bluuebunny/crossref_metadata_2025_split huggingface dataset:
Candidate Genes Underlying Wolbachia-Associated Plastic Recombination Revealed by Ovarian Transcriptomics of D. melanogaster
Authors: Frantz Sophia I. , Small Clayton M. , Cresko William A. , Singh Nadia D. 
Published: April 2022

AbstractPhenotypic plasticity is prevalent in nature and can facilitate the acclimation of organisms to changing environments. Recombination rate is plastic in a diversity of organisms and under a variety of stressful conditions. However, the recent finding that Wolbachia pipientis induces plastic recombination in Drosophila melanogaster was surprising because Wolbachia is not strictly considered a stressor to this host. We investigate the molecular mechanisms of Wolbachia-associated plastic recombination by comparing the ovarian transcriptomes of D. melanogaster infected and uninfected with Wolbachia. Our data suggest that infection explains a small amount of transcriptional variation but specifically affects genes related to cell cycle, translation, and metabolism. We also find enrichment of cell division and recombination processes among genes with infection-associated differential expression. Broadly, the transcriptomic changes identified in this study provide insight for the mechanisms of microbe-mediated plastic recombination, an important but poorly understood facet of host-microbe dynamics.Significance StatementThough it is documented that Wolbachia is associated with increased recombination in D. melanogaster, the underlying mechanisms remain unknown. Here we use ovarian transcriptomics in Wolbachia-infected and uninfected flies to identify candidate genes underlying Wolbachia-associated plastic recombination. We find that infection alters ovarian gene expression in subtle ways, and also identify exciting candidate genes for functional analysis in subsequent work. These candidate genes may be the first step in determining the molecular mechanisms underlying Wolbachia-associated plastic recombination. Moreover, our data contribute to the growing body of knowledge surrounding how Wolbachia affects host gene expression, and highlights how context-dependent these effects are.
Cryo-EM structure of the Agrobacterium tumefaciens T-pilus reveals the importance of positive charges in the lumen
Authors: Amro Jaafar , Black Corbin , Jemouai Zakaria , Rooney Nathan , Daneault Caroline , Zeytuni Natalie , Ruiz Matthieu , Bui Khanh Huy , Baron Christian 
Published: April 2022

AbstractAgrobacterium tumefaciens is a natural genetic engineer that transfers DNA into plants and this is the most frequently applied process for the generation of genetically modified plants. DNA transfer is mediated by a type IV secretion system localized in the cell envelope and extracellular T-pili. We here report the cryo-electron microscopic structures of the T-pilus at 3.2Å resolution and that of the related plasmid pKM101-determined N-pilus at 3Å resolution. Both pili contain a main pilus protein (VirB2 in A. tumefaciens and TraM in pKM101) and phospholipids arranged in a 5-start helical assembly. They contain positively charged amino acids in the pilus lumen and the lipids are positively charged in the T-pilus (phosphatidylcholine) conferring overall positive charge to the lumen. Mutagenesis of the lumen-exposed Arg91 residue in VirB2 resulted in protein destabilization and loss of pilus formation. Our results reveal that different phospholipids can be incorporated into type IV secretion system pili and that the charge of the lumen is of functional importance.
Induction of neutralizing antibodies against SARS-CoV-2 variants by a multivalent mRNA-lipid nanoparticle vaccine encoding SARS-CoV-2/SARS-CoV Spike protein receptor-binding domains
Authors: Zhang Qiong , Tiwari Shashi K. , Wang Shaobo , Wang Lingling , Li Wanyu , Zhang Lingzhi , Rawlings Stephen A. , Cheng Yong , Jokerst Jesse V. , Rana Tariq M. 
Published: April 2022

AbstractTo address the need for multivalent vaccines against Coronaviridae that can be rapidly developed and manufactured, we compared antibody responses against SARS-CoV, SARS-CoV-2, and several variants of concern in mice immunized with mRNA-lipid nanoparticle vaccines encoding homodimers or heterodimers of SARS-CoV/SARS-CoV-2 receptor-binding domains. All vaccine constructs induced robust anti-viral antibody responses, and the heterodimeric vaccine elicited an IgG response capable of cross-neutralizing SARS-CoV, SARS-CoV-2 Wuhan-Hu-1, B.1.351 (beta), and B.1.617.2 (delta) variants.
Allosteric inhibition of PRPS is moderated by filamentous polymerization
Authors: Hu Huan-Huan , Lu Guangming , Chang Chia-Chun , Li Yilan , Zhong Jiale , Guo Chen-Jun , Zhou Xian , Yin Boqi , Zhang Tianyi , Liu Ji-Long 
Published: April 2022

ABSTRACTPhosphoribosyl pyrophosphate (PRPP) is an important intermediate for the biosynthesis of purine and pyrimidine nucleotides, histidine, tryptophan, and cofactors NAD and NADP. Abnormal regulation of PRPP synthase (PRPS) has been associated with human disorders including Arts syndrome, retinal dystrophy and gouty arthritis. Recent studies have revealed that PRPS can form filamentous cytoophidia in prokaryotes and eukaryotes. Here we resolve two distinct filament structures of E. coli PRPS at near-atomic resolution under Cryo-EM. Formation of two types of filaments is controlled by the binding of different ligands. While the type A filament attenuates the allosteric inhibition of PRPS by ADP, the type B filament enhances the inhibition. In addition, a novel conformation of the regulatory flexible loop of PRPS was found occupying the ATP binding site. AMP/ADP bound at a noncanonical allosteric site interacts with the regulatory flexible loop and facilitates the binding of ATP. Our findings not only reveal molecular mechanisms of the regulation of PRPS with structural basis, but also suggest a distinctive bidirectional regulatory system for PRPP production via PRPS polymerization.
Joint effect of temperature and insect chitosan on the heat resistance of Bacillus cereus spores in rice derivatives
Authors: Valdez Maria Ines , Maria Ubeda , Cristian Narvaes , Dolores Rodrigo , Antonio Martinez 
Published: April 2022

SummaryThe heat resistance of Bacillus cereus spores inoculated in a rice substrate supplemented with insect chitosan as an alternative antimicrobial was studied. Two concentrations of insect chitosan were considered in order to assess the role of the insect chitosan concentration during the heat process as an antimicrobial replacement for crustacean chitosan.Results of the study indicated that the DT values were clearly higher in the substrate without chitosan than in the substrate containing chitosan thus indicating a greater heat resistance to heat treatment of the microorganism inoculated in the substrate without chitosan. This behaviour was also evidenced in the survival curves. There were no great differences between either of the insect chitosan concentrations tested regarding the DT values. The z values were 9.8 ºC on rice substrate. 8.9 ºC on rice substrate supplemented with insect chitosan at 150 µg/mL and 10.7 ºC on rice substrate supplemented with 250 µg/mL of insect chitosan, the chitosan concentration appears to affect the z value of the microorganism. Our results indicate that the combination of heat with insect chitosan as an antimicrobial on foodstuffs subjected to cooking is feasible and can improve the safety of rice derivatives.
Quantitative analysis of surface wave patterns of Min proteins
Authors: Meindlhumer Sabrina , Kerssemakers Jacob , Dekker Cees 
Published: April 2022

ABSTRACTThe Min protein system is arguably the best-studied model systems for biological pattern formation. It exhibits pole-to-pole oscillations in E. coli bacteria as well as a variety of surface wave patterns in in vitro reconstitutions. Such Min surface wave patterns pose particular challenges to quantification as they are typically only semi-periodic and non-stationary. Here, we present a methodology for quantitatively analyzing such Min patterns, aiming for reproducibility, user-independence, and easy usage. After introducing pattern-feature definitions and image-processing concepts, we present an analysis pipeline where we use autocorrelation analysis to extract global parameters such as the average spatial wavelength and oscillation period. Subsequently, we describe a method that uses flow-field analysis to extract local properties such as the wave propagation velocity. We provide descriptions on how to practically implement these quantification tools and provide Python code that can directly be used to perform analysis of Min patterns.
Dissecting the phase separation and oligomerization activities of the carboxysome positioning protein McdB
Authors: Basalla Joseph L. , Mak Claudia A. , Byrne Jordan , Ghalmi Maria , Hoang Y , Vecchiarelli Anthony G. 
Published: April 2022

ABSTRACTAcross bacteria, protein-based organelles called bacterial microcompartments (BMCs) encapsulate key enzymes to regulate their activities. The model BMC is the carboxysome that encapsulates enzymes for CO2fixation to increase efficiency and is found in many autotrophic bacteria, such as cyanobacteria. Despite their importance in the global carbon cycle, little is known about how carboxysomes are spatially regulated. We recently identified the two-factor system required for the maintenance of carboxysome distribution (McdAB). McdA drives the equal spacing of carboxysomes via interactions with McdB, which associates with carboxysomes. McdA is a ParA/MinD ATPase, a protein family well-studied in positioning diverse cellular structures in bacteria. However, the adaptor proteins like McdB that connect these ATPases to their cargos are extremely diverse. In fact, McdB represents a completely unstudied class of proteins. Despite the diversity, many adaptor proteins undergo phase separation, but functional roles remain unclear. Here, we define the domain architecture of McdB from the model cyanobacteriumSynechococcus elongatusPCC 7942, and dissect its mode of biomolecular condensate formation. We identify an N-terminal intrinsically disordered region (IDR) that modulates condensate solubility, a central coiled-coil dimerizing domain that drives condensate formation, and a C-terminal domain that trimerizes McdB dimers and provides increased valency for condensate formation. We then identify critical basic residues in the IDR, which we mutate to fine-tune condensate solubility. Finally, we find that a condensate-defective mutant of McdB has altered association with carboxysomes and influences carboxysome enzyme content. The results have broad implications for understanding spatial organization of BMCs and the molecular grammar of protein condensates.
Control becomes habitual early on when learning a novel motor skill
Authors: Yang Christopher S. , Cowan Noah J. , Haith Adrian M. 
Published: April 2022

AbstractWhen people perform the same task repeatedly, their behavior becomes habitual, or inflexible to changes in the goals or structure of a task. While habits have been hypothesized to be a key aspect of motor skill acquisition, there has been little empirical work investigating the relationship between skills and habits. To better understand this relationship, we examined whether and when people’s behavior would become habitual as they learned a challenging new motor skill. After up to ten days of practice, we altered the structure of the task to assess whether participants would flexibly adjust their behavior or habitually persist in performing the task the way they originally learned. We found that participants’ behavior became habitual early in practice—after only two days—at which point they were still relatively unskilled. These data demonstrate that motor skills become habitual after relatively little training, but can nevertheless further improve with practice.
An essential host dietary fatty acid stimulates TcpH inhibition of TcpP proteolysis enabling virulence gene expression in Vibrio cholerae
Authors: Demey Lucas M. , Sinha Ritam , DiRita Victor J. 
Published: April 2022

AbstractVibrio cholerae is a Gram-negative gastrointestinal pathogen responsible for the diarrheal disease cholera. Expression of key virulence factors, cholera toxin and toxin-coregulated pilus, is regulated indirectly by two single-pass membrane-localized transcription regulators (MLTR), ToxR and TcpP, that promote expression of the transcription activator toxT. TcpP abundance and activity are controlled by TcpH, a single-pass transmembrane protein, which protects TcpP from a two-step proteolytic process known as regulated intramembrane proteolysis (RIP). The mechanism of TcpH mediated protection of TcpP represents a major gap in our understanding of V. cholerae pathogenesis. Absence of tcpH leads to unimpeded degradation of TcpP in vitro and a colonization defect in a neonate mouse model of V. cholerae colonization. Here, we show that TcpH protects TcpP from RIP via direct interaction. We also demonstrate that a dietary fatty acid, α-linolenic acid, promotes TcpH-dependent inhibition of RIP via co-association of TcpP and TcpH molecules within detergent-resistant membranes (DRMs; also known as lipid rafts) in a mechanism requiring the TcpH transmembrane domain. Taken together our data support a model where V. cholerae cells use exogenous α-linolenic acid to remodel the phospholipid bilayer in vivo, leading to co-association of TcpP and TcpH within DRMs where RIP of TcpP is inhibited by TcpH, thereby promoting V. cholerae pathogenicity.Significance StatementV. cholerae continues to pose a significant global burden on health infection millions of people every year resulting in ∼100,000 deaths annually. The importance of toxT gene expression in V. cholerae pathogenesis has been well established. Our results show that TcpP, one of the major regulators of toxT gene expression, is protected from proteolysis by TcpH, via direct interaction, in the presence of α-linolenic acid, an essential dietary fatty acid. Here we identify a physiological relevant host factor that stimulates V. cholerae pathogenicity via TcpH-dependent antagonism of TcpP proteolysis.
Impact of human factors in aircraft accident mitigation and aircraft maintenance training needs in post COVID-19 aviation
Authors: C.S. Karunakaran , J. Ashok Babu 
Published: April 2022

Purpose
The purpose of this study is to analyze the effect of human factor training in aircraft maintenance accident mitigation and aircraft safety in post COVID-19 aviation scenarios. The cause of aircraft accidents and details of three decades of selective aircraft maintenance accidents are analyzed to arrive to the significant aviation safety factor. The effect of COVID-19 pandemic and related technological applications to maintain high standards of safety and their applications in aircraft maintenance with respect to the view of human factors are discussed in details.

Design/methodology/approach
This paper details the overview of the human errors, error mitigation and need of human factor applications in aircraft maintenance industry for safe air travel. The criticality of aircraft maintenance in keeping aircraft in airworthy condition to provide safe air transportation without delay and to support airline economy is discussed in this study.

Findings
The cause of aircraft accidents and details of three decades of selective aircraft maintenance accidents are analyzed to arrive to the significant aviation safety factor. The effect of COVID-19 pandemic and related technological applications to maintain high standards of safety and their applications in aircraft maintenance with respect to the view of human factors are discussed in details. The route of error mitigation and need of high standard technological training with human factor knowledge, to aircraft maintenance students are analyzed in detail with the opportunity of percentages of error reduction.

Originality/value
This study bridges, gained knowledge for aircraft maintenance error mitigation, current accident rates and future training needs for safest air travel through high standard quality maintenance in aircraft and its systems.
A guiding model for developing construction training programmes focusing on productivity and performance improvement for different qualification levels
Authors: Manoharan Kesavan , Dissanayake Pujitha , Pathirana Chintha , Deegahawature Dharsana , Silva Renuka 
Published: April 2022

Purpose
The effectiveness of the construction industry highly depends on the quality of the work practices, education and training. Based on the industry’s need to strengthen the productivity and performance improvement scopes in the construction education/training practices, this study aims to develop a guiding tool for designing new training programmes in different qualification levels considering the industry’s near-future challenges.

Design/methodology/approach
The study methodology encompassed literature reviews, experts’ discussions/reviews and problem-based communication approaches with qualitative methods to obtain a set of expected competency outcomes (COs) for each qualification level. The necessary mapping frameworks were used to display the cross section of each CO.

Findings
The study has presented a guiding model comprising three categories of qualification levels, where each consists of 12 COs with the mapping outcomes against learning domains of a conceptual framework. The guiding model also displays the detailed steps to develop detailed curriculums for different qualification levels of training.

Research limitations/implications
Though the scope of the study was limited to the Sri Lankan context, the findings can be beneficial to many other countries in similar scenarios.

Practical implications
Overall study outcomes are expected to make an impact on the industry’s reskilling and upskilling practices resulting in a considerable level of improvement in the quality and productivity of work operations.

Originality/value
The experts’ reviews highlight the developed model as a valuable tool that provides a platform for upgrading the construction education and training practices based on the industry’s near-future circumstances in productivity and performance improvement practices, also revealing its future influences in training accreditation processes.
Causes of cost overruns in building construction projects in Asian countries; Iran as a case study
Authors: Amini Shima , Rezvani Alireza , Tabassi Mohsen , Malek Sadati Seyed Saeed 
Published: April 2022

PurposeCost overruns have been identified as the most significant challenge for construction sector stakeholders. Like many developing countries, the Iranian construction industry suffers from poor cost performance. So, the current research aims to investigate the causes of cost overrun in Iranian construction projects. This paper also reviews the findings of similar studies conducted in several Asian countries.Design/methodology/approachThis paper includes a literature review and a quantitative method with a questionnaire survey. The review is limited to the studies investigating the causes of cost overrun in an Asian country in the last decade. Moreover, the current research was conducted through a questionnaire prepared based on 43 common factors identified through the literature review. The required data were gathered from the representatives involved in handling construction activities in Iran. The collected data were analyzed based on relative importance index (RII), using the SPSS software package.FindingsThe results showed that poor site management, improper planning, fluctuation of prices of materials, lack of experience, and poor economic condition are the critical reasons for cost overrun in Iranian construction projects. The findings also indicated that among the studies conducted in Asian countries, the first three factors have the highest frequency.Originality/valueThis paper highlighted most studies concerning the cost overrun factors in construction projects in different Asian countries in recent years. Up-to-date knowledge helps to understand the complexity of this field in various periods and therefore minimizes the risk of cost overrun. This research can also be used as a benchmark for further studies to clarify similar issues in other developing countries.
Investigating the role of spatial configuration on visitors’ spatial cognition in health-care spaces: case studies in Gilan, Iran
Authors: Mehrinejad Khotbehsara Elham , Safari Hossein , Askarizad Reza , Somasundaraswaran Kathirgamalingam 
Published: April 2022

Purpose
This study aims to explore the impact of spatial configuration on behavioral patterns of visitors in the ground floor of health-care spaces.

Design/methodology/approach
In this study, the Space Syntax analysis was used to combine visibility graph analysis and axial line analysis with empirical observation of visitors’ activities. Two types of observation methods on visitors were conducted to discover the behavioral patterns of individuals, respectively, named “gate counts” and “people following.”

Findings
The outcomes of this research revealed that the spatial arrangements of pathways, public areas, vertical circulations, entrance space, lobby, emergency department, reception desk and pharmacy have a significant influence on the way that visitors perceive the health-care environment.

Research limitations/implications
The current research is limited to two aspects of effective wayfinding (configuration of health care and geometry). Future work can investigate the other potential factors coupled with the current factor as an integrated research for enhancing wayfinding and sustaining accessibility. Another limitation is that the observation results for this study had been conducted before the COVID-19 pandemic and future studies can compare these results with the current COVID-19 situation within health care environments.

Originality/value
A large amount of research has focused on the needs of populations in developed countries. This topic has not been investigated thoroughly by professionals in developing countries such as Iran. Accordingly, this study benefits environmental psychologists and architects by revealing the effective characteristics of legible spaces in health-care environments.