bluuebunny/crossref_metadata_2025_split huggingface dataset:
Refactoring the formicamycin biosynthetic gene cluster to make high-level producing strains and new molecules
Authors: Devine Rebecca , McDonald Hannah , Qin Zhiwei , Arnold Corinne , Noble Katie , Chandra Govind , Wilkinson Barrie , Hutchings Matthew I. 
Published: September 2020

AbstractThe formicamycins are promising antibiotics with potent activity against Gram-positive pathogens including VRE and MRSA and display a high barrier to selection of resistant isolates. They were first identified inStreptomyces formicaeKY5, which produces the formicamycins at low levels on solid agar but not in liquid culture, thus hindering further investigation of these promising antibacterial compounds. We hypothesised that by understanding the organisation and regulation of theforbiosynthetic gene cluster, we could rationally refactor the cluster to increase production levels. Here we report that theforbiosynthetic gene cluster consists of 24 genes expressed on nine transcripts. Seven of these transcripts, including those containing all the major biosynthetic genes, are repressed by the MarR-regulator ForJ which also controls the expression of the ForGF two-component system that initiates biosynthesis. A third cluster-situated regulator, ForZ, autoregulates and controls production of the putative MFS transporter ForAA. Consistent with these findings, deletion offorJincreased formicamycin biosynthesis 5-fold, while over-expression offorGFin the ΔforJbackground increased production 10-fold compared to the wild-type. De-repression by deletingforJalso switched on biosynthesis in liquid-culture and induced the production of two novel formicamycin congeners. By combining mutations in regulatory and biosynthetic genes, six new biosynthetic precursors with antibacterial activity were also isolated. This work demonstrates the power of synthetic biology for the rational redesign of antibiotic biosynthetic gene clusters both to engineer strains suitable for fermentation in large scale bioreactors and to generate new molecules.ImportanceAntimicrobial resistance is a growing threat as existing antibiotics become increasingly ineffective against drug resistant pathogens. Here we determine the transcriptional organisation and regulation of the gene cluster encoding biosynthesis of the formicamycins, promising new antibiotics with activity against drug resistant bacteria. By exploiting this knowledge, we construct stable mutant strains which over-produce these molecules in both liquid and solid culture whilst also making some new compound variants. This will facilitate large scale purification of these molecules for further study including in vivo experiments and the elucidation of their mechanism of action. Our work demonstrates that understanding the regulation of natural product biosynthetic pathways can enable rational improvement of the producing strains.
Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases
Authors: Westberg Michael , Su Yichi , Zou Xinzhi , Ning Lin , Hurst Brett , Tarbet Bart , Lin Michael Z. 
Published: September 2020

ABSTRACTThe coronavirus main protease, Mpro, is a key protein in the virus life cycle and a major drug target. Based on crystal structures of SARSCoV2 Mprocomplexed with peptidomimetic inhibitors, we recognized a binding characteristic shared with proline-containing inhibitors of hepatitis C virus protease. Initial tests showed that this subclass of HCV protease inhibitors indeed exhibited activity against Mpro. Postulating a benefit for a preorganized backbone conformation, we designed new ketoamide-based Mproinhibitors based on central proline rings. One of the designed compounds, ML1000, inhibits Mprowith low-nanomolar affinity and suppresses SARSCoV2 viral replication in human cells at sub-micromolar concentrations. Our findings identify ML1000 as a promising new pre-organized scaffold for the development of anti-coronavirus drugs.
Transcription Factors STAT5A and SPI1 Reveals RHBDD2 as a Potential Biomarker in Sepsis and Septic Shock
Authors: Ali Arslan , Shehwana Huma , Hanif Ayesha , Fatima Abeera , Shabbir Maria , Rafiq Mehak 
Published: September 2020

ABSTRACTSepsis is a serious health situation caused by uncontrolled infection and septic shock is a severe condition of sepsis. RHBDD2 is a member of the rhomboid superfamily which is overexpressed in different types of cancer and associated with ER stress and estrogen receptor. Using microarray gene expression data and using different computational techniques this study investigated the role of RHBDD2 in sepsis and septic shock. Finds functional annotation of RHBDD2 using co-expression analysis and identified the deregulation of RHBDD2 in sepsis using differential expression analysis. Results show that RHBDD2 is overexpressed in sepsis and septic shock. The GO enrichment analysis, KEGG pathways, and biological functions of the RHBDD2 co-expressed genes module show that it is involved in most of the sepsis-related biological functions and also plays a role in most of the infection-related pathways which lead to sepsis and septic shock. RHBDD2 is regulated by STAT5A and SPI1 transcription factors in sepsis and septic shock. The identification of the RHBDD2 as a biomarker may facilitate in septic shock diagnosis, treatment, and prognosis.
Accuracy of predicting chemical body composition of growing pigs using dual-energy X-ray absorptiometry
Authors: Kasper Claudia , Schlegel Patrick , Ruiz-Ascacibar Isabel , Stoll Peter , Bee Giuseppe 
Published: September 2020

AbstractStudies in animal science assessing nutrient and energy efficiency or determining nutrient requirements necessitate gathering exact measurements of body composition or body nutrient contents. Wet chemical analysis methods or standardized dissection are commonly applied, but both are destructive. Harnessing human medical imaging techniques for animal science can enable repeated measurements of individuals over time and reduce the number of individuals required for research. Among imaging techniques, dual-energy X-ray absorptiometry (DXA) is particularly promising. However, the measurements obtained with DXA do not perfectly match dissections or chemical analyses, requiring the adjustment of the DXA via calibration equations. Several calibration regressions have been published, but comparative studies are pending. Thus, it is currently not clear whether existing regression equations can be directly used to convert DXA measurements into chemical values or whether each individual DXA device will require its own calibration. Our study builds prediction equations that relate body composition to the content of single nutrients in growing entire male pigs (body weight range 20-100 kg) as determined by both DXA and chemical analyses, with R2ranging between 0.89 for ash and 0.99 for water and crude protein. Moreover, we show that the chemical composition of the empty body can be satisfactorily determined by DXA scans of carcasses, with the prediction error rCV ranging between 4.3% for crude protein and 12.6% for ash. Finally, we compare existing prediction equations for pigs of a similar range of body weights with the equations derived from our DXA measurements and evaluate their fit with our chemical analyses data. We found that existing equations for absolute contents that were built using the same DXA beam technology predicted our data more precisely than equations based on different technologies and percentages of fat and lean mass. This indicates that the creation of generic regression equations that yield reliable estimates of body composition in pigs of different growth stages, sexes and genetic breeds could be achievable in the near future. DXA may be a promising tool for high-throughput phenotyping for genetic studies, because it efficiently measures body composition in a large number and wide array of animals.
Dynamic analysis of sugar metabolism reveals the mechanisms of action of synthetic sugar analogs
Authors: van Scherpenzeel Monique , Conte Federica , Büll Christian , Ashikov Angel , Hermans Esther , Willems Anke , van Tol Walinka , Kragt Else , Moret Ed E. , Heise Torben , Langereis Jeroen D. , Rossing Emiel , Zimmermann Michael , Rubio-Gozalbo M. Estela , de Jonge Marien I. , Adema Gosse J. , Zamboni Nicola , Boltje Thomas , Lefeber Dirk J. 
Published: September 2020

AbstractSynthetic sugar analogs are widely applied in metabolic oligosaccharide engineering (MOE) and as novel drugs to interfere with glycoconjugate biosynthesis. However, mechanistic insights on their exact metabolism in the cell and over time are mostly lacking. We developed sensitive ion-pair UHPLC-QqQ mass spectrometry methodology for analysis of sugar metabolites in organisms and in model cells and identified novel low abundant nucleotide sugars in human cells, such as ADP-glucose and UDP-arabinose, and CMP-sialic acid (CMP-NeuNAc) in Drosophila. Dynamic tracing of propargyloxycarbonyl (Poc) labeled analogs, commonly used for MOE, revealed that ManNPoc is metabolized to both CMP-NeuNPoc and UDP-GlcNPoc. Finally, combined treatment of B16-F10 melanoma cells with antitumor compound 3Fax-NeuNAc and13C-labeled GlcNAc revealed that endogenous CMP-NeuNAc levels started to decrease before a subsequent decrease of ManNAc 6-phosphate was observed. This implicates 3Fax-NeuNAc first acts as a substrate for cytosolic CMP-sialic acid synthetase and subsequently its product CMP-3Fax-NeuNAc functions as a feed-back inhibitor for UDP-GlcNAc 2-epimerase/N-acetylmannosamine kinase. Thus, dynamic analysis of sugar metabolites provides key insights into the time-dependent metabolism of synthetic sugars, which is important for the rational design of analogs with optimized effects.
The 5α-reductase inhibitor finasteride reduces opioid self-administration
Authors: Bosse Gabriel D. , Cadeddu Roberto , Floris Gabriele , Farero Ryan D. , Vigato Eva , Lee Suhjung J. , Zhang Tejia , Gaikwad Nilesh W. , Keefe Kristen A. , Philips Paul E.M. , Bortolato Marco , Peterson Randall T. 
Published: September 2020

AbstractOpioid use disorder (OUD) has become a leading cause of death in the US, yet current therapeutic strategies remain highly inadequate. To identify novel potential treatments for OUD, we screened a targeted selection of over 100 drugs, using a recently developed opioid self-administration assay in zebrafish. This paradigm showed that finasteride, a steroidogenesis inhibitor approved for the treatment of benign prostatic hyperplasia and androgenetic alopecia, reduced self-administration of multiple opioids without affecting locomotion or feeding behavior. These findings were confirmed in rats; furthermore, finasteride did not interfere with the antinociceptive effect of opioids in rat models of neuropathic pain. Steroidomic analyses of the brains of fish treated with finasteride revealed a significant increase in dehydroepiandrosterone sulfate (DHEAS). Treatment with precursors of DHEAS reduced opioid self-administration in zebrafish, in a fashion akin to the effects of finasteride. Our results highlight the importance of steroidogenic pathways as a rich source of therapeutic targets for OUD and point to the potential of finasteride as a new option for this disorder.
LOX-1+immature neutrophils predict severe COVID-19 patients at risk of thrombotic complications
Authors: Combadiere Béhazine , Adam Lucille , Quentric Paul , Rosenbaum Pierre , Dorgham Karim , Bonduelle Olivia , Parizot Christophe , Sauce Delphine , Mayaux Julien , Luyt Charles-Edouard , Boissonnas Alexandre , Amoura Zahir , Pourcher Valérie , Miyara Makoto , Gorochov Guy , Guihot Amélie , Combadière Christophe 
Published: September 2020

AbstractRationalLymphopenia and neutrophil/lymphocyte ratio may have prognostic value in coronavirus disease 2019 (COVID-19) severity.ObjectiveWe sought to investigate the representation of neutrophil subsets in severe and critical COVID-19 patients based on Intensive Care Units (ICU) and non-ICU admission.MethodsWe developed a multi-parametric neutrophil profiling strategy based on known neutrophil markers to distinguish COVID-19 phenotypes in critical and severe patients.ResultsOur results showed that 80% of ICU patients develop strong myelemia with CD10−CD64+immature neutrophils. Cellular profiling revealed two distinct neutrophil subsets expressing either the lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) or the Interleukin-3 receptor alpha (CD123), both significantly overrepresented in ICU patients compared to non-ICU patients. The proportion of LOX-1-expressing immature neutrophils positively correlated with clinical severity, with the cytokine storm (IL-1β, IL-6, IL-8, TNFα), and with intravascular coagulation. Importantly, high proportions of LOX-1+-immature neutrophils are associated with high risks of severe thrombosis.ConclusionsTogether these data suggest that point of care enumeration of LOX-1-immature neutrophils might help distinguish patients at risk of thrombosis complication and most likely to benefit from intensified anticoagulant therapy.
The maternal foam plug constitutes a reservoir for the desert locust’s bacterial symbionts
Authors: Lavy Omer , Gophna Uri , Ayali Amir , Gihaz Shalev , Fishman Ayelet , Gefen Eran 
Published: September 2020

AbstractA hallmark of the desert locust’s ancient and deserved reputation as a devastating agricultural pest is that of the long-distance, multi-generational migration of locust swarms to new habitats. The bacterial symbionts that reside within the locust gut comprise a key aspect of its biology, augmenting its immunity and having also been reported to be involved in the swarming phenomenon through the emission of attractant volatiles. However, it is still unclear whether and how these beneficial symbionts are transmitted vertically from parent to offspring. Using comparative 16S rRNA amplicon sequencing and direct experiments with engineered bacteria, we provide here evidence of the vertical transmission of locust gut bacteria. The females perform this activity by way of inoculation of the egg-pod’s foam plug, through which the larvae pass upon hatching. Furthermore, analysis of the biochemical structure of the foam revealed chitin to be its major component, along with immunity-related proteins such as lysozyme, which could be responsible for the inhibition of some bacteria in the foam while allowing other, more beneficial, strains to proliferate. Our findings reveal a potential vector for the transgenerational transmission of symbionts in locusts, which contributes to the locust swarm’s ability to invade and survive in new territories.
Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding
Authors: Scott Michael F. , Fradgley Nick , Bentley Alison R. , Brabbs Thomas , Corke Fiona , Gardner Keith A. , Horsnell Richard , Howell Phil , Ladejobi Olufunmilayo , Mackay Ian J. , Mott Richard , Cockram James 
Published: September 2020

AbstractBackgroundBreeding has helped improve bread wheat yield significantly over the last century. Understanding the potential for future crop improvement depends on relating segregating genetic variation to agronomic traits.ResultsWe bred NIAB Diverse MAGIC population, comprising over 500 recombinant inbred lines, descended from sixteen bread wheat varieties released between 1935-2004. We sequenced the founders’ exomes and promotors by capture. Despite being highly representative of North-West European wheat and capturing 73% of global polymorphism, we found 89% of genes contained no more than three haplotypes. We sequenced each line with 0.3x coverage whole-genome sequencing, and imputed 1.1M high-quality SNPs that were over 99% concordant with array genotypes. Imputation accuracy remained high at coverage as low as 0.076x, with or without the use of founder genomes as reference panels. We created a genotype-phenotype map for 47 traits over two years. We found 136 genome-wide significant associations, concentrated at 42 genetic loci with large and often pleiotropic effects. Outside of these loci most traits are polygenic, as revealed by multi-locus shrinkage modelling.ConclusionsHistorically, wheat breeding has reshuffled a limited palette of haplotypes; continued improvement will require selection at dozens of loci of diminishing effect, as most of the major loci we mapped are known. Breeding to optimise one trait generates correlated trait changes, exemplified by the negative trade-off between yield and protein content, unless selection and recombination can break critical unfavourable trait-trait associations. Finally, low coverage whole genome sequencing of bread wheat populations is an economical and accurate genotyping strategy.
RBM20 phosphorylation on serine/arginine domain is crucial to regulate pre-mRNA splicing and protein shuttling in the heart
Authors: Sun Mingming , Jin Yutong , Zhu Chaoqun , Zhang Yanghai , Liss Martin , Gotthardt Michael , Ren Jun , Ge Ying , Guo Wei 
Published: September 2020

AbstractMolecular and cellular mechanisms of mutations of splicing factors in heart function are not well understood. The splicing of precursor mRNA is dependent on an essential group of splicing factors containing serine-arginine (SR) domain(s) that are critical for protein-RNA and protein-protein interaction in the spliceosome assembly. Phosphorylation of SR domains plays a key role in splicing control and the distribution of splicing factors in the cell. RNA binding motif 20 (RBM20) is a splicing factor predominantly expressed in muscle tissues with the highest expression level in the heart. However, its phosphorylation status is completely unknown up-to-date. In this study, we identified sixteen amino acid residues that are phosphorylated by middle-down mass spectrometry. Four of them are located in the SR domain, and two out of the four residues, S638 and S640, play an essential role in splicing control and facilitate RBM20 shuttling from the nucleus to the cytoplasm. Re-localization of RBM20 promotes protein aggregation in the cytoplasm. We have also verified that SR-protein kinases (SRPKs), cdc2-like kinases (CLKs) and protein kinase B (PKB or AKT) phosphorylate S638 and S640. Mutations of S638A and S640G reduce RBM20 phosphorylation and disrupt the splicing. Taken together, we determine the phosphorylation status of RBM20 and provide the first evidence that phosphorylation on SR domain is crucial for pre-mRNA splicing and protein trafficking. Our findings reveal a new role of RBM20 via protein shuttling in cardiac function.
A transcriptomic taxonomy ofDrosophilacircadian neurons around the clock
Authors: Ma Dingbang , Przybylski Dariusz , Abruzzi Katharine C. , Schlichting Matthias , Li Qunlong , Long Xi , Rosbash Michael 
Published: September 2020

AbstractMany different functions are regulated by circadian rhythms, including those orchestrated by discrete clock neurons within animal brains. To comprehensively characterize and assign cell identity to the 75 pairs ofDrosophilacircadian neurons, we optimized a single cell RNA sequencing method and assayed clock neuron gene expression at different times of day. The data identify at least 17 clock neuron categories with striking spatial regulation of gene expression. Transcription factor regulation is prominent and likely contributes to the robust circadian oscillation of many transcripts, including those that encode cell-surface proteins previously shown to be important for cell recognition and synapse formation during development. We suggest that these molecules orchestrate the temporal regulation of synapse formation and/or strength. The many other clock-regulated genes also constitute an important resource for future mechanistic and functional studies between clock neurons and/or for temporal signaling to circuits elsewhere in the fly brain.
Transcriptomic responses and survival mechanisms of staphylococci to the antimicrobial skin lipid sphingosine
Authors: Chen Yiyun , Moran Josephine C. , Campbell-Lee Stuart , Horsburgh Malcolm J. 
Published: September 2020

AbstractSphingosines are antimicrobial lipids that form part of the innate barrier to skin colonisation by microbes. Sphingosine deficiencies can result in increased epithelial infections by bacteria includingStaphylococcus aureus. Recent studies have focused on the potential use of sphingosines as novel therapeutic agents, but there have been no investigations into sphingosine resistance or its potential mechanisms. We used RNA-Seq to identify the common D-sphingosine transcriptomic response of the transient skin coloniserS. aureusand the dominant skin coloniserS. epidermidis. A common D-sphingosine stimulon was identified that included downregulation of the SaeSR two-component system (TCS) regulon and upregulation of both the VraSR TCS and CtsR stress regulons. We show that the PstSCAB phosphate transporter, and VraSR offer intrinsic resistance to D-sphingosine. Further, we demonstrate increased sphingosine resistance in these staphylococci evolves readily through mutations in genes encoding the FarE-FarR efflux/regulator proteins. The ease of selecting mutants with resistance to sphingosine may impact upon staphylococcal colonisation of skin where the lipid is present and have implications with topical therapeutic applications.
Neural support of manual preference revealed by BOLD variations during right and left finger-tapping in a sample of 287 healthy adults balanced for handedness
Authors: Tzourio-Mazoyer Nathalie , Labache Loïc , Zago Laure , Hesling Isabelle , Mazoyer Bernard 
Published: September 2020

AbstractWe have identified the brain areas involved in Manual Preference (MP) in 143 left-handers (LH) and 144 right-handers (RH)). First, we selected the pairs of homotopic regions of interest (hROIs) of the AICHA atlas with significant contralateral activation and asymmetry during the right-hand and the left-hand Finger-Tapping (FT) both in RH and LH. Thirteen hROIs were selected, including the primary and secondary sensorimotor, and premotor cortices, thalamus, dorsal putamen and cerebellar lobule IV. Both contralateral activations and ipsilateral deactivations (reversed for the cerebellum) were seen in primary motor and somatosensory areas, with stronger asymmetries when the preferred hand was used. Comparing the prediction of MP with different combinations of BOLD variations in these 13 hROIs, the differences between movement of the preferred hand versus that of the non-preferred hand within the contralateral and/or ipsilateral cortices of 11 hROIS performed best at explaining handedness distribution, Handedness is thus supported by: 1-between-hand variations of ipsilateral deactivations of hand primary sensorimotor and secondary somatosensory cortices and 2-variations in regions showing the same profile in left and right-handers during the right or left FT. The present study demonstrates that right and left-handedness are not based on mirrored organization of hand control areas.
Non-redundant functions of H2A.Z.1 and H2A.Z.2 in chromosome segregation and cell cycle progression
Authors: Sales-Gil Raquel , de Castro Ines J. , Amin Hasnat , Spanos Christos , Vinciotti Veronica , Rappsilber Juri , Sisu Cristina , Vagnarelli Paola 
Published: September 2020

SUMMARYH2A.Z is a H2A-type histone variant essential for many aspects of cell biology ranging from gene expression to genome stability. From deuterostomes, H2A.Z evolved into two paralogues H2A.Z.1 and H2A.Z.2 that differ by only three amino acids and are encoded by different genes (H2AFZandH2AFVrespectively). Despite the importance of this histone variant in development and cellular homeostasis, very little is known about the individual functions of each paralogue in mammals. Here we investigated the distinct roles of two paralogues in cell cycle regulation. Using a specific siRNA approach for each paralogue in human cells, we unveiled non-redundant functions for H2A.Z.1 and H2A.Z.2 in cell division: H2A.Z.1 regulates the expression of important cell cycle genes (including Myc and Ki-67) and its depletion leads to a G1 arrest, whereas H2A.Z.2 is essential for centromere integrity and function, thus playing a key role in chromosome segregation.