bluuebunny/crossref_metadata_2025_split huggingface dataset:
Negative Electrospray Supercharging Mechanisms of Oligonucleotide Single Strands and G-quadruplexes
Authors: Ghosh Debasmita , Rosu Frédéric , Gabelica Valérie 
Published: July 2022

AbstractWhen sprayed from physiological ionic strength, nucleic acids typically end up with low levels of charging and in compact conformations. Increasing the electrospray negative charging of nucleic acids while preserving the native non-covalent interactions can help distinguish solution folds by ion mobility mass spectrometry. To get fundamental insight into the supercharging mechanisms of nucleic acids in the negative mode, we studied model G-quadruplex structures and single strand controls in 100 mM ammonium acetate. We found that adding 0.4% propylene carbonate, 0.4% sulfolane or 0.1% m-NBA induces native supercharging through the charged residue mechanism. However, although 0.4% m-NBA shows the highest supercharging ability, it induces unwanted unfolding of solution-folded G-quadruplexes. The supercharging effect resembles the effect of lowering the ionic strength, which could be explained by partial neutralization of the ampholytes when droplets become more concentrated in their non-aqueous components. The supercharging ability ranks: PC < sulfolane < m-NBA. m-NBA adducts to G-quadruplexes with high charge states confirms that the supercharging agent interacts directly with DNA. Surprisingly, in presence of supercharging agents, more negative charge states also bear more alkali metal ion adducts. This suggests that native supercharging results from larger droplets evaporating to the charged residue, leading to higher concentration of both the supercharging agent and of alkali counterions. However, when negative charge carriers from the electrolyte become too rare, chain ejection accompanied by denaturation, and hence non-native supercharging, can become predominant.
Phylogenomics oftrans-Andean tetras of the genusHyphessobryconDurbin 1908 and colonization patterns of Middle America
Authors: Elías Diego J. , McMahan Caleb D. , Alda Fernando , García-Alzate Carlos , Hart Pamela B. , Chakrabarty Prosanta 
Published: July 2022

AbstractHyphessobryconis one of the most species rich and widely distributed genera in the family Characidae, with more than 160 species ranging from Veracruz, Mexico to Argentina. The majority of the diversity ofHyphessobryconshows acis-Andean distribution; only nine species aretrans-Andean includingH. compressus(Meek 1908). It is well established thatHyphessobryconis not monophyletic but has been suggested that natural groups can be identified within the largerHyphessobryconspecies group. In this study, we test the monophyly oftrans-Andean species ofHyphessobryconand investigate the placement ofH. compressus. We have inferred the first phylogenomic hypothesis oftrans-AndeanHyphessobryconthat includes nearly complete taxonomic sampling (eight of nine valid species) using ultraconserved elements (UCEs). We analyzed 75% (1682 UCEs), 90% (1258 UCEs), and 95% (838 UCEs) complete data matrices, and inferred phylogenomic hypotheses under concatenation and coalescent approaches. In all cases, we recovered the monophyly oftrans-AndeanHyphessobryconinclusive ofH. compressus, and strong support for three species groups and evidence of cryptic diversity within the widespreadH. compressusandH. condotensis. We used our phylogenomic hypothesis to investigate the biogeographic history ofHyphessobryconin Middle America. Our ancestral range estimation analysis suggests a single event ofcis- totrans-Andean colonization followed by stepwise colonization from the Pacific slope of northwestern South America (Chocó block) to northern Middle America (Maya block). Our work supports the recognition of thetrans-Andean species asHyphessobryconsensu stricto and provides a robust evolutionary template to examine morphological characters that will allow us to better understand the diversity ofHyphessobryconin Middle America.
DNA methyltransferase enhanced Fusobacterium nucleatum genetics
Authors: Umaña Ariana , Nguyen Tam T.D. , Sanders Blake E. , Williams Kevin J. , Wozniak Bryce , Slade Daniel J. 
Published: July 2022

ABSTRACTBacterial restriction-modification (R-M) systems are a first line immune defense against foreign DNA from viruses and other bacteria. While R-M systems are critical in maintaining genome integrity, R-M nucleases unfortunately present significant barriers to targeted genetic modification. Bacteria of the genus Fusobacterium are oral, Gram-negative, anaerobic, opportunistic pathogens that are implicated in the progression and severity of multiple cancers and tissue infections, yet our understanding of their direct roles in disease have been severely hindered by their genetic recalcitrance. Here, we demonstrate a path to overcome these barriers in Fusobacterium by using native DNA methylation as a host mimicry strategy to bypass R-M system cleavage of user introduced plasmid DNA. We report the identification, characterization, and successful use of Fusobacterium nucleatum (Fn) Type II and III DNA methyltransferase (DMTase) enzymes to produce a multi-fold increase in gene knockout efficiency in the strain Fusobacterium nucleatum subsp. nucleatum 23726 (Fnn 23726), as well as the first efficient gene knockouts and complementations in Fnn 25586. We show plasmid protection can be accomplished in vitro with purified enzymes, as well as in vivo in an E. coli host that constitutively expresses Fnn DMTase enzymes. By characterizing specific DMTases that are critical for bypassing R-M systems, we have enhanced our understanding of potential enzyme combinations, with the goal of expanding these studies to genetically modify clinical isolates of Fusobacterium that have thus far been inaccessible to molecular characterization. This proof-of-concept study provides a roadmap to guide molecular microbiology efforts of the scientific community to facilitate the discovery of new Fusobacterium virulence genes, thereby leading to a new era of characterizing how an oral opportunistic pathogen contributes to an array of human infections and diseases.IMPORTANCEFusobacterium nucleatum is an oral opportunistic pathogen associated with diseases including cancer and preterm birth. Our understanding of how this bacterium modulates human disease has been hindered by a lack of genetic systems. Here we show that F. nucleatum DNA methyltransferase modified plasmid DNA overcomes the transformation barrier and allows the development of genetic systems in previously inaccessible strains. We present a strategy that can be expanded to enable the genetic modification of clinical isolates, thereby fostering investigational studies to uncover novel host-pathogen interactions in Fusobacterium.
Gabapentin Disrupts Binding of Perlecan to the α2δ1Voltage Sensitive Calcium Channel Subunit and Impairs Skeletal Mechanosensation
Authors: Reyes Fernandez Perla C. , Wright Christian S. , Masterson Adrianna N. , Yi Xin , Tellman Tristen V. , Bonteanu Andrei , Rust Katie , Noonan Megan L. , White Kenneth E. , Lewis Karl J. , Sankar Uma , Hum Julia M. , Bix Gregory , Wu Danielle , Robling Alexander G. , Sardar Rajesh , Farach-Carson Mary C. , Thompson William R. 
Published: July 2022

AbstractOur understanding of how osteocytes, the principal mechanosensors within bone, sense and perceive force remains unclear. Previous work identified “tethering elements” (TEs) spanning the pericellular space of osteocytes and transmitting mechanical information into biochemical signals. While we identified the heparan sulfate proteoglycan perlecan (PLN) as a component of these TEs, PLN must attach to the cell surface to induce biochemical responses. As voltage-sensitive calcium channels (VSCCs) are critical for bone mechanotransduction, we hypothesized that PLN binds the extracellular α2δ1subunit of VSCCs to couple the bone matrix to the osteocyte membrane. Here, we showed co-localization of PLN and α2δ1along osteocyte dendritic processes. Additionally, we quantified the molecular interactions between α2δ1and PLN domains and demonstrated for the first time that α2δ1strongly associates with PLN via its domain III. Furthermore, α2δ1is the binding site for the commonly used pain drug, gabapentin (GBP), which is associated with adverse skeletal effects when used chronically. We found that GBP disrupts PLN::α2δ1bindingin vitro, and GBP treatmentin vivoresults in impaired bone mechanosensation. Our work identified a novel mechanosensory complex within osteocytes composed of PLN and α2δ1, necessary for bone force transmission and sensitive to the drug GBP. This work provides insights into the mechanisms underlying mechanotransduction and will inform future studies to understand the mechanisms responsible for the negative effects of GBP on bone.
Actively replicating gut bacteria identified by 5-ethynyl-2’-deoxyuridine (EdU) click chemistry and cell sorting
Authors: Beauchemin Eve T. , Hunter Claire , Maurice Corinne F. 
Published: July 2022

AbstractThe composition of the intestinal bacterial community is well described, but recent research suggests that the metabolism of these bacteria plays a larger role in health than which species are present. One fundamental aspect of gut bacterial metabolism that remains understudied is bacterial replication. Indeed, there exist few techniques which can identify actively replicating gut bacteria. In this study, we aimed to address this gap by adapting 5-ethynyl-2’-deoxyuridine (EdU) click chemistry (EdU-click), a metabolic labeling method, coupled with fluorescence-activated cell sorting and sequencing (FACS-Seq) to characterize replicating gut bacteria. We first used EdU-click with human gut bacterial isolates and show that many of them are amenable to this technique. We then optimized EdU-click and FACS-Seq for murine fecal bacteria and reveal thatPrevotellaUCG-001 andIleibacteriumare enriched in the replicating fraction. Finally, we labelled the actively replicating murine gut bacteria during exposure to cell wall-specific antibioticsin vitro. We show that regardless of the antibiotic used, the actively replicating bacteria largely consist ofIleibacterium, suggesting the resistance of this taxon to perturbations. Overall, we demonstrate how combining EdU-click and FACSeq can identify the actively replicating gut bacteria and their link with the composition of the whole community in both homeostatic and perturbed conditions. This technique will be instrumental in elucidatingin situbacterial replication dynamics in a variety of other ecological states, including colonization and species invasion, as well as for investigating the relationship between the replication and abundance of bacteria in complex communities.
Developing cyanobacterial quorum sensing toolkits: towards interspecies coordination in mixed autotroph/heterotroph communities
Authors: Kokarakis Emmanuel J. , Rillema Rees , Ducat Daniel C. , Sakkos Jonathan K. 
Published: July 2022

1.AbstractThere has been substantial recent interest in the promise of sustainable, light-driven bioproduction using cyanobacteria, including developing efforts for microbial bioproduction using mixed autotroph/heterotroph communities, which could provide useful properties, such as division of metabolic labor. However, building stable mixed-species communities of sufficient productivity remains a challenge, partly due to the lack of strategies for synchronizing and coordinating biological activities across different species. To address this obstacle, we developed an inter-species communication system using quorum sensing (QS) modules derived from well-studied pathways in heterotrophic microbes. In the model cyanobacterium, Synechococcus elongatus PCC 7942 (S. elongatus), we designed, integrated, and characterized genetic circuits that detect acyl-homoserine lactones (AHLs), diffusible signals utilized in many QS pathways. We showed that these receiver modules sense exogenously supplied AHL molecules and activate gene expression in a dose-dependent manner. We characterized these AHL receiver circuits in parallel in Escherichia coli W (E. coli W) to dissect species-specific properties, finding broad agreement, albeit with increased basal expression in S. elongatus. Our engineered “sender” E. coli strains accumulated biologically synthesized AHLs within the supernatant and activated receiver strains similarly to exogenous AHL activation. Our results will bolster the design of sophisticated genetic circuits in cyanobacterial/heterotroph consortia and the engineering of QS-like behaviors across cyanobacterial populations.HighlightsDesigned, built, and tested an inter-species quorum sensing-based communication system.These genetic circuits can sense and respond to exogenous and secreted signals.Circuit function in S. elongatus was comparable to E. coli, albeit with increased basal expression and lower induction ratiosDemonstrated inter-species communication in direct co-cultivationFirst demonstration of inducible promoters and cross-species gene regulation in S. elongatus based on quorum sensing
Estimated Monkeypox Susceptible MSM Population in North Carolina
Authors: DeWitt Michael E. , Sampson Mindy M. , Fairman Robert T. , McNeil Candice J. , Polk Christopher , Passaretti Catherine L. , Sanders John W. 
Published: July 2022

AbstractUsing NHANES survey data we estimate that there are nearly 65,100 North Carolina residents who identify as men who have sex with men (MSM). Among those men, it is estimated nearly 15,700 have had at least one new sexual partner in the last year and represent the highest risk for infection and onward transmission of monkeypox. Vaccination strategies should consider vaccinating with highest priority those who are highly sexually active men who have sex with men as these sexual networks have the capacity to drive the monkeypox epidemic. Estimates of the number of MSM by county as well as the estimates of highly sexually active MSM are provided by North Carolina county in order to inform vaccination quantities and priorities given the current limited supply of vaccines.
Development of a framework for utilising Lean Six Sigma’s intangible impacts in creating organisational innovation climate
Authors: Alblooshi Mohamed , Shamsuzzaman Mohammad , Karim Azharul , Haridy Salah , Shamsuzzoha Ahm , Badar M. Affan 
Published: July 2022

PurposeThe purpose of this paper is to develop a framework that illustrates the role of Lean Six Sigma (LSS) in creating organisational innovation climate by investigating the relationship between LSS’s intangible impacts and organisational innovation climate factors.Design/methodology/approachA self-administrated survey questionnaire was distributed among 145 public sector officials to get their opinions on the relationship between various observable elements of LSS’s intangible impacts and organisational innovation climate factors, where a response rate of 73.8% was achieved. The collected data were demographically, descriptively and statistically analysed. Accordingly, a house-of-pillars-based framework that illustrates the role of LSS’s intangible impacts in creating innovation climate in an organisation was developed.FindingsResults from this study indicated that LSS’s intangible impacts on organisational structure and hierarchy, culture, change adaptability, utilisation of staff and staff’s behavioural aspects are positively related to many of organisational innovation climate factors such as trust and openness, challenge and involvement, support for ideas and freedom and autonomy.Research limitations/implicationsThe findings of this study are based on the data collected from public sector organisations in the UAE and are supported by relevant literature. However, this study can provide useful guidance for further research for the generalisation of the results to wider scopes in terms of sectors and geographical domains.Practical implicationsThe findings of this study will provide UAE public sector officials with a clear roadmap on how to use LSS for promoting innovation and fostering its implementation in practice. This study will also encourage professionals in public sectors to integrate LSS into their innovation strategies to enhance organisational innovativeness and improve service quality.Originality/valueIt is one of the first studies that explores LSS’s intangible impacts and assesses their relationship with organisational innovation climate factors. Hence, this study offers valuable insights for both academics and practitioners and is expected to lay a foundation for a better understanding of how LSS’s intangible impacts can be used in creating organisational innovation climate.
Staying, switching, and multiplatforming of user-generated content activities: a 12-year panel study
Authors: Hou Lei , Guan Lu , Zhou Yixin , Shen Anqi , Wang Wei , Luo Ang , Lu Heng , Zhu Jonathan J.H. 
Published: July 2022

PurposeUser-generated content (UGC) refers to semantic and behavioral traces created by users on various social media platforms. While several waves of platforms have come and gone, the long-term sustainability of UGC activities has become a critical question that bears significance for theoretical understanding and social media practices.Design/methodology/approachBased on a large and lengthy dataset of both blogging and microblogging activities of the same set of users, a multistate survival analysis was applied to explore the patterns of users' staying, switching and multiplatforming behaviors, as well as the underlying driving factors.FindingsUGC activities are generally unsustainable in the long run, and natural attrition is the primary reason, rather than competitive switching to new platforms. The availability of leisure time, expected gratification and previous experiences drive users' sustainability.Originality/valueThe authors adopted actual behavioral data from two generations of platforms instead of survey data on users' switching intentions. Four types of users are defined: loyal, switcher, multiplatformer and dropout. As measured by the transitions among the four states, the different sustainability behaviors are thereby studied via an integrated framework. These two originalities bridge gaps in the literature and offer new insights into exploring user sustainability in social media.
Promoting transformative encounters in libraries and archives
Authors: Lowe Carli V. 
Published: July 2022

PurposeIn several existing studies of Information Encountering (IE), a recurring sub-phenomenon of serendipity arises that indicates the potential for certain unexpected encounters with information to be transformative. The author labels this sub-phenomenon Transformative Information Encountering (TIE), deriving its definition from an application of Transformative Education (TE) theory to existing understandings of IE. This paper aims to discuss the potential for librarians and archivists to promote TIE through everyday practices.Design/methodology/approachAfter defining and identifying TIE in existing studies of IE, this article will put models of IE in conversation with theories of TE and propose ways in which TIE may arise in the everyday work of librarians and archivists.FindingsIn TE theory, there are three phases of the process of critical premise reflection that may be especially relevant to the work of libraries and archives. These are a disorienting dilemma (phase 1); recognition that the process of transformation is shared (phase 4); and acquiring knowledge and skills (phase 7). Each of these aligns with aspects of IE models.Practical implicationsUnderstanding how TIE might inform everyday Library and Information Science (LIS) work may increase the positive impact cultural institutions have on the communities they serve.Originality/valueWhile several IE studies have suggested the existence of TIE as a sub-phenomenon, none thus far have attempted to define it or apply an understanding of it to LIS work.
Conceptual design of a small production plant for eco-friendly packaging
Authors: Fiorineschi Lorenzo , Conti Leonardo , Rossi Giuseppe , Rotini Federico 
Published: July 2022

Purpose
This paper aims to present the application of a tailored systematic engineering design procedure to the concept design of a small production plant for compostable packaging made by straw fibres and bioplastic. In particular, the obtained boxes are intended to be used for wine bottles.

Design/methodology/approach
A systematic procedure has been adopted, which underpins on a comprehensive analysis of the design requirements and the function modelling of the process. By considering well-known models of the engineering design process, the work focuses on the early design stages that precede the embodiment design of the whole components of the plant.

Findings
The followed design approach allowed to preliminarily evaluate different alternatives of the process from a functional point of view, thus allowing to identify the preferred conceptual process solution. Based on the identified functional sequence, a first evaluation of the potential productivity and the required human resources has been performed.

Research limitations/implications
The procedure shown in this work has been applied only for the considered case of compostable packaging, and other applications are needed to optimize it. Nevertheless, the adopted systematic approach can be adapted for any context where it is necessary to conceive a new production plant for artefacts made by innovative materials.

Originality/value
The work presented in this paper represents one of the few practical examples available in the literature where systematic conceptual design procedures are presented. More specifically, to the best of the authors’ knowledge, this is the very first application of systematic design methods to compostable packaging production.
Exploring locally-produced design solutions for thermal comfort: a socio-technical assessment
Authors: Peker Ender 
Published: July 2022

PurposeThe purpose of this paper is to explore the role of locally-produced architectural design solutions for the provision of thermal comfort in the vernacular settlements of Mardin, Turkey.Design/methodology/approachWith an aim of extracting clues of climate responsive design, the paper develops a socio-technical assessment methodology and presents a comparative inquiry between the vernacular and contemporary built environments of Mardin.FindingsFindings display that the capacity of vernacular architecture in providing a more climate responsive living environment than contemporary one is in fact correlated with the design of living spaces in harmony with the local climatic conditions as well as how inhabitants traditionally use and behave in designed space.Originality/valueThe paper argues for a need for (re)conceptualization of thermal comfort within and through the production of housing, as well as by taking into account the ways in which end-users interact, adapt and sustain end-users' everyday life in accordance with the local climatic characteristics.