bluuebunny/crossref_metadata_2025_split huggingface dataset:
mtorHaploinsufficiency Ameliorates Renal Cyst Formation in Adult Zebrafishtmem67Mutants
Authors: Zhu Ping , Qiu Qi , Harris Peter C. , Xu Xiaolei , Lin Xueying 
Published: December 2019

AbstractAlthough zebrafish embryos have been utilized to study ciliogenesis and to model polycystic kidney disease (PKD), adult zebrafish remain unexplored. Here, we report the generation and characterization of a zebrafish mutant oftmem67, a homologue of the mammalian causative gene for Meckel syndrome type 3 (MKS3). Although a small population of homozygous embryos exhibited pronephric cysts, all mutants were able to survive to adulthood and developed progressive mesonephric cysts with full penetrance. The cysts in the adult zebrafish kidneys manifested features of mammalian PKD, including switching of cyst origin from the proximal tubules to the collecting ducts, increased proliferation of cyst-lining epithelial cells, and hyperactive mTOR signaling. Consistent ciliary abnormalities were observed in both the embryonic and adult zebrafish mutants compared with the wild-type fish, including shorter and fewer single cilia in the distal pronephros and all segments of the mesonephros and greater numbers of multiciliated cells (MCCs). Lack of single cilium preceded cystogenesis, suggestive of a primary defect. Expansion of MCCs occurred after pronephric cyst formation and was inversely correlated with the severity of cystogenesis in young adult zebrafish, suggesting an adaptive action. Interestingly, mTOR inhibition ameliorated renal cysts in both the embryonic and adult zebrafish models; however, it only rescued ciliary abnormalities in the adult mutants. In summary, we have established atmem67mutant as the first adult zebrafish PKD model, revealed a novel aspect of cilium regulation, and identified sustained mTOR inhibition as a candidate therapeutic strategy fortmem67-based PKD.Significance StatementWhile zebrafish embryos are well recognized for their value in studying ciliogenesis and polycystic kidney disease (PKD), adult zebrafish have not commonly been used. Here, we report the establishment of the first adult zebrafish model for PKD, which exhibits characteristics of mammalian PKD and shows kidney ciliary abnormalities consistent with those observed in an embryonic model. We also provide evidence for mTOR inhibition as a therapeutic strategy for this particular type of cystogenesis. Compared to the embryonic model, the adult fish model exhibits a spectrum of progressive pathogeneses and enables ciliary abnormalities to be discerned as either primary or secondary to cystogenesis. We believe that this novel adult fish model will facilitate mechanistic studies and therapeutic development for PKD.
Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease
Authors: Winkler Thomas W , Grassmann Felix , Brandl Caroline , Kiel Christina , Günther Felix , Strunz Tobias , Weidner Lorraine , Zimmermann Martina E , Korb Christina A. , Poplawski Alicia , Schuster Alexander K , Müller-Nurasyid Martina , Peters Annette , Rauscher Franziska G , Elze Tobias , Horn Katrin , Scholz Markus , Cañadas-Garre Marisa , McKnight Amy Jayne , Quinn Nicola , Hogg Ruth E , Küchenhoff Helmut , Heid Iris M , Stark Klaus J , Weber Bernhard HF 
Published: December 2019

ABSTRACTBackgroundAdvanced age-related macular degeneration (AMD) is a leading cause of blindness. While around half of the genetic contribution to advanced AMD has been uncovered, little is known about the genetic architecture of the preceding early stages of the diseases.MethodsTo identify genetic factors for early AMD, we conducted a genome-wide association meta-analysis with 14,034 early AMD cases and 91,214 controls from 11 sources of data including data from the International AMD Genomics Consortium (IAMDGC) and the UK Biobank (UKBB). We ascertained early AMD via color fundus photographs by manual grading for 10 sources and by using an automated machine learning approach for >170,000 images from UKBB. We searched for significant genetic loci in a genome-wide association screen (P<5×10-8) based on the meta-analysis of the 11 sources and via a candidate approach based on 13 suggestive early AMD variants from Holliday et al 2013 (P<0.05/13, additional 3,432 early AMD cases and 11,235 controls). For the novel AMD regions, we conducted in-silico follow-up analysis to prioritize causal genes and pathway analyses.ResultsWe identified 11 loci for early AMD, 9 novel and 2 known for early AMD. Most of these 11 loci overlapped with known advanced AMD loci (nearARMS2/HTRA1, CFH, APOE, C2, C3, CETP, PVRL2, TNFRSF10A, VEGFA), except two that were completely novel to any AMD. Among the 17 genes within the two novel loci, in-silico functional annotation suggestedCD46andTYRas the most likely responsible genes. We found the presence or absence of an early AMD effect to distinguish known pathways of advanced AMD genetics (complement/lipid pathways or extracellular matrix metabolism, respectively).ConclusionsOur data on early AMD genetics provides a resource comparable to the existing data on advanced AMD genetics, which enables a joint view. Our large GWAS on early AMD identified novel loci, highlighted shared and distinct genetics between early and advanced AMD and provides insights into AMD etiology. The ability of early AMD effects to differentiate the major pathways for advanced AMD underscores the biological relevance of a joint view on early and advanced AMD genetics.
Signature activities of 20S proteasome include degradation of the ubiquitin-tag with the protein under hypoxia
Authors: Sahu Indrajit , Mali Sachitanand M. , Sulkshane Prasad , Rozenberg Andrey , Xu Cong , Morag Roni , Sahoo Manisha Priyadarsini , Singh Sumeet K. , Ding Zhanyu , Wang Yifan , Day Sharleen , Cong Yao , Kleifeld Oded , Brik Ashraf , Glickman Michael H. 
Published: December 2019

AbstractCareful removal of unwanted proteins is necessary for cell survival. The primary constitutive intracellular protease is the 26S proteasome complex, often found in equilibrium with its free catalytic subcomplex– the 20S core particle. Protein degradation by 26S is tightly regulated by prior ubiquitination of substrates, whereas 20S is amenable to substrates with an unstructured segment. Differentiating their contributions to intracellular proteolysis is challenging due to their common catalytic sites. Here, by chemically synthesizing a synoptic set of homogenous ubiquitinated proteins, we ascribe signature features to 20S function and demonstrate a unique property: degrading the ubiquitin-tag along with the target protein. Cryo-EM confirms that a ubiquitinated substrate can induce asymmetric conformational changes to 20S. Mass-spectrometry of intracellular peptidome under hypoxia and in human failing heart identifies the signature properties of 20S in cells. Moreover, the ability of 20S proteasome to clear toxic proteins rapidly, contributes to better survival under these conditions.
Glutamatergic modulation of auditory cortex connectivity with attentional brain networks in unpredictable perceptual environment
Authors: Kompus K. , Volehaugen V. , Craven A. , Specht K. 
Published: December 2019

AbstractIn a stable environment the brain can minimize processing required for sensory input by forming a predictive model of the surrounding world and suppressing neural response to predicted stimuli. Unpredicted stimuli lead to a prediction error signal propagation through the perceptual network, and resulting adjustment to the predictive model. The inter-regional plasticity which enables the model-building and model-adjustment is hypothesized to be mediated via glutamatergic receptors. While pharmacological challenge studies with glutamate receptor ligands have demonstrated impact on prediction-error indices, it is not clear how inter-individual differences in the glutamate system affect the prediction-error processing in non-medicated state. In the present study we examined 20 healthy young subjects with resting-state proton MRS spectroscopy to characterize glutamate+glutamine (rs-Glx) levels in their Heschl’s gyrus (HG), and related this to HG functional connectivity during a roving auditory oddball protocol. No rs-Glx effects were found within the frontotemporal prediction-error network. Larger rs-Glx signal was related to stronger connectivity between HG and bilateral inferior parietal lobule during unpredictable auditory stimulation. We also found effects of rs-Glx on the coherence of default mode network (DMN) and frontoparietal network (FPN) during unpredictable auditory stimulation. Our results demonstrate the importance of Glx in modulating long-range connections and wider networks in the brain during perceptual inference.
Modelling the emergence of whisker barrels
Authors: James Sebastian S. , Krubitzer Leah A. , Wilson Stuart P. 
Published: December 2019

AbstractBrain development relies on an interplay between genetic specification and self-organization. Striking examples of this relationship can be found in the somatosensory brainstem, thalamus, and cortex of rats and mice, where the arrangement of the facial whiskers is preserved in the arrangement of cell aggregates to form precise somatotopic maps. We show in simulation how realistic whisker maps can self-organize, by assuming that information is exchanged between adjacent cells only, under the guidance of gene expression gradients. The resulting model provides a simple account of how patterns of gene expression can constrain spontaneous pattern formation to faithfully reproduce functional maps in subsequent brain structures.
Core-2O-glycans are required for galectin-3 interaction with the osteoarthritis related protein lubricin
Authors: Flowers Sarah A. , Thomsson Kristina A. , Ali Liaqat , Huang Shan , Mthembu Yolanda , Regmi Suresh C. , Holgersson Jan , Schmidt Tannin A. , Rolfson Ola , Björkman Lena I , Sundqvist Martina , Karlsson Anna , Jay Gregory D. , Eisler Thomas , Krawetz Roman , Karlsson Niclas G. 
Published: December 2019

ABSTRACTSynovial fluid lubricin (proteoglycan 4) is a mucin-typeO-linked glycosylated (60% of the mass) biological lubricant involved in osteoarthritis (OA) development. Lubricin has been reported to be cross-linked by synovial galectin-3 on the lubricating articular surface. Here, we confirm that binding to galectin-3 depended on core-2O-linked glycans, where surface plasmon resonance of a recombinant lubricin (rhPRG4) devoid of core-2 structures lacked binding capacity to recombinant galectin-3. Both galectin-3 levels and interactions with synovial lubricin were found to be decreased in late-stage OA patients coinciding with an increase of truncated and less sialylated core 1 O-glycans. These data suggest a defect cross-linking of surface active molecules in OA and provides novel insights into OA molecular pathology.
Genetic background and diet affect brown adipose gene co-expression – metabolic associations
Authors: Carson Caryn , Lawson Heather A 
Published: December 2019

AbstractAdipose is a dynamic endocrine organ that is critical for regulating metabolism and is highly responsive to nutritional environment. Brown adipose tissue is an exciting potential therapeutic target, however there are no systematic studies of gene-by-environment interactions affecting function of this organ. We leveraged a weighted gene co-expression network analysis to identify transcriptional networks in brown adipose tissue from LG/J and SM/J inbred mice fed high or low fat diets, and correlate these networks with metabolic phenotypes. We identified 8 primary gene network modules associated with variation in obesity and diabetes-related traits. Four modules were enriched for metabolically relevant processes such as immune and cytokine response, cell division, peroxisome functions, and organic molecule metabolic processes. The relative expression of genes in these modules is highly dependent on both genetic background and dietary environment. Genes in the immune/cytkine response and cell division modules are particularly highly expressed in high fat-fed SM/J mice, which show unique brown adipose-dependent remission of diabetes. The interconnectivity of genes in these modules is also heavily dependent on diet and strain, with most genes showing both higher expression and co-expression under the same context. We highlight 4 candidate genes,Col28a1, Cyp26b1, Bmp8b, andKcnj14, that have distinct expression patterns among strain-by-diet contexts and fall under metabolic QTL previously mapped in an F16generation of an advanced intercross between these two strains. Each of these genes have some connection to obesity and diabetes-related traits, but have not been studied in brown adipose tissue. In summary, our results provide important insights into the relationship between brown adipose and systemic metabolism by being the first gene-by-environment study of brown adipose transcriptional networks and introducing novel candidate genes for follow-up studies of biological mechanisms of action.Author SummaryResearch on brown adipose tissue is a promising new avenue for understanding and potentially treating metabolic dysfunction. However, we do not know how genetic background interacts with dietary environment to affect the brown adipose transcriptional response, and how this might affect systemic metabolism. Here we report the first investigation of gene-by-environment interactions on brown adipose gene expression networks associating with multiple obesity and diabetes-related traits. We identified 8 primary networks correlated with variation in these traits in mice, including networks enriched for immune and cytokine response, cell division, organic molecule metabolism, and peroxisome genes. Characterizing these networks and their distinct diet-by-strain expression and co-expression patterns is an important step towards understanding how brown adipose tissue responds to an obesogenic diet, how this response affects metabolism, and how this can be modified by genetic variation.
Functional NHE1 expression is critical to blood brain barrier integrity and sumatriptan blood to brain uptake
Authors: Liktor-Busa Erika , Blawn Kiera T. , Kellohen Kathryn L. , Wiese Beth M. , Verkhovsky Vani , Wahl Jared , Vivek Anjali , Davis Thomas P. , Vanderah Todd W. , Largent-Milnes Tally M. 
Published: December 2019

AbstractDisruption of blood-brain barrier integrity and dramatic failure of brain ion homeostasis including fluctuations of pH occurs during cortical spreading depression (CSD) events associated with several neurological disorders, including migraine with aura, traumatic brain injury and stroke. NHE1 is the primary regulator of pH in the central nervous system. The goal of the current study was to investigate the role of sodium-hydrogen exchanger type 1 (NHE1) in blood brain barrier (BBB) integrity during CSD events and the contributions of this antiporter on xenobiotic uptake. Using immortalized cell lines, pharmacologic inhibition and genetic knockdown of NHE1 mitigated the paracellular uptake of radiolabeled sucrose implicating functional NHE1 in BBB maintenance. In contrast, loss of functional NHE1 in endothelial cells facilitated uptake of the anti-migraine therapeutic, sumatriptan. In female rats, cortical KCl but not aCSF selectively reduced total expression of NHE1 in cortex and PAG with limited impact on trigeminal ganglia or trigeminal nucleus caudalis suggesting in vitro observations may have a significancein vivo. Pharmacological inhibition of NHE1 prior to cortical manipulations enhanced the efficacy of sumatriptan at early time-points but induced facial sensitivity alone. Overall, our results suggest that dysregulation of NHE1 contributes to breaches in BBB integrity, drug penetrance, and the behavioral sensitivity to the antimigraine agent, sumatriptan.
Horizontal gene transfer of thepirABgenes responsible for Acute Hepatopancreatic Necrosis Disease (AHPND) turns a non-Vibriostrain into an AHPND-positive pathogen
Authors: Muthukrishnan Sarmila , Defoirdt Tom , Shariff Mohamed , M. Y Ina-Salwany , Yusoff Fatimah Md , Natrah I. 
Published: December 2019

AbstractIn the past decade, shrimp farms, particularly those established in Asia, Mexico and South America suffered from the outbreak of an emergent penaeid shrimp disease known as Acute Hepatopancreatic Necrosis Disease (AHNPD). The PirA and PirB toxins produced by plasmid pVA1 inVibrio parahaemolyticuswere reported to cause the AHPND pathology. More recent research demonstrated thatV. parahaemolyticusis not the only species that can cause AHPND, as otherVibriospecies were also found to contain PirAB-containing plasmid. The present study assessed the Horizontal Gene Transfer (HGT) of AHPND that transforms genes (pirAandpirB) from AHPND positiveV. parahaemolyticusto non-AHPND and non-vibrio species identified asAlgoriphagussp. strain NBP. The HGT ofpirAandpirBgenes from the AHPND positiveV. parahaemolyticustoAlgoriphagussp. strain NBP was found to occur at different temperatures. The conjugation efficiency rate (n°) ofpirABfromV. parahaemolyticustoAlgoriphagussp. strain NBP at 30°C and 40°C showed 80-91% efficiency. Shrimp challenged with thepirAandpirBpositiveAlgoriphagussp. strain NBP also demonstrated typical pathognomonic AHPND lesions during the histopathologic examination.Author summaryAHPND is a significant threat to the shrimp industry leading to high losses. The results demonstrated that the conjugative transfer of thepirAandpirBpositiveV. parahaemolyticus(donor strain) to a non-Vibrioand non-pathogenic bacterium (recipient strain), successfully transformed the non-pathogenic bacterium into a disease-causing strain with a disease-causing capability similar to the donor strain. Initially,V. parahaemolyticusthat express the PirA and PirB toxins which encoded by a conjugative plasmid cause sloughing and degeneration of shrimp hepatopancreatic.
Wt1 positive neurons in the hindbrain are essential for respiration
Authors: Schnerwitzki Danny , Hayn Christian , Perner Birgit , Englert Christoph 
Published: December 2019

AbstractNeuronal networks commonly referred to as central pattern generator (CPG) networks coordinate the generation of rhythmic activity like locomotion and respiration. These networks are proposed to exhibit a high degree of homology in their development. Their establishment is influenced by a variety of transcription factors. One of them is the Wilms tumor protein Wt1 that is present in dI6 neurons of the ventral spinal cord, which are involved in the coordination of locomotion. Here we report about the so far undescribed presence of Wt1 in neurons of the caudoventral medulla oblongata and their impact on respiration. By performing marker analyses, we were able to characterize these Wt1 positive (+) cells as dB4 neurons. The temporal pattern of Wt1 occurrence suggests a role for Wt1 in the differentiation of dB4 neurons during embryonic and postnatal development. Conditional knockout ofWt1in these cells caused an altered population size of V0 neurons already in the developing hindbrain leading to a decline in the respiration rate in the adults. Thereby, we confirmed and extended the so far proposed homology between neurons of the dB4 domain in the hindbrain and dI6 neurons of the spinal cord in terms of development and function. Ablation of Wt1+ dB4 neurons resulted in the death of neonates due to the inability to initiate respiration suggesting a vital role for Wt1+ dB4 neurons in breathing. These results extend the role of Wt1 in the CNS and show that in addition to its function in differentiation of dI6 neurons it also contributes to the development of dB4 neurons in the hindbrain that are critically involved in the regulation of respiration.
Applying Nanopore sequencing to a One-Health scenario for colistin resistance transmission among pigs, cows and the farmer
Authors: Viñes Joaquim , Cuscó Anna , Napp Sebastian , Gonzalez Judith , de Rozas Ana Perez , Francino Olga , Migura-Garcia Lourdes 
Published: December 2019

AbstractOne-Health studies applying massive-parallel and single-molecule sequencing are a suitable approximation to try to understand how antibiotic resistances flow between the human-animal-environment scenario. Colistin has been withdrawn in human medicine due to its toxicity, limiting its usage as a last-resort treatment option for multidrug-resistant Gram-negative bacteria. However, it is still used orally to treatEnterobacteriaceaeinfections in veterinary medicine. Since 2015, colistin resistance appeared to be located in mobile genetic elements, raising the concern of the likelihood of transmission by horizontal gene transfer between animals and humans. In this study, 202 faecal samples were collected in a mixed farm from pigs, calves, and the farmer. PCR forthe mcr-1 gene was positive for 18 of the isolates, and Nanopore sequencing allowed us to determine the location of the gene, either on the chromosome or in plasmids. Three types of replicons were found within the positive isolates harbouring themcr-1: IncX4, IncI2, and IncHI2. Four different genetic contexts probably indicate different stages of gene stabilization, either in the chromosome or plasmid, withISApl1as the main insertion element flanking the gene. Moreover, 43 other resistance genes were found in our samples, related to more than six different antibiotic families (e.g. aminoglycosides, lincosamides, beta-lactams, macrolides, trimethoprim, phenicols, and sulphonamides). We found resistance genes against colistin and that six antibiotic families together in at least one of the isolates from human, swine, and bovine. Isolate 15B-22 harboured one plasmid with seven resistance genes related to four families of antibiotics other than polymyxins, meaning that there are more chances to maintain colistin resistance even with the withdrawn of colistin. Nanopore long reads allowed us to assemble the DNA elements within the isolates easily and determine the genetic context of themcr-1gene. Furthermore, they allowed us to describe and locate more antimicrobial resistance genes to other antibiotic families and antiseptic compounds.
A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants
Authors: Dhorne-Pollet Sophie , Barrey Eric , Pollet Nicolas 
Published: December 2019

AbstractBackgroundWe present here an approach to sequence whole mitochondrial genomes using nanopore long-read sequencing. Our method relies on the selective elimination of nuclear DNA using an exonuclease treatment and on the amplification of circular mitochondrial DNA using a multiple displacement amplification step.ResultsWe optimized each preparative step to obtain a 100 million-fold enrichment of horse mitochondrial DNA relative to nuclear DNA. We sequenced these amplified mitochondrial DNA using nanopore sequencing technology and obtained mitochondrial DNA reads that represented up to half of the sequencing output. The sequence reads were 2.3 kb of mean length and provided an even coverage of the mitochondrial genome. Long-reads spanning half or more of the whole mtDNA provided a coverage that varied between 118X and 488X. Finally, we identified SNPs with a precision of 98.1%; recall of 85.2% and a F1-score of 0.912.ConclusionsOur analyses show that our method to amplify mtDNA and to sequence it using the nanopore technology is usable for mitochondrial DNA variant analysis. With minor modifications, this approach could easily be applied to other large circular DNA molecules.