bluuebunny/crossref_metadata_2025_split huggingface dataset:
MeCP2 isoform e1 mutant mice recapitulate motor and metabolic phenotypes of Rett syndrome
Authors: LaSalle Janine M. 
Published: July 2018

AbstractMutations in the X-linked geneMECP2cause the majority of Rett syndrome (RTT) cases. Two differentially spliced isoforms of exons 1 and 2 (MeCP2-e1 and MeCP2-e2) contribute to the diverse functions of MeCP2, but only mutations in exon 1, not exon 2, are observed in RTT. We previously described an isoform-specific MeCP2-e1 deficient male mouse model of a human RTT mutation that lacks MeCP2-e1 while preserving expression of MeCP2-e2. However, RTT patients are heterozygous females that exhibit delayed and progressive symptom onset beginning in late infancy, including neurologic as well as metabolic, immune, respiratory, and gastrointestinal phenotypes. Consequently, we conducted a longitudinal assessment of symptom development in MeCP2-e1 mutant females and males. A delayed and progressive onset of motor impairments was observed in both female and male MeCP2-e1 mutant mice, including hind limb clasping and motor deficits in gait and balance. Because these motor impairments were significantly impacted by age-dependent increases in body weight, we also investigated metabolic phenotypes at an early stage of disease progression. Both male and female MeCP2-e1 mutants exhibited significantly increased body fat compared to sex-matched wild-type littermates prior to weight differences.Mecp2e1-/ymales exhibited significant metabolic phenotypes of hypoactivity, decreased energy expenditure, increased respiratory exchange ratio (RER), but decreased food intake compared to wildtype. Untargeted analysis of lipid metabolites demonstrated a distinguishable profile in MeCP2-e1 female mutant liver characterized by increased triglycerides. Together these results demonstrate that MeCP2-e1 mutation in mice of both sexes recapitulate early and progressive metabolic and motor phenotypes of human RTT.
Enhancing Percolation in Phosphatic Clay Using Diatoms under Laboratory Conditions
Authors: Horton Melba D. , Vital Dieff , Defino Paul , Spaulding Sarah , Albarelli Gary 
Published: July 2018

ABSTRACTClay settling areas are large impoundments brought about by phosphate mining with water-holding capacity that renders it very poor for agriculture and crop production. This study aims to enhance water percolation in phosphatic clay using porous diatom frustules under laboratory conditions. Phosphatic clay collected from settling areas was brought to the laboratory for the experiment. Diatom frustules were purchased commercially and dry samples of the diatom,Didymospheniawere provided by the University of Colorado-Boulder. Oven-dried clay was mixed with diatom frustules into 125 mL centrifuge tubes following a 1:1 volume ratio as experimental set-ups while pure phosphatic clay was used as control. Deionized water was poured into each set-up and the percentage of unpercolated water overlying the sediment, water retained in the sediment particles, water that percolated and passed through the hole of the centrifuge tube were monitored for 48 hours. Results showed that the addition of diatom frustules enhances the percolation of water in the sediment mixture especially those withDidymospheniafrustules. However, this mixture also showed higher percentage of water retained in the sediment particles which could be attributed to the high carbon and organic content brought about by the presence of stalks which is a major component of this species morphology. Considering howDidymospheniadisturbs freshwater habitats, proper management may render it useful for the mitigation of clay settling areas in the land environment. The implication of this on crop production remains to be explored and furtherin situexperimentations need to be conducted.IMPORTANCEClay settling areas abound in places where phosphate mining is conducted. The very fine particles and the chemical property of this phosphatic clay allows it to hold water more than normal clay sediments making the area unstable and less suitable for agricultural use. Studies show that mitigative measures to enhance surface drainage is very costly leaving most areas barren and unused. Diatoms are unicellular algae in various size and shapes with silicified cell walls that are porous and are ubiquitous in aquatic environments. The significance of our research is being able to demonstrate the potential use of diatoms, most especially the genusDidymospheniawhich is regarded as an environmental threat to some habitats, in mitigating the drainage problem in clay settling areas by mixing phosphatic clay with diatom frustules. This process is cost-effective and more importantly provides utilization of a resource that is regarded as nuisance in freshwater environments.
Utilisation of the Prestwick Chemical Library®to identify drugs that inhibit the growth of Mycobacteria
Authors: Kanvatirth Panchali , Jeeves Rose E. , Bacon Joanna , Besra Gurdyal S. , Alderwick Luke J. 
Published: July 2018

AbstractTuberculosis (TB) is an infectious bacterial disease that kills approximately 1.3 million people every year. Despite global efforts to reduce both the incidence and mortality associated with TB, the emergence of drug resistant strains has slowed any progress made towards combating the spread of this deadly disease. The current TB drug regimen is inadequate, takes months to complete and poses significant challenges when administering to patients suffering from drug resistant TB. New treatments that are faster, simpler and more affordable are urgently required. Arguably, a good strategy to discover new drugs is to start with an old drug. Here, we have screened a library of 1200 FDA approved drugs from the Prestwick Chemical library®using a GFP microplate assay. Drugs were screened against GFP expressing strains ofMycobacterium smegmatisandMycobacterium bovisBCG as surrogates forMycobacterium tuberculosis,the causative agent of TB in humans. We identified several classes of drugs that displayed antimycobacterial activity against bothM. smegmatisandM. bovisBCG, however each organism also displayed some selectivity towards certain drug classes. Variant analysis of whole genomes sequenced for resistant mutants raised to florfenicol, vanoxerine and pentamidine highlight new pathways that could be exploited in drug repurposing programmes.
Drosophilakinesin-8 stabilises the kinetochore-microtubule interaction
Authors: Edzuka Tomoya , Goshima Gohta 
Published: July 2018

AbstractKinesin-8 is required for proper chromosome alignment in a variety of animal and yeast cell types. However, how this conserved motor protein controls chromosome alignment remains unclear, as multiple biochemical activities, including inconsistent ones between studies, have been identified for this motor family. Here, we show thatDrosophilakinesin-8 Klp67A possesses both microtubule (MT) plus-end-stabilising and ‐destabilising activities in addition to commonly observed MT plus-end-directed motility and tubulin-binding activityin vitro, and is required for stable kinetochore-MT attachment during prometaphase in S2 cells In the absence of kinesin-8Klp67A, abnormally-long MTs interact in an “end-on” fashion with kinetochores at normal frequency. However, the interaction was not stable and, once-attached, MTs were frequently detached. This phenotype was rescued by ectopic expression of MT plus-end-stabilising factor CLASP, but not by artificial shortening of MTs. These results suggest that MT-stabilising activity of kinesin-8Klp67Ais critical for stable kinetochore-MT attachment. Finally, human kinesin-8KIF18Awas also shown important to ensure proper MT attachment.
“DoC-feeling”: a new behavioural tool to help diagnose the Minimally Conscious State
Authors: Hermann Bertrand , Goudard Gwen , Courcoux Karine , Valente Mélanie , Labat Sebastien , Despois Lucienne , Bourmaleau Julie , Richard-Gilis Louise , Faugeras Frédéric , Demeret Sophie , Sitt Jacobo D , Naccache Lionel , Rohaut Benjamin 
Published: July 2018

AbstractObjectivesThe clinical distinction between vegetative state/unresponsive wakefulness syndrome (UWS) and minimally conscious state (MCS) is a key step to elaborate a prognosis and formulate an appropriate medical plan for any patient suffering from disorders of consciousness (DoC). However, this assessment is often challenging and may require specialized expertise. In this study, we hypothesized that pooling subjective reports of the level of consciousness of a given patient across several nursing staff members can be used to clinically detect MCS.Setting and ParticipantsPatients referred for consciousness assessment were prospectively screened. MCS (target condition) was defined according to the best Coma Recovery Scale-Revised score (CRS-R) obtained from expert physicians (reference standard). “DoC-feeling” score consisted in the median value of multiple ratings of patient’s behavior observation pooled from multiple staff members during a week of hospitalisation (index test). Individual ratings were collected at the end of each shift using a 100mm visual analog scale, blinded from the reference standard. Diagnostic accuracy was evaluated using area under the receiver operating characteristic curve (AUC), sensitivity and specificity metrics.Results692 ratings performed by 83 nursing staff members were collected from 47 patients. Twenty patients were in a UWS and 27 in a MCS. DoC-feeling scores obtained by pooling all individual ratings obtained for a given patient were significantly greater in MCS than in UWS patients (59.2 mm [IQR: 27.3-77.3] vs. 7.2 mm [IQR: 2.4-11.4]; p<0.001) yielding an AUC of 0.92 (95%CI: 0.84-0.99).ConclusionsDoC-feeling capitalizes on the expertise of nursing staff to evaluate patients’ consciousness. Together with the CRS-R as well as with brain imaging, DoC-feeling might improve diagnostic and prognostic accuracy of DoC patients.Strengths and limitations of this studyWe designed a new behavioural tool called “DoC-feeling” to help face the clinical challenge of the detection of Minimally Conscious State in patients suffering from disorders of consciousness (DoC)“DoC-feeling score” quantifies nursing staff’s subjective perception of patient’s consciousness by pooling multiple assessments obtained from multiple caregivers (“wisdom of the crowds”)This score which requires no particular training showed a very good accuracy when compared to the gold standard (repeated expert clinical assessment using the Coma Recovery Scale – Revised (CRS-R))A validation in a separate cohort would help to determine its place in consciousness assessmentThis score should be tested not only against the CRS-R but also against brain-imaging techniques to test for its capacity to detect covert signs of consciousness
CHD8 Regulates Cellular Homeostasis and Neuronal Function Genes Across Multiple Models of CHD8 Haploinsufficiency
Authors: Wade A. Ayanna , Lim Kenneth , Catta-Preta Rinaldo , Nord Alex S. 
Published: July 2018

ABSTRACTThe packaging of DNA into chromatin determines the transcriptional potential of cells and is central to eukaryotic gene regulation. Recent sequencing of patient mutations has linked de novo loss-of-function mutations to chromatin remodeling factors with specific, causal roles in neurodevelopmental disorders. Characterizing cellular and molecular phenotypes arising from haploinsufficiency of chromatin remodeling factors could reveal convergent mechanisms of pathology. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeling factor gene and has among the highest de novo loss-of-function mutations rates in patients with autism spectrum disorder (ASD). Mutations to CHD8 are expected to drive neurodevelopmental pathology through global disruptions to gene expression and chromatin state, however, mechanisms associated with CHD8 function have yet to be fully elucidated. We analyzed published transcriptomic and epigenomic data across CHD8 in vitro and in vivo knockdown and knockout models to identify convergent mechanisms of gene regulation by CHD8. We found reproducible high-affinity interactions of CHD8 near promoters of genes necessary for basic cell functions and gene regulation, especially chromatin organization and RNA processing genes. Overlap between CHD8 interaction and differential expression suggests that reduced dosage of CHD8 directly relates to decreased expression of these genes. In addition, genes important for neuronal development and function showed consistent dysregulation, though there was a reduced rate and decreased affinity for CHD8 interactions near these genes. This meta-analysis verifies CHD8 as a critical regulator of gene expression and reveals a consistent set of high affinity CHD8 interaction targets observed across human and mouse in vivo and in vitro studies. Our findings highlight novel core functions of CHD8 and indicate direct and downstream gene regulatory impacts that are likely to be associated with neuropathology underlying CHD8-associated neurodevelopmental disorder.
Dynamic recruitment of single RNAs to processing bodies depends on RNA functionality
Authors: Pitchiaya Sethuramasundaram , Mourao Marcio D.A. , Jalihal Ameya , Xiao Lanbo , Jiang Xia , Chinnaiyan Arul M. , Schnell Santiago , Walter Nils G. 
Published: July 2018

SUMMARYCellular RNAs often colocalize with cytoplasmic, membrane-less ribonucleoprotein (RNP) granules enriched for RNA processing enzymes, termed processing bodies (PBs). Here, we track the dynamic localization of individual miRNAs, mRNAs and long non-coding RNAs (lncRNAs) to PBs using intracellular single-molecule fluorescence microscopy. We find that unused miRNAs stably bind to PBs, whereas functional miRNAs, repressed mRNAs and lncRNAs both transiently and stably localize within either the core or periphery of PBs, albeit to different extents. Consequently, translation potential and positioning of cis-regulatory elements significantly impact PB-localization dynamics of mRNAs. Using computational modeling and supporting experimental approaches we show that phase separation into large PBs attenuates mRNA silencing, suggesting that physiological mRNA turnover predominantly occurs outside of PBs. Instead, our data support a role for PBs in sequestering unused miRNAs to regulate their surveillance and provides a framework for investigating the dynamic assembly of RNP granules by phase separation at single-molecule resolution.
Determining the Mutation Bias of Favipiravir in Influenza Using Next-generation Sequencing
Authors: Goldhill Daniel H. , Langat Pinky , Xie Hongyao , Galiano Monica , Miah Shahjahan , Kellam Paul , Zambon Maria , Lackenby Angie , Barclay Wendy 
Published: July 2018

AbstractFavipiravir is a broad spectrum antiviral drug that may be used to treat influenza. Previous research has identified that favipiravir likely acts as a mutagen but the precise mutation bias that favipiravir induces in influenza virus RNAs has not been described. Here, we use next-generation sequencing (NGS) with barcoding of individual RNA molecules to accurately and quantitatively detect favipiravir-induced mutations and to sample orders of magnitude more mutations than would be possible through Sanger sequencing. We demonstrate that favipiravir causes mutations and show that favipiravir primarily acts as a guanine analogue and secondarily as an adenine analogue resulting in the accumulation of transition mutations. We also use a standard NGS pipeline to show that the mutagenic effect of favipiravir can be measured by whole genome sequencing of virus.ImportanceNew antiviral drugs are needed as a first line of defence in the event of a novel influenza pandemic. Favipiravir is a broad-spectrum antiviral which is effective against influenza. The exact mechanism of how favipiravir works to inhibit influenza is still unclear. We used next-generation sequencing (NGS) to demonstrate that favipiravir causes mutations in influenza RNA. The greater depth of NGS sequence information over traditional sequencing methods allowed us to precisely determine the bias of particular mutations caused by favipiravir. NGS can also be used in a standard diagnostic pipeline to show that favipiravir is acting on the virus by revealing the mutation bias pattern typical to the drug. Our work will aid in testing whether viruses are resistant to favipiravir and may help demonstrate the effect of
favipiravir on viruses in a clinical setting. This will be important if favipiravir is used during a future influenza pandemic.
Emergence of Multidrug-Resistant Uropathogens harboring ESBL, Carbapenem, Aminoglycosides and AmpC resistant genes from Northern India
Authors: Gajamer Varsha Rani , Bhattacharjee Amitabha , Paul Deepjyoti , Ingti Birson , Sarkar Arunabha , Kapil Jyotsna , Singh Ashish Kumar , Pradhan Nilu , Tiwari Hare Krishna 
Published: July 2018

ABSTRACTExtended-spectrum β-lactamase (ESBL) producing bacteria acts as a serious threat, and its co-existence with other antibiotic resistant gene makes the clinical scenario worse nowadays. Therefore in this study, we investigated the occurrence of ESBL genes coexisting with carbapenem, AmpC and aminoglycoside resistance gene in uropathogens. Out of 1516 urine samples, 454 showed significant bacteriuria with a prevalence rate of 29.94 %. Escherichia coli (n=340) were found to be the most predominant uropathogen followed by Klebsiella pneumoniae (n=92), Pseudomonas aeruginosa (n=10) and Proteus mirabilis (n=9). Among the total uropathogens, sixty-three ESBL-producers were identified which included blaCTX-M-15 (n=32), followed by blaCTX-M-15 + blaOXA-2 (n=15), blaCTX-M-15 + blaOXA-2 + blaTEM (n=6), blaOXA-2 (n=5), blaOXA-2 + blaSHV-76 (n=1), blaTEM+SHV-76 (n= 1) and blaTEM (n=1). All ESBL genes were found on plasmid incompatibility types: HI1, I1, FIA+FIB, FIA and Y and were horizontally transferable. Among 63 ESBL-producers, 59 isolates harboured carbapenem-resistant genes which included blaNDM-5 (n=48), blaNDM-5 + blaOXA-48 (n=5), blaNDM-5 + blaIMP (n=5) and blaNDM-5 + blaIMP + blaVIM (n=1). The ESBL producing uropathogens also harbored 16S rRNA methylase genes which included rmtB (n=9), rmtA (n=4), rmtC (n=1) and ArmA (n=1) followed by AmpC genes which includes CIT (n=8) and DHA-1 (n=1) genes. Imipenem and gentamicin were found to be more effective. We speculating, this is the first report showing the prevalence of multidrug-resistant uropathogens in this area demanding regular surveillance for such resistance mechanisms which will be useful for health personnel to treat ESBL infection and its co-existence with another antibiotic resistance gene.
Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole genome sequencing
Authors: Nordlund Jessica , Marincevic-Zuniga Yanara , Cavelier Lucia , Raine Amanda , Martin Tom , Lundmark Anders , Abrahamsson Jonas , Norén-Nyström Ulrika , Lönnerholm Gudmar , Syvänen Ann-Christine 
Published: July 2018

ABSTRACTStructural chromosomal rearrangements that may lead to in-frame gene-fusions represent a leading source of information for diagnosis, risk stratification, and prognosis in pediatric acute lymphoblastic leukemia (ALL). However, short-read whole genome sequencing (WGS) technologies struggle to accurately identify and phase such large-scale chromosomal aberrations in cancer genomes. We therefore evaluated linked-read WGS for detection of chromosomal rearrangements in an ALL cell line (REH) and primary samples of varying DNA quality from 12 patients diagnosed with ALL. We assessed the effect of input DNA quality on phased haplotype block size and the detectability of copy number aberrations (CNAs) and structural variants (SVs). Biobanked DNA isolated by standard column-based extraction methods was sufficient to detect chromosomal rearrangements even at low 10x sequencing coverage. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements and aneuploidy assessment. With use of haplotype information from the linked-reads, we also identified additional structural variants, such as a compound heterozygous deletion of ERG in a patient with the DUX4-IGH fusion gene. Thus, linked-read WGS allows detection of important pathogenic variants in ALL genomes at a resolution beyond that of traditional karyotyping or short-read WGS.
“Rapid Eye Movement sleep deprivation of rat generates ROS in the hepatocytes and makes them more susceptible to oxidative stress”
Authors: Pandey Atul , Kar Santosh K 
Published: July 2018

AbstractBackgroundRapid Eye Movement sleep deprivation (REMSD) of rats causes inflammation of the liver and apoptotic cell death of neurons and hepatocytes. Studies also suggest that REMSD are involved with muscle injury, cardiac injury and neurodegerative diseases.Objective and methodsThe aim of this research was to determine whether REMSD of rats would generate reactive oxygen species (ROS) and create oxidative stress in the hepatocytes. We selectively deprived the rats from REM sleep using the standard flower pot method.ResultsWe observed that when rats were subjected to REMSD, the levels of ROS in the hepatocytes increased with the increase in the number of days of REMSD by ∼265%, but it returned towards normal levels after recovery sleep for 5 days (∼36%) compared to controls. Nitric oxide synthase (iNOS) gene and protein was found elevated in hepatocytes in response to REM sleep loss as confirmed by real time PCR and western blot analysis compared to controls. The level of nitric oxide (NO) also increased by ∼ 675% in the hepatocytes of REMSD rats as compared to that of control group of animals.DiscussionWe have analyzed the oxidative stress generated and potentiation of hepatocytes against oxidative stress in response to REMSD. Since, REM sleep is known to play an important role for survival of most animals and has important role in maintenance of body physiology. Hence, our findings that loss of REM sleep in hepatocytes of rats can affect the ROS levels and induce iNOS & NO circulation, while making them more susceptible to oxidative stress assumes significance.Highlights of the studyWe observed elevated levels of ROS in the hepatocytes of REM sleep deprived rats.The hepatocytes of REMSD group of rats were found more susceptible to oxidative stress than that of control groups.We found increased expression of iNOS gene and nitric oxide synthase protein in the hepatocytes of REMSD rats.We observed that nitric oxide levels in the hepatocytes of REM sleep deprived rats increased positively with days of REMSD, but returned to its normal levels after 5 days of recovery sleep.