bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pipeline for species-resolved full-length16S rRNA amplicon nanopore sequencing analysis of low-complexity bacterial microbiota
Authors: Tandon Disha , Dong Yuan , Hapfelmeier Siegfried 
Published: December 2023

Abstract16S rRNA amplicon sequencing is a fundamental tool for characterizing prokaryotic microbial communities. While short-read 16S rRNA sequencing is a proven standard for examining complex microbiomes, it cannot achieve taxonomic classification beyond genus level. Third-generation sequencing technologies, particularly nanopore sequencing, have allowed for full-length 16S rRNA gene sequencing enabling enhanced taxonomic resolution to species and strain levels.Precise species-to-strain level classification is crucial in investigating low-complexity microbiota. This research presents an efficient pipeline using full-length 16S rRNA amplicon nanopore sequencing, spanning library prep to computational analysis for low-complexity microbiota composition analysis. We applied this pipeline to a defined intestinal bacterial community in gnotobiotic mice to evaluate different methods.Our findings revealed that the proprietary barcoded universal primers 27F-1492R from Oxford Nanopore Technologies(ONT) 16S amplicon sequencing kit did not efficiently amplify the 16S rRNA gene ofBifidobacteriumspecies. Addressing this constraint, we designed degenerate primers and employed ONT’s native barcoding kit for library preparation. We developed a customized wet lab and bioinformatics pipeline for processing and classifying amplicon reads at the species level.Validation of the protocol using a mock community DNA sample with known composition confirmed a reduced analytical bias. Additionally, our method surpassed Illumina short-read V3-V4 amplicon sequencing, achieving accurate species-level classification compared to Illumina’s genus-level accuracy.This pipeline is tailored for analyzing the composition of low-complexity microbiota from natural ecosystems and synthetic/gnotobiotic communities. It is cost- and time-effective and therefore accessible for small-scale studies that would otherwise be hindered by the typically long turnaround times of NGS services.Importance16S rRNA amplicon sequencing is conventionally used to identify microbes and determine their composition in microbial communities. Deep amplicon sequencing of complex microbiomes is well established using short-read sequencing targeting variable regions of the 16S rRNA gene. Short reads enable the classification of bacteria until the genus level in the taxa hierarchy, whereas long reads provide better chances of identifying bacteria to species and even strain levels. This study introduces a streamlined approach for analyzing simple microbial communities using full-length 16S rRNA amplicon nanopore long read sequencing. This approach surpasses Illumina sequencing in species accuracy, is cost-effective and time-efficient. Tailored for low-complexity microbiota, it facilitates studies in natural or synthetic communities, especially beneficial for smaller-scale projects with limited resources.
Probiotic bacteriaLacticaseibacillus rhamnosus L108andLacticaseibacillus delbrueckii R2increase lifespan and influence the expression ofCaenorhabditis eleganslongevity genes
Authors: Chelombitskaya D.S. , Teperin A.V. , Emelyantsev S.A. , Prazdnova E.V. 
Published: December 2023

AnnotationNumerous studies have shown that probiotics hold great promise in slowing down the aging process and extending life expectancy. Bacteria of the genusLacticaseibacillushave been found to possess antioxidant, antimutagenic and anti-inflammatory effects, as well as the ability to regulate the expression of genes that control signaling defense mechanisms in model objects. In this study, we used the nematodeCaenorhabditis elegansas a model organism to investigate the impact ofLacticaseibacillus rhamnosus L108(L.rhamnosus L108)andLacticaseibacillus delbrueckii R2on nematode lifespan and the expression levels of genes associated with healthy aging. Our results demonstrate that theLacticaseibacillus rhamnosusL108 strain exhibits antioxidant properties and increases the average lifespan of nematodes by 15%.Lacticaseibacillus delbrueckii R2also has a positive effect, extending the lifespan of the worms by 21.4%. Furthermore, analysis of longevity gene expression reveals a correlation between increased lifespan and activation of the insulin/insulin-like factor-1 pathway. Moreover, we observed a significant increase in the expression of the skn-1 gene, which encodes antioxidant proteins and enhances the antioxidant response. Our findings suggest that the expression of the skn-1 gene and the transcription factor SKN-1 are associated with activation of the p38 MAPK signaling pathway. Therefore, it seems that probiotic bacteriaLacticaseibacillus rhamnosus L108 and Lactobacillus delbrueckii R2have a positive effect on lifespan due to increased expression of genes that underlie the regulation of conserved signaling pathways related to host defense.
ERK3 Is Involved in Regulating Cardiac Fibroblast Function
Authors: Sahadevan Pramod , Dingar Dharmendra , Nawaito Sherin A. , Nair Reshma S. , Trépanier Joëlle , Sahmi Fatiha , Shi Yanfen , Gillis Marc-Antoine , Sirois Martin G. , Meloche Sylvain , Tardif Jean-Claude , Allen Bruce G. 
Published: December 2023

ABSTRACTERK3/MAPK6, an atypical MAPK, activates MAP kinase-activated protein kinase (MK)-5 in selected cell types. MK5 haplodeficient mice show reduced hypertrophy and attenuated increase inCol1a1mRNA in response to increased cardiac afterload. In addition, MK5 deficiency alters cardiac fibroblast function. This study was to determine the effect of reduced ERK3 on cardiac hypertrophy following transverse aortic constriction (TAC) and fibroblast biology. Three wk post-surgery, ERK3, but not ERK4 or p38α, was co-immunoprecipitated with MK5 from both sham and TAC heart lysates. The increase in left ventricular mass and myocyte diameter was lower in TAC-ERK3+/-than TAC-ERK3+/+hearts, whereas ERK3 haploinsufficiency did not alter systolic or diastolic function. Furthermore, the TAC-induced increase inCol1a1mRNA abundance was diminished in ERK3+/-hearts. ERK3 immunoreactivity was detected in atrial and ventricular fibroblasts but not myocytes. In both quiescent fibroblasts and ‘activated’ myofibroblasts isolated from adult mouse heart, siRNA-mediated knockdown of ERK3 reduced the TGF-β-induced increase inCol1a1mRNA. In addition, intracellular type 1 collagen immunoreactivity was reduced following ERK3 depletion in quiescent fibroblasts but not myofibroblasts. Finally, knocking down ERK3 impaired motility in both atrial and ventricular myofibroblasts. These results suggest that ERK3 plays an important role in multiple aspects of cardiac fibroblast biology.
Chromatin profiling data indicate regulatory mechanisms for differentiation during development in the acoelHofstenia miamia
Authors: Bump Paul , Loubet-Senear Kaitlyn , Arnold Sarah , Srivastava Mansi 
Published: December 2023

ABSTRACTChromatin profiling data can corroborate and generate hypotheses for regulatory events that underlie the control of gene expression in any biological process. Here, we applied the Assay for Transposase Accessible Chromatin (ATAC) sequencing to build a catalog of putative regulatory DNA during the process of embryonic development in an acoel. Acoels represent an enigmatic phylum-level lineage of animals, the Xenacoelomorpha, which is placed either as a sister-group to all other animals with bilateral symmetry or as an early-diverging ambulacrarian, two alternative phylogenetic placements that both position acoels equally well to inform the evolution of developmental mechanisms. We focused on the acoelHofstenia miamia, a.k.a. the three-banded panther worm, which has emerged as a new laboratory research organism for whole-body regeneration that also enables the study of development from zygote to hatching. We profiled chromatin landscapes over a time course encompassing many major morphological events, including gastrulation, axial patterning, and differentiation of tissues such as epidermis and muscle. Broad patterns of chromatin accessibility and predicted binding of various transcription factor (TF) motifs identified major biological processes and their putative regulators, and we noted that differential accessibility tended to precede major developmental transitions in embryogenesis. Focused analysis of TF binding combined with single-cell RNA-seq data provided regulatory linkages for genes in a previously hypothesized differentiation trajectory for epidermis and generated new hypotheses for gene regulatory networks associated with the formation of muscle. This work provides a platform for the identification of developmental mechanisms inHofsteniaand enables comparisons of embryogenesis in acoels to other animals as well as comparisons of embryogenesis to regeneration.
Discovery of a high-performance phage-derived promoter/repressor system for probiotic lactobacillus engineering
Authors: Blanch-Asensio Marc , Tadimarri Varun Sai , Wilk Alina , Sankaran Shrikrishnan 
Published: December 2023

ABSTRACTBackgroundTheLactobacillusfamily comprises many species of great importance for the food and healthcare industries, with numerous strains identified as beneficial for humans and used as probiotics. Hence, there is a growing interest in engineering these probiotic bacteria as live biotherapeutics for animals and humans. However, the genetic parts needed to regulate gene expression in these bacteria remain limited compared to model bacteria likeE. coliorB. subtilis. To address this deficit, in this study, we selected and tested several bacteriophage-derived genetic parts with the potential to regulate transcription in lactobacilli.ResultsWe screened genetic parts from 6 different lactobacilli-infecting phages and identified one promoter/repressor system with unprecedented functionality inL. plantarumWCFS1. The phage-derived promoter was found to achieve expression levels nearly 9-fold higher than the previously reported strongest promoter in this strain and the repressor was able to almost completely repress this expression by reducing it nearly 500-fold.ConclusionsThe new parts and insights gained from their engineering will enhance the genetic programmability of lactobacilli for healthcare and industrial applications.
Structural basis of tRNA recognition by the m3C-RNA-methyltransferase METTL6 in complex with SerRS seryl-tRNA synthetase
Authors: Throll Philipp , Dolce Luciano G. , Lastres Palma Rico , Arnold Katharina , Tengo Laura , Basu Shibom , Kaiser Stefanie , Schneider Robert , Kowalinski Eva 
Published: December 2023

SummaryMethylation of cytosine 32 in the anticodon loop of tRNAs to 3-methylcytosine (m3C) is crucial for cellular translation fidelity1. Misregulation of the RNA methyltransferases setting this modification can cause aggressive cancers and metabolic disturbances2,3. However, our understanding of the substrate selection and catalysis mode of the m3C RNA methyltransferases is currently still lacking. Here, we report the cryo-electron microscopy structure of the m3C tRNA methyltransferase METTL6 in complex with seryl-tRNA synthetase (SerRS) and their common substrate tRNASer. Through the complex structure, we identify the tRNA binding domain of METTL6. We show that SerRS acts as the tRNASersubstrate selection factor for METTL6. We reveal how METTL6 and SerRS jointly coordinate the long variable arm of tRNASerin their interface. We demonstrate that SerRS augments the methylation activity of METTL6 and that direct contacts between METTL6 and SerRS are necessary for efficient tRNASermethylation. Finally, based on the structure of METTL6 in complex with SerRS and tRNASer, we postulate a universal tRNA binding mode for m3C RNA methyltransferases including METTL2 and METTL8, suggesting that these mammalian paralogues use similar ways to engage their respective tRNA substrates and co-factors.
Packaging of supplemented urokinase into naked alpha-granules ofin vitro-grown megakaryocytes for targeted therapeutic delivery
Authors: Poncz Mortimer , Zaitsev Sergei V. , Ahn Hyunsook , Kowalska M. Anna , Bdeir Khalil , Camire Rodney M. , Cines Douglas B. , Stepanova Victoria 
Published: December 2023

AbstractOur prior finding that uPA endogenously expressed and stored in the platelets of transgenic mice prevented thrombus formation without causing bleeding, prompted us to develop a potentially clinically relevant means of generating anti-thrombotic human plateletsin vitrofrom CD34+hematopoietic cell-derived megakaryocytes. CD34+-megakaryocytes internalize and store in α-granules single-chain uPA (scuPA) and a uPA variant modified to be plasmin-resistant, but thrombin-activatable, (uPAT). Both uPAs co-localized with internalized factor V (FV), fibrinogen and plasminogen, low-density lipoprotein receptor-related protein 1 (LRP1), and interferon-induced transmembrane protein 3 (IFITM3), but not with endogenous von Willebrand factor (VWF). Endocytosis of uPA by CD34+-\megakaryocytes was mediated in part via LRP1 and αIIbβ3. scuPA-containing megakaryocytes degraded endocytosed intragranular FV, but not endogenous VWF, in the presence of internalized plasminogen, whereas uPAT-megakaryocytes did not significantly degrade either protein. We used a carotid-artery injury model in NOD-scid IL2rγnull (NSG) mice homozygous for VWFR1326H(a mutation switching binding VWF specificity from mouse to human glycoprotein IbmlIX) to test whether platelets derived from scuPA-MKs or uPAT-Mks would prevent thrombus formation. NSG/VWFR1326Hmice exhibited a lower thrombotic burden after carotid artery injury compared to NSG mice unless infused with human platelets or MKs, whereas intravenous injection of either uPA-containing megakaryocytes into NSG/VWFR1326Hgenerated sufficient uPA-containing human platelets to lyse nascent thrombi. These studies suggest the potential to deliver uPA or potentially other ectopic proteins within platelet α-granules fromin vitro-generated megakaryocytes.Key pointsUnlike platelets, in vitro-grown megakaryocytes can store exogenous uPA in its α-granules.uPA uptake involves LRP1 and αIIbβ3 receptors and is functionally available from activated platelets.
Navigating the landscape of academic coaching: a comprehensive bibliometric analysis
Authors: Mahdi Somayeh , Zeinabadi Hassanreza , Arasteh Hamidreza , Abbasian Hossein 
Published: December 2023

PurposeAcademic coaching (AC) has gained a significant attention to support student success and achievement in higher education, management and psychology. This study aimed to conduct a comprehensive bibliometric analysis of AC literature to identify the top authors, research patterns, hotspots and research topics in the field.Design/methodology/approachThe study utilized a bibliometric analysis of articles published between 1987 and 2023, using descriptive and network analysis methods with tools such as RStudio, Biblioshiny, Excel and VOSviewer. The study also conducted functional, mapping and content analysis, to identify AC literature's key themes and research areas.FindingsThe results revealed an increasing interest in AC, with increased publications. However, there are gaps in geographical diversity and authorship. Most studies were conducted in the United States of America and the UK, and were published in education, psychology and coaching journals. Common themes included coaching, professional development, higher education and mentoring. Emerging research areas include: coaching efficacy in education, AC as an online learning support and professional learning communities. More studies are needed in different contexts and with larger sample sizes.Originality/valueThis comprehensive bibliometric analysis adds to the existing literature by presenting a detailed analysis of the field of AC, filling a gap in the current literature. The study's unique contribution is its examination of emerging research areas and themes in AC literature, providing directions for future research. This study is particularly relevant for researchers, practitioners and policymakers interested in understanding AC's state of the art and identifying promising areas for future research.
Nexus between environmental sustainability, energy intensity and food security: evidence from emerging economies
Authors: Hasan Md. Mahadi , Adnan A.T.M. 
Published: December 2023

PurposeGrowing food insecurity is a leading cause of fatalities, particularly in developing nations like Sub-Saharan Africa and Southeast Asia. However, the rising energy consumption and carbon dioxide (CO2) emissions are mostly associated with food production. Balancing the trade-offs between energy intensity and food security remains a top priority for environmentalists. Despite the critical role of the environment in food security, there is a scarcity of substantial studies that explore the statistical connections among food security, CO2 emissions, energy intensity, foreign direct investment (FDI) and per capita income. Therefore, this study aims to provide more precise and consistent estimates of per capita CO2 emissions by considering the interplay of food security and energy intensity within the context of emerging economies.Design/methodology/approachTo examine the long-term relationships between CO2 emissions, food security, energy efficiency, FDI and economic development in emerging economies, this study employs correlated panel-corrected standard error, regression with Newey–West standard error and regression with Driscoll–Kraay standard error models (XTSCC). The analysis utilizes data spanning from 1980 to 2018 and encompasses 32 emerging economies.FindingsThe study reveals that increasing food security in a developing economy has a substantial positive impact on both CO2 emissions and energy intensity. Each model, on average, demonstrates that a 1 percent improvement in food security results in a 32% increase in CO2 levels. Moreover, the data align with the Environmental Kuznets Curve (EKC) theory, as it indicates a positive correlation between gross domestic product (GDP) in developing nations and CO2 emissions. Finally, all experiments consistently demonstrate a robust correlation between the Food Security Index (FSI), energy intensity level (EIL) and exchange rate (EXR) in developing markets and CO2 emissions. This suggests that these factors significantly contribute to environmental performance in these countries.Originality/valueThis study introduces novelty by employing diverse techniques to uncover the mixed findings regarding the relationship between CO2 emissions and economic expansion. Additionally, it integrates energy intensity and food security into a new model. Moreover, the study contributes to the literature by advocating for a sustainable development goal (SDG)-oriented policy framework that considers all variables influencing economic growth.
Asymmetric modelling predicting migrants versus refugees starting new ventures
Authors: Crisan-Mitra Catalina , Martín-de Castro Gregorio 
Published: December 2023

Purpose
This study aims to examine the entrepreneurship profiles of migrants and refugees relying on a neo-configurational approach that increases understanding of causal complexity, equifinality and causal asymmetry patterns to high entrepreneurial intentions in the two groups.

Design/methodology/approach
Using a fuzzy set qualitative comparative analysis method, the authors analysed 52 respondents – migrants and refugees. The findings show the existence of equifinality in which different configurations can lead to high and low entrepreneurial intentions, underlying that traumatic experiences have a major role in entrepreneurial intention. It also demonstrates that core conditions are associated with refugee’s configurations and causal asymmetry. The cross-sectional character of this research impedes the searching for a better causal relationship. The lack of studies that approach the subject of refugees makes it challenging to develop a robust theory in this sense.

Findings
The paper highlights five main configurations – two related to migrants’ profile and three related to refugees’ profile – that enable expanding the current knowledge and practices to better customize practices to increase entrepreneurial intention.

Originality/value
To the best of the authors’ knowledge, this is the first research using a configurational approach to explore migrant and refugee entrepreneurship intention profiles.
Finding a generic fixed brake force distribution through optimizing hydraulic brake system parameters to prevent wheel lock
Authors: Banik Indranil , Nandi Arup Kumar , Mondal Bittagopal 
Published: December 2023

Purpose
The paper aims to identify a suitable generic brake force distribution ratio (β) corresponding to optimal brake design attributes in a diminutive driving range, where road conditions do not exhibit excessive variations. This will intend for an appropriate allocation of brake force distribution (BFD) to provide dynamic stability to the vehicle during braking.

Design/methodology/approach
Two techniques are presented (with and without wheel slip) to satisfy both brake stability and performance while accommodating variations in load sharing and road friction coefficient. Based on parametric optimization of the design variables of hydraulic brake using evolutionary algorithm, taking into account both the laden and unladen circumstances simultaneously, this research develops an improved model for computing and simulating the BFD applied to commercial and passenger vehicles.

Findings
The optimal parameter values defining the braking system have been identified, resulting in effective β = 0.695 which enhances the brake forces at respective axles. Nominal slip of 3.42% is achieved with maximum deceleration of 5.72 m/s2 maintaining directional stability during braking. The results obtained from both the methodologies are juxtaposed and assessed governing the vehicle stability in straight line motion to prevent wheel lock.

Originality/value
Optimization results establish the practicality, efficacy and applicability of the proposed approaches. The findings provide valuable insights for the design and optimization of hydraulic drum brake systems in modern automobiles, which can lead to safer and more efficient braking systems.
Mutually exclusive feeding yields Holling type III functional response
Authors: Lehtinen Sami O. , Perälä Tommi A. , Uusi‐Heikkilä Silva K. , Kuparinen Anna K. 
Published: December 2023

Abstract

Many generalist predators, including fish, insects and mammals, temporarily focus on their search behaviour and can switch between prey species. Flexible and rapid behavioural plasticity enables a predator to forage optimally, as guided by search image formation and prey switching in response to changing prey abundances.

More than half a century of studies have used Holling type III functional response to model the impact of this feeding behaviour on population dynamics, yet a mechanistic understanding for the pathway between individual behaviour and feeding rates remains poorly understood.

To understand this common feeding behaviour, we developed three mechanistic models using first‐principles to provide direct derivations for the relationship between observed individual behaviour and feeding rates.

The derived models yield three novel, generalised functional responses for predators characterised by prey switching and mutually exclusive feeding (i.e. feeding is limited to one prey species at a time). We show how these functional responses act as Holling type III response, and how they can be used to predict predators' diet compositions.

Our results demonstrate that several behavioural forms of prey switching, as displayed in a wide range of predator species, consistently produce type III conforming functional responses.

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