bluuebunny/crossref_metadata_2025_split huggingface dataset:
KaiC-like proteins improve stress resistance in environmental Pseudomonas species
Authors: Terrettaz Céline , Cabete Bruno , Geiser Johan , Valentini Martina , Gonzalez Diego 
Published: January 2022

SummaryKaiC is the central cog of the circadian clock in Cyanobacteria. Close homologs of this protein are widespread among bacteria that are not known to have or need a circadian physiology. The function, interaction network, and mechanism of action of these KaiC homologs are still largely unknown. Here, we focus on KaiC-like proteins found in environmental Pseudomonas species. Using a bioinformatic approach, we describe the diversity and distribution of members of this protein family in the Pseudomonas genus and sketch, through comparative genomics, a conserved minimal interaction network comprising a histidine kinase and a response regulator. We then characterize experimentally the only KaiC homolog present in Pseudomonas putida KT2440 and Pseudomonas protegens CHA0. Through phenotypic assays and transcriptomics, we show that KaiC is involved in osmotic and oxidative stress resistance in P. putida and in sulfur uptake and alternative carbon source utilization in P. protegens. As expected, it physically interacts with its cognate histidine kinase and response regulator. Moreover, KaiC homologs are phosphorylated at one (P. putida) or two (P. protegens) sites and KaiC phosphorylation patterns change over time; however, in Pseudomonas species, changes in KaiC phosphorylation are driven by the age of the culture rather than by circadian cues as is the case in Cyanobacteria. In this study, through thorough bioinformatic and experimental analyses, we shed light onto the functional diversification and evolution of a unique protein family, diversely involved in bacterial rhythmic interactions with their environment. By so doing, we present a striking example of a protein whose general purpose is conserved in evolution, but whose molecular mechanics and participation in bacterial physiology can change dramatically across species.
ARZIMM: A Novel Analytic Platform for the Inference of Microbial Interactions and Community Stability from Longitudinal Microbiome Study
Authors: He Linchen , Wang Chan , Hu Jiyuan , Gao Zhan , Falcone Emilia , Holland Steven , Blaser Martin J. , Li Huilin 
Published: January 2022

AbstractDynamic changes of microbiome communities may play important roles in human health and diseases. The recent rise in longitudinal microbiome studies calls for statistical methods that can model the temporal dynamic patterns and simultaneously quantify the microbial interactions and community stability. Here, we propose a novel autoregressive zero-inflated mixed-effects model (ARZIMM) to capture the sparse microbial interactions and estimate the community stability. ARZIMM employs a zero-inflated Poisson autoregressive model to model the excessive zero abundances and the non-zero abundances separately, a random effect to investigate the underlining dynamic pattern shared within the group, and a Lasso-type penalty to capture and estimate the sparse microbial interactions. Based on the estimated microbial interaction matrix, we further derive the estimate of community stability, and identify the core dynamic patterns through network inference. Through extensive simulation studies and real data analyses we evaluated ARZIMM in comparison with the other methods.
Multivalent interactions essential for lentiviral integrase function
Authors: Ballandras-Colas Allison , Chivukula Vidya , Gruszka Dominika T. , Shan Zelin , Singh Parmit K. , Pye Valerie E. , McLean Rebecca K. , Bedwell Gregory J. , Li Wen , Nans Andrea , Cook Nicola J. , Fadel Hind J. , Poeschla Eric M. , Griffiths David J. , Vargas Javier , Taylor Ian A. , Lyumkis Dmitry , Yardimci Hasan , Engelman Alan N. , Cherepanov Peter 
Published: January 2022

AbstractA multimer of retroviral integrase (IN) synapses viral DNA ends within a stable intasome nucleoprotein complex for integration into a host cell genome. Reconstitution of the intasome from the maedi-visna virus (MVV), an ovine lentivirus, revealed a large assembly containing sixteen IN subunits (1). Herein, we report cryo-EM structures of the lentiviral intasome prior to engagement of target DNA and following strand transfer, refined at 3.4 and 3.5 Å resolution, respectively. The structures elucidate details of the protein-protein and protein-DNA interfaces involved in lentiviral intasome formation. We show that the homomeric interfaces involved in IN hexadecamer formation and the α-helical configuration of the linker connecting the C-terminal and catalytic core domains are critical for MVV IN strand transfer activity in vitro and for virus infectivity. Single-molecule microscopy in conjunction with photobleaching revealed that the MVV intasome can bind a variable number, up to sixteen molecules, of the lentivirus-specific host factor LEDGF/p75. Concordantly, ablation of endogenous LEDGF/p75 resulted in gross redistribution of MVV integration sites in human and ovine cells. Our data confirm the importance of the expanded architecture observed in cryo-EM studies of lentiviral intasomes and suggest that this organization underlies multivalent interactions with chromatin for integration targeting to active genes.
Convergent recruitment of Amh as the sex determination gene in two lineages of stickleback fish
Authors: Jeffries Daniel L. , Mee Jon , Peichel Catherine L. 
Published: January 2022

AbstractSex chromosomes vary greatly in their age and levels of differentiation across the tree of life. This variation is largely due to the rates of sex chromosome turnover in different lineages; however, we still lack an explanation for why sex chromosomes are so conserved in some lineages (e.g. Mammals, Birds) but so labile in others (e.g. Fish, Amphibians). Here we add to the information on sex chromosomes in stickleback, a valuable model lineage for the study of sex chromosome evolution, by identifying the sex chromosome and a strong candidate for the master sex determination gene in the brook stickleback, Culaea inconstans. Using whole genome sequencing of wild-caught samples and a lab cross, we identify AmhY, a male specific duplication of the gene Amh, as the candidate master sex determination gene. AmhY resides on Chromosome 20 in C. inconstans and is likely a recent duplication, as both AmhY and the sex linked region of Chromosome 20 show little sequence divergence. Importantly, this duplicate AmhY represents the second independent duplication and recruitment of Amh as the sex determination gene in stickleback and the eighth example now known across teleosts. We discuss this convergence in the context of sex chromosome turnovers and the role that the Amh/AmhrII pathway, which is crucial for sex determination, may play in the evolution of sex chromosomes in teleosts.
Marine Bacteria Chemotaxis to Crude Oil Components with Opposing Effects
Authors: Zhao Xueying , Ford Roseanne M. 
Published: January 2022

AbstractMarine microorganisms were critical to hydrocarbon removal from the Gulf of Mexico oil spill. Chemotaxis, a process attracting motile bacteria toward higher hydrocarbon concentrations, can increase biodegradation efficiency. However, crude oil also contains heavy metal ions that repel bacteria. Will bacteria migrate toward hydrocarbons or away from heavy metals? We exposed a marine isolate Halomonas sp. to decane and copper ions in a microfluidic device that maintained a constant concentration gradient across a channel. Bacterial distributions were used to quantify parameters in a mathematical model capturing bacteria motility and chemotaxis. This multi-scale model was adapted from the signal transduction mechanism of E. coli. For Halomonas sp., we used independent receptors for sensing attractant or repellent and chemotaxis parameter values were assessed. Predictions based on the multi-scale model correctly estimated the net attraction or repulsion responses of bacteria to the stimuli mixture. In some cases, the model yielded a stronger repulsion than what was observed experimentally, but still captured the general trends of bacteria distribution. Understanding how marine bacteria integrate information from multiple inputs to yield net migration toward or away from oil will improve predictions of hydrocarbon degradation rates.
T-lymphocyte Tyrosine Hydroxylase Regulates TH17 T-lymphocytes during Repeated Social Defeat Stress
Authors: Elkhatib Safwan K. , Moshfegh Cassandra M. , Watson Gabrielle F. , Case Adam J. 
Published: January 2022

AbstractPosttraumatic stress disorder (PTSD) is a debilitating psychiatric disorder which results in deleterious changes to psychological and physical health. Patients with PTSD are especially susceptible to co-morbid inflammation-driven pathologies, such as autoimmunity, while also demonstrating increased T-helper 17 (TH17) lymphocyte-driven inflammation. While the exact mechanism of this increased inflammation is unknown, overactivity of the sympathetic nervous system is a hallmark of PTSD. Neurotransmitters of the sympathetic nervous system (i.e., catecholamines) can alter T-lymphocyte function, which we have previously demonstrated to be partially mitochondrial redox-mediated. Furthermore, we have previously elucidated that T-lymphocytes generate their own catecholamines, and strong associations exist between tyrosine hydroxylase (TH; the rate-limiting enzyme in the synthesis of catecholamines) and pro-inflammatory interleukin 17A (IL-17A) expression within purified T-lymphocytes in a preclinical rodent model of PTSD. Therefore, we hypothesized that T-lymphocyte-generated catecholamines drive TH17 T-lymphocyte polarization through a mitochondrial superoxide-dependent mechanism during psychological trauma. To test this, T-lymphocyte-specific TH knockout mice (THT-KO) were subjected to repeated social defeat stress (RSDS). RSDS characteristically increased tumor necrosis factor-α (TNFα), IL-6, IL-17A, and IL-22, however, IL-17A and IL-22 (TH17 produced cytokines) were selectively attenuated in circulation and in T-lymphocytes of THT-KO animals. When activated ex vivo, secretion of IL-17A and IL-22 by THT-KO T-lymphocytes was also found to be reduced, but could be partially rescued with supplementation of norepinephrine specifically. Interestingly, THT-KO T-lymphocytes were still able to polarize to TH17 under exogenous polarizing conditions. Last, contrary to our hypothesis, we found RSDS-exposed THT-KO T-lymphocytes still displayed elevated mitochondrial superoxide, suggesting increased mitochondrial superoxide is upstream of T-lymphocyte TH induction, activity, and TH17 regulation. Overall, these data demonstrate TH in T-lymphocytes plays a critical role in RSDS-induced TH17 T-lymphocytes and offer a previously undescribed regulator of inflammation in RSDS.
The IMD and JNK pathways drive the functional integration of the immune and circulatory systems of mosquitoes
Authors: Yan Yan , Sigle Leah T. , Rinker David C. , Estévez-Lao Tania Y. , Capra John A. , Hillyer Julián F. 
Published: January 2022

AbstractThe immune and circulatory systems of animals are functionally integrated. In mammals, the spleen and lymph nodes filter and destroy microbes circulating in the blood and lymph, respectively. In insects, immune cells that surround the heart valves (ostia), called periostial hemocytes, destroy pathogens in the areas of the body that experience the swiftest hemolymph (blood) flow. An infection recruits additional periostial hemocytes, amplifying heart-associated immune responses. Although the structural mechanics of periostial hemocyte aggregation have been defined, the genetic factors that regulate this process remain less understood. Here, we conducted RNAseq in the African malaria mosquito, Anopheles gambiae, and discovered that an infection upregulates multiple components of the IMD and JNK pathways in the heart with periostial hemocytes. This upregulation is greater in the heart with periostial hemocytes than in the circulating hemocytes or the entire abdomen. RNAi-based knockdown then showed that the IMD and JNK pathways drive periostial hemocyte aggregation and alter phagocytosis and melanization on the heart, thereby demonstrating that these pathways regulate the functional integration between the immune and circulatory systems. Understanding how insects fight infection lays the foundation for novel strategies that could protect beneficial insects and harm detrimental ones.
Structural and mechanistic insights into the MCM8/9 helicase complex
Authors: Weng Zhuangfeng , Zheng Jiefu , Zhou Yiyi , Lu Zuer , Wu Yixi , Xu Dongyi , Li Huanhuan , Liang Huanhuan , Liu Yingfang 
Published: January 2022

AbstractMCM8 and MCM9 form a functional helicase complex (MCM8/9) that plays an essential role in DNA homologous recombination repair for DNA double-strand break. However, the structural characterization of MCM8/9 for DNA binding/unwinding remains unclear. Here, we report structures of the MCM8/9 complex using cryo-electron microscopy single particle analysis. The structures reveal that MCM8/9 is arranged into a heterohexamer through a three-fold symmetry axis, creating a central channel that accommodates DNA. Multiple characteristic hairpins from the N-terminal oligosaccharide/oligonucleotide (OB) domains of MCM8/9 protrude into the central channel and serve to unwind the duplex DNA. When activated by HROB, the structure of MCM8/9’s N-tier ring converts its symmetry fromC3toC1with a conformational change that expands the MCM8/9’s trimer interface. Moreover, our structural dynamic analyses revealed that the flexible C-tier ring exhibited rotary motions relative to the N-tier ring, which is required for the unwinding ability of MCM8/9. In summary, our structural and biochemistry study provide a basis for understanding the DNA unwinding mechanism of MCM8/9 helicase in homologous recombination.
Methacrylate-Modified Gold Nanoparticles Enable Non-Invasive Monitoring of Photocrosslinked Hydrogel Scaffolds
Authors: Li Lan , Gil Carmen J. , Finamore Tyler A. , Evans Connor J. , Tomov Martin L. , Ning Liqun , Theus Andrea , Kabboul Gabriella , Serpooshan Vahid , Roeder Ryan K. 
Published: January 2022

AbstractPhotocrosslinked hydrogels, such as methacrylate-modified gelatin (gelMA) and hyaluronic acid (HAMA), are widely utilized as tissue engineering scaffolds and/or drug delivery vehicles, but lack a suitable means for non-invasive, longitudinal monitoring of surgical placement, biodegradation, and drug release. Therefore, we developed a novel photopolymerizable X-ray contrast agent, methacrylate-modified gold nanoparticles (AuMA NPs), to enable covalent-linking to methacrylate-modified hydrogels (gelMA and HAMA) in one-step during photocrosslinking and non-invasive monitoring by X-ray micro-computed tomography (micro-CT). Hydrogels exhibited a linear increase in X-ray attenuation with increased Au NP concentration to enable quantitative imaging by contrast-enhanced micro-CT. The enzymatic and hydrolytic degradation kinetics of gelMA-Au NP hydrogels were longitudinally monitored by micro-CT for up to one monthin vitro, yielding results that were consistent with concurrent measurements by optical spectroscopy and gravimetric analysis. Importantly, AuMA NPs did not disrupt the hydrogel network, rheology, mechanical properties, and hydrolytic stability compared with gelMA alone. GelMA-Au NP hydrogels were thus able to be bioprinted into well-defined three-dimensional architectures supporting endothelial cell viability and growth. Overall, AuMA NPs enabled the preparation of both conventional photopolymerized hydrogels and bioprinted scaffolds with tunable X-ray contrast for noninvasive, longitudinal monitoring of placement, degradation, and NP release by micro-CT.
Detection of SARS-CoV-2 Omicron, Delta, Alpha and Gamma variants using a rapid antigen test
Authors: Salcedo Nol , Nandu Nidhi , Boucau Julie , Herrera Bobby Brooke 
Published: January 2022

AbstractThroughout the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have emerged with different infection and disease dynamics. Testing strategies, including clinical diagnosis, surveillance, and screening, have been deployed to help limit the spread of SARS-CoV-2 variants. Rapid antigen tests, in particular, have been approved for self-testing in many countries and governments are supporting their manufacturing and distribution. However, studies demonstrating the accuracy of rapid antigen tests in detecting SARS-CoV-2 variants, especially the new Omicron variant, are limited. We determined the analytical sensitivity of a CE-marked rapid antigen test against the Omicron, Delta, Alpha and Gamma variants. The rapid antigen test had the most sensitive limit of detection (10 plaque forming units [PFU]/mL) when tested with the Alpha and Gamma variants, followed by the Omicron (100 PFU/mL) and Delta (1,000 PFU/mL) variants. Given the increasing numbers of breakthrough infections and the need to surveil infectiousness, rapid antigen tests are effective public health tools to detect SARS-CoV-2 variants.
Large Registry Based Analysis of Genetic Predisposition to Tuberculosis Identifies Genetic Risk Factors at HLA
Authors: Tervi Anniina , Junna Nella , Broberg Martin , Jones Samuel E. , FinnGen  , Strausz Satu , Kreivi Hanna-Riikka , Heckman Caroline A. , Ollila Hanna M. 
Published: January 2022

AbstractTuberculosis is a significant public health concern resulting in the death of over 1 million individuals each year worldwide. While treatment options and vaccines exist, a substantial number of infections still remain untreated or are caused by treatment resistant strains. Therefore, it is important to identify mechanisms that contribute to risk and prognosis of tuberculosis as this may provide tools to understand disease mechanisms and provide novel treatment options for those with severe infection. Our goal was to identify genetic risk factors that contribute to the risk of tuberculosis and to understand biological mechanisms and causality behind the risk of tuberculosis. A total of 1,895 individuals in the FinnGen study had ICD-based tuberculosis diagnosis. GWAS analysis identified genetic variants with statistically significant association with tuberculosis at the Human leukocyte antigen (HLA) region (p<5e-8) and at rs560595454 in gene INPP5A. Fine mapping the HLA-association provided evidence for one protective haplotype tagged by HLA DQB1*05:01 (p=1.82E-06, OR = 0.81 [CI 95 % 0.74-0.88]), and predisposing alleles tagged by HLA DRB1*13:02 (p=0.00011, OR = 1.35 [CI 95% 1.16-1.57]). Furthermore, genetic correlation analysis showed association with earlier reported risk factors including smoking (p<0.05). Mendelian randomization supported smoking as a risk factor for tuberculosis (inverse-variance weighted p<0.05, OR = 1.83 [CI 95 % 1.15-2.93]) with no significant evidence of pleiotropy. Our findings indicate that specific HLA alleles and INPP5A associate with the risk of tuberculosis. In addition, lifestyle risk factors such as smoking contribute to the risk of developing tuberculosis.
Generation of stable microtubule superstructures by binding of peptide-fused tetrameric proteins to inside and outside
Authors: Inaba Hiroshi , Sueki Yurina , Ichikawa Muneyoshi , Kabir Arif Md. Rashedul , Iwasaki Takashi , Shigematsu Hideki , Kakugo Akira , Sada Kazuki , Matsuura Kazunori 
Published: January 2022

AbstractMicrotubules (MTs) play important roles in biological functions by forming superstructures, such as doublets, triplets, and branched structures, in vivo. Formation of these superstructures by exogenous molecules in vitro will be useful not only for understanding the functions of MTs but also as components of MT-based nanomaterials. Here, we developed a tetrameric fluorescent protein Azami-Green (AG) fused with a His-tag and Tau-derived peptide (TP), TP–AG, which can bind to the inside or outside of MTs depending on the polymerization conditions. The binding of TP–AG to the inside of MTs induced the formation, stabilized, and increased the rigidity of the MTs. The binding of TP–AG to the outside of MTs induced various types of MT superstructures, including doublets, multiplets, and branched structures, by recruiting tubulins to MTs. The formation of motile MT aster structures by TP–AG was also observed. The generation of MT superstructures by these exogenous proteins provides guidelines for the design of MT-based nanomaterials.
PfD123 modulates K13-mediated survival and recovery after artemisinin exposure
Authors: Nötzel Christopher , Kafsack Björn F. C. 
Published: January 2022

ABSTRACTRecent advances in curbing the deadly toll of malaria have been threatened by the emergence of parasites resistant to the front-line antimalarial artemisinin. Resistance is mediated by point-mutations in the parasite protein Kelch13, but the mechanism of resistance is multi-factorial and only partially understood. Resistance-conferring Kelch13 mutations have been shown to lead to low-level activation of the parasite’s integrated stress response (ISR) which has a protective effect against artemisinin through an unclear mechanism. Furthermore, only a subpopulation of resistant parasites ever survives drug exposure, implying an underlying heterogeneity. By applying scRNAseq to the resistance-relevant early ring stage, we found expansion of a subpopulation in Kelch13 mutant parasites that is chiefly characterized by transcription of the putative positive translational regulator D123, while we conversely observed reduced D123 protein levels at the same stage. Analogous inverse changes in D123 expression are produced by experimental activation of the ISR, and genetically manipulating D123 expression modulates sensitivity to artemisinin, establishing it as a stress-responsive gene that contributes to artemisinin resistance in Kelch13-mutant malaria parasites.
Transcription factor FOXM1 specifies the loading of chromatin DNA to extracellular vesicles
Authors: Zhang Yunsheng , Ding Nana , Li Yizhen , Zhao Xiaoyun , Yang Shiping , Fu Ping , Peng Yousong , Cheng Haojie , Ouyang Min , Wang Ruiping , Wang Yu , Liu Hanyun , Chen Yan , Huang Xiaoqin , Yu Li , Tan Yongjun 
Published: January 2022

AbstractExtracellular vesicle DNAs (evDNAs) possess the important diagnostic value for multiple diseases and play roles for horizontally transferring genetic materials among cells. In this study, we have found that transcription factor FOXM1 can mediate the loading of certain chromatin genes or DNA fragments (named FOXM1-chDNAs) to extracellular vesicles (EVs). FOXM1 interacts with LC3 in nucleus and FOXM1-chDNAs (such asDUX4gene and Telomere DNA) are specified by FOXM1 and translocated to cytoplasm. These DNAs are released to EVs through the process of an LC3-involved autophagosome-multivesicular body (MVB) transport. The roles of FOXM1 on loading FOXM1-chDNAs to EVs are further confirmed by DNA-FISH experiments, tracing the translocation of selected chromatin loci with the TetO/TetR-GFP method, and PCR analysis of the DNA samples from MVBs and EVs. Furthermore, disrupting the expression of FOXM1 or the process of autophagosome-MVB transport impairs the loading of FOXM1-chDNAs to EVs. This discovery suggests that transcription factor FOXM1 contributes the constitution of evDNAs from nuclear chromatin, providing the first example to explain how chromatin DNA fragments are specified and loaded to EVs. It also provide a foundation to further explore the roles of evDNAs in biological processes such as the horizontal gene transfer.