bluuebunny/crossref_metadata_2025_split huggingface dataset:
Black-necked spitting cobra (Naja nigricollis) phospholipases A2 cause Trypanosoma brucei death by blocking endocytosis through the flagellar pocket
Authors: Martos-Esteban Andrea , Macleod Olivia J. S. , Maudlin Isabella , Kalogeropoulos Konstantinos , Jürgensen Jonas A. , Carrington Mark , Laustsen Andreas H. 
Published: November 2021

AbstractAfrican trypanosomes, such as Trypanosoma brucei, are flagellated protozoa which proliferate in mammals and cause a variety of diseases in people and animals. In a mammalian host, the external face of the African trypanosome plasma membrane is covered by a densely packed coat formed of variant surface glycoprotein (VSG), which counteracts the host adaptive immune response by antigenic variation. The VSG is attached to the external face of the plasma membrane by covalent attachment of the C-terminus to a glycosylphosphatidylinositol. As the trypanosome grows, newly synthesised VSG is added to the plasma membrane by vesicle fusion to the flagellar pocket, the sole location of exo- and endocytosis. Snake venoms contain dozens of components including proteases and phospholipases. Here, we investigated the effect of Naja nigricollis on T. brucei with the aim of describing the response of the trypanosome to hydrolytic attack on the VSG. We found no evidence for VGS hydrolysis however N. nigricollis venom caused: (i) an enlargement of the flagellar pocket, (ii) the Rab11 positive endosomal compartments to adopt an abnormal dispersed localisation, and (iii) a cell cycle arrest prior to cytokinesis. A single protein family, the phospholipases A2s present in N. nigricollis venom, was necessary and sufficient for the effects. This study provides new molecular insight into T. brucei biology and possibly describes mechanisms that could be exploited for T. brucei targeting.
Maize root-associated microbes likely under adaptive selection by the host to enhance phenotypic performance
Authors: Meier Michael A. , Xu Gen , Lopez-Guerrero Martha G. , Li Guangyong , Smith Christine , Sigmon Brandi , Herr Joshua R. , Alfano James R. , Ge Yufeng , Schnable James C. , Yang Jinliang 
Published: November 2021

AbstractThe root-associated microbiome (rhizobiome) plays a non-negligible role in determining plant health, stress tolerance, and nutrient use efficiency. However, it remains unclear to what extent the composition of the rhizobiome is governed by intraspecific variation in host plant genetics in the field and the degree to which host plant selection can reshape the composition of the rhizobiome. Here we quantify the rhizosphere microbial communities associated with a replicated diversity panel of 230 maize (Zea mays L.) genotypes grown in agronomically relevant conditions under high N (+N) and low N (-N) treatments. We show that the abundance of many root-associated microbes within a functional core microbial community of 150 abundant and consistently reproducible microbial groups is explainable by natural genetic variation in the host plant, with a greater proportion of microbial variance attributable to plant genetic variation in low N conditions. Population genetic approaches identify signatures of purifying selection in the maize genome associated with the abundance of several groups of microbes in the maize rhizobiome. Genome-wide association studies conducted using rhizobiome phenotypes identified n = 467 microbe-associated plant loci (MAPLs) in the maize genome linked to variation in the abundance of n = 115 microbial groups in the maize rhizosphere. In 62/115 cases, which is more than expected by chance, the abundance of these same microbial groups was correlated with variation in plant vigor indicators derived from high throughput phenotyping of the same field experiment. This study provides insights into harnessing the full potential of root-associated microbial symbionts in maize production.
Development of a novel bioluminescent activity assay for peptide ligases
Authors: Zhang Cong-Hui , Shao Xiao-Xia , Wang Xin-Bo , Shou Li-Li , Liu Ya-Li , Xu Zeng-Guang , Guo Zhan-Yun 
Published: November 2021

ABSTRACTIn recent years, some peptide ligases have been identified, such as bacterial sortases and certain plant asparaginyl or prolyl endopeptidases. Peptide ligases have wide applications in protein labeling and cyclic peptide synthesis. To characterize known peptide ligases or identify new ones, we propose a novel bioluminescent activity assay via the genetic fusion of a recognition motif of a peptide ligase to the C-terminus of an inactive large NanoLuc fragment (LgBiT) and the chemical introduction of a nucleophilic motif preferred by the peptide ligase to the N-terminus of the low-affinity SmBiT complementation tag. When the inactive ligation version LgBiT protein was ligated with the low-affinity ligation version SmBiT tag by the expected peptide ligase, its luciferase activity would be restored and could be quantified sensitively according to the measured bioluminescence. In the present study, we first validated the novel bioluminescent activity assay using bacterial sortase A and plant butelase-1. Subsequently, we screened novel peptide ligases from crude extracts of selected plants using two LgBiT–SmBiT ligation pairs. Among 80 common higher plants, we identified that five of them likely express asparaginyl endopeptidase-type peptide ligase and four of them likely express prolyl endopeptidase-type peptide ligase, suggesting that peptide ligases are not so rare in higher plants and more of them await discovery. The novel bioluminescent activity assay is ultrasensitive, convenient for use, and resistant to protease interference, and thus would have wide applications for characterizing known peptide ligases or screening new ones from various sources in future studies.
The expression of essential selenoproteins during zebrafish development requires SECIS binding protein 2-like
Authors: Kiledjian Nora T. , Shah Rushvi , Vetick Michael B. , Copeland Paul R. 
Published: November 2021

AbstractThe dietary requirement for selenium is based on its incorporation into selenoproteins, which contain the amino acid selenocysteine (Sec). The Sec insertion sequence (SECIS) is an RNA structure found in the 3’ UTR of all selenoprotein mRNAs, and it is required to convert in-frame UGA codons from termination to Sec-incorporating codons. There are two proteins that bind to SECIS elements, but only one, SECIS binding protein 2 (Sbp2), has been shown to be required for Sec incorporation. The Sbp2 paralogue, SECIS binding protein 2-like (Secisbp2l) is conserved in all vertebrates and shares many features with Sbp2, but its function is unknown. Here we set out to determine the relative roles of Sbp2 and Secisbp2l by introducing CRISPR mutations in both genes in zebrafish. By monitoring selenoprotein synthesis with 75Se labeling during embryogenesis, we found that sbp2-/- embryos still make a select subset of selenoproteins but secisbp2l-/- embryos retain the full complement. Abrogation of both genes completely prevents selenoprotein synthesis and juveniles die at 14 days post fertilization. Embryos lacking Sbp2 are sensitive to oxidative stress and express the stress marker vtg1. We propose a model where Secisbp2l is required to promote essential selenoprotein synthesis during stress.
Oligomerization state of the functional bacterial twin arginine translocation (Tat) receptor complex
Authors: Sharma Ankith , Chowdhury Rajdeep , Musser Siegfried M. 
Published: November 2021

ABSTRACTThe twin-arginine translocation (Tat) system transports folded proteins across bacterial and plastid energy transducing membranes. Ion leaks are generally considered to be mitigated by the creation and destruction of the translocation conduit in a cargodependent manner, a mechanism that enables tight sealing around a wide range of cargo shapes and sizes. In contrast to the variable stoichiometry of the active translocon, the oligomerization state of the receptor complex is considered more consistently stable, but has proved stubbornly difficult to establish. Here, using a single molecule photobleaching analysis of individual inverted membrane vesicles, we demonstrate that Tat receptor complexes are tetrameric in native membranes with respect to both TatB and TatC. This establishes a maximal diameter for a resting state closed pore. A large percentage of Tat-deficient vesicles explains the typical low transport efficiencies observed. This individual reaction chamber approach will facilitate examination of the effects of stochastically distributed molecules.
E-cigarette aerosol exacerbates cardiovascular oxidative stress in mice with an inactive aldehyde dehydrogenase 2 enzyme
Authors: Yu Xuan , Zeng Xiaocong , Xiao Feng , Chen Ri , Sinharoy Pritam , Gross Eric R. 
Published: November 2021

ABSTRACTAimsE-cigarette aerosol containing aldehydes, including acetaldehyde, are metabolized by the enzyme aldehyde dehydrogenase 2 (ALDH2). However, little is known how aldehyde exposure from e-cigarettes, when coupled with an inactivating ALDH2 genetic variant, ALDH2*2 (present in 8% of the world population), affects cardiovascular oxidative stress. The aim of this study was to determine how e-cigarette aerosol exposure, when coupled with genetics, impacts cardiovascular oxidative stress in wild type ALDH2 and ALDH2*2 knock-in mice.Methods and ResultsUsing selective ion flow mass spectrometry, we determined that e-cigarette aerosol contains acetaldehyde that are 10-fold higher than formaldehyde or acrolein. Next, using wild type ALDH2 and ALDH2*2 knock-in rodents, we identified organ-specific differences in ALDH2 with the heart having ~1.5-fold less ALDH2 enzyme activity relative to the liver and lung. In isolated cardiac myocytes, acetaldehyde exposure (30 seconds, 0.1-1 μM) caused a 4-fold greater peak in calcium levels for ALDH2*2 relative to ALDH2 cardiomyocytes. ALDH2*2 cardiomyocytes exposed to acetaldehyde also demonstrated a 2-fold increase in ROS production and 2.5-fold increase in 4HNE protein adducts relative to ALDH2 cardiomyocytes. For intact rodents, ALDH2*2 knock-in mice exposed to e-cigarette aerosol had an increased heart rate beginning 5 days after exposure compared to wild type ALDH2 mice (775±30 bpm versus 679±33 bpm, respectively, *p<0.01, n=7-8/group). E-cigarette aerosol exposure also exacerbated oxidative stress in ALDH2*2 heart homogenates, including a 1.3-fold higher protein carbonyl level, a 1.7-fold higher lipid peroxide level and 1.5-fold greater phosphorylation of NF-κB relative to wild type ALDH2 homogenates.ConclusionsThe increased oxidative stress from e-cigarette aerosol aldehydes triggers the proinflammatory NF-κB pathway. As ALDH2 expression and activity is lower in the heart relative to the lung, the heart could be more susceptible to increases in cardiovascular oxidative stress from e-cigarette aerosol; particularly for those carrying an ALDH2*2 genetic variant which limits acetaldehyde metabolism.Graphical AbstractE-cigarette aerosol exposure triggers increases in ROS that lead to increased protein carbonylation, MDA production, and elevates phosphorylated NF-kB. This exposure to e-cigarette aerosol leads to increases in cardiovascular oxidative stress. For the ALDH2*2 variant, there is limited ability to metabolize the reactive aldehydes from e-cigarette aerosol and with increased levels of oxidative stress at baseline relative to wild type ALDH2, e-cigarette aerosol increased oxidative stress, protein carbonylation, and phosphorylation of NF-kB relative to wild type ALDH2 rodents.
Core circadian clock and light signaling genes brought into genetic linkage across the green lineage
Authors: Michael Todd P. 
Published: November 2021

AbstractThe circadian clock ensures that biological processes are phased to the correct time of day. In plants the circadian clock is conserved at both the level of transcriptional networks as well as core genes. In the model plantArabidopsis thaliana,the core circadiansingleMYB(sMYB) genesCCA1andRVE4are in genetic linkage with thePSEUDO-RESPONSE REGULATOR(PRR) genesPRR9andPRR7respectively. Leveraging chromosome-resolved plant genomes and syntenic ortholog analysis it was possible to trace this genetic linkage back to the basal angiospermAmborellaand identify an additional evolutionarily conserved genetic linkage betweenPIF3andPHYA. TheLHY/CCA1-PRR5/9, RVE4/8-PRR3/7andPIF3-PHYAgenetic linkages emerged in the bryophyte lineage and progressively moved within several genes of each other across an array of higher plant families representing distinct whole genome duplication and fractionation events. Soybean maintains all but two genetic linkages, and expression analysis revealed thePIF3-PHYAlinkage overlapping with the E4 maturity group locus was the only pair to robustly cycle with an evening phase in contrast to thesMYB-PRRmorning and midday phase. While most monocots maintain the genetic linkages, they have been lost in the economically important grasses (Poaceae) such as maize where the genes have been fractionated to separate chromosomes and presence/absence variation results in the segregation ofPRR7paralogs across heterotic groups. The evolutionary conservation of the genetic linkage as well as its loss in the grasses provides new insight in the plant circadian clock, which has been a critical target of breeding and domestication.Summary SentenceThe genetic linkage of the core circadian clock components has evolutionary origins in bryophytes and sheds light on the current functioning and selection on the circadian clock in crops.
Logistic planning for pharmaceutical supply chain using multi-objective optimization model
Authors: Ershadi Mohammad Mahdi , Ershadi Mohamad Sajad 
Published: November 2021

Purpose
Appropriate logistic planning for the pharmaceutical supply chain can significantly improve many financial and performance aspects. To this aim, a multi-objective optimization model is proposed in this paper that considers different types of pharmaceuticals, different vehicles with determining capacities and multi-period logistic planning. This model can be updated based on new information about resources and newly identified requests.

Design/methodology/approach
The main objective function of the proposed model in this paper is minimizing the unsatisfied prioritized requests for pharmaceuticals in the network. Besides, the total transportation activities of different types of vehicles and related costs are considered as other objectives. Therefore, these objectives are optimized hierarchically in the proposed model using the Lexicographic method. This method finds the best value for the first objective function. Then, it tries to optimize the second objective function while maintaining the optimality of the first objective function. The third objective function is optimized based on the optimality of other objective functions, as well. A non-dominated sorting genetic algorithm II-multi-objective particle swarm optimization heuristic method is designed for this aim.

Findings
The performances of the proposed model were analyzed in different cases and its results for different problems were shown within the framework of a case study. Besides, the sensitivity analysis of results shows the logical behavior of the proposed model against various factors.

Practical implications
The proposed methodology can be applied to find the best logistic plan in real situations.

Originality/value
In this paper, the authors have tried to use a multi-objective optimization model to guide and correct the pharmaceutical supply chain to deal with the related requests. This is important because it can help managers to improve their plans.
Financial crime in the decentralized finance ecosystem: new challenges for compliance
Authors: Wronka Christoph 
Published: November 2021

Purpose
As decentralized finance (DeFi) has collected substantial promotion, investment and cryptographic development as a new model for numerous financial operations over the last months. As DeFi models and technology are quite unique, authorities have not been engaged much yet. However, these non-regulated financial markets will be overlooked for no long by the regulators. Therefore, the purpose of this paper is to analyse and evaluate the new challenges for financial crime compliance which need to be tackled very soon.

Design/methodology/approach
The research relied on secondary sources of data, using secondary research to collect archival data in the form of documents. Content and thematic analyses were used to synthesize the collected data

Findings
DeFi is considered to be one of the major steps towards adopting crypto masses. It is expected that DeFi will play a significant role in future and provide the present banking system with a feasible alternative. Therefore, it is crucial that the DeFi industry must address the main risks to ensure its “user” full compliance.

Originality/value
This research is the first to analyse the emerging challenges of fighting financial crime in the DeFi ecosystem.
Understanding the leaky pipeline system: behavioural ecological approach to the social marketing of women thriving in STEM careers
Authors: Çelik Hafize , Watson Forrest 
Published: November 2021

Purpose
This paper aims to explore the complexity of the “leaky pipeline” of women in science, technology, engineering and maths (STEM) in the intriguing contexts where there are a high number of STEM graduates but a low number of women working in these fields.

Design/methodology/approach
The authors conducted in-depth interviews with eight STEM “leavers” and eight “persisters” in Turkey to understand the multi-level influences on their career paths.

Findings
The behavioural ecological model is applied to enrich the understanding of women’s attrition from STEM. The authors found a complex system of actors, relationships and influences that impact the negotiations of women’s felt misfit/love of their STEM career and changing self-actualisation.

Practical implications
The authors highlight that social marketers should consider the complex influences on even the most individualistic-looking decisions to produce systemic change.

Originality/value
This paper deepens the use of the behavioural ecological model in the ways that the layers of motivator and demotivator influences interact with women’s internal negotiations of career choice. The paper integrates classic theories (self-actualisation (Maslow, 1943) and two-factor model (Herzberg et al., 1959)) within systems social marketing.
Will the revisions to GRI 303 improve corporate water reporting? The challenges of defining and operationalising “water stress”
Authors: Hewawithana Dushyanthi , Hazelton James , Walkerden Greg , Tello Edward 
Published: November 2021

Purpose
This paper aims to examine whether the disclosure obligations in areas of water stress required under the revised Global Reporting Initiative standard (GRI) 303 Water and Effluents, 2018 will improve the quality of corporate water reporting. As a key new requirement is to disclose the impact of water withdrawals from (and discharges to) areas experiencing water stress, the authors examine the ambiguity of the term “water stress” and the extent to which following the GRI’s guidance to use the Aqueduct Water Risk Atlas and/or the Water Risk Filter will enable quality corporate water reporting.

Design/methodology/approach
The study is informed by the notion of public interest reporting, on the basis that the provision of contextual water information is in the public interest. To explore the ambiguity of the term “water stress”, the authors conduct a semi-systematic review of hydrology literature on water stress and water stress indices. To explore the efficacy of using the Aqueduct Water Risk Atlas and/or the Water Risk Filter, the authors review the operation and underlying data sources of both databases.

Findings
The term “water stress” has a range of definitions and the indicators of water stress encompass a wide variety of differing factors. The Aqueduct Water Risk Atlas and the Water Risk Filter use a combination of different risk indicators and are based on source data of varying quality and granularity. Further, different weightings of water risk information are available to the user, which yield different evaluations of water stress. A variety of approaches are permitted under GRI 303.

Practical implications
Effective implementation of GRI 303 may be impeded by the ambiguity of the term “water stress”, varying quality and availability of the water stress information and the fact that different water stress calculation options are offered by the water databases. The authors suggest that the GRI closely monitor compliance, implementation approaches and scientific developments in relation to the water stress requirements with a view to providing further guidance and improving future iterations of the standard.

Originality/value
Whilst there have been many calls for improved contextual water reporting, few previous studies have explored the challenges to implementing reporting requirements related to the determination of “water stress”.
Developing rightly culture on TQM - evidence from SMEs in the context of emerging economy
Authors: Gorondutse Abdullahi Hassan , Ali Gamal Abdualmajed , Hilman Haim 
Published: November 2021

Purpose
Total quality management (TQM) must include orientation towards quality awareness in the overall organisational processes in a firm. A successful TQM needs a supportive culture that can adapt to alterations and strengthen innovation. This study aims to confirm the association between the style of management known as organisational culture (OC) and TQM practices in manufacturing Small and Medium Enterprises (SMEs).

Design/methodology/approach
Data-driven research was drawn from self-assessment inquiries among 772 managers/owners of manufacturing SMEs of the Saudi Arabia Kingdom (KSA). The dominant culture was detected by means of a cross-sectional technique.

Findings
The findings enrich the literature by revealing a positive effect of OC on TQM execution in the manufacturing SMEs of KSA.

Research limitations/implications
Prior to the execution of TQM operations, administrators of manufacturing SMEs should be aware of the culture within organisations so that TQM may be implemented.

Practical implications
The study suggests that organisations, particularly manufacturing SMEs, should constantly strive to enhance the TQM culture.

Social implications
Amid intense competition among manufacturing SMEs, it is crucial to guarantee their high performance. This research assists society in evaluating the strength of a particular SME sector and further enables it to assess which SMEs really have a good OC–TQM relation.

Originality/value
The paper creates and presents various platforms of the OC and TQM as a unified body of knowledge.