bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antimycobacterial potential of Mycobacteriophage under disease-mimicking conditions
Authors: Kalapala Yeswanth Chakravarthy , Sharma Pallavi Raj , Agarwal Rachit 
Published: May 2020

AbstractAntibiotic resistance continues to be a major global health risk with an increase in multi-drug resistant infections seen across nearly all bacterial diseases. Mycobacterial infections such as Tuberculosis (TB) and Non-Tuberculosis infections have seen a significant increase in the incidence of multi-drug resistant and extensively drug-resistant infections. With this increase in drug-resistant Mycobacteria, mycobacteriophage therapy offers a promising alternative. However, a comprehensive study on the infection dynamics of mycobacteriophage against their host bacteria and the evolution of bacteriophage (phage) resistance in the bacteria remains elusive. We aim to study the infection dynamics of a phage cocktail against Mycobacteria under various pathophysiological conditions such as low pH, low growth rate and hypoxia. We show that mycobacteriophages are effective againstM. smegmatisunder various conditions and the phage cocktail prevents emergence of resistance for long durations. Although the phages are able to amplify after infection, the initial multiplicity of infection plays an important role in reducing the bacterial growth and prolonging efficacy. Mycobacteriophages are effective against antibiotic-resistant strains of Mycobacterium and show synergy with antibiotics such as rifampicin and isoniazid. Finally, we also show that mycobacteriophages are efficient againstM. tuberculosisboth under lag and log phase for several weeks. These findings have important implications for developing phage therapy for Mycobacterium.
Integrated information structure collapses with anesthetic loss of conscious arousal inDrosophila melanogaster
Authors: Leung Angus , Cohen Dror , van Swinderen Bruno , Tsuchiya Naotsugu 
Published: May 2020

AbstractThe physical basis of consciousness remains one of the most elusive concepts in current science. One influential conjecture is that consciousness is to do with some form of causality, measurable through information. The integrated information theory of consciousness (IIT) proposes that conscious experience, filled with rich and specific content, corresponds directly to a hierarchically organised, irreducible pattern of causal interactions; i.e. an integrated informational structure among elements of a system. Here, we tested this conjecture in a simple biological system (fruit flies), estimating the information structure of the system during wakefulness and general anesthesia. Consistent with this conjecture, we found that integrated interactions among populations of neurons during wakefulness collapsed to isolated clusters of interactions during anesthesia. We used classification analysis to quantify the accuracy of discrimination between wakeful and anesthetised states, and found that informational structures inferred conscious states with greater accuracy than a scalar summary of the structure, a measure which is generally championed as the main measure of IIT. In stark contrast to a view which assumes feedforward architecture for insect brains, especially fly visual systems, we found rich information structures, which cannot arise from purely feedforward systems, occurred across the fly brain. Further, these information structures collapsed uniformly across the brain during anesthesia. Our results speak to the potential utility of the novel concept of an “informational structure” as a measure for level of consciousness, above and beyond simple scalar values.Author summaryThe physical basis of consciousness remains elusive. Efforts to measure consciousness have generally been restricted to simple, scalar quantities which summarise the complexity of a system, inspired by integrated information theory, which links a multi-dimensional, informational structure to the contents of experience in a system. Due to the complexity of the definition of the structure, assessment of its utility as a measure of conscious arousal in a system has largely been ignored. In this manuscript we evaluate the utility of such an information structure in measuring the level of arousal in the fruit fly. Our results indicate that this structure can be more informative about the level of arousal in a system than even the single-value summary proposed by the theory itself. These results may push consciousness research towards the notion of multi-dimensional informational structures, instead of traditional scalar summaries.
MINPP1prevents intracellular accumulation of the cation chelator inositol hexakisphosphate and is mutated in Pontocerebellar Hypoplasia
Authors: Ucuncu Ekin , Rajamani Karthyayani , Wilson Miranda S.C. , Medina-Cano Daniel , Altin Nami , David Pierre , Barcia Giulia , Lefort Nathalie , Vasilache-Dangles Marie-Thérèse , Pitelet Gaële , Lorino Elsa , Rabasse Nathalie , Bieth Eric , Zaki Maha S. , Topcu Meral , Sonmez Fatma Mujgan , Musaev Damir , Stanley Valentina , Bole-Feysot Christine , Nitschké Patrick , Munnich Arnold , Bahi-Buisson Nadia , Fossoud Catherine , Giuliano Fabienne , Colleaux Laurence , Burglen Lydie , Gleeson Joseph G. , Boddaert Nathalie , Saiardi Adolfo , Cantagrel Vincent 
Published: May 2020

ABSTRACTInositol polyphosphates are vital metabolic and secondary messengers, involved in diverse cellular functions. Therefore, tight regulation of inositol polyphosphate metabolism is essential for proper cell physiology. Here, we describe an early-onset neurodegenerative syndrome caused by loss-of-function mutations in themultiple inositol polyphosphate phosphatase 1gene (MINPP1). Patients were found to have a distinct type of Pontocerebellar Hypoplasia with typical basal ganglia involvement on neuroimaging. We found that patient-derived and genome editedMINPP1-/-induced pluripotent stem cells (iPSCs) are not able to differentiate efficiently into neurons. MINPP1 deficiency results in an intracellular imbalance of the inositol polyphosphate metabolism. This metabolic defect is characterized by an accumulation of highly phosphorylated inositols, mostly inositol hexakiphosphate (IP6), detected in HEK293, fibroblasts, iPSCs and differentiating neurons lacking MINPP1. In mutant cells, higher IP6level is expected to be associated with an increased chelation of intracellular cations, such as iron or calcium, resulting in decreased levels of available ions. These data suggest the involvement of IP6-mediated chelation on Pontocerebellar Hypoplasia disease pathology and thereby highlight the critical role of MINPP1 in the regulation of human brain development and homeostasis.
Differential SP1 Interactions in SV40 Chromatin from Virions and Minichromosomes
Authors: Rowbotham Kincaid , Haugen Jacob , Milavetz Barry 
Published: May 2020

ABSTRACTSP1 binding in SV40 chromatin in vitro and in vivo was characterized in order to better understand its role during the initiation of early transcription. We observed that chromatin from disrupted virions, but not minichromosomes, was efficiently bound by HIS-tagged SP1in vitro, while the opposite was true for the presence of endogenous SP1 introduced in vivo. Using ChIP-Seq to compare the location of SP1 to nucleosomes carrying modified histones, we found that SP1 could occupy its whole binding site in virion chromatin but only the early side of its binding site in most of the minichromosomes carrying modified histones due to the presence of overlapping nucleosomes. The results suggest that during the initiation of an SV40 infection, SP1 binds to an open region in SV40 virion chromatin but quickly triggers chromatin reorganization and its own removal by a hit and run mechanism.
Senile plaques in Alzheimer’s disease arise from Aβ and Cathepsin D-enriched amyloidogenic mixtures out of intravascular hemolysis and Charcot-Bouchard aneurysm-related vascular degeneration
Authors: Fu Hualin , Li Jilong , Du Peng , Jin Weilin , Gao Guo , Cui Daxiang 
Published: May 2020

AbstractThe mechanism governing senile plaque generation in Alzheimer’s disease (AD) remains intensively debated. We analyzed AD brain tissues with histochemistry, immunohistochemistry and fluorescence imaging. We found little co-expression between neural markers and plaque Aβ while abundant co-expression between blood or plasma markers such as HBA, HbA1C, Hemin, ApoE and plaque Aβ. The cores of dense-core plaques were structured with vascular proteins and glial processes at the periphery and blood metabolites in the center. Senile plaques additionally co-localized with a characteristic Hoechst-staining-independent blue autofluorescence, likely also derived from red blood cells. Aβ interacts with hemoglobin in anin vitroassay and also at single cell levels in red blood cellsin vivo, showing as dots, stripes or diffusive patterns with its intensity correlated with coagulation, the elevation of calcium and blue autofluorescence. Interaction between Aβ and ApoE in the blood stream forms vascular amyloid plaques that restrict red blood cell passage. The interaction of Aβ and red blood cells associates with multiple blood and vascular defects besides CAA, including increased perivascular space, microaneurysm, intravascular hemolysis and vascular calcification. Senile plaque formation was intrinsically linked to vascular degeneration as shown by LRP1, ColIV and ACTA2 immunostaining. Aβ staining also overlapped with Cathepsin D expression in intravascular hemolysis, CAA, microaneurysm and senile plaques in AD brain tissues. Microaneurysms with chronic hemolysis were identified as important sites of amyloid formation besides CAA and intravascular hemolysis. In summary, our data suggested that senile plaques arise from Aβ and Cathepsin D-enriched amyloid mixtures out of intravascular hemolysis and Charcot-Bouchard aneurysm-related vascular degeneration. In addition, hemoglobin could be a primary physiological target of Aβ.
Detection of cerebral tauopathy in P301L mice using high-resolution large-field multifocal illumination fluorescence microscopy
Authors: Ni Ruiqing , Chen Zhenyue , Gerez Juan A. , Shi Gloria , Zhou Quanyu , Riek Roland , Nilsson K. Peter R. , Razansky Daniel , Klohs Jan 
Published: May 2020

AbstractCurrent intravital microscopy techniques visualize tauopathy with high-resolution, but have a small field-of-view and depth-of-focus. Herein, we report a transcranial detection of tauopathy over the entire cortex of P301L tauopathy mice using large-field multifocal illumination (LMI) fluorescence microscopy technique and luminescent conjugated oligothiophenes.In vitroassays revealed that fluorescent ligand h-FTAA is optimal forin vivotau imaging, which was confirmed by observing elevated probe retention in the cortex of P301L mice compared to non-transgenic littermates. Immunohistochemical staining further verified the specificity of h-FTAA to detect tauopathy in P301L mice. The new imaging platform can be leveraged in pre-clinical mechanistic studies of tau spreading and clearance as well as longitudinal monitoring of tau targeting therapeutics.
Distinct activities of bacterial condensins for chromosome management inPseudomonas aeruginosa
Authors: Lioy Virginia S. , Junier Ivan , Lagage Valentine , Vallet Isabelle , Boccard Frédéric 
Published: May 2020

AbstractBacteria encompass three types of structurally related SMC complexes referred to as condensins. Smc-ScpAB is present in most bacteria while MukBEF is found in enterobacteria and MksBEF is scattered over the phylogenic tree. The contributions of these condensins to chromosome management were characterized inPseudomonas aeruginosathat carries both Smc-ScpAB and MksBEF. In this bacterium, SMC-ScpAB controls chromosome disposition by juxtaposing chromosome arms. In contrast, MksBEF is critical for chromosome segregation in the absence of the main segregation system and affects the higher-order architecture of the chromosome by promoting DNA contacts in the megabase range. Strikingly, our results reveal a prevalence of Smc-ScpAB over MksBEF involving a coordination of their activities with the DNA replication process. They also show thatE. coliMukBEF can substitute for MksBEF inP. aeruginosawhile prevailing over Smc-ScpAB. Altogether, our results reveal a hierarchy between activities of bacterial condensins on the same chromosome.
Effects of TMS over the anterior intraparietal area on anticipatory fingertip force scaling and the size-weight illusion
Authors: van Polanen Vonne , Buckingham Gavin , Davare Marco 
Published: May 2020

ABSTRACTIn skilled object lifting, fingertip forces need to be carefully scaled to object weight, which can be inferred from object properties, such as size or material. This anticipatory force scaling ensures smooth and efficient lifting movements. However, even with accurate motor plans, weight perception can still be biased. In the size-weight illusion, objects of different size but equal weight are perceived to differ in heaviness, with the small object perceived to be heavier than the large object. The neural underpinnings of the size-weight illusion and anticipatory force scaling to object size are largely unknown. In this study, we hypothesized a possible role of the anterior intraparietal cortex (aIPS) in predictive force scaling and the size-weight illusion, which we investigated by applying continuous theta burst stimulation (cTBS) prior to participants lifting objects designed to induce the size-weight illusion. Participants received cTBS over aIPS, the primary motor cortex (control area), or sham stimulation. We found no evidence that aIPS stimulation affected the size-weight illusion. Small effects were, however, found on anticipatory force scaling, where grip force was less tuned to object size during initial lifts. These findings suggest that, while aIPS might be peripherally involved in sensorimotor prediction, other brain areas underpin the processes that mediate the size-weight illusion.
Expression of Separate Foreign Proteins from the Rotavirus NSP3 Genome Segment Using a Translational 2A Stop-Restart Element
Authors: Philip Asha A. , Patton John T. 
Published: May 2020

AbstractThe segmented 18.5-kB dsRNA genome of rotavirus expresses 6 structural and 6 nonstructural proteins. We investigated the possibility of using the recently-developed plasmid-based rotavirus reverse genetics (RG) system to generate recombinant viruses that express a separate foreign protein, in addition to the 12 viral proteins. To address this, we replaced the NSP3 open-reading-frame (ORF) of the segment 7 (pT7/NSP3) transcription vector used in the RG system with an ORF encoding NSP3 fused to a fluorescent reporter protein (i.e., UnaG, mRuby, mKate, or TagBFP). Inserted at the fusion junction was a teschovirus 2A-like self-cleaving element designed to direct the separate expression of NSP3 and the fluorescent protein. Recombinant rotaviruses made with the modified pT7/NSP3 vectors were well growing, generally genetically stable, and expressed NSP3 and a separate fluorescent protein detectable by live cell imaging. NSP3 made by the recombinant viruses was functional, inducing nuclear accumulation of cellular poly(A)-binding protein. Further modification of the NSP3 ORF showed that it was possible to generate recombinant viruses encoding 2 foreign proteins (mRuby and UnaG) in addition to NSP3. Our results demonstrate that, through modification of segment 7, the rotavirus genome can be increased in size to at least 19.8 kB and can be used to produce recombinant rotaviruses expressing a full complement of viral proteins and multiple foreign proteins. The generation of recombinant rotaviruses expressing fluorescent proteins will be valuable for the study of rotavirus replication and pathogenesis by live cell imagining and suggest that rotaviruses may prove useful as expression vectors.ImportanceRotaviruses are a major cause of severe gastroenteritis in infants and young children. Recently, a highly efficient reverse genetics system was developed that allows genetic manipulation of the rotavirus segmented double-stranded RNA genome. Using the reverse genetics system, we show that it is possible to modify one of the rotavirus genome segments (segment 7) such that virus gains the capacity to express a separate foreign protein, in addition to the full complement of viral proteins. Through this approach, we have generated wildtype-like rotaviruses that express various fluorescent reporter proteins, including UnaG (green), mRuby (far red), mKate (red), and TagBFP (blue). Such strains will be of value in probing rotavirus biology and pathogenesis by live-cell imagining techniques. Notably, our work indicates that the rotavirus genome is remarkably flexible and able to accommodate significant amounts of foreign RNA sequence, raising the possibility of using the virus as vaccine expression vector.
Repurposing Ribo-Seq to provide insights into structured RNAs
Authors: Fremin Brayon J. , Bhatt Ami S. 
Published: May 2020

AbstractRibosome profiling (Ribo-Seq) is a powerful method to study translation in bacteria. However, this method can enrich RNAs that are not bound by ribosomes, but rather, are protected from degradation in another way. For example, Escherichia coli Ribo-Seq libraries also capture reads from most non-coding RNAs (ncRNAs). These fragments of ncRNAs pass all size selection steps of the Ribo-Seq protocol and survive hours of MNase treatment, presumably without protection from the ribosome or other macromolecules or proteins. Since bacterial ribosome profiling does not directly isolate ribosomes, but instead uses broad size range cutoffs to fractionate actively translated RNAs, it is understandable that some ncRNAs are retained after size selection. However, how these ‘contaminants’ survive MNase treatment is unclear. Through analyzing metaRibo-Seq reads across ssrS, a well established structured RNA in E. coli, and structured direct repeats from Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) arrays in Ruminococcus lactaris, we observed that these RNAs are protected from MNase treatment by virtue of their secondary structure. Therefore, large volumes of data previously discarded as contaminants in bacterial Ribo-Seq experiments can, in fact, be used to gain information regarding the in vivo secondary structure of ncRNAs, providing unique insight into their native functional structures.ImportanceWe observe that ‘contaminant’ signals in bacterial Ribo-Seq experiments that are often disregarded and discarded, in fact, strongly overlap with structured regions of ncRNAs. Structured ncRNAs are pivotal mediators of bioregulation in bacteria and their functions are often reliant on their specific structures. We present an approach to access important RNA structural information through merely repurposing ‘contaminant’ signals in bacterial Ribo-Seq experiments. This powerful approach enables us to partially resolve RNA structures, identify novel structured RNAs, and elucidate RNA structure-function relationships in bacteria at a large-scale and in vivo.
Combined effect of biological and physical stress on artificial production of agarwood oleoresin inAquilaria malaccensis
Authors: Chhipa Hemraj , Kaushik Nutan 
Published: May 2020

AbstractAgarwood is the most expensive wood of the world and highly demanded wood in perfumery industry and ritual ceremonies of various religions. Agarwood is the infectious wood part ofAquilariatree. Naturally, production of agarwood inAquilariatakes 10-20 years of time and it can develop only in 1-2% ofAquilariatrees. Different types of biological, chemical and physical methods have been developed for artificial production of agarwood to fulfil the rising demand of the market. In the current article, we tried to explore combined effect of physical and biological stress in the form of stick method to improve agarwood production inAquilaria malaccensisand compared it with well-known artificial fungal infection syringe method. Total 21 fungal strains were applied alone (syringe method) and with bamboo sticks (stick method). We found maximum infection occurred in stick method by fungiPenicillium polonicumAQGGR1.1 with 10 cm infection length. Artificial induction of marker compounds of agarwood, benzyl acetone and anisyl acetone were measured mostly in stick method, induced by 71.4% fungal strains grown on bamboo sticks, while alone only 42.9% fungi can induced in syringe method.Penicillium aethiopicumAQGGR1.2 found highly agarwood oleoresin inducing fungus in stick method and shown high potential agent in stick method for artificial production of agarwood.
Human IgG neutralizing monoclonal antibodies block SARS-CoV-2 infection
Authors: Wan Jinkai , Xing Shenghui , Ding Longfei , Wang Yongheng , Zhu Dandan , Rong Bowen , Wang Siqing , Chen Kun , He Chenxi , Yuan Songhua , Qiu Chengli , Zhao Chen , Zhang Xiaoyan , Wang Xiangxi , Lu Yanan , Xu Jianqing , Lan Fei 
Published: May 2020

AbstractThe coronavirus induced disease 19 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a worldwide threat to human lives, and neutralizing antibodies present a great therapeutic potential in curing affected patients. We purified more than one thousand memory B cells specific to SARS-CoV-2 S1 or RBD (receptor binding domain) antigens from 11 convalescent COVID-19 patients, and a total of 729 naturally paired heavy and light chain fragments were obtained by single B cell cloning technology. Among these, 178 recombinant monoclonal antibodies were tested positive for antigen binding, and the top 13 binders with Kdbelow 0.5 nM are all RBD binders. Importantly, all these 13 antibodies could block pseudoviral entry into HEK293T cells overexpressing ACE2, with the best ones showing IC50s around 2-3 nM. We further identified 8 neutralizing antibodies against authentic virus with IC50s within 10 nM. Among these, 414-1 blocked authentic viral entry at IC50 of 1.75 nM and in combination with 105-38 could achieve IC50 as low as 0.45 nM. Meanwhile, we also found that 3 antibodies could cross-react with the SARS-CoV spike protein. Altogether, our study provided a panel of potent human neutralizing antibodies for COVID19 as therapeutics candidates for further development.
In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy
Authors: Uwizeye Clarisse , Decelle Johan , Jouneau Pierre-Henri , Gallet Benoit , Keck Jean-Baptiste , Moriscot Christine , Chevalier Fabien , Schieber Nicole L. , Templin Rachel , Curien Gilles , Schwab Yannick , Schoehn Guy , Zeeman Samuel C. , Falconet Denis , Finazzi Giovanni 
Published: May 2020

AbstractPhytoplankton is a minor fraction of the global biomass playing a major role in primary production and climate. Despite improved understanding of phytoplankton diversity and genomics, we lack nanoscale subcellular imaging approaches to understand their physiology and cell biology. Here, we present a complete Focused Ion Beam - Scanning Electron Microscopy (FIB-SEM) workflow (from sample preparation to image processing) to generate nanometric 3D phytoplankton models. Tomograms of entire cells, representatives of six ecologically-successful phytoplankton unicellular eukaryotes, were used for quantitative morphometric analysis. Besides lineage-specific cellular architectures, we observed common features related to cellular energy management:i)conserved cell-volume fractions occupied by the different organelles;ii)consistent plastid-mitochondria interactions,iii)constant volumetric ratios in these energy-producing organelles. We revealed detailed subcellular features related to chromatin organization and to biomineralization. Overall, this approach opens new perspectives to study phytoplankton acclimation responses to abiotic and biotic factors at a relevant biological scale.