bluuebunny/crossref_metadata_2025 huggingface dataset:
popDMS infers mutation effects from deep mutational scanning data
Authors: Hong Zhenchen , Barton John P.
Published: February 2024

Deep mutational scanning (DMS) experiments provide a powerful method to measure the functional effects of genetic mutations at massive scales. However, the data generated from these experiments can be difficult to analyze, with significant variation between experimental replicates. To overcome this challenge, we developed popDMS, a computational method based on population genetics theory, to infer the functional effects of mutations from DMS data. Through extensive tests, we found that the functional effects of single mutations and epistasis inferred by popDMS are highly consistent across replicates, comparing favorably with existing methods. Our approach is flexible and can be widely applied to DMS data that includes multiple time points, multiple replicates, and different experimental conditions.
Cutaneous leishmaniasis in British troops following jungle training in Belize: cumulative incidence and potential risk practices
Authors: Niba Rawlings Ngwa , Bailey Mark , Craig Peter , Courtenay Orin
Published: February 2024

Introduction

British soldiers undergoing jungle training (JT) in Belize typically experience a relatively low risk of developing cutaneous leishmaniasis (CL). However, an uncharacteristically large outbreak of CL occurred in 2022. This study aimed to determine the cumulative incidence (CUMI) of the disease and highlight potential shortcomings in personal protective measures (PPMs) to mitigate exposure to sand fly vector bites.

Methods

A retrospective analysis was conducted on medical records of CL cases between 2005 and 2022, as well as on questionnaire responses regarding PPMs administered to CL cases in 2022. Data were sourced from Defence Public Health Unit, Military Environmental Health Department and British Army Training Support Unit Belize.

Results

Eighty-one confirmed clinical CL cases were recorded between 2005 and 2022, with a substantial peak (38 cases) in 2022. Most cases occurred during the wet season. Pre-2022, the median CUMI per 8-week deployment was 0.90% (Q1–Q3: 0.34%–1.34%), with an annual variation of 0.2% to 2.0%. In 2022, the CUMI spiked to 4.22%, associated with a risk ratio of 5.3 (95% C.I.s: 3.41, 8.16), and rising to a CUMI of 7.3% in a single unit of 450 men (33 CL cases) in late 2022. These values are significantly higher than the median CUMI of all previous years, and to published reports for other CL-endemic regions. Troop responses identified limitations in the supply of optimal equipment, and in sand fly bite and leishmaniasis risk avoidance information provided by the pre-deployment health education (PDHE) programme. Compliance with PDHE advise was also suboptimal, with irregular use of insect repellents, protective clothing / head netting, and insecticide-treated hammocks.

Conclusions

The reasons behind the unusually high numbers of CL cases and CUMI in 2022 remain unclear, emphasising the need to improve PPM provision and implement a comprehensive PDHE programme for troops undergoing JT in Belize.
The collective application of shorebird tracking data to conservation
Authors: Harrison Autumn-Lynn , Stenzel Candace , Anderson Alexandra , Howell Jessica , Lanctot Richard B. , Aikens Marley , Aldabe Joaquín , Berigan Liam A. , Bêty Joël , Blomberg Erik , Bosi de Almeida Juliana , Boyce Andy J. , Bradley David W. , Brown Stephen , Carlisle Jay , Cheskey Edward , Christie Katherine , Christin Sylvain , Clay Rob , Dayer Ashley , Deppe Jill L. , English Willow , Flemming Scott A. , Gilg Olivier , Gilroy Christine , Heath Susan , Hill Jason M. , Hipfner J. Mark , Johnson James A. , Johnson Luanne , Kempenaers Bart , Knaga Paul , Kwon Eunbi , Lagassé Benjamin J. , Lamarre Jean-François , Latty Christopher , Léandri-Breton Don-Jean , Lecomte Nicolas , Loring Pam , McGuire Rebecca , Moorhead Scott , Navedo Juan G. , Newstead David , Nol Erica , Olalla-Kerstupp Alina , Olson Bridget , Olson Elizabeth , Paquet Julie , Pierce Allison K. , Rausch Jennie , Regan Kevin , Reiter Matt , Roth Amber M. , Russell Mike , Saalfeld Sarah T. , Scarpignato Amy L. , Schulte Shiloh , Senner Nathan R. , Smith Joseph A. M. , Smith Paul A. , Spector Zach , Srigley Werner Kelly , Stantial Michelle L. , Taylor Audrey R. , Valcu Mihai , Wehtje Walter , Winn Brad , Wunder Michael B.
Published: February 2024

Addressing urgent conservation issues, like the drastic declines of North American migratory birds, requires creative, evidence-based, efficient, and collaborative approaches. Over 50% of monitored North American shorebird populations have lost over 50% of their abundance since 1980. To address these declines, we developed a partnership of scientists and practitioners called the Shorebird Science and Conservation Collective (hereinafter “the Collective”). Here, we present this successful case study as an example for others engaged in translational science. The Collective acts as an intermediary whereby dedicated staff collate and analyze data contributions from scientists to support knowledge requests from conservation practitioners. Data contributions from 74 organizations include over 6.7 million shorebird locations forming movement paths of 3,345 individuals representing 36 species tracked across the Americas. We describe the founding and structure of the Collective and conservation activities we supported in our first two years. As the volume of scientific data on animal movements continues to grow, groups like the Collective can be vital liaisons to rapidly integrate and interpret research to support conservation action.
Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets
Authors: Kille Bryce , Nute Michael G. , Huang Victor , Kim Eddie , Phillippy Adam M. , Treangen Todd J.
Published: February 2024

Motivation

Since 2016, the number of microbial species with available reference genomes in NCBI has more than tripled. Multiple genome alignment, the process of identifying nucleotides across multiple genomes which share a common ancestor, is used as the input to numerous downstream comparative analysis methods. Parsnp is one of the few multiple genome alignment methods able to scale to the current era of genomic data; however, there has been no major release since its initial release in 2014.

Results

To address this gap, we developed Parsnp v2, which significantly improves on its original release. Parsnp v2 provides users with more control over executions of the program, allowing Parsnp to be better tailored for different use-cases. We introduce a partitioning option to Parsnp, which allows the input to be broken up into multiple parallel alignment processes which are then combined into a final alignment. The partitioning option can reduce memory usage by over 4x and reduce runtime by over 2x, all while maintaining a precise core-genome alignment. The partitioning workflow is also less susceptible to complications caused by assembly artifacts and minor variation, as alignment anchors only need to be conserved within their partition and not across the entire input set. We highlight the performance on datasets involving thousands of bacterial and viral genomes.

Availability

Parsnp is available athttps://github.com/marbl/parsnp
Temporal variability in host availability alters the outcome of competition between two parasitoid species
Authors: Wang Hua , Liu Tiantian , Sun Shucun , Lewis Owen T. , Xi Xinqiang
Published: February 2024

Variability in the availability of resources through time is a common attribute in trophic interactions, but its effects on the fitness of different consumer species and on interspecific competition between them are not clearly understood.

To investigate this, we allowed two parasitoid species,Trichopria drosophilaeandPachycrepoideus vindemiae, to exploitDrosophilahost pupae under three temporal variability treatments, either on their own or simultaneously.

When tested individually (in the absence of interspecific competition), both parasitoid species had lower fitness when hosts were exposed for a short duration at high density than when exposed for a long duration at low density. When both parasitoid species exploited hosts simultaneously, interspecific competition significantly decreased the number of offspring for both parasitoid species. The outcome of this interspecific competition depended on host temporal variability, withT. drosophilaeorP. vindemiaedominating in short and long host exposure treatments, respectively.

These results can be explained by the combination of host availability and egg load of female adult parasitoids. When abundant hosts are provided for a short period, the ample mature eggs of the proovigenicT. drosophilaeenable them to exploit hosts more efficiently thanP. vindemiae, which is synovigenic. However,P. vindemiaeis an intrinsically superior competitor and dominates when multiparasitism occurs. Multiparasitism is more frequent when hosts are at low levels relative to the egg load of the parasitoids.

Our results clearly demonstrate that resource temporal availability can alter the outcome of competition between consumers with different reproductive traits.
RNF43 is a gatekeeper for colitis-associated cancer
Authors: Dietl Alisa , Ralser Anna , Taxauer Karin , Dregelies Theresa , Sterlacci William , Stadler Mara , Olayo-Alarcon Roberto , Margaryan Shushan , Skerhut Martin , Groll Tanja , Steiger Katja , Singh Dharmesh , Li Xue , Oellinger Rupert , Rad Roland , Janssen Klaus Peter , Mueller Christian L. , Vieth Michael , Gerhard Markus , Mejías-Luque Raquel
Published: February 2024

Somatic mutations in the tumor suppressor Ring finger protein 43 (RNF43) were frequently found in colitis-associated cancer (CAC) and related to the duration of chronic inflammation, but their significance in inflammation and inflammation-associated carcinogenesis remained elusive.

We assessed the onset ofRNF43mutations at different stages of human CAC development by exome sequencing, and comprehensively characterizedRNF43loss-of-function-driven malignant transformation in mice by RNA sequencing, flow cytometry, immunohistochemistry, computational transcriptome-microbiome associations, and determined the underlying mechanisms by performing functional stem-cell derived organoid studies and fecal microbiota transfers.

Mutations inRNF43were frequent (12.9 %) in precancerous lesions of ulcerative colitis (UC) patients and eventually detectable in 24.4 % of CAC patients. In a bacterial-induced colitis mouse model,Rnf43mutations caused invasive colorectal carcinomas by aggravating and perpetuating inflammation due to impaired epithelial barrier integrity and pathogen control. We could demonstrate thatRnf43loss-of-function-mutations were even sufficient to cause spontaneous intestinal inflammation, resulting in UC-typical pathological features and subsequent invasive carcinoma development. In detail, mutantRnf43impaired intestinal epithelial and particularly goblet cell homeostasis in a cell-intrinsic manner, and caused dysbiosis. The altered microbiota composition induced epithelial DNA damage and spontaneous mucosal inflammation characterized by TGF-ß-activating dendritic cells and pro-inflammatory (IL-17+, IL-22+, TNFα+) T cells. Over time, the continuous epithelial and goblet cell dysfunction, combined with pro-tumorigenic and pro-inflammatory microbiota, resulted in accumulated epithelial damage with transformation into inflammation-associated cancer in the presence of constitutive WNT signaling activation.

We identified mutantRNF43as susceptibility gene for UC and bona fide driver of CAC.
Pyruvate metabolism dictates fibroblast sensitivity to GLS1 inhibition during fibrogenesis
Authors: Contento Greg , Wilson Jo-Anne A , Selvarajah Brintha , Platé Manuela , Guillotin Delphine , Morales Valle , Trevisani Marcello , Pitozzi Vanessa , Bianchi Katiuscia , Chambers Rachel C
Published: February 2024

Fibrosis is a chronic disease characterized by excessive extracellular matrix (ECM) production which leads to destruction of normal tissue architecture and disruption of organ function. Fibroblasts are key effector cells of this process and respond to a host of pro-fibrotic stimuli, including notably the pleiotropic cytokine, TGF-β1, which promotes fibroblast to myofibroblast differentiation. This is accompanied by the simultaneous rewiring of metabolic networks to meet the biosynthetic and bioenergetic needs of contractile and ECM-synthesizing cells, but the exact mechanisms involved remain poorly understood. In this study, we report that extracellular nutrient availability profoundly influences the TGF-β1transcriptome of primary human lung fibroblasts (pHLFs) and the “biosynthesis of amino acids” emerges as a top enriched transcriptional module influenced by TGF-β1. We subsequently uncover a key role for pyruvate in influencing the pharmacological impact of glutaminase (GLS1) inhibition during TGF-β1-induced fibrogenesis. In pyruvate replete conditions which mimic the physiological concentration of pyruvate in human blood, GLS1 inhibition is ineffective in blocking TGF-β1-induced fibrogenesis, as pyruvate is able to be used as the substrate for glutamate and alanine production via glutamate dehydrogenase (GDH) and glutamic-pyruvic transaminase 2 (GPT2), respectively. We further show that dual targeting of either GPT2 or GDH in combination with GLS1-inhibition is required to fully block TGF-β1-induced collagen synthesis. These findings embolden a therapeutic strategy aimed at additional targeting of mitochondrial pyruvate metabolism in the presence of a glutaminolysis inhibitor in order to interfere with the pathological deposition of collagen in the setting of pulmonary fibrosis and potentially other fibrotic conditions.
Protein language models learn evolutionary statistics of interacting sequence motifs
Authors: Zhang Zhidian , Wayment-Steele Hannah K. , Brixi Garyk , Wang Haobo , Dal Peraro Matteo , Kern Dorothee , Ovchinnikov Sergey
Published: February 2024

Protein language models (pLMs) have emerged as potent tools for predicting and designing protein structure and function, and the degree to which these models fundamentally understand the inherent biophysics of protein structure stands as an open question. Motivated by a discovery that pLM-based structure predictors erroneously predict nonphysical structures for protein isoforms, we investigated the nature of sequence context needed for contact predictions in the pLM ESM-2. We demonstrate by use of a “categorical Jacobian” calculation that ESM-2 stores statistics of coevolving residues, analogously to simpler modelling approaches like Markov Random Fields and Multivariate Gaussian models. We further investigated how ESM-2 “stores” information needed to predict contacts by comparing sequence masking strategies, and found that providing local windows of sequence information allowed ESM-2 to best recover predicted contacts. This suggests that pLMs predict contacts by storing motifs of pairwise contacts. Our investigation highlights the limitations of current pLMs and underscores the importance of understanding the underlying mechanisms of these models.

Significance Statement

Protein language models (pLMs) have exhibited remarkable capabilities in protein structure prediction and design. However, the extent to which they comprehend the intrinsic biophysics of protein structures remains uncertain. We present a suite of analyses that dissect how the flagship pLM ESM-2 predicts structure. Motivated by a consistent error of protein isoforms predicted as structured fragments, we developed a completely unsupervised method to uniformly evaluate any protein language model that allows for us to compare coevolutionary statistics to older linear models. We further identified t hat E SM-2 a ppears to have a precise context size that is needed to predict inter-residue contacts. Our study highlights the current limitations of pLMs and contributes to a deeper understanding of their underlying mechanisms, paving the way for more reliable protein structure predictions.
Cooperativity of c-MYC with Krüppel-Like Factor 6 Splice Variant 1 induces phenotypic plasticity and promotes prostate cancer progression and metastasis
Authors: Izadmehr Sudeh , Fernandez-Hernandez Heriberto , Wiredja Danica , Kirschenbaum Alexander , Lee-Poturalski Christine , Tavassoli Peyman , Yao Shen , Schlatzer Daniela , Hoon Divya , Difeo Analisa , Levine Alice C. , Mosquera Juan-Miguel , Galsky Matthew D. , Cordon-Cardo Carlos , Narla Goutham
Published: February 2024

Metastasis remains a major cause of morbidity and mortality in men with prostate cancer, and the functional impact of the genetic alterations, alone or in combination, driving metastatic disease remains incompletely understood. The proto-oncogene c-MYC, commonly deregulated in prostate cancer. Transgenic expression of c-MYC is sufficient to drive the progression to prostatic intraepithelial neoplasia and ultimately to moderately differentiated localized primary tumors, however, c-MYC-driven tumors are unable to progress through the metastatic cascade, suggesting that a “second-hit” is necessary in the milieu of aberrant c-MYC-driven signaling. Here, we identified cooperativity between c-MYC and KLF6-SV1, an oncogenic splice variant of the KLF6 gene. Transgenic mice that co-expressed KLF6-SV1 and c-MYC developed progressive and metastatic prostate cancer with a histological and molecular phenotype like human prostate cancer. Silencing c-MYC expression significantly reduced tumor burden in these mice supporting the necessity for c-MYC in tumor maintenance. Unbiased global proteomic analysis of tumors from these mice revealed significantly enriched vimentin, a dedifferentiation and pro-metastatic marker, induced by KLF6-SV1. c-MYC-positive tumors were also significantly enriched for KLF6-SV1 in human prostate cancer specimens. Our findings provide evidence that KLF6-SV1 is an enhancer of c-MYC-driven prostate cancer progression and metastasis, and a correlated genetic event in human prostate cancer with potential translational significance.
A Tale of Twins: The Distinct Roles of Intracellular and Extracellular Formate in Regulating Flagellar and Pathogenicity Island-1 Genes inSalmonellaTyphimurium
Authors: Mukherjee Debapriya , Chakravortty Dipshikha
Published: February 2024

Host-derived short-chain fatty acids (SCFAs) are extensively being studied for their role in the virulence and pathogenesis ofSalmonellaTyphimurium (STM). Formate, an SCFA present in the ileum, functions as a signalling molecule to enhance STM invasion. However, the role of intracellular formate inSalmonellavirulence remains poorly understood. To investigate this, we generated knockouts ofpflB(pyruvate-formate lyase) andfocA(formate transporter). Disruption of formate production throughpflBdeletion led to reduced flagellation and increasedhilAandprgHexpression, attributed to elevated intracellular pH and membrane damage. This suppression of flagellar machinery drives a shift from adhesion to invasion, regulated by RpoE via the CsrA/csrBpathway. Additionally, we demonstrate that upon compensation for intracellular deficiency of formate, STMΔpflBstarts to utilize formate as a signalling molecule to regulate downstream processes. To the best of our knowledge, this study is the first to establish the critical role of thepflBgene in maintaining intracellular pH and controlling virulence gene expression in STM. Lastly, our findings emphasize the importance of modulatingpflBexpression across intestinal regions to optimize STM invasion.

Graphical abstract
Integrated GWAS and Transcriptomic Analysis Identify New Candidate Genes for Seminal Root Growth Angle in Wheat (Triticum aestivumL.)
Authors: Paez-Garcia Ana , de Bang Louise , Maulana Frank , Kwon Taegun , Krom Nick , Kahn Rafeiza , Ma Xuefeng , Blancaflor Elison B.
Published: February 2024

Increased interest in root system architecture (RSA) and its major importance for nutrient and water uptake have intensified the efforts for a detailed study of the different root types within the homorhizic root system found in most monocotyledons as wheat. Mature homorhizic root system comprises two root types regarding their origin: embryonic and pot embryonic. However, knowledge of the different root type’ ss physiology and RSA plasticity is still limited. In wheat, embryonic roots are the first to develop after seed germination and have an important role in crop establishment. Wheat seedlings develop between 3 and 5 embryonic roots that have the same origin, but they differ in their spatial distribution. The first emerging root of a wheat seedling develops from the base of the embryo and grows vertically down. The rest of the seminal roots emerge from the lateral sides of the embryo and grow with a very specific set-point angle dependent on variety. In this study, we showed that seminal roots with different set-point angle displayed differences in response to gravity and in auxin transport. We hypothesized that the differences in RSA among root types will be directed by differences in their transcriptomic profiles. To that end, we performed an RNA sequencing analysis on both root types. With the aim of gaining a more complete understanding of the seminal root architecture plasticity, we also studied the genetic variability associated with root set-point angle performing a Genome-Wide Association Study in a wheat genetic panel of 200 accessions. Our results combined, uncovered a cluster of genes located in Chromosome 2B that comprises new players in wheat RSA with potential roles in plant response to abiotic stress.
Longitudinal fluctuations in protein concentrations and higher-order structures in the plasma proteome of kidney failure patients subjected to a kidney transplant
Authors: Nteak Sofia Kalaidopoulou , Völlmy Franziska , Lukassen Marie V. , van den Toorn Henk , den Boer Maurits A. , Bondt Albert , van der Lans Sjors P.A. , Haas Pieter-Jan , van Zuilen Arjan D. , Rooijakkers Suzan H. M. , Heck Albert J.R.
Published: February 2024

Using proteomics and complexome profiling we evaluated over a period of a year longitudinal variations in the plasma proteome of kidney failure patients, prior to and after a kidney transplantation, comparing this data with two healthy controls. The post-transplant period was complicated by numerous bacterial infections, resulting in dramatic changes in the plasma proteome, mostly related to an acute phase condition. As positive acute phase proteins, being elevated upon inflammation, we observed the well-described C-reactive protein (CRP) and Serum Amyloid A (SAA1 and SAA2), but our analyses added to that Fibrinogen (FGA, FGB and FGG), Haptoglobin (HP), Leucine-rich alpha-2-glycoprotein (LRG1), Lipopolysaccharide- binding protein (LBP), Alpha-1-antitrypsin (SERPINA1), Alpha-1-antichymotrypsin (SERPINA3), Protein S100 (S100A8, S100A9), Complement protein C4, C4b-binding protein alpha chain (C4BPA), Complement factor B (CFB) and Monocyte differentiation antigen CD14. As negative acute phase proteins, being downregulated upon inflammation, we identified the well-documented Serotransferrin (TF) and Transthyretin (TTR), but add on to that Kallistatin (SERPINA4), Heparin cofactor 2 (SERPIND1), Inter-alpha-trypsin inhibitor heavy chain H1 and H2 (ITIH1, ITIH2). For a patient with the most severe acute phase response, we furthermore performed plasma complexome profiling by SEC-LC-MS on all longitudinal samples. We observe that several plasma proteins displaying alike concentration patterns, co- elute and putatively form macromolecular complexes. These include a) FGA, FGB and FGG (as expected, b) ITIH1 and ITIH2, c) HP together with Hemoglobin (HB), d) the small acute phase biomarker proteins SAA1 and SAA2 with the Apolipoproteins A-I, A-II, A-IV (APOA1, APOA2, APOA4). By complexome profiling we expose how SAA1 and SAA2 become incorporated into high-density lipid particles, thereby replacing partly APOA1 and APOA4. Overall, our data highlight that the combination of in-depth longitudinal plasma proteome and complexome profiling can shed further light on the correlated variations in the abundance of several plasma proteins upon inflammatory events.
Virus-associated Inflammation Imprints an Inflammatory Profile on Long-lived Monocyte-derived Macrophages in the Human Liver
Authors: Sanchez Vasquez Juan Diego , Nkongolo Shirin , Traum Daniel , Kim Samuel C. , Mahamed Deeqa , Mehrotra Aman , Patel Anjali , Chen Diana , Fung Scott , Gaggar Anuj , Feld Jordan J. , Chang Kyong-Mi , Wallin Jeffrey J. , Janssen Harry L.A. , Gehring Adam J.
Published: February 2024

Chronic liver injury triggers the activation and recruitment of immune cells, causing antigen-independent tissue damage and liver disease progression. Tissue inflammation can reshape macrophage composition through monocyte replacement. Replacement of tissue macrophages with monocytes differentiating in an inflammatory environment can potentially imprint a phenotype that switches the liver from an immunotolerant organ to one predisposed to tissue damage. We longitudinally sampled the liver of chronic hepatitis B (CHB) patients with active liver inflammation starting antiviral therapy. Antiviral therapy suppressed viral replication and liver inflammation, which coincided with decreased myeloid activation markers. Single-cell RNA sequencing mapped peripheral inflammatory markers to a monocyte-derived macrophage population, distinct from Kupffer cells, with an inflammatory transcriptional profile. The inflammatory macrophages (iMacs) differentiated from blood monocytes and established a long-lived population. The iMacs retained their core transcriptional signature, consistent with trained immunity, resulting in a population of macrophages primed for inflammation potentially driving progressive liver disease.
ARX regulates cortical interneuron differentiation and migration
Authors: Lim Youngshin , Akula Shyam K , Myers Abigail K , Chen Connie , Rafael Katherine A , Walsh Christopher A , Golden Jeffrey A , Cho Ginam
Published: February 2024

Mutations in aristaless-related homeobox (ARX) are associated with neurodevelopmental disorders including developmental epilepsies, intellectual disabilities, and autism spectrum disorders, with or without brain malformations. Aspects of these disorders have been linked to abnormal cortical interneuron (cIN) development and function. To further understand ARX’s role in cIN development, multipleArxmutant mouse lines were interrogated. We found that ARX is critical for controlling cIN numbers and distribution, especially, in the developing marginal zone (MZ). Single cell transcriptomics and ChIP-seq, combined with functional studies, revealed ARX directly or indirectly regulates genes involved in proliferation and the cell cycle (e.g.,Bub3,Cspr3), fate specification (e.g.,Nkx2.1,Maf,Mef2c), and migration (e.g.,Nkx2.1,Lmo1,Cxcr4,Nrg1,ErbB4). Our data suggest that the MZ stream defects primarily result from disordered cell-cell communication. Together our findings provide new insights into the mechanisms underlying cIN development and migration and how they are disrupted in several disorders.
Analysis of arbuscular mycorrhizal fungi (AMF) community composition associated with alkaline saline sodic soils
Authors: Marquez N , Irazoqui JM , Ciacci MB , Amadio AF , Fernandez FD , Giachero ML
Published: February 2024

Marginal soils affected by salinity, sodicity and alkalinity decrease crop productivity. In this context, a viable alternative strategy lies in the remediation of degraded lands using beneficial microorganisms. This study aims to characterize native arbuscular mycorrhizal fungal (AMF) communities by sequencing PCR amplicons that cover most of the small subunit rRNA (SSU) gene, the complete internal transcribed spacer (ITS) region, and a portion of the large subunit (LSU) rRNA, employing Oxford Nanopore Technologies (ONT). Three field sites, with varying crop conditions, were selected: a patch with no crop growth (Site 1), a patch with corn stubble (Site 2), and a patch with wheat plants exhibiting 15 days of growth (Site 3). Soil analyses revealed distinct characteristics - alkaline saline sodic soil (ASS) for Site 1, moderately alkaline soil (A) for Site 2, and neutral soil (N) for Site 3. ONT sequencing yielded a total of 4,040,470 raw reads from which 19.13% survived after quality and length filter. Reads were grouped in 556 clusters, of which 222 remained after bioinformatic analysis. Despite moderate error rates in 9.4.1, flowcells chemistry, using a clustering and polishing approach facilitated the ecological analysis and allowed a better taxonomic resolution. Bioinformatic analysis showed no significant differences in AMF diversity among soils. However, results suggest the dominance ofGlomeraceaeandAcaulosporaceaefamilies, specifically the generaGlomusandAcaulosporain ASS soil. Further exploration is required to better understand their role in promoting plant growth under adverse conditions. The study highlights the significance of cutting-edge sequencing tools in advancing the comprehension of essential symbiotic relationships for sustainable agriculture in challenging environments.
1-Aminocyclopropane-1-carboxylic acid oxidase determines the fate of ethylene biosynthesis in a tissue-specific way to fine-tune development and stress resilience
Authors: Houben M. , Vaughan-Hirsch J. , Pattyn J. , Mou W. , Roden S. , Martinez Roig A. , Kabak E. , Rodrigues S. , Polko A. , De Coninck B. , Kieber J. J. , Voet A. , Van de Poel B.
Published: February 2024

Ethylene is involved in several developmental processes and responses towards (a)biotic stress. In seed plants, ethylene is produced from its precursor 1-aminocyclopropane-1-carboxylic acid (ACC) by the enzyme ACC-oxidase (ACO). Despite its key role in ethylene synthesis, theACOgene family has not yet been fully characterized. We investigated the fiveACOmembers ofArabidopsis thalianaand revealed a tissue-and developmentally specific expression pattern. Furthermore, the five ACO enzymes each have a different capacity to produce ethylene. Combined, this allows for a precise spatial and temporal regulation of ethylene synthesis. At the sub-cellular level, we uncovered that ACOs reside in the cytosol, where ethylene is likely synthesized, but surprisingly also in the nucleus. Using reverse genetics of single and higher orderacomutants we revealed a high degree of gene redundancy and minimal phenotypes. A lack of ethylene synthesis by knocking out all fiveACOsdid not impair normal vegetative and generative development but did influence processes associated with high rates of ethylene production such as petal abscission. This suggests that ethylene is not a prime regulator of development, but more a moderator. We also showed that the inability to synthesize ethylene impairs some abiotic (nutrient deficiency and metal toxicity) and biotic (Botrytis cinerea) stress responses, similar as plants insensitive towards ethylene, corroborating the role of ethylene in mediating stress responses. In conclusion, theACOgene family enables plants to fine-tune their ethylene synthesis rates, but a lack their off is not crucial for normal development and stress survival.
Identification of Editable Sites, Spacer Oligonucleotide Design, and Generation of the Gene-Targeting CRISPR–nCas9 Plasmid for Gene Disruption inStaphylococcus aureusUsing the CRISPR–nCas9 and Cytidine Deaminase System
Authors: Gründling Angelika , Ji Quanjiang
Published: February 2024

Methods for gene disruption are essential for functional genomics, and there are multiple approaches for altering gene function in bacteria. One of these methods involves introducing a premature stop codon in a gene of interest, which can be achieved by using the CRISPR–nCas9-cytidine deaminase system. The approach involves the mutation of editable cytidines to thymidines, with the goal of generating a novel stop codon that ultimately results in a nonfunctional gene product. The workflow involves two major sections, one for the identification of editable cytidines, the design of the targeting spacer oligonucleotides for introduction into the CRISPR–nCas9 cytidine deaminase plasmid, and the construction of the gene-targeting CRISPR–nCas9 cytosine deaminase plasmids, and one for the actual introduction of the mutation in the species of interest. Here, we describe the steps for the first part. To better illustrate the method and oligonucleotide design, we describe the construction ofStaphylococcus aureusRN4220gehmutants with C to T base changes at two different positions, leading to the construction of strains RN4220-geh(160stop) and RN4220-geh(712stop). We outline the steps for (1) the identification of editable cytidines within genes using the CRISPR-CBEI toolkit website, and (2) the design of the targeting spacer oligonucleotides for introduction into the CRISPR–nCas9 cytidine deaminase plasmid pnCasSA-BEC, followed by (3) the construction of the gene-targeting (in this example,gehgene-targeting) CRISPR–nCas9 cytosine deaminase plasmids pnCasSA-BEC-gehC160Tand pnCasSA-BEC-gehC712Tusing the Golden Gate assembly method, plasmid recovery inEscherichia coli, and confirmation by colony PCR and sequencing. The method can be easily adapted to construct gene-inactivation mutants in otherS. aureusgenes.
Introduction of a CRISPR–nCas9 Gene-Targeting Plasmid intoStaphylococcus aureusfor Gene Disruption
Authors: Gründling Angelika , Ji Quanjiang
Published: February 2024

Methods for gene disruption are essential for functional genomics, and there are multiple approaches for altering gene function in bacteria. One of these methods involves introducing a premature stop codon in a gene of interest, which can be achieved by using the CRISPR–nCas9-cytidine deaminase system. The approach involves the mutation of editable cytidines to thymidines, with the goal of generating a novel stop codon that ultimately results in a nonfunctional gene product. The workflow involves two major sections, one for the identification of editable cytidines, the design of the targeting spacer oligonucleotides for introduction into the CRISPR–nCas9 cytidine deaminase plasmid, and the construction of the gene-targeting CRISPR–nCas9 cytosine deaminase plasmids, and one for the actual introduction of the mutation in the species of interest. Here, we describe the steps for the second part. Specifically, we describe (1) how to introduce the gene-targeting pnCasSA-BEC plasmid intoStaphylococcus aureus, (2) how the gene inactivation inS. aureuscan be confirmed by PCR and sequencing, and (3) how, following successful gene inactivation, the strain can be cured of the pnCasSA-BEC plasmid. To better illustrate the method, and as specific example, two differentgehgene-inactivation mutations are generated here inS. aureusRN4220. The protocol, however, can easily be adapted to generate other gene-inactivating mutations.
Gate-tunable giant superconducting nonreciprocal transport in few-layer
Td−MoTe2
Authors: Wakamura T. , Hashisaka M. , Hoshino S. , Bard M. , Okazaki S. , Sasagawa T. , Taniguchi T. , Watanabe K. , Muraki K. , Kumada N.
Published: February 2024

We demonstrate gate-tunable giant field-dependent nonreciprocal transport (magnetochiral anisotropy) in a noncentrosymmetric superconductor Td−MoTe2 in the thin limit. Giant magnetochiral anisotropy (MCA) with a rectification coefficient (or a figure of merit) γ=3.1×106T−1A−1 is observed at 230 mK, below the superconducting transition temperature (Tc). This is one of the largest values reported so far and may be attributed to the reduced symmetry of the crystal structure. The temperature dependence of γ indicates that ratchetlike motion of magnetic vortices is the origin of the MCA, as supported by our theoretical model. For bilayer (2 L) Td−MoTe2, we can successfully modulate γ by gating. Our experimental results provide a new route to realizing electrically controllable superconducting rectification devices in a single material.

Published by the American Physical Society
2024
The prediction of single-molecule magnet properties via deep learning
Authors: Takiguchi Yuji , Nakane Daisuke , Akitsu Takashiro
Published: February 2024

This paper uses deep learning to present a proof-of-concept for data-driven chemistry in single-molecule magnets (SMMs). Previous discussions within SMM research have proposed links between molecular structures (crystal structures) and single-molecule magnetic properties; however, these have only interpreted the results. Therefore, this study introduces a data-driven approach to predict the properties of SMM structures using deep learning. The deep-learning model learns the structural features of the SMM molecules by extracting the single-molecule magnetic properties from the 3D coordinates presented in this paper. The model accurately determined whether a molecule was a single-molecule magnet, with an accuracy rate of approximately 70% in predicting the SMM properties. The deep-learning model found SMMs from 20 000 metal complexes extracted from the Cambridge Structural Database. Using deep-learning models for predicting SMM properties and guiding the design of novel molecules is promising.
Review on the application of stainless-clad bimetallic steel in the marine environment
Authors: Wang Dongsheng , Sun Xiaohan , Jiang Yingchang , Chang Xueting , Yonglei Xin
Published: February 2024

Purpose

Stainless-clad bimetallic steels (SCBS) are widely investigated in some extremely environmental applications areas, such as polar sailing area and tropical oil and gas platforms areas, because of their excellent anticorrosion performance and relatively lower production costs. However, the properties of SCBS, including the mechanical strength, weldability and the anticorrosion behavior, have a direct relation with the manufacturing process and can affect their practical applications. This paper aims to review the application and the properties requirements of SCBS in marine environments to promote the application of this new material in more fields.

Design/methodology/approach

In this paper, the manufacturing process, welding and corrosion-resistant properties of SCBS were introduced systematically by reviewing the related literatures, and some results of the authors’ research group were also introduced briefly.

Findings

Different preparation methods, such as rolling composite, casting rolling composite, explosive composite, laser cladding and plasma arc cladding, as well as the process parameters, including the vacuum degree, rolling temperature, rolling reduction ratio, volume ratios of liquid to solid, explosive ratio and the heat treatment, influenced a lot on the properties of the SCBS through changing the interface microstructures. Otherwise, the variations in rolling temperature, pass, reduction and the grain size of clad steel also brought the dissimilarities of the mechanical properties, microhardness, bonding strength and toughness. Another two new processes, clad teeming method and interlayer explosive welding, deserve more attention because of their excellent microstructure control ability. The superior corrosion resistance of SCBS can alleviate the corrosion problem in the marine environment and prolong the service life of the equipment, but the phenomenon of galvanic corrosion should be noted as much as possible. The high dilution rate, welding process specifications and heat treatment can weaken the intergranular corrosion resistance in the weld area.

Originality/value

This paper summarizes the application of SCBS in marine environments and provides an overview and reference for the research of stainless-clad bimetallic steel.
Can setting up inside debt accelerate the bank's digital transformation? Evidence from China
Authors: Bian Yuchen , Gu Haifeng
Published: February 2024

Purpose

Digital transformation is essential for commercial banks to maintain long-term competitiveness in the digital economy era. This study aims to investigate the relationship between inside debt and the bank's digital transformation.

Design/methodology/approach

This study set up a quasi-natural experiment based on implementing the executive compensation deferral system in the Chinese banking industry. Using the annual panel data of 180 commercial banks in China from 2007 to 2021, this study employed the difference-in-differences (DID) method to conduct an empirical analysis.

Findings

This study confirms a significant statistical relationship between inside debt and the bank's digital transformation, and managerial myopia is the transmission channel of inside debt affecting the bank's digital transformation. Furthermore, the development of Internet finance and the enhancement of bankers' confidence will improve the contributions of inside debt to the bank's digital transformation.

Originality/value

This study contributes to the literature on inside debt and the bank's digital transformation. It has specific policy value for the scientific design of the banking compensation mechanism and accelerating banks' digital transformation.
Development of central bank digital currencies: a bibliometric analysis
Authors: Kvedaravičiūtė Evelina , Šapkauskienė Alfreda
Published: February 2024

Purpose

We aim to conduct a bibliometric analysis that explores and maps quantitative data of the emerging field of central bank digital currencies in science and its implications in practice. We seek to clarify the underlying research structures and streams of the new phenomena, and our motivation is the rising number of pilots between governments seeking to implement different types of central bank digital currency.

Design/methodology/approach

We designed the unique set of keywords to explore ongoing projects on central bank digital currencies and the evolution of scientific thought on the topic. We conducted a descriptive analysis and an evaluating bibliometric analysis on the timeline from 2018 to April 18, 2023 and investigated 76 articles in the Web of Science database and 152 articles in the Scopus database using VOSviewer.

Findings

We highlight three main directions of discourse on central bank digital currencies in economics using authors keyword analysis, that are: (1) cash, (2) monetary policy and (3) financial stability. We conducted a map-based text analysis of the abstracts and identified the following main streams of discussion in the field: (1) policy-related research on financial systems, (2) a comprehensive review of the design and features of central bank digital currencies and (3) research on the impact of central bank digital currencies on the banking system.

Originality/value

The unique set of keywords allows us to continue the discourse on central bank digital currencies including implications of ongoing governmental projects on the topic and provide directions for future research. We brought the focus on the impact of central bank digital currencies on the banking sector and the new possible order for cash, deposits and payments.
Effect of sustainability measures on student satisfaction regarding accommodation services: practical study from the University of Northampton in the UK
Authors: Jrad Majida
Published: February 2024

Purpose

This study aims to examine the relationship between sustainability initiatives and student satisfaction in accommodation services at the University of Northampton.

Design/methodology/approach

Four main sustainability factors, including energy consumption, waste management, environmental responsibility and green infrastructure, are explored in relation to their impact on student satisfaction. A quantitative research approach was used, using a structured questionnaire distributed to 224 students. Correlation and regression analyses were conducted to assess the associations and predictive power of the sustainability factors on student satisfaction.

Findings

The findings underscore the pivotal role of sustainable initiatives in shaping student satisfaction with accommodation services. Particularly, energy consumption, environmental responsibility and green infrastructure emerged as significant factors influencing higher levels of student satisfaction. These outcomes align with the core principles of sustainability and emphasize the importance of implementing effective strategies in these domains to enhance student experiences. Existing literature supports these findings, indicating that sustainable practices significantly contribute to enhanced satisfaction levels. It is crucial to acknowledge that this study focused on a specific context, namely, the University of Northampton, and caution should be exercised when generalizing these findings to other settings.

Originality/value

This study contributes to the existing literature by providing empirical evidence of the specific sustainability factors that influence student satisfaction in university accommodation. Findings offer valuable guidance for universities and accommodation providers in developing and implementing sustainable practices to create a conducive living environment for students.
Analyzing predictors of pearl millet supply chain using an artificial neural network
Authors: Dhankar Nikita , Routroy Srikanta , Sharma Satyendra Kumar
Published: February 2024

Purpose

The internal (farmer-controlled) and external (non-farmer-controlled) factors affect crop yield. However, not a single study has identified and analyzed yield predictors in India using effective predictive models. Thus, this study aims to investigate how internal and external predictors impact pearl millet yield and Stover yield.

Design/methodology/approach

Descriptive analytics and artificial neural network are used to investigate the impact of predictors on pearl millet yield and Stover yield. From descriptive analytics, 473 valid responses were collected from semi-arid zone, and the predictors were categorized into internal and external factors. Multi-layer perceptron-neural network (MLP-NN) model was used in Statistical Package for the Social Sciences version 25 to model them.

Findings

The MLP-NN model reveals that rainfall has the highest normalized importance, followed by irrigation frequency, crop rotation frequency, fertilizers type and temperature. The model has an acceptable goodness of fit because the training and testing methods have average root mean square errors of 0.25 and 0.28, respectively. Also, the model has R2 values of 0.863 and 0.704, respectively, for both pearl millet and Stover yield.

Research limitations/implications

To the best of the authors’ knowledge, the current study is first of its kind related to impact of predictors of both internal and external factors on pearl millet yield and Stover yield.

Originality/value

The literature reveals that most studies have estimated crop yield using limited parameters and forecasting approaches. However, this research will examine the impact of various predictors such as internal and external of both yields. The outcomes of the study will help policymakers in developing strategies for stakeholders. The current work will improve pearl millet yield literature.