bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional analysis of cyclic diguanylate-modulating proteins inVibrio fischeri
Authors: Isenberg Ruth Y. , Holschbach Chandler S. , Gao Jing , Mandel Mark J. 
Published: July 2023

ABSTRACTAs bacterial symbionts transition from a motile free-living state to a sessile biofilm state, they must coordinate behavior changes suitable to each lifestyle. Cyclic diguanylate (c-di-GMP) is an intracellular signaling molecule that can regulate this transition, and it is synthesized by diguanylate cyclase (DGC) enzymes and degraded by phosphodiesterase (PDE) enzymes. Generally, c-di-GMP inhibits motility and promotes biofilm formation. While c-di-GMP and the enzymes that contribute to its metabolism have been well-studied in pathogens, considerably less focus has been placed on c-di-GMP regulation in beneficial symbionts.Vibrio fischeriis the sole beneficial symbiont of the Hawaiian bobtail squid (Euprymna scolopes) light organ, and the bacterium requires both motility and biofilm formation to efficiently colonize. C-di-GMP regulates swimming motility and cellulose exopolysaccharide production inV. fischeri. The genome encodes 50 DGCs and PDEs, and while a few of these proteins have been characterized, the majority have not undergone comprehensive characterization. In this study, we use protein overexpression to systematically characterize the functional potential of all 50V. fischeriproteins. All 28 predicted DGCs and 14 predicted PDEs displayed at least one phenotype consistent with their predicted function, and a majority of each displayed multiple phenotypes. Finally, active site mutant analysis of proteins with the potential for both DGC and PDE activities revealed potential activities for these proteins. This work presents a systems-level functional analysis of a family of signaling proteins in a tractable animal symbiont and will inform future efforts to characterize the roles of individual proteins during lifestyle transitions.IMPORTANCEC-di-GMP is a critical second messenger that mediates bacterial behaviors, andV. fischericolonization of its Hawaiian bobtail squid host presents a tractable model in which to interrogate the role of c-di-GMP during animal colonization. This work provides systems-level characterization of the 50 proteins predicted to modulate c-di-GMP levels. By combining multiple assays, we generated a rich understanding of which proteins have the capacity to influence c-di-GMP levels and behaviors. Our functional approach yielded insights into how proteins with domains to both synthesize and degrade c-di-GMP may impact bacterial behaviors. Finally, we integrated published data to provide a broader picture of each of the 50 proteins analyzed. This study will inform future work to define specific pathways by which c-di-GMP regulates symbiotic behaviors and transitions.
Dynamic regulatory phosphorylation of mouse CDK2 occurs during meiotic prophase I
Authors: Bradley Rachel A. , Wolff Ian D. , Cohen Paula E. , Gray Stephen 
Published: July 2023

AbstractDuring prophase I of meiosis, DNA double-strand breaks form throughout the genome, with a subset repairing as crossover events, enabling the accurate segregation of homologous chromosomes during the first meiotic division. The mechanism by which DSBs become selected to repair as crossovers is unknown, although the crossover positioning and levels in each cell indicate it is a highly regulated process. One of the proteins that localises to crossover sites is the serine/threonine cyclin-dependent kinase CDK2. Regulation of CDK2 occurs via phosphorylation at tyrosine 15 (Y15) and threonine 160 (T160) inhibiting and activating the kinase, respectively. In this study we use a combination of immunofluorescence staining on spread spermatocytes and fixed testis sections, and STA-PUT gravitational sedimentation to isolate cells at different developmental stages to further investigate the temporal phospho regulation of CDK2 during prophase I. Western blotting reveals differential levels of the two CDK2 isoforms (CDK233kDaand CDK239kDa) throughout prophase I, with inhibitory phosphorylation of CDK2 at Y15 occurring early in prophase I, localising to telomeres and diminishing as cells enter pachynema. Conversely, the activatory phosphorylation on T160 occurs later, specifically the CDK233kDaisoform, and T160 signal is detected in spermatogonia and pachytene spermatocytes, where it co-localises with the Class I crossover protein MLH3. Taken together, our data reveals intricate control of CDK2 both with regards to levels of the two CDK2 isoforms, and differential regulation via inhibitory and activatory phosphorylation.
Early-life stress triggers long-lasting organismal resilience and longevity via tetraspanin
Authors: Jiang Wei I. , Belly Henry De , Wang Bingying , Wong Andrew , Kim Minseo , Oh Fiona , DeGeorge Jason , Huang Xinya , Guang Shouhong , Weiner Orion D. , Ma Dengke K. 
Published: July 2023

AbstractEarly-life stress experiences can produce lasting impacts on organismal adaptation and fitness. How transient stress elicits memory-like physiological effects is largely unknown. Here we show that early-life thermal stress strongly up-regulatestsp-1, a gene encoding the conserved transmembrane tetraspanin inC. elegans. TSP-1 forms prominent multimers and stable web- like structures critical for membrane barrier functions in adults and during aging. The up- regulation of TSP-1 persists even after transient early-life stress. Such regulation requires CBP- 1, a histone acetyl-transferase that facilitates initialtsp-1transcription. Tetraspanin webs form regular membrane structures and mediate resilience-promoting effects of early-life thermal stress. Gain-of-function TSP-1 confers markedC. eleganslongevity extension and thermal resilience in human cells. Together, our results reveal a cellular mechanism by which early-life thermal stress produces long-lasting memory-like impact on organismal resilience and longevity.TeaserStudies reveal mechanisms of how early-life heat exposure produces long-lasting benefits on longevity in the nematodeC. elegans.
Extensive and diverse lanthanide-dependent metabolism in the ocean
Authors: Voutsinos Marcos Y. , Banfield Jillian F. , McClelland Harry-Luke O. 
Published: July 2023

AbstractLanthanide (Ln)-dependent enzymes have evolved roles in organic carbon metabolism despite low Ln availability in natural environments1–8. The oceans are the major reservoir of dissolved organic carbon (DOC) on the planet, yet the prevalence and diversity of Ln-dependent enzymes in the ocean, and their biogeochemical importance in the ocean carbon cycle is unknown. Here, we analyzed a global ocean metagenomic/metatranscriptomic dataset and found Ln-dependent methanol-, ethanol- and putative sorbose- and glucose-dehydrogenases in all metagenomes and 20% of all resolved microbial genomes, with several individual organisms hosting dozens of unique Ln-dependent genes. We find that biological methanol oxidation in the ocean is overwhelmingly Ln-dependent, and that methanol dehydrogenases are the most highly expressed Ln-dependent genes in most ocean regions, particularly in surface oceans. As Ln availability is a function of phosphate concentration and pH, Ln-dependent metabolism likely underpins complex biogeochemical feedbacks determining the efficiency of organic matter remineralization, thus impacting the oceanic DOC pool and Earth’s climate system. The widespread biological utility of Ln also explains their nutrient-like vertical concentration profiles observed in ocean waters, and shows that the preferential utilization of light lanthanides by biology must be considered when interpreting patterns of relative Ln concentrations in seawater.
A preliminary study exploring the nature of aggression supportive beliefs in a forensic psychiatric sample
Authors: Sebalo Ivan , Steene Lisa Maria Beethoven , Gaylor Lisa Lee Elaine , Ireland Jane Louise 
Published: July 2023

Purpose
This preliminary study aims to investigate and describe aggression-supportive normative beliefs among patients of a high-secure hospital.

Design/methodology/approach
Therapy data from a sample of high-secure forensic hospital patients (N = 11) who had participated in Life Minus Violence-Enhanced, a long-term violence therapy, was examined using interpretative phenomenological analysis (IPA). During therapy, cognitions linked to past incidences of aggression were explored using aggression choice chains.

Findings
IPA was applied to data generated through this process to examine the presence and nature of normative beliefs reported, identifying seven themes: rules for aggressive behaviour; use of violence to obtain revenge; processing emotions with violence; surviving in a threatening world; do not become a victim; using violence to maintain status; and prosocial beliefs.

Originality/value
Findings demonstrate that forensic patients have specific aggression-supportive normative beliefs, which may be malleable. Limitations and implications are discussed.
Learning and knowledge transfer by humans and digital platforms: which tools best support the decision-making process?
Authors: Russo Giuseppe , Manzari Alberto , Cuozzo Benedetta , Lardo Alessandra , Vicentini Francesca 
Published: July 2023

Purpose
This study aims to investigate the impact of technologies on the knowledge transfer process. In particular, the authors aim to analyze the topic of knowledge brokers and the relationship between broker and digital tools in the knowledge transfer process in the sport context. The study developed, therefore, aims to investigate the creating of this environment for knowledge transfer and knowledge sharing between man and machine, looking to improve the planning of technical sports projects of the clubs.

Design/methodology/approach
This paper presents a qualitative approach aimed at analyzing how platforms and the players’ agents can be useful tools in the knowledge transfer process. The research was conducted through a survey with a structured questionnaire via e-mail to 64 managers at the head of clubs playing in the Italian Series B basketball in the 2021–2022 championship. The total number of questions administered is 21.

Findings
The results demonstrate how sports directors, for the construction of a technical sports project, in addition to learning off the pitch by interactions with media, fans, pressure management, leadership skills, positive attitude, tolerance, understanding of other opinions, background and cultures, see the athletes’ agents as the main stakeholder of the managers. The research resulted, by the clubs’ managers, in both formal learning and informal-type learning. Informal learning, by far the most frequently used and most important in the general learning process of executives, is identified in the use that executives make of information available on digital platforms and of the fiduciary relationships that management has with players’ agents.

Originality/value
The results demonstrate the valuable opportunities for executives, coaches, managers and clubs to strategically manage learning and knowledge sharing. Improving and managing knowledge-sharing strategies would help increase knowledge, not only of the sports directors but also of the entire club, thus improving the absolute quality of the game within the Italian basketball divisions. The authors have developed an innovative framework regarding the construction of a “typed sports technical project”, and the authors have identified a series of crucial phases capable of determining the creation of a new roster of athletes.
Leveraging open data for reference services delivery in academic libraries
Authors: Oladokun Bolaji David , Gaitanou Panorea 
Published: July 2023

Purpose
Librarians play a critical role in curating, organizing and facilitating access to open data (OD) resources, supporting research, learning and information dissemination. This study aims to explore the use of OD for reference services delivery in academic libraries. It is believed that the concept of OD in librarianship refers to the practice of making publicly available data freely accessible, usable and shareable by anyone.

Design/methodology/approach
This research examined how the utilization of OD may affect library services and operations. This paper used the systematic review of literature to answer the research questions; hence, it was a desk study.

Findings
Given that there has been recently a research shift in linking OD to library metadata, this study revealed some interesting findings. More specifically, it discovered that incorporating OD into reference services can provide several benefits and enhance the quality and relevance of the information provided to library users. In addition, this paper reported that OD enriches reference services by providing comprehensive, current and interdisciplinary information, supporting evidence-based research, enabling data visualization and analysis, fostering community engagement and promoting innovation.

Originality/value
This paper proposes that libraries that possess extensive collections are in a favorable position to embrace the shift toward becoming OD and open big data libraries. It is also believed that academic libraries, through reference services, meet the challenge of providing access to their institutional repositories by holding many sets of data in various formats and providing various interfaces, developing metadata systems for various data streams, supporting all ecosystems of software and data products for reformatting and reusing large and complex data, and support for data sets identifiers. By actively engaging with OD, librarians can play a vital role in facilitating access to information and promoting the use of open knowledge for academic pursuits.
Militarization, globalization and liberal democracy: a nexus?
Authors: Kollias Christos , Tzeremes Panayiotis 
Published: July 2023

PurposeUsing composite indices, the paper examines the nexus between militarization, globalization and liberal democracy. The democratic peace theory, the conflict inhibiting effects of international trade – a key and dominant facet of globalization – and the democracy promoting globalization hypothesis form the theoretical underpinnings of the empirical investigation.Design/methodology/approachTo probe into the issue at hand, the paper adopts a dynamic panel VAR estimation procedure. Given the usual data constraints, the sample consists of 113 countries, and the estimations span the period 1995–2019.FindingsThe findings from the dynamic panel VAR estimations suggest the presence of a negative and statistically significant nexus between the level of globalization and the level of militarization. No statistically traceable nexus between globalization and liberal democracy was found.Research limitations/implicationsThe findings offer empirical support to the hypothesis that the strong links of interdependence shaped by globalization reduce the need for military preparedness. The results lead to a tentative inference in favor of the doux commerce thesis. Nonetheless, given that the estimations span a historically specific period – the entire post-bipolar era – the inferences that stem from the findings should be treated with caution.Originality/valueTo the best of the authors’ knowledge, the composite indices Bonn International Centre for Conflict Studies (BICC) militarization index, the globalization index of the Swiss Economic Institute (Konjunkturforschungsstelle) (KOF), LibDem, polyarchy have not hitherto been jointly used in previous studies to examine the nexus between militarization, globalization and liberal democracy.
How Tesla’s management innovations operationalize its “Deep Purpose” to save the planet
Authors: Denning Stephen 
Published: July 2023

Purpose
Instead of merely adding a socially popular mission to its existing business goals, Tesla’s CEO Elon Musk has innovated its operations by working backwards from its mission of saving the planet by making and selling a vast number of electric cars in order to help remove a principal cause of an approaching global environmental disaster.

Design/methodology/approach
When Elon Musk became CEO in 2008, Tesla’s mission of saving the planet by replacing gasoline-driven cars with electric cars seemed a preposterous overreach.

Findings
Tesla is not only making extraordinary progress towards the accomplishment of its mission, but the mission serves as an accelerator of its business generally and its innovations in particular.

Practical implications
The example of CEO Musk showing up on the factory floor, and working shoulder to shoulder with the staff in teams and mobs to solve urgent bottleneck issues sets the tone of Tesla’s workplace. The overriding preoccupation with accelerating innovation is enabled by modularity in design.

Originality/value
A unique study of Tesla’s post-Agile management innovations by an expert on Agile teams and practices.
Litter quality controls tradeoffs in soil carbon decomposition and replenishment in a subtropical forest
Authors: Lyu Maokui , Homyak Peter M. , Xie Jinsheng , Peñuelas Josep , Ryan Michael G. , Xiong Xiaoling , Sardans Jordi , Lin Weisheng , Wang Minhuang , Chen Guangshui , Yang Yusheng 
Published: July 2023

Abstract

Species‐rich forests can produce litter of varying carbon (C) and nitrogen (N) composition (i.e. quality), which can affect decomposition and play a central role in long‐term soil organic carbon (SOC) accumulation. However, how differences in litter quality affect SOC decomposition and formation remains unclear over the full litter decomposition trajectory.

We followed the in situ complete decomposition of added 13C‐labelled high‐ (low C:N) and low‐quality (high C:N) leaf‐litter and its effect on particulate organic matter (POM) and mineral‐associated organic matter (MAOM) fractions over 2 years in a natural subtropical forest.

We found that during early stages of decomposition, low‐quality litter inputs decreased SOC via a positive priming effect (i.e. new C inputs favoured decomposition of native SOC), but these SOC losses were offset by SOC gains observed via a negative priming effect during decomposition of high‐quality litter. In contrast, this pattern reversed during late stages of decomposition—SOC losses via a positive priming effect induced by high‐quality litter were offset by SOC gains via a negative priming effect induced by low‐quality litter. Over the full decomposition of litter, both high‐ and low‐quality litter stimulated microbial breakdown of SOC tied to POM, but also replenished more persistent SOC that associated with soil minerals (MAOM). Altogether, we observed that low‐quality litter formed twice as much new SOC as high‐quality litter (24% vs. 12% of added litter‐C). We extend the notion of the priming effect from primarily a negative role promoting losses of native SOC, to a functional role that can replenish persistent SOC.

Synthesis. Our measurements raise the possibility that, in species‐rich forests, high‐ and low‐quality litter decomposition play opposite but dynamically complementary roles in renewing POM—both by inducing its decomposition and formation—while exclusively favouring MAOM formation, which can help explain how differences in litter quality favour SOC accumulation and persistence. Global change factors that shift plant community composition may ultimately affect the fate of soil C, as changes in litter quality may force soil transitions from sinks to sources or sources to sinks of atmospheric CO2.
Alternative relay regulates the adenosine triphosphatase activity of Locusta migratoria striated muscle myosin
Authors: Hao Jie , Liu Chang , Zhang Ning , Li Jing , Ni Tong , Qu Mingbo , Li Xiang‐dong 
Published: July 2023

AbstractLocust (Locusta migratoria) has a single striated muscle myosin heavy chain (Mhc) gene, which contains 5 clusters of alternative exclusive exons and 1 differently included penultimate exon. The alternative exons of Mhc gene encode 4 distinct regions in the myosin motor domain, that is, the N‐terminal SH3‐like domain, one lip of the nucleotide‐binding pocket, the relay, and the converter. Here, we investigated the role of the alternative regions on the motor function of locust muscle myosin. Using Sf9‐baculovirus protein expression system, we expressed and purified 5 isoforms of the locust muscle myosin heavy meromyosin (HMM), including the major isoform in the thorax dorsal longitudinal flight muscle (FL1) and 4 isoforms expressed in the abdominal intersegmental muscle (AB1 to AB4). Among these 5 HMMs, FL1‐HMM displayed the highest level of actin‐activated adenosine triphosphatase (ATPase) activity (hereafter referred as ATPase activity). To identify the alternative region(s) responsible for the elevated ATPase activity of FL1‐HMM, we produced a number of chimeras of FL1‐HMM and AB4‐HMM. Substitution with the relay of AB4‐HMM (encoded by exon‐14c) substantially decreased the ATPase activity of FL1‐HMM, and conversely, the relay of FL1‐HMM (encoded by exon‐14a) enhanced the ATPase activity of AB4‐HMM. Mutagenesis showed that the exon‐14a‐encoded residues Gly474 and Asn509 are responsible for the elevated ATPase activity of FL1‐HMM. Those results indicate that the alternative relay encoded by exon‐14a/c play a key role in regulating the ATPase activity of FL1‐HMM and AB4‐HMM.
Origin matters: Using a local reference genome improves measures in population genomics
Authors: Thorburn Doko‐Miles J. , Sagonas Kostas , Binzer‐Panchal Mahesh , Chain Frederic J. J. , Feulner Philine G. D. , Bornberg‐Bauer Erich , Reusch Thorsten B. H. , Samonte‐Padilla Irene E. , Milinski Manfred , Lenz Tobias L. , Eizaguirre Christophe 
Published: July 2023

AbstractGenome sequencing enables answering fundamental questions about the genetic basis of adaptation, population structure and epigenetic mechanisms. Yet, we usually need a suitable reference genome for mapping population‐level resequencing data. In some model systems, multiple reference genomes are available, giving the challenging task of determining which reference genome best suits the data. Here, we compared the use of two different reference genomes for the three‐spined stickleback (Gasterosteus aculeatus), one novel genome derived from a European gynogenetic individual and the published reference genome of a North American individual. Specifically, we investigated the impact of using a local reference versus one generated from a distinct lineage on several common population genomics analyses. Through mapping genome resequencing data of 60 sticklebacks from across Europe and North America, we demonstrate that genetic distance among samples and the reference genomes impacts downstream analyses. Using a local reference genome increased mapping efficiency and genotyping accuracy, effectively retaining more and better data. Despite comparable distributions of the metrics generated across the genome using SNP data (i.e. π, Tajima's D and FST), window‐based statistics using different references resulted in different outlier genes and enriched gene functions. A marker‐based analysis of DNA methylation distributions had a comparably high overlap in outlier genes and functions, yet with distinct differences depending on the reference genome. Overall, our results highlight how using a local reference genome decreases reference bias to increase confidence in downstream analyses of the data. Such results have significant implications in all reference‐genome‐based population genomic analyses.