bluuebunny/crossref_metadata_2025_split huggingface dataset:
The regulatory role of anti-sigma factor, RsbW, in Clostridioides difficile stress response, persistence and infection
Authors: Cheng Jeffrey K. J. , Đapa Tanja , Chan Ivan Y. L. , MacCreath Thomas , Slater Ross , Unnikrishnan Meera 
Published: August 2022

SummaryThe anaerobic pathogen Clostridioides difficile, a primary cause of antibiotic-associated diarrhoea, faces a variety of stresses in the environment and in the mammalian gut. To cope with environmental stresses, it uses the alternative sigma factor B (σB) to modulate gene transcription, which is regulated by an anti-sigma factor, RsbW. To understand the role of RsbW in C. difficile physiology, a rsbW mutant (ΔrsbW) where σB is ‘always on’, was generated. ΔrsbW did not have deleterious fitness defects but tolerated acidic environments and detoxified reactive oxygen and nitrogen species better. ΔrsbW was defective in spore and biofilm formation, adhered better to human gut epithelia and was less virulent in a Galleria mellonella infection model. A transcriptomic analysis to understand this unique phenotype showed a change in expression of some σB-controlled genes along with several non-σB controlled genes. Interestingly, sinRR’ locus that encodes a pleiotropic regulator, was highly upregulated in ΔrsbW indicating a potential indirect role for σB or RsbW in control of sinRR’. Furthermore, the unexpected lower intracellular levels of σB observed suggest post translational control mechanisms. Our study thus provides new insight into the regulatory role of RsbW and the complexity of regulatory networks in C. difficile.ImportancePathogens, like C. difficile, face a range of stresses in the environment and within the host. Alternate transcriptional factors such as sigma factor B (σB) enables the bacterium to respond quickly to different types of stresses and are conserved across bacteria. Anti-sigma factors like RsbW control the activation of genes via these pathways. Such transcriptional control systems provide pathogens like C. difficile a route to tolerance and detoxification of harmful compounds. In this study we investigate the role of RsbW in C. difficile physiology. We demonstrate distinctive phenotypes for a rsbW mutant in growth, persistence and virulence. Our data suggest new σB regulatory circuits in C. difficile. Understanding bacterial responses to external stress is key to designing better strategies to combat this highly resilient bacterial pathogen.
Human conflict with wild carnivores and herbivores: a comparison of socio-economics, damage and prey preference of wild carnivores
Authors: Bayani Abhijeet , Dandekar Nikhil 
Published: August 2022

AbstractHuman-wildlife conflict (HWC) at the fringes of protected areas is a major concern in the conservation biology. Although damage caused by carnivores and herbivores may vary in their magnitude, more attention has been given to carnivores due to various reasons. In Tadoba-Andhari Tiger Reserve (TATR) we compared economic dependence of locals on agriculture and livestock independently and found that income from livestock is only additional, whereas agriculture is the major source of livelihood. We also studied the relative abundance of wild herbivores and diet of tiger, leopard and sloth bear and found that these carnivores have largely been dependent on chital, nilgai and wild pig despite livestock population being higher. We found HWC mitigation in TATR effective but biased towards big cats while the damage in main livelihood (agriculture) being higher. We recommend higher attention to crop-raiding problem for the successful wildlife conservation in central India.
A Peronophythora litchii RXLR effector PlAvh202 enhances plant susceptibility by destabilizing host SAMS
Authors: Li Peng , Li Wen , Zhou Xiaofan , Situ Junjian , Xie Lizhu , Xi Pinggen , Yang Bo , Kong Guanghui , Jiang Zide 
Published: August 2022

AbstractOomycete pathogens can secret hundreds of effectors into plant cells to interfere with plant immune system during infection. Here we identified a cytoplasmic RXLR effector from the most destructive pathogen of litchi, Peronophythora litchii, and named it as PlAvh202. PlAvh202 could suppress cell death triggered by INF1 and Avr3a/R3a in Nicotiana benthamiana, and was essential for P. litchii virulence. In addition, PlAvh202 also suppressed plant immune responses and promoted the susceptibility of N. benthamiana to Phytophthora capsici. Further research revealed that PlAvh202 could suppress ethylene (ET) production by targeting and destabilizing plant S-adenosyl-L-methionine synthetase (SAMS), a key enzyme in ET biosynthesis pathway, in a 26S proteasome-dependent manner. Transient expression of LcSAMS3 induced ET production and enhanced plant resistance, whereas inhibition of ET biosynthesis promoted P. litchii infection, supporting that LcSAMS and ET positively regulate litchi immunity towards P. litchii. Overall, these findings highlight that SAMS can be targeted by oomycete RXLR effector to manipulate ET-mediated plant immunity.
Development of molecular markers of the Kunitz trypsin inhibitor mutant alleles generated by CRISPR/Cas9-mediated mutagenesis in soybean
Authors: Wang Zhibo , Shea Zachary , Rosso Luciana , Shang Chao , Li Jianyong , Bewick Patrick , Li Qi , Zhao Bingyu , Zhang Bo 
Published: August 2022

AbstractThe digestibility of soybean meal can be severely impacted by trypsin inhibitor (TI), one of the most abundant anti-nutritional factors present in soybean seeds. TI can restrain the function of trypsin, a critical enzyme that breaks down proteins in the digestive tract. Soybean accessions with low TI content have been identified. However, it is challenging to breed the low TI trait into elite cultivars due to a lack of molecular markers associated with low TI traits. We identified Kunitz trypsin inhibitor 1 (KTI1, Glyma01g095000) and KTI3 (Glyma08g341500) as two seed-specific TI genes. Mutant kti1 and kti3 alleles carrying small deletions or insertions within the gene open reading frames were created in the soybean cultivar Glycine max cv. Williams 82 (WM82) using the CRISPR/Cas9-mediated genome editing approach. The KTI content and TI activity both remarkably reduced in kti1/3 mutants compared to the WM82 seeds. There was no significant difference in terms of plant growth or maturity days of kti1/3 transgenic and WM82 plants in greenhouse condition. We further identified a T1 line, #5-26, that carried double homozygous kti1/3 mutant alleles, but not the Cas9 transgene. Based on the sequences of kti1/3 mutant alleles in #5-26, we developed markers to co-select for these mutant alleles by using a gel-electrophoresis-free method. The kti1/3 mutant soybean line and associated selection markers will assist in accelerating the introduction of low TI trait into elite soybean cultivars in the future.
Local adaptation of host-species specific gut microbiota
Authors: Sprockett Daniel D. , Price Jeffrey D. , Juritsch Anthony F. , Schmaltz Robert J. , Real Madalena V. F. , Goldman Samantha , Sheehan Michael , Ramer-Tait Amanda E. , Moeller Andrew H. 
Published: August 2022

AbstractMammalian species harbor compositionally distinct gut microbial communities, but the mechanisms that maintain specificity of symbionts to host species remain unclear. Here we show that natural selection within house mice (Mus musculus domesticus) drives deterministic assembly of the house-mouse gut microbiota from mixtures of native and non-native microbiotas. Competing microbiotas from wild-derived lines of house mice and other mouse species (Mus and Peromyscus spp.) within germ-free wildtype (WT) and Rag1-knockout (Rag1−/−) house mice revealed widespread fitness advantages for native gut bacteria. Certain native Bacteriodetes and Firmicutes favored by selection in WT hosts were not favored or disfavored in Rag1−/− hosts, which lack adaptive immunity, indicating that Rag1 mediates fitness advantages of these strains. This study demonstrates local adaptation of gut microbiota to a mammalian species.One-Sentence SummaryAdaptive advantages for native bacteria underlie the assembly of the mouse gut microbiota.
Direct control of translational elongation by TAOK2β highlights altered protein synthesis as a fundamental underlying component of autism
Authors: Henis Melad , Rücker Tabitha , Scharrenberg Robin , Richter Melanie , Baltussen Lucas , Meka Durga Praveen , Schwanke Birgit , Neelagandan Nagammal , Daaboul Danie , Murtaza Nadeem , Krisp Christoph , Harder Sönke , Schlüter Hartmut , Kneussel Matthias , Hermans-Borgmeyer Irm , de Wit Joris , Singh Karun K. , Duncan Kent E. , de Anda Froylan Calderón 
Published: August 2022

AbstractMicrodeletions in the 16p11.2 region of the human genome are frequently associated with autism spectrum disorders (ASDs), but how these genomic rearrangements cause ASD remains unclear. Here, we reveal that TAOK2β, a protein isoform encoded by the human TAOK2 gene located in the 16p11.2 locus, regulates mRNA translation. To identify key functional interaction partners of TAOK2β, we performed proteomic screening from Neuro-2a (N2a) cells, mouse cortices, and cultured neurons. This revealed translation factors as a major class of enriched interacting proteins. Consistently, TAOK2β is present in mouse cortical polyribosomes and cortices from Taok2 knockout mice show increased ribosome density on mRNAs and enhanced protein synthesis. Several lines of evidence support an effect of TAOK2β on translation elongation via phosphorylation of eukaryotic elongation factor (eEF2). TAOK2 can directly phosphorylate eEF2 on Threonine 56 and this phosphorylation is reduced in cortices from Taok2 knockout mice. TAOK2β WT overexpression increased eEF2 phosphorylation levels and reduced protein synthesis, whereas a kinase-dead allele of TAOK2β showed opposite effects. Finally, we show that cortices from the mouse model of the human 16p11.2 microdeletion have increased polysome/monosome (P/M) ratios and protein synthesis, phenocopying Taok2 loss of function. Importantly, defective translation phenotypes observed in the mouse 16p11.2 microdeletion model of ASD could be normalized either by reintroducing Taok2 in vivo or by delivering TAOK2β to cortical neurons derived from 16p11.2 microdeletion mice. Our results uncover a critical role of TAOK2β as a regulator of protein synthesis and support the idea that translational control is a common endpoint of ASD-associated signaling pathways.
Infrared videography of a subcutaneous knee tattoo as a simple and inexpensive method to overcome skin motion artifact in rodent kinematics
Authors: Moukarzel George , Rauscher Bradley C. , Patil Chetan A. , Spence Andrew J. 
Published: August 2022

AbstractKinematic analyses of rodent behavior are frequently used in neuroscience research, and commonly in spinal cord injury (SCI) studies. Unfortunately, skin motion artifact introduces significant errors into these data, because the skin is only loosely coupled to the underlying skeleton by connective tissue. In rats, these errors can be as large as 50-75%,as quantified by past work using x-ray fluoroscopy. Here we show that infrared videography of a subcutaneous tattoo can overcome skin motion artifact in rodent kinematics. The method yields data similar to gold standard x-ray fluoroscopy systems at a fraction of the cost, does not affect the animals’ locomotion, and results in markers that persist for at least 10 weeks. We found that, compared to a gold-standard x-ray fluoroscopy study that directly tracked the skeleton, our method reduced the error in mean hip angle from 17 ± 6.0 to 3.1 ± 2.4 degrees (mean ± SEM), and the root-mean-square (RMS) error across the mean hip angle waveform from 20 to 5.3 degrees (n=4 rats). The knee joint angle waveform derived from infra-red imaging tightly matched the shape of the x-ray waveform after allowing for a constant offset, having RMS error reduced from 8.1 to 1.2 degrees. The method stands to significantly reduce between-animal errors, and hence between laboratory errors, in these ubiquitous model systems, especially important in SCI studies where individuals are assigned to different treatments.
Direction mutation pressure of SARS-CoV-2 helps to understand the past and predict the future evolution: C>U and G>U biased mutagenesis forces the majority of amino-acid substitutions to be from CG-rich losers to U-rich gainers
Authors: Voronka Alexandr , Efimenko Bogdan , Oreshkov Sergey , Franco Melissa , Fleischmann Zoe , Yurov Valerian , Trufanova Arina , Timonina Valeria , Ree Natalia , Zalevsky Arthur , Penfrat Emma , Junier Thomas , Agranovsky Alexey , Khrapko Konstantin , Gunbin Konstantin , Fellay Jacques , Popadin Konstantin 
Published: August 2022

AbstractEvolution is a function of mutagenesis and selection. To analyse the role of mutagenesis on the structure of the SARS-CoV-2 genome, we reconstructed the mutational spectrum, which was highly C>U and G>U biased. This bias forces the SARS-CoV-2 genome to become increasingly U-rich unless selection cancels it. We analysed the consequences of this bias on the composition of the most neutral (four-fold degenerate synonymous substitutions) and the least neutral positions (nonsynonymous substitutions). The neutral nucleotide composition is already highly saturated by U and, according to our model, it is at equilibrium, suggesting that in the future, we don’t expect any more increase in U. However, nonsynonymous changes continue slowly evolve towards equilibrium substituting CG-rich amino-acids (“losers”) with U-rich ones (“gainers”). This process is universal for all genes of SARS-CoV-2 as well as for other coronaviridae species. In line with the direction mutation pressure hypothesis, we show that viral-specific amino acid content is associated with the viral-specific mutational spectrum due to the accumulation of effectively neutral slightly deleterious variants (losers to gainers) during the molecular evolution. The tuning of a protein space by the mutational process is expected to be typical for species with relaxed purifying selection, suggesting that the purging of slightly-deleterious variants in the SARS-CoV-2 population is not very effective, probably due to the fast expansion of the viral population during the pandemic. Understanding the mutational process can help to design more robust vaccines, based on gainer-rich motifs, close to the mutation-selection equilibrium.
Endogenous RNAi silences a burgeoning sex chromosome arms race
Authors: Vedanayagam Jeffrey , Lin Ching-Jung , Papareddy Ranjith , Nodine Michael , Flynt Alex S. , Wen Jiayu , Lai Eric C. 
Published: August 2022

AbstractAlthough the biological utilities of endogenous RNAi (endo-RNAi) have been largely elusive, recent studies reveal its critical role in the non-model fruitfly Drosophila simulans to suppress selfish genes, whose unchecked activities can severely impair spermatogenesis. In particular, hairpin RNA (hpRNA) loci generate endo-siRNAs that suppress evolutionary novel, X-linked, meiotic drive loci. The consequences of deleting even a single hpRNA (Nmy) in males are profound, as such individuals are nearly incapable of siring male progeny. Here, comparative genomic analyses of D. simulans and D. melanogaster mutants of the core RNAi factor dcr-2 reveal a substantially expanded network of recently-emerged hpRNA-target interactions in the former species. The de novo hpRNA regulatory network in D. simulans bears compelling signatures of sex chromosome conflict and provides insight into molecular strategies that underlie hpRNA emergence. In particular, our data support the existence of ongoing rapid evolution of Nmy/Dox-related networks, recurrent targeting of testis HMG Box loci by hpRNAs, and connections to the piRNA pathway. Importantly, the impact of the endo-RNAi network on gene expression flips the convention for regulatory networks, since we observe strong derepression of targets of the youngest hpRNAs, but only mild effects on the targets of the oldest hpRNAs. These data suggest that endo-RNAi are especially critical during incipient stages of intrinsic sex chromosome conflicts, and that continual cycles of distortion and resolution may contribute to the segregation of species.
Targeting Plasmodium falciparum calcium dependent protein kinase-1: Computational modelling approach towards the discovery of antimalarial drug from medicinal herbs and clinically approved anti-malarial drugs pharmacophores
Authors: Adelusi Temitope Isaac , Ojo Taiwo Ooreoluwa , Quadri Bolaji Olawale , Oyewole Precious Moyosoluwa , Oladipo Elijah Kolawole 
Published: August 2022

ABSTRACTThe Key participants in the calcium signaling process in the malaria parasite are calcium dependent protein kinases. It has been established that Plasmodium falciparum calcium dependent protein kinase 1 (PfCDPK1) is essential for the invasion of host erythrocytes as well as for the parasite’s asexual development. Due to malaria’s resistance to currently available anti-malarial medications, it has become necessary to create effective inhibitory agents that target invasion-dependent proteins. In this study, libraries of 856 chemicals were screened using a variety of computational methods. Physicochemical property testing, molecular docking analysis, and pharmacokinetic ADMET profiling were used to determine these drugs’ capacity to inhibit PfCDPK1. 88 of the 856 compounds derived from known antimalarial botanicals and clinically approved antimalarial drug pharmacophores have demonstrated a potent inhibitory effect on PfCDPK1. Additionally, based on research done on the purported inhibitory standard of PfCDPK1 (Purfalcamine), which had a binding affinity of −8.8 KJ/mol, twelve compounds, which include 17-hydroxyazadiradione, Nimbaflavone, Dehydrocarpaine-II, Picracin, Epicatechin gallate, and Naringin, ZINC000012504271, ZINCC000100029905, ZINC000004149268, ZINC000078832372, ZINC000102739374 and ZINC000198562314 had exhibited better binding affinities (−8.8, −8.8, −9.2, −9.1, −9.3, −10.0, −8.1, −7.9, −7.9, −8.2, −8.3, −7.9 KJ/mol respectively), pharmacokinectics, and physicochemical properties. According to our findings, 88 compounds are likely pharmacological targets with domiciled PfCDPK1 inhibitory effects. Nevertheless, our findings highlight these twelve stand-out compounds, suggesting that they may be the best candidates with regard to therapeutic efficacy.
Loss of chromosome Y in primary tumors
Authors: Qi Meifang , Pang Jiali , Mitsiades Irene , Lane Andrew A. , Rheinbay Esther 
Published: August 2022

AbstractIt has long been recognized that certain cancer types afflict female and male patients disproportionately. The reasons for this disparity include differences in male/female physiology, effect of sex hormones, risk behavior and environmental exposures, and different copy number of the sex chromosomes X and Y. Loss of Y (LOY) is common in peripheral blood cells in aging men, and this phenomenon is associated with several diseases. However, the frequency and role of LOY in tumors is little understood. Here, we present a comprehensive catalog of LOY in >5,000 primary tumors from male patients in the TCGA. We show that LOY rates vary by tumor type, and provide evidence for LOY being either a passenger or driver event depending on context. LOY in uveal melanoma specifically is associated with age, survival and is an independent predictor of poor outcome. LOY creates common dependencies on DDX3X and EIF1AX in male cell lines, suggesting that LOY generates unique vulnerabilities that could be therapeutically exploited.
Robust total X-ray scattering workflow to study correlated motion of proteins in crystals
Authors: Meisburger Steve P. , Case David A. , Ando Nozomi 
Published: August 2022

AbstractThe breathing motions of proteins are thought to play a critical role in function. However, current techniques to study key collective motions are limited to spectroscopy and computation. We present a high-resolution experimental approach based on the total scattering from protein crystals at room temperature (TS/RT-MX) that captures both structure and collective motions. To reveal the scattering signal from protein motions, we developed a general workflow that enables robust subtraction of lattice disorder. The workflow introduces two new methods: GOODVIBES, a detailed and refinable lattice disorder model based on the rigid-body vibrations of a crystalline elastic network; and DISCOBALL, an independent method of validation that estimates the displacement covariance between proteins in the lattice in real space. We demonstrate the robustness of this workflow and further demonstrate how it can be interfaced with MD simulations towards obtaining high-resolution insight into functionally important protein motions.
Autocrine Proteinase Activated Receptor (PAR) mediated signaling in prostate cancer cells
Authors: Chandrabalan Arundhasa , Ramachandran Rithwik 
Published: August 2022

ABSTRACTProteinase activated receptors (PARs) are G protein-coupled receptors (GPCRs) activated by limited N-terminal proteolysis. A variety of proteolytic enzymes derived from the coagulation cascade and inflammatory milieu activate PARs, however specific activators in different physiological and pathophysiological contexts remain poorly defined. PARs are highly expressed in many cancer cells and regulate various aspects of tumor growth and metastasis. Endogenous proteinases that regulate PARs in the setting of various tumors however remains unresolved. Prostate cancer (PCa) remains a major cause of mortality in men despite advances in early detection and clinical intervention. PAR expression has been reported in PCa, however, their role here remains poorly defined. In androgen independent PC3 cells, we find functional expression of PAR1 and PAR2 but not PAR4. Using genetically encoded PAR cleavage biosensors, we find that PCa cells secrete proteolytic enzymes that cleave PARs and trigger autocrine signaling. Deletion of PAR1 and PAR2 using CRISPR/Cas9 combined with microarray analysis revealed genes that are differentially regulated by this autocrine signalling mechanism. Interestingly, several genes that are known PCa prognostic factors or biomarker were differentially expressed in PAR1-KO and PAR2-KO PC3 cells. We also examined PAR1 and PAR2 regulation of PCa cell proliferation and migration using PAR1 and PAR2-KO PC3 cells, as well as PAR1 and PAR2 specific agonists and antagonists. We find that PAR1 and PAR2 have opposite effects on PC3 cell proliferation and migration. In summary, we have identified an autocrine signaling mechanism through PARs as a regulator of PCa cell function.