bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic and environmental circadian disruption induce metabolic impairment through changes in the gut microbiome
Authors: Altaha Baraa , Heddes Marjolein , Pilorz Violetta , Niu Yunhui , Gorbunova Elizaveta , Gigl Michael , Kleigrewe Karin , Oster Henrik , Haller Dirk , Kiessling Silke 
Published: July 2022

AbstractObjectiveInternal clocks time behavior and physiology, including the gut microbiome in a circadian (∼24 h) manner. Mismatch between internal and external time, e.g. during shift work, disrupts circadian system coordination promoting the development of obesity and type 2 diabetes (T2D). Conversely, body weight changes induce microbiota dysbiosis. The relationship between circadian disruption and microbiota dysbiosis in metabolic diseases, however, remains largely unknown.MethodsCore and accessory clock gene expression in different gastrointestinal (GI) tissues were determined by qPCR in two different models of circadian disruption - mice with Bmal1 deficiency in the circadian pacemaker, the suprachiasmatic nucleus (Bmal1SCNfl/-), and wild-type mice exposed to simulated shift work (SSW). Body composition and energy balance were evaluated by nuclear magnetic resonance (NMR), bomb calorimetry, food intake and running-wheel activity. Intestinal permeability was measured in an Ussing chamber. Microbiota composition and functionality were evaluated by 16S rRNA gene amplicon sequencing, PICRUST2.0 analysis and targeted metabolomics. Finally, microbiota transfer was conducted to evaluate the functional impact of SSW-associated microbiota on the host’s physiology.ResultsBoth chronodisruption models show desynchronization within and between peripheral clocks in GI tissues and reduced microbial rhythmicity, in particular in taxa involved in short-chain fatty acid (SCFA) fermentation and lipid metabolism. In Bmal1SCNfl/- mice, loss of rhythmicity in microbial functioning associates with previously shown increased body weight, dysfunctional glucose homeostasis and adiposity. Similarly, we observe an increase in body weight in SSW mice. Germ-free colonization experiments with SSW- associated microbiota mechanistically link body weight gain to microbial changes. Moreover, alterations in expression of peripheral clock genes as well as clock-controlled genes (CCGs) relevant for metabolic functioning of the host were observed in recipients, indicating a bidirectional relationship between microbiota rhythmicity and peripheral clock regulation.ConclusionsCollectively, our data suggest that loss of rhythmicity in bacteria taxa and their products, which likely originates in desynchronization of intestinal clocks, promotes metabolic abnormalities during shift work.
Chemoenzymatic Synthesis of Heparan Sulfate Oligosaccharides having a Domain Structure
Authors: Sun Lifeng , Chopra Pradeep , Boons Geert-Jan 
Published: July 2022

AbstractHeparan sulfate (HS) have domain structures in which regions that are substantially modified by epimerization and sulfation (NS domains) are interspersed by unmodified fragments (NA domains). There is data to support that the domain structure of HS can regulate protein binding, however, such a binding mode has been difficult to probe. Here, we report a chemoenzymatic methodology that can provide HS oligosaccharides composed of two or more NS domains separated by NA domains of different length. It is based on the chemical synthesis of a sulfated HS oligosaccharide that enzymatically could be extended by various GlcA-GlcNAc units and terminated in a GlcNAc-6N3 moiety. HS oligosaccharides having an azide and alkyne moiety could assembled by copper catalyzed alkyne-azide cycloaddition (CuAAC) to give compounds having various NS domains separated by unsulfated regions. Competition binding studies showed that the length of an NA domain modulates the binding of the chemokines CCL5 and CXCL8.
Genomic evaluation of BC4, a consortium of four Alkalihalobacillus clausii isolates, confirms its probiotic potential and safety in usage
Authors: Dhakephalkar Tanisha , Wagh Shilpa , Yadav Kunal , Engineer Anupama S. , Pore Soham D. , Dhakephalkar Prashant K. 
Published: July 2022

AbstractFour strains of Alkalihalobacillus clausii B603/Nb (resistant to rifampicin), B619/R (resistant to streptomycin), B637/Nm (resistant to tetracyclin) and B106 (resistant to chloramphenicol) were isolated from various sources and used to prepare a consortium designated as BC4. Genomes of the constituent strains of the BC4 consortium were evaluated to investigate their genetic makeup and determine their probiotic potential. Gene prediction and functional annotation were performed using RAST. The data obtained was mined for genes encoding various phenotypic traits. This analysis revealed the presence of several genes encoding probiotic attributes like (i) survivability in the presence of low pH, bile, oxidative stress; (ii) bacterial aggregation and adhesion to gut epithelium, etc.; and (iii) enzymes/ molecules conferring health benefits. Further, the genome analysis also confirmed the genes required for enhancing the nutritional amenability, health-promoting, and disease-preventing traits were present. Several genes encoding multiple antibiotic resistance were detected; however, none of these genes was located on mobile elements such as plasmids, transposons, etc. The absence of genes encoding virulence factors, pathogenic islands, emetic toxins, etc., as well as mobile genetic elements, underscored the safety of BC4 isolates.
Sudan black lipid blot – a rapid and simple method for quantification of lipids in biological samples
Authors: Homolak Jan , Joja Mihovil , Markovic Pavel , Salkovic-Petrisic Melita 
Published: July 2022

AbstractBioanalytical techniques for the isolation and quantification of total lipids in biological samples are an integral part of lipidomic workflows and widely used tools for metabolic assessment at the cellular and organismic levels. The most widely used protocol for the isolation, extraction, and quantification of total lipids in biological tissues was originally introduced by Folch et al.. It requires a relatively large amount of tissue and large volumes of lipid extracts for reliable assessment of lipid content using the gravimetric technique. Here, we propose a new method to overcome the aforementioned challenges based on the hypothesis that the partitioning coefficient of the widely used lysochrome diazo dye Sudan Black B between the lipid extract and ethylene glycol can be used to indirectly estimate the absolute concentration of lipids. The proposed method demonstrates great precision and linearity, requires minimal equipment, and enables the analysis of total lipid content in biological specimens available only in limited amounts by reducing the requirements for the input quantity by >300-fold for some tissues (e.g. fecal samples).
Honey Bees Get Map Coordinates from the Dance
Authors: Wang Zhengwei , Chen Xiuxian , Becker Frank , Greggers Uwe , Walter Stefan , Werner Marleen , Gallistel Charles R. , Menzel Randolf 
Published: July 2022

AbstractHoneybees (Apis mellifera carnica) communicate the rhumb line to a food source (its direction and distance from the hive) by means of a waggle dance. We ask whether bees recruited by the dance use it only as a flying instruction or also translate it into a location vector in a map-like memory, so that information about spatial relations of environmental cues informs their attempts to find the source. The flights of recruits captured on exiting the hive and released at distant sites were tracked by radar. The recruits performed first a straight flight in the direction of the rhumb line. However, the vector portions of their flights and the ensuing tortuous search portions were strongly and differentially affected by the release site. Searches were biased toward the true location of the food and away from the location specified by translating the rhumb line origin to the release site. We conclude that by following the dance a recruit gets two messages, a polar flying instruction (the rhumb line) and its conversion to Cartesian map coordinates.
The role of division stochasticity on the robustness of bacterial size dynamics
Authors: Nieto César , Arias-Castro Juan Carlos , Sánchez Carlos , Vargas-García César , Singh Abhyudai , Pedraza Juan Manuel 
Published: July 2022

AbstractVariables of bacterial division such as size at birth, growth rate, division time, and the position of the septal ring, all vary from cell to cell. Currently, it is unknown how these random fluctuations can combine to produce a robust mechanism of homeostasis. To address this question, we studied the dynamics of the cell division process from both experimental and theoretical perspectives. Our model predicts robustness in division times as sustained oscillations in metrics of the cell size distribution, such as the mean, variability, and the cell size autocorrelation function. These oscillations do not get damped, even considering stochasticity in division timing and the cell size at the beginning of the experiment. Damping appears just after inducing stochasticity in either the septum position or the growth rate. We compare the predictions of the full model with the size dynamics of E. coli bacteria growing in minimal media using either glucose or glycerol as carbon sources. We observe that growth in poorer media increases the noise in both partitioning position and growth rate. This additional noise results in oscillations with more damping. Although intracellular noise is known as a source of phenotypic variation, our results show that it can play a similar but subtler role in maintaining population-level homeostasis by causing rapid desynchronization of cell cycles..
SEQUENCE VARIATIONS ASSOCIATED WITH NOVEL PURPLE-PERICARP SUPER-SWEETCORN COMPARED TO ITS PURPLE-PERICARP MAIZE AND WHITE SUPER-SWEETCORN PARENTS
Authors: Anirban Apurba , Masouleh Ardashir Kharabian , Henry Robert J , O’Hare Tim J 
Published: July 2022

AbstractRecently, a novel purple-pericarp super-sweetcorn line, ‘Tim1’ (A1A1.sh2sh2) is derived from the purple-pericarp maize ‘Costa Rica’ (A1Sh2.A1Sh2) and white shrunken2 (sh2) super-sweetcorn ‘Tims-white’ (a1sh2.a1sh2), however information regarding purple colour controlling anthocyanin biosynthesis genes and sweetcorn gene is lacking. Specific sequence differences in the CDS (coding DNA sequence) and promoter regions of the anthocyanin biosynthesis structural genes, anthocyanin1 (A1), purple aleurone1 (Pr1) and regulatory genes, purple plant1 (Pl1), plant colour1 (B1), coloured1 (R1), and the sweetcorn structural gene, shrunken2 (sh2) were investigated using the publicly available annotated yellow starchy maize, B73 (NAM5.0) as a reference genome. In the CDS region, the A1, Pl1 and R1 gene sequence differences of ‘Tim1’ and ‘Costa Rica’ were similar, as they control purple-pericarp pigmentation, however the B1 gene showed similarity between the ‘Tim1’ and ‘Tims-white’ lines, which may indicate that it does not have a role in controlling pericarp colour, unlike a previous study. In case of Pr1 gene, unlike ‘Costa Rica’, 6- and 8-bp dinucleotide (TA) repeats were observed in the promoter region of the ‘Tims-white’ and ‘Tim1’ lines, respectively, indicating the defective functionality (redder colour in ‘Tim1’ than purple in ‘Costa Rica’) of the recessive pr1 allele. In the sweetcorn structural gene (sh2), sequence similarity was observed between purple-sweet ‘Tim1’ and its white-sweet parent ‘Tims-white’, as both display a shrunken phenotype in their mature kernels. These findings revealed that the developed purple-sweet line is different than the reference yellow-nonsweet line regarding both the anthocyanin biosynthesis and sweetcorn genes.
Bringing Plant Immunity to Light: A Genetically Encoded, Bioluminescent Reporter of Pattern Triggered Immunity inNicotiana benthamiana
Authors: Garcia Anthony G. K. , Steinbrenner Adam D. 
Published: July 2022

AbstractPlants rely on innate immune systems to defend against a wide variety of biotic attackers. Key components of innate immunity include cell-surface pattern recognition receptors (PRRs), which recognize pest/pathogen-associated molecular patterns (PAMPs). Unlike other classes of receptors which often have visible cell death immune outputs upon activation, PRRs generally lack rapid methods for assessing function. Here, we describe a genetically encoded bioluminescent reporter of immune activation by heterologously-expressed PRRs in the model organismNicotiana benthamiana.We characterizedN. benthamianatranscriptome changes in response toAgrobacterium tumefaciens (Agrobacterium)and subsequent PAMP treatment to identify PTI-associated marker genes, which were then used to generate promoter-luciferase fusion fungal bioluminescence pathway (FBP) constructs. A reporter construct termedpFBP_2xNbLYS1::LUZallows for robust detection of PTI activation by heterologously expressed PRRs. Consistent with known PTI signaling pathways, activation by receptor-like protein (RLP) PRRs is dependent on the known adaptor of RLP PRRs, SOBIR1. This system minimizes the amount of labor, reagents, and time needed to assay function of PRRs and displays robust sensitivity at biologically relevant PAMP concentrations, making it ideal for high throughput screens. The tools described in this paper will be powerful for studying PRR function and investigations to characterize the structure-function of plant cell surface receptors.
Knowledge sharing processes and the role of attachment patterns
Authors: McLarnon Matthew J.W. , R. Gellatly Ian , A. Richards David , Arazy Ofer 
Published: July 2022

Purpose
Past research on the motivational processes underpinning knowledge sharing has assumed that the sharing processes are similar for all individuals. Yet, sharing is a fundamental affiliative behavior, and the sharing processes can differ between people. This study aims to propose and test a model of the moderating influence that employee attachment patterns have on the theory of reasoned action (TRA)-defined knowledge sharing processes.

Design/methodology/approach
The authors administered a questionnaire to 1,103 employees from a range of industries who participated in an online Qualtrics survey. Advanced forms for structural equation modeling and latent profile analysis were used to assess the proposed model.

Findings
The results revealed that participants in the study exhibited the latent profiles corresponding to secure, dismissive, preoccupied and fearful patterns. The preoccupied cohort had the lowest knowledge sharing behavior, yet the strongest links within the sharing process. Secure, dismissive and fearful had similar sharing levels, but the strength of the TRA-defined processes differed. These findings underscore equifinality: although sharing may be approximately equal across different attachment patterns, the fundamental processes underpinning sharing differ.

Research limitations/implications
The authors used self-report data, given that sharing attitudes, norms and intentions may not be overly amenable to ratings even from well-acquainted others. Further, the use of advanced analytical methods helps to minimize common method concerns. Additionally, causal mechanisms underscoring the TRA have been demonstrated (Ajzen and Fishbein, 2005), allowing us to explore the moderating role of attachment patterns.

Practical implications
This study speaks to the importance of considering employees’ attachment patterns, and developing comprehensive intra-organizational norms, policies and systems that support and encourage knowledge sharing from employees with a variety of attachment patterns.

Originality/value
This study uniquely contributes to knowledge sharing literatures by incorporating attachment patterns as moderators within the TRA-defined sharing processes. The authors provide important insights on the role of individuals’ attachment patterns have for knowledge sharing behaviors, but also highlight how structure of knowledge sharing differed across subgroups of employees, determined based on their dispositional attachment pattern.
Analyst forecast quality and corporate social responsibility: the mediation effect of corporate governance
Authors: Shan Yuan George , Yang Joey Wenling , Zhang Junru , Chang Millicent 
Published: July 2022

Purpose
This study aims to examine the mediating role played by corporate governance (CG) in the relationship between corporate social responsibility (CSR) and analyst forecast quality.

Design/methodology/approach
The authors raise three specific questions: Does CG play a mediating role in the relationship between CSR and analyst forecast quality? If so, is such mediation effect of CG reduced for firms with weak governance? Do firms with superior CSR performance experience higher analyst forecast quality through the mediation effect of CG?

Findings
The present results suggest that CG serves as a partial mediator that facilitates CSR’s positive influence on analyst forecast quality. However, further analyses show that in firms with a low governance score, CG does not have a mediation effect. Conversely, the authors find that firms with superior CSR performance have higher forecast quality through the mediation effect of CG. The authors also find that the mediation effect of CG is more pronounced for the environmental component than for the social component of CSR.

Originality/value
To the best of the authors’ knowledge, this study is the first to investigate the role of CG as a mediator between CSR and analyst forecast quality and to reveal that the strength of this effect varies depending on firms’ CG level and CSR commitment.
The evolution of carotenoid‐based plumage colours in passerine birds
Authors: Delhey Kaspar , Valcu Mihai , Dale James , Kempenaers Bart 
Published: July 2022

Abstract

Many birds use carotenoids to colour their plumage yellow to red. Because birds cannot synthesise carotenoids, they need to obtain these pigments from food, although some species metabolise dietary carotenoids (which are often yellow) into derived carotenoids (often red).

Here, we study the occurrence of yellow and red carotenoid‐based plumage colours in the passerines, the largest bird radiation and quantify the effects of potential ecological and life‐history drivers on their evolution.

We scored the presence/absence of yellow and red carotenoid‐based plumage in nearly 6,000 species and use Bayesian phylogenetic mixed models to assess the effects of carotenoid‐availability in diet, primary productivity, body size, habitat and sexual selection. We also test the widespread assumption that red carotenoid‐based colours are more likely to be the result of metabolization. Finally, we analyse the pattern of evolutionary transitions between yellow and red carotenoid‐based plumage colours to determine whether, as predicted, the evolution of yellow carotenoid‐based colours precedes red.

We show that, as expected, both colours are more likely to evolve in smaller species and in species with carotenoid‐rich diets. Yellow carotenoid‐based plumage colours, but not red, are more prevalent in species that inhabit environments with higher primary productivity and closed vegetation. In general, females were more likely to have yellow and males more likely to have red carotenoid‐based plumage colours, closely matching the effects of sexual selection. Our analyses also confirm that red carotenoid‐based colours are more likely to be metabolised than yellow carotenoid‐based colours. Evolutionary gains and losses of yellow and red carotenoid‐based plumage colours indicate that red colours evolved more readily in species that already deposited yellow carotenoids, while the reverse was rarely the case.

Our study provides evidence for a general, directional evolutionary trend from yellow to red carotenoid‐based colours, which are more likely to be the result of metabolization. This may render them potentially better indicators of quality, and thus favoured by sexual selection.
Radical shift in the genetic composition of New England chicory populations
Authors: Závada Tomáš , Malik Rondy J. , Mazumder Lisa , Kesseli Rick V. 
Published: July 2022

Abstract

Human activities have been altering the flora and fauna across the planet. Distributions and the diversity of species, and the phenotypes of individuals in those species are changing. New England with its rapidly changing human demographics is an ideal place to investigate these temporal changes in the habitat. The flora of New England consists of both native and nonnative species. Non‐indigenous plant species have been introduced since the first Europeans arrived in North America in the 15th century. Cichorium intybus (chicory), native to Eurasia, was first recorded in North America in 1774. Subsequently, chicory spread and became naturalized throughout much of the continent.

In this study, we used chloroplast DNA sequences and 12 microsatellite nuclear markers to assess the temporal genetic changes in New England populations of chicory. We analysed 84 herbarium specimens and 18 contemporary extant populations (228 individuals in total).

Three chloroplast DNA haplotypes were detected and all were present in New England prior to 1890; however, Hap3 was rare prior to the 1950s. The nuclear DNA markers showed a major shift in the genetic diversity and composition, with all historical herbarium collections belonging to a single genetic cluster and 16 out of 18 contemporary chicory populations belonging to different genetic clusters. This change occurred regionally and also on a local scale with contemporary populations being very different from herbarium specimens collected previously in the corresponding localities.

Synthesis. Our results indicate that the genetic diversity and structure of Cichorium intybus populations have changed substantially since the founding populations in New England. These changes may have contributed to the success of this nonnative species and helped to fuel its rapid expansion and adaptation to the changing landscapes in both New England and the rest of North America.
Inclusive recovery planning for incremental systemic change: A methodology, early outcomes, and limitations from the Falkland Islands' Covid‐19 recovery planning experience
Authors: Cochrane Kate , Cornish Flora , Murphy Annette , Denton Neil , Bracken Louise 
Published: July 2022

AbstractCrises do not affect populations equally but expose and exacerbate long‐standing vulnerabilities and inequalities. Recovery language such as ‘build back better’, or ‘bounce forward’ has been criticised for neglecting underlying inequalities. This paper reports on the process and early outcomes of an inclusive Community Recovery Planning process for the Falkland Islands, in response to Covid‐19. The Falkland Islands is home to a complex community, with close ties and short power distances (due to its small size and remoteness), with differences institutionalised in citizenship statuses and entitlements, and shaped by geopolitical tensions. We aimed to use the ‘pandemic as a portal’, seeking out previously ‘less heard’ voices, to make visible previously hidden impacts, and initiate incremental systemic change to tackle them. Community Impact Assessments evidenced specific areas of vulnerability (e.g., housing and income insecurity) and inequalities, largely shaped by differing citizenship status. In tandem with other government currents, the Community Recovery Planning process has contributed to progressive policy changes in Equalities legislation and Income Support. We offer this paper as a demonstration of our methodology for inclusive recovery planning that could be adapted elsewhere. We argue that the inclusion of previously unheard voices contributed to incremental systemic change to reduce inequalities.