bluuebunny/crossref_metadata_2025 huggingface dataset:
Primate homologs of mouse cortico-striatal circuits
Authors: Balsters Joshua H. , Zerbi Valerio , Sallet Jérôme , Wenderoth Nicole , Mars Rogier B.
Published: November 2019

With the increasing necessity of animal models in biomedical research, there is a vital need to harmonise findings across species by establishing similarities and differences in rodent and primate neuroanatomy. Using a connectivity fingerprint matching approach, we compared cortico-striatal circuits across humans, non-human primates, and mice using resting state fMRI data in all species. Our results suggest that the connectivity patterns for both the nucleus accumbens and cortico-striatal motor circuits (posterior/lateral putamen) were conserved across species, making them reliable targets for cross-species comparisons. However, a large number of human and macaque striatal voxels were not matched to any mouse cortico-striatal circuit (mouse->human: 85% unassigned; mouse->macaque 69% unassigned; macaque->human; 31% unassigned). These unassigned voxels were largely localised to the caudate nucleus and anterior putamen, overlapping with executive function and social/language regions of the striatum, and connected to prefrontal-projecting cerebellar lobules and anterior prefrontal cortex, forming circuits that seem to be unique for non-human primates and humans. Our results demonstrate the potential of connectivity fingerprint matching to bridge the gap between rodent and primate neuroanatomy.
Spatial regulation of clathrin-mediated endocytosis through position-dependent site maturation
Authors: Pedersen Ross TA , Hassinger Julian E , Marchando Paul , Drubin David G
Published: November 2019

During clathrin-mediated endocytosis (CME), over 50 different proteins assemble on the plasma membrane to reshape it into a cargo-laden vesicle. It has long been assumed that cargo triggers local CME site assembly in Saccharomyces cerevisiae based on the discovery that cortical actin patches clustered near exocytic sites are CME sites. Quantitative imaging data reported here lead to a radically different view of which CME steps are regulated and which steps are deterministic. We quantitatively and spatially describe progression through the CME pathway and pinpoint a cargo-sensitive regulatory transition point that governs progression from the initiation phase of CME to the internalization phase. Thus, site maturation, rather than site initiation, accounts for the previously observed polarized distribution of actin patches in this organism. While previous studies suggested that cargo ensures its own internalization by regulating either CME initiation rates or frequency of abortive events, our data instead identify maturation through a checkpoint in the pathway as the cargo-sensitive step.

Pedersen, Hassinger, et al. investigate steps of the clathrin-mediated endocytosis pathway that are subject to regulation. They report position-dependent differences in endocytic site maturation rates in polarized cells and suggest that cargo controls endocytic internalization through tuning site maturation rather than site initiation.
Multiple evidences suggest sox2 as the main driver of a young and complex sex determining ZW/ZZ system in turbot (Scophthalmus maximus)
Authors: Martínez Paulino , Robledo Diego , Taboada Xoana , Blanco Andrés , Gómez-Tato Antonio , Álvarez-Blázquez Blanca , Cabaleiro Santiago , Piferrer Francesc , Bouza Carmen , Viñas Ana M.
Published: November 2019

A major challenge in evolutionary biology is to find an explanation for the variation in sex-determining (SD) systems across taxa and to understand the mechanisms driving sex chromosome differentiation. We studied the turbot, holding a ZW/ZZ SD system and no sex chromosome heteromorphism, by combining classical genetics and genomics approaches to disentangle the genetic architecture of this trait. RAD-Seq was used to genotype 18,214 SNPs on 1,135 fish from 36 families and a genome wide association study (GWAS) identified a ∼ 6 Mb region on LG5 associated with sex (P < 0.05). The most significant associated markers were located close to sox2, dnajc19 and fxr1 genes. A segregation analysis enabled narrowing down the associated region and evidenced recombination suppression in a region overlapping the candidate genes. A Nanopore/Illumina assembly of the SD region using ZZ and WW individuals identified a single SNP fully associated with Z and W chromosomes. RNA-seq from 5-90 day-old fish detected the expression along the gonad differentiation period of a short non-coding splicing variant (ncRNA) included in a vertebrate-conserved long non-coding RNA overlapping sox2. qPCR showed that sox2 was the only differentially expressed gene between males and females at 50-55 days post fertilization, just prior the beginning of gonad differentiation. More refined information on the involvement of secondary genetic and environmental factors and their interactions on SD was gathered after the analysis of a broad sample of families. Our results confirm the complex nature of SD in turbot and support sox2 as its main driver.
Boosting Brain Signal Variability Underlies Liberal Shifts in Decision Bias
Authors: Kloosterman Niels A. , Kosciessa Julian Q. , Lindenberger Ulman , Fahrenfort Johannes Jacobus , Garrett Douglas D.
Published: November 2019

Strategically adopting decision biases allows organisms to tailor their choices to environmental demands. For example, a liberal response strategy pays off when target detection is crucial, whereas a conservative strategy is optimal for avoiding false alarms. Using conventional time-frequency analysis of human electroencephalographic (EEG) activity, we previously showed that bias setting entails adjustment of evidence accumulation in sensory regions (Kloosterman et al., 2019), but the presumed prefrontal signature of a strategic conservative-to-liberal bias shift has remained elusive. Here, we show that a liberal bias shift relies on frontal regions adopting a more unconstrained neural regime (boosted entropy) that is suited to the detection of unpredictable events. Overall EEG variation, spectral power and event-related potentials could not explain this relationship, highlighting the unique contribution of moment-to-moment neural variability to bias shifts. Neural variability modulation through prefrontal cortex appears instrumental for permitting an organism to tailor its decision bias to environmental demands.

Impact statement

Moment-to-moment variability is a prominent feature of neural activity. Rather than representing mere noise, this variability might enable us to flexibly adapt our decision biases to the environment.
Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika
Authors: Tran Patricia Q. , Bachand Samantha C. , McIntyre Peter B. , Kraemer Benjamin M. , Vadeboncoeur Yvonne , Kimirei Ismael A. , Tamatamah Rashid , McMahon Katherine D. , Anantharaman Karthik
Published: November 2019

Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth’s surface. LT’s mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT’s 1470 m deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 21 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change which is predicted to bring increased stratification and anoxia to freshwater lakes.
A high-fat/high-protein, Atkins-type diet exacerbates Clostridioides (Clostridium) difficile infection in mice, whereas a high-carbohydrate diet protects
Authors: Mefferd Chrisabelle C. , Bhute Shrikant S. , Phan Jacqueline R. , Villarama Jacob V. , Do Dung M. , Alarcia Stephanie , Abel-Santos Ernesto , Hedlund Brian P.
Published: November 2019

Clostridioides difficile (formerly Clostridium difficile) infection (CDI) can result from the disruption of the resident gut microbiota. Western diets and popular weight-loss diets drive large changes in the gut microbiome; however, the literature is conflicted with regard to the effect of diet on CDI. Using the hypervirulent strain C. difficile R20291 (RT027) in a mouse model of antibiotic-induced CDI, we assessed disease outcome and microbial community dynamics in mice fed two high-fat diets in comparison with a high-carbohydrate diet and a standard rodent diet. The two high-fat diets exacerbated CDI, with a high-fat/high-protein, Atkins-like diet leading to severe CDI and 100% mortality, and a high-fat/low-protein, medium-chain triglyceride (MCT)-like diet inducing highly variable CDI outcomes. In contrast, mice fed a high-carbohydrate diet were protected from CDI, despite high refined carbohydrate and low fiber content. 28 members of the Lachnospiraceae and Ruminococcaceae decreased in abundance due to diet and/or antibiotic treatment; these organisms may compete with C. difficile for amino acids and protect healthy animals from CDI in the absence of antibiotics. Together, these data suggest that antibiotic treatment might lead to loss of C. difficile competitors and create a favorable environment for C. difficile proliferation and virulence that is intensified by high-fat/high-protein diets; in contrast, high-carbohydrate diets might be protective regardless of the source of carbohydrate.
Comparative genomic analyses and a novel linkage map for cisco (Coregonus artedi) provide insights into chromosomal evolution and rediploidization across salmonids
Authors: Blumstein Danielle M. , Campbell Matthew A. , Hale Matthew C. , Sutherland Ben J. G. , McKinney Garrett J. , Stott Wendylee , Larson Wesley A.
Published: November 2019

Whole-genome duplication (WGD) is hypothesized to be an important evolutionary mechanism that can facilitate adaptation and speciation. Genomes that exist in states of both diploidy and residual tetraploidy are of particular interest, as mechanisms that maintain the ploidy mosaic after WGD may provide important insights into evolutionary processes. The Salmonidae family exhibits residual tetraploidy, and this, combined with the evolutionary diversity formed after an ancestral autotetraploidization event, makes this group a useful study system. In this study, we generate a novel linkage map for cisco (Coregonus artedi), an economically and culturally important fish in North America and a member of the subfamily Coregoninae, which previously lacked a high-density haploid linkage map. We also conduct comparative genomic analyses to refine our understanding of chromosomal fusion/fission history across salmonids. To facilitate this comparative approach, we use the naming strategy of protokaryotype identifiers (PKs) to associate duplicated chromosomes to their putative ancestral state. The female linkage map for cisco contains 20,292 loci, 3,225 of which are likely within residually tetraploid regions. Comparative genomic analyses revealed that patterns of residual tetrasomy are generally conserved across species, although interspecific variation persists. To determine the broad-scale retention of residual tetrasomy across the salmonids, we analyze sequence similarity of currently available genomes and find evidence of residual tetrasomy in seven of the eight chromosomes that have been previously hypothesized to show this pattern. This interspecific variation in extent of rediploidization may have important implications for understanding salmonid evolutionary histories and informing future conservation efforts.
The ocellate river stingray (Potamotrygon motoro) exploits vortices of sediment to bury into the substrate
Authors: Seamone S.G. , Syme D.A.
Published: November 2019

Particle image velocimetry and video analysis were employed to discern and describe the mechanism used by the stingrayPotamotrygon motoroto bury into the substrate.P. motororepeatedly and rapidly pumped the body up and down while folding the posterior portion of the pectoral fins up and over, drawing water in and suspending sediment beneath the pectoral disc. As the fins folded up and over, vortices of fluidized sediment travelled along the ventral surface of the fins toward the fin tips, and were then directed onto the dorsal surface of the fins and towards the dorsal midline of the fish, where they dissipated and the sediment settled over the dorsal surface of the ray. As displacement and speed of the body pumping and finbeat motions increased, the speed of the sediment translating across the dorsal surface increased, and accordingly, sediment coverage of the dorsal surface increased. Mean sediment coverage was 82.5% ± 3.0 S.E.M, and appeared to be selectively controlled, whereby the pectoral fins tended to bury more than the body, head and tail, and the body more than the head and the tail. In the most vigorous burying events, vortices of sediment shed from each fin collided at the midline and annihilated, reorienting the sediment flow and sending jets of sediment towards the head and the tail, covering these locations with sediment. Hence, this study demonstrates that the mechanism of burying employed byP. motoropermits effective control of sediment vortices and flows to modulate the extent of burying.
A causal role for mouse superior colliculus in visual perceptual decision-making
Authors: Wang Lupeng , McAlonan Kerry , Goldstein Sheridan , Gerfen Charles R. , Krauzlis Richard J.
Published: November 2019

The superior colliculus (SC) is arguably the most important visual structure in the mouse brain and is well-known for its involvement in innate responses to visual threats and prey items. In other species, the SC plays a central role in voluntary as well as innate visual functions, including crucial contributions to selective attention and perceptual decision-making. In the mouse, the possible role of the SC in voluntary visual choice behaviors has not been established. Here, we demonstrate that the mouse SC plays a causal role in visual perceptual decision-making by transiently inhibiting SC activity during an orientation-change detection task. First, unilateral SC inhibition induced spatially specific deficits in detection. Hit rates were reduced and reaction times increased for orientation changes in the contralateral but not ipsilateral visual field. Second, the deficits caused by SC inhibition were specific to a temporal epoch coincident with early visual burst responses in the SC. Inhibiting SC during this 100-ms period caused a contralateral detection deficit, whereas inhibition immediately before or after did not. Third, SC inhibition reduced visual detection sensitivity. Psychometric analysis revealed that inhibiting SC visual activity significantly increased detection thresholds for contralateral orientation changes. In addition, effects on detection thresholds and lapse rates caused by SC inhibition were larger in the presence of a competing visual stimulus, indicating a role for the mouse SC in visual target selection. Together, our results demonstrate that the mouse SC plays a crucial role in voluntary visual choice behaviors.

Significance statement

The mouse superior colliculus has become a popular model for studying the circuit organization and development of the visual system. Although the SC is a fundamental component of the visual pathways in mice, its role in visual perceptual decision-making is not clear. By investigating how temporally precise SC inhibition influenced behavioral performance during a visually guided orientation change detection task, we identified a 100-ms temporal epoch of SC visual activity that is crucial for the ability of mice to detect behaviorally relevant visual changes. In addition, we found that SC inhibition also caused deficits in visual target selection. Thus, our findings highlight the importance of the SC for visual perceptual choice behavior in the mouse.
Genomic characterization of the non-O1/non-O139 Vibrio cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018
Authors: Arteaga Mónica , Velasco Juliana , Rodriguez Shelly , Vidal Maricel , Arellano Carolina , Silva Francisco , Carreño Leandro J. , Vidal Roberto , Montero David A.
Published: November 2019

Vibrio cholerae is a human pathogen, which is transmitted by the consumption of contaminated food or water. V. cholerae strains belonging to the serogroups O1 and O139 can cause cholera outbreaks and epidemics, a severe life-threatening diarrheal disease. In contrast, serogroups other than O1 and O139, denominated as non-O1/non-O139, have been mainly associated with sporadic cases of moderate or mild diarrhea, bacteremia and wound infections. Here we investigated the virulence determinants and phylogenetic origin of a non-O1/non-O139 V. cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018. We found that this outbreak strain lacks the classical virulence genes harboured by O1 and O139 strains, including the cholera toxin (CT) and the toxin-coregulated pilus (TCP). However, this strain carries genomic islands (GIs) encoding Type III and Type VI secretion systems (T3SS/T6SS) and antibiotic resistance genes. Moreover, we found these GIs are wide distributed among several lineages of non-O1/non-O139 strains. Our results suggest that the acquisition of these GIs may enhance the virulence of non-O1/non-O139 strains that lack the CT and TCP-encoding genes. Our results highlight the pathogenic potential of these V. cholerae strains.

DATA SUMMARY

Sequence data were submitted to GenBank under the accession number SRLP00000000. The authors confirm that all supporting data and protocols have been provided within the article or through supplementary data files.

Data statement

All supporting data, code and protocols have been provided within the article or through supplementary data files. Four supplementary tables are available with the online version of this article.
The early local and systemic Type I interferon responses to ultraviolet B light exposure are cGAS dependent
Authors: Skopelja-Gardner Sladjana , An Jie , Tai Joyce , Tanaka Lena , Sun Xizhang , Hermanson Payton , Baum Rebecca , Kawasumi Masaoki , Green Richard , Gale Michael , Kalus Andrea , Werth Victoria P. , Elkon Keith B.
Published: November 2019

Most systemic lupus erythematosus (SLE) patients are photosensitive and ultraviolet B light (UVB) exposure worsens cutaneous disease and precipitates systemic flares of disease. The pathogenic link between skin disease and systemic exacerbations in SLE remains elusive. In an acute model of UVB-triggered inflammation, we observed that a single UV exposure triggered a striking IFN-I signature not only in the skin, but also in the blood and kidneys. The early IFN-I signature was significantly higher in female compared to male mice. The early IFN-I response in the skin was almost entirely, and in the blood partly, dependent on the presence of cGAS, as was skin inflammatory cell infiltration. Inhibition of cGAMP hydrolysis augmented the UVB-triggered IFN-I response. UVB skin exposure leads to cGAS-activation and both local and systemic IFN-I signature and could contribute to acute flares of disease in susceptible subjects such as patients with SLE.
mir-71 mediates age-dependent opposing contributions of the stress activated kinase KGB-1 inCaenorhabditis elegans
Authors: Ruediger Cyrus , Shapira Michael
Published: November 2019

Studying the evolutionary processes that shaped aging offers a path for understanding the causes of aging. The Antagonistic Pleiotropy theory for the evolution of aging proposes that the inverse correlation between natural selection strength and aging allows positive selection of gene variants with early-life beneficial contributions to fitness in spite of detrimental late-life consequences. However, mechanistic understanding of how this principle manifests in aging is still lacking. We previously identified antagonistic pleiotropy in the function of theCaenorhabditis elegansJNK homolog KGB-1, which provided stress protection in developing larvae, but sensitized adults to stress and shortened their lifespan. To a large extent, KGB-1’s contributions depended on age-dependent and opposing regulation of the stress transcription factor DAF-16, but the underlying mechanisms remained unknown. Here we describe a role for the microRNA mir-71 in mediating effects of KGB-1 on DAF-16 and on downstream phenotypes. Fluorescent imaging along with genetic and survival analyses revealed age-dependent regulation ofmir-71expression by KGB-1 – upregulation in larvae, but downregulation in adults, and showed thatmir-71was required both for late-life effects of KGB-1 (infection sensitivity and shortened lifespan), as well as for early life resistance to cadmium. Whilemir-71disruption did not compromise development under protein folding stress (known to depend on KGB-1), disruption of the argonaute genealg-1, a central component of the microRNA machinery, did. These results suggest that microRNAs play a role in mediating age-dependent antagonistic contributions of KGB-1 to survival, with mir-71 playing a central role and additional microRNAs contributing redundantly.
Fast-evolving alignment sites are highly informative for reconstructions of deep Tree of Life phylogenies
Authors: Thibério Rangel L. , Fournier Gregory P.
Published: November 2019

The trimming of fast-evolving sites, often known as “slow-fast” analysis, is broadly used in microbial phylogenetic reconstruction under assumption that fast-evolving sites do not retain accurate phylogenetic signal due to substitution saturation. Therefore, removing sites that have experienced multiple substitutions would improve the signal-to-noise ratio in phylogenetic analyses, with the remaining slower-evolving sites preserving a more reliable record of evolutionary relationships. Here we show that, contrary to this assumption, even the fastest evolving sites, present in conserved proteins often used in Tree of Life studies, contain reliable and valuable phylogenetic information, and that the trimming of such sites can negatively impact the accuracy of phylogenetic reconstruction. Simulated alignments modeled after ribosomal protein datasets used in Tree of Life studies consistently show that slow-evolving sites are less likely to recover true bipartitions than even the fastest-evolving sites. Furthermore, site specific substitution-rates are positively correlated with the frequency of accurately recovered short-branched bipartitions, as slowly evolving sites are less likely to have experienced substitutions along these intervals. Using published Tree of Life sequence alignment datasets, we additionally show that both slow-and fast-evolving sites contain similarly inconsistent phylogenetic signals, and that, for fast-evolving sites, this inconsistency can be attributed to poor alignment quality. Furthermore, trimming fast sites, slow sites, or both is shown to have substantial impact on phylogenetic reconstruction across multiple evolutionary models. This is perhaps most evident in the resulting placements of Eukarya and Asgardarchaeota groups, which are especially sensitive to the implementation of different trimming schemes.

Significance Statement

It is common practice among comprehensive microbial phylogenetic studies to trim fast-evolving sites from the source alignment in the expectation to increase the signal to noise ratio. Here we show that despite fast-evolving sites being more sensitive to parameter misspecifications than mid-rate evolving sites, such sensitivity is comparable, if not smaller, than what we observe among slow-evolving sites. Through the use of both empirical and simulated datasets we also show that, besides the lack of evidences regarding the noisy nature of fast-evolving sites, such sites are of core importance for the reliable the reconstruction of short-branched bipartitions. Such points are exemplified by the variations in the Eukarya+Archaea Tree of Life when subjective alignment trimming strategies are employed.
Identifying Integrative Molecular Pathways for Predictive Modeling of Infectious Disease
Authors: Schaper Charles D.
Published: November 2019

The signs and symptoms of infectious disease are similar in presentation, such as fever and fatigue, but differ in magnitude, duration, and sequence. Although observable responses of dysfunction are well characterized, the integrative system mechanisms driving such trajectories are poorly known, even during normative circumstances. Here, molecular pathways are presented that enable predictive modeling of autonomic dysfunction due to infectious agents, and that illustrate a coordinating integration of body system dynamics. To arrive at this result, a molecular model is presented which shows, for the first time, that the hormone cortisol (CORT) and prostaglandin E2 (PGE2) have approximately equivalent chemical affinity, as indicated by the positioning of functional groups in hydrogen bonding and hydrophobicity, with the ligand binding domain of the glucocorticoid receptor (GR). A mathematical model is developed to predict that the signs and symptoms of illnesses are associated with the competitive inhibition at the GR of CORT and PGE2 within the hypothalamus that prevents normal gene expression during DNA transcription. To validate the pathways and model, a case study is presented to analyze the cause and presentation of fever and fatigue over multiple days due to the injection of a pneumococcal vaccine as influenced by physical activity. The research provides quantitative understanding of the root causes of signs and symptoms of infectious disease, which for example can offer a quantitative explanation of common symptomatic concerns of illness, such as fever, and can result in optimal drug treatment plans to minimize the effects of ailments.

Graphical Abstract
Individual differences in haemoglobin concentration influence BOLD fMRI functional connectivity and its correlation with cognition
Authors: Ward Phillip G. D. , Orchard Edwina R. , Oldham Stuart , Arnatkevičiūtė Aurina , Sforazzini Francesco , Fornito Alex , Storey Elsdon , Egan Gary F. , Jamadar Sharna D.
Published: November 2019

Resting-state connectivity measures the temporal coherence of the spontaneous neural activity of spatially distinct regions, and is commonly measured using BOLD-fMRI. The BOLD response follows neuronal activity, when changes in the relative concentration of oxygenated and deoxygenated haemoglobin cause fluctuations in the MRI T2* signal. Since the BOLD signal detects changes in relative concentrations of oxy/deoxy-haemoglobin, individual differences in haemoglobin levels may influence the BOLD signal-to-noise ratio in a manner independent of the degree of neural activity. In this study, we examined whether group differences in haemoglobin may confound measures of functional connectivity. We investigated whether relationships between measures of functional connectivity and cognitive performance could be influenced by individual variability in haemoglobin. Finally, we mapped the neuroanatomical distribution of the influence of haemoglobin on functional connectivity to determine where group differences in functional connectivity are manifest.

In a cohort of 518 healthy elderly subjects (259 men) each sex group was median split into two groups with high and low haemoglobin concentration. Significant differences were obtained in functional connectivity between the high and low haemoglobin groups for both men and women (Cohen’s d 0.17 and 0.03 for men and women respectively). The haemoglobin connectome in males showed a widespread systematic increase in functional connectivity correlational scores, whilst the female connectome showed predominantly parietal and subcortical increases and temporo-parietal decreases. Despite the haemoglobin groups having no differences in cognitive measures, significant differences in the linear relationships between cognitive performance and functional connectivity were obtained for all 5 cognitive tests in males, and 4 out of 5 tests in females.

Our findings confirm that individual variability in haemoglobin levels that give rise to group differences are an important confounding variable in BOLD-fMRI-based studies of functional connectivity. Controlling for haemoglobin variability as a potentially confounding variable is crucial to ensure the reproducibility of human brain connectome studies, especially in studies that compare groups of individuals, compare sexes, or examine connectivity-cognition relationships.

Highlights

Individual differences in haemoglobin significantly impact measures of functional connectivity in the elderly.

Significant differences in connectivity-cognition relationships are shown between groups separated by haemoglobin values without accompanying cognitive differences.

The influence of haemoglobin on functional connectivity differs between men and women.
Outer Membrane Vesicles Mediated Horizontal Transfer of an Aerobic Denitrification Gene betweenEscherichia coli
Authors: Luo Yang , Miao Jiahui , Qiao Weichuan
Published: November 2019

Bacterial genetic material can be horizontally transferred between microorganisms via outer membrane vesicles (OMVs) released by bacteria. Up to now, the application of vesicle-mediated horizontal transfer of “degrading genes” in environmental remediation has not been reported. In this study, thenirSgene from an aerobic denitrification bacterium,Pseudomonas stutzeri, was enclosed in a pET28a plasmid, transformed intoEscherichia coli(E. coli) DH5α and expressed inE. coliBL21. TheE. coliDH5α released OMVs containing the recombination plasmid pET28a–nirS. Moreover, the amount of released OMVs-protein and DNA in OMVs increase as heavy metal concentrations and temperature increased. When compared with the free pET28a–nirSplasmid’s inability to transform,nirSin OMVs could be transferred intoE. coliBL21 with the transformation frequency of 2.76×106CFU/g when the dosage of OMVs was 200 µg under natural conditions, andnirScould express successfully in recipient bacteria. Furthermore, the recipient bacteria that received OMVs could produce 18.16 U ml-1activity of nitrite reductase. Vesicle-mediated HGT of aerobic denitrification genes provides a novel bioaugmentation technology of nitrogen removal.

Importance

Previous studies have reported that bacterial genetic material can be horizontally transferred between microorganisms via outer membrane vesicles(OMVs) released by bacteria. However, the application of vesicle-mediated horizontal transfer of “degrading genes” in environmental remediation has not been reported. In this study, we found that OMVs could mediate horizontal transfer of pET28a–nirSplasmid between E. coli under natural condition. The transformation frequency reached to 2.76×106, which was higher than that of the free plasmid. Vesicle-mediated HGT of aerobic denitrification genes provides a novel bioaugmentation technology of nitrogen removal.
Hippocampus has lower oxygenation and weaker control of brain blood flow than cortex, due to microvascular differences
Authors: Shaw K. , Bell L. , Boyd K. , Grijseels D.M. , Clarke D. , Bonnar O. , Crombag H.S. , Hall C.N.
Published: November 2019

The hippocampus is essential for spatial and episodic memory but is damaged early in Alzheimer’s disease and is very sensitive to hypoxia. Understanding how it regulates its oxygen supply is therefore key for designing interventions to preserve its function. However, studies of neurovascular function in the hippocampusin vivohave been limited by its relative inaccessibility. Here we compared hippocampal and visual cortical neurovascular function in awake mice, using two photon imaging of individual neurons and vessels and measures of regional blood flow and haemoglobin oxygenation. We show that blood flow, blood oxygenation and neurovascular coupling were decreased in the hippocampus compared to neocortex, because of differences in both the vascular network and pericyte and endothelial cell function. Modelling oxygen diffusion indicates that these features of the hippocampal vasculature could explain its sensitivity to damage during neurological conditions, including Alzheimer’s disease, where the brain’s energy supply is decreased.
Mendelian randomisation for mediation analysis: current methods and challenges for implementation
Authors: Carter Alice R , Sanderson Eleanor , Hammerton Gemma , Richmond Rebecca C , Smith George Davey , Heron Jon , Taylor Amy E , Davies Neil M , Howe Laura D
Published: November 2019

Mediation analysis seeks to explain the pathway(s) through which an exposure affects an outcome. Mediation analysis experiences a number of methodological difficulties, including bias due to confounding and measurement error. Mendelian randomisation (MR) can be used to improve causal inference for mediation analysis. We describe two approaches that can be used for estimating mediation analysis with MR: multivariable Mendelian randomisation (MVMR) and two-step Mendelian randomisation. We outline the approaches and provide code to demonstrate how they can be used in mediation analysis. We review issues that can affect analyses, including confounding, measurement error, weak instrument bias, and analysis of multiple mediators. Description of the methods is supplemented by simulated and real data examples. Although Mendelian randomisation relies on large sample sizes and strong assumptions, such as having strong instruments and no horizontally pleiotropic pathways, our examples demonstrate that it is unlikely to be affected by confounders of the exposure or mediator and the outcome, reverse causality and non-differential measurement error of the exposure or mediator. Both MVMR and two-step MR can be implemented in both individual-level MR and summary data MR, and can improve causal inference in mediation analysis.
PCA-based source-space contrast maps reveal psychologically meaningful individual differences in continuous MEG activity
Authors: Heinilä Erkka , Hyvärinen Aapo , Ristaniemi Tapani , Parkkonen Lauri , Parviainen Tiina
Published: November 2019

Within the field of neuroimaging, there has been an increasing trend towards studying brain activity in naturalistic conditions, and it is possible to robustly estimate networks of on-going oscillatory activity in the brain. However, not many studies have focused on differences between individuals in on-going brain activity that would be associable to psychological or behavioral characteristics. Existing standard methods can perform well at single-participant level, but generalizing the methodology across many participants is challenging due to individual differences of brains. As an example of a clinically relevant, naturalistic condition we consider here mindfulness. Trait mindfulness, as well as a mindfulness-based intervention cultivating focused attention, is often associated with benefits for psychological health. Therefore, the manner in which the brain engages in focused attention vs. mind wandering is likely to associate with individual differences in psycho–behavioral tendencies.

We recorded MEG from 29 participants both in a state of focused attention and in a state of simulated mind wandering. We used Principal Component Analysis to decompose spatial average activation maps of focused attention contrasted with two different mind wandering states. The first principal component, which reflected differential engagement of bilateral parietal areas during focused attention vs. mind wandering, was associated with behavioral characteristics of inhibition, anxiousness and depression, as measured by standard questionnaires. We demonstrated that such decomposition of time-averaged contrast maps can overcome some of the challenges in methods based on concatenated data, especially from the perspective of behaviorally and clinically relevant characteristics in the ongoing brain oscillatory activity.

Highlights

We present a specific method to analyse/establish associations between brain oscillations and behavioral characteristics.

We found that activity levels in parietal areas during mind wandering compared to focused attention were associated with the behavioral trait of inhibition and anxiety.
gplas: a comprehensive tool for plasmid analysis using short-read graphs
Authors: Arredondo-Alonso Sergio , Bootsma Martin , Hein Yaïr , Rogers Malbert R.C. , Corander Jukka , Willems Rob JL , Schürch Anita C.
Published: November 2019

Plasmids can horizontally transmit genetic traits, enabling rapid bacterial adaptation to new environments and hosts. Short-read whole-genome sequencing data is often applied to large-scale bacterial comparative genomics projects but the reconstruction of plasmids from these data is facing severe limitations, such as the inability to distinguish plasmids from each other in a bacterial genome. We developed gplas, a new approach to reliably separate plasmid contigs into discrete components using sequence composition, coverage, assembly graph information and clustering based on a pruned network of plasmid unitigs. Gplas facilitates the analysis of large numbers of bacterial isolates and allows a detailed analysis of plasmid epidemiology based solely on short read sequence data.

Availability and implementation

Gplas is written in R, Bash and uses a Snakemake pipeline as a workflow management system. Gplas is available under the GNU General Public License v3.0 at https://gitlab.com/sirarredondo/gplas.git

Contact

a.c.schurch@umcutrecht.nl
Integrated effect of plant growth regulators with boron sources on some biological parameters of sugar beet
Authors: Qotob Marwa A. , Nasef Mostafa A. , Elhakim Heba K. A. , Shaker Olfat G. , Habashy Nader R. , Abdelhamid Ismail A.
Published: November 2019

Any improvement in agricultural systems that results higher production aimed to reduce negative environmental impacts and enhance sustainability plant growth regulators (PGRs) such as gibberellin have similar physiological and biological effects to those of plant hormones, and therefore used widely in agriculture to minimize unwanted shoot growth without lowering plant productivity.

An experimental field was conducted at Giza Experimental Station Egypt, on sugar beet plants (Beta vulgarisL.var.Sara poly) with some plant growth regulators (gibberellin and proline) foliar application at three rates of zero (control), 100 and 200 mg l−1and boron sources (Boric acid and B-NPs) with 75% of macro-nutrients from full dose.

The main target of this study to evaluate another plant growth regulator source like proline which is safer than gibberellin for maximizing sugar beet biological parameters to reduce the gap between sugar consumption and production in presence of boron sources.

Data showed that the foliar applications of gibberellin (GA3) at rate 100 mg l−1and proline at 200 mg l−1were found to be the more effective without significant differences for plant growth, productivity and quality may be due to increased N use efficiency, especially at sub-optimal macro nutrient fertilizers. Regard to boron sources, B-NPs had positive effect on all biological parameters under study due to sugar transport, cell membrane synthesis, nitrogen fixation, respiration, carbohydrate metabolisms, root growth, functional characteristics and development.
Reflections on interdisciplinary critical intellectual capital accounting research
Authors: Dumay John , Guthrie James
Published: November 2019

Purpose

In 2001, the Accounting, Auditing & Accountability Journal (AAAJ) published a special issue entitled “Managing, measuring and reporting intellectual capital for the new millennium”. After 20 years, we revisit the eight articles in this special issue to trace early developments in interdisciplinary intellectual capital (IC) accounting research, link these developments to the current state of play, and set out an agenda for future research. The paper aims to discuss this issue.

Design/methodology/approach

This paper, written reflectively, includes an impact assessment of the articles using citation analysis and a thematic framing of the prominent issues they discussed. We critically reflect on the status of these eight foundational papers after 20 years, before presenting propositions for a multidisciplinary IC research future.

Findings

We find that IC research needs to extend beyond organisational boundaries to help improve human rights, human dignity and the human condition as part of the wider interdisciplinary accounting project. We argue that fifth stage IC research can assist because it explores beyond organisational boundaries and helps address the wicked problems of the world.

Research limitations/implications

This paper only investigates the themes found in the AAAJ special issue. However, the implications for researchers are intended to be transformational because, to go forward and help resolve the material issues facing society and the planet, researchers need to move from being observers to participants.

Originality/value

We argue that IC researchers must embrace both interdisciplinary and multidisciplinary IC research. This requires IC researchers to reflect on what they are trying to achieve and which issues facing the planet are material.
Does a creative identity encourage innovative behaviour? Evidence from knowledge-intensive IT service firms
Authors: Uddin Md. Aftab , Priyankara H.P. Rasika , Mahmood Monowar
Published: November 2019

Purpose

The purpose of this paper is to investigate the influence of an employee’s personal creative identity on their innovation behaviour in knowledge-intensive information technology (IT) service provider firms. It further investigates the mediating role of an employee’s creative process engagement (CPE) and the moderating effects of the organizational creative climate on creative identity-innovative behaviour (IB) relationships.

Design/methodology/approach

This study follows a quantitative method. Using a multi-item survey instrument, a total of 316 questionnaires were collected from the employees of IT service provider firms in Chittagong, Bangladesh. The collected data were analysed using structural equation modelling, factor analysis and path analysis to test the hypotheses and to assess the moderating and mediating effects of the variables.

Findings

The results revealed the significant influence of an employee’s creative personal identity (CPI) on their IB. The mediation analysis revealed that CPE mediates the association between a CPI and IB. The study also found a significant moderating effect of a creative organizational climate between a CPI and CPE.

Research limitations/implications

Based on the premise of the interactionist approach of creativity and role identity theory, this study contributes to the creativity and innovation literature by providing empirical support for the relationship between a personal creative identity, organizational creative culture, CPE and IB in IT service organizations.

Originality/value

This study adopts a distinct model comprising four different variables to investigate an employee’s IB from a multi-level perspective, i.e., a creative identity and CPE at the individual level and a creative climate and IB at the organizational level. This integrated model using predictors from multiple levels supports the theoretical assumption that IB results from the interaction of individual and organizational level factors.
Globalization and innovation with Chinese characteristics: the case of the automotive industry
Authors: Petti Claudio , Spigarelli Francesca , Lv Ping , Biggeri Mario
Published: November 2019

Purpose

The purpose of this paper is to analyze the internationalization of Chinese new global players through innovation-oriented Mergers and Acquisitions (M&As).

Design/methodology/approach

The paper combines the analysis of East-Asian and Chinese multinationals’ international expansion within international business (IB) and innovation domains, with the “latecomer” perspective. It is a conceptual contribution, based on the role of local institutions and firm’s absorptive capacity. A theoretical framework is developed, and further elucidated with two illustrative cases of Chinese M&As abroad in the automotive sector. Implications for theoretical development and practical application are then drawn.

Findings

Chinese firms’ M&As abroad have become one of the preferential modes of developing innovation capabilities. The success of these endeavors is argued to be the result of a combination of a strong push from government industrial policies, along with significant internal knowledge assimilation and transformation capabilities.

Originality/value

The paper extends IB literature integrating the latecomer firms’ perspective within a novel conceptual framework, which adds to the traditional resource-based arguments about incumbent MNEs asset and knowledge-seeking internationalization modes, as well as institutional and multi-dimensional absorptive capacity perspectives.
Study of chiroptical effects on the novel chiral photonic structure
Authors: Zara Chemseddine , Mezache Zinelabiddine , Benabdelaziz Fatiha
Published: November 2019

Purpose

The purpose of this paper is to demonstrate a novel chiral photonic crystal with thin thickness and small unit cells via numerical calculations. The multi-band circular dichroism is found in a wide frequency range from 400 to 600 THz by studying the transmission properties.

Design/methodology/approach

To investigate this chiral photonic structure, refection coefficients are analytically computed using finite element method. Numerical results are given, and physical properties are discussed, including the optical rotation, the circular dichroism and the absorption.

Findings

The results of this modeling and simulation under COMSOL multiphysics environment have led the authors to study the scattered parameters such as the coefficient of transmission (S21) and the coefficient of reflection (S11) for a 2D CPC nanostructure. The authors have also developed script under the Matlab environment which studies absorption and circular dichroism and ensure the existence of optical activity. According to the obtained results, the coefficient of transmission is proportional to the parameter of chirality.

Originality/value

The authors have designed a novel chiral photonic structure that exhibits larger circular dichroism. The CD spectrum has typically both positive and negative bands. The design principles defined in this work, which combine the concepts of the photonic crystal with the chiral structure (optical activity, circular dichroism and absorption), represent a model for simulation of the properties of a more complex chiral photonic structure. These results led to realization of novel circularly polarized devices in nanotechnologies.