bluuebunny/crossref_metadata_2025 huggingface dataset:
Tornadic shear stress induces a transient, calcineurin-dependent hyper-virulent phenotype in Mucorales molds
Authors: Wurster Sebastian , Tatara Alexander M. , Albert Nathaniel D. , Ibrahim Ashraf S. , Heitman Joseph , Lee Soo Chan , Shetty Amol C. , McCracken Carrie , Graf Karen T. , Mikos Antonios G. , Bruno Vincent M. , Kontoyiannis Dimitrios P.
Published: February 2020

Trauma-related necrotizing myocutaneous mucormycosis (NMM) has a high morbidity and mortality in victims of combat-related injuries, geo-meteorological disasters, and severe burns. Inspired by the observation that several recent clusters of NMM have been associated with extreme mechanical forces (e.g. during tornados), we studied the impact of mechanical stress on Mucoralean biology and virulence in aDrosophila melanogasterinfection model. In contrast to other experimental procedures to exert mechanical stress, tornadic shear challenge (TSC) by magnetic stirring induced a hyper-virulent phenotype in several clinically relevant Mucorales species but not inAspergillusorFusarium. Whereas fungal growth rates, morphogenesis, and susceptibility to noxious environments or phagocytes were not altered by TSC, soluble factors released in the supernatant of shear-challengedR. arrhizusspores rendered static spores hyper-virulent. Consistent with a rapid decay of TSC-induced hyper-virulence, minimal transcriptional changes were revealed by comparative RNA sequencing analysis of static and shear-challengedRhizopus arrhizus. However, inhibition of the calcineurin/heat shock protein 90 (hsp90) stress response circuitry by cyclosporine A (CsA) and tanespimycin abrogated the increased pathogenicity ofR. arrhizusspores following TSC. Similarly, calcineurin loss-of-function mutants ofMucor circinelloidesdisplayed no increased virulence capacity in flies after undergoing TSC. Collectively, these results establish that TSC induces hyper-virulence specifically in Mucorales and point out the calcineurin/hsp90 pathway as a key orchestrator of this phenotype. Our findings invite future studies of topical calcineurin inhibitor treatment of wounds as an adjunct mitigation strategy for NMM following high-energy trauma.

Significance

Given the limited efficacy of current medical treatments in trauma-related necrotizing mucormycosis, there is a dire need to better understand the Mucoralean pathophysiology in order to develop novel strategies to counteract fungal tissue invasion following severe trauma. Here, we describe that tornadic shear stress challenge transiently induces a hyper-virulent phenotype in various pathogenic Mucorales species but not in other molds known to cause wound infections. Our data support a model whereby shear stress-induced hyper-virulence is primarily driven by soluble factors and orchestrated by the calcineurin/hsp90 pathway. Importantly, pharmacological and genetic inhibition of calcineurin signaling abrogated hyper-virulence in shear stress-challenged Mucorales, encouraging further evaluation of (topical) calcineurin inhibitors to improve therapeutic outcomes of NMM after combat-related blast injuries or violent storms.
Increased mTOR activity and metabolic efficiency in mouse and human cells containing the African-centric tumor-predisposing p53 variant Pro47Ser
Authors: Gnanapradeepan Keerthana , Basu Subhasree , Barnoud Thibaut , Leu Julia I-Ju , Good Madeline , Lee Joyce V. , Quinn William J. , Kung Che-Pei , Ahima Rexford S. , Baur Joseph A. , Wellen Kathryn E. , Liu Qin , Schug Zachary T. , George Donna L. , Murphy Maureen E.
Published: February 2020

The Pro47Ser variant of p53 exists in African-descent populations, and is associated with increased cancer risk in humans and mice. This variant, hereafter S47, shows altered regulation of the cystine importerSlc7a11, and S47 cells possess increased cysteine and glutathione (GSH) accumulation compared to cells with wild type p53. In this study we show that mice containing the S47 variant have increased mTOR activity, increased oxidative metabolism, larger size, and improved metabolic efficiency. Mechanistically, we show that there is increased association between mTOR and its positive regulator Rheb in S47 cells, due to altered redox state of GAPDH, which normally binds and sequesters Rheb. Compounds that decrease glutathione in S47 cells normalize GAPDH-Rheb complex formation and mTOR activity. The enhanced metabolic efficiency may have been selected for in early Africa, making the S47 variant one of a growing number of cancer-predisposing genetic variants that possesses other positive, potentially selectable attributes.
GPU accelerated partial order multiple sequence alignment for long reads self-correction
Authors: Peverelli Francesco , Tucci Lorenzo Di , Santambrogio Marco D. , Ding Nan , Hofmeyr Steven , Buluç Aydın , Oliker Leonid , Yelick Katherine
Published: February 2020

As third generation sequencing technologies become more reliable and widely used to solve several genome-related problems, self-correction of long reads is becoming the preferred method to reduce the error rate of Pacific Biosciences and Oxford Nanopore long reads, that is now around 10-12%. Several of these self-correction methods rely on some form of Multiple Sequence Alignment (MSA) to obtain a consensus sequence for the original reads. In particular, error-correction tools such as RACON and CONSENT use Partial Order (PO) graph alignment to accomplish this task. PO graph alignment, which is computationally more expensive than optimal global pairwise alignment between two sequences, needs to be performed several times for each read during the error correction process. GPUs have proven very effective in accelerating several compute-intensive tasks in different scientific fields. We harnessed the power of these architectures to accelerate the error correction process of existing self-correction tools, to improve the efficiency of this step of genome analysis.

In this paper, we introduce a GPU-accelerated version of the PO alignment presented in the POA v2 software library, implemented on an NVIDIA Tesla V100 GPU. We obtain up to 6.5x speedup compared to 64 CPU threads run on two 2.3 GHz 16-core Intel Xeon Processors E5-2698 v3. In our implementation we focused on the alignment of smaller sequences, as the CONSENT segmentation strategy based on k-mer chaining provides an optimal opportunity to exploit the parallel-processing power of GPUs. To demonstrate this, we have integrated our kernel in the CONSENT software. This accelerated version of CONSENT provides a speedup for the whole error correction step that ranges from 1.95x to 8.5x depending on the input reads.
Temporal discounting in adolescents and adults with Tourette syndrome
Authors: Schüller Canan Beate , Wagner Ben Jonathan , Schüller Thomas , Baldermann Juan Carlos , Huys Daniel , auch Koerner Julia Kerner , Niessen Eva , Münchau Alexander , Brandt Valerie , Peters Jan , Kuhn Jens
Published: February 2020

Background

Tourette syndrome is a neurodevelopmental disorder with the clinical hallmarks of motor and phonic tics which are associated with hyperactivity in dopaminergic networks. Dopaminergic hyperactivity in the basal ganglia has previously been linked to increased sensitivity to positive reinforcement and increases in choice impulsivity.

Objective

We address whether this extends to changes in temporal discounting, where impulsivity is operationalized as an increased preference to choose smaller-but-sooner over larger-but-later rewards. Results are discussed with respect to neural models of temporal discounting, dopaminergic alterations in Tourette syndrome and the developmental trajectory of temporal discounting.

Methods

In the first study we included nineteen adolescent patients with Tourette syndrome and nineteen age- and education matched controls. In the second study, we compared twenty-five adult patients with Tourette syndrome and twenty-five age- and education-matched controls.

Results

In the light of the dopaminergic hyperactivity model, we predicted differences in temporal discounting in patients with Tourette syndrome. However, computational modeling of choice behavior using hierarchical Bayesian parameter estimation revealed reduced impulsive choice in adolescent patients, and no group differences in adults.

Conclusion

We speculate that adolescents might show reduced discounting due to improved inhibitory functions that also affect choice impulsivity and/or the developmental trajectory of executive control functions. The absence of an effect in adults might be due to differences in the clinical population (e.g. patients who acquired successful tic inhibition during adolescence might have gone into remission). Future studies would benefit from adopting longitudinal approaches to further elucidate the developmental trajectory of these effects.
The binding of palonosetron and other antiemetic drugs to the serotonin 5-HT3 receptor
Authors: Zarkadas Eleftherios , Zhang Hong , Cai Wensheng , Effantin Gregory , Perot Jonathan , Neyton Jacques , Chipot Christophe , Schoehn Guy , Dehez Francois , Nury Hugues
Published: February 2020

Inaccurately perceived as niche drugs, antiemetics are key elements of cancer treatment alleviating the most dreaded side effect of chemotherapy. Serotonin 5-HT3 receptor antagonists are the most commonly prescribed class of drugs to control chemotherapy-induced nausea and vomiting (CINV). These antagonists have been clinically successful drugs since the 1980s, yet our understanding of how they operate at the molecular level has been hampered by the difficulty of obtaining structures of drug-receptor complexes. Here, we report the cryo-EM structure of the palonosetron-bound 5-HT3 receptor. We investigate the binding of palonosetron, granisetron, dolasetron, ondansetron, and cilansetron using molecular dynamics, covering the whole set of antagonists used in the clinical practice. The structural and computational results yield detailed atomic insight into the binding modes of the drugs. In light of our data, we establish a comprehensive framework underlying the inhibition mechanism by the -setron drug family.
Disulfide bridge formation prevents CaMKII/Calmodulin interaction in Parkinson’s disease
Authors: Di Maio Roberto , General Ignacio J. , Furbee Emily , Ayoob Joseph C. , Castro Sandra L. , Bahar Ivet , Greenamyre J. Timothy , Pullara Filippo
Published: February 2020

There is increasing evidence for disordered Ca2+signaling in dopamine neurons in Parkinson’s disease (PD), and this likely involves altered Ca2+/calmodulin-dependent protein kinase II (CaMKII) function. Previous work suggests that oxidative stress - a major feature in PD pathogenesis - affects regulatory methionine residues that sustain CaMKII activity in a Ca2+/CaM-independent manner. Here, applying computational modeling, we predicted formation of a defined disulfide bridge close to the CaMKII docking site for Ca2+/CaM binding.In vitroandin vivoinvestigations using PD models revealed formation of a disulfide bridge and loss of the CaMKII–calmodulin interaction. Mutagenesis of the relevant cysteine residues abrogated disulfide bridge formation and recovered the CaMKII–calmodulin interaction. Importantly, dopamine neurons from post-mortem PD brain specimens also lost this regulatory protein-protein interaction, providing relevance in the human disease. This study provides novel insights into oxidative CaMKII-CaM dysfunction, which may contribute to the pathophysiology of PD.
In Silicoidentification of potential drug targets by subtractive genome analysis ofEnterococcus faecium DO
Authors: Karim Marwah , Islam MD Nazrul , Azad Jewel G. M. Nurnabi
Published: February 2020

Once believed to be a commensal bacteria,Enterococcus faeciumhas recently emerged as an important nosocomial pathogen worldwide. A recent outbreak ofE. faeciumunrevealed natural andin vitroresistance against a myriad of antibiotics namely ampicillin, gentamicin and vancomycin due to over-exposure of the pathogen to these antibiotics. This fact combined with the ongoing threat demands the identification of new therapeutic targets to combatE. faecium infections.

In this present study, comparative proteome analysis, subtractive genomic approach, metabolic pathway analysis and additional drug prioritizing parameters were used to propose a potential novel drug targets forE. faecium strainDO. Comparative genomic analysis of Kyoto Encyclopedia of Genes and Genomes annotated metabolic pathways identified a total of 207 putative target proteins inE. faecium DOthat showed no similarity to human proteins. Among them 105 proteins were identified as essential novel proteins that could serve as potential drug targets through further bioinformatic approaches; such as-prediction of subcellular localization, calculation of molecular weight, and web-based investigation of 3D structural characterization. Eventually 19 non-homologous essential proteins ofE. faecium DOwere prioritized and proved to have the eligibility to become novel broad-spectrum antibiotic targets. Among these targets aldehyde-alcohol dehydrogenase was found to be involved in maximum pathways, and therefore, was chosen as novel drug target. Interestingly, aldehyde-alcohol dehydrogenase enzyme contains two domains namely acetaldehyde dehydrogenase and alcohol dehydrogenase, on which a 3D structure homology modeling andin silicomolecular docking were performed. Finally, eight molecules were confirmed as the most suitable ligands for aldehyde-alcohol dehydrogenase and hence proposed as the potential inhibitors of this target.

In conclusion, being human non-homologous, aldehyde-alcohol dehydrogenase protein can be targeted for potential therapeutic drug development in future. However, laboratory based experimental research should be performed to validate our findingsin vivo.
Central vestibular tuning arises from patterned convergence of otolith afferents
Authors: Liu Zhikai , Kimura Yukiko , Higashijima Shin-ichi , Hildebrand David G. , Morgan Joshua L. , Holy Timothy E. , Bagnall Martha W.
Published: February 2020

As sensory information moves through the brain, higher-order areas exhibit more complex tuning than lower areas. Though models predict this complexity is due to convergent inputs from neurons with diverse response properties, in most vertebrate systems convergence has only been inferred rather than tested directly. Here we measure sensory computations in zebrafish vestibular neurons across multiple axesin vivo. We establish that whole-cell physiological recordings reveal tuning of individual vestibular afferent inputs and their postsynaptic targets. An independent approach, serial section electron microscopy, supports the inferred connectivity. We find that afferents with similar or differing preferred directions converge on central vestibular neurons, conferring more simple or complex tuning, respectively. Our data also resolve a long-standing contradiction between anatomical and physiological analyses by revealing that sensory responses are produced by sparse but powerful inputs from vestibular afferents. Together these results provide a direct, quantifiable demonstration of feedforward input convergencein vivo.
Cerebrospinal fluid metabolomics identifies 19 brain-related phenotype associations
Authors: Panyard Daniel J. , Kim Kyeong M. , Darst Burcu F. , Deming Yuetiva K. , Zhong Xiaoyuan , Wu Yuchang , Kang Hyunseung , Carlsson Cynthia M. , Johnson Sterling C. , Asthana Sanjay , Engelman Corinne D. , Lu Qiongshi
Published: February 2020

Advances in technology have allowed for the study of metabolomics in the context of disease, enabling the discovery of new potential risk factors, diagnostic markers, and drug targets. For neurological and psychiatric phenotypes, the cerebrospinal fluid (CSF) is of particular biomedical importance as it is in direct contact with the brain and spinal cord. However, the CSF metabolome is difficult to study on a large scale due to the relative complexity of the procedure needed to collect the fluid compared to blood or urine studies. Here, we present a metabolome-wide association study (MWAS), an analysis using individual-level genetic and metabolomic data from two cohorts to impute metabolites into large samples with genome-wide association summary statistics. We conducted a metabolome-wide genome-wide association analysis with 338 CSF metabolites, identifying 16 genotype-metabolite associations, 6 of which were novel. Using these results, we then built prediction models for all available CSF metabolites and tested for associations with 27 neurological and psychiatric phenotypes in large cohorts, identifying 19 significant CSF metabolite-phenotype associations. Our results demonstrate the potential of MWAS to overcome the logistic challenges inherent in cerebrospinal fluid research to study the role of metabolomics in brain-related phenotypes and the feasibility of this framework for similar studies of omic data in scarce sample types.
Effects of Sodium tanshinone IIA sulfonate on H9C2 cardiomyocyte injury induced by sodium arsenite
Authors: Xu Heli , Zhang Xinsheng , Liu Mengyao , Li Jiayu , Dou Wenjing , Wang Xiyan , Tan Hongyou , Ding Jian , Xie Juhua , Zhang Yue
Published: February 2020

Arsenic is a grade I human carcinogen that can cause kinds of damage to the body. The heart is one of the main target organs of arsenic damage, but the preventive and curative measures underlying arsenic poisoning are not clear. To investigate the effect of tanshinone IIA sulfonate (STS) on the injury of H9C2 cardiomyocytes induced by NaAsO2,H9C2 cardiomyocyteswere divided into four groups where control group with general medium, arsenic (As) group received sodium arsenite (NaAsO2)-containing general medium, STS pretreatment+As group and finally the STS alone group. Compared with the control group, different concentrations of STS had no significant effect on the cell viability (n = 6, P > 0.05); Compared with the control group, there was no significant change in the viability of cells treated with arsenic for 12 h after STS pretreatment for 6 h (n = 6, P > 0.05),the viability of cells treated with NaAsO2 alone was decreased(n = 6, P < 0.05);Compared with the control group, the cell viability was decreased after STS pretreatment for 12h and arsenic for 24h, the cell viability of NaAsO2 group was also decreased, the viability of NaAsO2 cells was lower than that of STS pretreated for 12h with NaAsO2 for 24h(n=6,p<0.05).The content of Caspase 3/7 in the NaAsO2 group was higher than that in the STS and NaAsO2 group and the Control group and STS group after 12h, the differences were statistically significant(n=6,p<0.05).After STS pretreatment for 12h and NaAsO2 for 24 h, there was no significant difference in Caspase 8 content between NaAsO2 group and other groups(n=6,P>0.05) As a result, Sodium tanshinone IIA sulfonate can attenuate the injury of H9C2 cardiomyocytes induced by sodium arsenite.
SPRTN protease and SUMOylation coordinate DNA-protein crosslink repair to prevent genome instability
Authors: Vaz Bruno , Ruggiano Annamaria , Popovic Marta , Rodriguez-Berriguete Gonzalo , Kilgas Susan , Singh Abhay N. , Higgins Geoffrey S. , Kiltie Anne E. , Ramadan Kristijan
Published: February 2020

DNA-protein crosslinks (DPCs) are a specific type of DNA lesions where proteins are covalently attached to DNA. Unrepaired DPCs lead to genomic instability, cancer, neurodegeneration and accelerated ageing. DPC proteolysis was recently discovered as a specialised pathway for DPC repair. The DNA-dependent SPRTN protease and 26S proteasome emerged as as two independent proteolytic systems for DPC repair. DPCs are also repaired by homologous recombination (HR), a canonical DNA repair pathway. While studying the role of ubiquitin and SUMO in DPC repair, we identified mutually exclusive signalling mechanisms associated with DPC repair pathway choice. DPC modification by SUMO-1 favours SPRTN proteolysis as the preferred pathway for DPC repair. DPC SUMOylation counteracts DPC ubiquitination, which promotes DNA breaks and the switch to HR. We propose that modification of DPCs by SUMO-1 promotes SPRTN proteolysis, which is essential for DPC removal to prevent DNA replication defects, chromosomal recombination and genomic instability.
Delivery of oligonucleotides to bone marrow to modulate ferrochelatase splicing in a mouse model of Erythropoietic Protoporphyria
Authors: Halloy François , Iyer Pavithra S. , Ćwiek Paulina , Ghidini Alice , Barman-Aksözen Jasmin , van Wijk Nicole Wildner-Verhey , Theocharides Alexandre , Minder Elisabeth I. , Schneider-Yin Xiaoye , Schümperli Daniel , Hall Jonathan
Published: February 2020

Erythropoietic protoporphyria (EPP) is a rare genetic disease in which patients experience acute phototoxic reactions after sunlight exposure. It is caused by a deficiency in ferrochelatase (FECH) in the heme biosynthesis pathway. Most patients exhibit a loss-of-function mutation intransto an allele bearing a SNP that favours aberrant splicing of transcripts. One viable strategy for EPP is to deploy splice-switching oligonucleotides (SSOs) to increase FECH synthesis, whereby an increase of a few percent would provide therapeutic benefit. However, successful application of SSOs in bone marrow cells is not described. Here, we show that SSOs comprising methoxyethyl-chemistry increase FECH levels in cells. We conjugated one SSO to three prototypical targeting groups and administered them to a mouse model of EPP in order to study their biodistribution, their metabolic stability and their FECH splice-switching ability. The SSOs exhibited distinct distribution profiles, with increased accumulation in liver, kidney, bone marrow and lung. However, they also underwent substantial metabolism, mainly at their linker groups. An SSO bearing a cholesteryl group increased levels of correctly spliced FECH transcript by 80% in the bone marrow. The results provide a promising approach to treat EPP and other disorders originating from splicing dysregulation in the bone marrow.
Long-term implicit memory for sequential auditory patterns in humans
Authors: Bianco Roberta , Harrison Peter M. C. , Hu Mingyue , Bolger Cora , Picken Samantha , Pearce Marcus T. , Chait Maria
Published: February 2020

To understand auditory scenes, listeners track and retain the statistics of sensory inputs as they unfold over time. We combined behavioural manipulation and modelling to investigate how sequence statistics are encoded into long-term memory and used to interpret incoming sensory signals. In a series of experiments, participants detected the emergence of regularly repeating patterns in novel rapid sound sequences. Unbeknownst to them, a few regular patterns reoccurred sparsely (every ∼3 minutes). Reoccurring sequences showed a rapidly growing detection time advantage over novel sequences. This effect was implicit, robust to interference, and persisted up to 7 weeks. Human performance was reproduced by a memory-constrained probabilistic model, where sequences are stored as n-grams and are subject to memory decay. Results suggest that similar psychological mechanisms may underlie integration processes over different-time scales in memory formation and flexible retrieval.
Diversity of culturable actinobacteria producing protease inhibitors isolated from the intertidal zones of Maharashtra, India
Authors: Shintre Neha , Baig Ulfat , Pund Anagha , Patwardhan Rajashree , Tamhane Vaijayanti , Deshpande Neelima
Published: February 2020

Phylogenetic diversity of culturable actinobacteria isolated from the intertidal regions of west coast of Maharashtra, India was studied using 16S rRNA gene sequencing. Total of 140 actinobacterial isolates were obtained, which belonged to 14 genera, 10 families and 65 putative species withStreptomycesbeing the most dominant (63%) genus followed byNocardiopsisandMicromonospora. They were screened for production of extracellular protease inhibitors (PI) against three pure proteases viz. chymotrypsin, trypsin, subtilisin and one crude extracellular protease fromPseudomonas aeruginosa. Eighty percent of the isolates showed PI activity against at least one of the four proteases, majority of them belonged to genusStreptomyes. Actinobacterial diversity from two sites Ade (17°52′ N, 73°04′ E) and Harnai (17°48′ N, 73°05′ E) with varying degree of anthropological pressure showed that more putative species diversity was obtained from site with lower human intervention i.e Ade (Shannon’s H 3.45) than from Harnai (Shannon’s H 2.83), a site with more human intervention. Further, in Ade percentage of isolates not showing PI activity against any of the proteases was close to 21% and that in Harnai was close to 9%. Considering human activities in the coastal region might be contributing to increasing the organic load and in turn increasing the presence of extracellular enzymes in the intertidal environments it would be interesting to look at the association of PI production and organic load in these habitats.
In vitro biosynthesis of poly-β-1,4-glucan derivatives using a pro-miscuous glycosyltransferase
Authors: Bulmer Gregory S. , Mattey Ashley P. , Parmeggiani Fabio , Williams Ryan , Ledru Helene , Marchesi Andrea , Seibt Lisa S. , Both Peter , Huang Kun , Galan M. Carmen , Flitsch Sabine L. , Green Anthony P. , van Munster Jolanda M.
Published: February 2020

The β-1,4-glucose linkage of cellulose is the most abundant polymeric linkage on earth and as such is of considerable interest in biology and biotechnology. It remains challenging to synthesize this linkage in vitro due to a lack of suitable biocatalysts; the natural cellulose biosynthetic machinery is a membrane-associated complex with processive activity that cannot be easily manipulated to synthesize tailor-made oligosaccharides and their derivatives. Here we identify a promiscuous activity of a soluble recombinant biocatalyst,Neisseria meningitidisglycosyltransferase LgtB, suitable for the polymerization of glucose from UDP-glucose via the generation of β-1,4-glycosidic linkages. We employed LgtB to synthesize natural and derivatized cello-oligosaccharides and we demonstrate how LgtB can be incorporated in biocatalytic cascades and chemo-enzymatic strategies to synthesize cello-oligosaccharides with tailored functionalities. We also show how the resulting glycan structures can be applied as chemical probes to report on activity and selectivity of plant cell wall degrading enzymes, including lytic polysaccharide monooxygenases. We anticipate that this biocatalytic approach to derivatized cello-oligosaccharides via glucose polymerization will open up new applications in biology and nanobiotechnology.
RanBP2-mediated SUMOylation promotes human DNA polymerase lambda nuclear localization and DNA repair
Authors: Moreno-Oñate M. , Herrero-Ruiz A.M. , García-Dominguez M. , Cortés-Ledesma F. , Ruiz J.F.
Published: February 2020

Cellular DNA is under constant attack by a wide variety of agents, both endogenous and exogenous. To counteract DNA damage, human cells have a large collection of DNA repair factors. Among them, DNA polymerase lambda (Polλ) stands out for its versatility, as it participates in different DNA repair and damage tolerance pathways in which gap-filling DNA synthesis is required. In this work we show that human Polλ is conjugated with Small Ubiquitin-like MOdifier (SUMO) proteins bothin vitroandin vivo, with Lys27 being the main target of this covalent modification. Polλ SUMOylation takes place in the nuclear pore complex and is mediated by the E3 ligase RanBP2. This post-translational modification promotes Polλ entry into the nucleus, which is required for its recruitment to DNA lesions and stimulated by DNA damage induction. Our work represents an advance in the knowledge of molecular pathways that regulate cellular localization of human Polλ, which are essential to be able to perform its functions during repair of nuclear DNA, and that might constitute an important point for the modulation of its activity in human cells.
“Enteric glia as a source of neural progenitors in adult zebrafish”
Authors: McCallum Sarah , Obata Yuuki , Fourli Evangelia , Boeing Stefan , Peddie Christopher J , Xu Qiling , Horswell Stuart , Kelsh Robert , Collinson Lucy , Wilkinson David , Pin Carmen , Pachnis Vassilis , Heanue Tiffany
Published: February 2020

The presence and identity of neural progenitors in the enteric nervous system (ENS) of vertebrates is a matter of intense debate. Here we demonstrate that the non-neuronal ENS cell compartment of teleosts shares molecular and morphological characteristics with mammalian enteric glia but cannot be identified by the expression of canonical glia markers. However, unlike their mammalian counterparts, which are generally quiescent and do not undergo neuronal differentiation during homeostasis, we show that a relatively high proportion of zebrafish enteric glia proliferate under physiological conditions giving rise to progeny that differentiate into enteric neurons. We also provide evidence that, similar to brain neural stem cells, the activation and neuronal differentiation of enteric glia are regulated by Notch signalling. Our experiments reveal remarkable similarities between enteric glia and brain neural stem cells in teleosts and open new possibilities for use of mammalian enteric glia as a potential source of neurons to restore the activity of intestinal neural circuits compromised by injury or disease.
SingleChlamydomonas reinhardi(C. reinhardtii) cell separation from bacterial cells and auto-fluorescence tracking with a nano-sieve device
Authors: Korensky Grant , Chen Xinye , Bao Mengdi , Miller Abbi , Lapizco-Encinas Blanca , Park Myeongkee , Du Ke
Published: February 2020

A planar, transparent, and adaptable nano-sieve device is developed for efficient microalgae/bacteria separation. In our strategy, a sacrificial layer is applied in the dual photolithography patterning to achieve a one-dimensional channel with a very low aspect ratio (1:10,000). Microalgae/bacteria mixture is then introduced into the deformable polydimethylsiloxane (PDMS) nano-channel. The hydrodynamic deformation of the nano-channel is regulated to allow the bacteria cells to pass through while leaving the microalgae cells trapped in the device. At a flow rate of 4 μl/min, ~100% of the microalgae cells are trapped in the device. Additionally, this device is capable of immobilizing single cells in a transparent channel for auto-fluorescence tracking. These microalgae cells demonstrate minimal photo-bleaching over 250 s laser exposure and can be used to monitor hazardous compounds in the sample with a continuous flow fashion. Our method will be valuable to purify microalgae samples containing contaminations and study single cell heterogeneity.
Viral channelrhodopsins: calcium-dependent Na+/K+selective light-gated channels
Authors: Zabelskii D. , Alekseev A. , Kovalev K. , Oliviera A.-S. , Balandin T. , Soloviov D. , Bratanov D. , Volkov D. , Vaganova S. , Astashkin R. , Chizhov I. , Yutin N. , Rulev M. , Popov A. , Rokitskaya T. , Antonenko Y. , Rosselli R. , Rodriguez-Valera F. , Armeev G. , Shaitan K. , Bueldt G. , Vivaudou M. , Kirpichnikov M. , Koonin E. , Bamberg E. , Gordeliy V.
Published: February 2020

Phytoplankton is the base of the marine food chain, oxygen, carbon cycle playing a global role in climate and ecology. Nucleocytoplasmic Large DNA Viruses regulating the dynamics of phytoplankton comprise genes of rhodopsins of two distinct families. We present a function-structure characterization of two homologous proteins representatives of family 1 of viral rhodopsins, OLPVR1 and VirChR1. VirChR1 is a highly selective, Ca2+-dependent, Na+/K+- conducting channel and, in contrast to known cation channelrhodopsins (ChRs), is impermeable to Ca2+ions. In human neuroblastoma cells, upon illumination, VirChR1 depolarizes the cell membrane to a level sufficient to fire neurons. It suggests its unique optogenetic potential. 1.4 Å resolution structure of OLPVR1 reveals their remarkable difference from the known channelrhodopsins and a unique ion-conducting pathway. The data suggest that viral channelrhodopsins mediate phototaxis of algae enhancing the host anabolic processes to support virus reproduction, and therefore, their key role in global phytoplankton dynamics.
DeepHE: Accurately Predicting Human Essential Genes based on Deep Learning
Authors: Zhang Xue , Xiao Wangxin , Xiao Weijia
Published: February 2020

Motivation

Accurately predicting essential genes using computational methods can greatly reduce the effort in finding them via wet experiments at both time and resource scales, and further accelerate the process of drug discovery. Several computational methods have been proposed for predicting essential genes in model organisms by integrating multiple biological data sources either via centrality measures or machine learning based methods. However, the methods aiming to predict human essential genes are still limited and the performance still need improve. In addition, most of the machine learning based essential gene prediction methods are lack of skills to handle the imbalanced learning issue inherent in the essential gene prediction problem, which might be one factor affecting their performance.

Results

We proposed a deep learning based method, DeepHE, to predict human essential genes by integrating features derived from sequence data and protein-protein interaction (PPI) network. A deep learning based network embedding method was utilized to automatically learn features from PPI network. In addition, 89 sequence features were derived from DNA sequence and protein sequence for each gene. These two types of features were integrated to train a multilayer neural network. A cost-sensitive technique was used to address the imbalanced learning problem when training the deep neural network. The experimental results for predicting human essential genes showed that our proposed method, DeepHE, can accurately predict human gene essentiality with an average AUC higher than 94%, the area under precision-recall curve (AP) higher than 90%, and the accuracy higher than 90%. We also compared DeepHE with several widely used traditional machine learning models (SVM, Naïve Bayes, Random Forest, Adaboost). The experimental results showed that DeepHE greatly outperformed the compared machine learning models.

Conclusions

We demonstrated that human essential genes can be accurately predicted by designing effective machine learning algorithm and integrating representative features captured from available biological data. The proposed deep learning framework is effective for such task.

Availability and Implementation

The python code will be freely available upon the acceptance of this manuscript athttps://github.com/xzhang2016/DeepHE.

Contact

xue.zhang@tufts.edu
MCT2 Overexpression Rescues Metabolic Vulnerability and Protects Retinal Ganglion Cells in Two Models of Glaucoma
Authors: Harun-Or-Rashid Mohammad , Pappenhagen Nathaniel , Zubricky Ryan , Coughlin Lucy , Jassim Assraa Hassan , Inman Denise M.
Published: February 2020

Improving cellular access to energy substrates is one strategy to overcome observed declines in energy production and utilization in the aged and pathologic central nervous system. Monocarboxylate transporters (MCTs), the movers of lactate, pyruvate, and ketone bodies into or out of a cell, are significantly decreased in the DBA/2J mouse model of glaucoma. In order to confirm MCT decreases are disease-associated, we decreased MCT2 in the retinas of MCT2fl/+mice using an injection of AAV2-cre, observing significant decline in ATP production and visual evoked potential. Restoring MCT2 levels in retinal ganglion cells (RGCs) via intraocular injection of AAV2-GFP-MCT2 in two models of glaucoma, the DBA/2J (D2), and a magnetic bead model of ocular hypertension (OHT), preserved RGCs and their function. Viral-mediated overexpression of MCT2 increased RGC density and axon number, reduced energy imbalance, and increased mitochondrial function as measured by cytochrome c oxidase and succinate dehydrogenase activity in both models of glaucoma. Ocular hypertensive mice injected with AAV2:MCT2 had significantly greater P1 amplitude as measured by pattern electroretinogram than mice with OHT alone. These findings indicate overexpression of MCT2 improves energy homeostasis in the glaucomatous visual system, suggesting that expanding energy input options for cells is a viable option to combat neurodegeneration.

Highlights

Loss of MCT2 in retina compromises visual function and ATP production in optic nerve

MCT2 overexpression preserves RGC soma and axon number in two glaucoma models

MCT2 overexpression improves energy homeostasis in optic nerve
A meiosis-specific factor C19orf57/4930432K21Rik/BRME1 modulates localization of RAD51 and DMC1 recombinases to DSBs in mouse meiotic recombination
Authors: Takemoto Kazumasa , Tani Naoki , Takada-Horisawa Yuki , Fujimura Sayoko , Tanno Nobuhiro , Yamane Mariko , Okamura Kaho , Sugimoto Michihiko , Araki Kimi , Ishiguro Kei-ichiro
Published: February 2020

Meiotic recombination is critical for genetic exchange and generation of chiasmata that ensures faithful chromosome segregation during meiosis I. Meiotic recombination is initiated by DNA double-strand break (DSB) followed by multiple processes of DNA repair. The exact mechanisms how recombinases localize to DSB remained elusive. Here we show that C19orf57/4930432K21Rik/BRME1 is a new player for meiotic recombination in mice. C19orf57/4930432K21Rik/BRME1 associates with ssDNA binding proteins, BRCA2 and MEILB2/HSF2BP, critical recruiters of recombinases onto DSB sites. Disruption of C19orf57/4930432K21Rik/BRME1 shows severe impact on DSB repair and male fertility. Remarkably, removal of single stranded DNA (ssDNA) binding proteins from DSB sites is delayed, and reciprocally the loading of RAD51 and DMC1 onto resected ssDNA is impaired inBrme1KO spermatocytes. We propose that C19orf57/4930432K21Rik/BRME1 modulates localization of recombinases to meiotic DSB sites through the interaction with the BRCA2-MEILB2/HSF2BP complex during meiotic recombination.
Faster and better CRISPR guide RNA design with the Crackling method
Authors: Bradford Jacob , Chappell Timothy , Perrin Dimitri
Published: February 2020

The design of CRISPR-Cas9 guide RNAs is not trivial, and is a computationally demanding task. Design tools need to identify target sequences that will maximise the likelihood of obtaining the desired cut, whilst minimising off-target risk. There is a need for a tool that can meet both objectives while remaining practical to use on large genomes.

Here, we present Crackling, a new method that is more suitable for meeting these objectives. We test its performance on 12 genomes and on data from validation studies. Crackling maximises guide efficiency by combining multiple scoring approaches. On experimental data, the guides it selects are better than those selected by others. It also incorporates Inverted Signature Slice Lists (ISSL) for faster off-target scoring. ISSL provides a gain of an order of magnitude in speed, while preserving the same level of accuracy. Overall, this makes Crackling a faster and better method to design guide RNAs at scale.

Crackling is available athttps://github.com/bmds-lab/Cracklingunder the Berkeley Software Distribution (BSD) 3-Clause license.
Revealing Atomic-scale Molecular Diffusion of a Plant Transcription Factor WRKY domain protein along DNA
Authors: Dai Liqiang , Xu Yongping , Du Zhenwei , Su Xiao-dong , Yu Jin
Published: February 2020

Transcription factor (TF) target search on genome is highly essential for gene expression and regulation. High-resolution determination of TF diffusion along DNA remains technically challenging. Here we constructed a TF model system of the plant WRKY domain protein in complex with DNA from crystallography and demonstrated microsecond diffusion dynamics of WRKY on the DNA employing all-atom molecular dynamics (MD) simulations. Notably, we found that WRKY preferentially binds to the Crick strand of DNA with significantly stronger energetic association than to the Watson strand. The preferential binding becomes highly prominent from non-specific to specific DNA binding, but less distinct from static binding to diffusive movements of WRKY on the DNA. Remarkably, without employing acceleration forces or bias, we captured a complete one-base pair (bp) stepping cycle of WRKY tracking along major groove of DNA with homogenous (AT)n sequence, as individual protein-DNA contacts break and reform at the binding interface. Continuous tracking of WRKY forward or backward, with occasional sliding as well as strand crossing to the minor groove of DNA, have also been captured in the simulation. The processive diffusion of WRKY had been confirmed by accompanied single-molecule fluorescence assays and coarse-grained (CG) structural simulations. The study thus provides unprecedented structural dynamics details on the TF diffusion, suggests how TF possibly approaches to gene target, and supports further high-precision experimental follow-up. The stochastic movements revealed in the TF diffusion also provide general clues on how other nucleic acid walkers step and slide along DNA.

Significance Statement

How transcription factors search for target genes impact on how quickly and accurately the genes are transcribed and expressed. To locate target sufficiently fast, 1D diffusion of the protein along DNA appears essential. Experimentally, it remains challenging to determine diffusional steps of protein on DNA. Here, we report all-atom equilibrium simulations of a WRKY protein binding and diffusing on DNA, revealing structural dynamics details which have not been identified previously. We unprecedently demonstrate a complete stepping cycle of the protein for one base pair on DNA within microseconds, along with stochastic stepping or sliding, directional switching, and strand crossing. Additionally, we have found preferential DNA strand association of WRKY. These suggest how protein factors approach toward target DNA sequences.
Histogenesis of the reticulum of non- descript goat (Capra hircus) of India
Authors: Gupta Varsha , Farooqui Muneer Mohhamad , Sharma Ajay Prakash , Pathak Archana
Published: February 2020

The study was conducted on 36 developing reticulum from healthy and normal embryos/ foeti of Indian goat. Embryos/foeti were assigned into three groups. Histo-differentiation of reticulum of goat stomach took place at 38 days of gestation. The wall of foetal reticulum was made up of three strata i. e. epithelium, pleuripotent blastemic tissue and serosa up to 49 days of fetal age and definite four layersviz.epithelium, propria-submucosa, tunica muscularis and serosa were observed first at 51 days of gestation. Upto 100 days of gestation the reticulum was lined by undifferentiated stratified epithelium and thereafter gradually transformed into stratified squamous epithelium. Keratinization was noticed at term. Primary and secondary reticular crests made their appearance at 60 and 112 days of gestation, respectively. Corial papillae were detected in primary and secondary reticular crests at 121 and 145 days of gestation, respectively. Near term, the core of the reticular crest also contained muscularis mucosae in its proximal 1/3rdregion while core of the corial papillae contained only lamina propria. Reticular, collagen and elastic fibers came into sight at 46, 100 and 134 days of gestation, respectively.

Summary statement

The study was conducted on intrauterine reticulum of Indian goat. From this study it can be concluded that the histogenesis of reticulum was almost completed in prenatal life. However, to become functional it still required more time as the relative sizes of reticulum and process of keratinization were yet to be completed.
Seneca Valley virus intercellular transmission mediated by exosomes
Authors: Zhang Keshan , Xu Guowei , Xu Shouxing , Shi Xijuan , Shen Chaochao , hao Junhong , yan Minhao , zhang dajun , Liu Xiangtao , Zheng Haixue
Published: February 2020

Exosomes are cup-shaped vesicles that are secreted by cells and are involved in the intercellular transport of a variety of substances, including proteins, RNA, and liposomes. Studies have shown that pathogenic microorganisms are contained in exosomes extracted from pathogenic micro-infected cells. The Seneca Valley virus (SVV) is a non-encapsulated single-stranded positive-strand RNA virus that causes ulceration in the pig’s nose, the appearance of blisters, and other clinical symptoms similar to foot-and-mouth disease (FMD). Whether exosomes from SVV-infected cells can mediate SVV intercellular transmission is of great significance. There have been no studies showing whether exosomes can carry SVV in susceptible and non-susceptible cells. Here, we first extracted and identified exosomes from SVV-infected IBRS-2 cells. It was confirmed that replication of SVV can be inhibited when IBRS-2 cells treated with exosomes inbihitor GW4869. Furthermore, laser confocal microscopy and qRT-PCR experiments were performed to investigate whether exosomes can carry SVV and enable the virus to proliferate in susceptible and non-susceptible cells. Finally, exosome-mediated intercellular transmission can not be completely blocked by SVV-specific neutralizing antibodies. Taken together, this study showed that exosomes extracted from the SVV-infected IBRS-2 cells can carry SVV and transmit productive SVV infection between SVV susceptible and non-susceptible cells, this transmit infection is resistant to SVV specific neutralization antibody.

IMPORTANCE

Exosomes participate in intercellular communnication between cells. Exosomes derived from virus-infected cells can mediate virus transmission or/and regulate immune response. However, the function of exosomes that from SVV-infected host cells during SVV transmission is unclear. Here, we demonstrate SVV can utilize host exosomes to establish productive infection in intercellular transmission. Furthermore, exosome-mediated SVV transmission is resistant to SVVV-specific neutralizing antibodies. This discovery sheds light on neutralizing antibodies resistant to SVVV transmission by exosomes as a potential immune evasion mechanism.
mTORC1 induces eukaryotic translation initiation factor 4E interaction with TOS-S6 kinase 1 and its activation
Authors: Majeed Sheikh Tahir , Batool Asiya , Majeed Rabiya , Bhat Nadiem Nazir , Andrabi Khurshid Iqbal
Published: February 2020

Eukaryotic translation initiation factor 4E was recently shown to be a substrate of mTORC1, suggesting it may be a mediator of mTORC1 signaling. Here, we present evidence that eIF4E phosphorylated at S209 interacts with TOS motif of S6 Kinase1 (S6K1). We also show that this interaction is sufficient to overcome rapamycin sensitivity and mTORC1 dependence of S6K1. Furthermore, we show that eIF4E-TOS interaction relieves S6K1 from auto-inhibition due to carboxy terminal domain (CTD) and primes it for hydrophobic motif (HM) phosphorylation and activation in mTORC1 independent manner. We conclude that the role of mTORC1 is restricted to engaging eIF4E with S6K1-TOS motif to influence its state of HM phosphorylation and inducing its activation.

Highlights

Phosphorylated eIF4E interacts with TOS motif of S6 Kinase1

eIF4E-TOS interaction relieves S6 Kinase 1 from carboxy terminal domain auto-inhibition and primes it for activation.