bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding priority ribosomes for future structural and pathogen research based upon global RNA and protein sequence analysis
Authors: Cooper Helena B. , Krause Kurt L. , Gardner Paul P. 
Published: June 2021

AbstractRibosome-targeting antibiotics comprise over half of antibiotics used in medicine, but our fundamental knowledge of their binding sites is derived primarily from ribosome structures from non-pathogenic species. These include Thermus thermophilus, Deinococcus radiodurans and Haloarcula marismortui, as well as commensal and pathogenic Escherichia coli. Advancements in electron cryomicroscopy have allowed for the determination of more ribosome structures from pathogenic bacteria, with each study highlighting species-specific differences that had not been observed in the non-pathogenic structures. These observed differences suggest that more novel ribosome structures, particularly from pathogens, are required for a more accurate understanding of the level of diversity of the entire bacterial ribosome, potentially leading to potential advancements in antibiotic research. In this study, high accuracy covariance and hidden Markov models were used to annotate ribosomal RNA and protein sequences respectively from genomic sequence, allowing us to determine the underlying ribosomal sequence diversity using phylogenetic methods. This analysis provided evidence that the current non-pathogenic ribosome structures are not sufficient representatives of some pathogenic bacteria, such as Campylobacter pylori, or of whole phyla such as Bacteroidetes.Significance StatementThe growing number of antibiotic resistance pathogenic bacteria are of critical concern to the health profession. Many of the current classes of antibiotics target the bacterial ribosome, the protein making factory for these species. However, much of our knowledge of the bacterial ribosome is based upon non-pathogenic bacteria that are highly divergent from the major pathogens of concern. We have analysed the genetic variation of the RNA and protein components of all available bacterial ribosomes. This has led us to identify the highest priority groups of bacteria that would benefit most from further analysis of their ribosome structures, from both a medical and evolutionary perspective.
Daily Patterns of Foraging and Aggressive Behaviors in Great-tailed Grackle (Quiscallus mexicanus) at an Urban Patch with Availability or Absence of Resources
Authors: Rodrigo Alejandro , Ávila-Chauvet Laurent , Buriticá Jonathan 
Published: June 2021

AbstractThe Great-tailed Grackle (Quiscalus mexicanus) seems to take advantage of inhospitable environments such as cities. However, it is not yet fully understood how these birds exploit hostile environments to their advantage. Casual observation seems to suggest that this species can obtain resources of biological importance such as food or nesting material from the trash. As a first approach to the problem, we located a patch outside a residential building, in a high-density urban area, where the residents left their trash for pick-up, and a group of wild Great-tailed grackles was identified as regular visitors. In total, 25 days were recorded at the site (November 2017 - January 2018). Events such as foraging, number of subjects present at the foraging site, aggressive behaviors between members of the group, and their relation with the presence or absence of the garbage collector truck were registered. The results show a higher number of grackles at the observation site and a higher frequency of foraging behaviors in the presence of garbage collection than in its absence. In its presence, the distribution of foraging during the day follows a normal distribution. In the absence, the distribution shows more variability towards the day. The highest frequency of interactions occurred between two grackles, yet there were records of up to eight subjects. The highest number of aggressions registered took place in the absence of garbage collection than in its presence. Moreover, the focal subject exhibits fewer agonistic behaviors compared to other members of the group, a result expected if the producer-scrounger game literature is considered. The outcome is explained in terms of deprivation and availability of resources. Finally, we conclude that grackles can exploit hazardous environments such as cities due to the highly social behaviors exhibited during foraging.
Sequencing uracil in DNA at single-nucleotide resolution
Authors: Jiang Liudan , Yin Jiayong , Qian Maoxiang , Rong Shaoqin , Chen Kejing , Zhao Chengchen , Tan Yuanqing , Guo Jiayin , Chen Hao , Gao Siyun , Liu Tingting , Liu Yi , Shen Bin , Yang Jian , Zhang Yong , Meng Fei-Long , Hu Jinchuan , Ma Honghui , Chen Yi-Han 
Published: June 2021

ABSTRACTAs an aberrant base in DNA, uracil is generated by dUMP misincorporation or cytosine deamination, and involved in multiple physiological and pathological processes. Current methods for whole-genome mapping of uracil all rely on uracil-DNA N-glycosylase (UNG) and are limited in resolution or specificity. Here, we present a UNG-independent Single-Nucleotide resolution Uracil Sequencing (SNU-seq) method utilizing the UdgX protein which specifically excises the uracil and forms a covalent bond with the resulting deoxyribose. SNU-seq was validated on synthetic DNA and applied to mammalian genomes. We found that the uracil content of pemetrexed-treated cells fluctuated along with DNA replication timing. We also accurately detected uracil introduced through cytosine deamination by the cytosine base editor (nCas9-APOBEC) and verified uracil occurrence in “WRC” motif within Activation-Induced Cytidine Deaminase (AID) hotspot regions in CSR-activated UNG−/− B cells.
The contribution of genetic and environmental effects to Bergmann’s rule and Allen’s rule in house mice
Authors: Ballinger Mallory A. , Nachman Michael W. 
Published: June 2021

AbstractDistinguishing between genetic, environmental, and genotype-by-environment effects is central to understanding geographic variation in phenotypic clines. Two of the best-documented phenotypic clines are Bergmann’s rule and Allen’s rule, which describe larger body sizes and shortened extremities in colder climates, respectively. Although numerous studies have found inter- and intraspecific evidence for both ecogeographic patterns, we still have a poor understanding of the extent to which these patterns are driven by genetics, environment, or both. Here, we measured the genetic and environmental contributions to Bergmann’s rule and Allen’s rule across introduced populations of house mice (Mus musculus domesticus) in the Americas. First, we documented clines for body mass, tail length, and ear length in natural populations, and found that these conform to both Bergmann’s rule and Allen’s rule. We then raised descendants of wild-caught mice in the lab and showed that these differences persisted in a common environment and are heritable, indicating that they have a genetic basis. Finally, using a full-sib design, we reared mice under warm and cold conditions. We found very little plasticity associated with body size, suggesting that Bergmann’s rule has been shaped by strong directional selection in house mice. However, extremities showed considerable plasticity, as both tails and ears grew shorter in cold environments. These results indicate that adaptive phenotypic plasticity as well as genetic changes underlie major patterns of clinal variation in house mice and likely facilitated their rapid expansion into new environments across the Americas.
Iron-dependent mutualism between Chlorella sorokiniana and Ralstonia pickettii forms the basis for a sustainable bioremediation system
Authors: Rawat Deepak , Sharma Udita , Poria Pankaj , Finlan Arran , Parker Brenda , Sharma Radhey Shyam , Mishra Vandana 
Published: June 2021

AbstractMutualism between microalgae and bacteria is ubiquitous, but remains underexplored as a basis for biodegradation of anthropogenic pollutants. In industrial systems, poor iron uptake by microalgae limits growth, bioprocessing efficacy, and bioremediation potential. Iron supplementation is costly and ineffective because iron remains insoluble in aqueous medium and biologically unavailable. In aquatic environments, microalgae develop an association with bacteria that solubilize iron by production of siderophore, which increases the bioavailability of iron as a public good. Algae, in exchange, provides dissolved organic matter to bacteria to sustain such interkingdom associations. Therefore, using a case study of azo dye degradation, we combine environmental isolations and synthetic ecology as a workflow, establishing a microbial community to degrade industrially relevant Acid Black 1 dye. We create a mutualism between previously non-associated chlorophyte alga Chlorella sorokiniana and siderophore-producing bacterium Ralstonia pickettii, based on the eco-evolutionary principle of exchange of iron and carbon. This siderophore-mediated increased iron bioavailability increases reductive iron uptake, growth rate, and azoreductase-mediated dye degradation of microalga. In exchange, C. sorokiniana produces galactose, glucose, and mannose as major extracellular monosaccharides, supporting bacterial growth. We propose a mechanism whereby extracellular ferrireductase is crucial for azoreductase-mediated dye degradation in microalgae. Our work demonstrates that bioavailability of iron, which is often overlooked in industrial bio-designs, governs microalgal growth and enzymatic processes. Our results suggest that algal-bacterial consortia based on the active association are a self-sustainable mechanism to overcome existing challenges of micronutrient availability in bioremediation systems and their industrial translation.
Stem cell therapy for skin regeneration using mesenchymal stem cells derived from the progeroid Werner syndrome-specific iPS cells
Authors: Funayama Shinichiro , Kato Hisaya , Kaneko Hiyori , Kosaka Kentaro , Sawada Daisuke , Takada-Watanabe Aki , Minamizuka Takuya , Baba Yusuke , Koshizaka Masaya , Shimamoto Akira , Ouchi Yasuo , Iwama Atsushi , Endo Yusuke , Takayama Naoya , Eto Koji , Maezawa Yoshiro , Yokote Koutaro 
Published: June 2021

AbstractAdult progeria, Werner syndrome (WS), is an autosomal recessive disorder that develops accelerated aging-associated symptoms after puberty. Refractory skin ulcer of limbs, which is one of the symptoms specific to WS, is seriously painful and sometimes results in amputation. In recent years, cell therapy using mesenchymal stem cells (MSCs) has been attracting attention; however, the effect of WS-derived MSCs on skin ulcers is still unclear. In this study, we generated iPS cells from a patient with WS and a normal subject, differentiated them into MSCs (WS- and NM-iMSC, respectively), and performed cell therapy to a refractory skin ulcer mouse model. As a result, WS-iMSC recapitulated premature senescence phenotypes in vitro. Upon subcutaneous injection around the wounds of mice, WS-iMSC was significantly inferior in wound healing effect compared to NM-iMSC. Proteome and transcriptome analysis revealed altered expression of genes related to angiogenesis, inflammation, and proliferation in WS-iMSC with remarkable downregulation of VEGF, a potent angiogenic factor. In addition, simultaneous administration of recombinant human VEGF and WS-iMSC improved the wound healing effect in vivo. These results indicate that the expression of angiogenic factors is reduced in WS-iMSC, and its supplementation restores the wound healing ability. This finding may pave the way to develop the treatment of intractable skin ulcers of WS.
Predicting drug targets by homology modelling of Pseudomonas aeruginosa proteins of unknown function
Authors: Babic Nikolina , Kovacic Filip 
Published: June 2021

AbstractEfficacies of antibiotics to treat bacterial infections rapidly decline due to antibiotic resistance. This stimulated the development of novel antibiotics, but most attempts failed. As a response, the idea of mining uncharacterised genes of pathogens to identify potential targets for entirely new classes of antibiotics raised. Without knowing the biochemical function of a protein it is difficult to validate its potential for drug targeting; therefore progress in the functional characterisation of bacterial proteins of an unknown function must be accelerated. Here we present a paradigm for comprehensively predicting biochemical functions of a large set of proteins encoded by hypothetical genes in human pathogens, to identify candidate drug targets. A high-throughput approach based on homology modelling with ten templates per target protein was applied on the set of 2103 P. aeruginosa proteins encoded by hypothetical genes. Obtained >21000 homology modelling results and available biological and biochemical information about several thousand templates was scrutinised to predict the function of reliably modelled proteins of unknown function. This approach resulted in assigning, one or often multiple, putative functions to hundreds of enzymes, ligand-binding proteins and transporters. New biochemical functions were predicted for 41 proteins whose essential or virulence-related roles in P. aeruginosa were already experimentally demonstrated. Eleven of them were shortlisted as promising drug targets which participate in essential pathways (maintaining genome and cell wall integrity), virulence-related processes (adhesion, cell motility, host recognition) or antibiotic resistance, which are general drug targets. These proteins are conserved among other WHO priority pathogens but not in humans, therefore they represent high-potential targets for pre-clinical studies. These and many more biochemical functions assigned to uncharacterised proteins of P. aeruginosa, available as PaPUF database may guide the design of experimental screening of inhibitors which is a crucial step toward validation of the most potential targets for the development of novel drugs against P. aeruginosa and other high-priority pathogens.
The Fusarium graminearum transporters Abc1 and Abc6 are important for xenobiotic resistance, trichothecene accumulation, and virulence to wheat
Authors: O’Mara Sean P. , Broz Karen , Dong Yanhong , Kistler H. Corby 
Published: June 2021

AbstractThe plant pathogenic fungus Fusarium graminearum is the causal agent of Fusarium Head Blight (FHB) disease on small grain cereals. F. graminearum produces trichothecene mycotoxins such as deoxynivalenol (DON) that are required for full virulence. DON must be exported outside the cell to cause FHB disease, a process that may require the involvement of membrane-bound transporters. In this study we how the deletion of membrane-bound transporters results in reduced DON accumulation as well as reduced FHB symptoms on wheat. Deletion of the ATP-Binding Cassette (ABC) transporter Abc1 results in the most severe reduction in DON accumulation and virulence. Deletion of another ABC transporter, Abc6, also reduces FHB symptoms to a lesser degree. Combining deletions fails to reduce DON accumulation or virulence in an additive fashion, even when including an Δabc1 deletion. Heterologous expression of F. graminearum transporters in a DON-sensitive strain of yeast confirms Abc1 as a major DON resistance mechanism. Yeast expression further indicates that multiple transporters, including Abc1 play an important role in resistance to the wheat phytoalexin 2-benzoxazolinone (BOA) and other xenobiotics. Thus, Abc1 may contribute to wheat virulence both by allowing export of DON and by providing resistance to the wheat phytoalexin BOA. This research provides useful information which may aid in designing novel management techniques of FHB or other destructive plant diseases.
Graduate certificate in local development planning, land use management and disaster risk management: a knowledge, attitude and practice (KAP) evaluation
Authors: Sarmiento Juan Pablo , Sarmiento Catalina , Hoberman Gabriela , Chabba Meenakshi 
Published: June 2021

PurposeThis study aims to assess knowledge retention of the graduates of the online graduate certificate on local development planning, land use management and disaster risk management (PDLOTGR, the abbreviation of the certificate's Spanish title). The certificate was offered to practitioners and faculty members of Latin American countries since 2016.Design/methodology/approachThe authors reviewed the knowledge, attitude and practice (KAP) method to develop a specific approach, which included the preparation of a KAP survey, a composite KAP index and three sub-indices. The survey targeted two groups: (1) experimental group, composed of the certificate's 76 graduates, and (2) control group, comprised of 25 certificate's candidates, who had not yet undergone the training/intervention. The statistical analysis included a one-way multivariate analysis of variance to compare the mean scores on the KAP index and sub-indices for individuals in the experimental and control groups.FindingsThe study results showed significant differences in the knowledge sub-index between those who had completed the PDLOTGR training and those who had not, while the attitudes and practices sub-indices did not show significant differences. When using the KAP index, a statistically significant difference was also observed between the two groups.Originality/valuePerceived knowledge assessment offers an acceptable and non-intimidating option for evaluating continuing education and professional development programs associated to disaster risk. It is particularly helpful in determining whether an intervention or program has a lasting impact. It is not, however, a substitute for direct knowledge assessment, and the use of other methods to evaluate the performance of a capacity building program's graduates.
A comparative analysis on digital libraries and academic search engines from the dual-route perspective
Authors: Cao Fenfang , Zhang Jinchao , Zha Xianjin , Liu Kunfeng , Yang Haijuan 
Published: June 2021

Purpose
Digital libraries and academic search engines have developed as two important online scholarly information sources with different features. The purpose of this study is to compare digital libraries and academic search engines from the perspective of the dual-route model.

Design/methodology/approach
Research hypotheses were developed. Potential participants were recruited to answer an online survey distributing at Chinese social media out of which 251 responses were deemed to be valid and used for data analysis. The paired samples t-test was used to compare the means.

Findings
Both information quality (central route) and source credibility (peripheral route) of digital libraries are significantly higher than those of academic search engines, while there is no significant difference between digital libraries and academic search engines in terms of affinity (peripheral route).

Practical implications
In the digital information society, the important status of digital libraries as conventional information sources should be spread by necessary measures. Academic search engines can act as complementary online information sources for seeking academic information rather than the substitute for digital libraries. Practitioners of digital libraries should value the complementary role of academic search engines and encourage users to use academic search engines while emphasizing the importance of digital libraries as conventional information sources.

Originality/value
According to the dual-route model, this study compares digital libraries and academic search engines in terms of information quality, source credibility and affinity, which the authors believe presents a new lens for digital libraries research and practice alike.
Invisibility not invincibility: Pakistani women and the lack of career ascendance
Authors: Waqar Shaista , Hanif Rubina , Loh Jennifer 
Published: June 2021

PurposeThe purpose of this paper is to investigate the role of gender in the relationships between employee’s work experience and their chances of obtaining a job promotion.Design/methodology/approachFive hundred middle to lower management Pakistan employees from service industries were surveyed. Measures used to obtain data included work experience, job promotions and gender. Gender was dummy coded. Moderation analyses via SPSS was used to investigate the moderating effect of gender in the relationship between employee’s work experience and job promotions.FindingsThe results indicated that work experience was positively associated with job promotion. However, the results indicated that gender fully moderated the relationship between work experience and job promotion. Specifically, female employees were less likely to get promoted compared to male employees despite having similar work experiences.Research limitations/implicationsDrawing together the human capital theory, social role theory and cultural factors, this study highlighted the socioeconomic/cultural barriers’ impact on Pakistani women’s career ascendance.Practical implicationsThere is a lack of empirical evidence about career ascendance among Pakistani women. Therefore, the aim of the present study is to conduct and provide empirical evidence so that relevant agencies within Pakistan can develop more gender-equitable promotional policies and processes.Originality/valueThis study responded to the call for more empirical investigation of career ascendancy among women in developing countries. While this issue has been discussed in many developed western countries, there is a lack of empirical evidence in Muslim Pakistan.
Intrinsic factors affecting online impulsive shopping during the COVID-19 in emerging markets
Authors: Lavuri Rambabu 
Published: June 2021

PurposeIn an emerging market, understanding shoppers' behavior in an online market is essential to developing online retail strategies. This research study examines the effects of intrinsic factors, namely, perceived utilitarian, hedonic value, materialism, fashion interest and enjoyment, on impulsive online shopping with mediating role of trust and online shopping attitude in the Indian emerging market.Design/methodology/approachData are collected from 443 Indian respondents, using purposive and snowball sampling. The data were analyzed using the IBM Statistical Product and Service Solutions (SPSS) and Analysis of Moment Structures (AMOS) package using structural equation modeling.FindingsThe results showed that perceived utilitarian, hedonic value, materialism and enjoyment factors significantly impacted perceived trust and online shopping attitude, but fashion interest had no effect. Mediating factors positively impacted impulsive online shopping and showed a significant association between intrinsic factors and impulsive online shopping.Research limitations/implicationsThe geographical area of study was limited to only India. Consequently, the findings and conclusions of the study had their limits. The research used the information continuum with a purposive and snowball approach that does not necessarily generalize the findings of the analysis. This work looked at factors stimulating the impulsive online shopping pattern of Indian shoppers in an emerging market.Practical implicationsThis research would help e-retailers develop new strategies and plans to increase sales volume and create strong relationships with online customers by providing trustworthiness and security in buying practices.Social implicationsThis study helps to understand the consumer impulsive buying during coronavirus disease 2019 (COVID-19), and it helps e-retailers to adopt a new online store to draw the attention of the consumers and enhance their online sales.Originality/valueIn this COVID-19 situation, this study explores the inherent factors influencing impulsive online shopping in the emerging Indian market. As a result, it contributes to visual identity literature by expanding the field of impulsive online shopping behavior.