bluuebunny/crossref_metadata_2025 huggingface dataset:
Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting
Authors: Rad SM Ali Hosseini , McLellan Alexander D.
Published: May 2020

The SARS-CoV-2 virus is a recently-emerged zoonotic pathogen already well adapted to transmission and replication in humans. Although the mutation rate is limited, recently introduced mutations in SARS-CoV-2 have the potential to alter viral fitness. In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral life cycle, or interfere with sequences targeted by host miRNAs. We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson-Crick pairing, with resultant changes in predicted secondary structure. Filtering to targets matching miRNAs expressed in SARS-CoV-2 permissive host cells, we identified twelve separate target sequences in the SARS-CoV-2 genome; eight of these targets have been lost through conserved mutations. A genomic site targeted by the highly abundant miR-197-5p, overexpressed in patients with cardiovascular disease, is lost by a conserved mutation. Our results are compatible with a model that SARS-CoV-2 replication within the human host could be constrained by host miRNA defence. The impact of these and further mutations on secondary structures, miRNA targets or potential splice sites offers a new context in which to view future SARS-CoV-2 evolution, and a potential platform for engineered viral attenuation and antigen presentation.
Mitigation of radiation damage in biological macromolecules via tunable picosecond pulsed transmission electron microscopy
Authors: Choe Hyeokmin , Ponomarev Ilya , Montgomery Eric , Lau June W. , Zhu Yimei , Zhao Yubin , Liu Ao , Kanareykin Alexei , Jing Chunguang
Published: May 2020

We report mitigation of electron-beam-induced radiation damage in biological macromolecules using rapid, low-dose transmission electron microscopy (TEM) with a new, tunable, retrofittable picosecond pulser. Damage mitigation strategies historically consisted of sample cryoprotection and ultra-low beam current; ultrafast laser-pulsed systems have shown promise, but with day-long acquisition times. We show the first practical, fast, laser-free tunable system, with acquisition of diffraction series in minutes at 5.2 GHz and 10 pA. This is the largest study to date: two materials (C36H74paraffin and purple membrane), two beam energies (200 keV and 300 keV), two independent microscopes (Schottky and LaB6), two modes (pulsed and continuous), and unsurpassed repetition rate tunability. Critical dose at room temperature doubled versus continuous beam for ∼100 MHz single-electron repetition rates. Results herald a new class of highly-tunable, ultrafast pulsers with future applications in cryogenic electron microscopy (CryoEM), high resolution single particle imaging, and rapid low-dose TEM.
Genomic diversity of 39 samples ofPyropiaspecies grown in Japan
Authors: Nagano Yukio , Kimura Kei , Kobayashi Genta , Kawamura Yoshio
Published: May 2020

SomePyropiaspecies, such as nori (P. yezoensis), are important marine crops. We conducted a phylogenetic analysis of 39 samples ofPyropiaspecies grown in Japan using organellar genome sequences. A comparison of the chloroplast DNA sequences with those from China showed a clear genetic separation between Japanese and ChineseP. yezoensis. Conversely, comparing the mitochondrial DNA sequences did not separate Japanese and ChineseP. yezoensis. Analysis of organellar genomes showed that the genetic diversity of JapaneseP. yezoensisused in this study is lower than that of Chinese wildP. yezoensis. To analyze the genetic relationships between samples of JapanesePyropia, we used whole-genome resequencing to analyze their nuclear genomes. In the offspring resulting from cross-breeding betweenP. yezoensisandP. tenera, nearly 90% of the genotypes analyzed by mapping were explained by the presence of different chromosomes originating from two different parental species. Although the genetic diversity of JapaneseP. yezoensisis low, analysis of nuclear genomes genetically separated each sample. Samples isolated from the sea were often genetically similar to those being farmed. Study of genetic heterogeneity of samples within a single aquaculture strain ofP. yezoensisshowed that samples were divided into two groups and the samples with frequent abnormal budding formed a single, genetically similar group. The results of this study will be useful for breeding and the conservation ofPyropiaspecies.
Trialstreamer: a living, automatically updated database of clinical trial reports
Authors: Marshall Iain J , Nye Benjamin , Kuiper Joël , Noel-Storr Anna , Marshall Rachel , Maclean Rory , Soboczenski Frank , Nenkova Ani , Thomas James , Wallace Byron C
Published: May 2020

Objective
Randomized controlled trials (RCTs) are the gold standard method for evaluating whether a treatment works in healthcare, but can be difficult to find and make use of. We describe the development and evaluation of a system to automatically find and categorize all new RCT reports.
Materials and Methods
Trialstreamer, continuously monitors PubMed and the WHO International Clinical Trials Registry Platform (ICTRP), looking for new RCTs in humans using a validated classifier. We combine machine learning and rule-based methods to extract information from the RCT abstracts, including free-text descriptions of trial populations, interventions and outcomes (the 'PICO') and map these snippets to normalised MeSH vocabulary terms. We additionally identify sample sizes, predict the risk of bias, and extract text conveying key findings. We store all extracted data in a database which we make freely available for download, and via a search portal, which allows users to enter structured clinical queries. Results are ranked automatically to prioritize larger and higher-quality studies.
Results
As of May 2020, we have indexed 669,895 publications of RCTs, of which 18,485 were published in the first four months of 2020 (144/day). We additionally include 303,319 trial registrations from ICTRP. The median trial sample size in the RCTs was 66.
Conclusions
We present an automated system for finding and categorising RCTs. This yields a novel resource: A database of structured information automatically extracted for all published RCTs in humans. We make daily updates of this database available on our website (trialstreamer.robotreviewer.net).
Mathematical Modeling and Simulation of SIR Model for COVID-2019 Epidemic Outbreak: A Case Study of India
Authors: Yadav Ramjeet Singh
Published: May 2020

The present study discusses the spread of COVID-2019 epidemic of India and its end by using SIR model. Here we have discussed about the spread of COVID-2019 epidemic in great detail using Euler's method. The Euler’s method is a method for solving the ordinary differential equations. The SIR model has the combination of three ordinary differential equations. In this study, we have used the data of COVID-2019 Outbreak of India on 8 May, 2020. In this data, we have used 135710 susceptible cases, 54340 infectious cases and 1830 reward/removed cases for the initial level of experimental purpose. Data about a wide variety of infectious diseases has been analyzed with the help of SIR model. Therefore, this model has been already well tested for infectious diseases by various scientists and researchers. Using the data to the number of COVID-2019 outbreak cases in India the results obtained from the analysis and simulation of this proposed SIR model showing that the COVID-2019 epidemic cases increase for some time and there after this outbreak decrease. The results obtained from the SIR model also suggest that the Euler’s method can be used to predict transmission and prevent the COVID-2019 epidemic in India. Finally, from this study, we have found that the outbreak of COVID-2019 epidemic in India will be at its peak on 25 May 2020 and after that it will work slowly and on the verge of ending in the first or second week of August 2020.
Red blood cell classification using image processing and CNN
Authors: Parab Mamata Anil , Mehendale Ninad Dileep
Published: May 2020

In the medical field, the analysis of the blood sample of the patient is a critical task. Abnormalities in blood cells are accountable for various health issues. Red blood cells (RBCs) are one of the major components of blood. Classifying the RBC can allow us to diagnose different diseases. The traditional time consuming technique of visualizing RBC manually under the microscope is a tedious task and may lead to wrong interpretation because of the human error. The various health conditions can change the shape, texture, and size of normal RBCs. The proposed method has involved the use of image processing to classify the RBCs with the help of Convolution Neural Networks (CNN). The algorithm can extract the feature of each segmented cell image and classify it in various types as Microcytes, Elliptocytes, Stomatocytes, Macrocytes, Teardrop RBCs, Codocytes, Spherocytes, Sickel cell RBCs and Howell jolly RBCs. Classification is done with respect to the size, shape, and appearance of RBCs. The experiment was conducted on the blood slide collected from the hospital and RBC images were extracted from those blood slide images. The obtained results compared with reports obtained by the pathology lab and realized 98.5% accuracy. The developed system provides accurate and fast results due to which it may save the life of patients.
Evidence for enhancer noncoding RNAs (enhancer-ncRNAs) with gene regulatory functions relevant to neurodevelopmental disorders
Authors: Asgari Yazdan , Heng Julian I.T. , Lovell Nigel , Forrest Alistair R. R. , Alinejad-Rokny Hamid
Published: May 2020

Noncoding RNAs (ncRNAs) comprise a significant proportion of the mammalian genome, but their biological significance in neurodevelopment disorders is poorly understood. In this study, we identified 908 brain-enriched noncoding RNAs comprising at least one nervous system-related eQTL polymorphism that is associated with protein coding genes and also overlap with chromatin states characterised as enhancers. We referred to such noncoding RNAs with putative enhancer activity as brain ‘enhancer-ncRNAs’. By integrating GWAS SNPs and Copy Number Variation (CNV) data from neurodevelopment disorders, we found that 265 enhancer-ncRNAs were either mutated (CNV deletion or duplication) or contain at least one GWAS SNPs in the context of such conditions. Of these, the eQTL-associated gene for 82 enhancer-ncRNAs did not overlap with either GWAS SNPs or CNVs suggesting in such contexts that mutations to neurodevelopment gene enhancers disrupt ncRNA interaction. Taken together, we identified 49 novel NDD-associated ncRNAs that influence genomic enhancers during neurodevelopment, suggesting enhancer mutations may be relevant to the functions for such ncRNAs in neurodevelopmental disorders.
Human.miRFFL.DB-A curated resource for human miRNA coregulatory networks and associated regulatory-circuits
Authors: Khurana Pankaj , Varshney Rajeev , Sugadev R , Sharma YK
Published: May 2020

Gene regulation is viewed as a complex process where regulatory elements and their targets form highly complex network interactions thus affecting normal biological physiology and also disease-initiation and progress. Transcription factors (TF) and microRNA (miRNA) are fundamental transcriptional and post-transcriptional regulators of the gene expression controlling important biological processes. In recent years, many high throughput studies revealed that the complex regulatory interactions are mediated by the complex interplay between miRNA and TF regulating a Target Gene (TG) in conjunction. miRNAs and TFs are also known to regulate each other. This complex coregulatory mechanism may be represented in the form of miRNA:TF:TG coregulatory network. This network can be used to identify several small recurring subgraphs known as regulatory-circuits. One of these regulatory-circuits also called the Feed-Forward Loops (FFLs) is a three-node pattern which is composed of a miRNA and a TF, one of which regulates the other and both jointly regulate a TG. These regulatory-circuits have proven useful in elucidating the complex interplay of gene regulation during many physiological and pathological conditions.

Human.miRFFL.DB is a comprehensive integrated resource for human miRNA:TF:TG coregulatory directed networks and their associated regulatory-circuits. In-house scripts based on the graph theory principle have been used to identify both types of FFL motifs i.e. miRNA-FFL and TF-FFL. The database additionally provides an interactive visualization of the coregulatory networks and associated FFLs. Human.miRFFL.DB can be used as a comprehensive ready reference for human miRNA:TF:TG coregulatory networks and associated FFLs for decrypting complex cellular interactions of these regulatory biomolecules. Human.miRFFL.DB is available online athttp://mirffldb.in/human/
Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies
Authors: Slater Luke T , Gkoutos Georgios V , Hoehndorf Robert
Published: May 2020

Background

Ontologies are widely used throughout the biomedical domain. These ontologies formally represent the classes and relations assumed to exist within a domain. As scientific domains are deeply interlinked, so too are their representations. While individual ontologies can be tested for consistency and coherency using automated reasoning methods, systematically combining ontologies of multiple domains together may reveal previously hidden contradictions.

Results

We developed a method that tests for hidden unsatisfiabilities in an ontology that arise when combined with other ontologies. For this purpose, we combine sets of ontologies and use automated reasoning to determine whether unsatisfiable classes are present. We test the mutual consistency of the OBO Foundry and the OBO ontologies and find that the combined OBO Foundry gives rise to at least 636 unsatisfiable classes, while the OBO ontologies give rise to more than 300,000 unsatisfiable classes.

We design and implement a novel algorithm that can determine justifications for contradictions across extremely large and complicated ontologies, and use these justifications to semi-automatically repair ontologies by identifying the minimal set of axioms that, when removed, result in a consistent and coherent set of ontologies. We applied our algorithm to each combination of OBO ontologies that resulted in unsatisfiable classes.

Conclusions

We identified a large set of hidden unsatisfiability across a broad range of biomedical ontologies, and we find that this large set of unsatisfiable classes is the result of a relatively small amount of axiomatic disagreements. Our results show that hidden unsatisfiability is a serious problem in ontology interoperability; however, our results also provide a way towards more consistent ontologies by addressing the issues we identified.
Cryopreservation of Ghagus chicken semen: effect of cryoprotectants diluents and thawing temperature
Authors: Murugesan Shanmugam , Mahapatra Ramkrishna
Published: May 2020

The present study evaluated the effects of cryoprotectants, semen diluents and thawing temperature during Ghagus chicken semen cryopreservation. Four different experiments were conducted; Experiment 1- semen was cryopreserved using 6% dimethylacetamide (DMA) and 2% dimethylsulfoxide (DMSO) in Sasaki diluent (SD) and Lake and Ravie diluent (LRD), Experiment 2 and 3- semen was cryopreserved using 8% Ethylene Glycol (EG) in SD, LRD and Red Fowl Extender (RFE), Experiment 4- semen was cryopreserved using 6% dimethylformamide (DMF) in SD, LRD and Beltsville Poultry Semen Extender (BPSE). Semen was cryopreserved in 0.5 ml French straws. Thawing was done at 5°C for 100 sec in ice water in Experiments 1, 2 and 4, whereas in Experiment 3 thawing was done at 37°C for 30 sec. The post-thaw sperm motility, live sperm and percent acrosome intact sperm were significantly (P<0.05) lower in cryopreserved samples in all the experiments. No fertile eggs were obtained from cryopreserved samples in Experiments 1 and 2, except for 8% EG RFE treatment where the fertility was 0.83%. In Experiments 3 and 4, highest fertility was obtained in LRD treatment 48.12 and 30.89% respectively. In conclusion, using cryoprotectant EG (8%) and thawing at 37°C for 30 sec, and DMF (6%) resulted in acceptable level of fertility in Ghagus chicken. Though the diluents influenced post-thaw in vitro semen parameters the fertility was not affected. In addition, results indicated that thawing temperature may be a critical stage in the cryopreservation protocol.
Dual Role of a Rubisco Activase in Metabolic Repair and Carboxysome Organization
Authors: Flecken Mirkko , Wang Huping , Popilka Leonhard , Hartl F. Ulrich , Bracher Andreas , Hayer-Hartl Manajit
Published: May 2020

Rubisco, the key enzyme of CO2fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone Rubisco activase (Rca) in a process that is not well understood. Here we performed a structural and mechanistic analysis of cyanobacterial Rca, a close homolog of plant Rca. In the Rca:Rubisco complex, Rca is positioned over the Rubisco catalytic site under repair and pulls the N-terminal tail of the large Rubisco subunit (RbcL) into the hexamer pore. Simultaneous displacement of the C-terminus of the adjacent RbcL opens the catalytic site for inhibitor release. An alternative interaction of Rca with Rubisco is mediated by C-terminal domains that resemble the small Rubisco subunit. These domains, together with the N-terminal AAA+ hexamer, ensure that Rca is packaged with Rubisco into carboxysomes. Cyanobacterial Rca is a dual-purpose protein with functions in Rubisco repair and carboxysome organization.
Acoustically driven cortical delta oscillations underpin perceptual chunking
Authors: Rimmele J.M. , Poeppel D. , Ghitza O.
Published: May 2020

Oscillation-based models of speech perception postulate a cortical computational principle by which decoding is performed within a window structure derived by a segmentation process. In the syllable level segmentation is realized by a theta oscillator. We provide evidence for an analogous role of a delta oscillator at the phrasal level. We recorded MEG while participants performed a target identification task. Random-digit strings, with phrasal chunks of two digits, were presented at chunk rates inside or outside of the delta range. Strong periodicities were elicited by acoustic-driven chunk rates inside of delta, in superior and middle temporal areas and speech-motor integration areas. Periodicities were diminished or absent for chunk rates outside of the delta range, closely in line with behavioral performance. No periodicities were observed for top-down driven chunking conditions. Our findings show that phrasal chunking is correlated with acoustic-driven delta oscillations, expressing anatomically specific patterns of neuronal periodicities.
Spatiotemporal variation in drivers of parasitism in a wild wood mouse population
Authors: Sweeny A.R. , Albery G.F. , Venkatesan S.V. , Fenton A. , Pedersen A.B.
Published: May 2020

Host-parasite interactions in nature are driven by a range of factors across several ecological scales, so observed relationships are often context-dependent. Importantly, if these factors vary across space and time, practical sampling limitations can limit or bias inferences, and the relative importance of different drivers can be hard to discern.

We collected a replicated, longitudinal dataset of >1000 individual wood mice (Apodemus sylvaticus) encompassing 6 years of sampling across 5 different woodland sites to investigate how environmental, host and within-host factors determine infection intensity of a highly prevalent gastrointestinal nematode,Heligmosomoides polygyrus.

We used a Bayesian modelling approach to further quantify if and how each factor varied in space and time. Finally, we examined the extent to which a lack of spatially or temporally replication (i.e., within single years or single sites) and single (cross-sectional) versus repeated (longitudinal) sampling of individuals would affect which drivers were found to predictH. polygyrusinfection.

Season, host body condition, and sex were the three most important determinants of infection intensity; however, the strength and even direction of these effects varied in time, but not in space. Additionally, longitudinal datasets, in which we can control for within-individual variation through repeat observations, provided more robust estimates of the drivers of parasite intensity compared to cross-sectional data.

These results highlight the importance of accounting for spatiotemporal variation in drivers of disease dynamics and the need to incorporate spatiotemporal replication when designing sampling regimes. Furthermore, they suggest that embracing rather than simply controlling for spatiotemporal variation can reveal important insight into host-parasite relationships in the wild.
Reoxygenation after Evofosfamide Treatment in Pancreatic Ductal Adenocarcinoma Xenografts is due to Decreased Oxygen Consumption and not Increased Oxygen Supply
Authors: Kishimoto Shun , Brender Jeffrey R. , Saida Yu , Yamamoto Kazutoshi , Mitchell James B. , Krishna Murali C.
Published: May 2020

Evofosfamide is designed to release a cytotoxic bromo-isophosphoramide (Br-IPM) moiety in a hypoxic microenvironment. This drug therefore preferentially attacks hypoxic regions in tumors where other standard anti-cancer treatments such as chemotherapy and radiation therapy are often ineffective. Various combination therapies with evofosfamide have been proposed and tested in preclinical and clinical settings. However, the treatment effect of evofosfamide monotherapy on tumor hypoxia has not been fully understood, partly due to the lack of quantitative methods to assess tumor pO2 in vivo. Here, we use quantitative pO2 imaging by EPR to evaluate the change in tumor hypoxia in response to evofosfamide treatment using two pancreatic ductal adenocarcinom a xenograft models; MIA Paca-2 tumors responding to evofosfamide and Su.86.86 tumors which do not respond. EPR imaging showed oxygenation improved globally after evofosfamide treatment in hypoxic MIA Paca-2 tumors, in agreement with the ex vivo results obtained from hypoxia staining by pimonidazole and in apparent contrast to the decrease in Ktransobserved in DCE MRI. This suggests reoxygenation after treatment is due to decreased oxygen demand rather than improved prefusion. Following the change in pO2 after treatment may therefore yield a way of monitoring treatment response. The observation that evofosfamide not only kills the hypoxic region of the tumor but also improves oxygenation in the residual tumor regions provides a rationale for combination therapies using radiation and anti-proliferatives post evofosfamide for improved outcomes.
NAIP–NLRC4-deficient mice are susceptible to shigellosis
Authors: Mitchell Patrick S. , Roncaioli Justin L. , Turcotte Elizabeth A. , Goers Lisa , Chavez Roberto A. , Lee Angus Y. , Lesser Cammie F. , Rauch Isabella , Vance Russell E.
Published: May 2020

Bacteria of the genusShigellacause shigellosis, a severe gastrointestinal disease that is a major cause of diarrhea-associated mortality in humans. Shigellosis develops upon oral ingestion of as few as 100 bacteria, but million-fold higher doses fail to cause disease in mice. The lack of a physiologically relevant mouse model of shigellosis has impeded our understanding of this important human disease, but why mice are resistant is unknown. Here we show that in human cells, but not in mice,Shigellaevades detection by the NAIP–NLRC4 inflammasome, an immune sensor present in intestinal epithelial cells (IECs). We find that NAIP–NLRC4-deficient mice are highly susceptible to oralShigellainfection and recapitulate the clinical features of human shigellosis, including bacterial replication in IECs and neutrophilic inflammation of the colon. Confirming a role for bacterial replication in IECs in our new model, aShigellamutant lacking IcsA, a factor required for cell-to-cell spread among IECs, is attenuated in otherwise susceptible NAIP–NLRC4-deficient mice. Although inflammasome-mediated cell death is widely held to promoteShigellainfection and pathogenesis, we instead demonstrate that IEC-specific NAIP–NLRC4-induced cell death is sufficient to protect the host from shigellosis. Thus, NAIP–NLRC4-deficient mice are a physiologically relevant and experimentally tractable model for shigellosis. More broadly, our results suggest that the lack of an inflammasome response in IECs may help explain the extreme susceptibility of humans to shigellosis.
A unique and evolutionarily conserved retinal interneuron relays rod and cone input to the inner plexiform layer
Authors: Young Brent K. , Ramakrishnan Charu , Ganjawala Tushar , Li Yumei , Kim Sangbae , Wang Ping , Chen Rui , Deisseroth Karl , Tian Ning
Published: May 2020

Neurons in the CNS are distinguished from each other by their morphology, the types of the neurotransmitter they release, their synaptic connections, and their genetic profiles. While attempting to characterize the retinal bipolar cell (BC) input to retinal ganglion cells (RGCs), we discovered a previously undescribed type of interneuron in mice and primates. This interneuron shares some morphological, physiological, and molecular features with traditional BCs, such as having dendrites that ramify in the outer plexiform layer (OPL) and axons that ramify in the inner plexiform layer (IPL) to relay visual signals from photoreceptors to inner retinal neurons. It also shares some features with amacrine cells, particularly Aii amacrine cells, such as their axonal morphology and possibly the release of the inhibitory neurotransmitter glycine, along with the expression of some amacrine cell specific markers. Thus, we unveil an unrecognized type of interneuron, which may play unique roles in vision.

Significance Statement

Cell types are the building blocks upon which neural circuitry is based. In the retina, it is widely believed that all neuronal types have been identified. We describe a cell type, which we call the Campana cell, that does not fit into the conventional neuronal retina categories but is evolutionarily conserved. Unlike retinal bipolar cells, the Campana cell receives synaptic input from both rods and cones, has broad axonal ramifications, and may release an inhibitory neurotransmitter. Unlike retinal amacrine cells, the Campana cell receives direct photoreceptor input has bipolar-like ribbon synapses. With this discovery, we open the possibility for new forms of visual processing in the retina.
The low complexity motif of cytoplasmic polyadenylation element binding protein 3 (CPEB3) is critical for the trafficking of its targets in neurons
Authors: Ford Lenzie , Asok Arun , Tripp Arielle D. , Parro Cameron , Fitzpatrick Michelle , de Solis Christopher A. , Shafiian Neeva , Fioriti Luana , Soni Rajesh Kumar , Kandel Eric R.
Published: May 2020

Biomolecular condensates, membraneless organelles found throughout the cell, play critical roles in many aspects of cellular function. Ribonucleoprotein granules (RNPs), a type of biomolecular condensate found in neurons that are necessary for local protein synthesis and are involved in long-term potentiation (LTP). Several RNA-binding proteins present in RNPs are necessary for the synaptic plasticity involved in LTP and long-term memory. Most of these proteins possess low complexity motifs, allowing for increased promiscuity. We explore the role the low complexity motif plays for RNA binding protein cytoplasmic polyadenylation element binding protein 3 (CPEB3), a protein necessary for long-term memory persistence. We found that RNA binding and SUMOylation are necessary for CPEB3 localization to the P body, thereby having functional implications on translation. Here, we investigate the role of the low complexity motif of CPEB3 and find that it is necessary for P body localization and downstream targeting for local protein synthesis.
Antimycobacterial potential of Mycobacteriophage under disease-mimicking conditions
Authors: Kalapala Yeswanth Chakravarthy , Sharma Pallavi Raj , Agarwal Rachit
Published: May 2020

Antibiotic 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.
ELF4 Expression is Associated with Worse Disease Outcomes and Increased Resistance to Anticancer Agents in Human Cancers
Authors: Kafita Doris , Daka Victor , Nkhoma Panji , Zulu Mildred , Zulu Ephraim , Tembo Rabecca , Ngwira Zifa , Mwaba Florence , Sinkala Musalula , Munsaka Sody
Published: May 2020

The malignant phenotype of tumour cells is fuelled by changes in the expression of various transcription factors, which include some of the well-studied proteins such as p53 and Myc. Despite significant progress made, little is known about several other transcription factors, including ELF4, and how they help shape the oncogenic processes that occur in cancer cells. To this end, we performed a bioinformatics analysis to facilitate a detailed understanding of how the transcriptional variations of ELF4 in human cancers are related to disease outcomes and the cancer cell drug responses. Here, using mRNA transcription data of ELF4 from the Cancer Genome Atlas pan-cancer project of 9,350 samples, we identify two groups of patient's tumours: those that expressed high ELF4 transcripts and those that expressed low ELF4 transcripts across 32 different human cancers. We uncover that patients segregated into these two groups are associated with different clinical outcomes. Further, we found that, besides being associated with comparatively worse disease outcomes, tumours that express high ELF4 mRNA transcript tend to be of a higher-grade, afflict a significantly older patient population and have a significantly higher mutation burden. By analysing dose-response profiles to 397 anti-cancer drugs of 612 well-characterised human cancer cell lines from the Genomics of Drug Sensitivity in Cancer, we discover that cell lines that express high ELF4 mRNA transcript are significantly less responsive to 129 anti-cancer drugs. Collectively our analyses have shown that, across the 32 different human cancers, the patients afflicted with tumours that overexpress ELF4 tended to have a more aggressive disease that is also is more likely more refractory to most anti-cancer drugs, a finding upon which we could devise novel categorisation of patient tumours, treatment and prognostic strategies.
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

The 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 summary

The 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

Inositol 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.
The importance of orangutans in small fragments for maintaining metapopulation dynamics
Authors: Ancrenaz Marc , Oram Felicity , Nardiyono Nardiyono , Silmi Muhammad , Jopony Marcie Elene Marcus , Voigt Maria , Seaman David J.I. , Sherman Julie , Lackman Isabelle , Traeholt Carl , Wich Serge , Struebig Matthew J. , Santika Truly , Meijaard Erik
Published: May 2020

Orangutans (Pongo spp.) occur at low densities and therefore large areas are necessary to sustain viable metapopulations, defined here as sets of conspecific units of individuals linked by dispersal. Historically, orangutans lived in large contiguous areas of intact rainforest, but are now increasingly found in agricultural and other landscapes modified by people. Here we collate evidence of orangutans utilizing isolated forest fragments (< 500 ha) within multiple-use landscapes dominated by oil palm monoculture across Borneo. Orangutan signs (i.e. nests) were evident in 76 fragments surveyed by helicopter, and in 50 of 70 additional fragments surveyed on the ground; on average 63 ha in size. This includes presence of adult resident females with dependent young confirmed in 40% of the fragments assessed by ground survey. Our study revealed some resident females are raising offspring in isolated forest patches within mature oil palm stands. This not only confirms that some forest patches can sustain orangutans, but indicates migratory males are capable of reaching these fragments scattered throughout the multiple-use landscape. Therefore, orangutans that use or live in even small isolated forest patches are an essential part of the overall metapopulation by maintaining gene flow between, and genetic connectivity within, populations distributed across larger multiple-use landscapes. Orangutan survival is commonly thought to be low in small, isolated forest patches, and the customary management strategy is to remove (translocate) these individuals and release them in larger forests. In some cases, translocations may be necessary, i.e. in case of fire or when the animals are in eminent danger of being killed and have no other refuge. However, the small amount of data available indicates that mortality rates during and after translocations are high, while the impacts of removing animals from spatially dispersed metapopulations are unknown. Therefore, we argue the current policy of routine translocation rather than conserving the species within human-modified landscapes could inadvertently decrease critical metapopulation functionality necessary for long-term viability. It is clear that orangutans need natural forest to survive, but our findings show that fragmented agricultural landscapes can also serve as complementary conservation areas in addition to fully protected areas if they are well designed with ecological connections, and if orangutan killing can be prevented. To achieve this, we call for a paradigm shift from the traditional large single forest model to one that emphasizes metapopulation functionality in the fragmented forest - human use matrix characteristic of the Anthropocene.
Differential SP1 Interactions in SV40 Chromatin from Virions and Minichromosomes
Authors: Rowbotham Kincaid , Haugen Jacob , Milavetz Barry
Published: May 2020

SP1 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

The 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

Current 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

Bacteria 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

In 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.