bluuebunny/crossref_metadata_2025_split huggingface dataset:
Horizontal gene transfer and CRISPR targeting drive phage-bacterial host interactions and coevolution in pink berry marine microbial aggregates
Authors: Kosmopoulos James C. , Campbell Danielle E. , Whitaker Rachel J. , Wilbanks Elizabeth G. 
Published: February 2023

ABSTRACTBacteriophages (phages), viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. The study of phage-host interactions, however, is made difficult by a paucity of model systems from natural environments and known and cultivable phage-host pairs. Here, we investigate phage-host interactions in the ”pink berry” consortia, naturally-occurring, low-diversity, macroscopic aggregates of bacteria found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPR), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect the known pink berry symbiontsDesulfofustissp. PB-SRB1,Thiohalocapsasp. PB-PSB1, andRhodobacteraceaesp. A2, and belong to entirely novel viral taxa, except for one genome which represents the second member of theKnuthellervirusgenus. We further observed increased nucleotide variation over a region of a conserved phage capsid gene that is commonly targeted by host CRISPR systems, suggesting that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary, emphasizing the role of phages in bacterial evolution in pink berries. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages, and provide evidence for phage-host co-evolution via multiple mechanisms in a natural microbial system.IMPORTANCEPhages (viruses that infect bacteria) are important components of all microbial systems, where they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and co-evolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms are CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate bacteria and phage populations from a simple marine microbial community known as “pink berries” found in salt marshes of Falmouth, Massachusetts, as a model of phage-host co-evolution. We identify eight novel phages, and characterize a case of putative CRISPR-driven phage evolution and an instance of HGT between phage and host, together suggesting that phages have large evolutionary impacts in a naturally-occuring microbial community.
Non-destructive DNA metabarcoding of arthropods using collection medium from passive traps
Authors: Sire Lucas , Schmidt Yáñez Paul , Bézier Annie , Courtial Béatrice , Mbedi Susan , Sparmann Sarah , Larrieu Laurent , Rougerie Rodolphe , Bouget Christophe , Monaghan Michael T. , Herniou Elisabeth A. , Lopez-Vaamonde Carlos 
Published: February 2023

AbstractBackgroundBroad-scale monitoring of arthropods is often carried out with passive traps (e.g. Malaise traps) that can collect thousands of specimens per sample. The identification of individual specimens requires time and taxonomic expertise, limiting the geographical and temporal scale of research and monitoring studies. DNA metabarcoding of bulk-sample homogenates is faster and has been found to be efficient and reliable, but is destructive and prevents a posteriori validation of species occurrences and/or relative abundances. Non-destructive DNA metabarcoding from the collection medium has been applied in a limited number of studies, but further tests of efficiency are required in a broader range of circumstances to assess the consistency of the method.MethodsWe quantified the detection rate of arthropod species when applying non-destructive DNA metabarcoding with a short (127-bp) fragment of mitochondrial COI on two types of passive traps and collection media: 1) water with monopropylene glycol (H2O–MPG) used in window-flight traps (WFT, 53 in total); 2) ethanol with monopropylene glycol (EtOH–MPG) used in Malaise traps (MT, 27 in total). We then compared our results with those obtained for the same samples using morphological identification (for WFTs) or destructive metabarcoding of bulk homogenate (for MTs). This comparison was applied as part of a larger study of arthropod species richness in silver fir (Abies alba) stands across a range of climate-induced tree dieback levels and forest management strategies.ResultsOf the 53 H2O-MPG samples from WFTs, 16 produced no metabarcoding results, while the remaining 37 samples yielded 77 arthropod MOTUs in total. None of those MOTUs were shared species with the 389 morphological taxa (343 of which were Coleoptera) obtained from the same traps. Metabarcoding of 26 EtOH–MPG samples from MTs detected more arthropod MOTUs (233) and insect orders (11) than destructive metabarcoding of homogenate (146 MOTUs, 8 orders). Arachnida and Collembola were more diverse in EtOH-MPG samples, but Hymenoptera, Coleoptera and Lepidoptera were less represented than in homogenate. Overall, MOTU richness per trap similar for EtOH–MPG (21.81 MOTUs) than for homogenate (32.4 MOTUs). Arthropod communities from EtOH–MPG and homogenate metabarcoding were relatively distinct, with 162 MOTUs (53%) unique to the collection medium and only 71 MOTUs (23%) present in both treatments. Finally, collection medium did not reveal any significant changes in arthropod richness along a disturbance gradient in silver fir forests. We conclude that DNA metabarcoding of collection medium can be used to complement homogenate metabarcoding in inventories to favour the detection of soft-bodied arthropods like spiders.
Widespread natural selection on metabolite levels in humans
Authors: Timasheva Yanina , Lepik Kaido , Liska Orsolya , Papp Balázs , Kutalik Zoltán 
Published: February 2023

AbstractNatural selection acts ubiquitously on complex human traits, predominantly constraining the occurrence of extreme phenotypes (stabilizing selection). These constrains propagate to DNA sequence variants associated with traits under selection. The genetic imprints of such evolutionary events can thus be detected via combining effect size estimates from genetic association studies and the corresponding allele frequencies. While this approach has been successfully applied to high-level traits, the prevalence and mode of selection acting on molecular traits remains poorly understood. Here, we estimate the action of natural selection on genetic variants associated with metabolite levels, an important layer of molecular traits. By leveraging summary statistics of published genome-wide association studies with large sample sizes, we find strong evidence of stabilizing selection for 15 out of 97 plasma metabolites, with an overrepresentation of amino acids among such cases. Mendelian randomization analysis revealed that metabolites under stronger stabilizing selection display larger effects on key cardiometabolic traits, suggesting that maintaining a healthy cardiometabolic profile may be an important source of selective constraints on the metabolome. Metabolites under strong stabilizing selection in humans are also more conserved in their concentrations among diverse mammalian species, suggesting shared selective forces across micro and macroevolutionary time scales. Finally, we also found evidence for both disruptive and directional selection on specific lipid metabolites, potentially indicating ongoing evolutionary adaptation in humans. Overall, this study demonstrates that variation in metabolite levels among humans is frequently shaped by natural selection and this may be acting indirectly through maintaining cardiometabolic fitness.
A novel chimeric RNA originating from BmCPV S4 andBombyx moriHDAC11 transcripts regulates virus proliferation
Authors: Pan Jun , Wei Shulin , Qiu Qunnan , Tong Xinyu , Shen Zeen , Zhu Min , Hu Xiaolong , Gong Chengliang 
Published: February 2023

Polymerases encoded by segmented negative-strand RNA viruses cleave 5’-m7G-capped host transcripts to prime viral mRNA synthesis (‘‘cap-snatching’’) to generate chimeric RNA, and trans-splicing occurs between viral and cellular transcripts.Bombyx moricytoplasmic polyhedrosis virus (BmCPV), an RNA virus belonging to Reoviridae, is a major pathogen of silkworm (B. mori). The genome of BmCPV consists of 10 segmented double-stranded RNAs (S1-S10) from which viral RNAs encoding a protein are transcribed. In this study, chimeric silkworm-BmCPV RNAs, in which the sequence derived from the silkworm transcript could fuse with both the 5’ end and the 3’ end of viral RNA, were identified in the midgut of BmCPV-infected silkworms by RNA_seq and further confirmed by PCR and Sanger sequencing. A novel chimeric RNA, HDAC11-S4 RNA 4, derived from silkworm histone deacetylase 11 (HDAC11) and the BmCPV S4 transcript encoding viral structural protein 4 (VP4), was selected for validation byin situhybridization and Northern blotting. Interestingly, our results indicated that HDAC11-S4 RNA 4 was generated in a BmCPV RNA-dependent RNA polymerase (RdRp)-independent manner and could be translated into a truncated BmCPV VP4 with a silkworm HDAC11-derived N-terminal extension. Moreover, it was confirmed that HDAC11-S4 RNA 4 inhibited BmCPV proliferation, decreased the level of H3K9me3 and increased the level of H3K9ac. These results indicated that during infection with BmCPV, a novel mechanism, different from that described in previous reports, allows the genesis of chimeric silkworm-BmCPV RNAs with biological functions.Graphical abstract
A Cas9-fusion proximity-based approach generates anIrak1-Mecp2tandem duplication mouse model for the study of MeCP2 duplication syndrome
Authors: Maino Eleonora , Scott Ori , Rizvi Samar Z. , Visuvanathan Shagana , Zablah Youssif Ben , Li Hongbin , Sengar Ameet S. , Salter Michael W. , Jia Zhengping , Rossant Janet , Cohn Ronald D. , Gu Bin , Ivakine Evgueni A. 
Published: February 2023

AbstractMECP2 duplication syndrome (MDS) is a neurodevelopmental disorder caused by tandem duplication of theMECP2locus and its surrounding genes, includingIRAK1. Current MDS mouse models involve transgenic expression ofMECP2only, limiting their applicability to the study of the disease. Herein, we show that an efficient and precise CRISPR/Cas9 fusion proximity-based approach can be utilized to generate anIrak1-Mecp2tandem duplication mouse model. TheMecp2 Dupmodel displays a neurological phenotype in keeping with MDS and demonstrates an abnormal immune response to infection not previously observed in other mouse models, possibly stemming from concurrentIrak1overexpression. TheMecp2 Dupmouse line thus provides an innovative tool to investigate disease mechanisms and potential therapeutic development.
Two decades of workplace ecological behaviour: a systematic literature review
Authors: Farooq Khalid , Yusliza Mohd Yusoff 
Published: February 2023

PurposeThis research offered a systematic and comprehensive literature review in analysing current studies on employee ecological behaviour (EEB) strategies and settings to determine various emphasised workplace ecological behaviour areas and contribute a precise mapping for future research.Design/methodology/approachThis systematic literature review method involved 106 peer-reviewed articles published in reputable academic journals (between 2000 and the first quarter of 2021). This study was confined to a review of empirical papers derived from digital databases encompassing the terms ‘Employee green behaviour’, ‘Green behaviour at workplace’, ‘Employee ecological behaviour’, ‘Employee Pro-environmental behaviour’ and ‘Pro-environmental behaviour at workplace’ in the titles.FindingsThis study identified relevant journal articles (classified as EEB at work) from the current body of knowledge. Notably, much emphasis was identified on EEB over the past two decades. Overall, most studies employing quantitative approaches in both developed and emerging nations. Notably, ecological behaviour application garnered the most significant attention from scholars among the four focus areas in the literature review: (i) EEB concepts, models, or reviews, (ii) EEB application, (iii) EEB determinants and (iv) EEB outcomes.Practical implicationsSignificant literature gaps indicate this field to be a relatively novel phenomenon. Thus, rigorous research on the topic proves necessary to develop a holistic understanding of the subject area.Originality/valueThis study expands the current body of knowledge by providing the first comprehensive systematic review on EEB themes, methods, applications, determinants, contextual focus, outcomes and recommending future research agenda.
Does investment committee mitigate the risk of financial distress in GCC? The role of investment inefficiency
Authors: Al-Dhamari Redhwan , Al-Wesabi Hamid , Farooque Omar Al , Tabash Mosab I. , El Refae Ghaleb A. 
Published: February 2023

Purpose
The purpose of this study is to empirically examine how the voluntary formation of a specialised investment committee (IC) and IC characteristics affect financial distress risk (FDR) and whether such impact is influenced by the level of investment inefficiency.

Design/methodology/approach
The authors use a large sample of Gulf Cooperation Council (GCC) non-financial companies during 2006–2016. A principal component analysis is done to aggregate and derive a factor score for IC characteristics (i.e. independence, size and meeting) as a proxy for the effectiveness of IC. This study also uses three measurements of FDR to corroborate the findings and partitions sample firms into overinvesting and underinvesting companies to examine the potential impact of investment inefficiency on the IC–FDR nexus.

Findings
Using feasible generalised least square estimation method, the authors document that the likelihood of financial distress occurrence decreases for firms with separate ICs. The authors also find that firms with effective ICs enjoy lower FDR. In other words, the probability of financial distress minimises if the IC is large, meets frequently and has a high number of independent directors. However, the authors find neither any moderation nor any mediation effect of investment inefficiency for the impact of IC and IC attributes on FDR. The additional analysis indicates the expected benefits of an actively performing IC are amplified for firms with risk of both over- and underinvestment. These findings are robust to alternative measures of FDR and investment inefficiency, sub-sample analysis and endogeneity concerns.

Originality/value
This study, to the best of researchers’ knowledge, is the first to provide evidence in GCC firms’ perspective, suggesting that the existence of an effective IC is associated with a lower risk of financial distress, and to some extent, the economic benefits of IC are aggrandised for companies with a high probability of over- and underinvestment problems. These results are unique and contribute to a small but growing body of literature documenting the need for effective ICs and their economic consequences on investment efficiency in the FDR environment. The findings of this study carry valuable practical implications for regulatory bodies, policymakers, investors and other interested parties in the GCC region.
The relationship between macroeconomic variables on residential property price: case study in Malaysia before and during COVID-19
Authors: Zulkarnain Siti Hafsah , Nawi Abdol Samad 
Published: February 2023

Purpose
The purpose of this study is to analyse numerous aspects affecting residential property price in Malaysia against macroeconomics issues such as gross domestic product (GDP), exchange rate, unemployment and wage.

Design/methodology/approach
The hedonic pricing model has been adopted as econometric model for this research to investigate the relationship between residential property price against macroeconomics indicator. The data for residential property price and macroeconomic variables were collected from 1991 to 2019. Multiple linear regression had been adopted to find the relationship between the dependent and independent variables.

Findings
The result shows that the GDP has a significant positive impact on residential property price, while exchange rate has no significant impact although it was positive. In addition, the unemployment rate has a significant impact on the residential property price and has a negative relationship. Similar to the wage that shows the negative relationship with residential property prices. Moreover, during the pandemic COVID-19 in Malaysia, this research shows a more transparent view of the relationship between residential property price and the macroeconomic issues of GDP, exchange rate, unemployment and wage.

Originality/value
The findings of this research found that macroeconomics issue cannot be eliminated due to Malaysia is a developing country, and there will always be an issue that will happen, but the issues can be reduced to maximise the advantages, e.g. during COVID-19, the solution to fight against COVID-19 were crucial and weaken the macroeconomics issues.
A Choquet integral-based TODIM method for q-rung trapezoidal fuzzy numbers and its application in group decision-making
Authors: Wan Benting , Huang Juelin 
Published: February 2023

PurposeThe purpose of this paper is to develop a multi-attribute group decision-making (MAGDM) method under the q-rung orthopair trapezoidal fuzzy environment, which calculates the interaction between the criteria depending on the proposed q-rung orthopair trapezoidal fuzzy aggregation Choquet integral (q-ROTrFACI) and employ TODIM (an acronym in Portuguese of Interactive and Multi-criteria Decision Making) to consider the risk psychology of decision-makers, to determine the optimal ranking of alternatives.Design/methodology/approachIn MAGDM, q-rung orthopair trapezoidal fuzzy numbers (q-ROTrFNs) are efficient to indicate the quantitative vagueness of decision-makers. The q-ROTrFACI operator is defined and some properties are proved. Then, a novel similarity measure is developed by fusing the area and coordinates of the q-rung orthopair trapezoidal fuzzy function. Based on the above, a Choquet integral-based TODIM (CI-TODIM) method to consider the risk psychology of decision-makers is proposed and two cases are provided to prove superiority of the method.FindingsThe paper investigates q-ROTrFACI operator to productively solve problems with interdependent criteria. Then, an approach is proposed to determine the center point of q--ROTrFNs and a q-rung orthopair trapezoidal fuzzy similarity is constructed. Furthermore, CI-TODIM method is devised based on the proposed q-ROTrFACI operator and similarity in q-rung orthopair trapezoidal fuzzy context. The illustration example of business models' solutions and hypertension health management are given to demonstrate the effectiveness and superiority of proposed method.Originality/valueThe paper develops a novel CI-TODIM method that effectively solves the MAGDM problems under the premise of fully considering the priority of criteria and the risk preference of decision-makers, which provides guiding advantages for practical decision-making and enriches the application of decision-making theory.
Exploring colliding logics of supply chains and business ecosystems in purchasing and supply management
Authors: Andersen Poul Houman , Laursen Linda Nhu , Møller Morten Munkgaard 
Published: February 2023

Purpose
A shift in supply management is underway. Nonlinear connections of buyers and sellers in business ecosystems challenge conventional supply management practice. Digital technologies and network connectivity lower the costs of connecting and collaborating with loosely related external parties. This paper aims to explore how this challenges conventional purchasing and supply management (PSM) practice.

Design/methodology/approach
This paper builds on the extended case research method. It is based on a theoretical conceptualization, which is explored through a case study.

Findings
The authors find that both supply management’s contribution to value creation, value appropriation and collaborative interfaces change with the emergence of multifaceted business systems.

Research limitations/implications
The paper is developed within a specific industrial context, and the findings are not directly transferrable to other contexts. However, the authors believe that on an analytical level, there is value in transferring the insights into other manufacturing contexts.

Practical implications
Managers must challenge the taken-for-granted thinking that follows from linear supply management practices and start rehearsing the role of PSM when dealing with supplies from business ecosystem lead firms.

Originality/value
This research takes up a novel issue, highly relevant for PSM practitioners as well as for theory. To the best of the authors’ knowledge, nothing has been written about the colliding business logics of conventional PSM and that of business ecosystems.
Earnings performance of financial and non-financial IPOs in India: an empirical analysis based on market timing
Authors: Dhanda Sunaina , Singh Shveta 
Published: February 2023

PurposeThe purpose of this study is to see if market timing predicts the first reporting of earnings performance after the issue, i.e. the issue-year earnings performance. Furthermore, this study examines the behaviour of financial and non-financial issuers’ performance in the light of varied market timings.Design/methodology/approachThis study focuses on 785 NSE-listed initial public offerings that took place between April 2010 and December 2021. This study evaluates market timing by using moving averages. Using multiple regression analysis, the research further investigates the impact of market timing on issue-year earnings performance for financial and non-financial issuers on the basis of an interaction (moderation) effect.FindingsThis study finds that there is a significant presence of market timing in India, which predicts issue-year earnings performance. This study also demonstrates that hot market issuers’ performance is heavily influenced by market timing for non-financial issuers only. However, financial companies are not influenced by market timing.Research limitations/implicationsThe findings of this study will assist the potential investors, analysts and stakeholders about performance of public issuers in India. Lower earnings performance for hot market non-financial issuers implies that the issuers’ market performance may not be supported by earnings figures. A market performance that is not synchronous with earnings will not last long. The findings of this study hold implications to the regulators as well to keep an eye on issuers’ earnings performance alongside the stock performance. Apart from that, the observations in context of financial and non-financial issuers provide insight about the variation in performance of public issues on the basis of background.Originality/valueTo the best of the authors’ knowledge, this is the only study to examine earnings performance in the context of market timing in India. This study holds significance in terms of methodology for anticipating the presence of market timing and the study of interaction effects. Moreover, it is one of the few studies that has focused on comparing financial and non-financial issuers around the world.