April 2020

ABSTRACTHepatocellular carcinoma (HCC) is the fourth leading cause of cancer death in the world. Although most cases occur in stiff, cirrhotic livers, and stiffness is a significant risk factor, HCC can also arise in non-cirrhotic livers in the setting of non-alcoholic fatty liver disease (NAFLD). We hypothesized that lipid droplets in NAFLD might apply mechanical forces to the nucleus, functioning as mechanical stressors akin to stiffness. We investigated the effect of lipid droplets on cellular mechanosensing and found that primary human hepatocytes loaded with the fatty acids oleate and linoleate exhibited decreased stiffness-induced cell spreading and disrupted focal adhesions and stress fibers. The presence of large lipid droplets in hepatocytes resulted in increased nuclear localization of the mechano-sensor Yes-associated protein (YAP). In cirrhotic livers from patients with NAFLD, hepatocytes filled with large lipid droplets showed significantly higher nuclear localization of YAP as compared to cells with small lipid droplets. This work suggests that lipid droplets induce a mechanical signal that disrupts the ability of the hepatocyte to sense its underlying matrix stiffness, and that the presence of lipid droplets can induce intracellular mechanical stresses.GRAPHICAL ABSTRACT
Molecular Docking Analysis Of Some Phytochemicals On Two SARS-CoV-2 Targets: Potential Lead Compounds Against Two Target Sites of SARS-CoV-2 Obtained from Plants
Authors: Ubani Amaka , Agwom Francis , RuthMorenikeji Oluwatoyin , Nathan Shehu , Luka Pam , Umera Arinze , Umar Usal , Omale Simeon , Nnadi Nnaemeka Emmanuel , Aguiyi John Chineye 
Published: April 2020

AbstractCOV spike (S) glycoprotein and Mproare two key targets that have been identified for vaccines and drug development against the COVID-19 disease. Virtual screening of some compounds of plants origin that have shown antiviral activities were carried out on the two targets, 6lu7 and 6vsb by docking with the PyRx software. The binding affinities were compared with other compounds and drugs already identified as potential ligands for 6lu7 and 6vsb as well as Chloroquine and hydroxychloroquine. The docked compounds with best binding affinities were also filtered for drug likeness using the SwissADME and PROTOX platforms on the basis of Physicochemical properties and toxicity respectively. The docking results revealed that scopodulcic acid and dammarenolic acid had the best binding affinity on the s-glycoprotein and Mproprotein targets respectively. Silybinin also demonstrated a good binding affinity to both protein targets making it a potential candidate for further evaluation as repurposed candidate for SARS COV2 with likelihood of having a multitarget activity.
Decision making and best practices for taxonomy-free eDNA metabarcoding in biomonitoring using Hill numbers
Authors: Mächler Elvira , Walser Jean-Claude , Altermatt Florian 
Published: April 2020

AbstractEnvironmental DNA (eDNA) metabarcoding raises expectations for biomonitoring to cover organisms that have hitherto been neglected or excluded. To bypass current limitations in taxonomic assignments due to incomplete or erroneous reference data bases, taxonomic-free approaches are proposed for biomonitoring at the level of operational taxonomic unites (OTUs). However, this is challenging, because OTUs cannot be annotated and directly compared to classically derived data. The application of good stringency treatments to infer validity of OTUs and the clear understanding of the consequences to such treatments is thus especially relevant for biodiversity assessments. We investigated how common practices of stringency filtering affect diversity estimates based on Hill numbers derived from eDNA samples. We collected eDNA at 61 sites across a 740 km2river catchment, reflecting a spatially realistic scenario in biomonitoring. After bioinformatic processing of the data, we studied how different stringency treatments affect conclusions with respect to biodiversity at the catchment and site levels. The applied stringency treatments were based on the consistent appearance of OTUs across filter replicates, a relative abundance cut-off and rarefaction. We detected large differences in diversity estimates when accounting for presence/absence only, such that the detected diversity at the catchment scale differed by an order of magnitude between the treatments. These differences disappeared between the stringency treatments with increasing weighting of the OTUs’ abundances. Our study demonstrated the usefulness of Hill numbers for comparisons between data sets with large differences in diversity, and suggests best practice for data stringency filtering for biomonitoring.
Regulation of polyphosphate glucokinase gene expression through co-transcriptional processing inMycobacterium tuberculosisH37Rv
Authors: Bokolia Naveen Prakash , Khan Inshad Ali 
Published: April 2020

AbstractTranscription is the process that allows the simultaneous folding of RNA molecules, known as co-transcriptional folding. This folding determines the functional properties of RNA molecules and possibly having a critical role during the synthesis as well. This functioning includes the characterized properties of riboswitches and ribozymes as well, which is significant when the transcription rate is comparable to the cellular environment. This study aims to discover a novel non-coding region that is important in the genetic expression ofMycobacterium tuberculosis. In this work, we identified a novel non-coding element of polyphosphate glucokinase (ppgk) gene that undergoes cleavage activity during the transcriptional process inMycobacterium tuberculosis. We revealed that cleavage occurs within the nascent RNA, and the resultant cleaved 3’RNA fragment carries the Shine-Dalgarno (SD) sequence and expression platform. Site-specific mutations provide a strong correlation between the disruption of cleavage activity and expression ofppgkgene. We concluded that co-transcriptional processing at the noncoding region as the required mechanism forppgkexpression that remains constitutive within the bacterial environment. The underlying reason forppgkmRNA processing and expression is correlated because the non-coding counterpart adopts a hairpin domain that sequesters ribosomal binding site. Thus, the mRNA processing at the immediate upstream of Shine-Dalgarno sequence is required to prevent this sequestration and subsequent expression as well. This study defines the molecular mechanism that is dependent on the transient but highly active structural features of the nascent RNA.
Single-molecule imaging reveals translation of mRNAs localized to stress granules
Authors: Mateju Daniel , Eichenberger Bastian , Eglinger Jan , Roth Gregory , Chao Jeffrey A. 
Published: April 2020

SUMMARYCellular stress leads to reprogramming of mRNA translation and formation of stress granules (SGs), membraneless organelles consisting of mRNA and RNA-binding proteins. Although the function of SGs remains largely unknown, it is widely assumed they contain exclusively nontranslating mRNA. Here we re-examine this hypothesis using single-molecule imaging of mRNA translation in living cells. While our data confirms that non-translating mRNAs are preferentially recruited to SGs, we find unequivocal evidence for translation of mRNA localized to SGs. Our data indicate that SG-associated translation is not rare and that the entire translation cycle (initiation, elongation and termination) can occur for these transcripts. Furthermore, translating mRNAs can be observed transitioning between the cytosol and SGs without changing their translational status. Together, these results argue against a direct role for SGs in inhibition of mRNA translation.
Echocardiography-guided percutaneous left ventricular intracavitary injection as a cell delivery approach in infarcted mice
Authors: Nong Yibing , Guo Yiru , Tomlin Alex , Zhu Xiaoping , Wysoczynski Marcin , Li Qianhong , Bolli Roberto 
Published: April 2020

AbstractBackgroundIn the field of cell therapy for heart disease, a new paradigm of repeated dosing of cells has recently emerged. However, the lack of a repeatable cell delivery method in preclinical studies in rodents is a major obstacle to investigating this paradigm.Methods and ResultsWe have established and standardized a method of echocardiography-guided percutaneous left ventricular intracavitary injection (echo-guided LV injection) as a cell delivery approach in infarcted mice. Here, we describe the method in detail and address several important issues regarding it. First, by integrating anatomical and echocardiographic considerations, we have established strategies to determine a safe anatomical window for injection in infarcted mice. Second, we summarize our experience with this method (734 injections). The overall survival rate was 91.4%. Previous studies results suggest that 1×106cells delivered via this method yielded similar retention in the heart at 24 h as 1×105cells delivered via intracoronary or intramyocardial injection. Lastly, we examined the efficacy of this cell delivery approach. Compared with vehicle treatment, cardiac mesenchymal cells (CMCs) delivered via this method improved cardiac function assessed both echocardiographically and hemodynamically. Furthermore, repeated injections of CMCs via this method yielded greater cardiac function improvement than single dose administration.ConclusionEcho-guided LV injection is a feasible, reproducible, relatively less invasive and effective delivery method for cell therapy in heart disease. It is an important approach that could move the field of cell therapy forward, especially with regard to repeated cell administrations.
A recombinant gp145 Env glycoprotein from HIV-1 expressed in two different cell lines: effects on glycosylation and antigenicity
Authors: González-Feliciano José A. , Akamine Pearl , Capó-Vélez Coral M. , Delgado-Vélez Manuel , Dussupt Vincent , Krebs Shelly J. , Wojna Valerie , Polonis Victoria R. , Baerga-Ortiz Abel , Lasalde-Dominicci José A. 
Published: April 2020

AbstractThe envelope glycoprotein (Env) of the human immunodeficiency virus (HIV), has been the primary target for the development of a protective vaccine against infection. The extensiveN-linked glycosylation on Env is an important consideration as it may affect efficacy, stability, and expression yields. The expression host has been shown to influence the extent and type of glycosylation that decorates the protein target. Here, we report the glycosylation profile of the candidate subtype C immunogen CO6980v0c22 gp145 produced in two different host cells: CHO-K1 and Expi293F. The amino acid sequence for both glycoproteins was confirmed to be identical by peptide mass fingerprinting. However, the isoelectric point of the proteins differed; 4.5-5.5 and 6.0-7.0 for gp145 produced in CHO-K1 and Expi293F, respectively. These differences in pI were eliminated by enzymatic treatment with sialidase, indicating a large difference in the incorporation of sialic acid between hosts. This dramatic difference in the number of sialylated glycans between hosts was confirmed by analysis of PNGase F-released glycans using MALDI-ToF MS. These differences in glycosylation, however, did not greatly translate into differences in antibody recognition. Biosensor assays showed that gp145 produced in CHO-K1 had similar affinity toward the broadly neutralizing antibodies, 2G12 and PG16, as the gp145 produced in Expi293F. Additionally, both immunogens showed the same reactivity against plasma of HIV-infected patients. Taken together, these results support the notion that there are sizeable differences in the glycosylation of Env depending on the expression host. How these differences translate to vaccine efficacy remains unknown.
Adipose depot-specific upregulation of Ucp1 or mitochondrial oxidative complex proteins are early consequences of genetic insulin reduction in mice
Authors: Botezelli Jose Diego , Overby Peter , Lindo Lorenzo , Wang Su , Haïda Obélia , Lim Gareth E. , Templeman Nicole M. , Pauli Jose Rodrigo , Johnson James D. 
Published: April 2020

AbstractHyperinsulinemia plays a causal role in adipose tissue expansion. Mice with reduced insulin have increased energy expenditure, but the mechanisms remained unclear. Here we investigated the effects of genetically reducing insulin production on uncoupling and oxidative mitochondrial proteins in liver, skeletal muscle, white adipose tissue (WAT), and brown adipose tissue (BAT). Male Ins1+/+ or Ins1+/- littermates were fed either a low-fat diet (LFD) or a high-fat diet (HFD) for 4 weeks, starting at 8 weeks of age. Replicating our previous observations, HFD increased fasting hyperinsulinemia, and Ins1+/- mice had significantly lower circulating insulin compared with Ins1+/+ littermates. Fasting glucose and body weight were not different between genotypes. We did not observe significant differences in liver in skeletal muscle. In mesenteric WAT, Ins1+/- mice had reduced Ndufb8 and Sdhb. Ucp1 was increased in the context of the HFD, and HFD alone had a dramatic inhibitory effect on Pparg abundance. In inguinal WAT, Ins1+/- mice exhibited significant increases in oxidative complex proteins, independent of diet, without affecting Ucp1, Pparg, or Prdm16:Pparg association. In BAT, lowered insulin increased Sdhb protein levels that had been reduced by HFD. Ucp1 protein, Prdm16:Pparg association, and Sirt3 abundance were all increased in the absence of diet-induced hyperinsulinemia. Our data show that reducing insulin upregulates oxidative proteins in inguinal WAT without affecting Ucp1, while in mesenteric WAT and BAT, reducing insulin upregulates Ucp1 in the context of HFD. Preventing hyperinsulinemia has early depot-specific effects on adipose tissue metabolism and help explain the increased energy expenditure previously reported in Ins1+/- mice.
Helminth infection in a suburban ungulate population is driven more by age than landscape variables
Authors: Vannatta J. Trevor 
Published: April 2020

ABSTRACTWildlife are increasingly common in suburban environments as towns and cities spread into surrounding rural areas. Many wildlife species have adapted to these new environments; however, we know comparatively little about how parasites respond urbanization of host habitats. Parasites are important members within ecological communities and alterations to transmission dynamics are known to alter host population dynamics. For complex life cycle parasites (parasites that use multiple different host species), suburban environments are thought to decrease transmission. Here, infection metrics of two parasites of white-tailed deer, giant liver flukes and thin-necked bladderworms, are examined to determine how successful these parasites are in a suburban environment. Additionally, land cover variables within suburban deer hunting areas are used to test if infection prevalence is associated with certain landscape level metrics. Results indicate that both parasites are common across the suburban landscape and are commonly found coinfecting the same hosts. Prevalence of neither parasite was strongly related to landscape variables within deer hunting areas, but fluke intensity was negatively correlated with the proportion of human development on the landscape. Overall, the scale of transmission events and host-parasite biology may explain why landscape metrics are weak predictors of infection risk in this system.
Nuclear Import of the HIV-1 Core Precedes Reverse Transcription and Uncoating
Authors: Selyutina Anastasia , Persaud Mirjana , Lee Kyeongeun , KewalRamani Vineet , Diaz-Griffero Felipe 
Published: April 2020

SUMMARYHIV-1 particles contain a core formed by ~1500 capsid protein monomers housing viral RNA. HIV-1 core uncoating---disassembly---is required for infection. HIV-1 reverse transcription (RT) occurs before or during uncoating, but the cellular compartment where RT and uncoating occurs is unknown. Using imaging and biochemical assays to track HIV-1 capsids in nuclei during infection, we demonstrated that higher-order capsid complexes or complete cores containing viral genome are imported into nuclear compartments. Additionally, inhibition of RT that stabilizes the core during infection does not prevent capsid nuclear import; thus, RT may occur in nuclear compartments. We separated infected cells into cytosolic and nuclear fractions to measure RT during infection. Most observable RT intermediates were enriched in nuclear fractions, suggesting that most HIV-1 RT occurs in the nuclear compartment alongside uncoating. Thus, nuclear import precedes RT and uncoating, fundamentally changing our understanding of HIV-1 infection.
Demystifying “drop-outs” in single cell UMI data
Authors: Kim Tae , Zhou Xiang , Chen Mengjie 
Published: April 2020

AbstractAnalysis of scRNA-seq data has been challenging particularly because of excessive zeros observed in UMI counts. Prevalent opinions are that many of the detected zeros are “drop-outs” that occur during experiments and that those zeros should be accounted for through procedures such as normalization, variance stabilization, and imputation. Here, we extensively analyze publicly available UMI datasets and challenge the existing scRNA-seq workflows. Our results strongly suggest that resolving cell-type heterogeneity should be the foremost step of the scRNA-seq analysis pipeline because once cell-type heterogeneity is resolved, “drop-outs” disappear. Additionally, we show that the simplest parametric count model, Poisson, is sufficient to fully leverage the biological information contained in the UMI data, thus offering a more optimistic view of the data analysis. However, if the cell-type heterogeneity is not appropriately taken into account, pre-processing such as normalization or imputation becomes inappropriate and can introduce unwanted noise. Inspired by these analyses, we propose a zero inflation test that can select gene features contributing to cell-type heterogeneity. We integrate feature selection and clustering into iterative pre-processing in our novel, efficient, and straightforward framework for UMI analysis, HIPPO (Heterogeneity Inspired Pre-Processing tOol). HIPPO leads to downstream analysis with much better interpretability than alternatives in our comparative studies.
Progress Towards Plant Community Transcriptomics: Pilot RNA-Seq Data from 24 Species of Vascular Plants at Harvard Forest
Authors: Marx Hannah E. , Jorgensen Stacy A. , Wisely Eldridge , Li Zheng , Dlugosch Katrina M. , Barker Michael S. 
Published: April 2020

ABSTRACTPremise of the study:Large scale projects such as NEON are collecting ecological data on entire biomes to track and understand plant responses to climate change. NEON provides an opportunity for researchers to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA-seq data from phylogenetically diverse NEON plant communities, including species with diploid and polyploid genomes.Methods:We used Illumina NextSeq to generate >20 Gb of RNA-seq for each of 24 vascular plant species representing 12 genera and 9 families at the Harvard Forest NEON site. Each species was sampled twice, in July and August 2016. We used Transrate, BUSCO, and GO analyses to assess transcriptome quality and content.Results:We obtained nearly 650 Gb of RNA-seq data that assembled into more than 755,000 translated protein sequences across the 24 species. We observed only modest differences in assembly quality scores across a range of k-mer values. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated genes between diploid and polyploid transcriptomes.Discussion:Our resource provides new RNA-seq datasets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers clear opportunities for large scale studies at the intersection of ecology and genomics.
Impact of glycan positioning on HIV-1 Env glycan shield density, function, and antibody recognition
Authors: Wei Qing , Hargett Audra A. , Knoppova Barbora , Duverger Alexandra , Rawi Reda , Shen Chen-Hsiang , Farney S. Katie , Hall Stacy , Brown Rhubell , Keele Brandon F. , Heath Sonya L. , Saag Michael S. , Kutsch Olaf , Chuang Gwo-Yu , Kwong Peter D. , Moldoveanu Zina , Raska Milan , Renfrow Matthew B. , Novak Jan 
Published: April 2020

AbstractN-glycans, which represent >50% mass of the HIV-1 envelope (Env) trimer, play important roles for virus-cell entry and immune evasion. How each glycan unit interacts to shape the Env protein-sugar complex and affects Env function is not well understood. Here, high-resolution glycomics analysis of two Env variants from the same donor, with differing functional characteristics and N-glycosylation-site composition, revealed that changes to key N-glycosylation-site not only affected the Env structure at distant locations, but also had a ripple effect on Env-wide glycan processing, virus infectivity, and antibody recognition and virus neutralization. Specifically, the N262 glycan, although not located in the CD4-binding site, controlled Env binding to the CD4 receptor, affected the recognition of Env by several glycan-dependent broadly neutralizing antibodies, and altered heterogeneity of glycosylation at several sites, with N156, N160, and N448 displaying limited glycan processing. Molecular dynamic simulations visualized how specific oligosaccharide positions can move to compensate for loss of a glycan. This study demonstrates how changes in individual glycan units can alter molecular dynamics and processing of the Env-glycan shield and, consequently, Env function.
On the Relation of Gene Essentiality to Intron Structure: A Computational and Deep Learning Approach
Authors: Schonfeld Ethan , Vendrow Edward , Vendrow Joshua , Schonfeld Elan 
Published: April 2020

AbstractIdentification and study of human-essential genes has become of practical importance with the realization that disruption or loss of nearby essential genes can introduce latent-vulnerabilities to cancer cells. Essential genes have been studied by copy-number-variants and deletion events, which are associated with introns. The premise of our work is that introns of essential genes have characteristic properties that are distinct from the introns of nonessential genes. We provide support for the existence of characteristic properties by training a deep learning model on introns of essential and nonessential genes and demonstrated that introns alone can be used to classify essential and nonessential genes with high accuracy (AUC of 0.846). We further demonstrated that the accuracy of the same deep-learning model limited to first introns will perform at an increased level, thereby demonstrating the critical importance of introns and particularly first introns in gene essentiality. Using a computational approach, we identified several novel properties of introns of essential genes, finding that their structure protects against deletion and intron-loss events, and that these traits are especially centered on the first intron. We showed that GC density is increased in the first introns of essential genes, allowing for increased enhancer activity, protection against deletions, and improved splice-site recognition. Furthermore, we found that first introns of essential genes are of remarkably smaller size than their nonessential counterparts, and to protect against common 3’ end deletion events, essential genes carry an increased number of (smaller) introns. To demonstrate the importance of the seven features we identified, we trained a feature–based model using only information from these features and achieved high accuracy (AUC of 0.787).