bluuebunny/crossref_metadata_2025_split huggingface dataset:
DivIVA phosphorylation at threonine affects its dynamics and cell cycle in Deinococcus radiodurans
Authors: Chaudhary Reema , Kota Swathi , Misra Hari S. 
Published: June 2022

AbstractRqkA, a γ radiation responsive Ser/Thr quinoprotein kinase, is characterized for its role in radioresistance in Deinoocccus radiodurans. DivIVA is a cell division protein involved in determination of cell pole and division site in bacteria. RqkA phosphorylated cognate DivIVA (drDivIVA) at Threonine 19 (T19) residue located in its pole recognition motif. The phospho-mimetic replacement of T19 (T19E) functioned differently than phospho-ablative (T19A) and drDivIVA proteins. T19E-RFP expressing in wild type background showed arrest in dynamics of drDivIVA, and loss of interaction with genome segregation protein. divIVA is shown to be an essential gene in this bacterium. The allelic replacement of divIVA with T19E-RFP was not tolerated unless drDivIVA was expressed episomally while there was no effect of this replacement with T19A-RFP and drDivIVA-RFP. These results suggested that the T19 phosphorylation in drDivIVA by RqkA has affected in vivo functions of DivIVA that would render cell cycle arrest in this bacterium.
Fundamental limits to progression of cellular life in frigid environments
Authors: Trip Diederik S. Laman , Maire Théo , Youk Hyun 
Published: June 2022

ABSTRACTLife on Earth, including for microbes and cold-blooded animals, often occurs in frigid environments. At frigid temperatures, nearly all intracellular processes slow down which is colloquially said to decelerate life’s pace and, potentially, aging. But even for one cell, an outstanding conceptual challenge is rigorously explaining how the slowed-down intracellular processes collectively sustain a cell’s life and set its pace. Here, by monitoring individual yeast cells for months at near-freezing temperatures, we show how global gene-expression dynamics and Reactive Oxygen Species (ROS) act together as the primary factors that dictate and constrain the pace at which a budding yeast’s life can progresses in frigid environments. We discovered that yeast cells help each other in surviving and dividing at frigid temperatures. By investigating the underlying mechanism, involving glutathione secretion, we discovered that ROS is the primary determinant of yeast’s ability to survive and divide at near-freezing temperatures. Observing days-to-months-long cell-cycle progression in individual cells revealed that ROS inhibits S-G2-M (replicative) phase while elongating G1 (growth) phase up to a temperature-dependent threshold duration, beyond which yeast cannot divide and bursts as an unsustainably large cell. We discovered that an interplay between global gene-expression speed and ROS sets the threshold G1-duration by measuring rates of genome-wide transcription and protein synthesis at frigid temperatures and then incorporating them into a mathematical model. The same interplay yields unbeatable “speed limits” for cell cycling – shortest and longest allowed doubling times – at each temperature. These results establish quantitative principles for engineering cold-tolerant microbes and reveal how frigid temperatures can fundamentally constrain microbial life and cell cycle at the systems-level.
Phase variation as a major mechanism of adaptation inMycobacterium tuberculosiscomplex
Authors: Vargas Roger , Luna Michael J. , Freschi Luca , Murphy Kenan C. , Ioerger Thomas R. , Sassetti Christopher M. , Farhat Maha R. 
Published: June 2022

ABSTRACTPhase variation induced by insertions and deletions (INDELs) in genomic homopolymeric tracts (HT) can silence and regulate genes in pathogenic bacteria but this process is not characterized in MTBC adaptation. We leverage 31,428 diverse clinical isolates to identify genomic regions including phase-variants under positive selection. Of 87,651 INDEL events that emerge repeatedly across the phylogeny, 12.4% are phase-variants within HTs (0.02% of the genome by length). We estimated thein-vitroframeshift rate in a neutral HT at 100x the neutral substitution rate at 1.1 × 10−5frameshifts/HT/year. Using neutral evolution simulations, we identified 4,098 substitutions and 45 phase-variants to be putatively adaptive to MTBC (P<0.002). We experimentally confirm that a putatively adaptive phase-variant alters the expression ofespA,a critical mediator of ESX-1 dependent virulence. Our evidence supports a new hypothesis that phase variation in the ESX-1 system of MTBC can act as a toggle between antigenicity and survival in the host.
Innate Conformational Dynamics Drive Binding Specificity in Anti-Apoptotic Proteins Mcl-1 and Bcl-2
Authors: Wolf Esther , Lento Cristina , Pu Jinyue , Dickinson Bryan C. , Wilson Derek J. 
Published: June 2022

AbstractThe structurally conserved B-cell Lymphoma 2 (Bcl-2) family of proteins function to promote or inhibit apoptosis through an exceedingly complex web of specific, intrafamilial protein-protein interactions. The critical role of these proteins in lymphomas and other cancers has motivated a widespread interest in understanding the molecular mechanisms that drive specificity in Bcl-2 family interactions. However, the substantial structural similarity amongst Bcl-2 homologues has made it difficult to rationalize the highly specific (and often divergent) binding behavior exhibited by these proteins using conventional structural arguments. In this work, we use millisecond hydrogen deuterium exchange mass spectrometry to explore shifts in conformational dynamics associated with binding partner engagement in Bcl-2 family proteins Bcl-2 and Mcl-1. Using this approach, we reveal that, specifically for Mcl-1, binding specificity arises largely from protein-specific dynamic modes that are accessed in the unbound state. This work has implications for exploring the evolution of internally regulated biological systems composed of structurally similar proteins, and for the development of drugs targeting Bcl-2 family proteins for promotion of apoptosis in cancer.General Interest StatementThis work reveals how a group of proteins, which are highly similar in structure, can form a complex web of highly specific protein-protein interactions that drive programmed cell death (apoptosis) in cancer.
Genome-wide analysis of heat stress-stimulated transposon mobility in the human fungal pathogenCryptococcus deneoformans
Authors: Gusa Asiya , Yadav Vikas , Roth Cullen , Williams Jonathan D. , Shouse Eva Mei , Magwene Paul , Heitman Joseph , Jinks-Robertson Sue 
Published: June 2022

AbstractWe recently reported transposon mutagenesis as a significant driver of spontaneous mutations in the human fungal pathogenCryptococcus deneoformansduring murine infection. Mutations caused by transposable element (TE) insertion into reporter genes were dramatically elevated at high temperature (37° versus 30°) in vitro, suggesting that heat stress stimulates TE mobility in the Cryptococcus genome. To explore the genome-wide impact of TE mobilization, we generated transposon accumulation lines by in vitro passage ofC. deneoformansstrain XL280α for multiple generations at both 30° and at the host-relevant temperature of 37°. Utilizing whole-genome sequencing, we identified native TE copies and mapped multiplede novoTE insertions in these lines. Movements of the T1 DNA transposon occurred at both temperatures with a strong bias for insertion between gene-coding regions. By contrast, the Tcn12 retrotransposon integrated primarily within genes and movement occurred exclusively at 37°. In addition, we observed a dramatic amplification in copy number of the Cnl1 (C. neoformansLINE-1) retrotransposon in sub-telomeric regions under heat-stress conditions. Comparing TE mutations to other sequence variations detected in passaged lines, the increase in genomic changes at elevated temperature was primarily due to mobilization of the retroelements Tcn12 and Cnl1. Finally, we found multiple TE movements (T1, Tcn12 and Cnl1) in the genomes of singleC. deneoformansisolates recovered from infected mice, providing evidence that mobile elements are likely to facilitate microevolution and rapid adaptation during infection.Significance StatementRising global temperatures and climate change are predicted to increase fungal diseases in plants and mammals. However, the impact of heat stress on genetic changes in environmental fungi is largely unexplored. Environmental stressors can stimulate the movement of mobile DNA elements (transposons) within the genome to alter the genetic landscape. This report provides a genome-wide assessment of heat stress-induced transposon mobilization in the human fungal pathogen Cryptococcus. Transposon copies accumulated in genomes more rapidly following growth at the higher, host-relevant temperature. Additionally, movements of multiple elements were detected in the genomes of cryptococci recovered from infected mice. These findings suggest that heat stress-stimulated transposon mobility contributes to rapid adaptive changes in fungi both in the environment and during infection.
ALegionellatoxin mimics tRNA and glycosylates the translation machinery to trigger a ribotoxic stress response
Authors: Subramanian Advait , Wang Lan , Moss Tom , Voorhies Mark , Sangwan Smriti , Stevenson Erica , Pulido Ernst H. , Kwok Samentha , Krogan Nevan J. , Swaney Danielle L. , Floor Stephen N. , Sil Anita , Walter Peter , Mukherjee Shaeri 
Published: June 2022

AbstractPathogens often secrete proteins or nucleic acids that mimic the structure and/or function of molecules expressed in their hosts. Molecular mimicry empowers pathogens to subvert critical host processes and establish infection. We report that the intracellular bacteriumLegionella pneumophilasecretes the toxin SidI (substrate of icm/dot transporter I), which possesses a transfer RNA (tRNA)-like shape and functions as a mannosyl transferase. The 3.1 Å cryo-EM structure of SidI reveals an N-terminal domain that exhibits a characteristic ‘inverted L-shape’ and charge distribution that is present in two other known protein mimics of tRNAs, the bacterial elongation factor EF-G and the mammalian release factor eRF1. In addition, we show that SidI’s C-terminal domain adopts a glycosyl transferase B fold similar to a mannosyl transferase. This molecular coupling of the protein’s fold and enzymatic function allows SidI to bind and glycosylate components of the host translation apparatus, including the ribosome, resulting in a robust block of protein synthesis that is comparable in potency to ricin, one of the most powerful toxins known. Additionally, we find that translational pausing activated by SidI elicits a stress response signature reminiscent of the ribotoxic stress response that is activated by elongation inhibitors that induce ribosome collisions. SidI-mediated effects on the ribosome activate the stress kinases ZAKα and p38, which in turn drive an accumulation of the protein activating transcription factor 3 (ATF3). Intriguingly, ATF3 escapes the translation block imposed by SidI, translocates to the nucleus, and orchestrates the transcription of stress-inducible genes that promote cell death. Thus, usingLegionellaand its effectors as tools, we have unravelled the role of a ribosome-to-nuclear signalling pathway that regulates cell fate.
Current Situation of Breeding Bird Species in the Gediz Delta, Turkey
Authors: Arslan Şafak , Kaya Ahmet , Akyol Adem , Kaya Mehmet 
Published: June 2022

AbstractGediz Delta, one of the most important wetland ecosystems in the Mediterranean Basin, also is one of the most important areas for birds in Turkey. Breeding bird atlas studies were carried out in 2002, and 2006 and extensive breeding species were revealed. In 2021, we conducted an atlas of breeding birds using the same method as previous studies and observed the change over the last 15 years. Bird species seen and heard between May 3 and June 15 in 294 1x1 square kilometres were recorded and classified with internationally accepted breeding codes. Breeding codes were given to 113 species belonging to 48 families throughout the study. Of these, 32 species are classified as possible breeding, 34 species as probable breeding and 47 species as confirmed breeding. Threat factors of species and habitats are grouped under five main topics. According to previous studies, we observed that the number of breeding bird species increased. It is thought that the number of breeding bird species will increase with the elimination of threats and carrying out the necessary restoration works.
Sturgeons: An Evolutionary Insight to The α-globin Protein Speciation and Diversification
Authors: Ariaeenejad Shohreh , Kavousi Kaveh , Elahi Elaheh , Banaei-Moghaddam Ali Mohammad , Moosavi-Movahedi Ali A. 
Published: June 2022

AbstractSturgeons are living fossils and among the oldest surviving vertebrate species, and Caspian Sea is habitat of the vast majority of sturgeon species. It is tempting to assume that speciation of sturgeons occurred in response to the severe environmental changes during the formation of Caspian Sea from the ancient Paratethys Sea. Hemoglobin (Hb) reflects the evolutionary history of fishes. Changes in the Hb sequences will affect the protein structure and consequently the vital function of oxygen delivery. As complete sequence data for any sturgeon hemoglobin gene or protein was hitherto not available, we determined the complete gene and protein sequences of an α-globin chain (as one of the constituents of Hb complex) from six Caspian Sea sturgeons of different species and compared these sequences mutually and with all available fish α-globin sequences. The phylogenetic analyses based on alpha globin sequences can highlight the essentiality of proper changes in globin chains in the speciation process. Estimating the divergence time of α-globin genes for different fish families discloses important facts about the rate of evolution and decodes. The results support the hypothesis of simultaneity between the time of morphological speciation of fish families and their α-globin divergence. The correlation and concurrency between morphological and molecular changes can be interpreted as a sign of struggling to acquire more fitness to changing environment.
Envisioning legitimacy: visual dimensions of NGO annual reports
Authors: Dhanani Alpa , Kennedy Denis 
Published: June 2022

PurposeThis paper explores the communication of legitimacy in the annual reports of non-governmental organizations (NGOs), focusing specifically on the function of images. The visual mode of discourse and meaning construction has to date only scarcely been explored in legitimacy research, especially in the NGO context.Design/methodology/approachDistinguishing between normative, regulatory, cognitive and outcome legitimacy, the paper inquires into the kinds of legitimacy that NGOs communicate to their constituents and the claims that predominate. Turning to research on impression management, the paper explores whether and how organizations use images as symbolic mechanisms of legitimacy. Finally, the paper considers the socio-cultural implications of these legitimation strategies for beneficiary groups, donor communities and the organizations themselves.FindingsA qualitative content analysis of images in the reports of the eight influential members of the US-based Global Emergency Response Coalition confirms the widespread presence of legitimacy claims in NGO visual communications, with normative (especially need) and output (especially implementation) categories predominating. However, these practices are potentially contradictory; measures to increase legitimacy to and of donors result in forms of beneficiary exclusion and reduction. Strategies of impression management, namely self-promotion, ingratiation and exemplification, appear to shape these NGO representative logics.Originality/valueThe results of this study extend prior research into legitimacy, legitimation and impression management in and beyond the non-governmental sector by differentiating among categories of legitimacy and incorporating images as the object of analysis. In this capacity, they also support and augment the emerging literature on imagery use in NGO annual reports.
Thrust modelling of a target drone engine with nonlinear least – squares estimation based on series expansions
Authors: Kaba Aziz , Yurdusevimli Metin Ece , Turan Onder 
Published: June 2022

Purpose
The purpose of this study is to build a high accuracy thrust model under various small turbojet engine shaft speeds by using robust, ordinary, linear and nonlinear least squares estimation methods for target drone applications.

Design/methodology/approach
The dynamic shaft speeds from the test experiment of a target drone engine is conducted. Then, thrust values are calculated. Based on these, the engine thrust is modeled by robust linear and nonlinear equations. The models are benefited from quadratic, power and various series expansion functions with several coefficients to optimize the model parameters.

Findings
The error terms and accuracy of the model are given using sum of squared errors, root mean square error (RMSE) and R-squared (R2) error definitions. Based on the multiple analyses, it is seen that the RMSE values are no more than 17.7539 and the best obtained result for robust least squares estimation is 15.0086 for linear at all cases. Furthermore, the R2 value is found to be 0.9996 as the highest with the nonlinear Fourier series expansion model.

Originality/value
The motivation behind this paper is to propose robust nonlinear thrust models based on power, Fourier and various series expansion functions for dynamic shaft speeds from the test experiments.
Can the digital transformation of manufacturing enterprises promote enterprise innovation?
Authors: Zhao Xueqi , Sun Xiaozhe , Zhao Longwen , Xing Yibing 
Published: June 2022

PurposeThe purpose of this paper is to investigate the relations between the digital transformation of manufacturing enterprises and enterprise innovation to provide inspiration for promoting the digitization and upgrading of China's manufacturing industry and facilitate enterprises' innovative development.Design/methodology/approachBased on a panel data of 584 listed manufacturing companies in China from 2016 to 2020, and using a fixed effects approach, this paper empirically examines the impact of digital transformation on corporate innovation in manufacturing enterprises, as well as examining the influential mechanisms and heterogeneity.FindingsThe research shows that the digital transformation of manufacturing enterprises has effectively improved the innovation capacity of enterprises and verifies different situations through heterogeneity. At the same time, the research clarifies the mediating effect of the innovation investment mechanism, cost control mechanism, and profit guarantee mechanism on the relations between the digital transformation of manufacturing enterprises and the innovation capacity of enterprises.Originality/valueBased on Chinese manufacturing enterprise samples, this paper empirically tests the influential mechanism of digital transformation on the innovation capability of manufacturing enterprises, therefore clarifying the main mediating effects. This paper could provide inspiration for manufacturing companies to make good use of digital transformation rules according to their own situation and improve their innovation capabilities, thereby enhancing competitiveness in the digital economy era.
Understanding the BIM actor role: a study of employer and employee preference and availability in the construction industry
Authors: Adekunle Samuel Adeniyi , Aigbavboa Clinton Ohis , Ejohwomu Obuks Augustine 
Published: June 2022

PurposeThe implementation of BIM in the construction industry requires the coevolution of the various aspects of the BIM ecosystem. The human dimension is a very important dimension of the ecosystem necessary for BIM implementation. It is imperative to study this aspect of the BIM ecosystem both from the employer perspective and employee availability to provide insights for stakeholders (job seekers, employers, students, researchers, policymakers, higher education institutions, career advisors and curriculum developers) interested in the labour market dynamics.Design/methodology/approachTo understand the BIM actor roles through the employer lens and the actual BIM actors in the construction industry, this study employed data mining of job adverts from LinkedIn and Mncjobs website. Content analysis was employed to gain insights into the data collected. Also, through a quantitative approach, the existing BIM actor roles were identified.FindingsThe study identified the employers' expectations of BIM actors; however, it is noted that the BIM actor recruitment space is still a loose one as recruiters put out open advertisements to get a large pool of applicants. From the data analysed, it is concluded that the BIM actor role is not an entirely new profession. However, it simply exists as construction industry professionals with BIM tool skills. Also, the professional development route is not well defined yet.Originality/valueThis study presents a realistic angle to BIM actor roles hence enhancing BIM implementation from the human perspective. The findings present an insight into the preferred against the actual.
Knowledge management enablers and knowledge management processes: a direct and configurational approach to stimulate green innovation
Authors: Shehzad Muhammad Usman , Zhang Jianhua , Dost Mir , Ahmad Muhammad Shakil , Alam Sajjad 
Published: June 2022

PurposeGiven the critical importance of green innovation (GI) for organizations in developing economies, this study aims to examine the interrelationship between knowledge management (KM) enablers, KM processes and GI. The research also indicates that certain combinations of KM enabler dimensions and KM processes can lead to better GI.Design/methodology/approachThe study sample consists of 328 participants from Pakistan's medium- and large-sized manufacturing enterprises. Smart PLS 3.2.9 is used to verify the relationships. Moreover, the fuzzy set qualitative comparative analysis (fsQCA) investigates configurational paths for improving GI.FindingsThe results demonstrate that KM enablers significantly affect two aspects of GI – green product and process innovation – and KM processes. Moreover, KM processes significantly enhance two aspects of GI. The fsQCA findings indicate multiple combinations of KM enablers and KM processes dimensions that result in better GI.Research limitations/implicationsTo better understand the critical role of knowledge resources, future studies should explore the potential mediating mechanisms of KM processes or the moderating effects of strategic organizational factors in the relationship between KM enablers and GI.Practical implicationsThe study offers valuable insight and a unique approach for policymakers and executives of corporations in developing countries to enhance their organizations' GI capacity through KM enablers and KM processes.Originality/valueThis research contributes to bridging research gaps in the literature and advances insights into the interrelationship among KM enablers, KM processes and GI. In addition, the study offers methodological significance by combining direct and configurational techniques to address two distinct facets of GI.