bluuebunny/crossref_metadata_2025 huggingface dataset:
OvirusTdb: A Repository of Oncolytic Viruses used in Cancer Treatment
Authors: Lathwal Anjali , Kumar Rajesh , Raghava Gajendra P.S.
Published: January 2020

One of the emerging technologies to fight against cancer is oncolytic virus-based immunotherapy which directly lysis tumor cells. Recently, the FDA approved an oncolytic virus named T-vec for the treatment of melanoma; several hundred other viruses are in clinical trials. In order to facilitate the scientific community to fight against cancer, we build a repository of oncolytic viruses called OvirusTdb (https://webs.iiitd.edu.in/raghava/ovirustdb/). This is a manually curated repository where information is curated from research papers and patents. The current version of the repository maintains comprehensive information on therapeutically important oncolytic viruses with 5927 records where each record has 25 fields such as the virus species, cancer cell line, synergism with anti-cancer drugs, and many more. It stores information on 09 types of DNA and 15 types of RNA viruses; 300 recombinant and 09 wildtype viral strains; tested against 124 cancer types and 427 cancer cell lines. Approximately, 1047 records show improved anti-cancer response using combinatorial approach of chemotherapeutic agents with virus strains. Nearly, 3243 and 1506 records show cancer cell death via apoptosis induction and immune activation, respectively. In summary, a user-friendly web repository of oncolytic viruses for information retrieval and analysis have been developed to facilitate researchers in designing and discovering new oncolytic viruses for effective cancer treatment.
Molecular Mechanisms of Non-ionotropic NMDA Receptor Signaling
Authors: Stein Ivar S. , Park Deborah K. , Jahncke Jennifer N. , Flores Juan C. , Zito Karen
Published: January 2020

Structural plasticity of dendritic spines is a key component of the refinement of synaptic connections during learning. Recent studies highlight a novel role for the NMDA receptor (NMDAR), independent of ion flow, in driving spine shrinkage and LTD. Yet little is known about the molecular mechanisms that link conformational changes in the NMDAR to changes in spine size and synaptic strength. Here, using two-photon glutamate uncaging to induce plasticity in hippocampal CA1 neurons from mice and rats, we demonstrate that p38 MAPK is required downstream of conformational NMDAR signaling to drive both spine shrinkage and LTD at individual dendritic spines. In a series of pharmacological and molecular genetic experiments, we identify key components of the non-ionotropic NMDAR signaling pathway driving dendritic spine shrinkage, including the interaction between NOS1AP and nNOS, nNOS enzymatic activity, activation of MK2 and cofilin, and signaling through CaMKII. Our results represent a large step forward in delineating the molecular mechanisms of non-ionotropic NMDAR signaling that drive the shrinkage and elimination of dendritic spines during synaptic plasticity.
Independent domestications shape the genetic pattern of a reproductive isolation system in rice
Authors: Xu Xun , Ge Song , Zhang Fu-Min
Published: January 2020

Severe reproductive isolation (RI) exists between the two subspecies of rice,IndicaandJaponica, but in the wild ancestors no post-zygotic RI was found. The studies about the establishment of the interspecies RI of rice are still rear. A pair of rice hybrid sterility genes,DOPPELGANGER 1(DPL1) andDOPPELGANGER 2(DPL2), offers a convenient example to study the evolutionary history of RI genes. Either of the two loci has one non-functional allele (DPL1-andDPL2-). The hybrid pollen carrying bothDPL1-andDPL2-will be sterility.

We collected 811 individuals:Oryza sativa(132), the two wild ancestorsO. nivara(296) andO. rufipogon(383) as well as 20DPL1and 34DPL2sequences ofO. sativafrom on-line databases. We analysed the genetic and geographic pattern ofDPLsin all three species to determine the origination regions ofDPL1-andDPL2-. The neutral test as well as the diversities of nucleotide and haplotype were used to detect if selection shaped the pattern ofDPLs.

We found thatDPL1-andDPL2-of rice emerged from wild ancestor populations in South Asia and South China through two respective domestications. Comparing with the ancestral populations,DPL1-andDPL2-both showed reduce of diversities, however their frequencies increased in rice. We assume that the reduce of diversities due to the bottleneck effect of domestication while the loss of one copy was preferred by artificial selection for cost savings.
Catabolism of 3-hydroxypyridine byEnsifer adhaerensHP1: a novel four-component gene encoding 3-hydroxypyridine dehydrogenase HpdA catalyzes the first step of biodegradation
Authors: Wang Haixia , Wang Xiaoyu , Ren Hao , Wang Xuejun , Lu Zhenmei
Published: January 2020

3-Hydroxypyridine (3HP) is an important natural pyridine derivative.Ensifer adhaerensHP1 can utilize 3HP as the sole source of carbon, nitrogen and energy to grow. However, the genes responsible for the degradation of 3HP remain unknown. In this study, we predicted that a gene cluster, designated3hpd, may be responsible for the degradation of 3HP. The initial hydroxylation of 3HP is catalyzed by a four-component dehydrogenase (HpdA1A2A3A4), leading to the formation of 2,5-dihydroxypyridine (2,5-DHP) inE. adhaerensHP1. In addition, the SRPBCC component in HpdA existed as a separate subunit, which is different from other SRPBCC-containing molybdohydroxylases acting on N-heterocyclic aromatic compounds. Our findings provide a better understanding of the microbial degradation of pyridine derivatives in nature. Additionally, research on the origin of the discovered four-component dehydrogenase with a separate SRPBCC domain may be of great significance.

Importance

3-Hydroxypyridine is an important building block for synthesizing drugs, herbicides and antibiotics. Although the microbial degradation of 3-hydroxypyridine has been studied for many years, the molecular mechanisms remain unclear. Here, we show that3hpdis responsible for the catabolism of 3-hydroxypyridine. The3hpdgene cluster was found to be widespread inActinobacteria,Rubrobacteria,Thermoleophilia, andAlpha-,Beta-, andGammaproteobacteria, and the genetic organization of the3hpdgene clusters in these bacteria showed high diversity. Our findings provide new insight into the catabolism of 3-hydroxypyridine in bacteria.
Tissue engineered model of hepatic breast cancer micrometastasis shows host-dependent colonization patterns and drug responses
Authors: Guller Anna , Rozova Vlada , Kuschnerus Inga , Khabir Zahra , Nadort Annemarie , Garcia-Bennett Alfonso , Liang Liuen , Qian Yi , Goldys Ewa M. , Zvyagin Andrei V.
Published: January 2020

Early stages of colonization of distant organs by metastatic cancer cells (micrometastasis) remain almost inaccessible to study due to lack of relevant experimental approaches. Here, we show the first 3D tissue engineered model of hepatic micrometastasis of triple negative breast cancer (TNBC). It reproduces characteristic histopathological features of the disease and reveals that metastatic TNBC cells colonize liver parenchymal and stromal extracellular matrix with different speed and by different strategies. These engineered tumors induce the angiogenic switch when grafted in vivo, confirming their metastatic-specific behaviour. Furthermore, we proved feasibility and biological relevance of our model for drug and nanoparticle testing and found a down-regulatory effect of the liver microenvironment of the sensitivity of TNBC cells to chemotherapeutic drug doxorubicin in free and nanoformulated forms. The convenient and affordable methodology established here can be translated to other types of metastatic tumors for basic cancer biology research and adapted for high-throughput assays.
NAChRDB: A Web Resource of Structure-Function Annotations to Unravel the Allostery of Nicotinic Acetylcholine Receptors
Authors: Chareshneu Aliaksei , Pant Purbaj , José Tristão Ramos Ravi , Gökbel Tuğrul , Ionescu Crina-Maria , Koča Jaroslav
Published: January 2020

Due to their paramount importance, near-ubiquitous presence, and complex nature, nicotinic acetylcholine receptors (nAChRs) have remained the focus of intensive research for over 50 years. The vast amount of knowledge accumulated on the topic has become extremely difficult to navigate. NAChRDB addresses this challenge by providing web-based, real-time access to curated residue-level functional annotations of neuromuscular nAChRs with interactive 3D visualization and sequence alignment. NAChRDB provides systematic access to experimental observations and predictions from computational studies reported in the literature or performed specifically to complement current knowledge, which allows new findings to be interpreted in a more holistic context, both from a structural and a functional perspective. NAChRDB aims to serve as an invaluable resource for identifying gaps in knowledge and for guiding discovery through structural and molecular biology experiments, especially when exploring the allosteric mechanisms underlying neuromuscular nAChR function and pathology.

Availability and Implementation

NAChRDB is freely available online, with a self-explanatory interface and useful tool tips (https://crocodile.ncbr.muni.cz/Apps/NAChRDB/). No installation or user registration is required. NAChRDB content is stored in .json format, queried using Python, and rendered in browser using Javascript and WebGL (LiteMol). NAChRDB is highly responsive and accessible through any modern Internet browser on desktop and mobile devices.

Contact

jkoca@ceitec.cz

Supplementary information

Supplementary data are available online.
In vivocontrol of the ezrin/radixin/moesin protein ERM-1 inC. elegans
Authors: Ramalho João J. , Nicolle Ophélie , Michaux Grégoire , Boxem Mike
Published: January 2020

ERM proteins are conserved regulators of cortical membrane specialization, that function as membrane–actin linkers and molecular hubs. Activity of ERM proteins requires a conformational switch from an inactive cytoplasmic form into an active membrane- and actin-bound form, which is thought to be mediated by sequential PIP2-binding and phosphorylation of a conserved C-terminal threonine residue. Here, we use the singleC. elegansERM ortholog, ERM-1, to study the contribution of these regulatory events to ERM activity and tissue formationin vivo. Using CRISPR/Cas9-generatederm-1mutant alleles we demonstrate that PIP2-binding is critically required for ERM-1 function. In contrast, dynamic regulation of C-terminal T544 phosphorylation is not essential but modulates ERM-1 apical localization and dynamics in a tissue-specific manner, to control cortical actin organization and drive lumen formation in epithelial tubes. Our work highlights the dynamic nature of ERM protein regulation during tissue morphogenesis and the importance of C-terminal phosphorylation in fine-tuning ERM activity in a tissue-specific context.
Changes in the gene expression profile during spontaneous migraine attacks
Authors: Kogelman Lisette J.A. , Falkenberg Katrine , Buil Alfonso , Erola Pau , Courraud Julie , Laursen Susan Svane , Michoel Tom , Olesen Jes , Hansen Thomas F.
Published: January 2020

Objective

Migraine occurs in clearly defined attacks and thus lends itself to investigate changes during and outside attack. Gene expression fluctuates according to environmental and endogenous events and therefore is likely to reveal changes during a migraine attack. We examined the hypothesis that changes in RNA expression during and outside of a spontaneous migraine attack exist which are specific to the migraine attack.

Methods

We collected blood samples from 27 migraine patients during an attack, two hours after treatment with subcutaneous sumatriptan, on a headache-free day and after a cold pressor test. All patients were deeply phenotyped, including headache characteristics and treatment effect during the sampling. RNA-Sequencing, genotyping, and steroid profiling was performed on all samples. RNA-Sequences were analyzed at gene level (differential expression analysis) and at network level, and we integrated transcriptomic and genomic data.

Results

We found 29 differentially expressed (DE) genes between ‘attack’ and ‘after treatment’, after subtracting non-migraine specific genes, i.e. genes related to a general pain/stress response. DE genes were functioning in fatty acid oxidation, signaling pathways and immune-related pathways. Network analysis revealed molecular mechanisms affected by change in gene interactions during the migraine attack, e.g. ‘ion transmembrane transport’ and ‘response to stress’. Integration of genomic and transcriptomic data revealed pathways related to sumatriptan treatment, i.e. ‘5HT1 type receptor mediated signaling pathway’.

Interpretation

Using a paired-sample design, we uniquely investigated intra-individual changes in the gene expression during a migraine attack. We revealed both genes and pathway potentially involved in the pathophysiology of migraine.
A phospho-switch in the N-terminus of NRT2.1 affects nitrate uptake by controlling the interaction of NRT2.1 with NAR2.1
Authors: Li Zhi , Wu Xu Na , Jaquot Aurore , Lejay Larence , Schulze Waltraud X
Published: January 2020

NRT2.1 can be phosphorylated at five different sites within N- and C-terminus. Here, we provide a systematic functional characterization of phosphorylation at S21 and S28 within the N-terminus of NRT2.1. We used existing phosphoproteomic data sets of nitrate starvation and nitrate resupply to construct a site-specific correlation network identifying kinase candidates to phosphorylate NRT2.1. By this approach, we identified NITRATEUPTAKEREGULATORYKINASE1 (AT5G49770) which itself was regulated by phosphorylation at S839 and S870 within its kinase domain. In the active state, when S839 was dephosphorylated and S870 was phosphorylated, NURK1 was found to interact with NRT2.1 at dephosphorylated S28. Upon that interaction, NURK1 can phosphorylate NRT2.1 at S21. Phosphorylation of NRT2.1 at S21 resulted in low interaction of NRT2.1 with its activator protein NAR2.1. By contrast, phosphorylation of NRT2.1 at S28 by a yet unknown kinase enhanced the interaction with NAR2.1, but inhibited the interaction with NURK1. We propose that serines S21 and S28 are involved in a phospho-switch mechanism and by which the interaction of NRT2.1 with its activator NAR2.1, and thus NRT2.1 activity, is modulated. NURK1 here was identified as the kinase affecting this phospho-switch through phosphorylation of NRT2.1 at S21 leading to inactivation of NRT2.1.
Crystal structure of calcium bound outer membrane phospholipase A (OmpLA) fromSalmonella typhiandin silicoanti-microbial screening
Authors: Perumal Perumal , Raina Rahul , Narayanan Sundara Baalaji , Arockiasamy Arulandu
Published: January 2020

Antimicrobial resistance is widespread inSalmonellainfections that affect millions worldwide.Salmonella typhiand other Gram-negative bacterial pathogens encode an outer membrane phospholipase A (OmpLA), crucial for their membrane integrity. Further, OmpLA is implicated in pathogen internalization, haemolysis, acid tolerance, virulence and sustained infection in human hosts. OmpLA is an attractive drug target for developing novel anti-microbials that attenuate virulence, as the abrogation of OmpLA encodingpldAgene causes loss of virulence. Here, we present the crystal structure ofSalmonella typhiOmpLA in dimeric calcium bound activated state at 2.95 Å. Structure analysis suggests that OmpLA is a potential druggable target. Further, we have identified and shortlisted small molecules that bind at the dimer interface using structure basedin silicoscreening, docking and molecular dynamics. While it requires further experimental validation, anti-microbial discovery targeting OmpLA from gram-negative pathogens offers an advantage as OmpLA is required for virulence.
Preventing Jacob-induced transcriptional inactivation of CREB protects synapses from β-amyloid in Alzheimer’s Disease
Authors: Grochowska Katarzyna M. , Gomes Guilherme M. , Raman Rajeev , Kaushik Rahul , Sosulina Liudmila , Kaneko Hiroshi , Oelschlegel Anja M. , Yuanxiang PingAn , Reyes-Resina Irene , Bayraktar Gonca , Samer Sebastian , Spilker Christina , Woo Marcel S. , Morawski Markus , Goldschmidt Jürgen , Friese Manuel A. , Rossner Steffen , Navarro Brugal Gemma , Remy Stefan , Reissner Carsten , Karpova Anna , Kreutz Michael R.
Published: January 2020

Synaptic dysfunction caused by soluble β-Amyloid (Aβ) is a hallmark of the early stage of Alzheimer’s disease (AD) and is tightly linked to cognitive decline. Aβ induces by yet unknown mechanisms disruption of transcriptional activity of cAMP– responsive element-binding protein (CREB), a master regulator of cell survival and plasticity-related gene expression. Here, we report that Aβ elicits cytonuclear trafficking of Jacob, a protein serves as a mobile signaling hub that docks a signalosome to CREB, which induces transcriptional inactivation and subsequent synapse impairment and eventually loss in AD. The small chemical compound Nitarsone selectively hinders assembly of this signalosome and thereby restores CREB transcriptional activity. Nitarsone prevents impairment of synaptic plasticity as well as cognitive decline in mouse models of AD. Collectively, the data suggest that targeting Jacob induced CREB shutoff is a therapeutic avenue against early synaptic dysfunction in AD.
CD4+follicular helper-like T cells are key players in anti-tumor immunity
Authors: Singh D , Ganesan AP , Panwar B , Eschweiler S , Hanley CJ , Madrigal A , Ramírez-Suástegui C , Wang A , Clarke J , Wood O , Garrido-Martin EM , Chee SJ , Seumois G , Belanger S , Alzetani A , Woo E , Friedmann PS , Crotty S , Thomas GJ , Sanchez-Elsner T , Ay F , Ottensmeier CH , Vijayanand P
Published: January 2020

To determine the nature of CD4+T cells that provide ‘help’ for generating robust anti-tumor CD8+cytotoxic T cell (CTL) responses, we profiled the transcriptomes of patient-matched CD4+and CD8+T cells present in the tumor micro-environment (TME) and analyzed them jointly using integrated weighted gene correlation network analysis. We found the follicular helper T cell (TFH) program in CD4+T cells was strongly associated with proliferation and tissue-residency in CD8+CTLs. Single-cell analysis demonstrated the presence of TFH-like cells and features linked to cytotoxic function and their provision of CD8+T cell ‘help’. Tumor-infiltrating TFH-like cells expressed PD-1 and were enriched in tumors following checkpoint blockade, suggesting that they may respond to anti-PD-1 therapy. Adoptive transfer or induction of TFHcells in mouse models resulted in augmented CD8+CTL responses and impairment of tumor growth, indicating an important role of TFH-like CD4+T cells in anti-tumor immunity.
4DNvestigator: Time Series Genomic Data Analysis Toolbox
Authors: Lindsly Stephen , Chen Can , Liu Sijia , Ronquist Scott , Dilworth Samuel , Perlman Michael , Rajapakse Indika
Published: January 2020

Data on genome organization and output over time, or the 4D Nucleome (4DN), require synthesis for meaningful interpretation. Development of tools for the efficient integration of these data is needed, especially for the time dimension. We present the “4DNvestigator”, a user-friendly network based toolbox for the analysis of time series genome-wide genome structure (Hi-C) and gene expression (RNA-seq) data. Additionally, we provide methods to quantify network entropy, tensor entropy, and statistically significant changes in time series Hi-C data at different genomic scales.

Availability

https://github.com/lindsly/4DNvestigator
Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju
Authors: Tovo Anna , Menzel Peter , Krogh Anders , Lagomarsino Marco Cosentino , Suweis Samir
Published: January 2020

Characterizing species diversity and composition of bacteria hosted by biota is revolutionizing our understanding of the role of symbiotic interactions in ecosystems. However, determining microbiomes diversity implies the classification of taxa composition within the sampled community, which is often done via the assignment of individual reads to taxa by comparison to reference databases. Although computational methods aimed at identifying the microbe(s) taxa are available, it is well known that inferences using different methods can vary widely depending on various biases. In this study, we first apply and compare different bioinformatics methods based on 16S ribosomal RNA gene and whole genome shotgun sequencing for taxonomic classification to three small mock communities of bacteria, of which the compositions are known. We show that none of these methods can infer both the true number of taxa and their abundances. We thus propose a novel approach, named Core-Kaiju, which combines the power of shotgun metagenomics data with a more focused marker gene classification method similar to 16S, but based on emergent statistics of core protein domain families. We thus test the proposed method on the three small mock communities and also on medium- and highly complex mock community datasets taken from the Critical Assessment of Metagenome Interpretation challenge. We show that Core-Kaiju reliably predicts both number of taxa and abundance of the analysed mock bacterial communities. Finally we apply our method on human gut samples, showing how Core-Kaiju may give more accurate ecological characterization and fresh view on real microbiomes.
Intergenic RNA mainly derives from nascent transcripts of known genes
Authors: Federico Agostini , Julian Zagalak , Jan Attig , Jernej Ule , Luscombe Nicholas M.
Published: January 2020

Background

Eukaryotic genomes undergo pervasive transcription, leading to the production of many types of stable and unstable RNAs. Transcription is not restricted to regions with annotated gene features but includes almost any genomic context. Currently, the source and function of most RNAs originating from intergenic regions in the human genome remains unclear.

Results

We hypothesised that many intergenic RNA can be ascribed to the presence of as-yet unannotated genes or the ‘fuzzy’ transcription of known genes that extends beyond the annotated boundaries. To elucidate the contributions of these two sources, we assembled a dataset of >2.5 billion publicly available RNA-seq reads across 5 human cell lines and multiple cellular compartments to annotate transcriptional units in the human genome. About 80% of transcripts from unannotated intergenic regions can be attributed to the fuzzy transcription of existing genes; the remaining transcripts originate mainly from putative long non-coding RNA loci that are rarely spliced. We validated the transcriptional activity of these intergenic RNA using independent measurements, including transcriptional start sites, chromatin signatures, and genomic occupancies of RNA polymerase II in various phosphorylation states. We also analysed the nuclear localisation and sensitivities of intergenic transcripts to nucleases to illustrate that they tend to be rapidly degraded either ‘on-chromatin’ by XRN2 or ‘off-chromatin’ by the exosome.

Conclusions

We provide a curated atlas of intergenic RNAs that distinguishes between alternative processing of well annotated genes from independent transcriptional units based on the combined analysis of chromatin signatures, nuclear RNA localisation and degradation pathways.
Loss of Complement Factor H impairs antioxidant capacity and energy metabolism of human RPE cells
Authors: Armento Angela , Honisch Sabina , Panagiotakopoulou Vasiliki , Sonntag Inga , Jacob Anke , Kilger Ellen , Deleidi Michela , Clark Simon , Ueffing Marius
Published: January 2020

Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly population. About 50% of AMD patients present polymorphisms in the Complement Factor H (CFH) gene, coding for Factor H protein (FH). AMD-associatedCFHrisk variants, Y402H in particular, impair FH function leading to complement overactivation. In AMD, retinal homeostasis is compromised due to dysfunction of retinal pigment epithelium (RPE) cells. Whether FH contributes to AMD pathogenesis only via complement system dysregulation remains unclear. To investigate the potential role of FH on energy metabolism and oxidative stress in RPE cells, we silencedCFHin human hTERT-RPE1 cells. FH-deprived RPE cells exposed to oxidative insult, showed altered metabolic homeostasis, including reduction of glycolysis and mitochondrial respiration, paralleled by an increase in lipid peroxidation. Our data suggest that FH protects RPE cells from oxidative stress and metabolic reprogramming, highlighting a novel function for FH in AMD pathogenesis.

Graphical abstract
Transcriptional elongation machinery controls vulnerability of breast cancer cells to PRC2 inhibitors
Authors: Chan Ngai Ting , Liu Peng , Huang Junfeng , Wang Yidan , Ong Irene , Li Lingjun , Xu Wei
Published: January 2020

CTR9 is the scaffold subunit in Paf1c, a multifunctional complex regulating multiple steps of RNA Pol II-mediated transcription. Using inducible and stable CTR9 knockdown breast cancer cell lines, we discovered that the expression of a subset of KDMs, including KDM6A and Jarid2, is strictly controlled by CTR9. Global analyses of histone modifications revealed a significant increase of H3K27me3 upon loss of CTR9. Loss of CTR9 results in a decrease of H3K4me3 and H3K36me3 in gene bodies, and elevated levels and genome-wide expansion of H3K27me3. Mechanistically, CTR9 depletion triggers a PRC2 subtype switching from PRC2.2 to PRC2.1. As a consequence, CTR9 depletion generates vulnerability that renders breast cancer cells hypersensitive to PRC2 inhibitors. Our findings that CTR9 demarcates PRC2-mediated H3K27me3 levels and genomic distribution, provide a unique mechanism of transition from transcriptionally active to repressive chromatin states and sheds light on the biological functions of CTR9 in development and cancer.
A working memory intervention weakens the reconsolidation of a threat memory and its biases processing towards threat
Authors: Picco Soledad , Bavassi Luz , Fernández Rodrigo S. , Pedreira María E.
Published: January 2020

BACKGROUND

Threat-conditioning (TC) memory plays a central role in anxiety disorders, but not in a simple way. This memory impacts on complex cognitive systems by modifying behavioral responses with a bias to fearful stimuli and overestimating potential threats. In this study we proposed a global approach analyzing the scope of disrupting TC memory reconsolidation in the implicit memory, the declarative contingency and the cognitive biases.

METHODS

Day 1: Subjects were trained on TC. Day 2: after Threat-memory reactivation, one group performed a high demanding working memory task (HWM) and the other a low demanding working memory task (LWM). The last group, only performed the HWM task. Day 3: TC memory was tested by an extinction session followed by reinstatement. Finally, all subjects completed tasks targeting stimuli representation, valuation and attentional bias towards threat.

RESULTS

Disrupting reconsolidation of TC memory with a HWM weakened the implicit memory retention and faded the representation and valuation towards threat but it had no effect on attentional bias. Moreover, we revealed that subjects’ performance during the working memory task was specifically associated in TC memory retention.

CONCLUSIONS

Our findings reveal a strong impairment of the threat-memory restabilization and associated emotional biases. This may result from the competition between defensive survival and central-executive control networks. Our results fits with Experimental Psychopathology approach, disentangling the relation between the implicit memory, cognitive, valenced systems and the possibility to weaken both the threatening memory and the systems associated with the maintenance of anxiety profile.
Assessing the Intra- and Inter-Subject Reliability of the Perturbational Complexity Index (PCI) of Consciousness for Three Brain Regions Using TMS-EEG
Authors: Caulfield Kevin A. , Savoca Matthew T. , Lopez James W. , Summers Philipp M. , Li Xingbao , Fecchio Matteo , Casarotto Silvia , Massimini Marcello , George Mark S.
Published: January 2020

Background

The perturbational complexity index (PCI) is a useful measure of consciousness that combines transcranial magnetic stimulation (TMS) with electroencephalography (EEG). However, the PCI has not been assessed for reliability between sessions nor is there a clear best stimulation target to acquire a PCI.

Objective/Hypothesis

We assessed the reliability of within-subject PCIs between 3 sessions with stimulation over the same premotor, motor, and parietal targets between visits, hypothesizing that we could determine a most reliable TMS-EEG target to acquire PCIs in healthy, conscious adults.

Methods

PCIs were acquired for 9 participants (5 women) over 3 sessions within a week. A 64 channel EEG system was used with all electrode impedances ≤ 10kΩ. Premotor, motor, and parietal stimulation targets were identified using a real-time Matlab graphical user interface (GUI). Neuronavigation using an MRI-template brain ensured that every TMS pulse was delivered within 3.0mm and 5° of the stimulation target.

Results

Premotor, motor, and parietal PCIs all had significant PCIs (all p < 0.05). However, parietal and motor PCIs had excellent reliability (ICCs = 0.927 and 0.857 respectively) whereas premotor PCIs had good reliability (ICC = 0.737). PCIs were similar between brain sites within each subject in a single visit, but with only a moderate effect (p = 0.024, ICC = 0.480). PCIs on a group level did not differ between brain sites (p = 0.589).

Conclusions

The PCI is a reliable measure over this timeframe within each subject for single brain targets. PCIs for parietal and motor sites are most similar between visits. Due to only moderate similarity between PCIs from three brain sites within each session, PCIs should be acquired over at least two brain sites, with parietal and motor regions as the top candidates.
Red Panda: A novel method for detecting variants in single-cell RNA sequencing
Authors: Cornish Adam , Roychoudhury Shrabasti , Sarma Krishna , Pramanik Suravi , Bhakat Kishor , Dudley Andrew , Mishra Nitish K , Guda Chittibabu
Published: January 2020

Single-cell sequencing enables us to better understand genetic diseases, such as cancer or autoimmune disorders, which are often affected by changes in rare cells. Currently, no existing software is aimed at identifying single nucleotide variations or micro (1-50bp) insertions and deletions in single-cell RNA sequencing (scRNA-seq) data. Generating high-quality variant data is vital to the study of the aforementioned diseases, among others. In this study, we report the design and implementation of Red Panda, a novel method to accurately identify variants in scRNA-seq data. Variants were called on scRNA-seq data from human articular chondrocytes, mouse embryonic fibroblasts (MEFs), and simulated data stemming from the MEF alignments. Red Panda had the highest Positive Predictive Value at 45.0%, while other tools—FreeBayes, GATK HaplotypeCaller, GATK UnifiedGenotyper, Monovar, and Platypus—ranged from 5.8%-41.53%. From the simulated data, Red Panda had the highest sensitivity at 72.44%. We show that our method provides a novel and improved mechanism to identify variants in scRNA-seq as compared to currently-existing software.

Availability

Source code freely available under the MIT License athttps://github.com/adambioi/red_panda, and is supported on Linux
Serum cytokine levels are modulated by specific frequencies, amplitudes, and pulse widths of vagus nerve stimulation
Authors: Tsaava Téa , Datta-Chaudhuri Timir , Addorisio Meghan E. , Masi Emily Battinelli , Silverman Harold A. , Newman Justin E. , Imperato Gavin H. , Bouton Chad , Tracey Kevin J. , Chavan Sangeeta S. , Chang Eric H.
Published: January 2020

Electrical stimulation of peripheral nerves is a widely used technique to treat a variety of conditions including chronic pain, motor impairment, headaches, and epilepsy. Nerve stimulation to achieve efficacious symptomatic relief depends on the proper selection of electrical stimulation parameters to recruit the appropriate fibers within a nerve. Recently, electrical stimulation of the vagus nerve has shown promise for controlling inflammation and clinical trials have demonstrated efficacy for the treatment of inflammatory disorders. This application of vagus nerve stimulation activates the inflammatory reflex, reducing levels of inflammatory cytokines during inflammation. Here, we wanted to test whether altering the parameters of electrical vagus nerve stimulation would change circulating cytokine levels of normal healthy animals in the absence of increased inflammation. To examine this, we systematically tested a set of electrical stimulation parameters and measured serum cytokine levels in healthy mice. Surprisingly, we found that specific combinations of pulse width, pulse amplitude, and frequency produced significant increases of the pro-inflammatory cytokine tumor necrosis factor alpha (TNFα), while other parameters selectively lowered serum TNFα levels, as compared to sham-stimulated mice. In addition, serum levels of the anti-inflammatory cytokine interleukin-10 (IL-10) were significantly increased by select parameters of electrical stimulation but remained unchanged with others. These results indicate that electrical stimulation parameter selection is critically important for the modulation of cytokines via the cervical vagus nerve and that specific cytokines can be increased by electrical stimulation in the absence of inflammation. As the next generation of bioelectronic therapies and devices are developed to capitalize on the neural regulation of inflammation, the selection of nerve stimulation parameters will be a critically important variable for achieving cytokine-specific changes.
TheGossypium longicalyxgenome as a resource for cotton breeding and evolution
Authors: Grover Corrinne E. , Pan Mengqiao , Yuan Daojun , Arick Mark A. , Hu Guanjing , Brase Logan , Stelly David M. , Lu Zefu , Schmitz Robert J. , Peterson Daniel G. , Wendel Jonathan F. , Udall Joshua A.
Published: January 2020

Cotton is an important crop that has made significant gains in production over the last century. Emerging pests such as the reniform nematode have threatened cotton production. The rare African diploid speciesGossypium longicalyxis a wild species that has been used as an important source of reniform nematode immunity. While mapping and breeding efforts have made some strides in transferring this immunity to the cultivated polyploid species, the complexities of interploidal transfer combined with substantial linkage drag have inhibited progress in this area. Moreover, this species shares its most recent common ancestor with the cultivated A-genome diploid cottons, thereby providing insight into the evolution of long, spinnable fiber. Here we report a newly generatedde novogenome assembly ofG. longicalyx. This high-quality genome leveraged a combination of PacBio long-read technology, Hi-C chromatin conformation capture, and BioNano optical mapping to achieve a chromosome level assembly. The utility of theG. longicalyxgenome for understanding reniform immunity and fiber evolution is discussed.
Using regions of homozygosity to evaluate the use of dogs as preclinical models in human drug development
Authors: Smieszek SP. , Polymeropoulos MP.
Published: January 2020

Animals are used as preclinical models for human diseases in drug development. Dogs, especially, are used in preclinical research to support the clinical safety evaluations during drug development. Comparisons of patterns of regions of homozygosity (ROH) and phenotypes between dog and human are not well known. We conducted a genome-wide homozygosity analysis (GWHA) in the human and the dog genomes.

We calculated ROH patterns across distinct human cohorts including the Amish, the 1000 genomes, Wellderly, Vanda 1k genomes, and Alzheimer’s cohort. The Amish provided a large cohort of extended kinships allowing for in depth family oriented analyses. The remaining human cohorts served as statistical references. We then calculated ROH across different dog breeds with emphasis on the beagle - the preferred breed used in drug development.

Out of five studied human cohorts we reported the highest mean ROH in the Amish population. We calculated the extent of the genome covered by ROH (FROH) (human 3.2Gb, dog 2.5Gb). Overall FROHdiffered significantly between the Amish and the 1000 genomes, and between the human and the beagle genomes. The mean FROHper 1Mb was ∼16kb for Amish, ∼0.6kb for Vanda 1k, and ∼128kb for beagles. This result demonstrated the highest degree of inbreeding in beagles, far above that of the Amish, one of the most inbred human populations.

ROH can contribute to inbreeding depression if they contain deleterious variants that are fully or partially recessive. The differences in ROH characteristics between human and dog genomes question the applicability of dog models in preclinical research, especially when the goal is to gauge the subtle effects on the organism’s physiology produced by candidate therapeutic agents. Importantly, there are huge differences in a subset of ADME genes, specifically cytochrome P450 family (CYPs), constituting major enzymes involved in drug metabolism. We should hesitate to generalize from dog to human, even if human and beagle are relatively close species phylogenetically
Theory of Visual Attention (TVA) in Action: Assessing Premotor Attention in Simultaneous Eye-Hand Movements
Authors: Kreyenmeier Philipp , Deubel Heiner , Hanning Nina M.
Published: January 2020

Attention shifts that precede goal-directed eye and hand movements are regarded as markers of motor target selection. Whether effectors compete for a single, shared attentional resource during simultaneous eye-hand movements or whether attentional resources can be allocated independently towards multiple target locations is controversially debated. Independent, effector-specific target selection mechanisms underlying parallel allocation of visuospatial attention to saccade and reach targets would predict an increase of the overall attention capacity with the number of active effectors. We test this hypothesis in a modified Theory of Visual Attention (TVA; Bundesen, 1990) paradigm. Participants reported briefly presented letters during eye, hand, or combined eye-hand movement preparation to centrally cued locations. Modeling the data according to TVA allowed us to assess both the overall attention capacity and the deployment of visual attention to individual locations in the visual work space. In two experiments, we show that attention is predominantly allocated to the motor targets – without pronounced competition between effectors. The parallel benefits at eye and hand targets, however, have concomitant costs at non-motor locations, and the overall attention capacity does not increase by the simultaneous recruitment of both effector systems. Moreover, premotor shifts of attention dominate over voluntary deployment of processing resources, yielding severe impairments of voluntary attention allocation. We conclude that attention shifts to multiple effector targets without mutual competition given that sufficient processing resources can be withdrawn from movement-irrelevant locations.
Semecarpus anacardiumLinn. leaf extract exhibits activities against breast cancer and prolongs the survival of tumor-bearing mice
Authors: Singh Rajesh Kumar , Mallik Bhagaban , Ranjan Amit , Tripathi Ruchita , Verma Sumit Singh , Sharma Vinamra , Gupta Subash Chandra , Singh Anil Kumar
Published: January 2020

Semecarpus anacardiumLinn. is commonly used in various traditional medicines from ancient times. The nuts have been described in Ayurveda medication systems to treat numerous clinical ailments. However, isolating phytochemical constituents from nuts remains challenging and exhibits cytotoxic effects on other cells. In this study, we have standardized procedures for isolating phytochemicals from the leaf extract. The ethyl acetate leaf extract selectively affects cancer cells in a dose-dependent manner (IC50: 0.57 μg/ml in MCF-7 cells) in various cancer cell lines.

Next, we examined if the extract incubation could induce cell cycle arrest and suppress cell migration in the cell culture model. Consistent with this idea, the leaf extract could potentially affect the aggressive migration nature of cancer cells. Moreover, oral administration of extract significantly restored tumor growth in mice. Together, these observations suggest the anti-cancer activities ofS. anacardiumleaf potential for both in vitro and in vivo models.

Graphical Abstract
A hybrid optimal contribution approach to drive short-term gains while maintaining long-term sustainability in a modern plant breeding program
Authors: Santantonio Nicholas , Robbins Kelly
Published: January 2020

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Plant breeding programs must adapt genomic selection to an already complex system. Inbred or hybrid plant breeding programs must make crosses, produce inbred individuals, and phenotype inbred lines or their hybrid test-crosses to select and validate superior material for product release. These products are few, and while it is clear that population improvement is necessary for continued genetic gain, it may not be sufficient to generate superior products. Rapid-cycle recurrent truncation genomic selection has been proposed to increase genetic gain by reducing generation time. This strategy has been shown to increase short-term gains, but can quickly lead to loss of genetic variance through inbreeding as relationships drive prediction. The optimal contribution of each individual can be determined to maximize gain in the following generation while limiting inbreeding. While optimal contribution strategies can maintain genetic variance in later generations, they suffer from a lack of short-term gains in doing so. We present a hybrid approach that branches out yearly to push the genetic value of potential varietal materials while maintaining genetic variance in the recurrent population, such that a breeding program can achieve short-term success without exhausting long-term potential. Because branching increases the genetic distance between the phenotyping pipeline and the recurrent population, this method requires sacrificing some trial plots to phenotype materials directly out of the recurrent population. We envision the phenotypic pipeline not only for selection and validation, but as an information generator to build predictive models and develop new products.
The small protein RmpD drives hypermucoviscosity inKlebsiella pneumoniae
Authors: Walker Kimberly A. , Treat Logan P. , Miller Virginia L.
Published: January 2020

Klebsiella pneumoniaehas a remarkable ability to cause a wide range of human diseases. It is divided into two broad classes: Classical strains that are a notable problem in healthcare settings due to multidrug resistance, and hypervirulent (hv) strains that are drug sensitive, but able to establish disease in immunocompetent hosts. Alarmingly, there has been an increased frequency of clinical isolates that have both drug resistance andhv-associated genes. One such gene isrmpAthat encodes a transcriptional regulator required for maximal capsule (cps) gene expression and confers hypermucoviscosity (HMV). This link has resulted in the assumption that HMV is caused by elevated capsule production. However, we recently reported a newcpsregulator, RmpC, and ΔrmpCmutants have reducedcpsexpression but remain HMV, suggesting that capsule and HMV may be separable traits. Here, we report the identification of a small protein, RmpD, that is essential for HMV, but does not impact capsule. RmpD is 58 residues with a putative N-terminal transmembrane domain and highly positively charged C-terminal half, and it is conserved among otherhv K. pneumoniaestrains. Expression ofrmpD in transcomplements both ΔrmpDand ΔrmpAmutants for HMV, suggesting that RmpD is the key driver of this phenotype. ThermpDgene is located betweenrmpAandrmpC, within an operon regulated by RmpA. This data, combined with our previous work, suggests a model in which the RmpA-associated phenotypes are largely due to RmpA activating the expression ofrmpDto produce HMV andrmpCto stimulatecpsexpression.

SIGNIFICANCE

Capsule is a critical virulence factor inKlebsiella pneumoniae, in both antibiotic-resistant classical strains and hypervirulent strains. Hypervirulent strains usually have a hypermucoviscous (HMV) phenotype that contributes to their heightened virulence capacity, but the production of HMV is not understood. The transcriptional regulator RmpA is required for HMV and also activates capsule gene expression, leading to the assumption that HMV is caused by hyperproduction of capsule. We have identified a new gene (rmpD) required for HMV but does not contribute to capsule production. This distinction between HMV and capsule production will promote a better understanding of the mechanisms of hypervirulence, which is in great need given the alarming increase in clinical isolates with both drug resistance and hypervirulence traits.
Cryo-EM structures reveal two distinct conformational states in a picornavirus cell entry intermediate
Authors: Shah Pranav N.M. , Filman David J. , Karunatilaka Krishanthi S. , Hesketh Emma L. , Groppelli Elisabetta , Strauss Mike , Hogle James M.
Published: January 2020

The virions of enteroviruses such as poliovirus undergo a global conformational change after binding to the cellular receptor, characterized by a 4% expansion, and opening of holes at the two and quasi-three-fold symmetry axes of the capsid. The resultant particle is called a 135S particle or A-particle and is thought to be on the pathway to a productive infection. Previously published studies have concluded that the membrane interactive peptides, namely VP4 and the N-terminus of VP1, are irreversibly externalized in the 135S particle. However, using established protocols to produce the 135S particle, and single particle cryo-electron microscopy methods, we have identified at least two unique states that we call the early and late 135S particle. Surprisingly, only in the “late” 135S particles have detectable levels of the VP1 N-terminus trapped outside the capsid. Moreover, we observe a distinct density inside the capsid that can be accounted for by VP4 that remains associated with the genome. Taken together our results conclusively demonstrate that the 135S particle is not a unique conformation, but rather a family of conformations that could exist simultaneously.

AUTHOR SUMMARY

Nonenveloped viruses need to provide mechanisms that allow their genomes to be delivered across membrane. This process remains poorly understood. For enterovirus such as poliovirus, genome delivery involves a program of conformational changes that include expansion of the particle and externalization of two normal internal peptides, VP4 and the VP1 N-terminus, which then insert into the cell membrane, triggering endocytosis and the creation of pores that facilitate the transfer of the viral RNA genome across the endosomal membrane. This manuscript describes five high-resolution cryo-EM structures of altered poliovirus particles that represent a number of intermediates along this pathway. The structures reveal several surprising findings, including the discovery of a new intermediate that is expanded but has not yet externalized the membrane interactive peptides, the clear identification of a unique exit site VP1 N-terminus, the demonstration that the externalized VP1 N-terminus partitions between two different sites in a temperature-dependent fashion, direct visualization of an amphipathic helix at the N-terminus of VP1 in an ideal position for interaction with cellular membranes, and the observation that a significant portion of VP4 remains inside the particle and accounts for a feature that had been previously ascribed to part of the viral RNA. These findings represent significant additions to our understanding of the cell entry process of an important class of human pathogens.