bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase transitions in natural C-O-H-N-S fluid inclusions - implications for gas mixtures and the behavior of solid H2S at low temperatures
Authors: Sośnicka Marta , Lüders Volker 
Published: November 2021

AbstractC–O–H–N–S-bearing fluids are known as one of the most challenging geochemical systems due to scarcity of available experimental data. H2S-rich fluid systems were recognized in a wide array of world-class mineral deposits and hydrocarbon reservoirs. Here we report on a nature of low-temperature (T ≥ −192 °C) phase transitions observed in natural CH4–H2S–CO2–N2–H2O fluid inclusions, which are modeled as closed thermodynamic systems and thus serve as natural micro-laboratories representative of the C–O–H–N–S system. For the first time, we document solid–solid H2S (α ↔ β ↔ γ) transitions, complex clathrates and structural transformations of solid state H2S in natural inclusion gas mixtures. The new data on Raman spectroscopic features and a complete sequence of phase transition temperatures in the gas mixtures contribute to scientific advancements in fluid geochemistry. Enhanced understanding of the phase equilibria in the C–O–H–N–S system is a prerequisite for conscientious estimation of P-T-V-X properties, necessary to model the geologic evolution of hydrocarbon and mineral systems. Our findings are a driver for the future research expeditions to extraterrestrial H2S-rich planetary systems owing to their low temperature environments.
Crystal structures of phosphatidyl serine synthase PSS reveal the catalytic mechanism of CDP-DAG alcohol O-phosphatidyl transferases
Authors: Centola Martin , van Pee Katharina , Betz Heidi , Yildiz Özkan 
Published: November 2021

AbstractPhospholipids are the major components of the membrane in all type of cells and organelles. They also are critical for cell metabolism, signal transduction, the immune system and other critical cell functions. The biosynthesis of phospholipids is a complex multi-step process with high-energy intermediates. Several enzymes in different metabolic pathways are involved in the initial phospholipid synthesis and its subsequent conversion. While the “Kennedy pathway” is the main pathway in mammalian cells, in bacteria and lower eukaryotes the precursor CDP-DAG is used in the de novo pathway by CDP-DAG alcohol O-phosphatidyl transferases to synthetize the basic lipids. Here we present the high-resolution structures of phosphatidyl serine synthase from Methanocaldococcus jannaschii crystallized in four different states. Detailed structural and functional analysis of the different structures allowed us to identify the substrate binding site and show how CDP-DAG, serine and two essential metal ions are bound and oriented relative to each other. In close proximity to the substrate binding site, two anions were identified that appear to be highly important for the reaction. The structural findings were confirmed by functional activity assays and suggest a model for the catalytic mechanism of CDP-DAG alcohol O-phosphatidyl transferases, which synthetize the phospholipids essential for the cells.
A rechargeable aqueous manganese-ion battery based on intercalation chemistry
Authors: Bi Songshan , Wang Shuai , Yue Fang , Tie Zhiwei , Niu Zhiqiang 
Published: November 2021

AbstractAqueous rechargeable metal batteries are intrinsically safe due to the utilization of low-cost and non-flammable water-based electrolyte solutions. However, the discharge voltages of these electrochemical energy storage systems are often limited, thus, resulting in unsatisfactory energy density. Therefore, it is of paramount importance to investigate alternative aqueous metal battery systems to improve the discharge voltage. Herein, we report reversible manganese-ion intercalation chemistry in an aqueous electrolyte solution, where inorganic and organic compounds act as positive electrode active materials for Mn2+ storage when coupled with a Mn/carbon composite negative electrode. In one case, the layered Mn0.18V2O5·nH2O inorganic cathode demonstrates fast and reversible Mn2+ insertion/extraction due to the large lattice spacing, thus, enabling adequate power performances and stable cycling behavior. In the other case, the tetrachloro-1,4-benzoquinone organic cathode molecules undergo enolization during charge/discharge processes, thus, contributing to achieving a stable cell discharge plateau at about 1.37 V. Interestingly, the low redox potential of the Mn/Mn2+ redox couple vs. standard hydrogen electrode (i.e., −1.19 V) enables the production of aqueous manganese metal cells with operational voltages higher than their zinc metal counterparts.
Engineering of a fluorescent chemogenetic reporter with tunable color for advanced live-cell imaging
Authors: Benaissa Hela , Ounoughi Karim , Aujard Isabelle , Fischer Evelyne , Goïame Rosette , Nguyen Julie , Tebo Alison G. , Li Chenge , Le Saux Thomas , Bertolin Giulia , Tramier Marc , Danglot Lydia , Pietrancosta Nicolas , Morin Xavier , Jullien Ludovic , Gautier Arnaud 
Published: November 2021

AbstractBiocompatible fluorescent reporters with spectral properties spanning the entire visible spectrum are indispensable tools for imaging the biochemistry of living cells and organisms in real time. Here, we report the engineering of a fluorescent chemogenetic reporter with tunable optical and spectral properties. A collection of fluorogenic chromophores with various electronic properties enables to generate bimolecular fluorescent assemblies that cover the visible spectrum from blue to red using a single protein tag engineered and optimized by directed evolution and rational design. The ability to tune the fluorescence color and properties through simple molecular modulation provides a broad experimental versatility for imaging proteins in live cells, including neurons, and in multicellular organisms, and opens avenues for optimizing Förster resonance energy transfer (FRET) biosensors in live cells. The ability to tune the spectral properties and fluorescence performance enables furthermore to match the specifications and requirements of advanced super-resolution imaging techniques.
WFS1 functions in ER export of vesicular cargo proteins in pancreatic β-cells
Authors: Wang Linlin , Liu Hongyang , Zhang Xiaofei , Song Eli , Wang You , Xu Tao , Li Zonghong 
Published: November 2021

AbstractThe sorting of soluble secretory proteins from the endoplasmic reticulum (ER) to the Golgi complex is mediated by coat protein complex II (COPII) vesicles and thought to required specific ER membrane cargo-receptor proteins. However, these receptors remain largely unknown. Herein, we show that ER to Golgi transfer of vesicular cargo proteins requires WFS1, an ER-associated membrane protein whose loss of function leads to Wolfram syndrome. Mechanistically, WFS1 directly binds to vesicular cargo proteins including proinsulin via its ER luminal C-terminal segment, whereas pathogenic mutations within this region disrupt the interaction. The specific ER export signal encoded in the cytosolic N-terminal segment of WFS1 is recognized by the COPII subunit SEC24, generating mature COPII vesicles that traffic to the Golgi complex. WFS1 deficiency leads to abnormal accumulation of proinsulin in the ER, impeding the proinsulin processing as well as insulin secretion. This work identifies a vesicular cargo receptor for ER export and suggests that impaired peptide hormone transport underlies diabetes resulting from pathogenic WFS1 mutations.
Differential susceptibility of reef-building corals to deoxygenation reveals remarkable hypoxia tolerance
Authors: Johnson Maggie D. , Swaminathan Sara D. , Nixon Emily N. , Paul Valerie J. , Altieri Andrew H. 
Published: November 2021

AbstractOcean deoxygenation threatens the persistence of coastal ecosystems worldwide. Despite an increasing awareness that coastal deoxygenation impacts tropical habitats, there remains a paucity of empirical data on the effects of oxygen limitation on reef-building corals. To address this knowledge gap, we conducted laboratory experiments with ecologically important Caribbean coralsAcropora cervicornisandOrbicella faveolata. We tested the effects of continuous exposure to conditions ranging from extreme deoxygenation to normoxia (~ 1.0 to 6.25 mg L−1dissolved oxygen) on coral bleaching, photophysiology, and survival. Coral species demonstrated markedly different temporal resistance to deoxygenation, and within a species there were minimal genotype-specific treatment effects.Acropora cervicornissuffered tissue loss and mortality within a day of exposure to severe deoxygenation (~ 1.0 mg L−1), whereasO. faveolataremained unaffected after 11 days of continuous exposure to 1.0 mg L−1. Intermediate deoxygenation treatments (~ 2.25 mg L−1, ~ 4.25 mg L−1) elicited minimal responses in both species, indicating a low oxygen threshold for coral mortality and coral resilience to oxygen concentrations that are lethal for other marine organisms. These findings demonstrate the potential for variability in species-specific hypoxia thresholds, which has important implications for our ability to predict how coral reefs may be affected as ocean deoxygenation intensifies. With deoxygenation emerging as a critical threat to tropical habitats, there is an urgent need to incorporate deoxygenation into coral reef research, management, and action plans to facilitate better stewardship of coral reefs in an era of rapid environmental change.
Structural exploration with AlphaFold2-generated STAT3α structure reveals selective elements in STAT3α-GRIM-19 interactions involved in negative regulation
Authors: Mishra Seema , Kumar Santosh , Choudhuri Kesaban Sankar Roy , Longkumer Imliyangla , Koyyada Praveena , Kharsyiemiong Euphinia Tiberius 
Published: November 2021

AbstractSTAT3, an important transcription factor constitutively activated in cancers, is bound specifically by GRIM-19 and this interaction inhibits STAT3-dependent gene expression. GRIM-19 is therefore, considered as an inhibitor of STAT3 and may be an effective anti-cancer therapeutic target. While STAT3 exists in a dimeric form in the cytoplasm and nucleus, it is mostly present in a monomeric form in the mitochondria. Although GRIM-19-binding domains of STAT3 have been identified in independent experiments, yet the identified domains are not the same, and hence, discrepancies exist. Human STAT3-GRIM-19 complex has not been crystallised yet. Dictated by fundamental biophysical principles, the binding region, interactions and effects of hotspot mutations can provide us a clue to the negative regulatory mechanisms of GRIM-19. Prompted by the very nature of STAT3 being a challenging molecule, and to understand the structural basis of binding and interactions in STAT3α-GRIM-19 complex, we performed homology modelling and ab-initio modelling with evolutionary information using I-TASSER and avant-garde AlphaFold2, respectively, to generate monomeric, and subsequently, dimeric STAT3α structures. The dimeric form of STAT3α structure was observed to potentially exist in an anti-parallel orientation of monomers. We demonstrate that during the interactions with both unphosphorylated and phosphorylated STAT3α, the NTD of GRIM-19 binds most strongly to the NTD of STAT3α, in direct contrast to the earlier works. Key arginine residues at positions 57, 58 and 68 of GRIM-19 are mainly involved in the hydrogen-bonded interactions. An intriguing feature of these arginine residues is that these display a consistent interaction pattern across unphosphorylated and phosphorylated monomers as well as unphosphorylated dimers in STAT3α-GRIM-19 complexes. MD studies verified the stability of these complexes. Analysing the binding affinity and stability through free energy changes upon mutation, we found GRIM-19 mutations Y33P and Q61L and among GRIM-19 arginines, R68P and R57M, to be one of the top-most major and minor disruptors of binding, respectively. The proportionate increase in average change in binding affinity upon mutation was inclined more towards GRIM-19 mutants, leading to the surmise that GRIM-19 may play a greater role in the complex formation. These studies propound a novel structural perspective of STAT3α-GRIM-19 binding and inhibitory mechanisms in both the monomeric and dimeric forms of STAT3α as compared to that observed from the earlier experiments, these experimental observations being inconsistent among each other.
In vivo optical imaging-guided targeted sampling for precise diagnosis and molecular pathology
Authors: Sahu Aditi , Oh Yuna , Peterson Gary , Cordova Miguel , Navarrete-Dechent Cristian , Gill Melissa , Alessi-Fox Christi , Gonzalez Salvador , Phillips William , Wilson Steven , Afzalneia Reza , Rose Raven , Mohsen Abu-Akeel , Bello Danielle , Marghoob Ashfaq , Rossi Anthony , Wolchok Jedd D. , Merghoub Taha , Rotemberg Veronica , Jason Chen Chih-Shan , Rajadhyaksha Milind 
Published: November 2021

AbstractConventional tissue sampling can lead to misdiagnoses and repeated biopsies. Additionally, tissue processed for histopathology suffers from poor nucleic acid quality and/or quantity for downstream molecular profiling. Targeted micro-sampling of tissue can ensure accurate diagnosis and molecular profiling in the presence of spatial heterogeneity, especially in tumors, and facilitate acquisition of fresh tissue for molecular analysis. In this study, we explored the feasibility of performing 1–2 mm precision biopsies guided by high-resolution reflectance confocal microscopy (RCM) and optical coherence tomography (OCT), and reflective metallic grids for accurate spatial targeting. Accurate sampling was confirmed with either histopathology or molecular profiling through next generation sequencing (NGS) in 9 skin cancers in 7 patients. Imaging-guided 1–2 mm biopsies enabled spatial targeting for in vivo diagnosis, feature correlation and depth assessment, which were confirmed with histopathology. In vivo 1-mm targeted biopsies achieved adequate quantity and high quality of DNA for next-generation sequencing. Subsequent mutational profiling was confirmed on 1 melanoma in situ and 2 invasive melanomas, using a 505-gene mutational panel called Memorial Sloan Kettering-Integrated mutational profiling of actionable cancer targets (MSK-IMPACT). Differential mutational landscapes, in terms of number and types of mutations, were found between invasive and in situ melanomas in a single patient. Our findings demonstrate feasibility of accurate sampling of regions of interest for downstream histopathological diagnoses and molecular pathology in both in vivo and ex vivo settings with broad diagnostic, therapeutic and research potential in cutaneous diseases accessible by RCM-OCT imaging.
Immunoprotective effect of an in silico designed multiepitope cancer vaccine with BORIS cancer-testis antigen target in a murine mammary carcinoma model
Authors: Mahdevar Elham , Kefayat Amirhosein , Safavi Ashkan , Behnia Amirhossein , Hejazi Seyed Hossein , Javid Amaneh , Ghahremani Fatemeh 
Published: November 2021

AbstractIn our previous study, immunoinformatic tools were used to design a novel multiepitope cancer vaccine based on the most immunodominant regions of BORIS cancer-testis antigen. The final vaccine construct was an immunogenic, non-allergenic, and stable protein consisted of multiple cytotoxic T lymphocytes epitopes, IFN-γ inducing epitopes, and B cell epitopes according to bioinformatic analyzes. Herein, the DNA sequence of the final vaccine construct was placed into the pcDNA3.1 vector as a DNA vaccine (pcDNA3.1-VAC). Also, the recombinant multiepitope peptide vaccine (MPV) was produced by a transfected BL21 E. coli strain using a recombinant pET-28a vector and then, purified and screened by Fast protein liquid chromatography technique (FPLC) and Western blot, respectively. The anti-tumor effects of prophylactic co-immunization with these DNA and protein cancer vaccines were evaluated in the metastatic non-immunogenic 4T1 mammary carcinoma in BALB/c mice. Co-immunization with the pcDNA3.1-VAC and MPV significantly (P < 0.001) increased the serum levels of the MPV-specific IgG total, IgG2a, and IgG1. The splenocytes of co-immunized mice exhibited a significantly higher efficacy to produce interleukin-4 and interferon-γ and proliferation in response to MPV in comparison with the control. The prophylactic co-immunization regime caused significant breast tumors’ growth inhibition, tumors’ weight decrease, inhibition of metastasis formation, and enlarging tumor-bearing mice survival time, without any considerable side effects. Taking together, this cancer vaccine can evoke strong immune response against breast tumor and inhibits its growth and metastasis.
Anti-breast cancer synthetic peptides derived from the Anabas testudineus skin mucus fractions
Authors: Najm Ahmed Abdul Kareem , Azfaralariff Ahmad , Dyari Herryawan Ryadi Eziwar , Othman Babul Airianah , Shahid Muhammad , Khalili Nahid , Law Douglas , Syed Alwi Sharifah Sakinah , Fazry Shazrul 
Published: November 2021

AbstractPrevious study has shown the antimicrobial activities of mucus protein extracted from Anabastestudineus. In this study, we are interested in characterizing the anticancer activity of the A.testudineus antimicrobial peptides (AMPs). The mucus was extracted, fractioned, and subjected to antibacterial activity testing to confirm the fish's AMPs production. The cytotoxic activity of each fraction was also identified. Fraction 2 (F2), which shows toxicity against MCF7 and MDA-MB-231 were sent for peptide sequencing to identify the bioactive peptide. The two peptides were then synthetically produced and subjected to cytotoxic assay to prove their efficacy against cancer cell lines. The IC50 for AtMP1 against MCF7 and MDA-MB-231 were 8.25 ± 0.14 μg/ml and 9.35 ± 0.25 μg/ml respectively, while for AtMP2 it is 5.89 ± 0.14 μg/ml and 6.97 ± 0.24 μg/ml respectively. AtMP1 and AtMP2 treatment for 48 h induced breast cancer cell cycle arrest and apoptosis by upregulating the p53, which lead to upregulate pro-apoptotic BAX gene and downregulate the anti-apoptotic BCL-2 gene, consequently, trigger the activation of the caspase-3. This interaction was supported by docking analysis (QuickDBD, HPEPDOCK, and ZDOCK) and immunoprecipitation. This study provided new prospects in the development of highly effective and selective cancer therapeutics based on antimicrobial peptides.
Characterization of gliadin, secalin and hordein fractions using analytical techniques
Authors: Rani Monika , Sogi Dalbir Singh , Gill Balmeet Singh 
Published: November 2021

AbstractProlamins, alcohol soluble storage proteins of the Triticeae tribe of Gramineae family, are known as gliadin, secalin and hordein in wheat, rye and barley respectively. Prolamins were extracted from fifteen cultivars using DuPont protocol to study their physiochemical, morphological and structural characteristics. SDS-PAGE of prolamins showed well resolved low molecular weight proteins with significant amount of albumin and globulin as cross-contaminant. The β-sheet (32.72–37.41%) and β-turn (30.36–37.91%) were found higher in gliadins, while α-helix (20.32–28.95%) and random coil (9.05–10.28%) in hordeins. The high colloidal stability as depicted by zeta-potential was observed in gliadins (23.5–27.0 mV) followed secalins (11.2–16.6 mV) and hordeins (4.1–7.8 mV). Surface morphology by SEM illustrated the globular particle arrangement in gliadins, sheet like arrangement in secalins and stacked flaky particle arrangement in hordeins fraction. TEM studies showed that secalin and hordein fractions were globular in shape while gliadins in addition to globular structure also possessed rod-shaped particle arrangement. XRD pattern of prolamin fractions showed the ordered crystalline domain at 2θ values of 44.1°, 37.8° and 10.4°. The extracted prolamins fractions showed amorphous as well as crystalline structures as revealed by XRD and TEM analysis. Space saving hexagonal molecular symmetry was also observed in TEM molecular arrangement of prolamins which has profound application in development of plant-based polymers and fibres.
The significance of neural inter-frequency power correlations
Authors: Savolainen Oscar W. 
Published: November 2021

AbstractIt is of great interest in neuroscience to determine what frequency bands in the brain have covarying power. This would help us robustly identify the frequency signatures of neural processes. However to date, to the best of the author’s knowledge, a comprehensive statistical approach to this question that accounts for intra-frequency autocorrelation, frequency-domain oversampling, and multiple testing under dependency has not been undertaken. As such, this work presents a novel statistical significance test for correlated power across frequency bands for a broad class of non-stationary time series. It is validated on synthetic data. It is then used to test all of the inter-frequency power correlations between 0.2 and 8500 Hz in continuous intracortical extracellular neural recordings in Macaque M1, using a very large, publicly available dataset. The recordings were Current Source Density referenced and were recorded with a Utah array. The results support previous results in the literature that show that neural processes in M1 have power signatures across a very broad range of frequency bands. In particular, the power in LFP frequency bands as low as 20 Hz was found to almost always be statistically significantly correlated to the power in kHz frequency ranges. It is proposed that this test can also be used to discover the superimposed frequency domain signatures of all the neural processes in a neural signal, allowing us to identify every interesting neural frequency band.