bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repeated introduction of micropollutants enhances microbial succession despite stable degradation patterns
Authors: Izabel-Shen Dandan , Li Shuang , Luo Tingwei , Wang Jianjun , Li Yan , Sun Qian , Yu Chang-Ping , Hu Anyi 
Published: August 2021

AbstractThe increasing-volume release of micropollutants into natural surface waters has raised great concern due to their environmental accumulation. Persisting micropollutants can impact multiple generations of organisms, but their microbially-mediated degradation and their influence on community assembly remain understudied. Here, freshwater microbes were treated with several common micropollutants, alone or in combination, and then transferred every 5 days to fresh medium containing the same micropollutants to mimic the repeated exposure of microbes. Metabarcoding of 16S rRNA gene makers was chosen to study the succession of bacterial assemblages following micropollutant exposure. The removal rates of micropollutants were then measured to assess degradation capacity of the associated communities. The degradation of micropollutants did not accelerate over time but altered the microbial community composition. Community assembly was dominated by stochastic processes during early exposure, via random community changes and emergence of seedbanks, and deterministic processes later in the exposure, via advanced community succession. Early exposure stages were characterized by the presence of sensitive microorganisms such as Actinobacteria and Planctomycetes, which were then replaced by more tolerant bacteria such as Bacteroidetes and Gammaproteobacteria. Our findings have important implication for ecological feedback between microbe-micropollutants under anthropogenic climate change scenarios.
Bi-reporter vaccinia virus for tracking viral infections in vitro and in vivo
Authors: Chiem Kevin , Lorenzo Maria , Rangel-Moreno Javier , De La Luz Garcia-Hernandez Maria , Park Jun-Gyu , Nogales Aitor , Blasco Rafael , Martínez-Sobrido Luis 
Published: August 2021

ABSTRACTRecombinant viruses expressing reporter genes allow visualization and quantification of viral infections and can be used as valid surrogates to identify the presence of the virus in infected cells and animal models. However, one of the limitations of recombinant viruses expressing reporter genes is the use of either fluorescent or luciferase proteins that are used alternatively for different purposes. Vaccinia virus (VV) is widely used as a viral vector, including recombinant (r)VV singly expressing either fluorescent or luciferase reporter genes that are useful for specific purposes. In this report, we engineered two novel rVV stably expressing both fluorescent (Scarlet or GFP) and luciferase (Nluc) reporter genes from different loci in the viral genome. In vitro, these bi-reporter expressing rVV have similar growth kinetics and plaque phenotype than those of the parental WR VV isolate. In vivo, rVV Nluc/Scarlet and rVV Nluc/GFP effectively infected mice and were easily detected using in vivo imaging systems (IVIS) and ex vivo in the lungs from infected mice. We used these bi-reporter expressing rVV to assess viral pathogenesis, infiltration of immune cells in the lungs, and to directly identify the different subsets of cells infected by VV in the absence of antibody staining. Collectively, these rVV expressing two reporter genes open the feasibility to study the biology of viral infections in vitro and in vivo, including host-pathogen interactions and dynamics or tropism of viral infections. Moreover, they represent an excellent approach for the discovery of new prophylactics and/or therapeutics for the treatment of poxvirus infections.IMPORTANCEDespite the eradication of variola virus (VARV), the causative agent of smallpox, poxviruses still represent an important threat to human health due to their possible use as bioterrorism agents and the emergence of zoonotic poxvirus diseases. Recombinant vaccinia viruses (rVV) expressing easily traceable fluorescent or luciferase reporter genes have significantly contributed to the progress of poxvirus research. However, rVV expressing one marker gene have several constraints for in vitro and in vivo studies, since both fluorescent and luciferase proteins impose certain limitations for specific applications. To overcome these limitations, we generated optimized rVV stably expressing both fluorescent (Scarlet or GFP) and luciferase (Nluc) reporter genes to easily track viral infection in vitro and in vivo. This new generation of double reporter-expressing rVV represent an excellent option to study viral infection dynamics in cultured cells and validated animal models of infection, and for the discovery of new poxvirus antiviral treatments.
Longevity of SARS-CoV-2 Antibody in Health Care Workers: 6-Months Follow Up
Authors: Brant-Zawadzki Michael , Fridman Deborah , Robinson Philip A. , German Randy , Shapiro Arell , Breit Marcus , Wilton Stacy , Burke Elmira , Bock Jason R. , Hara Junko 
Published: August 2021

AbstractThe prevalence and longevity of acquired immunity to coronavirus disease 2019 (COVID-19) in health care workers (HCWs) is of great interest, especially with the roll-out of vaccines for SARS-CoV-2. Determining such immunity may enhance knowledge about susceptibility of HCWs to COVID-19, frequency of vaccine administration, and degree of workplace risk, and may also support enactment of better workplace policies and procedures.The present study reports on 6-months follow-up serosurveillance to determine the longevity of SARS-CoV-2 antibodies in HCWs.Sub-sample (n=35) of the original serosurveillance in HCWs (n = 3,458) with baseline, 8-week, and 6-month blood sampling were analyzed. Information on job duties, location, COVID-19 symptoms, polymerase chain reaction test history, travel since January 2020, and household contacts with COVID-19 was collected.Of 35 subjects, 13 were seropositive at baseline and maintained positivity at 8-week follow-up, with 3 losing positivity at 6-month follow-up. Among 22 subjects who were seronegative at baseline and seropositive at 8-week follow-up, all but one maintained positivity at 6-month follow-up. There was no significant effect of all factors (e.g., age, gender, job duties) examined at the .05 level on seropositivity at 6-month follow-up. The observed antibody longevity was 7.0+/-0.6 months for seropositive subjects (n=13), and 4.5+/-0.8 months for those seronegative subjects (n=22), at baseline. The longest duration of seropositivity observed in this cohort was 7.9 months (236 days).With reported COVID-19-related symptoms up to 4.7 months prior to baseline blood sampling, possibly longer antibody presence is suggested. Similarly, seropositivity at 6-month follow-up further suggests greater antibody longevity than observed in this study.
Multiscale modeling of tumor adaption and invasion following anti-angiogenic therapy
Authors: Cess Colin G. , Finley Stacey D. 
Published: August 2021

ABSTRACTIn order to promote continued growth, a tumor must recruit new blood vessels, a process known as tumor angiogenesis. Many therapies have been tested that aim to inhibit tumor angiogenesis, thus starving the tumor of nutrients and preventing tumor growth. However, many of these therapies have been unsuccessful and can paradoxically further tumor development by leading to increased local tumor invasion and metastasis. In this study, we use agent-based modeling to examine how hypoxic and acidic conditions following anti-angiogenic therapy can influence tumor development. Under these conditions, we find that cancer cells experience a phenotypic shift to a state of higher survival and invasive capability, spreading further away from the tumor into surrounding tissue. Although anti-angiogenic therapy alone promotes tumor cell adaptation and invasiveness, we find that augmenting chemotherapy with anti-angiogenic therapy improves chemotherapeutic response and delays the time it takes for the tumor to regrow. Overall, we use computational modeling to explain the behavior of tumor cells in response to anti-angiogenic treatment in the dynamic tumor microenvironment.
Epitopedia: identifying molecular mimicry between pathogens and known immune epitopes
Authors: Balbin Christian A , Nunez-Castilla Janelle , Stebliankin Vitalii , Baral Prabin , Sobhan Masrur , Cickovski Trevor , Mondal Ananda Mohan , Narasimhan Giri , Chapagain Prem , Mathee Kalai , Siltberg-Liberles Jessica 
Published: August 2021

AbstractUpon infection, foreign antigenic proteins stimulate the host’s immune system to produce antibodies targeting the pathogen. These antibodies bind to regions on the antibody called epitopes. Structural similarity (molecular mimicry) of epitopes between an infecting pathogen and host proteins or other pathogenic proteins the host has previously encountered can impact the host immune response to the pathogen and may lead to cross-reactive antibodies. The ability to identify potential regions of molecular mimicry in a pathogen can illuminate immune effects which are especially important to pathogen treatment and vaccine design. Here we present Epitopedia, a software pipeline that facilitates the identification of regions that may exhibit potential three-dimensional molecular mimicry between an antigenic pathogen protein and known immune epitopes as catalogued by the immune epitope database (IEDB). Epitopedia is open-source software released under the MIT license and is freely available on GitHub, including a Docker container with all other software dependencies preinstalled. We performed an analysis describing how various secondary structure states, identity between pentapeptide pairs, and identity between the parent sequences of pentapeptide pairs affects RMSD. We found that pentapeptides pairs in a helical conformation had considerably lower RMSD values than those in Extended or Coil conformations. We also found that RMSD is significantly increased when pentapeptide pairs are from non-homologous sequences.
Extrinsic KRAS signaling shapes the pancreatic microenvironment through fibroblast reprogramming
Authors: Velez-Delgado Ashley , Donahue Katelyn L. , Brown Kristee L. , Du Wenting , Irizarry-Negron Valerie , Menjivar Rosa E. , Lasse Opsahl Emily L. , Steele Nina G. , The Stephanie , Lazarus Jenny , Sirihorachai Veerin R. , Yan Wei , Kemp Samantha B. , Kerk Samuel A. , Bollampally Murali , Lima Fatima , Lyssiotis Costas A. , Rao Arvind , Crawford Howard C. , Bednar Filip , Frankel Timothy L. , Zhang Yaqing , Pasca di Magliano Marina 
Published: August 2021

ABSTRACTOncogenic KRAS is the hallmark mutation of human pancreatic cancer and a driver of tumorigenesis in genetically engineered mouse models of the disease. While the tumor cell-intrinsic effects of oncogenic Kras expression have been widely studied, its role in regulating the extensive pancreatic tumor microenvironment is less understood. Using a genetically engineered mouse model of inducible and reversible oncogenic Kras expression and a combination of approaches that include mass cytometry and single cell RNA sequencing, we have discovered that non-cell autonomous (i.e., extrinsic) oncogenic KRAS signaling reprograms pancreatic fibroblasts, activating an inflammatory gene expression program. As a result, fibroblasts become a hub of extracellular signaling, mediating the polarization and function of pro-tumorigenic myeloid cells while also preventing tissue repair. Our study provides fundamental new knowledge on the mechanisms underlying the formation of the fibroinflammatory stroma in pancreatic cancer and highlights stromal pathways with the potential to be exploited therapeutically.
Subsurface Hydrocarbon Degradation Strategies in Low- and High-Sulfate Coal Seam Communities Identified with Activity-Based Metagenomics
Authors: Schweitzer Hannah , Smith Heidi , Barnhart Elliott P. , McKay Luke , Gerlach Robin , Cunningham Alfred B. , Malmstrom Rex R. , Goudeau Danielle , Fields Matthew W. 
Published: August 2021

AbstractEnvironmentally relevant metagenomes and BONCAT-FACS derived translationally active metagenomes from Powder River Basin coal seams were investigated to elucidate potential genes and functional groups involved in hydrocarbon degradation to methane in coal seams with high- and low-sulfate levels. An advanced subsurface environmental sampler allowed the establishment of coal-associated microbial communities underin situconditions for metagenomic analyses from environmental and translationally active populations. Metagenomic sequencing demonstrated that biosurfactants, aerobic dioxygenases, and anaerobic phenol degradation pathways were present in active populations across the sampled coal seams. In particular, results suggested the importance of anaerobic degradation pathways under high-sulfate conditions with an emphasis on fumarate addition. Under low-sulfate conditions, a mixture of both aerobic and anaerobic pathways were observed but with a predominance of aerobic dioxygenases. The putative low-molecular weight biosurfactant, lichysein, appeared to play a more important role compared to rhamnolipids. The methods used in this study—subsurface environmental samplers in combination with metagenomic sequencing of both total and translationally active metagenomes—offer a deeper and environmentally relevant perspective on community genetic potential from coal seams poised at different redox conditions broadening the understanding of degradation strategies for subsurface carbon.One Sentence SummaryIdentifying hydrocarbon degradation strategies across different redox conditions via metagenomic analysis of environmental and translationally active (BONCAT-FACS) samples from subsurface coal beds.
An efficient and robust HPLC method to determine the sialylation levels of human epithelial cells
Authors: Kim Hyo Jeong , Schweiker Stephanie , Powell Katie , Levonis Stephan M 
Published: August 2021

AbstractSialyltransferase, an enzyme responsible for attaching sialic acid to the cell surface, is reported to play a key role in cancer, making sialyltransferase a potent therapeutic target in drug development for cancer. Hence, this paper aimed to develop a simple method to detect and quantify sialic acids in cancer cells. An efficient method was developed using a reverse-phase ion-pairing HPLC-UV using triisopropanolamine as the ion-pairing agent with a C18 column. Neu5Ac was successfully eluted with the retention time 6.344 min with a flow rate of 0.4 mL/min. The proposed method was validated appropriately according to the AOAC guidelines (2013). This work demonstrates that the proposed method is not only relatively simple but also cost and time effective compared to pre-existing methods to successfully determine both free and protein-bound Neu5Ac in a complex cancer cell matrix. Furthermore, by applying the proposed method, a statistically significant decrease was observed for both HeLa and HuCCT1 cell lines with the application of deoxycholic acid – a known sialyltransferase inhibitor. Hence, the proposed method may be applicable to evaluate the effectiveness of sialyltransferase inhibitors.
A tetrameric assembly of saposin A: increasing structural diversity in lipid transfer proteins
Authors: Shamin Maria , Spratley Samantha J. , Graham Stephen C. , Deane Janet E. 
Published: August 2021

AbstractSaposins are lipid transfer proteins required for the degradation of sphingolipids in the lysosome. These small proteins bind lipids by transitioning from a closed, monomeric state to an open conformation exposing a hydrophobic surface that binds and shields hydrophobic lipid tails from the aqueous environment. Saposins form a range of multimeric assemblies to encompass these bound lipids and present them to hydrolases in the lysosome. This lipid-binding property of human saposin A has been exploited to form lipoprotein nanodiscs suitable for structural studies of membrane proteins. Here we present the crystal structure of a unique tetrameric assembly of murine saposin A produced serendipitously, following modifications of published protocols for making lipoprotein nanodiscs. The structure of this new saposin oligomer highlights the diversity of tertiary arrangement that can be adopted by these important lipid transfer proteins.
Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes
Authors: Borges Adair L. , Lou Yue Clare , Sachdeva Rohan , Al-Shayeb Basem , Jaffe Alexander L. , Lei Shufei , Santini Joanne M. , Banfield Jillian F. 
Published: August 2021

AbstractThe genetic code is a highly conserved feature of life. However, some “alternative” genetic codes use reassigned stop codons to code for amino acids. Here, we survey stop codon recoding across bacteriophages (phages) in human and animal gut microbiomes. We find that stop codon recoding has evolved in diverse clades of phages predicted to infect hosts that use the standard code. We provide evidence for an evolutionary path towards recoding involving reduction in the frequency of TGA and TAG stop codons due to low GC content, followed by acquisition of suppressor tRNAs and the emergence of recoded stop codons in structural and lysis genes. In analyses of two distinct lineages of recoded virulent phages, we find that lysis-related genes are uniquely biased towards use of recoded stop codons. This convergence supports the inference that stop codon recoding is a strategy to regulate the expression of late stage genes and control lysis timing. Interestingly, we identified prophages with recoded stop codons integrated into genomes of bacteria that use standard code, and hypothesize that recoding may control the lytic-lysogenic switch. Alternative coding has evolved many times, often in closely related lineages, indicating that genetic code is plastic in bacteriophages and adaptive recoding can occur over very short evolutionary timescales.
Crossover patterning through kinase-regulated condensation and coarsening of recombination nodules
Authors: Zhang Liangyu , Stauffer Weston , Zwicker David , Dernburg Abby F. 
Published: August 2021

AbstractMeiotic recombination is highly regulated to ensure precise segregation of homologous chromosomes. Evidence from diverse organisms indicates that the synaptonemal complex (SC), which assembles between paired chromosomes, plays essential roles in crossover formation and patterning. Several additional “pro-crossover” proteins are also required for recombination intermediates to become crossovers. These typically form multiple foci or recombination nodules along SCs, and later accumulate at fewer, widely spaced sites. Here we report that in C. elegans CDK-2 is required to stabilize all crossover intermediates and stabilizes interactions among pro-crossover factors by phosphorylating MSH-5. Additionally, we show that the conserved RING domain proteins ZHP-3/4 diffuse along the SC and remain dynamic following their accumulation at recombination sites. Based on these and previous findings we propose a model in which recombination nodules arise through spatially restricted biomolecular condensation and then undergo a regulated coarsening process, resulting in crossover interference.
The standalone and resource-bundling effects of government and nongovernment institutional support on early internationalizing firms’ performance
Authors: Faroque Anisur R. , Sultana Hafiza , Ahmed Jashim Uddin , Ahmed Farhad Uddin , Rahman Mahabubur 
Published: August 2021

PurposeThis study aims to analyze the individual and joint effects of institutional support by government and nongovernment institutions on early internationalizing firms’ (EIFs) performance. It also investigated the moderating impact of firm age and size on the institutional support-firms’ export performance relationships.Design/methodology/approachData were collected from 705 EIFs in the apparel industry of Bangladesh and analyzed with hierarchical regression.FindingsThe positive influence of institutional support on exporting firms’ financial performance is stronger for the joint effect of government and nongovernment assistance than the individual impact. Firms’ size positively moderates the impact of individual government and nongovernment assistance, while age positively moderates their resource-bundling effect.Research limitations/implicationsThe findings suggest the necessity of integrating resources from diverse but complementary sources of institutional support for superior export performance. The findings also show the presence of the liability of smallness and liability of newness in the standalone and joint influence of institutional support, respectively.Practical implicationsFirms need to bundle resources obtained from the government (unrequited) and nongovernment (reciprocal) institutional support to overcome the liability of smallness they might encounter while availing of support from only one source.Originality/valueDistinguishing between government and nongovernment institutional support, this paper sheds light on exporting firms’ resource-bundling mechanism for these two sources of support in the backdrop of an emerging economy. It also offers fresh insights into the critical role of the liabilities of newness and smallness in early internationalization, especially with regard to the home-country institutional environment.
Characterisation of the drivers of environmental management system implementation
Authors: Oladinrin Olugbenga Timo , Ojo Lekan Damilola 
Published: August 2021

PurposeThe detrimental impacts of the construction industry activities, namely, toxicity of cement and concrete to the health of construction workers and the general public, have been reported in previous studies. Several environmental management measures were put in place by international organisations to reduce these impacts on humans and the entire ecosystem. Sadly, such environmental management measures are not widely embraced in the construction industry of developing countries. This contributes to the poor quality of life of construction stakeholders, amongst other outcomes. Therefore, this study investigated the drivers to facilitate an environmental management system (EMS) in the Nigerian construction industry (NCI).Design/methodology/approachquestionnaires retrieved from construction professionals in the micro, small, medium and large enterprises were used to conduct both descriptive and inferential statistics, namely, mean score, standard deviation, Kruskal–Wallis H test, post hoc test and factor analysis.FindingsThe analyses show that the drivers of EMS implementation in the NCI could be grouped into intellectual enhancement strategies, documentation and cultural strategies, and motivation and tracking strategies. The study concluded that training and education of relevant stakeholders, tracking compliance levels of organisations and recognising firms acting in compliance with stipulated “environmental” policy are essential. It was recommended that the collaboration of all construction stakeholders be upheld to aid EMS implementation in the NCI.Originality/valueThis paper investigated the drivers of EMS with the opinions of construction professionals in the mainstream of the NCI through survey using to ensure wide coverage of respondents. Investigating the view of construction professionals in the micro, small, medium and large enterprises helped determine possible significant differences. Thus, practical implications of the study were also provided in a systematic manner.