bluuebunny/crossref_metadata_2025_split huggingface dataset:
LoopViz: A uLoop Assembly Clone Verification Tool for Nanopore Sequencing Reads
Authors: Lensink Mariele , Abramson Bradley W. , Hartwick Nolan , Poire Alfonzo , Bielinski Vincent A. , Michael Todd P. 
Published: February 2021

AbstractCloning has been an integral part of most laboratory research questions and continues to be an essential tool in defining the genetic elements determining life. Cloning can be difficult and time consuming as each plasmid is unique to a particular project and each sequence must be carefully selected, cloned and sequenced to determine correctness. Loop assembly (uLOOP) is a recursive, Golden Gate-like assembly method that allows rapid cloning of domesticated DNA fragments to robustly refactor novel pathways. With uLOOP methodologies, one can clone several sequences directionally to generate a library of transcriptional units (TUs) in plasmids within a single reaction but analysis of the plasmid population has been impeded by current sequencing and analysis methods. Here we develop LoopViz, a quality control tool that quantifies and visualizes results from assembly reactions using long-read Oxford Nanopore Technologies (ONT) sequencing. LoopViz identifies full length reads originating from a single plasmid in the population, and visualizes them in terms of a user input DNA fragments file, and provides QC statistics. This methodology enables validation and analysis of cloning and sequencing reactions in less than a day, determination of the entire plasmid’s sequence, and sequencing through repetitive meta-regions that cannot be meaningfully assembled. Finally, LoopViz represents a new paradigm in determining plasmid sequences that is rapid, cost-effective and performed in-lab. LoopViz is made publicly available athttps://gitlab.com/marielelensink325/loopseq
Nanotraps for the containment and clearance of SARS-CoV-2
Authors: Chen Min , Rosenberg Jillian , Cai Xiaolei , Lee Andy Chao Hsuan , Shi Jiuyun , Nguyen Mindy , Wignakumar Thirushan , Mirle Vikranth , Edobor Arianna Joy , Fung John , Donington Jessica Scott , Shanmugarajah Kumaran , Chang Eugene , Randall Glenn , Penaloza-MacMaster Pablo , Tian Bozhi , Madariaga Maria Lucia , Huang Jun 
Published: February 2021

SummarySARS-CoV-2 enters host cells through its viral spike protein binding to angiotensin-converting enzyme 2 (ACE2) receptors on the host cells. Here we show functionalized nanoparticles, termed “Nanotraps”, completely inhibited SARS-CoV-2 infection by blocking the interaction between the spike protein of SARS-CoV-2 and the ACE2 of host cells. The liposomal-based Nanotrap surfaces were functionalized with either recombinant ACE2 proteins or anti-SARS-CoV-2 neutralizing antibodies and phagocytosis-specific phosphatidylserines. The Nanotraps effectively captured SARS-CoV-2 and completely blocked SARS-CoV-2 infection to ACE2-expressing human cell lines and primary lung cells; the phosphatidylserine triggered subsequent phagocytosis of the virus-bound, biodegradable Nanotraps by macrophages, leading to the clearance of pseudotyped and authentic virus in vitro. Furthermore, the Nanotraps demonstrated excellent biosafety profile in vitro and in vivo. Finally, the Nanotraps inhibited pseudotyped SARS-CoV-2 infection in live human lungs in an ex vivo lung perfusion system. In summary, Nanotraps represent a new nanomedicine for the inhibition of SARS-CoV-2 infection.HighlightsNanotraps block interaction between SARS-CoV-2 spike protein and host ACE2 receptorsNanotraps trigger macrophages to engulf and clear virus without becoming infectedNanotraps showed excellent biosafety profiles in vitro and in vivoNanotraps blocked infection to living human lungs in ex vivo lung perfusion systemProgress and PotentialTo address the global challenge of creating treatments for SARS-CoV-2 infection, we devised a nanomedicine termed “Nanotraps” that can completely capture and eliminate the SARS-CoV-2 virus. The Nanotraps integrate protein engineering, immunology, and nanotechnology and are effective, biocompatible, safe, stable, feasible for mass production. The Nanotraps have the potential to be formulated into a nasal spray or inhaler for easy administration and direct delivery to the respiratory system, or as an oral or ocular liquid, or subcutaneous, intramuscular or intravenous injection to target different sites of SARS-CoV-2 exposure, thus offering flexibility in administration and treatment. More broadly, the highly versatile Nanotrap platform could be further developed into new vaccines and therapeutics against a broad range of diseases in infection, autoimmunity and cancer, by incorporating with different small molecule drugs, RNA, DNA, peptides, recombinant proteins, and antibodies.
Telomere maintenance pathway activity analysis enables tissue- and gene-level inferences
Authors: Nersisyan Lilit , Simonyan Arman , Binder Hans , Arakelyan Arsen 
Published: February 2021

ABSTRACTTelomere maintenance is one of the mechanisms ensuring indefinite divisions of cancer and stem cells. Good understanding of telomere maintenance mechanisms (TMM) is important for studying cancers and designing therapies. However, molecular factors triggering selective activation of either the telomerase dependent (TEL) or the alternative lengthening of telomeres (ALT) pathway are poorly understood. In addition, more accurate and easy-to-use methodologies are required for TMM phenotyping. In this study, we have performed literature based reconstruction of signaling pathways for the ALT and TEL TMMs. Gene expression data were used for computational assessment of TMM pathway activities and compared with experimental assays for TEL and ALT. Explicit consideration of pathway topology makes bioinformatics analysis more informative compared to computational methods based on simple summary measures of gene expression. Application to healthy human tissues showed high ALT and TEL pathway activities in testis, and identified genes and pathways that may trigger TMM activation. Our approach offers a novel option for systematic investigation of TMM activation patterns across cancers and healthy tissues for dissecting pathway-based molecular markers with diagnostic impact.
Metagenomic screening for lipolytic genes reveals an ecology-clustered distribution pattern
Authors: Lu Mingji , Schneider Dominik , Daniel Rolf 
Published: February 2021

AbstractLipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phylaActinobacteria, Proteobacteria, Firmicutes, BacteroidetesandChloroflexi.Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique genes encoding lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integral classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.
EMC is required for biogenesis and membrane insertion of Xport-A, an essential chaperone of rhodopsin-1 and the TRP channel
Authors: Gaspar Catarina J. , Vieira Lígia C. , Christianson John C. , Jakubec David , Strisovsky Kvido , Adrain Colin , Domingos Pedro M. 
Published: February 2021

SUMMARYInsertion of hydrophobic transmembrane domains (TMDs) into the endoplasmic reticulum (ER) lipid bilayer is an essential step during eukaryotic membrane protein biogenesis. The ER membrane complex (EMC) functions as an insertase for TMDs of low hydrophobicity and is required for the biogenesis of a subset of tail-anchored (TA) and polytopic membrane proteins, including rhodopsin-1 (Rh1) and the TRP channel. To better understand the physiological implications of membrane protein biogenesis dependent on the EMC, we performed a bioinformatic analysis to predict TA proteins present in theDrosophilaproteome. From 254 predicted TA proteins, subsequent genetic screening inDrosophilalarval eye discs led to the identification of 2 proteins that require EMC for their biogenesis: farinelli (fan) and Xport-A. Fan is required for sperm individualization and male fertility inDrosophilaand we now show that EMC is also required for these important biological processes. Interestingly, Xport-A is essential for the biogenesis of both Rh1 and TRP, raising the possibility that disruption of Rh1 and TRP biogenesis in EMC loss of function mutations is secondary to the Xport-A defect. We show that EMC is required for Xport-A TMD membrane insertion and increasing the hydrophobicity of Xport-A TMD rendered its membrane insertion to become EMC-independent. Moreover, these EMC-independent Xport-A mutants rescued Rh1 and TRP biogenesis in EMC mutants. Our data establish that EMC can impact the biogenesis of polytopic membrane proteins indirectly, by controlling the biogenesis and membrane insertion of an essential protein co-factor.
Non-Canonical Projections from Ventral CA1 and Subicular Complex to CA3 Augments the Feedforward Hippocampal Trisynaptic Pathway
Authors: Lin Xiaoxiao , Amalraj Michelle , Blanton Crisylle , Avila Brenda , Holmes Todd C. , Nitz Douglas A. , Xu Xiangmin 
Published: February 2021

AbstractThe hippocampal formation is well documented as having a feedforward, unidirectional circuit organization termed the trisynaptic pathway. This circuit organization exists along the septotemporal axis of the hippocampal formation, but the circuit connectivity across septal to temporal regions is less well described. The emergence of viral-genetic mapping techniques enhances our ability to determine the detailed complexity of hippocampal formation circuitry. In earlier work, we mapped a subiculum back-projection to CA1 prompted by the discovery of theta wave back-propagation from the subiculum to CA1 and CA3. We reason that this circuitry may represent multiple extended non-canonical pathways involving the subicular complex and hippocampal subregions CA1 and CA3. In the present study, multiple retrograde viral tracing approaches produced robust mapping results, which supports this prediction. We find significant non-canonical synaptic inputs to dorsal hippocampal CA3 from ventral CA1, perirhinal cortex, and the subicular complex. Thus, CA1 inputs to CA3 run opposite the trisynaptic pathway and in a temporal to septal direction. Our retrograde viral tracing results are confirmed by anterograde-directed viral mapping of projections from input mapped regions to hippocampal dorsal CA3. Together, our data provide a circuit foundation to explore novel functional roles contributed by these non-canonical hippocampal circuit connections to hippocampal dynamics and behavior.
Variation inLeishmaniachemokine suppression driven by diversification of the GP63 virulence factor
Authors: Antonia Alejandro L. , Martin Amelia T. , Wang Liuyang , Ko Dennis C. 
Published: February 2021

AbstractLeishmaniasis is a neglected tropical disease with diverse infection outcomes ranging from self-healing lesions, to progressive non-healing lesion, to metastatic spread and destruction of mucous membranes. Although resolution of cutaneous leishmaniasis is a classic example of type-1 immunity leading to well controlled self-healing lesions, an excess of type-1 related inflammation can contribute to immunopathology and metastatic spread of disease.Leishmaniagenetic diversity can contribute to variation in polarization and robustness of the immune response through differences in both pathogen sensing by the host and immune evasion by the parasite. In this study, we observed a difference in parasite chemokine suppression between theLeishmania (L.)subgenus and theViannia (V.)subgenus, which is associated with severe immune mediated pathology such as mucocutaneous leishmaniasis. WhileLeishmania (L.)subgenus parasites utilize the virulence factor and metalloprotease glycoprotein-63(gp63)to suppress the type-1 associated host chemokine CXCL10,L. (V.) panamensisdid not suppress CXCL10. To understand the molecular basis for the inter-species variation in chemokine suppression, we usedin silicomodeling of the primary amino acid sequence and protein crystal structures to identify a putative CXCL10-binding site on GP63. We found the putative CXCL10 binding site to be located in a region ofgp63under significant positive selection and that it varies from theL. majorwild-type sequence in allgp63alleles identified in theL. (V.) panamensisreference genome. We determined that the predicted binding site and adjacent positively selected amino acids are required for CXCL10 suppression by mutating wild-typeL. (L.) major gp63to theL. (V.) panamensisallele and demonstrating impaired cleavage of CXCL10 but not a non-specific protease substrate. Notably,Vianniaclinical isolates confirmed thatL. (V.) panemensisprimarily encodes non-CXCL10-cleavinggp63alleles. In contrast,L. (V.) braziliensishas an intermediate level of activity, consistent with this species having more equal proportions of both alleles at the CXCL10 binding site, possibly due to balancing selection. Our results demonstrate how parasite genetic diversity can contribute to variation in the host immune response toLeishmaniaspp. infection that may play critical roles in the outcome of infection.
Electrospun fibers for vaginal administration of tenofovir disoproxil fumarate and emtricitabine in the context of topical pre-exposure prophylaxis
Authors: Nunes Rute , Bogas Sarah , Faria Maria João , Gonçalves Hugo , Lúcio Marlene , Viseu Teresa , Sarmento Bruno , das Neves José 
Published: February 2021

AbstractWomen are particularly vulnerable to sexual HIV-1 transmission. Oral pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate and emtricitabine (TDF/FTC) is highly effective in avoiding new infections in men, but protection has only been shown moderate in women. Such differences have been associated, at least partially, to poor drug penetration of the lower female genital tract and the need for strict adherence to continuous daily oral intake of TDF/FTC. On-demand topical microbicide products could help circumventing these limitations. We developed electrospun fibers based on polycaprolactone (PCL fibers) or liposomes associated to poly(vinyl alcohol) (liposomes-in-PVA fibers) for the vaginal co-delivery of TDF and FTC, and assessed their pharmacokinetics in mice. PCL fibers and liposomes-in-PVA fibers were tested for morphological and physicochemical properties using scanning electron microscopy, differential scanning calorimetry and X-ray diffractometry. Fibers featured organoleptic and mechanical properties compatible with their suitable handling and vaginal administration. Fluorescent quenching of mucinin vitro– used as a proxy for mucoadhesion – was intense for PCL fibers, but mild for liposomes-in-PVA fibers. Both fibers were shown safein vitroand able to rapidly release drug content (15-30 min) under sink conditions. Liposomes-in-PVA fibers allowed increasing genital drug concentrations after a single intravaginal administration when compared to continuous daily treatment with 25-times higher oral doses. For instance, the levels of tenofovir and FTC in vaginal lavage were around 4- and 29-fold higher, respectively. PCL fibers were also superior to oral treatment, although to a minor extent (approximately 2-fold higher drug concentrations in lavage). Vaginal tissue drug levels were generally low for all treatments, while systemic drug exposure was negligible in the case of fibers. These data suggest that proposed fibers may provide an interesting alternative or an ancillary option to oral PrEP in women.
Crystal structure of fungal tannase from Aspergillus niger
Authors: Dong Liangbo , McKinstry William J. , Pan Li , Newman Janet , Ren Bin 
Published: February 2021

Tannases are serine esterases that were first discovered in fungi more than one and half centuries ago. They catalyze the hydrolysis of the gallolyl ester bonds in gallotannins to release gallic acid, which is an important intermediate in the chemical and pharmaceutical industries. Since their discovery, fungal tannases have found wide industrial applications, although there is scarce knowledge about these enzymes at the molecular level, including their catalytic and substrate-binding sites. While this lack of knowledge hinders engineering efforts to modify the enzymes, many tannases have been isolated from various fungal strains in a search for the desired enzymatic properties. Here, the first crystal structure of a fungal tannase, that from Aspergillus niger, is reported. The enzyme possesses a typical α/β-hydrolase-fold domain with a large inserted cap domain, which together form a bowl-shaped hemispherical shape with a surface concavity surrounded by N-linked glycans. Gallic acid is bound at the junction of the two domains within the concavity by forming two hydrogen-bonding networks with neighbouring residues. One is formed around the carboxyl group of the gallic acid and involves residues from the hydrolase-fold domain, including those from the catalytic triad, which consists of Ser206, His485 and Asp439. The other is formed around the three hydroxyl groups of the compound, with the involvement of residues mainly from the cap domain, including Gln238, Gln239, His242 and Ser441. Gallic acid is bound in a sandwich-like mode by forming a hydrophobic contact with Ile442. All of these residues are found to be highly conserved among fungal and yeast tannases.
The effect of conservative financial reporting and tax aggressiveness on the market valuation of unrecognized tax benefits
Authors: Jiménez-Angueira Carlos E. , Nwaeze Emeka , Park Sung-Jin 
Published: February 2021

PurposePrior studies document a positive relation between stock prices and tax-related contingent liability, unrecognized tax benefits (UTBs) and interpret the finding as evidence that investors reward tax aggressiveness. The purpose of this paper is to explore the nature of this puzzle finding by considering a link between UTBs and financial reporting strategy and propose that financial reporting conservatism may explain the positive association between UTBs and stock prices.Design/methodology/approachTo estimate the incremental valuation weights on UTBs, the authors employ the Ohlson (1995) valuation model and regress stock prices on UTBs and its interactions with the proxies for financial reporting conservatism and tax aggressiveness. Further, the authors adopt a UTB estimation model to decompose its balance into the predicted and unpredicted components.FindingsThe authors find that the reporting conservatism has a positive effect on the market valuation of UTBs. The authors also find some evidence that tax aggressiveness increases the valuation weight of UTBs. When UTBs are decomposed into predicted and unpredicted components, the authors find that the effect of financial reporting conservatism is more pronounced for the market valuation of predicted UTBs. Collectively, the evidence suggests that conservative financial reporting is a major driver of the positive valuation of UTBs and that tax aggressiveness plays a less significant role in investors' valuation decisions.Originality/valueWhile prior studies focus on how UTBs are associated with stock prices, this paper is the first attempt to explain why UTBs are positively valued by investors.
Examining antecedents of retail employees' propensity to leave
Authors: Park Jungkun , Ahn Jiseon , Hyun Hyowon , Rutherford Brian N. 
Published: February 2021

PurposeIn this study, the authors examine the impacts of two facets of retail employees' cognitive support and affective commitment on emotional labor-related outcomes.Design/methodology/approachTo test the study hypotheses, 521 retail service employees participated in the survey. By using the structural equation modeling, the results show that employees' perceived organizational support directly and positively employees' affective organizational commitment and emotional exhaustion.FindingsBy using the structural equation modeling, the results show that employees' perceived organizational support directly and positively influence employees' affective organizational commitment and emotional exhaustion. The extent of employees' affective organizational commitment directly and negatively influences emotional labor and exhaustion. Furthermore, employees' emotional exhaustion exerts an influence on retail employees' propensity to leave.Research limitations/implicationsDrawing on social exchange and conservation of resources theories, this study contributes to emotional labor research and practices by examining factors that potentially influences employees' propensity to leave. For future studies, researchers can expand the proposed framework of the current study to other retailing settings.Practical implicationsFindings of the study suggest that retail organizations need to manage employees' support and commitment concerning to understand emotional labor.Originality/valueThe current study found that employees' affective commitment influences key emotional labor constructs including emotional labor and emotional exhaustion. Employees who have a high level of identification, involvement and emotional attachment toward the organization, they are less likely to feel of overload and inefficiency. Given the importance of emotional labor in the retailing setting, the proposed model and findings of this study contribute the existing knowledge of retail employees' behavior.