bluuebunny/crossref_metadata_2025 huggingface dataset:
Early Tactile Stimulation Influences the Development of Alzheimer Disease in Gestationally Stressed APPNL-G-FAdult OffspringNL-G-F/NL-G-Fmice
Authors: Hossain Shakhawat R. , Karem Hadil , Jafari Zahra , Kolb Bryan E. , Mohajerani Majid H.
Published: March 2022

Alzheimer Disease (AD) is associated with cerebral plaques and tangles, reduced synapse number, and shrinkage in several brain areas and these morphological effects are associated with the onset of compromised cognitive, motor, and anxiety-like behaviours. The focus of this study was to examine the effect of neonatal tactile stimulation on AD-like behavioural and neurological symptoms on APPNL-G-F/NL-G-Fmice, a mouse model of AD. Our findings indicate that neonatal tactile stimulation improves cognition, motor skills, and anxiety-like symptoms in both gestationally stressed and non-stressed adult APP mice and that these alterations are associated with reduced Aβ plaque formation. Thus, tactile stimulation appears to be a promising non-invasive preventative strategy for slowing the onset of dementia in aging animals.
MAPLE: A Hybrid Framework for Multi-Sample Spatial Transcriptomics Data
Authors: Jeon Hyeongseon , Allen Carter , Ovando-Ricárdez José Antonio , Chang Yuzhou , Rosas Lorena , Vanegas Natalia-Del Pilar , Cheng Hao , Xie Juan , Wang Cankun , Mora Ana L. , Rojas Mauricio , Ma Qin , Chung Dongjun
Published: March 2022

High throughput spatial transcriptomics (HST) technologies provide unprecedented opportunity to identify spatially resolved cell sub-populations in tissue samples. However, existing methods preclude joint analysis of multiple HST samples, do not allow for differential abundance analysis (DAA), and ignore uncertainty quantification. To address this, we developed MAPLE: a hybrid deep learning and Bayesian modeling framework for joint detection of spatially informed sub-populations, DAA, and uncertainty quantification. We demonstrate the capability of MAPLE to achieve these multi-sample analyses through four case studies that span a variety of organs in both humans and animal models. AnRpackagemapleis available on GitHub athttps://github.com/carter-allen/maple.
Genomic resolution of cryptic species diversity in chipmunks
Authors: Herrera Nathanael D. , Bell Kayce C. , Callahan Colin M. , Nordquist Erin , Sarver Brice A. J. , Sullivan Jack , Demboski John R. , Good Jeffrey M.
Published: March 2022

Discovery of cryptic species is essential to understanding the process of speciation and assessing the impacts of anthropogenic stressors. Here, we used genomic data to test for cryptic species diversity within an ecologically well-known radiation of North American rodents, western chipmunks (Tamias). We assembled a de novo reference genome for a single species (Tamias minimus) combined with new and published targeted sequence-capture data for 21,551 autosomal and 493 X-linked loci sampled from 121 individuals spanning 22 species. We identified at least two cryptic lineages corresponding with an isolated subspecies of least chipmunk (T. minimus grisescens) and with a restricted subspecies of the yellow-pine chipmunk (T. amoenus cratericus) known only from around the extensive Craters of the Moon lava flow. Additional population-level sequence data revealed that the so-called Crater chipmunk is a distinct species that is abundant throughout the coniferous forests of southern Idaho. This cryptic lineage does not appear to be most closely related to the ecologically and phenotypically similar yellow-pine chipmunk but does show evidence for recurrent hybridization with this and other species.
Transcranial random noise stimulation of the primary visual cortex but not retina modulates visual contrast sensitivity
Authors: Potok Weronika , Post Alain , Bächinger Marc , Kiper Daniel , Wenderoth Nicole
Published: March 2022

Transcranial random noise stimulation (tRNS) has been shown to significantly improve visual perception. Previous studies demonstrated that tRNS delivered over cortical areas acutely enhances visual contrast detection of stimuli when tRNS intensity is optimized for the individual. However, it is currently unknown whether tRNS-induced signal enhancement could be achieved within different neural substrates along the retino-cortical pathway and whether the beneficial effect of optimal tRNS intensities can be reproduced across sessions.

In 3 experimental sessions, we tested whether tRNS applied to the primary visual cortex (V1) and/or to the retina improves visual contrast detection. We first measured visual contrast detection threshold (VCT; N=24, 16 females) during tRNS delivery separately over V1 (no tRNS, 0.75, 1, 1.5mA) and over the retina (no tRNS, 0.1, 0.2, 0.3mA), determined the optimal tRNS intensities for each individual (ind-tRNS), and retested the effects of ind-tRNS within the sessions. We further investigated whether we could reproduce the ind-tRNS-induced modulation on a different session (N=19, 14 females). Finally, we tested whether the simultaneous application of ind-tRNS to the retina and V1 causes additive effects.

We found that at the group level tRNS of 0.75mA decreases VCT compared to baseline when delivered to the V1. Beneficial effects of ind-tRNS could be replicated when retested within the same experimental session but not when retested in a separate session. Applying tRNS to the retina did not cause a systematic reduction of VCT, irrespective of whether the individually optimized intensity was considered or not. We also did not observe consistent additive effects of V1 and retina stimulation.

Our findings demonstrate that V1 seems to be more sensitive than the retina to tRNS-induced modulation of visual contrast processing.

Significance statement

Our findings confirm previous evidence showing acute online benefits of tRNS of V1 on visual contrast detection in accordance with the stochastic resonance phenomenon. We further extend it, demonstrating that the optimal tRNS intensity varies among participants, but when individually tailored it can improve visual processing when re-tested within the experimental session. The tRNS-induced enhancement in visual sensitivity seems to be specific for cortical contrast processing as stimulation of the retina did not lead to systematic effects.
Social media mining and photo-identification detects the shift of long-term seasonal foraging habitat for a juvenile loggerhead sea turtle
Authors: Papafitsoros Kostas
Published: March 2022

Animal imagery uploaded on social media has been identified as an important tool in wildlife research and conservation and has been used in a variety of recent studies. Here a case study is presented, where a detailed analysis of social media content revealed a shift of a long-term foraging habitat for a juvenile loggerhead sea turtle (Caretta caretta) in Greece. In particular, this individual was a long term resident of Zakynthos island, Greece, from 2016 until 2020 (5 consecutive summer seasons), regularly foraging on a nearshore reef, with no observations of it being made during the 2021 season. However regular social media image mining combined with photo-identification, detected this individual foraging in the Gulf of Corinth in August 2021, more that 200km away from his previous foraging habitat. This case study (i) shows the possibility for juvenile loggerheads to shift their foraging site even after long term use, with implications in capture-mark-recapture studies and (ii) once more highlights the usefulness of social media mining and citizen science in diverse aspects of sea turtle studies.
Genomic patterns of divergence in the early and late steps of speciation of the deep-sea vent thermophilic worms of the genusAlvinella
Authors: Thomas–Bulle Camille , Bertrand Denis , Nagarajan Niranjan , Copley Richard , Corre Erwan , Hourdez Stéphane , Bonnivard Éric , Claridge-Chang Adam , Jollivet Didier
Published: March 2022

Background

The transient and fragmented nature of the deep-sea hydrothermal environment made of ridge subduction, plate collision and the emergence of new rifts is currently acting to the separation of vent populations, local adaptation and is likely to promote bursts of speciation and species specialization. The tube-dwelling wormsAlvinella pompejanacalled the Pompeii worm and its sister speciesA. caudatalive syntopically on the hottest part of deep-sea hydrothermal chimneys along the East Pacific Rise. They are exposed to extreme thermal and chemical gradients, which vary greatly in space and time, and thus represent ideal candidates for understanding the evolutionary mechanisms at play in the vent fauna evolution.

Results

In the present study, we explored genomic patterns of divergence in the early and late steps of speciation of these emblematic worms using transcriptome assemblies and the first draft genome to better understand the relative role of geographic isolation and habitat preference in their genome evolution. Analyses were conducted on allopatric populations ofAlvinella pompejana(early stage of separation) and betweenA. pompejanaand its syntopic speciesAlvinella caudata(late stage of speciation). We first identified divergent genomic regions and targets of selection as well as their position in the genome over collections of orthologous genes and, then, described the speciation dynamics by documenting the annotation of the most divergent and/or positively selected genes involved in the isolation process. Gene mapping clearly indicated that divergent genes associated with the early stage of speciation, although accounting for nearly 30% of genes, are highly scattered in the genome without any island of divergence and not involved in gamete recognition or mito-nuclear incompatibilities. By contrast, genomes ofA. pompejanaandA. caudataare clearly separated with nearly all genes (96%) exhibiting high divergence. This congealing effect however seems to be linked to habitat specialization and still allows positive selection on genes involved in gamete recognition, as a possible long-duration process of species reinforcement.

Conclusion

Our analyses pointed out the non-negligible role of natural selection on both the early and late stages of speciation in the emblematic thermophilic worms living on the walls of deep-sea hydrothermal chimneys. They shed ligth on the evolution of gene divergence during the process of speciation and species specialization over a very long period of time.
A tale of two connectivities: intra- and inter-subject functional connectivity jointly enable better prediction of social abilities
Authors: Xie Hua , Redcay Elizabeth
Published: March 2022

Naturalistic functional magnetic resonance imaging (fMRI) paradigms, such as movie viewing, are attracting increased attention, given their ability to mimic the real-world cognitive demands on attention and multimodal sensory integration. Moreover, naturalistic paradigms allow for characterizing brain network responses associated with dynamic social cognition in a model-free manner using inter-subject functional connectivity (ISFC). While intra-subject functional connectivity (FC) characterizes the individual’s brain functional architecture, ISFC characterizes the neural coupling driven by time-locked extrinsic dynamic stimuli across individuals. Here, we hypothesized that ISFC and FC provide distinct and complementary information about individual differences in social cognition. To test this hypothesis, we examined a public movie-viewing fMRI dataset with 32 healthy adults and 90 typically developing children. Building three partial least squares regression (PLS) models to predict social abilities using FC and/or ISFC, we compared predictive performance to determine whether combining two connectivity measures could improve the prediction accuracy of individuals’ social-cognitive abilities measured by a Theory of Mind (ToM) assessment. Our results indicated that the joint model (ISFC+FC) yielded the highest predictive accuracy and significantly predicted individuals’ social cognitive abilities (rho = 0.34, p < 0.001). We also confirmed that the improved accuracy was not due to the increased feature dimensionality. In conclusion, we demonstrated that intra-/inter-subject connectivity encodes unique information about social abilities, and a joint investigation could help us gain a more complete understanding of the complex processes supporting social cognition.
LIN-35 is necessary in both the soma and germline for preserving fertility in Caenorhabditis elegans under moderate temperature stress
Authors: Mikeworth Brian P. , Compere Frances V. , Quaglia Kristen , Petrella Lisa N.
Published: March 2022

Maintenance of germline function under stress conditions is crucial for species survival. The germline across many species is especially sensitive to elevated temperature stress. We have investigated the role that the pocket protein LIN-35 plays in preserving fertility in C. elegans under moderate high temperature stress. Here we show that lin-35 mutants have a number of temperature sensitive germline defects. The decreased brood size seen at elevated temperatures is more severe in lin-35 mutants than wild type. This loss of fertility under temperature stress is primarily due to loss of zygotic but not maternal LIN-35. Additionally, we have found that expression of LIN-35 is necessary in both the germline and soma for the preserving fertility at elevated temperature. Specifically, germline expressed LIN-35 is primarily what is important for maintaining fertility in hermaphrodites, but broad somatic expression of LIN-35 is also necessary for oocyte formation and/or function at elevated temperatures. Additionally, we found that overexpression of LIN-35 in the germline only can stabilize the formation of P granules in primordial germ cells. Our data adds to the emerging critical role that LIN-35 plays in buffering tissues against stress.
Regional variation in cholinergic terminal activity determines the non-uniform occurrence of cortical slow-wave activity during REM sleep
Authors: Nazari Mojtaba , Abadchi Javad Karimi , Naghizadeh Milad , Bermudez-Contreras Edgar J. , McNaughton Bruce L. , Tatsuno Masami , Mohajerani Majid H.
Published: March 2022

Sleep consists of two basic stages: non-rapid eye movement (NREM) and rapid eye movement (REM) sleep. NREM sleep is characterized by slow high-amplitude cortical EEG signals, while REM sleep is characterized desynchronized cortical rhythms. While, until recently, it has been widely believed that cortical activity during REM sleep is globally desynchronized, recent electrophysiological studies showed slow waves (SW) in some cortical areas during REM sleep. Electrophysiological techniques, however, have been unable to resolve the regional structure of these activities, due to relatively sparse sampling. We mapped functional gradients in cortical activity during REM sleep using mesoscale imaging in mice, and observed local SW patterns occurring mainly in somatomotor and auditory cortical regions, with minimum presence within the default mode network. The role of the cholinergic system in local desynchronization during REM sleep was also explored by calcium imaging of cholinergic terminal activity within the mouse cortex. Terminal activity was weaker in regions exhibiting SW activity more frequently during REM sleep. We also analyzed Allen Mouse Brain Connectivity dataset and found that these regions have weaker cholinergic projections from the basal forebrain.
Environmental thresholds in the functional mycobiome of global drylands
Authors: Egidi Eleonora , Delgado-Baquerizo Manuel , Berdugo Miguel , Guirado Emilio , Albanese Davide , Singh Brajesh K. , Coleine Claudia
Published: March 2022

Fungi are major drivers of ecosystem functions. Increases in aridity are known to negatively impact fungal communities in dryland ecosystems globally, however, much less is known on the potential influence of other environmental drivers. To fill this knowledge gap, we reanalyzed fungal data from 912 soil samples, providing the largest and most complete fungal community dataset from global drylands. We used machine learning tools to examine geographical patterns in community composition and spatial, edaphic, and climatic factors driving them. Further, we determined critical thresholds of community turnover along those gradients. Our analysis identifies UV index, climate seasonality, and sand content as the most important environmental predictors of community shifts, harbouring greatest association with the richness of putative plant pathogens and saprobes. Important nonlinear relationships existed with each of these fungal guilds, with increases in UV and temperature seasonality above 7.5 and 900 SD, respectively, being associated with an increased probability of plant pathogens and unspecified saprotrophs occurrence. Conversely, these environmental parameters had a negative relationship with litter and soil saprotrophs richness. Consequently, these functional groups might be differentially sensitive to environmental changes, which might result in an inevitable disturbance of current plant-soil dynamics in drylands.
Retinal neuroblast migration and laminar organization requires the cytoskeletal-interacting protein Mllt11
Authors: Blommers Marley , Stanton-Turcotte Danielle , Iulianella Angelo
Published: March 2022

Background

The vertebrate retina is an organized laminar structure comprised of distinct cell types populating three nuclear layers. During development, each retinal cell type follows a stereotypical temporal order of genesis, differentiation, and migration, giving rise to its stratified organization. Once born, the precise positioning of cells along the apico-basal (radial) axis of the retina is critical for subsequent connections to form, relying on orchestrated migratory processes. While these processes are critical for visual function to arise, the regulators of cellular migration and retinal lamination remain largely unexplored.

Results

We report a role for a microtubule-interacting protein, Mllt11 (Myeloid/lymphoid or mixed-lineage leukemia; translocated to chromosome 11/All1 Fused Gene From Chromosome 1q) in mammalian retinal cell migration during retinogenesis. We show that Mllt11 loss-of-function in mouse retinal neuroblasts affected the migration of ganglion and amacrine cells into the ganglion cell layer, and led to their ectopic accumulation in the inner plexiform layer.

Conclusions

We demonstrate that Mllt11 plays a critical role in the migration and lamination of neurons in the retina, and its loss impacted formation of the basal-most retinal layers.
Symbiosis with rhizobia limits range expansion only in polyploid legumes
Authors: Parshuram Zoe A. , Harrison Tia L. , Simonsen Anna K. , Stinchcombe John R. , Frederickson Megan E.
Published: March 2022

Both mutualism and polyploidy are thought to influence invasion success in plants but few studies have tested their joint effects. Mutualism can limit range expansion when plants cannot find a compatible partner in a novel habitat, or facilitate range expansion when mutualism increases a plant’s niche breadth. Polyploids are also expected to have greater niche breadth because of greater self-compatibility and phenotypic plasticity, increasing invasion success.

For 839 legume species, we compiled data from published sources to estimate ploidy, symbiotic status with rhizobia, specificity on rhizobia, and the number of introduced ranges.

We found that diploid species have had limited spread around the globe regardless of whether they are symbiotic or how many partners of rhizobia they can host. Polyploids, in contrast, have been successfully introduced to many new ranges, but interactions with rhizobia constrain their range expansion. In a hidden state model of trait evolution, we also found evidence of a high rate of re-diploidization in symbiotic legume lineages, suggesting that symbiosis and ploidy may interact at macroevolutionary scales.

Overall, our results suggest that symbiosis with rhizobia affects range expansion only in polyploid legumes.
Machine learning-aided multidimensional phenotyping of Parkinson’s disease patient stem cell-derived midbrain dopaminergic neurons
Authors: Vuidel Aurore , Cousin Loïc , Weykopf Beatrice , Haupt Simone , Hanifehlou Zahra , Wiest-Daesslé Nicolas , Segschneider Michaela , Peitz Michael , Ogier Arnaud , Brino Laurent , Brüstle Oliver , Sommer Peter , Wilbertz Johannes H.
Published: March 2022

Combining multiple Parkinson’s disease (PD) relevant cellular phenotypes might increase the accuracy of midbrain dopaminergic (mDA) in vitro models. We differentiated patient-derived induced pluripotent stem cells (iPSCs) with a LRRK2 G2019S mutation, isogenic control and genetically unrelated iPSCs into mDA neurons. Using automated fluorescence microscopy in 384-well plate format, we identified elevated levels of α-synuclein and Serine 129 phosphorylation (pS129), reduced dendritic complexity, and mitochondrial dysfunction. Next, we measured additional image-based phenotypes and used machine learning (ML) to accurately classify mDA neurons according to their genotype. Additionally, we show that chemical compound treatments, targeting LRRK2 kinase activity or α-synuclein levels, are detectable when using ML classification based on multiple image-based phenotypes. We validated our approach using a second isogenic patient derived SNCA gene triplication mDA neuronal model. This phenotyping and classification strategy improves the exploitability of mDA neurons for disease modelling and the identification of novel PD drug targets.
Feeding growing mushrooms
Authors: Sonnenberg Anton S.M. , Baars Johan J.P. , Straatsma Gerben , Hendrickx Patrick M. , Hendrix Ed , Blok Chris , Peer Arend van
Published: March 2022

A number of experiments were done to further our understanding of the substrate utilization in button mushroom crops (Agaricus bisporus). An analysis of the degradation of dry matter of the substrate during a crop cycle revealed that for pin formation the upper layer is used, for the production of flush one all layers are involved and for flush two mainly the lower layer is used. A reduction in substrate depth leads to a decrease in yield/m2 but an apparent increase in yield per ton of substrate but with a lower mushroom quality. A short daily interruption of the connection between the casing soil with all the substrate results in a delay of the first flush. Repetitive interruption of the connection with all or only part of the substrate leads to a shift in yield from flush one to flush two but the total yield remains unchanged. The mycelial biomass in the substrate increases from filling up to pinning, a steeper increase during flush one, levelling off during flush two, indicating that in the period of venting and up to/including flush one, enzymes are secreted by growing hyphae generating nutrients to feed a fixed amount of mushroom biomass for two flushes. A sidewise extension of the substrate (without casing soil, thus not producing mushrooms) showed that the substrate at a distance more than 20-50 cm away from the casing soil does not contribute to feeding mushrooms in the first two flushes. The observations are discussed with respect to relevant previous research.

Importance

Button mushrooms (Agaricus bisporus) are cultivated on a substrate prepared of composted wheat straw, chicken and/or horst manure and gypsum. This manuscript describes a number of experiments indicating that in a harvesting strategy towards quality mushrooms there is a fixed amount of nutrients prepared/available to feed two flushes. The increase of mycelial biomass in the substrate after venting and especially during the development of flush one indicates that likely a branching of mycelium occurs during this period, leading to a substantial number of growing hyphal tips excreting lignocellulolytic enzymes that degrade substrate and make nutrients available during flush one which are utilised in flush one and two. The presently used substrate seems to have reached its limits and there are hardly opportunities for further improvement. Research on alternative, more energy dense, substrates are needed to improve the efficiency of the present production system.
Non-occupational physical activity and risk of 22 cardiovascular disease, cancer, and mortality outcomes: a dose-response meta-analysis of large prospective studies
Authors: Garcia Leandro , Pearce Matthew , Abbas Ali , Mok Alexander , Strain Tessa , Ali Sara , Crippa Alessio , Dempsey Paddy C , Golubic Rajna , Kelly Paul , Laird Yvonne , McNamara Eoin , Moore Samuel , de Sa Thiago Herick , Smith Andrea D , Wijndaele Katrien , Woodcock James , Brage Søren
Published: March 2022

Objective

To estimate dose-response associations between non-occupational physical activity and multiple chronic disease outcomes in the general adult population.

Eligibility criteria

Prospective cohort studies with (a) general population samples >10,000 adults, (b) ≥3 exposure categories, and (c) risk measures and confidence intervals for all-cause mortality, total cardiovascular disease, coronary heart disease, stroke, heart failure, total cancer, and site-specific cancers (head and neck, myeloid leukemia, myeloma, gastric cardia, lung, liver, endometrium, colon, breast, bladder, rectum, esophagus, prostate, kidney).

Information sources

PubMed, Scopus, Web of Science, and reference lists of published studies, searched in February 2019.

Data extraction and synthesis

Independent extraction and double-checking of study characteristics, exposure, and outcome assessment by two reviewers for each paper. Primary exposure was non-occupational physical activity volume, harmonized to physical activity energy expenditure in marginal MET-hours per week (mMET-h/week). The current minimum recommendations for physical activity (150 min/week of moderate-to-vigorous physical activity) equate to 8.75 mMET-h/week. Outcomes were risks of mortality, cardiovascular diseases, and cancers. We used restricted cubic splines in random-effects meta-analyses. Potential population impact was quantified using impact fractions.

Results

196 articles were included, covering 94 cohorts. The evidence base was largest for all-cause mortality (50 independent results; 163,415,543 person-years; 811,616 events), and incidence of cardiovascular disease (37 independent results; 28,884,209 person-years; 74,757 events) and cancer (31 independent results; 35,500,867 person-years; 185,870 events). In general, inverse non-linear associations were observed, steeper between 0 and 8.75 mMET-h/week, with smaller marginal reductions in risk above this level to 17.5 mMET-h/week, beyond which additional reductions were small and uncertain. Associations were stronger for all-cause and cardiovascular disease mortality than for cancer mortality. If all insufficiently active individuals had met the recommended physical activity level, 15.7% (95%CI: 13.1 to 18.2%) of all premature deaths would have been averted.

Conclusions

Inverse non-linear dose-response associations suggest substantial protection against a range of chronic disease outcomes from small increases in non-occupational physical activity in inactive adults.

Review registration

PROSPERO CRD42018095481.
Flipped Over U: Structural Basis for dsRNA Cleavage by the SARS-CoV-2 Endoribonuclease
Authors: Frazier Meredith N. , Wilson Isha M. , Krahn Juno M. , Butay Kevin John , Dillard Lucas B. , Borgnia Mario J. , Stanley Robin E.
Published: March 2022

Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, coronaviruses employ Nsp15, which is uridine-specific endoribonuclease. Nsp15 is proposed to associate with the coronavirus replication-transcription complex within double-membrane vesicles to cleave these dsRNA intermediates. How Nsp15 recognizes and processes dsRNA is poorly understood because previous structural studies of Nsp15 have been limited to small single-stranded (ss) RNA substrates. Here we present cryo-EM structures of SARS-CoV-2 Nsp15 bound to a 52nt dsRNA. We observed that the Nsp15 hexamer forms a platform for engaging dsRNA across multiple protomers. The structures, along with site-directed mutagenesis and RNA cleavage assays revealed critical insight into dsRNA recognition and processing. To process dsRNA Nsp15 utilizes a base-flipping mechanism to properly orient the uridine within the active site for cleavage. Our findings show that Nsp15 is a distinctive endoribonuclease that can cleave both ss- and dsRNA effectively.
Nematode histone H2A variant evolution reveals diverse histories of retention and loss and evidence for conserved core-like variants
Authors: Singh Swadha , Chu Diana , Roy Scott
Published: March 2022

Histone variants are paralogs that replace canonical histones in nucleosomes, often imparting novel functions. Despite their importance, how histone variants arise and evolve is poorly understood. Reconstruction of histone protein evolution is challenging due to high amino acid conservation and large differences in evolutionary rates across gene lineages and sites. Here we combined amino acid sequences and intron position data from 108 nematode genomes to trace the evolutionary histories of the three H2A variants found in Caenorhabditis elegans: the ancient H2A.ZHTZ-1, the sperm-specific HTAS-1, and HIS-35, which differs from canonical H2A by a single glycine-to-alanine C-terminal change. We find disparate evolutionary histories. Although the H2A.ZHTZ-1 protein is highly conserved, its gene exhibits recurrent intron gain and loss. This pattern suggests that it is intron presence, rather than specific intron sequences or positions, that may be important to H2A.Z functionality. In contrast, for HTAS-1 and HIS-35, we find variant-specific intron positions that are conserved across species. HIS-35 arose in the ancestor of Caenorhabditis and its sister group, including the genus Diploscapter, while the sperm-specific variant HTAS-1 arose more recently in the ancestor of a subset of Caenorhabditis species. HIS-35 exhibits gene retention in some descendent lineages but also recurrent gene loss in others, suggesting that histone variant use or functionality is highly flexible in this case. We also find that the single amino acid differentiating HIS-35 from core H2A is ancestral and common across canonical Caenorhabditis H2A sequences and identify one nematode species that bear identical HIS-35 and canonical H2A proteins, findings that are not predicted from the hypothesis that HIS-35 has a distinct function. Instead, we speculate that HIS-35 enables H2A expression across the cell cycle or in distinct tissues; genes encoding such partially-redundant functions may be advantageous yet relatively replaceable over evolutionary times, consistent with the patchwork pattern of retention and loss of both genes. Our study shows the evolutionary trajectory for histone H2A variants with distinct functions and the utility of intron positions for reconstructing the evolutionary history of gene families, particularly those undergoing idiosyncratic sequence evolution.
Inducible CRISPR/Cas9 allows for multiplexed and rapidly segregated single target genome editing in Synechocystis sp. PCC 6803
Authors: Cengic Ivana , Cañadas Inés C. , Minton Nigel P. , Hudson Elton P.
Published: March 2022

Establishing various synthetic biology tools is crucial for the development of cyanobacteria for biotechnology use, especially tools that allow for precise and markerless genome editing in a time-efficient manner. Here we describe a riboswitch-inducible CRISPR/Cas9 system, contained on one single replicative vector, for the model cyanobacteria Synechocystis sp. PCC 6803. A theophylline-responsive riboswitch allowed tight control of Cas9 expression, which enabled reliable transformation of the CRISPR/Cas9 vector into Synechocystis. Induction of the CRISPR/Cas9 mediated various types of genomic edits, specifically deletions and insertions of varying size. The editing efficiency varied depending on the target and intended edit; smaller edits overall performed better, reaching e.g. 100% for insertion of a FLAG-tag onto rbcL. Importantly, the single-vector CRISPR/Cas9 system described herein was also shown to mediate multiplexed editing of up to three targets in parallel in Synechocystis. All single-target and several double-target mutants were also fully segregated after the first round of induction, adding to the usefulness of this system. Further, a vector curing system that is separately induced by nickel and contained on the CRISPR/Cas9 vector itself, improved curing efficiencies by roughly 4-fold, enabling the final mutants to become truly markerless.
Sights and sounds of dolphins, Tursiops truncatus, preying on native fish of San Diego Bay and offshore in the Pacific Ocean
Authors: Ridgway Sam H. , Dibble Dianna S. , Baird Mark
Published: March 2022

For the first time, dolphins wearing video cameras were observed capturing and eating live native fish. While freely swimming in San Diego Bay, one dolphin caught 69 resident fish, 64 demersal, 5 near surface, while the other caught 40, 36 demersal and 4 near the surface. Two other dolphins were observed capturing 135 live native fish in a sea water pool. Two additional dolphins were observed feeding opportunistically during open water sessions in the Pacific Ocean. Notably, one of these dolphins was observed to consume 8 yellow-bellied sea snakes (Hydrophis platurus). Searching dolphins clicked at intervals of 20 to 50 ms. On approaching prey, click intervals shorten into a terminal buzz and then a squeal. Squeals were bursts of clicks that varied in duration, peak frequency, and amplitude. Squeals continued as the dolphin seized, manipulated and swallowed the prey. If fish escaped, the dolphin continued the chase and sonar clicks were heard less often than the continuous terminal buzz and squeal. During captures, the dolphins’ lips flared to reveal nearly all of the teeth. The throat expanded outward. Fish continued escape swimming even as they entered the dolphins’ mouth, yet the dolphin appeared to suck the fish right down.
A dynamic kissing model for enhancer-promoter communication on the surface of transcriptional condensate
Authors: Zhang Qing , Shi Hualin , Zhang Zhihua
Published: March 2022

Enhancers are key DNA elements that regulate gene transcription by activating promoters in eukaryotes. Many potential mechanistic models have been proposed to account for enhancer-promoter communication, including the formation of the condensed enhancer-promoter clusterings that may result from liquid-liquid phase separation. However, the detailed kinetic mechanisms by which condensates may mediate enhancer-promoter contacts remain unclear. Here, we characterized enhancer-promoter communication in condensates using a self-avoiding polymer chain model under several possible spatial constraints. When the chain was confined to the spherical surface or interior, we discovered a distinct relationship between average end-to-end distance and contour length, as well as a distinct distribution of end-to-end distance. Experimental molecular tracking data showed strong preference in support of the spherical surface confinement hypothesis. Based on such observation, we proposed a novel enhancer-promoter communication model in which enhancers dynamically “kiss” promoters along the surface of transcriptional condensate. The theoretical results may guide future experiments, as researchers continue to elucidate the regulation dynamics of gene expression.
Optimal shape design of a class of permanent magnet motors in a multiple-objectives context
Authors: Di Barba Paolo , Mognaschi Maria Evelina , Petkovska Lidija , Cvetkovski Goga Vladimir
Published: March 2022

Purpose

This paper aims to deal with the optimal shape design of a class of permanent magnet motors by minimizing multiple objectives according to an original interpretation of Pareto optimality. The proposed method solves a many-objective problems characterized by five objective functions and five design variables with evolution strategy algorithms, classically used for single- and multi-objective (two objective functions) optimization problems.

Design/methodology/approach

Two approaches are proposed in the paper: the All-Objectives (AO) and the Many-Objectives (MO) optimization approach. The former is based on a single-objective optimization of a preference function, i.e. a normalized weighted sum. In contrast, in the MO a multi-objective optimization algorithm is applied to the minimization of a weight-free preference function and simultaneously to a maximization of the distance of the current solution from the prototype. The optimizations are based on an equivalent circuit model of the Permanent Magnet (PM) motor, but the results are assessed by means of finite element analyses (FEAs).

Findings

An extensive study of the solutions obtained by means of the different optimization approaches is provided by means of post-processing analyses. Both the approaches find non-dominated solutions with respect to the prototype that are substantially improving the initial solution. The points of strength along with the weakness points of each solution with respect to the prototype are analysed in depth.

Practical implications

The paper gives a good guide to the designers of electric motors, focussed on a shape design optimization.

Originality/value

Considering simultaneously five objective functions in an automated optimal design procedure is challenging. The proposed approach, based on a well-known and established optimization algorithm, but exploiting a new concept of degree of conflict, can lead to new results in the field of automated optimal design in a many-objective context.
Neural network inverse model for multi-band unequal Wilkinson power divider
Authors: Sallam Tarek , Attiya Ahmed M.
Published: March 2022

Purpose

The purpose of this paper is to build a neural network (NN) inverse model for the multi-band unequal-power Wilkinson power divider (WPD). Because closed-form expressions of the inverse input–output relationship do not exist, the NN becomes an appropriate choice, because it can be trained to learn from the data in inverse modeling. The design parameters of WPD are the characteristic impedances, lengths of the transmission line sections and the isolation resistors. The design equations used to train the NN inverse model are based on the even–odd mode analysis.

Design/methodology/approach

An inverse model of a multi-band unequal WPD using NNs is presented. In inverse modeling of a microwave component, the inputs to the model are the required electrical parameters such as reflection coefficients, and the outputs of the model are the geometrical or the physical parameters.

Findings

For verification purposes, a quad-band WPD and a penta-band WPD are designed. The results of the full-wave simulations verify the validity of the design procedure. The resulting NN model outperforms traditional time-consuming optimization procedures in terms of computation time with acceptable accuracy. The designed WPDs using NN are implemented by microstrip lines and verified by using full-wave analysis based on high-frequency structure simulator (HFSS). The results of the microstrip WPDs have good agreements with the corresponding results obtained by using ideal transmission line sections.

Originality/value

The associated time-consuming procedure and computational burden in realizing WPD through optimization are major disadvantages; needless to mention the substantial increase in optimization time because of the multi-band design. NNs are one of the best candidates in addressing the abovementioned challenges, owing to their ability to process the interrelation between electrical and geometrical/physical characteristics of the WPD in a superfast manner.
Employee participation in performance measurement system: focusing on job satisfaction and leadership
Authors: Jang Soojeen , Chung Yanghon , Son Hosung
Published: March 2022

Purpose

This study examines how employee participation in the performance measurement system affects the relationship between authentic leadership and job satisfaction.

Design/methodology/approach

Survey data for this study were obtained from 322 employees in South Korea. Structural equation modeling and bootstrapping method were applied to test the proposed hypotheses.

Findings

This study first confirmed that authentic leadership positively affects job satisfaction. In addition, the results showed that employees' participation in developing performance measures partially mediated the relationship between authentic leadership and job satisfaction.

Practical implications

The findings imply that employees' participation in developing performance measures, which is promoted by authentic leadership, can be a strategy for enhancing job satisfaction. Therefore, in order to increase employees' job satisfaction, organizations need to promote employee participation in the performance measurement system and develop authenticity in leaders.

Originality/value

Employees' participation in developing performance measures has not been investigated sufficiently from the leadership perspective. This study expands the literature on the influence of employee participation in the performance measurement system on work-related outcomes by demonstrating that employees' participation in developing performance measures partially mediates the effect of authentic leadership on employee job satisfaction.
Australian consumers and environmental characteristics of wine: price premium indications
Authors: Gow Jeff , Rana Rezwanul Hasan , Moscovici Daniel , Ugaglia Adeline Alonso , Valenzuela Lionel , Mihailescu Radu , Coelli Robert
Published: March 2022

Purpose

There has been increasing consumer interest in recent times in the environmental providence of what they eat and drink. A number of different environmental wine certifications have been created and these include biodynamic, fairtrade, organic, natural and sustainable. The purpose of this study is to survey wine consumers in Australia about their interest in these eco-certifications and their willingness to pay (WTP) a price premium for wine with one of these eco-certifications.

Design/methodology/approach

An online survey was developed to capture the knowledge and attitudes of consumers and their socio-demographic characteristics about their WTP for eco-certified wine. Data from 454 wine consumers in Australia were collected and analysed. Descriptive statistics and Pearson’s chi-squared test analysed the significant factors which determine consumers’ attitudes towards eco-certified wines. Ordinal logistic regression with marginal effects was used to examine whether the WTP a premium for different certified wines differs significantly based on wine knowledge, attitudes and socio-demographic characteristics.

Findings

The findings of this study indicate that consumers often buy pro-environmental goods. The majority have a positive (greater than 0) WTP a premium for biodynamic, fairtrade, organic, natural and sustainable-labelled wines. The main factors influencing eco-certified wine purchase decisions by Australian consumers are previously bought eco-certified goods, previously bought eco-certified wine and respondent age. Income, education or previous wine knowledge did not positively influence WTP a price premium for eco-certified wines. Gender was not significant in the ordinal logistic regression.

Research limitations/implications

Most studies in the literature use stated preference experiments to elicit WTP and these are valuable exercises, as they can provide an indication of consumer preferences for potential certifications, before they have been introduced to the market. In this study, we used an ordinal dependent variable in the logistic regression instead of a continuous variable (because of data limitations). Using ordinal dependent variables provides information on the probability or likelihood of occurring an event.

Originality/value

The study results provide the first price premium indications that Australian consumers are willing to pay for eco-certified wines (other than organic).
The role of wages, skills development and R&D on productivity: evidence from Thai manufacturing firms
Authors: Amornkitvikai Yot , Harvie Charles , Sangkaew Piyapong
Published: March 2022

Purpose

The objectives of this study are to investigate the role of wages, skills development and R&D on the productivity of Thai manufacturing firms, using data from the 2017 Industrial Census of Thailand.

Design/methodology/approach

The paper uses two-stage least squares (2SLS) to examine the role of wages, skills development and R&D, as well as other vital factors, impacting productivity as measured by labour productivity and total factor productivity.

Findings

Thai manufacturing firms' technology in aggregate exhibits decreasing returns to scale. Increasing wages and skills development promote the labour productivity and total factor productivity (TFP) of Thai manufacturers. R&D is also shown to be vital in promoting the labour productivity and TFP of large firms, but not small firms. Foreign direct investment (FDI) and government support can significantly increase large and medium-sized firms' labour productivity and TFP. Financially constrained firms tend to perform more productively. However, older firms, larger firms, labour supply shortages and political instability adversely affect labour productivity and TFP.

Practical implications

Upskilling and improving HRD policies could move Thailand towards a knowledge-based and high-income country in the future. Intellectual property protection should be strengthened to boost the country's R&D. The government should consider lifting restrictions on FDI to encourage international openness. The Thai Board of Investment’s promotion should target Thai manufacturing firms and FDI.

Originality/value

This study is the first to examine in detail the role of wages, skills development and R&D on the productivity of Thai firms based on the 2017 Thailand Industrial Census.
The relationship between collaboration, productivity and publications: an empirical analysis in field of family business
Authors: Kinias Ioannis , Kampouris Ilias , Polyzos Stathis
Published: March 2022

Purpose

It is widely accepted that coauthorship and collaboration promotes intellectual partnerships and improves the quality of publications. This paper examines the relationship between collaboration, productivity and publications in the field of family business.

Design/methodology/approach

The authors identify the most prolific authors, affiliations and countries and focus on the evolution of research in the field of family business. In doing so, the authors employ social network analysis to discover the structure of the networks and the ways in which authors, institutions and countries interact.

Findings

The empirical results show that collaboration is positively related to productivity, and there is significant evidence that the shaped networks exhibit small-world characteristics, a condition in which collaboration within authors becomes integrated in conjunction with time.

Practical implications

The findings highlight the mechanics of collaborative research production and can be useful to understand the importance of collaboration patterns to be followed in the field of family business.

Originality/value

The contributions are as follows: (a) application of social network analysis to model the coauthorship patterns among individuals, institutions and countries in family business; (b) distinguishing the most degree-central authors in the social network of collaborating academics; (c) investigation of the academic collaborations in family business that have the characteristics of a small-world social network and (d) suggesting a unique connection, through published keywords, between the research priorities of the most central or prolific authors with the research trends in the family business literature. The authors demonstrate that authors' collaboration becomes integrated in conjunction with time.