bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer’s fields in western Burkina Faso
Authors: Barro Mariam , Wonni Issa , Simonin Marie , Kassankogno Abalo Itolou , Klonowska Agnieszka , Moulin Lionel , Béna Gilles , Somda Irénée , Brunel Caroline , Tollenaere Charlotte 
Published: March 2022

AbstractAs a consequence of its potential applications for food safety, there is a growing interest in rice root-associated microbial communities, but some systems remain understudied. Here, we compare the assemblage of root-associated microbiota in rice sampled in 19 small farmer’s fields from irrigated and rainfed lowlands in western Burkina Faso, using an amplicon metabarcoding approach 16S (Prokaryotes, three plant sample per field) and ITS (fungi, one sample per field). In addition to the expected structure according to the root compartment (root vs. rhizosphere) and geographical zones, we show that the rice production system is a major driver of microbiome structure, both for prokaryotes and fungi. In irrigated systems, we found a higher diversity of prokaryotic communities from rhizosphere and more complex co-occurrence networks, compared to rainfed lowlands. Core taxa were different between the two systems, and indicator species were identified: mostly within Bacillaceae and Bradyrhizobiaceae families in rainfed lowlands, and within Burkholderiaceae and Moraxellaceae in irrigated areas. Finally, phylotypes assigned to putative phytobeneficial and pathogen species were found. Mycorrhizal fungi Glomeromycetes abundance was higher in rainfed lowlands. Our results highlight deep microbiome differences induced by contrasted rice production systems that should consequently be considered for potential microbial engineering applications.
Toward a first principles understanding of the activation and deactivation mechanisms of class A G-protein coupled receptors and voltage-gated cation channels
Authors: Wan Hongbin , Pearlstein Robert A. 
Published: March 2022

AbstractWe previously reported a first principles multi-scale theory called Biodynamics that attributes cellular functions to sets of coupled molecular and ionic fluxes operating in the non-equilibrium/non-linear dynamic regime. Fluxes build and decay over time and undergo dynamic non-covalent intra- and intermolecular state transitions powered principally by the storage and release of free energy to/from the H-bond networks of external and internal solvation (that we refer to as solvation dynamics) at rates governed by the desolvation and resolvation costs incurred during their entry and exit, respectively. We have thus far examined the functional state transitions of cereblon and COVID Mproin this context, and now turn to the agonist-induced activating and deactivating state transitions of class A G-protein coupled receptors (GPCRs) and membrane potential-/dipole potential-induced activating and deactivating state transitions of voltage-gated cation channels (VGCCs). We analyzed crystal structures of the activated and deactivated forms of the human β2-adrenergic receptor (β2-AR) and cryo-EM structures of the activated and deactivated forms of Nav1.7 channels. We postulate that activation and deactivation of the β2-AR is conveyed by switchable changes in transmembrane helix (TMH) orientations relative to extracellular loop 2 (ECL2) and curvature of TMH6 and TMH7, all of which are powered by solvation free energy and kickstarted by agonist binding. The known activation and deactivation mechanisms of Nav1.7 consist of S4 translations toward and away from the extracellular membrane surface, respectively, resulting in S4-S5 linker repositioning, followed by rearrangements of the S5 and S6 helices. The latter TMH conveys channel opening and closing by respectively curving away from and toward the central pore axis. We postulate that all of these rearrangements are likewise powered by solvation free energy and kickstarted by changes in the membrane and dipole potentials. The results of our study may facilitate structure-based design of GPCR agonists/antagonists and mitigation of drug-induced ion channel blockade.
Automated identification and registration of anatomical landmarks inC. elegans
Authors: Laird Nicolette M. , Pincus Zachary 
Published: March 2022

AbstractThe physiology of the nematodeC. eleganscan be visualized with many microscopy techniques. However, quantitative microscopy ofC. elegansis complicated by the flexible and deformable nature of the nematode. These differences in posture and shape must be addressed in some fashion in any automated or manual analysis. Manual approaches are time intensive and require hand-labeling anatomical regions of interest. Automated tools exist, but generally rely on high-magnification imaging using labeled nuclei as fiducial markers. Here we describe a suite of new tools that allows for high-throughput analysis of whole-body images, aligned using anatomical landmarks identified from brightfield images. We show how these tools can be used in basic morphometric tasks and examine anatomical variation and morphological changes in a population over time.
Induction of Bacteriophage PinR Facilitates the Evolution of Antibiotic Resistance
Authors: Zhang Le , Guan Yunpeng , Su Qian Peter , Liao Yan , Duggin Iain , Jin Dayong 
Published: March 2022

AbstractA recent work reports that the single treatment of β-lactams can cause a SOS-independent superfast evolution of multi-drug resistance in the DNA repair deficiency Escherichia coli (E. coli), but the mechanism is not yet clear. Here, we find that the induction of PinR, a lambdoid prophage Rac, is involved in this process and facilitates the evolution of antibiotic resistance in DNA repair deficiency bacteria through the repression on the transcription of antioxidative genes and the thereafter ROS burst in cells. It is highlighted that the bacteriophage PinR can orchestrate the mutagenesis induced by the overaccumulation of ROS in cells. More importantly, we for the first time demonstrate that the deletion of pinR can avoid the rapid evolution of antibiotic resistance induced by either the single or long-term exposure to antibiotics, while strategies to target RecA, e.g., the inactivation on RecA, can be safely implemented to disarm the bacterial resistance to other antibiotics. Therefore, from a drug development perspective, our work suggests future studies on the “evolutionary potentiators” towards a safe and more effective strategy to be developed for infectious disease treatment.
THRONCAT: Efficient metabolic labeling of newly synthesized proteins using a bioorthogonal threonine analog
Authors: Ignacio Bob J. , Dijkstra Jelmer , Garcia Natalia Mora , Slot Erik F.J. , van Weijsten Margot J. , Storkebaum Erik , Vermeulen Michiel , Bonger Kimberly M. 
Published: March 2022

AbstractProfiling the nascent cellular proteome and capturing early proteomic changes in response to external stimuli provides valuable insight into cellular physiology. Existing metabolic protein labeling approaches based on bioorthogonal methionine-or puromycin analogs allow for the selective visualization and enrichment of the newly synthesized proteins. However, their applications are limited as they require methionine-free conditions, auxotrophic cells and/or are toxic to cells. Here, we introduce THRONCAT, a novel threonine-derived non-canonical amino acid tagging method based on bioorthogonal threonine analog β-ethynylserine (βES) that enables efficient and non-toxic labeling of the nascent proteome in complete growth media within minutes. We used THRONCAT for the visualization and enrichment of nascent proteins in bacteria, mammalian cells and Drosophila melanogaster. We profiled immediate proteome dynamics of Ramos B-cells in response to receptor activation, demonstrating the ease-of-use of the method and its potential to address diverse biological questions. In addition, using a Drosophila model of Charcot-Marie-Tooth peripheral neuropathy, we show that THRONCAT enables visualization and quantification of relative protein synthesis rates in vivo.
A machine learning method for estimating the probability of presence using presence-background data
Authors: Wang Yan , Samarasekara Chathuri L. , Stone Lewi 
Published: March 2022

AbstractEstimating the prevalence or the absolute probability of presence of a species from presence-background data has become a controversial topic in species distribution modelling. In this paper we propose a new method by combining both statistics and machine learning algorithms that helps overcome some of the known existing problems. We have also revisited the popular but highly controversial Lele and Keim (LK) method by evaluating its performance and assessing the RSPF condition it relies on. Simulations show that the LK method with unfounded model assumptions would render fragile estimation/prediction of the desired probabilities. Rather we propose the local knowledge condition, which relaxes the pre-determined population prevalence condition that has so often been used in much of the existing literature. Simulations demonstrate the performance of the CLK method utilising the local knowledge assumption to successfully estimate the probability of presence. The local knowledge extends the local certainty or the prototypical presence location assumption, and has significant implications for demonstrating the necessary condition for identifying absolute (rather than relative) probability of presence without absence data in species distribution modelling.
Inositol hexakisphosphate (IP6) accelerates immature HIV-1 Gag protein assembly towards kinetically-trapped morphologies
Authors: Pak Alexander J. , Gupta Manish , Yeager Mark , Voth Gregory A. 
Published: March 2022

AbstractDuring the late stages of the HIV-1 lifecycle, immature virions are produced by the concerted activity of Gag polyproteins, primarily mediated by the capsid (CA) and spacer peptide 1 (SP1) domains, which assemble into a spherical lattice, package viral genomic RNA, and deform the plasma membrane. Recently, inositol hexakisphosphate (IP6) has been identified as an essential assembly cofactor that efficiently produces both immature virions in vivo and immature virus-like particles in vitro. To date, however, several distinct mechanistic roles for IP6 have been proposed on the basis of independent functional, structural, and kinetic studies. In this work, we investigate the molecular influence of IP6 on the structural outcomes and dynamics of CA/SP1 assembly using coarse-grained (CG) molecular dynamics (MD) simulations and free energy calculations. Here, we derive a bottom-up, low-resolution, and implicit-solvent CG model of CA/SP1 and IP6, and simulate their assembly under conditions that emulate both in vitro and in vivo systems. Our analysis identifies IP6 as an assembly accelerant that promotes curvature generation and fissure-like defects throughout the lattice. Our findings suggest that IP6 induces kinetically-trapped immature morphologies, which may be physiologically important for later stages of viral morphogenesis and potentially useful for virus-like particle technologies.
Optimal inference of molecular interactions in live FRET imaging
Authors: Kamino Keita , Kadakia Nirag , Aoki Kazuhiro , Shimizu Thomas S. , Emonet Thierry 
Published: March 2022

AbstractIntensity-based live-cell fluorescence resonance energy transfer (FRET) imaging converts otherwise unobservable molecular interactions inside cells into fluorescence time-series signals. However, inferring the degree of molecular interactions from these observables is challenging, due to experimental complications such as spectral crosstalk, photobleaching, and measurement noise. Conventional methods solve this inverse problem through algebraic manipulations of the observables, but such manipulations inevitably accumulate measurement noise, limiting the scope of FRET analysis. Here, we introduce a Bayesian inference framework, B-FRET, which estimates molecular interactions from FRET data in a statistically optimal manner. B-FRET requires no additional measurements beyond those routinely conducted in standard 3-cube FRET imaging methods, and yet, by using the information contained in the data more efficiently, dramatically improves the signal-to-noise ratio (SNR). We validate B-FRET using simulated data, and then apply it to FRET data measured from single bacterial cells, a system with notoriously low SNR, to reveal signaling dynamics that are otherwise hidden in noise.
Predicting Protein Function and Orientation on a Gold Nanoparticle Surface Using a Residue-Based Affinity Scale
Authors: Xu Joanna Xiuzhu , Alom Md Siddik , Yadav Rahul , Fitzkee Nicholas C. 
Published: March 2022

ABSTRACTThe orientation adopted by proteins on nanoparticle surfaces determines the nanoparticle’s bioactivity and its interactions with living systems. Here, we present a residue-based affinity scale for predicting protein orientation on citrate-gold nanoparticles (AuNPs). Competitive binding between protein variants accounts for thermodynamic and kinetic aspects of adsorption in this scale. For hydrophobic residues, the steric considerations dominate, whereas electrostatic interactions are critical for hydrophilic residues. The scale rationalizes the well-defined binding orientation of the small GB3 protein, and it subsequently predicts the orientation and active site accessibility of two enzymes on AuNPs. Additionally, our approach accounts for the AuNP-bound activity of five out of six additional enzymes from the literature. The model developed here enables high-throughput predictions of protein behavior on nanoparticles, and it enhances our understanding of protein orientation in the biomolecular corona, which should greatly enhance the performance and safety of nanomedicines used in vivo.
scAllele: a versatile tool for the detection and analysis of variants in scRNA-seq
Authors: Valdez Giovanni Quinones , Fu Ting , Chan Tracey , Xiao Xinshu (Grace) 
Published: March 2022

AbstractSingle-cell RNA sequencing (scRNA-seq) data contain rich information at the gene, transcript, and nucleotide levels. Most analyses of scRNA-seq have focused on gene expression profiles, and it remains challenging to extract nucleotide variants and isoform-specific information. Here, we present scAllele, an integrative approach that detects single nucleotide variants, insertions, deletions, and their allelic linkage with splicing patterns in scRNA-seq. We demonstrate that scAllele achieves better performance in identifying nucleotide variants than other commonly used tools. In addition, the read-specific variant calls by scAllele enables allele-specific splicing analysis, a unique feature not afforded by other methods. Applied to a lung cancer scRNA-seq data set, scAllele identified variants with strong allelic linkage to alternative splicing, some of which being cancer-specific. scAllele represents a versatile tool to uncover multi-layer information and novel biological insights from scRNA-seq data.
More than names on a roster: the many meanings behind Sgaw Karen names
Authors: Gilhooly Daniel , Htoo Chris Mu 
Published: March 2022

Purpose
The purpose of this paper is to demonstrate how teachers can use their Sgaw Karen students’ names as a means to gaining awareness of their students’ home culture, language and personal stories.

Design/methodology/approach
This case study uses interviews with four Karen families to explore the meanings behind the names and nicknames given to Karen individuals.

Findings
The findings of this study reveal that Karen names can provide teachers important insights into Karen culture, history and language. Moreover, Karen names can also provide important biographical information about the student.

Research limitations/implications
This study only focuses on Sgaw Karen names and does not include other Karen subgroups like the Pwo Karen, who are also resettling in the USA. This study does not include all Sgaw Karen names, but the authors have made efforts to include Karen names from various regions of Burma and of different religious backgrounds.

Practical implications
Teachers and others working with culturally and linguistically diverse students like the Karen will gain a better understanding of the various ways that names are given across cultures. While this paper focuses on one particular ethnic group, it is believed that teachers need to expand their notions about how other non-European groups name their children and how these names may reveal something about the student’s heritage culture, history, language and the unique lived experiences of their students.

Social implications
Too often teachers and others working cross-culturally do not realize that other cultures follow different naming practices than those used in the USA. Teachers often mispronounce or misunderstand students’ names when the student comes from a cultural group unfamiliar to them. This paper helps a general audience better realize the unique approach Karen culture takes to naming children and how these names are often transformed to fit American naming conventions. As the title suggests, Karen students often feel embarrassed and take on a negative opinion of their given name as a result of a lack of awareness by teachers and others.

Originality/value
This paper provides a unique perspective in the literature on the ways cultural naming conventions can serve teachers aspiring to incorporate biography-driven instruction into their classroom practices.
Study on the dyeing process of fast-growing fir veneer with reactive dyes
Authors: Guan Xuemei , Li Wenfeng , Huang Jingyi 
Published: March 2022

Purpose
The purpose of this paper is to improve the dyeing effect of fast-growing fir wood dyed with reactive dyes.

Design/methodology/approach
In this study, five factors including temperature, the dosage of dye accelerator, dyeing time, the dosage of fixing agent and fixing time were investigated. Then, the color difference and light resistance of the wood surface after dyeing were used as the evaluation indicators; the best dyeing process under the two indicators was obtained through the range analysis. Finally, the two indicators were considered comprehensively, and the fuzzy comprehensive evaluation method was used to obtain the best dyeing process under the comprehensive indicators.

Findings
The results show that when the comprehensive index was used as the evaluation index, the optimal dyeing process for reactive red X-3B dyeing fast-growing fir veneer was that the dyeing temperature was 65°C; the amount of dye accelerator was 25 g L−1; the dyeing time was 2 h; the amount of fixing agent was 15 g L−1; and the fixing time was 35 min.

Originality/value
The technique of wood dyeing is an important method to increase the value of wood products. When using different kinds of dyes or dyeing substrates for wood dyeing, the dyeing process is different. This study determined the best process for reactive dye dyeing of fast-growing fir veneer and provided a solution for improving the value of fast-growing fir wood.
Discovery of 3‐(2‐aminoethyl)‐thiazolidine‐2,4‐diones as a novel chemotype of sigma‐1 receptor ligands
Authors: Elkholy Nada , Abdelwaly Ahmad , Mohamed Karim , Amata Emanuele , Lombino Jessica , Cosentino Giuseppe , Intagliata Sebastiano , Helal Mohamed A. 
Published: March 2022

AbstractSigma receptor is a transmembrane non‐GPCR protein expressed mainly in the endoplasmic reticulum membrane associated with mitochondria. It is classified into two types: Sigma‐1 (S1R) and Sigma‐2 (S2R) based on their biological functions. S1R has been implicated in many neurological disorders such as anxiety, schizophrenia, and depression. Therefore, S1R ligands possess a variety of potential clinical applications with a great interest in the treatment of neuropathic pain. In this study, we report the discovery of a novel lead compound for S1R binding, based on the thiazolidine‐2,4‐dione nucleus. We have explored hydrophobic groups of different sizes on both sides of the five‐membered ring scaffold guided by the crystal structure of S1R. Six compounds showed more than 50% displacement of the radioligand at 10 µM concentration with compound 6c resulting in 100% displacement and a Ki of 95.5 nM. Moreover, compounds 6c and 6e showed a significant selectivity over S2R. In addition, molecular docking predicted that all the compounds showed the critical salt bridge with Glu172 with variable degrees of π‐stacking interaction with Tyr103. Upon optimization, this series of compounds could represent potential clinically useful S1R ligands for pain management.
Expanding genotypic and phenotypic spectrums of LTBP3 variants in dental anomalies and short stature syndrome
Authors: Kantaputra Piranit , Guven Yeliz , Kalayci Tugba , Özer Pelin Karaca , Panyarak Wannakamon , Intachai Worrachet , Olsen Bjorn , Carlson Bruce M. , Praditsap Oranud , Tongsima Sissades , Ngamphiw Chumpol , Jatooratthawichot Peeranat , Tucker Abigail S. , Ketudat Cairns James R. 
Published: March 2022

AbstractMutations in LTBP3 are associated with Dental Anomalies and Short Stature syndrome (DASS; MIM 601216), which is characterized by hypoplastic type amelogenesis imperfecta, hypodontia, underdeveloped maxilla, short stature, brachyolmia, aneurysm and dissection of the thoracic aorta. Here we report a novel (p.Arg545ProfsTer22) and a recurrent (c.3107‐2A > G) LTBP3 variants, in a Turkish family affected with DASS. The proband, who carried compound heterozygous variant c.3107‐2A > G, p.Arg545ProfsTer22, was most severely affected with DASS. The proband's father, who carried the heterozygous variant c.3107‐2A > G had short stature and prognathic mandible. The mother and brother of the proband carried the heterozygous variant p.Arg545ProfsTer22, but only the mother showed any DASS characteristics. The c.3107‐2A > G and the p.Arg545ProfsTer22 variants are expected to result in abnormal LTPB3 protein, failure of TGFβ‐LAP‐LTBP3 complex formation, and subsequent disruption of TGFβ secretion and activation. This is the first report of heterozygous carriers of LTBP3 variants showing phenotypes. The new findings of DASS found in this family include taurodontism, single‐rooted molars, abnormal dentin, calcified dental pulp blood vessels, prognathic mandible, failure of mandibular tooth eruption, interatrial septal aneurysm, secundum atrial septal defect, tricuspid valve prolapse, and a recurrent glenohumeral joint dislocation.
The relationship between occupational dust exposure and incidence of diabetes in male workers: A retrospective cohort study
Authors: Yun Byungyoon , Sim Juho , Lee Seunghyun , Cho Ara , Oh Juyeon , Kim Seunghan , Yoon Jin‐Ha 
Published: March 2022

AbstractAimPrevious studies have focused on the association between ambient particulate matter and diabetes. However, the relationship between subacute exposure to occupational dust and diabetes has not been explored. We aimed to assess this relationship.MethodsMen who worked in dust‐related process factories between January 2013 and December 2017 were recruited from a Korea Health Worker Examination Common Data Model cohort. A history of physician‐diagnosed diabetes, use of an anti‐diabetic drug, or a fasting blood glucose level of ≥7 mmol/L were considered the criteria to diagnose diabetes. Multivariable time‐dependent Cox analysis estimated hazard ratios (HRs) and 95% CIs for incident diabetes associated with exposure to occupational dust exposure; interactions with lifestyle factors were analysed. Sensitivity analyses used propensity score matching and landmark analysis.ResultsAmong 5141 male participants (median follow‐up duration, 3.85 years), 349 participants had diabetes. Occupational dust exposure was related to an increased risk of diabetes in the time‐dependent Cox analysis (entire cohort: HR 1.66 [95% CI 1.25–2.19], matched cohort: HR 1.65 [95% CI 1.22–2.24]). The findings showed the same direction in the landmark analysis (HR 1.42 [95% CI 1.01–1.99]).ConclusionsA significant relationship exists between occupational dust exposure and increased risk of diabetes in male workers. Further studies should be conducted to confirm that occupational dust exposure is a possible risk factor for diabetes.