bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants
Authors: Nikolova Christina , Ijaz Umer Zeeshan , Magill Clayton , Kleindienst Sara , Joye Samantha B. , Gutierrez Tony 
Published: December 2020

AbstractBackgroundAlthough synthetic dispersants are effective in dispersing crude oil, they can alter the natural microbial response to oil and potentially hinder its biodegradation. Biosurfactants, however, are naturally derived products that play a similar role to synthetic dispersants in oil spill response but are easily biodegradable and less toxic. This study investigated the microbial community dynamics, ecological drivers, functional diversity, and oil biodegradation potential of a northeast Atlantic marine microbial community to crude oil when exposed to rhamnolipid or synthetic dispersant Finasol OSR52.ResultsWe found the microbial community composition and diversity were markedly different in the rhamnolipid-amended treatment compared to that with Finasol, with key aromatic hydrocarbon-degrading bacteria likeCycloclasticusbeing suppressed in the Finasol treatment but not in oil-only and rhamnolipid-amended treatments. PsychrophilicColwelliaandOleispiradominated the community in both the rhamnolipid and Finasol OSR52 treatments initially but later community structure across treatments diverged significantly:RhodobacteraceaeandVibriodominated the Finasol-amended treatment andColwellia, Oleispira, and laterCycloclasticusandAlcanivorax, dominated the rhamnolipid-amended treatment.Vibrioabundance increased substantially in treatments receiving Finasol, suggesting a potentially important role for these organisms in degrading dispersant components. In fact, Finasol was linked with a negative impact on alpha diversity. Deterministic environmental filtering played a dominant role in regulating the community assembly in all treatments but was strongest in the dispersant-amended treatments. Rhamnolipid-amended and oil-only treatments had the highest functional diversity, however, the overall oil biodegradation was greater in the Finasol treatment, but aromatic biodegradation was highest in the rhamnolipid treatment.ConclusionOverall, the natural marine microbial community in the northeast Atlantic responded differently to crude oil dispersed with either synthetic or biogenic surfactants over time, but oil degradation was more enhanced by the synthetic dispersant. Collectively, our results advance the understanding of how rhamnolipid biosurfactants affect the natural marine microbial community, supporting their potential application in oil spills.
Connexin-36-expressing Gap Junctions in VTA GABA Neurons Sustain Opiate Dependence
Authors: Maal-Bared Geith , Yee Mandy , Harding Erika K. , Ghebreselassie Martha , Bergamini Michael , Choy Roxanne , Kim Ethan , Di Vito Stephanie , Patel Maryam , Amirzadeh Mohammadreza , Grieder Taryn E. , Nagy James I. , Bonin Robert P. , van der Kooy Derek 
Published: December 2020

AbstractDrug dependence is characterized by a switch in motivation wherein a positively reinforcing substance becomes negatively reinforcing. Ventral tegmental area (VTA) GABA neurons form a point of divergence between two double dissociable pathways responsible for these respective motivational states. Here we show that this switch from drug-naïve to opiate-dependent and withdrawn (ODW) motivation is contingent upon the gap junction-forming protein, connexin-36 (Cx36), in VTA GABA neurons. Intra-VTA infusions of the Cx36 blocker, mefloquine, in ODW rats resulted in a reversion to a drug-naïve motivational state and a loss of opiate withdrawal aversions. Consistent with these data, conditional knockout mice lacking Cx36 in GABA neurons (GAD65-Cre;Cx36fl(CFP)/fl(CFP)) were perpetually drug-naïve and never experienced opiate withdrawal aversions. Further, viral-mediated rescue of Cx36 in VTA GABA neurons was sufficient to restore their susceptibility to ODW motivation. Our findings reveal a functional role for VTA gap junctions that has eluded prevailing circuit models of addiction.SignificanceThe motivation to seek drugs can vary depending on prior exposure. For instance, recreational and habitual drug use can stem from a desire to experience the pleasurable or relieving properties of the substance, respectively. Here we identify a subpopulation of midbrain neurons that dictate opiate-seeking motivation via expression of the gap junction protein, connexin-36. We show that connexin-36 expression increases upon opiate dependence and withdrawal. We then demonstrate that this is not merely a correlation, as pharmacological or genetic manipulations that interfere with connexin-36 function prevent the development of opiate dependence in rats and mice. Our results identify gap junctions as a critical node in the pathogenesis of opiate addiction, and a potential new target for substance use disorder pharmacotherapies.
Low force unfolding of a single-domain protein by parallel pathways
Authors: Zhuravlev Pavel I. , Hinczewski Michael , Thirumalai D. 
Published: December 2020

AbstractDeviations from linearity in the dependence of the logarithm of protein unfolding rates, logku(f), as a function of mechanical force,f, measurable in single molecule experiments, can arise for many reasons. In particular, upward curvature in logku(f) as a function of f implies that the underlying energy landscape must be multidimensional with the possibility that unfolding ensues by parallel pathways. Here, simulations using the SOP-SC model of a wild typeβ-sandwich protein and several mutants, with immunoglobulin folds, show upward curvature in the unfolding kinetics. There are substantial changes in the structures of the transition state ensembles as force is increased, signaling a switch in the unfolding pathways. Our results, when combined with previous theoretical and experimental studies, show that parallel unfolding of structurally unrelated single domain proteins can be determined from the dependence of logku(f) as a function of force (or logku[C] where [C] is the denaturant concentration).
Isoform-level transcriptome Atlas of Macrophage Activation
Authors: Vollmers Apple Cortez , Mekonen Honey E. , Campos Sophia , Carpenter Susan , Vollmers Christopher 
Published: December 2020

AbstractRNA-seq is routinely used to measure gene expression changes in response to cell perturbation. Genes that are up or down-regulated following perturbation in RNA-seq studies are designated as target genes for follow-up. However, RNA-seq is limited in its ability to capture the complexity of gene isoforms, defined by the exact composition of exons and transcription start sites (TSS) and poly(A) sites they contain, as well as the expression of these isoforms. Without knowing the composition of the most dominant isoform(s) of a target gene, a minority or non-existent isoform could be selected for follow-up solely based on available annotations for that target gene from databases that are incomplete, or by their nature not tissue specific, or do not provide key information on expression levels. In all, this can lead to loss in valuable resources and time. As the vast majority of genes in the human genome express more than one isoform, there is a great need to identify the complete range of isoforms present for each gene along with their corresponding levels of expression.Here, using the long-read nanopore-based R2C2 method, we generated an Isoform-level transcriptome Atlas of Macrophage Activation (IAMA) that identifies full-length isoforms in primary human monocyte-derived macrophages (MDMs). Macrophages are critical innate immune cells important for recognizing pathogens through use of Toll-like receptors (TLRs), culminating in the initiation of host defense pathways. We characterized isoforms for most moderate to highly expressed genes in resting and TLR-activated MDMs and generated a user-friendly portal built into the UCSC Genome Browser to explore the data (https://genome.ucsc.edu/s/vollmers/IAMA). Our atlas represents a valuable resource for innate immune research as it provides unprecedented isoform information for primary human macrophages.
ADe Novoregulation design shows an effectiveness in altering plant secondary metabolism
Authors: Li Mingzhuo , He Xianzhi , La Hovary Christophe , Zhu Yue , Dong Yilun , Liu Shibiao , Xing Hucheng , Liu Yajun , Jie Yucheng , Ma Dongming , Yuzuak Seyit , Xie De-Yu 
Published: December 2020

AbstractIntroductionTranscription factors (TFs) and cis-regulatory elements (CREs) control gene transcripts involved in various biological processes. We hypothesize that TFs and CREs can be effective molecular tools forDe Novoregulation designs to engineer plants.ObjectivesWe selected two Arabidopsis TF types and two tobacco CRE types to design aDe Novoregulation and evaluated its effectiveness in plant engineering.MethodsG-box and MYB recognition elements (MREs) were identified in fourNicotiana tabacum JAZs(NtJAZs) promoters. MRE-like and G-box like elements were identified in one nicotine pathway gene promoter. TF screening led to select Arabidopsis Production of Anthocyanin Pigment 1 (PAP1/MYB) and Transparent Testa 8 (TT8/bHLH). TwoNtJAZand two nicotine pathway gene promoters were cloned from commercial Narrow Leaf Madole (NL) and KY171 (KY) tobacco cultivars. Electrophoretic mobility shift assay (EMSA), cross-linked chromatin immunoprecipitation (ChIP), and dual luciferase assays were performed to test the promoter binding and activation by PAP1 (P), TT8 (T), PAP1/TT8 together, and the PAP1/TT8/Transparent Testa Glabra 1 (TTG1) complex. A DNA cassette was designed and then synthesized for stacking and expressing PAP1 and TT8 together. Three years of field trials were performed by following industrial and GMO protocols. Gene expression and metabolic profiling were completed to characterize plant secondary metabolism.ResultsPAP1, TT8, PAP1/TT8, and the PAP1/TT8/TTG1 complex bound to and activatedNtJAZpromoters but did not bind to nicotine pathway gene promoters. The engineered red P+T plants significantly upregulated fourNtJAZsbut downregulated the tobacco alkaloid biosynthesis. Field trials showed significant reduction of five tobacco alkaloids and four carcinogenic tobacco specific nitrosamines in most or all cured leaves of engineered P+T and PAP1 genotypes.ConclusionG-boxes, MREs, and two TF types are appropriate molecular tools for aDe Novoregulation design to create a novel distant-pathway cross regulation for altering plant secondary metabolism.
Identification of Aorta-Specific DNA Methylation Patterns in Cell-Free DNA from Patients with Bicuspid Aortic Valve-Associated Aortopathy and Correlation with Aortic Wall Cell Death
Authors: Maredia Ashna , Guzzardi David , Aleinati Mohammad , Iqbal Fatima , Madhu Aiswarya , Wang Xuemei , Barker Alex J. , McCarthy Patrick M. , Fedak Paul W. M. , Greenway Steven C. 
Published: December 2020

ABSTRACTObjectiveIn a proof-of-concept study we sought to identify aorta-specific differentially methylated regions (DMRs) detectable in plasma cell-free DNA (cfDNA) obtained from patients with bicuspid aortic valve (BAV)-associated aortopathy.MethodsWe used bioinformatics and publicly-available human methylomes to identify aorta-specific DMRs. We used data from 4D-flow cardiac magnetic resonance imaging to identify regions of elevated aortic wall shear stress (WSS) in patients with BAV-associated aortopathy undergoing surgery and correlated WSS regions with aortic tissue cell death assessed using TUNEL staining. Cell-free DNA was isolated from patient plasma and levels of candidate DMRs were correlated with aortic diameter and aortic wall cell death.ResultsAortic wall cell death was not associated with maximal aortic diameter but was significantly associated with elevated WSS. We identified 24 candidate aorta-specific DMRs and selected 4 for further study. A DMR on chromosome 11 showed acceptable specificity for the aorta and correlated significantly with aortic wall cell death. Plasma levels of total and aorta-specific cfDNA did not correlate with aortic diameter.ConclusionsElevated WSS created by abnormal flow hemodynamics is associated with increased aortic wall cell death which supports the use of aorta-specific cfDNA as a potential tool to identify aortopathy and stratify patient risk.Date and Number of Institutional Review Board ApprovalREB17-0207
Grey and White Matter Pathways Underlying the Relationship Between Aerobically Active Lifestyle, Cardiorespiratory Function, and Episodic Memory in the Aging Human Brain
Authors: Eisenstein Tamir , Giladi Nir , Havakuk Ofer , Lerner Yulia 
Published: December 2020

AbstractAging is associated with structural alterations of the hippocampus, a key region in episodic memory processes. Aerobic activity and maximal aerobic capacity (MAC), a key measure of cardiorespiratory function and a physiological adaptation of aerobic exercise, have been associated with biological and cognitive resilience of the brain. However, investigations of their relationship with the hippocampus in humans had resulted with inconsistent findings. This study aimed to investigate the relationship between lifestyle’s aerobic activity and MAC and hippocampal grey and white matter structure, as well as episodic memory performance in cognitively healthy older adults. In addition, we examined the relationship between aerobic activity and MAC, and cerebrovascular pathology expressed as white matter lesions (WML). Next, we used a regression-based mediation analysis to examine possible biological pathways which may underlie the relationship between MAC and hippocampal volume, which was demonstrated in previous works, and was confirmed in the current study. Fifty cognitively healthy older adults (70.92 ± 3.9 years) were divided into aerobically active (n=27) and non-active (n=23) groups, and performed structural and diffusion MRI. Forty-two participants were also evaluated for MAC. Aerobically active lifestyle and higher MAC were associated with increased hippocampal volume and microstructural integrity, as well as increased fornix microstructural integrity, and lower WML burden (p<.05). In addition, both factors were correlated with increased episodic memory performance (p<.05). Mediation analysis revealed two pathways potentially mediating the relationship between MAC, hippocampal volume, and episodic memory – a white matter pathway consisted of WML and fornix microstructure, and grey matter pathway including hippocampal microstructure. These findings shed light on possible neurobiological mechanisms that could potentially underlie the neuroprotective effect of cardiorespiratory function and aerobic physical activity on hippocampal macrostructure and memory function in the aging human brain.
Rapid Detection of SARS-CoV-2 Antigen from Serum in a Hospitalized Population
Authors: McAulay K , Kaleta EJ , Grys TE 
Published: December 2020

AbstractSARS-CoV-2 viremia has been demonstrated in some patients using molecular assays. Here we demonstrate detection of SARS-CoV-2 antigen in a cohort of hospitalized patients using a rapid diagnostic test from Anhui Deepblue Medical Technology Co., Ltd. We detected antigen in serum from 11 of 13 patients at time points ranging from three to eighteen days from symptom onset and observed that the disappearance of an antigen signal was associated with seroconversion. These results demonstrate proof of principle use of a rapid antigen test with serum samples in a format compatible with point of care testing.
PKA drives paracrine crisis and WNT4-dependent testis tumor in Carney complex
Authors: Djari C. , Sahut-Barnola I. , Septier A. , Plotton I. , Montanier N. , Dufour D. , Levasseur A. , Wilmouth J. , Pointud JC. , Faucz FR. , Kamilaris C. , Lopez AG. , Guillou F. , Swain A. , Vainio S. , Tauveron I. , Val P. , Lefebvre H. , Stratakis CA. , Martinez A. , Lefrançois-Martinez AM. 
Published: December 2020

ABSTRACTLarge Cell Calcifying Sertoli Cell Tumors (LCCSCTs) are among the most frequent lesions occurring in Carney complex (CNC) male patients. Although they constitute a key diagnostic criterion for this rare multiple neoplasia syndrome resulting from inactivating mutations of the tumor suppressorPRKAR1Aleading to unrepressed PKA activity, the LCCSCT pathogenesis and origin remain elusive. Mouse models targetingPrkar1ainactivation in all somatic populations or separately in each cell type were generated to decipher the molecular and paracrine networks involved in the CNC testis lesion induction. We demonstrate thatPrkar1amutation is required in both stromal and Sertoli cells for the occurrence of LCCSCT. Integrative analyses comparing transcriptomic, immunohistological data and phenotype of mutant mouse combinations led to understand the human LCCSCT pathogenesis and demonstrated unprecedented PKA-induced paracrine molecular circuits in which the aberrant WNT4 signal production is a limiting step in shaping intratubular lesions and tumor expansion both in mouse model and human CNC testes.
Efficient target cleavage by Type V Cas12a effector programmed with split CRISPR RNA
Authors: Tkach Regina , Nikitchina Natalia , Shebanov Nikita , Mekler Vladimir , Ulashchik Egor , Sharko Olga , Shmanai Vadim , Tarassov Ivan , Severinov Konstantin , Entelis Nina , Mazunin Ilya 
Published: December 2020

ABSTRACTCRISPR RNAs (crRNAs) directing target DNA cleavage by type V-A Cas12a nucleases consist of repeat-derived 5’-scaffold moiety and 3’-spacer moiety. We demonstrate that removal of most of the 20-nucleotide scaffold has only a slight effect onin vitrotarget DNA cleavage by Cas12a ortholog from Acidaminococcus sp (AsCas12a). In fact, residual cleavage was observed even in the presence of a 20-nucleotide crRNA spacer part only, while crRNAs split into two individual moieties (scaffold and spacer RNAs) catalyzed highly specific and efficient cleavage of target DNA. Our data also indicate that AsCas12a combined with split crRNA forms a stable complex with the target. These observations were also confirmed in lysates of human cells expressing AsCas12a. The ability of the AsCas12a nuclease to be programmed with split crRNAs opens new lines of inquiry into the mechanisms of target recognition and cleavage and will further facilitate genome editing techniques based on Cas12a nucleases.
Binding strength and hydrogen bond numbers between Covid-19 RBD and HVR of antibody
Authors: Wang Ryan Taoran , Xu Alex Fan , Zhou Qi , Song Tinglu , Xu Kelvin J. , Xu Gu 
Published: December 2020

AbstractThe global battle against the Covid-19 pandemic relies strongly on the human defence of antibody, which is assumed to bind the antigen’s Receptor Binding Domain with its Hypervariable Region. Due to the similarity to other viruses such as SARS, however, our understanding of the antibody-virus interaction has been largely limited to the genomic sequencing, which poses serious challenges to the containment, vaccine exploration and rapid serum testing. Based on the physical/chemical nature of the interaction, infrared spectroscopy was employed to reveal the binding disparity, when unusual temperature dependence was discovered from the 1550cm-1absorption band, attributed to the hydrogen bonds by carboxyl/amino groups, binding the SARS-CoV-2 spike protein and closely resembled SARS-CoV-2 or SARS-CoV-1 antibodies. The infrared absorption intensity, associated with the number of hydrogen bonds, was found to increase sharply between 27°C and 31°C, with the relative absorbance matches at 37°C the hydrogen bonding numbers of the two antibody types (19 vs 12). Meanwhile the ratio of bonds at 27°C, calculated by thermodynamic exponentials rather than by the layman’s guess, produces at least 5% inaccuracy. As a result, the specificity of the SARS-CoV-2 antibody will be more conclusive beyond 31°C, instead of at the usual room temperature of 20°C - 25°C, when the vaccine research and antibody diagnosis would likely be undermined. Beyond genomic sequencing, the temperature dependence, as well as the bond number match at 37°C between relative absorbance and the hydrogen bonding numbers of the two antibody types, are not only of clinical significance in particular, but also of a sample for the physical/chemical understanding of the vaccine-antibody interactions in general.
Microbial regulation of hexokinase 2 links mitochondrial metabolism and cell death in colitis
Authors: Hamm Jacob , Hinrichsen Finn , Schröder Lena , Mishra Neha , Shima Kensuke , Walker Alesia , Sommer Nina , Klischies Kenneth , Prasse Daniela , Zimmermann Johannes , Kaiser Sina , Bordoni Dora , Fazio Antonella , Laue Georg , Tremaroli Valentina , Basic Marijana , Häsler Robert , Schmitz Ruth A. , Krautwald Stefan , Wolf Andrea , Stecher Bärbel , Schmitt-Kopplin Philippe , Kaleta Christoph , Rupp Jan , Bäckhed Fredrik , Rosenstiel Philip , Sommer Felix 
Published: December 2020

SummaryHexokinases (HK) catalyze the first step of glycolysis and thereby limit its pace. HK2 is highly expressed in the gut epithelium, plays a role in immune responses and is upregulated in inflammation and ulcerative colitis1–3. Here, we examined the microbial regulation of HK2 and its impact on intestinal inflammation by generating mice lacking HK2 specifically in intestinal epithelial cells (Hk2ΔIEC).Hk2ΔIECmice were less susceptible to acute intestinal inflammation upon challenge with dextran sodium sulfate (DSS). Analyzing the epithelial transcriptome fromHk2ΔIECmice during acute colitis revealed downregulation of cell death signaling and mitochondrial dysfunction dependent on loss of HK2. Using intestinal organoids derived fromHk2ΔIECmice and Caco-2 cells lacking HK2, we identified peptidyl-prolyl cis-trans isomerase (PPIF) as a key target of HK2-mediated regulation of mitochondrial permeability and repression of cell-death during intestinal inflammation. The microbiota strongly regulated HK2 expression and activity. The microbially-derived short-chain fatty acid (SCFA) butyrate repressed HK2 expression and oral supplementation protected wildtype but notHk2ΔIECmice from DSS colitis. Our findings define a novel mechanism how butyrate may act as a protective factor for intestinal barrier homeostasis and suggest targeted HK2 inhibition as a promising therapeutic avenue in intestinal inflammation.