bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding land-use response of bird communities in an arid ecosystem of India
Authors: Varun K , Dutta Sutirtha
Published: September 2020

The Indian Thar desert has lost much of its grasslands over the last few decades, mainly due to land-use change from pastoralism to agriculture. Expanding croplands and intensifying grazing pressures are popularly hypothesized to be major drivers of biodiversity loss in the region. Our study aims to investigate the effects of contemporary land-use change on bird communities of the Western Thar Desert.

We surveyed 58 randomly laid line transects in a c2000 sq.km study area, to quantify parameters of bird community structure in three predominant land-use types viz. protected grasslands, rangelands, and non-irrigated croplands. Fieldwork for the study was conducted in the dry season (winter and summer) between December 2018 and April 2019.

During winter, overall bird richness and abundance were highest in protected grasslands followed by non-irrigated croplands and rangelands. Protected grasslands also had a higher abundance of diet and habitat specialists. Compared to protected grasslands, density was lower in non-irrigated croplands and rangelands for 35% and 10% of species, respectively. A majority of the negatively affected species were insectivorous grassland specialists.

Contrary to the pattern in winter, overall bird richness, abundance, community composition, and guild structure in summer were similar across three land-use types. Only one of the 17 analysed species had lower density in modified land-use types.

Overall, protected grassland was the best habitat for birds and was specifically important for specialists, particularly during the winter. Rangelands and fallow croplands sustained most generalists at comparable densities but had severe negative impacts on specialists.

Synthesis and application: Our results point out that low-intensity agro-pastoral land-uses can supplement, but not replace, protected areas in conservation of Thar desert’s avifaunal diversity. Our results are consistent with the idea of managing dryland habitats as agro-grassland mosaics with embedded protected areas, in order to reconcile human needs and biodiversity conservation at a landscape scale.
Glutamic acid promotes hair growth in mice
Authors: Jara Carlos Poblete , de Andrade Berti Beatriz , Mendes Natalia Ferreira , Engel Daiane F. , Zanesco Ariane Maria , Souza Gabriela Freitas , Velloso Lício Augusto , de Araujo Eliana Pereira
Published: September 2020

Glutamic Acid is the main excitatory neurotransmitter in neurons. Abnormal distributions of the glutamic acid receptors have been shown in hyper proliferative models such as psoriasis and skin regeneration. However, the biological function of glutamic acid in the skin remains unclear. Usingex vivo, in vivoandin silicoapproaches, we showed for the first time that exogenous glutamic acid promotes hair growth and keratinocyte proliferation. Topical application of glutamic acid decreased expression of genes related to apoptosis signaling in the skin. Also, we showed Glutamic acid increased viability and proliferation in cultured human keratinocyte. For the first time, we identified the excitotoxic GA concentration and we provided evidence for the existence of a novel skin signaling pathway mediated by a neurotransmitter controlling keratinocyte and hair follicle proliferation. In perspective, we anticipate our results could be the starting point to elucidate how exogenous glutamic acid from food intake or even endogenous GA from neuropsychiatric disorders modulate skin diseases.
A Tethered Ligand Assay to Probe the SARS-CoV-2 ACE2 Interaction under Constant Force
Authors: Bauer Magnus S. , Gruber Sophia , Milles Lukas F. , Nicolaus Thomas , Schendel Leonard C. , Gaub Hermann E. , Lipfert Jan
Published: September 2020

The current COVID-19 pandemic has a devastating global impact and is caused by the SARS-CoV-2 virus. SARS-CoV-2 attaches to human host cells through interaction of its receptor binding domain (RBD) located on the viral Spike (S) glycoprotein with angiotensin converting enzyme-2 (ACE2) on the surface of host cells. RBD binding to ACE2 is a critical first step in SARS-CoV-2 infection. Viral attachment occurs in dynamic environments where forces act on the binding partners and multivalent interactions play central roles, creating an urgent need for assays that can quantitate SARS-CoV-2 interactions with ACE2 under mechanical load and in defined geometries. Here, we introduce a tethered ligand assay that comprises the RBD and the ACE2 ectodomain joined by a flexible peptide linker. Using specific molecular handles, we tether the fusion proteins between a functionalized flow cell surface and magnetic beads in magnetic tweezers. We observe repeated interactions of RBD and ACE2 under constant loads and can fully quantify the force dependence and kinetics of the binding interaction. Our results suggest that the SARS-CoV-2 ACE2 interaction has higher mechanical stability, a larger free energy of binding, and a lower off-rate than that of SARS-CoV-1, the causative agents of the 2002-2004 SARS outbreak. In the absence of force, the SARS-CoV-2 RBD rapidly (within ≤1 ms) engages the ACE2 receptor if held in close proximity and remains bound to ACE2 for 400-800 s, much longer than what has been reported for other viruses engaging their cellular receptors. We anticipate that our assay will be a powerful tool investigate the roles of mutations in the RBD that might alter the infectivity of the virus and to test the modes of action of neutralizing antibodies and other agents designed to block RBD binding to ACE2 that are currently developed as potential COVID-19 therapeutics.
TALE: Transformer-based protein function Annotation with joint sequence–Label Embedding
Authors: Cao Yue , Shen Yang
Published: September 2020

Motivation

Facing the increasing gap between high-throughput sequence data and limited functional insights, computational protein function annotation provides a high-throughput alternative to experimental approaches. However, current methods can have limited applicability while relying on data besides sequences, or lack generalizability to novel sequences, species and functions.

Results

To overcome aforementioned barriers in applicability and generalizability, we propose a novel deep learning model, named Transformer-based protein function Annotation through joint sequence–Label Embedding (TALE). For generalizbility to novel sequences we use self attention-based transformers to capture global patterns in sequences. For generalizability to unseen or rarely seen functions, we also embed protein function labels (hierarchical GO terms on directed graphs) together with inputs/features (sequences) in a joint latent space. Combining TALE and a sequence similarity-based method, TALE+ outperformed competing methods when only sequence input is available. It even outperformed a state-of-the-art method using network information besides sequence, in two of the three gene ontologies. Furthermore, TALE and TALE+ showed superior generalizability to proteins of low homology and never/rarely annotated novel species or functions compared to training data, revealing deep insights into the protein sequence–function relationship. Ablation studies elucidated contributions of algorithmic components toward the accuracy and the generalizability.

Availability

The data, source codes and models are available athttps://github.com/Shen-Lab/TALE

Contact

yshen@tamu.edu

Supplementary information

Supplementary data are available atBioinformaticsonline.
Structural characterization of an RNA bound antiterminator protein reveal a successive binding mode
Authors: Walshe James L. , Patel Karishma , Ataide Sandro F.
Published: September 2020

In bacteria, rho-independent termination occurs through the formation of an intrinsic RNA terminator loop, which disrupts the RNA polymerase elongation complex, resulting in dissociation from the DNA template. ANTAR domains are a class of antiterminator that bind and stabilise mutually exclusive dual hexaloop motifs within the nascent RNA chain to prevent terminator loop formation. We have determined the structures of the dimeric ANTAR domain protein EutV, fromE. faecialis,both in the absence of and in complex with the dual hexaloop RNA target. The structures illustrate the conformational changes that occur upon RNA binding and reveal the molecular interactions between the ANTAR domains and RNA are restricted to a single hexaloop of the motif. Our findings thereby redefine the minimal ANTAR domain binding motif to a single hexaloop and revise the current model for ANTAR-mediated antitermination. These insights will inform and facilitate the discovery of novel ANTAR domain RNA targets.
MonaGO: a novel Gene Ontology enrichment analysis visualisation system
Authors: Xin Ziyin , Cai Yujun , Dang Louis T. , Burke Hannah M.S. , Revote Jerico , Nim Hieu T. , Li Yuan-Fang , Ramialison Mirana
Published: September 2020

MonaGO is a novel web-based visualisation system that provides an intuitive, interactive and responsive interface for performing gene ontology (GO) enrichment analysis and visualising the results. MonaGO combines dynamic clustering and interactive visualisation as well as customisation options to assist biologists in obtaining meaningful representation of overrepresented GO terms, producing simplified outputs in an unbiased manner. MonaGO supports gene lists as well as GO terms as inputs. Visualisation results can be exported as high-resolution images or restored in new sessions, allowing reproducibility of the analysis. An extensive comparison between MonaGO and 11 state-of-the-art GO enrichment visualisation tools based on 9 features revealed that MonaGO is the only platform that simultaneously allows interactive visualisation within one single output page, directly accessible through a web browser with customisable display options. In summary, MonaGO will facilitate the interpretation of GO analysis and will assist the biologists into the representation of the results.
Task-Free Recovery and Spatial Characterization of a P3-Like Global Network from Resting-State EEG
Authors: Tang Akaysha C. , Privitera Adam John
Published: September 2020

Diagnosis of mental illness, testing of treatment effects, and design of prevention strategies all require brain-based biomarkers that can serve as effective targets of evaluation. The search for such markers often starts with a search for neural correlates from brain imaging studies with measures of functions and behavior of interest. Yet such an approach can produce erroneous results for correlations do not guarantee causation. Only when the markers map onto neurocomputationally-relevant parameters can such markers best serve the intended function. Here we take an alternative approach to begin with targeting the neuroanatomically and neurophysiologically well-defined neuromoduatory systems that are well positioned to serve the computational role of generating globally synchronized neural activity for the purpose of functional integration [1]. By applying second-order blind identification (SOBI) [2], a blind source separation algorithm (BSS), to five minutes of resting-state EEG data (n=13), we provide evidence to support our conclusion that neuroelectrical signals associated with synchronized global network activity can be extracted using the detailed temporal information in the on-going continuously recorded EEG, instead of event-related potentials (ERPs). We report reliable extraction of a SOBI component, which we refer to as the P3-like component, in every individual studied, replicating our earlier report on data from a single participant [3]. We show that individual differences in the neural networks underlying this P3-like component can be revealed in high dimensional space by a vector of hits-based measures [4] for each of the P3-like network’s constituent structures. Given that resting-state EEG can be obtained with greater ease at natural non-hospital settings and at much lower cost in comparison with fMRI, and that mobile EEG systems have become increasingly available, the present work offers an enabling technology to support rapid and low-cost assessment of much larger and diverse populations of individuals, addressing several methodological limitations in our current investigation of brain function. Future opportunities and current limitations will be discussed.
Discovery and Development of Human SARS-CoV-2 Neutralizing Antibodies using an Unbiased Phage Display Library Approach
Authors: Cao Xia , Maruyama Junki , Zhou Heyue , Kerwin Lisa , Sattler Rachel , Manning John T. , Johnson Sachi , Richards Susan , Li Yan , Shen Weiqun , Blair Benjamin , Du Na , Morais Kyndal , Lawrence Kate , Lu Lucy , Pai Chin-I , Li Donghui , Brunswick Mark , Zhang Yanliang , Ji Henry , Paessler Slobodan , Allen Robert D.
Published: September 2020

SARS-CoV-2 neutralizing antibodies represent an important component of the ongoing search for effective treatment of and protection against COVID-19. We report here on the use of a naïve phage display antibody library to identify a panel of fully human SARS-CoV-2 neutralizing antibodies. Following functional profilingin vitroagainst an early pandemic isolate as well as a recently emerged isolate bearing the D614G Spike mutation, the clinical candidate antibody, STI-1499, and the affinity-engineered variant, STI-2020, were evaluated forin vivoefficacy in the Syrian golden hamster model of COVID-19. Both antibodies demonstrated potent protection against the pathogenic effects of the disease and a dose-dependent reduction of virus load in the lungs, reaching undetectable levels following a single dose of 500 micrograms of STI-2020. These data support continued development of these antibodies as therapeutics against COVID-19 and future use of this approach to address novel emerging pandemic disease threats.
A genomic variant of ALPK2 is associated with increased liver fibrosis risk in HIV/HCV coinfected women
Authors: McIntosh Alec T. , Wei Renhuizi , Ahn Jaeil , Aouizerat Brad E. , Kassaye Seble G. , Augenbraun Michael H. , Price Jennifer C. , French Audrey L. , Gange Stephen J. , Anastos Kathryn M. , Goldman Radoslav
Published: September 2020

HIV coinfection is associated with more rapid liver fibrosis progression in hepatitis C (HCV) infection. Recently, much work has been done to improve outcomes of liver disease and to identify targets for pharmacological intervention in coinfected patients. In this study, we analyzed clinical data of 1,858 participants from the Women’s Interagency HIV Study (WIHS) to characterize risk factors associated with changes in the APRI and FIB-4 surrogate measurements for advanced fibrosis. We assessed 887 non-synonymous single nucleotide variants (nsSNV) in a subset of 661 coinfected participants for genetic associations with changes in liver fibrosis risk. The variants utilized produced amino acid substitutions that either altered an N-linked glycosylation (NxS/T) sequon or mapped to a gene related to glycosylation processes. Seven variants were associated with an increased likelihood of liver fibrosis. The most common variant, ALPK2 rs3809973, was associated with liver fibrosis in HIV/HCV coinfected patients; individuals homozygous for the rare C allele displayed elevated APRI (0.61, 95% CI, 0.334 to 0.875) and FIB-4 (0.74, 95% CI, 0.336 to 1.144) relative to those coinfected women without the variant. Although warranting replication, ALPK2 rs3809973 may show utility to detect individuals at increased risk for liver disease progression.
The influence of socioeconomic deprivation on dementia mortality, age at death and quality of diagnosis: a nationwide death records study in England and Wales 2001-2017
Authors: Jitlal Mark , Amirthalingam Guru NK , Karania Tasvee , Parry Eve , Neligan Aidan , Dobson Ruth , Noyce Alastair J , Marshall Charles R
Published: September 2020

Background

Socioeconomic deprivation is postulated to be an important determinant of dementia risk, mortality, and access to diagnostic services. Nevertheless, premature mortality from other causes and under-representation of deprived individuals in research cohorts may lead to this effect being overlooked.

Methods

We obtained Office of National Statistics (ONS) mortality data where dementia was recorded as a cause of death in England and Wales from 2001 to 2017, stratified by age, diagnosis code and UK Index of Multiple Deprivation (IMD) decile. We calculated standardised mortality ratios (SMR) for each IMD decile, adjusting for surviving population size in each IMD decile and age stratum. In those who died of dementia, we used ordinal logistic regression to examine the effect of deprivation on likelihood of being older at death. We used logistic regression to test the effect of deprivation on likelihood of receiving a diagnosis of unspecified dementia, a proxy for poor access to specialist diagnostic care.

Results

578,623 deaths due to dementia in people over the age of 65 were identified between 2001-2017. SMRs were similar across the three most deprived deciles (1-3) but progressively declined through deciles 4-10 (Mean SMR [95%CI] in decile 1: 0.528 [0.506 to 0.550], decile 10: 0.369 [0.338 to 0.400]). This effect increased over time with improving ascertainment of dementia. In 2017, 14,837 excess dementia deaths were attributable to deprivation (21.5% of the total dementia deaths that year). There were dose-response effects of deprivation on likelihood of being older at death with dementia (odds ratio [95%CI] for decile 10 (least deprived): 1.31 [1.28 to 1.33] relative to decile 1), and on likelihood of receiving a diagnosis of unspecified dementia (odds ratio [95%CI] for decile 10: 0.78 [0.76 to 0.80] relative to decile 1).

Conclusions

Socioeconomic deprivation in England and Wales is associated with increased dementia mortality, younger age at death with dementia, and poorer access to specialist diagnosis. Reducing social inequality may be an important strategy for prevention of dementia mortality.
Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis
Authors: Munjal Akankshi , Hannezo Edouard , Mitchison Timothy J. , Megason Sean G.
Published: September 2020

How tissues acquire complex shapes is a fundamental question in biology and regenerative medicine. Zebrafish semicircular canals form from invaginations in the otic epithelium (buds) that extend and fuse to form the hubs of each canal. We find that conventional actomyosin-driven behaviors are not required. Instead, local secretion of hyaluronan, made by the enzymesugdhandhas3, drives canal morphogenesis. Charged hyaluronate polymers osmotically swell with water and generate isotropic extracellular pressure to deform the overlying epithelium into buds. The mechanical anisotropy needed to shape buds into tubes is conferred by a polarized distribution of cellular protrusions, linked between cells, that we term cytocinches. Most work on tissue morphogenesis ascribes actomyosin contractility as the driving force, while the extracellular matrix shapes tissues through differential stiffness. Our work inverts this expectation. Hyaluronate-pressure shaped by anisotropic tissue stiffness may be a widespread mechanism for powering morphological change in organogenesis and tissue engineering.
Regulation of lipid accumulation-induced ROS in myeloid-derived suppressor cells via targeting fatty-acid transport protein 2 enhanced anti-PD-L1 tumor immunotherapy
Authors: Adeshakin Adeleye Oluwatosin , Liu Wan , Adeshakin Funmilayo O. , Afolabi Lukman O. , Zhang Mengqi , Zhang Guizhong , Wang Lulu , Li Zhihuan , Lin Lilong , Yan Dehong , Wan Xiaochun
Published: September 2020

Despite the remarkable success and efficacy of immune checkpoint blockade (ICB) therapy against the PD-1/PD-L1 axis, it induces sustained responses in a sizeable minority of cancer patients due to the activation of immunosuppressive factors such as myeloid-derived suppressor cells (MDSCs). Inhibiting the immunosuppressive function of MDSCs is critical for successful cancer ICB therapy. Interestingly, lipid metabolism is a crucial factor in modulating MDSCs function. Fatty acid transport protein 2 (FATP2) conferred the function of PMN-MDSCs in cancer via the upregulation of arachidonic acid metabolism. However, whether regulating lipid accumulation in MDSCs by targeting FATP2 could block MDSCs reactive oxygen species (ROS) production and enhance PD-L1 blockade-mediated tumor immunotherapy remains unexplored. Here we report that FATP2 regulated lipid accumulation, ROS, and immunosuppressive function of MDSCs in tumor-bearing mice. Tumor cells-derived granulocyte macrophage-colony stimulating factor (GM-CSF) induced FATP2 expression in MDSCs by activation of STAT3 signaling pathway. Pharmaceutical blockade of FATP2 expression in MDSCs by lipofermata decreased lipid accumulation, reduced ROS, blocked immunosuppressive activity, and consequently inhibited tumor growth. More importantly, lipofermata inhibition of FATP2 in MDSCs enhanced anti-PD-L1 tumor immunotherapy via the upregulation of CD107a and reduced PD-L1 expression on tumor-infiltrating CD8+T-cells. Furthermore, the combination therapy blocked MDSC’s suppressive role on T-cells thereby enhanced T-cell’s ability for the production of IFN-γ. These findings indicate that FATP2 plays a key role in modulating lipid-induced ROS in MDSCs and targeting FATP2 in MDSCs provides a novel therapeutic approach to enhance anti-PD-L1 cancer immunotherapy.

Research highlights

FATP2 inhibition in MDSCs blocked ROS-mediated immunosuppressive function and promoted MDSCs differentiation to immune-stimulatory phenotype.

GM-CSF mediated FATP2 expression via activation of STAT3 signaling leading to lipid accumulation-induced ROS in MDSCs.

FATP2 inhibition enhanced anti-PD-L1 tumor immunotherapy by reducing MDSCs immunosuppressive activity in blocking T-cell’s ability to produce IFN-γ.

Combination of anti-PD-L1 antibody and FATP2 inhibitor decreased MDSCs accumulation and PD-L1 surface expression in the spleens of LLC-bearing mice.

Combined treatment of FATP2 inhibitor and PD-L1 blockade-mediated tumor immunotherapy enhanced tumor-infiltrating CD8+T cells activation via increased CD107a and reduced PD-L1 surface expression.
DEELIG: A Deep Learning-based approach to predict protein-ligand binding affinity
Authors: Ahmed Asad , Mam Bhavika , Sowdhamini Ramanathan
Published: September 2020

Protein-ligand binding prediction has extensive biological significance. Binding affinity helps in understanding the degree of protein-ligand interactions and has wide protein applications. Protein-ligand docking using virtual screening and molecular dynamic simulations are required to predict the binding affinity of a ligand to its cognate receptor. In order to perform such analyses, it requires intense computational power and it becomes impossible to cover the entire chemical space of small molecules. Recent developments using deep learning has enabled us to make sense of massive amounts of complex datasets where the ability of the model to “learn” intrinsic patterns in a complex plane of data is the strength of the approach. Here, we have incorporated Convolutional Neural Networks to find spatial relationships amongst data to help us predict affinity of binding of proteins in whole superfamilies towards a diverse set of ligands without the need of a docked pose or complex as input. The models were trained and validated using a detailed methodology for feature extraction. We have also tested DEELIG on protein complexes relevant to the current public health scenario. Our approach to network construction and training on protein-ligand dataset prepared in-house has yielded novel insights.
Deciphering the Genome Protection Roles of Autophagy in Primary Human Dermal Fibroblasts (HDFs) against Ultraviolet-(B) –Induced Skin Photodamage
Authors: Umar Sheikh Ahmad , Tasduq Sheikh Abdullah
Published: September 2020

Ultraviolet-B (UV-B) exposure to skin causes photo-damage and acts as the primary etiological agent in photo-carcinogenesis. UV-B exposure induces photodamage in epidermal cells and is the major factor that challenges skin homeostasis. Autophagy allows fundamental adaptation of cells to metabolic needs and stresses. Cellular dysfunction is observed in aged tissues and in toxic insults to cells that undergo through stress. Conversely, promising anti-aging strategies aimed at inhibiting the mTOR pathway has been found to significantly improve the aging related disorders. Recently, autophagy has been found to positively regulate skin homeostasis by enhancing DNA damage recognition. Here we investigated the Geno-protective roles of autophagy in UV-B exposed primary HDFs. We found that improving autophagy levels in HDFs regulates UV-B mediated cellular stress by decreasing the formation of DNA photo adducts, alleviates oxidative and ER stress response and by regulating the expression levels of cell cycle regulatory proteins P21 and P27. Autophagy also prevents HDFs from UV-B -induced nuclear damage as is evident from Tunnel assay and Acridine Orange/Ethidium Bromide co-staining. Salubrinal, (an eIf2α inhibitor) significantly decreases the DNA damage response in HDFs. P62 silenced HDFs show enhanced DNA damage response and disturbs the tumor suppressor axis PTEN/pAKT towards damage whereas ATG7 silenced HDFs reveal an unexpected consequence by decreasing the UV-B -induced DNA damage compared to UV-B treated HDFs. Together, our results suggest that autophagy is essential in protecting skin cells from UV-B radiation -induced photo-damage and holds great promise in devising it as a suitable therapeutic strategy against skin photo-damage.

Highlights

Autophagy is an immediate molecular event induced following exposure of primary HDFs to UV-B –irradiation

Autophagy offers pro-survival capacity to HDFs under UV-B induced genotoxic stress

Autophagy regulates DNA Damage Response via regulation of oxidative and ER stress in UV-B exposed HDFs

Relieving ER stress response offers significant protection to primary HDFs from UV-B by decreasing the DNA damage

Autophagy deprivation to HDFs via P62 silencing potentiates UV-B -induced DNA damage response

ATG7 silencing in UV-B exposed HDFs unexpectedly alleviates the DNA Damage Response in primary HDFs
Parietal cell-Specific SLC26A9 Deletion induces spontaneous Gastric Carcinogenesis in Mice
Authors: Liu Xuemei , Li Taolang , Yuan Dumin , Riederer Brigitte , Ma Zhiyuan , Zhu Jiaxing , Li Yunhua , An Jiaxing , Wen Guorong , Jin Hai , Hu Chunli , Zhang Minglin , Yang Xiao , Seidler Ursula , Tuo Biguang
Published: September 2020

Previous study showed that Slc26a9 loss impairs parietal cell function and survival. We investigated whether Slc26a9 loss causes spontaneous gastric carcinogenesis in mice and plays a role in the development and progression in human gastric cancer (GC). Gastric histopathology and potential molecular mechanism were explored in Slc26a9 knockout mice and wild-type littermates as well as Slc26a9fl/fl/Atp4b-Cre and Slc26a9fl/fl mice from 8 days to 18 months by histological and immunohistochemical analyses, quantitative PCR, in situ hybridization, and RNA microarray analysis, respectively. We demonstrated that loss of parietal cell expression of Slc26a9 is the key event to induce spontaneous gastric carcinogenesis in mice, and clarified the sequence of events leading to malignant transformation, including Slc26a9 deficiency in parietal cells resulted in dysregulated differentiation of stem cells in an inflammatory environment, activated Wnt signaling pathway to induce gastric epithelia cell hyperproliferation and apoptosis inhibition, as well as spontaneous epithelial to mesenchymal transition-induced cancer stem cell phenotypes. Downregulation of SLC26A9 correlated with GC patient’s short survival.

Graphical Abstract

Loss of parietal cell expression of Slc26a9 is the key event to induce spontaneous gastric carcinogenesis in transgenic mice.
Structural and dynamical heterogeneity of water trapped inside Na+-pumping KR2 rhodopsin in the dark state
Authors: Santra Mantu , Seal Aniruddha , Bhattacharjee Kankana , Chakrabarty Suman
Published: September 2020

Photoisomerisation in retinal leads to a channel opening in the rhodopsins that triggers translocation or pumping of an ion/proton. Crystal structures of rhodopsins contain several structurally conserved water molecules. It has been suggested that water plays an active role in facilitating the ion pumping/translocation process by acting as a lubricant in these systems. In this work, we systematically investigate the localisation, structure, dynamics and energetics of the water molecules along the channel for the resting/dark state of KR2 rhodopsin. Employing several microseconds long atomistic molecular dynamics (MD) simulation of this trans-membrane protein system, we demonstrate the presence of five distinct water containing pockets/cavities separated by gateways controlled by the protein side-chains. There exists a strong hydrogen bonded network involving these buried water molecules and functionally important key residues. We present evidence of significant structural and dynamical heterogeneity in the water molecules present in these cavities with very rare exchange between them. The exchange time-scale of these buried water with bulk has an extremely wide range from tens of nanoseconds to > 1.5μs! The translational and rotational dynamics of buried water are found to be strongly dependent on the protein cavity size and local interactions with classic signature of trapped diffusion and rotational anisotropy.
The impact of size on particle drainage dynamics and antibody response
Authors: Zinkhan Simon , Ogrina Anete , Balke Ina , Reseviča Gunta , Zeltins Andris , de Brot Simone , Lipp Cyrill , Chang Xinyue , Zha Lisha , Vogel Monique , Bachmann Martin F. , Mohsen Mona O.
Published: September 2020

Vaccine-induced immune response can be greatly enhanced by mimicking pathogen properties. The size and the repetitive geometric shape of virus-like particles (VLPs) influence their immunogenicity by facilitating drainage to secondary lymphoid organs and enhancing interaction with and activation of B-cells and other innate humoral immune components. VLPs derived from the plant Bromovirus genus, specifically cowpea chlorotic mottle virus (CCMV), are T=3 icosahedron particles. They can be easily expressed in anE. coli host system and package ssRNA during the expression process. Recently, we have engineered CCMV-VLPs by incorporating the universal tetanus toxoid (TT) epitope at the N-terminus. The modified CCMVTT-VLPs successfully form icosahedral particlesT=3, with a diameter of ∼30nm analogous to the parental VLPs. Interestingly, incorporating TT epitope at the C-terminus of CCMVTT-VLPs results in the formation of Rod-shaped VLPs, ∼1µm in length and ∼30nm in width. In this study, we have investigated the draining kinetics and immunogenicity of both engineered forms (termed as Round-shaped CCMVTT-VLPs and Rod-shaped CCMVTT-VLPs) as potential B cell immunogens using differentin vitroandin vivoassays. Our results reveal that Round-shaped CCMVTT-VLPs are more efficient in draining to secondary lymphoid organs to charge antigen-presenting cells as well as B-cells. Furthermore, compared to Rod-shaped CCMVTT-VLPs, Round-shaped CCMVTT-VLPs led to more than 100-fold increased systemic IgG and IgA responses accompanied by prominent formation of splenic germinal centers. Round-shaped CCMVTT-VLPs could also polarize the induced immune response towards TH1. Up to our knowledge, this is the first study investigating and comparing the draining kinetics and immunogenicity of one and the same VLP monomer forming nano-sized icosahedrons or rods in the micrometer size.
ISRIB blunts the integrated stress response by allosterically antagonising the inhibitory effect of phosphorylated eIF2 on eIF2B
Authors: Zyryanova Alisa F. , Kashiwagi Kazuhiro , Rato Claudia , Harding Heather P. , Crespillo-Casado Ana , Perera Luke A. , Sakamoto Ayako , Nishimoto Madoka , Yonemochi Mayumi , Shirouzu Mikako , Ito Takuhiro , Ron David
Published: September 2020

The small molecule ISRIB antagonises the activation of the integrated stress response (ISR) by phosphorylated translation initiation factor 2, eIF2(αP). ISRIB and eIF2(αP) bind distinct sites in their common target, eIF2B, a guanine nucleotide exchange factor (GEF) for eIF2. We have found that ISRIB-mediated acceleration of eIF2B activity in vitro is observed preferentially in the presence of eIF2(αP) and is attenuated by mutations that desensitise eIF2B to the inhibitory effects of eIF2(αP). ISRIB’s efficacy as an ISR inhibitor in cells also depends on presence of eIF2(αP). Cryo-EM showed that engagement of both eIF2B regulatory sites by two eIF2(αP) molecules remodels both the ISRIB-binding pocket and the pockets that would engage eIF2α during active nucleotide exchange, thereby discouraging both binding events. In vitro, eIF2(αP) and ISRIB reciprocally opposed each other’s binding to eIF2B. These findings point to antagonistic allostery in ISRIB action on eIF2B, culminating in inhibition of the ISR.
The landscape of interactions between cancer polygenic risk scores and somatic alterations in cancer cells
Authors: Porta-Pardo Eduard , Sayaman Rosalyn , Ziv Elad , Valencia Alfonso
Published: September 2020

Over the last 15 years we have identified hundreds of inherited variants that increase the risk of developing cancer. Polygenic risk scores (PRS) summarize the genetic risk of each individual by accounting for the unique combination of risk alleles in their genome. So far, most studies of PRS in cancer have focused on their predictive value: i.e. to what extent the PRS can predict which individuals will develop a particular cancer type. In parallel, for most cancers, we have identified several subtypes based on their somatic molecular properties. However, little is known about the relationship between the somatic molecular subtypes of cancer and PRS and it is possible that PRS preferentially predict specific cancer subtypes. Since cancer subtypes can have very different outcomes, treatment options and molecular vulnerabilities, answering this question is very important to understand the consequences that widespread PRS use would have in which tumors are detected early.

Here we used data from The Cancer Genome Atlas (TCGA) to study the correlation between PRS for different forms of cancer and the landscape of somatic alterations in the tumors developed by each patient. We first validated the predictive power of 8 different PRS in TCGA and describe how PRS for some cancer types are associated with specific molecular subtypes or somatic cancer driver events. Our results highlight important questions that could improve the predictive power of PRS and that need to be answered before their widespread clinical implementation.
SOCS-1 inhibition of type I interferon limitsStaphylococcus aureusskin host defense
Authors: Klopfenstein Nathan , Brandt Stephanie , Castellanos Sydney , Serezani C. Henrique
Published: September 2020

The innate immune response to methicillin-resistantStaphylococcus aureus(MRSA) skin infection culminates in forming an abscess that prevents the bacterial spread and tissue damage. Pathogen recognition receptors (PRRs) dictate the balance between microbial control and tissue damage. Therefore, intracellular brakes are of fundamental importance to tune the appropriate host defense while preventing injury. The intracellular inhibitor suppressor of cytokine signaling 1 (SOCS-1); is a classic JAK/STAT inhibitor that prevents PRR responses by influencing the expression and actions of PRR adaptors and downstream effectors. Whether SOCS-1 is a molecular component of skin host defense remains to be determined. Here, we hypothesized that SOCS-1 decreases type I interferon production and IFNAR-mediated antimicrobial effector functions of the inflammatory response during MRSA skin infection. Our data show that MRSA skin infection enhances SOCS-1 expression, and both SOCS-1 inhibitor peptide treated and myeloid-specific SOCS-1 deficient mice display decreased lesion size, bacterial loads, and increased abscess thickness when compared to wild-type mice treated or not with scrambled peptide control. SOCS-1 deletion/inhibition increases phagocytosis and bacterial killing, dependent on nitric oxide release. SOCS-1 inhibition also increases antimicrobial effector function correlated with type I and type II interferon levelsin vivo. IFNAR deletion and antibody blockage abolished the beneficial effects of SOCS-1 inhibitionin vivo. Notably, we unveiled that hyperglycemia triggers aberrant SOCS-1 expression that correlates with decreased overall IFN signatures in the skin. SOCS-1 inhibition restores skin host defense in highly susceptible hyperglycemic mice. Overall, these data demonstrate a role for type I interferons in enhancing microbial clearance and host defense during MRSA skin infection.
ColwelliaandMarinobactermetapangenomes reveal species-specific responses to oil and dispersant exposure in deepsea microbial communities
Authors: Peña-Montenegro Tito David , Kleindienst Sara , Allen Andrew E. , Eren A. Murat , McCrow John P. , Sánchez-Calderón Juan David , Arnold Jonathan , Joye Samantha B.
Published: September 2020

Over 7 million liters of Corexit EC9500A and EC9527A were applied to the Gulf of Mexico in response to the Deepwater Horizon oil spill. The impacts of dispersants remain under debate and negative, positive, and inconclusive impacts have been reported. Here, metatrancriptomics was applied in the context of metapangenomes to microcosms that simulated environmental conditions comparable to the hydrocarbon-rich 1,100 m deep plume. Within this microcosm study, negative effects of dispersants on microbial hydrocarbon degradation were previously reported based on activity measurements and geochemical data. Transcriptional enrichment ofColwellia, a potential dispersant degrader, followed variable time-dependent trajectories due to interactions between oil, dispersants, and nutrients. TheColwelliametapangenome captured a mixture of environmental responses linked to theColwellia psychrerythraea34H genome and to the genomes of other members of theColwelliagenus. The activation of genes involved in lipid degradation, nitrogen metabolism, and membrane composition under oil or nutrient availability, suggested an opportunistic growth strategy forColwellia. In contrast, transcripts ofMarinobacter, a natural hydrocarbon degrader, increased only in oil treatments.Marinobactertranscripts largely recruited to the accessory metapangenome ofMarinobactersp. C18, the closest genomic reference. A complex response involving carbon and lipid metabolism, chemotaxis and a type IV secretion system suggested active energy-dependent processes inMarinobacter. These findings highlight chemistry-dependent responses in the metabolism of key hydrocarbon-degrading bacteria and underscore that dispersant-driven selection could temper the ability of the community to respond to hydrocarbon injection.
Regulation of RUVBL1-RUVBL2 AAA-ATPases by the nonsense-mediated mRNA decay factor DHX34, as evidenced by Cryo-EM
Authors: López-Perrote Andrés , Hug Nele , González-Corpas Ana , Rodríguez Carlos F. , Serna Marina , García-Martín Carmen , Boskovic Jasminka , Fernandez-Leiro Rafael , Caceres Javier F. , Llorca Oscar
Published: September 2020

Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that degrades aberrant mRNAs and also regulates the expression of a wide range of physiological transcripts. RUVBL1 and RUVBL2 AAA-ATPases form an hetero-hexameric ring that is part of several macromolecular complexes such as INO80, SWR1 and R2TP. Interestingly, RUVBL1-RUVBL2 ATPase activity is required for NMD activation by an unknown mechanism. Here, we show that DHX34, an RNA helicase regulating NMD initiation, directly interacts with RUVBL1-RUVBL2in vitroand in cells. Cryo-EM reveals that DHX34 induces extensive changes in the N-termini of every RUVBL2 subunit in the complex, stabilizing a conformation that does not bind nucleotide and thereby down-regulates ATP hydrolysis of the complex. Using ATPase-deficient mutants, we find that DHX34 acts exclusively on the RUVBL2 subunits. We propose a model, where DHX34 acts to couple RUVBL1-RUVBL2 ATPase activity to the assembly of factors required to initiate the NMD response.
Preclinical characterization of mobocertinib highlights the putative therapeutic window of this novel EGFR inhibitor to EGFR exon 20 insertion mutations
Authors: Vasconcelos Pedro E. N. S. , Kobayashi Ikei S. , Kobayashi Susumu S. , Costa Daniel B.
Published: September 2020

Background

Epidermal growth factor receptor (EGFR) exon 20 insertion mutations account for 10% of all EGFR mutations and are mostly insensitive to approved EGFR-tyrosine kinase inhibitors (EGFR-TKIs). Novel EGFR-TKIs have been developed or repurposed for these mutants. A limited number of preclinical studies have detailed these EGFR-TKIs. We sought to use commercially available mobocertinib (TAK-788) to characterize the preclinical therapeutic window of this EGFR-TKI against EGFR mutations and to probe possible on-target mechanisms of resistance (EGFR-C797S).

Methods

We used models of EGFR mutations to probe representative 1st, 2nd, 3rdgeneration, and in-development EGFR exon 20-active (poziotinib, mobocertinib) TKIs. We also introduced EGFR-C797S to these models to identify mechanisms of resistance.

Results

Cells driven by the most common EGFR exon 20 insertion mutations (A767_V769dupASV, D770_N771insSVD, H773_V774insH and others) were inhibited by in-development EGFR TKIs at doses below those affecting EGFR-wildtype; albeit more common EGFR mutations (exon 19 deletions and L858R) were inhibited more readily by mobocertinib and poziotinib. Mobocertinib was able to inhibit phosphorylation of EGFR in multiple preclinical models. The presence of EGFR-C797S led to >200-fold resistance in proliferation assays probing mobocertinib and osimertinib. Review of clinical studies of mobocertinib disclosed responses that could be lasting.

Conclusions

This is one of the initial reports to characterize the novel EGFR TKI mobocertinib and highlights its broad activity against EGFR mutants plus the therapeutic window to EGFR exon 20 insertion mutations; as well as EGFR-C797S as a possible mechanism of resistance. Further clinical development of mobocertinib merits continuation.
TRAIL signalling promotes entosis in colorectal cancer
Authors: Bozkurt Emir , Düssmann Heiko , Salvucci Manuela , Cavanagh Brenton L. , Van Schaeybroeck Sandra , Longley Daniel B. , Martin Seamus J. , Prehn Jochen H. M.
Published: September 2020

Entosis is a form of non-phagocytic cell-in-cell (CIC) interaction where a living cell enters into another. Tumours show evidence of entosis, however factors controlling entosis remain to be elucidated. Here we find that the death receptor ligand TRAIL is a potent activator of entosis in colon cancer cells. CLEM/3D confocal microscopy analysis revealed ultrastructural features of entosis and subsequent entotic cell death of inner cells upon TRAIL treatment. Induction of entosis and apoptosis by TRAIL were mutually exclusive events but both required the presence of caspase-8.Bax/Bakdouble knock-out or caspase inhibition altered the fate of inner cells from entotic cell death to survival and escape. Analysis of colorectal cancer tumours showed a significant association between expression levels of TRAIL and CICs. Notably, the presence of CICs in the invasive front regions of colorectal tumours was significantly correlated with adverse patient prognosis.
An evolutionarily diverged mitochondrial protein controls biofilm growth and virulence inCandida albicans
Authors: Mamouei Zeinab , Singh Shakti , Lemire Bernard , Gu Yiyou , Alqarihi Abdullah , Nabeela Sunna , Li Dongmei , Ibrahim Ashraf , Uppuluri Priya
Published: September 2020

A forward genetic screening approach identified orf19.2500, as a gene controllingCandida albicansbiofilm dispersal and biofilm detachment. Three-dimensional (3-D) protein modeling and bioinformatics revealed that orf19.2500 is a conserved mitochondrial protein, structurally similar to, but functionally diverged from, the squalene/phytoene synthases family. TheC. albicansorf19.2500 is distinguished by three evolutionarily acquired stretches of amino acid inserts, absent from all other eukaryotes except a small number of ascomycete fungi. Biochemical assays showed that orf19.2500 is required for the assembly and activity of theNADHubiquinone oxidoreductase Complex I of the respiratory electron transport chain, and was thereby namedNDU1.NDU1is essential for respiration and growth on alternative carbon sources, important for immune evasion, required for virulence in a mouse model of hematogenously disseminated candidiasis, and for potentiating resistance to antifungal drugs. Our study is the first report on a protein that sets theCandida-like fungi phylogenetically apart from all other eukaryotes, based solely on evolutionary “gain” of new amino acid inserts that are also the functional hub of the protein.
Small-angle X-ray scattering as a multifaceted tool for structural characterization of covalent organic frameworks
Authors: Maia Renata Avena , Carneiro Leonardo Simões de Abreu , Cifuentes Jhonny Mauricio Cerón , Buarque Camilla Djenne , Esteves Pierre Mothé , Percebom Ana Maria
Published: September 2020

Small-angle X-ray scattering (SAXS) is an accurate nondestructive method that requires a minimum of sample preparation and is employed to study porosity, morphology and hierarchical structures. Zeolites and silica are among the porous materials that are widely investigated by SAXS. However, studies of covalent organic frameworks (COFs) are still scarce. In the present study, SAXS was employed to investigate meso- and microporous COFs, affording insightful information about their nanostructure textural properties. SAXS is especially useful when combined with other characterization techniques, such as powder X-ray diffraction and N2 adsorption isotherms, emerging as an efficient tool to further characterize COFs. For microporous COFs, SAXS was used mainly to obtain quantitative values of surface roughness as a function of fractal parameters, in all cases indicating surface fractals of the large-scale scattering object, namely the `grain'. Mesoporous COF studies allowed elucidation of their hexagonal structure on the basis of their structure peaks; however, the main result lies in the distinction between the pore and the grain, which are described as a hierarchical structure by the Beaucage model and evaluated according to their fractality. These COFs generally exhibit pores with mass fractal features and grains with surface fractal features when they are submitted to post-functionalization, which may be due to the poor diffusivity of the functionalizing agents into the pores. In addition, a proposed aggregation description of the porous scattering objects was envisioned, based on small-angle scattering premises, which was confirmed for a microporous COF by high-resolution transmission electron microscopy.
Structure of the substrate-binding domain of Plasmodium falciparum heat-shock protein 70-x
Authors: Schmidt Julia , Vakonakis Ioannis
Published: September 2020

The malaria parasite Plasmodium falciparum extensively modifies erythrocytes that it invades by exporting a large complement of proteins to the host cell. Among these exported components is a single heat-shock 70 kDa class protein, PfHsp70-x, that supports the virulence and growth rate of the parasite during febrile episodes. The ATP-binding domain of PfHsp70-x has previously been resolved and showed the presence of potentially druggable epitopes that differ from those on human Hsp70 chaperones. Here, the crystallographic structure of the substrate-binding domain (SBD) of PfHsp70-x is presented in complex with a hydrophobic peptide. The PfHsp70-x SBD is shown to be highly similar to the counterpart from a human erythrocytic Hsp70 chaperone. The binding of substrate at the interface between β-sandwich and α-helical subdomains of this chaperone segment is also conserved between the malaria parasite and humans. It is hypothesized that the parasite may partly exploit human chaperones for intra-erythrocytic trafficking and maintenance of its exported proteome.