bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using LanM Enzymes to Modify Glucagon-Like Peptides 1 and 2 inE.coli
Authors: Larsen Camilla Kjeldgaard , Lindquist Peter , Rosenkilde Mette , Madsen Alice Ravn , Haselmann Kim , Glendorf Tine , Olesen Kjeld , Kodal Anne Louise Bank , Tørring Thomas 
Published: March 2023

AbstractSelective modification of peptides is often exploited to improve pharmaceutically relevant properties of bioactive peptides like stability, circulation time, and potency. In Nature, natural products belonging to the class of ribosomally synthesized and post-translationally modified peptides (RiPPs) are known to install a number of highly attractive modifications with high selectivity. These modifications are installed by enzymes guided to the peptide by corresponding leader peptides removed as the last step of biosynthesis. Here, we exploit leader peptides and their matching enzymes to investigate the installment of D-Ala post-translationally in a critical position in the hormones, glucagon-like peptides (GLP) 1 and 2. We also offer insight into how precursor peptide design can modulate the modification pattern achieved.
Amino acid usage and tRNA expression underlies proteome adaptation inPlasmodium falciparum
Authors: Li Qian , Vetter Leonie , Veith Ylva , Christ Elena , Végvári Ákos , Sahin Cagla , Ribacke Ulf , Wahlgren Mats , Ankarklev Johan , Larsson Ola , Chan Sherwin Chun-Leung 
Published: March 2023

AbstractParasites often depend on metabolic adaptation to the host environment. An adaptive feature of malaria-causing parasites is digestion of hemoglobin (HB) to acquire amino acids (AAs). Here we describe a link between nutrient availability and translation elongation-dependent regulation of gene expression as an adaptive strategy. We show that, unexpectedly, tRNA expression inP. falciparumdoes not match the decoding need as tRNAs decoding AAs that are rare in HB are lowly expressed. This discrepancy renders codons of HB-rare AAs inefficiently decoded and transcripts levels negatively correlated with the requirement of HB-rare AAs for protein synthesis, which are consistent with poor codon optimality causing co-translational mRNA decay. Intriguingly, proliferation-related genes have evolved to require a high level of HB-rare AAs in their encoded proteins, thereby allowing the parasite to control its proliferation by repressing protein synthesis of these genes during nutrient stress. We conclude that the parasite modulates translation elongation by maintaining a discordant tRNA profile as a mechanism to exploit variations in AA-composition among genes as an adaptation strategy.
Aβ*56 is a stable oligomer that correlates with age-related memory loss in Tg2576 mice
Authors: Liu Peng , Lapcinski Ian P. , Shapiro Samantha L. , Kemper Lisa J. , Ashe Karen H. 
Published: March 2023

SummaryAmyloid-β (Aβ) oligomers consist of fibrillar and non-fibrillar soluble assemblies of the Aβ peptide. Tg2576 human amyloid precursor protein (APP)-expressing transgenic mice modeling Alzheimer’s disease produce Aβ*56, a non-fibrillar Aβ assembly that has been shown by several groups to relate more closely to memory deficits than plaques. Previous studies did not decipher specific forms of Aβ present in Aβ*56. Here, we confirm and extend the biochemical characterization of Aβ*56. We used anti-Aβ(1-x), anti-Aβ(x-40), and A11 anti-oligomer antibodies in conjunction with western blotting, immunoaffinity purification, and size-exclusion chromatography to probe aqueous brain extracts from Tg2576 mice of different ages. We found that Aβ*56 is a ∼56-kDa, SDS-stable, A11-reactive, non-plaque-related, water-soluble, brain-derived oligomer containing canonical Aβ(1-40) that correlates with age-related memory loss. The unusual stability of this high molecular-weight oligomer renders it an attractive candidate for studying relationships between molecular structure and effects on brain function.
Septum site placement inMycobacteria- Identification and Characterization of mycobacterial homologues ofEscherichia coliMinD
Authors: Kishore Vimal , Gaiwala Sharma Sujata S. , Raghunand Tirumalai R. 
Published: March 2023

ABSTRACTA major virulence trait ofMycobacterium tuberculosis(M. tb) is its ability to enter a dormant state within its human host. Since cell division is intimately linked to metabolic shut down, understanding the mechanism of septum formation and its integration with other events in the division pathway is likely to offer clues to the molecular basis of dormancy. TheM. tbgenome lacks obvious homologues of several conserved cell division proteins, and this study aimed at identifying and functionally characterising mycobacterial homologues of theE.coliseptum site specification protein MinD (EcMinD). Sequence homology based analyses suggested that the genomes of bothM.tband the saprophyteMycobacterium smegmatis(M. smegmatis) encode two putativeEcMinD homologues-Rv1708/MSMEG_3743 and Rv3660c/MSMEG_6171. BothRv1708andMSMEG_3743were observed to fully complement the mini-cell phenotype of theE.coliΔminDEmutantHL1,but the other homologues only partially complemented the mutant phenotype. Over-expression ofMSMEG_3743but notMSMEG_6171inM. smegmatisled to cell elongation and a drastic decrease in CFU counts, indicating the essentiality ofMSMEG_3743in cell-division. Sequence analysis of MSMEG_3743 showed a conserved Walker A motif, the functional role of which was confirmed by a radiolabelled ATPase activity assay. Rv1708 was observed to interact with the chromosome associated proteins ScpA and ParB, pointing to a link between its septum formation role and chromosome segregation. Comparative structural analyses showed Rv1708 to be closer in similarity toEcMinD than Rv3660c. In summary we have demonstrated that Rv1708 and MSMEG_3743 are true mycobacterial homologues ofEcMinD, adding a critical missing piece to the mycobacterial cell division puzzle.
Potential selection and maintenance of manure-originated multi-drug resistant plasmids at sub-clinical antibiotic concentrations
Authors: Tran Tam T. , Cole Marlena , Tomas Emily , Scott Andrew , Topp Edward 
Published: March 2023

ABSTRACTThe goal of this study was to determine minimum selection concentrations of various antibiotics using four manure-originated multi-drug resistant plasmids in a surrogateEscherichia colihost. These plasmids carried genes conferring resistance phenotypes to several antibiotic classes including β-lactams, lincosamides, phenicols, macrolides, sulfonamides and tetracyclines. The minimum selection concentrations of antibiotics tested in nutrient-rich medium were determined: 14.1-28.2 mg/L for penicillin G, 0.1 mg/L for oxytetracycline, 0.45 mg/L for chlortetracycline, 2 mg/L for lincomycin, 1 mg/L for florfenicol, 1.3-4 mg/L for azithromycin, 0.13-0.25 mg/L for tetracycline, 0.004-0.01 mg/L for cefotaxime. Penicillin G, oxytetracycline, chlortetracycline, lincomycin and florfenicol had minimum selection concentrations in nutrient-defined medium slightly changed within 3.5-fold range compared to those in nutrient-rich medium. The minimum selection concentrations of antibiotics interfering folic acid synthesis in bacteria were also determined: 63 mg/L for sulfamethoxazole, 11.2 mg/L for sulfisoxazole and 0.06 mg/L for trimethoprim. Mixing two antibiotics changed minimum selection concentrations within 3.7-fold range compared to those in single antibiotic tests. Relatively high plasmid loss rates (> 90%) were observed when culturing plasmid-bearing strains in antibiotic-free nutrient-rich and nutrient-defined media. Overall results suggested that these plasmids can be maintained at concentrations environmentally relevant in waste water treatment plants, sewage, manure and manured soil although they are not stable in antibiotic-free environments.IMPORTANCEAntibiotic resistance crisis is a grave concern in healthcare systems around the world. To combat this crisis, we sought to find out how likely manure-originated multi-drug resistant plasmids are to be selected and maintained in different environment matrices. Our study showed that these plasmids conferring resistance to β-lactams, lincosamides, phenicols, macrolides, sulfonamides and tetracyclines can be selected at minimum selection concentrations which are lower than minimum inhibition concentrations of theE. colihost strain. Lincomycin, oxytetracycline, chlortetracycline, tetracycline, chloramphenicol, trimethoprim had minimum selection concentrations lower than the antibiotic concentrations in several environment matrices reported previously. Our findings suggest that despite the burden and the high rate of plasmid loss, these plasmids can still be selected, maintained and circulated well in some polluted environments.
Genetic characterization of extended-β-lactamase (ESBL) plasmids captured from dairy manures
Authors: Tran Tam , Thorne Joe , Scott Andrew , Robertson James , Nash John HE , Carrillo Catherine , Topp Edward 
Published: March 2023

ABSTRACTThis study was to assess the gene diversity and characterize a large set of plasmids harboring extended β-lactamase (ESBL) genes from raw and digested dairy manure. A total of eighty-four plasmids that were captured in thisE. colirecipient were sequenced using Illumina MiSeq sequencing technology. Twenty-four plasmids of interest were subsequently sequenced using MinION technology in order that a hybrid assembly could be performed on short-and long-read sequences to circularize and complete these plasmids. The size of sequenced plasmids ranged between 40 and 260 kb with various incompatibility groups: IncC, IncI1, IncN, IncY, IncB/O/K/Z, IncX1, IncHI2, IncHI2A, IncFIB(K), IncFII. A variety of extended β-lactamase genes were identified:blaCTXM -1,blaCTXM -14,blaCTXM -15, blaCTXM-27, blaCTXM-55,blaCTXM-61,blaPER-1,blaIMP-27. Interestingly, theblaIMP-27gene, a novel metallo-β-lactamase discovered in the last decade, was found located on an integrated region in the host chromosome. And one plasmid carrying theblaCMY-2gene, an AmpC gene, also expressed ESBL phenotype. Four virulence factors, includingcia, cib, traTandterC,were detected on some of these plasmids. In addition, six type-2 toxin-antitoxin systems were detected: MazF/E, PemK/I, HipA/B, YdcE/D, RelB/E and HigB/A. Twenty-two out of twenty-four complete plasmids carried putative prophage regions; and most of prophage hits were marked as incomplete, except that the largest plasmid pT525A and the IncY plasmid pT415A had prophage hits with higher scores.IMPORTANCEThe widespread of antibiotic resistant bacteria is largely due to the exchange of mobile genetic elements such as plasmids. Plasmids harboring extended β-lactamase (ESBL) genes originated from dairy manure potentially become entrained in manured soil, which subsequently enter the human food chain. Currently there is a lack of detailed information on these plasmids in the environment, specifically in dairy manure. This study unveils the abundance and diversity of ESBL-carrying plasmids from both raw and digested manures which were captured ingfp-labelledE. coliCV601. In addition, the study provides insightful information of plasmid characteristics including incompatibility groups, ESBL genes combined with other resistance genes, mobile genetic elements (transposons, insertion sequence), toxin-antitoxin systems, virulence factors and prophage sequences.
Meiotic prophase length modulates Tel1-dependent DNA double-strand break interference
Authors: Ruiz Luz María López , Johnson Dominic , Gittens William H. , Brown George , Allison Rachal M. , Neale Matthew J. 
Published: March 2023

ABSTRACTDuring meiosis, genetic recombination is initiated by the formation of many DNA double-strand breaks (DSBs) catalysed by the evolutionarily conserved topoisomerase-like enzyme, Spo11, in preferred genomic sites known as hotspots. DSB formation activates the Tel1/ATM DNA damage responsive (DDR) kinase, locally inhibiting Spo11 activity in adjacent hotspots via a process known as DSB interference. Intriguingly, inS. cerevisiae, over short genomic distances (<15 kb), Spo11 activity displays characteristics of concerted activity or clustering, wherein the frequency of DSB formation in adjacent hotspots is greater than expected by chance. We have proposed that clustering is caused by a limited number of sub-chromosomal domains becoming primed for DSB formation. Here, we demonstrate that DSB clustering is abolished when meiotic prophase timing is extended via deletion of theNDT80transcription factor. We propose that extension of meiotic prophase enables most cells, and therefore most chromosomal domains within them, to reach an equilibrium state of similar Spo11-DSB potential, reducing the impact that priming has on estimates of coincident DSB formation. Consistent with this view, genome-wide maps of Spo11-DSB formation generated in the absence of Tel1 are skewed towards regions that load pro-DSB factors early—revealing regions of preferential priming—but this effect is abolished whenNDT80is deleted. Our work highlights how the stochastic nature of Spo11-DSB formation in individual cells within the limited temporal window of meiotic prophase can cause localised DSB clustering—a phenomenon that is exacerbated intel1Δ cells due to the dual roles that Tel1 has in DSB interference and meiotic prophase checkpoint control.
Reduction of aggressive behaviour following hypothalamic deep brain stimulation: involvement of 5-HT1Aand testosterone
Authors: Gouveia Flavia Venetucci , Diwan Mustansir , Martinez Raquel CR , Giacobbe Peter , Lipsman Nir , Hamani Clement 
Published: March 2023

ABSTRACTBackgroundAggressive behaviour (AB) may occur in patients with different neuropsychiatric disorders. Although most patients respond to conventional treatments, a small percentage continue to experience AB despite optimized pharmacological management and are considered to be treatment-refractory. For these patients, hypothalamic deep brain stimulation (pHyp-DBS) has been investigated. The hypothalamus is a key structure in the neurocircuitry of AB. An imbalance between serotonin (5-HT) and steroid hormones seems to exacerbate AB.ObjectivesTo test whether pHyp-DBS reduces aggressive behavior in mice through mechanisms involving testosterone and 5-HT.MethodsMale mice were housed with females for two weeks. These resident animals tend to become territorial and aggressive towards intruder mice placed in their cages. Residents had electrodes implanted in the pHyp. DBS was administered for 5h/day for 8 consecutive days prior to daily encounters with the intruder. After testing, blood and brain were recovered for measuring testosterone and 5-HT receptor density, respectively. In a second experiment, residents received WAY-100635 (5-HT1Aantagonist) or saline injections prior to pHyp-DBS. After the first 4 encounters, the injection allocation was crossed, and animals received the alternative treatment during the next 4 days.ResultsDBS-treated mice showed reduced AB that was correlated with testosterone levels and an increase in 5-HT1Areceptor density in the orbitofrontal cortex and amygdala. Pre-treatment with WAY-100635 blocked the anti-aggressive effect of pHyp-DBS.ConclusionsThis study shows that pHyp-DBS reduces AB in mice via changes in testosterone and 5-HT1Amechanisms.HIGHLIGHTS-Posterior hypothalamus DBS reduces aggressive behavior in mice-Aggressive behavior was correlated with plasma testosterone levels-DBS increased 5-HT1A receptor density in the orbitofrontal cortex and amygdala-Pre-treatment with 5-HT1A antagonist (WAY) blocked the anti-aggressive effect of DBS
AN ARTIFICIAL INTELLIGENCE FOR RAPID IN-LINE LABEL-FREE HUMAN PLURIPOTENT STEM CELL COUNTING AND QUALITY ASSESSMENT
Authors: Ragunton Britney , Van Buskirk Steve , Wakefield Devin , Ranadive Ninad , Pipathsouk Andrew , Pei Baikang , Zhou Hong , Yamawaki Tracy , Berke Mike , Li Chi-Ming , Hale Christopher , Wang Songli , Chambers Stuart M. 
Published: March 2023

AbstractThe current state-of-the-art in hPSC culture is a bespoke and user-dependent process limiting the scale and complexity of the experiments performed and introducing operator-to-operator and day-to-day variation. Artificial intelligence (AI) offers the speed and flexibility to bridge the gap between a human-dependent process and industrial-scale automation.We evaluated an AI approach for counting exact cell numbers of undifferentiated human induced pluripotent stem cells in brightfield images for automating hPSC culture. The neural network generates a topological density map for accurate cell counts. We found that the image-based AI algorithm can determine a precise number of hPSCs and is superior to fluorescence-labeled object detection; the algorithm can ignore well edges, meniscus effects, and dust, achieving an average error of 5.6%. We have built a prototype capable of making a go/no go decision for stem cell passaging to perform 26,400 individual well-level counts from 422,400 images in 12 hours at low cost.
Different mechanisms of synapsin-induced vesicle clustering at inhibitory and excitatory synapses
Authors: Song Sang-Ho , Augustine George J. 
Published: March 2023

SummarySynapsins cluster synaptic vesicles (SVs) to provide a reserve pool (RP) of SVs that maintains synaptic transmission during sustained activity. However, it is unknown how synapsins cluster SVs. Here we show that either liquid-liquid phase separation (LLPS) or tetramerization-dependent cross-linking can cluster SVs, depending upon whether a synapse is excitatory or inhibitory. Cell-free reconstitution revealed that both mechanisms can cluster SVs, with tetramerization bring more effective. At inhibitory synapses, perturbing synapsin-dependent LLPS impairs SV clustering and synchronization of GABA release, while perturbing synapsin tetramerization does not. At glutamatergic synapses, the opposite is true: synapsin tetramerization enhances clustering of glutamatergic SVs and mobilization of these SVs from the RP, while synapsin LLPS does not. Comparison of inhibitory and excitatory transmission during prolonged synaptic activity revealed that synapsin LLPS serves as a brake to limit GABA release, while synapsin tetramerization enables rapid mobilization of SVs from the RP to sustain glutamate release.
An integrated RNA-proteomic landscape of drug induced senescence in a cancer cell line
Authors: Stevenson Thomas , Al-Roshdi Maha , Görtler Franziska , Grellscheid Sushma Nagaraja 
Published: March 2023

AbstractSenescent cells are characterized by an arrest in proliferation. In addition to replicative senescence resulting from telomere exhaustion, sub-lethal genotoxic stress resulting from DNA damage, oncogene activation, mitochondrial dysfunction or reactive metabolites also elicits a senescence phenotype. Senescence is a controlled programme affecting a wide variety of biological processes with some core hallmarks of senescence as well as tissue specific changes. This study presents an integrative multi-omic analysis of proteomic and RNA-seq from proliferating and senescent osteosarcoma cells. This study demonstrates senescence induction in a widely used cell line which can be used as a model system for characterising cancer cell responses to sub-lethal doses of chemotherapeutic agents, and makes available both RNA-seq and proteomic data from proliferating and senescent cells in open access repositories to aid reuse by the community.
The antecedents of university loyalty: a study of postgraduate students in Malaysia
Authors: Mutum Dilip S. , Hussein Ahmad Hata , Ghazali Ezlika M. 
Published: March 2023

PurposeThis study investigates the antecedents of student loyalty towards universities. This study offers new insights into postgraduate loyalty in the context of the Malaysian higher education industry.Design/methodology/approachPartial least squares structural equation modelling is used to analyse data obtained from a survey of 231 postgraduate students in Malaysia.FindingsThe findings indicate that there is a significant relationship between price value and both student satisfaction and student loyalty. There are also strong relationships between learning environment and student satisfaction and between student satisfaction and student loyalty. While university prestige showed a significant relationship with student satisfaction, it is not related to student loyalty. Another important finding is that price value has a strong and direct relationship with both student satisfaction and student loyalty.Originality/valueThis study presents an updated empirical model of student loyalty. Contrary to previous studies, the results indicate that service quality is not related to student satisfaction. However, it is found to influence student loyalty towards the University. The results also indicate the important mediating effect of student satisfaction. This is the first study to look specifically at student satisfaction and loyalty of postgraduate students in Malaysia.
Depressive mood and compulsive social media usage: the mediating roles of contingent self-esteem and social interaction fears
Authors: Ali Fayaz , Tauni Muhammd Zubair , Ashfaq Muhammad , Zhang Qingyu , Ahsan Tanveer 
Published: March 2023

PurposeGiven the limited literature on depression as a contributing factor to compulsive social media use, the present research examines the role of perceived depressive mood (PDM) in developing compulsive social media use behavior. The authors also identify and hypothesize channels such as contingent self-esteem (CSE), social interaction anxiety (SIA) and fear of negative evaluation (FNE), which may explain how PDM affects compulsive social media use.Design/methodology/approachThe research model was empirically tested with a survey of 367 Chinese university students using structural equation modeling by drawing on the escape and self-presentation lenses.FindingsThe findings indicate that PDM contributes to compulsive social media use behavior both directly and indirectly through CSE. Furthermore, the impact of CSE on compulsive social media use is mediated by the FNE, whereas SIA fails to mediate this effect.Practical implicationsThe results can advance the authors’ knowledge of the role and process by which depressive mood impacts compulsive social media use. These findings may add insights into psychological treatment and help in, for example, developing counseling programs or coping strategies for depressed people to protect them from using social media excessively.Originality/valueThis research identifies the pathway mechanism between PDM and compulsive use of social media. It also increases the understanding of how CSE and social interaction deficiencies contribute to compulsive social media usage (CSMU).
Role of inter-organizational systems in driving tourism businesses forward in the post-COVID-19 new normal
Authors: Ku Edward C.S. 
Published: March 2023

Purpose
This study aims to explore how inter-organizational systems (IOSs) drive tourism businesses to a new normal based on the resource-based view through the supply chain of tourism and information and computer technology used in IOSs.

Design/methodology/approach
Data were collected from the management of tourism businesses, and stratified sampling was used in the study. The authors selected 1,000 travel agencies as the study sample, mailed the research questionnaire to their managers and received 252 completed questionnaires. The authors analyzed the data using the partial least squares approach.

Findings
IOS is seen as a transformational service mechanism that provides a dynamic support weapon for members of the tourism supply chain. Tourism businesses should look for suppliers providing comprehensive services through IOS, excellent quality tourism products and customized tourism products to enhance the competitiveness of tourism businesses in the new normal.

Originality/value
This study provides an industrial marketing research perspective on tourism businesses facing the challenges of the new normal. For tourism businesses, technological innovation allows for changes in the strategies and procedures for their transformation and improves the business model of tourism businesses in the new normal.