bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strand-switching mechanism of Pif1 helicase induced by its collision with a G-quadruplex embedded in dsDNA
Authors: Valle-Orero Jessica , Rieu Martin , Tran Phong Lan Thao , Joubert Alexandra , Allemand Jean-François , Croquette Vincent , Boulé Jean-Baptiste 
Published: January 2022

AbstractG-rich sequences found at multiple sites throughout all genomes may form secondary structures called G-quadruplexes (G4), which act as roadblocks for molecular motors. Among the enzymes thought to process these structures, the Pif1 DNA helicase is considered as an archetypical G4-resolvase and its absence has been linked to G4-related genomic instabilities in yeast. Here we developed a single-molecule assay to observe Pif1 opening a DNA duplex and resolving the G4 in real time. In support of former enzymological studies, we show that the helicase reduces the lifetime of G4 from hours to seconds. However, we observe that in presence of a G4, Pif1 exhibits a strong strand switching behavior, which can lead to Pif1 escaping G4 resolution, depending on the structural context surrounding the substrate. This behavior is also detected in presence of other roadblocks (LNA or RNA). We propose that the efficiency of Pif1 to remove a roadblock (G4 or other) is affected by its strand switching behavior and depends on the context surrounding the obstacle. We discuss how this switching behavior may explain several aspects of Pif1 substrate preference and affect its activity as a G4 resolvase in vivo.
A thalamo-preoptic pathway promoting social touch
Authors: Keller Dávid , Láng Tamás , Cservenák Melinda , Puska Gina , Barna János , Csillag Veronika , Farkas Imre , Zelena Dóra , Dóra Fanni , Barteczko Lara , Usdin Ted B. , Palkovits Miklós , Hasan Mazahir T. , Grinevich Valery , Dobolyi Arpád 
Published: January 2022

SummarySocial touch is an important form of communication, it is still unknown how it is processed. Here, we discovered a functional role for a neuronal pathway projecting from the posterior intralaminar thalamic nucleus (PIL) to the medial preoptic area (MPOA) in controlling social contact. Neurons in the PIL and the MPOA were activated by physical contact between female rodents and also by chemogenetic stimulation of PIL neurons. Chemogenetic stimulation of PIL neurons tagged by social contact experience increased direct physical interactions between familiar female rats without affecting other forms of social behavior. Furthermore, selective stimulation of the PIL-MPOA pathway, and the local activation of PIL terminals within the MPOA, elevated direct social contact between the animals suggesting the role of pathway-specific activated cell assemblies. Neurons projecting from the PIL to the MPOA contain the neuropeptide parathyroid hormone 2 (PTH2). The expression of the peptide was induced by social housing, the presence of PTH2 receptor was identified in MPOA neurons, and local injection of PTH2 increased the firing rate of identified preoptic area GABAergic neurons via the PTH2 receptor suggesting that PTH2 acts as a neurotransmitter in the PIL-MPOA pathway. We also found a homologous PIL to MPOA neuronal pathway in the human brain. Altogether, we discovered a direct thalamo-preoptic pathway, which bypasses the cerebral cortex and controls social touch. This pathway originates in neurons expressing PTH2, a neuropeptide recently shown in fish to respond to the social environment. These observations provide evidence for common evolutionary-conserved PTH2-containing social-touch specific engram circuits.
Cross-kingdom analysis of microbial communities in Cystic Fibrosis and Bronchiectasis
Authors: Cuthbertson L. , Ish-Horowicz J. , Felton I.C. , James P. , Turek E. , Cox M.J. , Loebinger M.R. , Simmonds N.J. , Filippi S. , Moffatt M.F. , Cookson W.O.C. 
Published: January 2022

AbstractBackgroundCystic fibrosis (CF) and non-CF bronchiectasis (BX) are characterised by severe chronic infections. Fungal and bacterial components of infection are both recognized. Little however is known about how fungal and bacterial organisms interact and whether these interactions impact on disease outcomes.MethodsQuantitative PCR and next-generation sequencing of ITS2 and 16S rRNA gene was carried out on 107 patients with CF or BX with clinically defined fungal infection status for all patients. The relationship between fungal and bacterial community composition was extensively explored using: random forest modelling, correlation network analysis, multi-omics factor analysis, and sample-wise clustering, to understand associations both within and between the microbial communities and their relationship to respiratory disease.ResultsRandom forest modelling demonstrated distinct fungal and bacterial communities within CF and BX patients. The inclusion of both kingdoms in the models did not improve discrimination between the two diseases. Within the CF patients, bacterial community composition was independent of clinical fungal disease status. Bacterial and fungal communities did not relate to the presence of CF pulmonary exacerbations (CFPE). Correlation network analysis found intra-kingdom interactions were predominant in the data. Multi-omics factor analysis (MOFA) revealed latent factors corresponding to single kingdoms. Thus, in the bacterial community we identified two distinct clusters characterised by the presence or absence ofPseudomonas-domination. This was independent of fungal community which was characterised by a second set of independent clusters dominated bySaccharomycetes.ConclusionsIn this study we were unable to detect clear evidence of clinically significant inter-kingdom interactions between the bacterial and fungal communities. While further work is required to fully understand microbial interaction within the lung, our data suggests that interkingdom interactions may not be the primary driver of patient outcomes, particularly in the context of fungal infection.
Evaluation of the anti-tumor activities of Sulfonylurea Derivatives
Authors: Lu Sen , Guo Chenchen , Wu Lei , Zheng Zhanying , Hua Xuewen , Wei Wei , Zhang Wenqin , Zhou Shaa , Li Ruo , Zhou Sha 
Published: January 2022

AbstractThis study prepared 25 sulfonylurea compounds to evaluate anti-tumor activity. Through experimental investigations in MDA-MB-231 and MCF-7, i.e., cell lines of breast carcinoma of human, we have concluded that some compounds can significantly suppress breast carcinoma cells from growing and proliferating. Moreover, the compound M’s inhibitory effect on cells of breast carcinoma is concentration-dependent under a certain treatment time; and the inhibitory effect of the compound M on breast carcinoma cells is time-dependent under a certain concentration. In addition, we also found that the compound M can effectively suppress cells of breast carcinoma from migration and independent survival. The results can show the prospect of research and development of new breast carcinoma treatment drug.
Phylogenetic and protein prediction analysis reveals the taxonomically diverse distribution of virulence factors in the Bacillus cereus group
Authors: Zhang Ming , Liu Jun , Yin Zhenzhen , Zhang Li 
Published: January 2022

AbstractBacillus cereus is a food contaminant with widely varying enterotoxic potential of its virulence proteins. In this article, phylogenetic analysis of the whole-genome amino acid sequences of 41 strains, evolutionary distance calculation of the amino acid sequences of the virulence genes, and functional and structural prediction of the virulence proteins were performed to reveal the taxonomically diverse distribution of virulence factors. The genome evolution of the strains showed a clustering trend based on the coding virulence genes. The strains of B. cereus have evolved into non-toxic risk and toxic risk clusters with medium-high- and medium-low-risk clusters. The distances of evolutionary transfer relative to housekeeping genes of incomplete virulence genes were greater than those of complete virulence genes, and the distance values of HblACD were higher than those of nheABC and CytK among the complete virulence genes. Cytoplasmic localization was impossible for all the virulence proteins, and NheB, NheC, Hbl-B, and Hbl-L1 were extracellular according to predictive analysis. Nhe and Hbl proteins except CytK had similar spatial structures. The predicted structures of Nhe and Hbl mainly showed ‘head’ and ‘tail’ domains. The ‘head’ of NheA and Hbl-B, including two α-helices separated by β-tongue strands, might play a special role in Nhe trimers and Hbl trimers, respectively. The ‘cap’ of CytK, which includes two ‘latches’ with many β-sheets, formed a β-barrel structure with pores, and a ‘rim’ balanced the structure. The evolution of B. cereus strains showed a clustering tendency based on the coding virulence genes, and the complete virulence-gene operon combination had higher relative genetic stability. The beta-tongue or latch associated with β-sheet folding might play an important role in the binding of virulence structures and pore-forming toxins in B. cereus.
Performance evaluation of three DNA sample tracking tools in a whole exome sequencing workflow
Authors: Wils Gertjan , Helsmoortel Céline , Volders Pieter-Jan , Vereecke Inge , Milazzo Mauro , Vandesompele Jo , Coppieters Frauke , De Leeneer Kim , Lefever Steve 
Published: January 2022

AbstractIntroductionNext-generation sequencing applications are becoming indispensable for clinical diagnostics. These experiments require numerous wet and dry lab steps, each one increasing the probability of a sample swap or contamination. Therefore, an identity confirmation at the end of the process is recommended to ensure the right data is used for each patient.MethodsWe tested three commercially available, SNP based sample tracking kits in a diagnostic workflow to evaluate their ease of use and performance. The coverage uniformity, on-target specificity, sample identification and genotyping performance were determined to assess the reliability and the cost-effectiveness of each kit.Results and discussionHands-on time and manual steps are almost identical for the kits from pxlence and Nimagen. The Swift kit has an extra purification step, making it the longest and most demanding protocol. Furthermore, the Swift kit failed to correctly genotype 26 out of the 46 samples. The Nimagen kit identified all but one sample and the pxlence kit unambiguously identified all samples, making it the most reliable and robust kit of this evaluation. The Nimagen kit showed poor on-target mapping rates, resulting in deeper sequencing needs and higher sequencing costs compared to the other two kits. Our conclusion is that the Human Sample ID kit from pxlence is the most cost-effective of the three tested tools for DNA sample tracking and identification.Key pointsKits from pxlence and Nimagen are easy to use.Unambiguous identification of all samples possible with the pxlence kit.Only 20 out of 46 samples were correctly identified with the Swift kit.Poor on-target rates for the Nimagen kit results in higher sequencing costs.
SARS-CoV-2 Triggers Complement Activation through Interactions with Heparan Sulfate
Authors: Lo Martin W. , Amarilla Alberto A. , Lee John D. , Albornoz Eduardo A. , Modhiran Naphak , Clark Richard J. , Ferro Vito , Chhabra Mohit , Khromykh Alexander A. , Watterson Daniel , Woodruff Trent M. 
Published: January 2022

ABSTRACTThe complement system has been heavily implicated in severe COVID-19 with clinical studies revealing widespread gene induction, deposition, and activation. However, the mechanism by which complement is activated in this disease remains incompletely understood. Herein we examined the relationship between SARS-CoV-2 and complement by inoculating the virus in lepirudin-anticoagulated human blood. This caused progressive C5a production after 30 minutes and 24 hours, which was blocked entirely by inhibitors for factor B, C3, C5, and heparan sulfate. However, this phenomenon could not be replicated in cell-free plasma, highlighting the requirement for cell surface deposition of complement and interactions with heparan sulfate. Additional functional analysis revealed that complement-dependent granulocyte and monocyte activation was delayed. Indeed, C5aR1 internalisation and CD11b upregulation on these cells only occurred after 24 hours. Thus, SARS-CoV-2 is a non-canonical complement activator that triggers the alternative pathway through interactions with heparan sulfate.
Microscopic and ultramicroscopic anatomical characteristics of root nodules in Podocarpus macrophyllus during development
Authors: Zhu Li-Qiong , Chen Hui-Xin , Zhao Li-Jun , Jiang Wei-Xin 
Published: January 2022

AbstractTo understand the morphological and structural characteristics of root nodules in Podocarpus macrophyllus and their development, this study prepared P. macrophyllus root nodule samples at the young, mature, and senescent stages. Optical microscopy and transmission electron microscopy (SEM) revealed that new nodules can be formed on roots and senescent nodules; new nodules formed on the roots are nearly spherical and have an internal structure similar to finite nodules; new nodules on senescent nodules are formed by extension and differentiation of the vascular cylinder of the original nodules; and these new nodules are nested at the base of the original nodules, which create growth space for new nodules by dissociating the cortical tissue; clusters of nodules are formed after extensive accumulation, and the growth pattern is similar to that of infinite nodules; the symbiotic bacteria of P. macrophyllus root nodules mainly invade from the epidermal intercellular space of the roots and migrate along the intercellular space of the nodule cortex; infected nodule cortex cells have a well-developed inner membrane system and enlarged and loose nuclei; and unique Frankia vesicles, and rhizobia cysts, and bacteriophages can all develop. Compared with common leguminous and nonleguminous plant nodules, P. macrophyllus root nodules are more complex in morphology, structure and composition. From the perspective of plant system evolution, the rhizobium nodules in leguminous angiosperms and Frankia nodules in nonleguminous angiosperms are most likely two branches derived from the nodules in gymnosperms, such as P. macrophyllus. The conclusions of this study can provide a theoretical basis for the developmental biology of P. macrophyllus root nodules and the evolutionary pattern of plant symbionts.HighlightsWe discuss from the perspective of cell developmental biology, the rhizobium nodules in leguminous angiosperms and Frankia nodules in nonleguminous angiosperms are most likely two branches derived from the nodules in gymnosperms, such as Podocarpus macrophyllus.
A new class of protein sensor links spirochete pleomorphism, persistence, and chemotaxis
Authors: Muok A.R. , Kurniyati K. , Ortega D.R. , Olsthoorn F.A. , Mabrouk A. Sidi , Li C. , Briegel A. 
Published: January 2022

AbstractPathogenic spirochetes can alter their morphologies and behaviors to infect and survive within their hosts. Previous reports demonstrate that the formation of so-called ‘round bodies’ and biofilms, and chemotaxis are involved in spirochete pathogenesis. Here, in the spirocheteTreponema denticola, we report a direct link between these cellular states that involves a new class of protein sensor (CheWS) with hitherto unclear function. Using cryo-EM methods, protein modeling, bioinformatics, genetics methods, and behavioral assays we demonstrate that spirochetes regulate these behaviors in response to the small molecule s-adenosylmethionine (SAM) via a SAM sensor that is anchored to chemotaxis arrays. CheWS influences chemotaxis, biofilm and round body formation under nonstressed conditions by a novel sporulation-like mechanism. Taken together, we establish an improved model for round body formation, we discovered a direct link between this SAM sensor and changes in cellular states, as well as characterized a new sensor class involved in chemotaxis.
In situ structure and priming mechanism of the rhoptry secretion system in Plasmodium revealed by cryo-electron tomography
Authors: Martinez Matthew , Chen William David , Cova Marta Mendonça , Molnár Petra , Mageswaran Shrawan Kumar , Guérin Amandine , Odom John Audrey R. , Lebrun Maryse , Chang Yi-Wei 
Published: January 2022

AbstractApicomplexan parasites secrete the contents of rhoptries into host cells to permit their invasion and establishment of an infectious niche. The rhoptry secretory apparatus (RSA), which is critical for rhoptry secretion, was recently discovered in Toxoplasma and Cryptosporidium. It is positioned at the cell apex and associates with an enigmatic apical vesicle (AV), which docks one or two rhoptries at the site of exocytosis. The interplay among the rhoptries, the AV, and the parasite plasma membrane for secretion remains unclear. Moreover, it is unknown if a similar machinery exists in the deadly malaria parasite Plasmodium falciparum. In this study, we use in situ cryo-electron tomography to investigate the rhoptry secretion system in P. falciparum merozoites. We identify the presence of an RSA at the cell apex and a morphologically distinct AV docking the tips of the two rhoptries to the RSA. We also discover two new organizations: one in which the AV is absent with one of the two rhoptry tips docks directly to the RSA, and a second in which the two rhoptries fuse together and the common tip docks directly to the RSA. Interestingly, rhoptries among the three states show no significant difference in luminal volume and density, suggesting that the exocytosis of rhoptry contents has not yet occurred, and that these different organizations likely represent sequential states leading to secretion. Using subtomogram averaging, we reveal different conformations of the RSA structure corresponding to each state, including the opening of a gate-like density in the rhoptry-fused state. These conformational changes of the RSA uncover structural details of a priming process for major rhoptry secretion, which likely occur after initial interaction with a red blood cell. Our results highlight a previously unknown step in the process of rhoptry secretion and indicate a regulatory role for the conserved apical vesicle in host invasion by apicomplexan parasites.
Clinically Relevant Pathogens on Surfaces Display Differences in Survival and Transcriptomic Response in Relation to Probiotic and Traditional Cleaning Strategies
Authors: Hu Jinglin , Shuai Weitao , Sumner Jack T. , Moghadam Anahid A. , Hartmann Erica M. 
Published: January 2022

AbstractIndoor surfaces are paradoxically presumed to be both colonized by pathogens, necessitating disinfection, and “microbial wastelands.” In these resource-poor, dry environments, competition and decay are thought to be important drivers of microbial community composition. However, the relative contributions of these two processes have not been specifically evaluated. To bridge this knowledge gap, we used microcosms to specifically evaluate whether interspecies interactions occur on surfaces. We combined transcriptomics and traditional microbiology techniques to investigate whether competition occurred between two clinically important pathogens, Acinetobacter baumannii and Klebsiella pneumoniae, and a probiotic cleaner containing a consortium of Bacillus species. Probiotic cleaning seeks to take advantage of ecological principles such as competitive exclusion, thus using benign microorganisms to inhibit viable pathogens, but there is limited evidence that competitive exclusion in fact occurs in environments of interest (i.e., indoor surfaces). Our results indicate that competition in this setting has a negligible impact on community composition but may influence the functions expressed by active organisms. Although Bacillus spp. remained viable on surfaces for an extended period of time after application, viable colony forming units (CFUs) of A. baumannii recovered following exposure to a chemical-based detergent with and without Bacillus spp. showed no statistical difference. Similarly, for K. pneumoniae, there were small statistical differences in CFUs between cleaning scenarios with or without Bacillus spp. in the chemical-based detergent. The transcriptome of A. baumannii with and without Bacillus spp. exposure shared a high degree of similarity in overall gene expression, but the transcriptome of K. pneumoniae differed in overall gene expression, including reduced response in genes related to antimicrobial resistance. Together, these results highlight the need to fully understand the underlying biological and ecological mechanisms for community assembly and function on indoor surfaces, as well as having practical implications for cleaning and disinfection strategies for infection prevention.
The RNA-Binding Protein SAM68 regulates cardiomyocyte differentiation by enhancing Gata4 translation
Authors: Dasti Alessandro , Antonelli Maria Carla , Segura Magdalena Arnal , Armaos Alexandros , Bonnin Sarah , Graf Thomas , Paronetto Maria Paola , Tian Tian V , Bechara Elias , Tartaglia Gian Gaetano 
Published: January 2022

AbstractThe signal transduction and activation of RNA (STAR) family is composed of RNA-binding proteins (RBPs) that play a central role in mammalian development. Nonetheless, the functions and modes of action that STAR proteins have in lineage specification are still poorly understood. Here, we characterized the role of STAR proteins SAM68 and QUAKING (QKI) in pluripotency and differentiation by performing their depletion through CRISPR-Cas9 in mouse embryonic stem cells (mESCs). Combining RNA-sequencing, ribosome profiling and advanced computational predictions, we found that both SAM68 and QKI regulate the mESCs self-renewal and are indispensable for cardiomyocyte differentiation. At the molecular level, we discovered that SAM68 and QKI antagonistically control the expression of cardiogenic factors. Our calculations indicated that SAM68, unlike QKI, binds the cardiogenic-specific transcription factor Gata4 in a region spanning nucleotides 500 to 1000 of the mRNA corresponding to part of the 5’ untranslated region and the first exon. We validated the predictions by electrophoretic mobility shift assay and RNA immunoprecipitation showing that SAM68 controls the translation of Gata4 during mESCs differentiation towards the cardiomyocyte lineage.
GenomeBits insight into omicron and delta variants of coronavirus pathogen
Authors: Canessa Enrique , Tenze Livio 
Published: January 2022

AbstractWe apply the new GenomeBits method to uncover underlying genomic features of omicron and delta coronavirus variants. This is a statistical algorithm whose salient feature is to map the nucleotide bases into a finite alternating (±) sum series of distributed terms of binary (0,1) indicators. We show how by this method, distinctive signals can be uncovered out of the intrinsic data organization of amino acid progressions along their base positions. Results reveal a sort of ‘ordered’ (or constant) to ‘disordered’ (or peaked) transition around the coronavirus S-spike protein region. Together with our previous results for past variants of coronavirus: Alpha, Beta, Gamma, Epsilon and Eta, we conclude that the mapping into GenomeBits strands of omicron and delta variants can help to characterize mutant pathogens.