bluuebunny/crossref_metadata_2025 huggingface dataset:
Underground gibberellin activity: differential gibberellin response in tomato shoots and roots
Authors: Ramon Uria , Weiss David , Illouz-Eliaz Natanella
Published: July 2020

Gibberellins (GAs) are growth-promoting hormones that regulate organ growth, mainly via cell elongation. Contradicting reports leave an open question of whether GA is as important for root elongation as it is for stem elongation.

Here we have addressed this question focusing on tomato (Solanum lycopersicum) primary-root elongation. We used a combination of physiological, molecular and genetic approaches to tackle this question.

Tomato has three GA receptors; GID1a, GID1b1 and GID1b2. The loss of all three receptors, strongly suppressed stem elongation and leaf expansion, but had a relatively minor effect on primary root elongation. The effect of GA on cell elongation and gene-expression was much weaker in roots, than in shoots, reaching saturation at lower hormone concentrations. Our results imply that this differential response to GA in shoots and roots is caused by the lower expression of the dominant GA receptor GID1a in roots.

We show that the differential activity of GA between shoots and roots affects root-to-shoot ratio, and speculate that this evolved as an adaptive mechanism to changing environments.
Changes in salt-marsh vegetation weakly affect top consumers of aquatic food webs
Authors: Denis Lafage , Alexandre Carpentier , Duhamel Sylvain , Dupuy Christine , Feunteun Eric , Lesourd Sandric , Julien Pétillon
Published: July 2020

Salt marshes are under high, and increasing, anthropogenic pressures that have notably been reported to affect the diet of several fish species, probably resulting in nursery function alterations. Most of the previous studies in Europe were yet based on gut content analysis of fish, which can be considered a snapshot of immediate impacts of salt-marsh changes, and hardly of long-term effects of disturbances. In this study, we investigated the impact of vegetation type (resulting from both plant invasion and sheep grazing) by assessing trophic network (and especially fish diet and position) of different salt-marsh conditions. Replicated samples of basic sources (particular organic matter and microphytobenthos), dominant vegetation, potential aquatic and terrestrial prey and fish of 3 main species were taken during summer 2010 in two bays from Western France (Mont -Saint-Michel Bay and Seine Estuary) and analysed using C and N stable isotope compositions. All response variables tested (overall trophic organization, trophic niche and trophic position) provided consistent results, i.e. a dominant site effect and a weaker effect of vegetation type. Site effect was attributed to differences in anthropogenic Nitrogen inputs and tidal regime between the two bays, with more marine signatures associated with a higher frequency of flooding events. A second hypothesis is thatE. acuta, which has recently totally replaced typical salt-marsh vegetation in Mont Saint-Michel Bay strongly impacted the nursery function. The trophic status of dominant fish species was unchanged by local salt-marsh vegetation, and considered consistent with their diet, i.e. high for predatory species (the sea bassDicentrarchus labraxand the common gobyPomatoschistus microps) and lower for biofilm grazing species (the thinlip mulletChelon ramada). This study finally highlights the relevance of stable isotopes analyses for assessing long-term and integrative effects of changes in vegetation resulting from human disturbances in salt marshes.

Highlights

Cross-ecosystem subsidies are of high functional importance, notably in salt marshes

Fish are vectors of exchanges, most European studies being based on their gut content

Using stable isotopes we analysed the effect of surrounding vegetation on food webs

Surprisingly we found weak vegetation and strong site effects on all metrics

Nitrogen inputs, site accessibility and loss of nursery function can explain this fact

Abstract Figure
Unequal access to resources undermines global sustainability
Authors: Henderson Kirsten , Loreau Michel
Published: July 2020

We are a global society with various land use patterns, inequality, and the movement of people and goods. The various practices and behaviours associated with our current society raise questions about the future sustainability of the human population and the natural environment. We derive a model of a global socio-ecological system to explore the connections between human well-being and land resources, specifically looking at resource accessibility, conservation initiatives and human migration between two economically diverse regions. We find that the spatial aspect of a global system with two distinct regions, allows for faster development of technology, higher peaks in population size, greater natural land degradation, and generally speaking lower population well-being in the long-term. The unequal access to resources and differences in technological progress, alter the outcome of land management (i.e., conservation) and social behaviours (i.e., migration). We conclude that any socio-ecological management practices should be conscientious of the diversity in land access, population size, population well-being and development within the global society, as the potential for unintended consequences is high. Inequality needs to be addressed to promote sustainability.
Agricultural land use and the sustainability of social-ecological systems
Authors: Paz Diego Bengochea , Henderson Kirsten , Loreau Michel
Published: July 2020

Agricultural land expansion and intensification, driven by human consumption of agricultural goods, are among the major threats to environmental degradation and biodiversity conservation. Land degradation can ultimately hamper agricultural production through a decrease in ecosystem services. Thus, designing viable land use strategies is a key sustainability challenge. We develop a model describing the coupled dynamics of human demography and landscape composition, while imposing a trade-off between agricultural expansion and intensification. We model land use strategies spanning from low-intensity agriculture and high land conversion rates per person to high-intensity agriculture and low land conversion rates per person; and explore their consequences on the long-term dynamics of the coupled human-land system. We seek to characterise the strategies’ viability in the long run; and understand the mechanisms that potentially lead to large-scale land degradation and population collapse due to resource scarcity. We show that the viability of land use strategies strongly depends on the land’s intrinsic recovery rate. We also find that socio-ecological collapses occur when agricultural intensification is not accompanied by a sufficient decrease in land conversion. Based on these findings we stress the dangers of naive land use planning and the importance of precautionary behaviour for land use management.
Minimizing ion competition boosts volatile metabolome coverage by secondary electrospray ionization orbitrap mass spectrometry
Authors: Lan Jiayi , Kaeslin Jérôme , Greter Giorgia , Zenobi Renato
Published: July 2020

Secondary electrospray ionization high-resolution mass spectrometry (SESI-HR-MS) is an emerging technique for the detection of volatile metabolites. However, sensitivity and reproducibility of SESI-HRMS have limited its applications in untargeted metabolomics profiling. Ion suppression in the SESI source has been considered to be the main cause. Here, we show that besides ion suppression, ion competition in the C-trap of Orbitrap instruments is another important factor that influences sensitivity and reproducibility of SESI-MS. Instead of acquiring the full mass-to-charge ratio (m/z) range, acquisition of consecutivem/zwindows to minimize the ion competition effect allows the detection of more features.m/zwindow ranges are optimized to fill the C-trap either with an equal number of features or an equal cumulative intensity per window. Considering a balance between maximizing scanning speed and minimizing ion competition, splitting them/z= 50-500 range into 4 windows is selected for measuring human breath and bacterial culture samples on SESI-Orbitrap MS, corresponding to a duty cycle of 2.3 s at a resolution of 140’000. In a small cohort of human subjects, the proposed splitting into 4 windows allows three times more features to be detected compared to the classical fullm/zrange method.
Genome-Wide Mapping of Cisplatin Damaged Gene Loci
Authors: Qi Luyu , Luo Qun , Xu Yan , Yu Wanchen , Liu Xingkai , Zhang Yanyan , Jia Feifei , Fang Tiantian , Wang Shijun , Li Xiangjun , Zhao Yao , Wang Fuyi
Published: July 2020

Cisplatin is a DNA targeting anticancer drug, yet its damaged gene loci have remained unclear. In the present work, combining affinity isolation and high throughput sequencing, we genome-widely mapped 17729 gene loci containing platination lesions, which mainly function as enzymes, transcription regulators, transporters and kinases, and of which 445 genes account for 71% of potential gene targets for cancer therapy reported in the literature. The most related core signaling pathway, disease and tissue toxicity of 7578 genes with an enrichment fold (EFG) of >12, where EFGrefers to the ratio of total read counts of a gene detected in cells with and without cisplatin treatment, are sperm motility, cancer and hepatotoxicity with associationPvalues of < 1×10−22. Among 616 kinase genes damaged by cisplatin, 427 are protein kinases which account for 82% of putative protein kinases, suggesting that cisplatin may act as broad-spectrum protein kinase inhibitor. Western Blot assays verified that expression of 8 important protein kinase genes was significantly reduced due to cisplatin damage.SPAG9is closely related to 147 of 361 cancer diseases which the cisplatin damaged genes are associated with and was severely damaged by cisplatin. GivenSPAG9abundantly expresses JIP-4, a upstream mediator of protein kinase signaling, in testis, it may be responsible for the high sensitivity of testicular cancer to cisplatin, thus being a potential therapeutic target for precise treatment of testicular cancer. These findings provide novel insights into better understanding in molecular mechanism of anticancer activity and toxicity of cisplatin, more importantly inspire further studies in prioritizing gene targets for precise treatment of cancers.
Feeling the beat: Temporal and spatial perception of heartbeat sensations
Authors: Betka Sophie , Łukowska Marta , Silva Marta , King Joshua , Garfinkel Sarah , Critchley Hugo
Published: July 2020

The majority of interoceptive tasks (i.e. measuring the sensitivity to bodily signals) are based upon the heartbeat sensations perception. However, temporal perception of heartbeats varies among individuals and confidence and spatial perception of heartbeats in relation to temporal judgements have not yet been systematically investigated. This study examined the perception of heartbeat sensations in both time and spatial domains, using a multi-interval heartbeat discrimination task. The relationship between these domains was investigated, as well as the contribution of mental health conditions and cardiovascular parameters. Heartbeat sensations occurred on average ~250ms after the ECG R-wave and were more frequently sampled from the left part of the chest. Participants’ confidence in their experience of heartbeat sensations was maximal for the 0 ms interval. Interestingly, higher confidence was related to reduced dispersion of sampling locations but we found evidence toward the absence of relationship between temporal and spatial heartbeat sensations perception, using Bayesian statistics. Finally, we found evidence toward a relationship between spatial precision of heartbeat sensations and state anxiety score, which seems independent from the cardiovascular parameters. This systematic investigation of heartbeat sensations perception provides important fresh insights, informing the mechanistic understanding of the interoceptive signaling contribution to emotion, cognition and behaviour.
Atomistic Basis of Force Generation, Translocation, and Coordination in a Viral Genome Packaging Motor
Authors: Pajak Joshua , Dill Erik , Reyes-Aldrete Emilio , White Mark A. , Kelch Brian A. , Jardine Paul , Arya Gaurav , Morais Marc C.
Published: July 2020

Double-stranded DNA viruses package their genomes into pre-assembled capsids using virally-encoded ASCE ATPase ring motors. We present the first atomic-resolution crystal structure of a multimeric ring form of a viral dsDNA packaging motor and characterize its atomic-level dynamicsvialong timescale molecular dynamics simulations. Based on the results, we deduce an overall packaging mechanism that is driven by helical-to-planar transitions of the ring motor. These transitions are coordinated by inter-subunit interactions that regulate catalytic and force-generating events. Stepwise ATP binding to individual subunits increase their affinity for the helical DNA phosphate backbone, resulting in distortion away from the planar ring towards a helical configuration, inducing mechanical strain. Subsequent sequential hydrolysis events alleviate the accumulated mechanical strain, allowing a stepwise return of the motor to the planar conformation, translocating DNA in the process. This type of helical-to-planar mechanism could serve as a general framework for ring ATPases that exhibit burst-dwell dynamics.
The impact of chromatin remodeling on gene expression at the single cell level inArabidopsis thaliana
Authors: Farmer Andrew , Thibivilliers Sandra , Ryu Kook Hui , Schiefelbein John , Libault Marc
Published: July 2020

Similar to other complex organisms, plants consist of diverse and highly specialized cell types. The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-type-specific transcriptional programs and their associated regulatory mechanisms. Recently, single cell transcriptomic approaches have been applied onArabidopsis thalianaroot protoplasts allowing the accurate characterization of the transcriptional profiles of the cell-types composing seedling roots. As a first step in gaining a deeper understanding of the regulatory mechanisms controlling Arabidopsis gene expression, we report the use of single nucleus RNA sequencing (sNucRNA-seq) and single nucleus Assay for Transposase Accessible Chromatin sequencing (sNucATAC-seq) technologies on Arabidopsis roots. The comparison of our single nuclei transcriptomes to previously published protoplast transcriptomes validated the use of nuclei as biological entities to establish cell-type specific transcriptomes from multicellular organs. Furthermore, our sNucRNA-seq results uncovered the transcriptome of additional cell subtypes not identified by scRNA-seq. Similar to our transcriptomic approach, the sNucATAC-seq approach led to the distribution of the Arabidopsis nuclei into distinct clusters suggesting the differential remodeling of the chromatin between groups of cells according to their identity. To reveal the impact of chromatin remodeling on gene transcription, we integrated sNucRNA-seq and sNucATAC-seq data and demonstrated that cell-type-specific marker genes also display cell-type-specific pattern of chromatin accessibility. Our data suggest that the differential remodeling of the chromatin is a critical mechanism to regulate gene activity at the cell-type level.
Systemic inflammation causes microglial dysfunction with a mixed AD-like pathology
Authors: Bathini Praveen , Dupanloup Isabel , Zenaro Elena , Terrabuio Eleonora , Fischer Amrei , Ballabani Edona , Doucey Marie-Agnes , Alberi Lavinia
Published: July 2020

Background

Alzheimer’s disease (AD) is the primary cause of cognitive deficit in elderly humans. Late-onset AD (LOAD) is sporadic, multifactorial, non-Mendelian accounting at present for 95% of the cases in contrast to the genetic form. Risk factors for sporadic AD include Gene: Environment interactions. There is increasing evidence that lifestyle and environmental stress such as infection and chronic inflammation are underlying culprits of neurodegenerative dementia. Dementias that share or mimic pathological processes of AD include cerebrovascular diseases, Lewy body disease, TDP-43 proteinopathy. To date, very few mouse models reproduce the pathophysiological progression of mixed-vascular-AD, while the majority of studies have employed transgenic animals reproducing the familial form.

Methods

We have re-engineered the Polyinosinic:polycytidylic acid (PolyI:C) sterile infection model in wildtype C57Bl6 mice to obtain chronic low-grade systemic inflammation. We have conducted a cross-sectional analysis of aging PolyI:C and Saline control mice (3 months, 6 months, 9 months and 16 months), taking the hippocampus as a reference brain region, based on its vulnerability, and compared the brain aging phenotype to AD progression in humans with mild AD, severe AD and Controls (CTL), parallely in Vascular dementia (VaD) patient specimens.

Results

We found that PolyI:C mice display both peripheral and central inflammation with a peak at 6 months, associated with memory deficits. The hippocampus is characterized by a pronounced and progressive tauopathy. In PolyI:C brains, microglia undergo aging-dependent morphological rearrangements progressively adopting a phagocytic phenotype. Transcriptomic analysis reveals a profound change in gene expression over the course of aging, with a peak in differential expression at 9 months. We confirm that the proinflammatory markerLcn2is one of the genes with the strongest upregulation in PolyI:C mice upon aging. Validation in brains from patients with increasing severity of AD and VaD shows a reproducibility of some gene targets in vascular dementia specimens rather than AD ones, in which only GFAP is strongly increased at the severe stages.

Conclusions

The PolyI:C model of sterile infection demonstrates that peripheral chronic inflammation is sufficient to cause neuropathological processes resembling a mixed-VaD-AD phenotype, with progressive tau hyperphosphorylation, changes in microglia morphology, astrogliosis and gene reprogramming reflecting increased neuroinflammation, vascular remodeling and the loss of neuronal functionality seen to some extent in humans.
BRN2 and MITF together impact AXL expression in melanoma
Authors: Simmons Jacinta L. , Neuendorf Hannah M. , Boyle Glen M.
Published: July 2020

The inverse relationship between transcription factor MITF and receptor tyrosine kinase AXL has received much attention recently. It is thought that melanoma tumors showing AXLhigh/MITFlowlevels are resistant to therapy. We show here that a population of cells within melanoma tumors with extremely high expression of AXL are negative/low for both MITF and the transcription factor BRN2. Depletion of both transcription factors from cultured melanoma cell lines produced an increase in AXL expression greater than depletion of MITF alone. Further, re-expression of BRN2 led to decreased AXL expression, indicating a role for BRN2 in regulation of AXL levels unrelated to effects on MITF level. As AXL has been recognized as a marker of therapy resistance these cells may represent a population of cells responsible for disease relapse and as potential targets for therapeutic treatment.
Gut Microbiota Changes in Nonalcoholic Fatty Liver Disease and Concomitant Cardiovascular Diseases
Authors: Kurinna Olena H.
Published: July 2020

Nonalcoholic fatty liver disease (NAFLD) bears serious economic consequences for the health care system worldwide and Ukraine, in particular. Cardiovascular diseases (CVD) are the main cause of mortality in NAFLD patients. Changes in the gut microbiota composition can be regarded as a potential mechanism of CVD in NAFLD patients.

The purpose of this work was to investigate changes in major gut microbiota phylotypes,Bacteroidetes, FirmicutesandActinobacteriawith quantification ofFirmicutes/Bacteroidetesin NAFLD patients with concomitant CVD.

The author enrolled 120 NAFLD subjects (25 with concomitant arterial hypertension (AH) and 24 with coronary artery disease (CAD)). The gut microbiota composition was assessed by qPCR.

Results

the author found a marked tendency towards an increase in the concentration ofBacteroidetes(by 37.11% and 21.30%, respectively) with a decrease inFirmicutes(by 7.38% and 7.77%, respectively) in both groups with comorbid CAD and AH with the identified changes not reaching a statistical significance. The author quantified a statistically significant decrease in the concentration ofActinobacteriain patients with NAFLD with concomitant CAD at 41.37% (p<0.05) as compared with those with an isolated NAFLD. In patients with concomitant AH, the content ofActinobacteriadropped by 12.35%, which was statistically insignificant.

Conclusions

the author established changes in the intestinal microbiota, namely decrease inActinobacteriain patients with CAD, which requires further research.
Association between stress and depressive symptoms and the Covid-19 pandemic
Authors: Novotný Jan S. , Gonzalez-Rivas Juan P. , Kunzová Šárka , Skladaná Mária , Pospíšilová Anna , Polcrová Anna , Medina-Inojosa Jose R. , Lopez-Jimenez Francisco , Geda Yonas E. , Stokin Gorazd B.
Published: July 2020

Objective

To date, cross-sectional surveys reported frequency and distribution of mental health disorders on convenience samples impacted by Covid-19. Longitudinal assessment of mental health during Covid-19 in a representative population-based sample, however, is currently largely missing. The aim of this study was to investigate changes in perceived stress levels and depressive symptoms measured before and during Covid-19 pandemic in a representative population-based sample.

Methods

Baseline data on stress levels and depressive symptoms from a well-established population-based sample were compared with those obtained from self-administered e-questionnaires distributed during Covid-19 pandemic. A total of 715 participants completed e-questionnaires. Wilcoxon signed-rank test was used to test repeated-measure differences, while between-group differences were analysed using Mann-Whitney and the Kruskal-Wallis tests.

Results

Perceived stress levels and depressive symptoms increased 1.4 and 5.5 times, respectively, during the Covid-19 pandemic compared to the time prior Covid-19. Changes in stress and depressive symptoms were most significant in females and did not depend on whether one quarantined alone or with others. Feeling of loneliness during Covid-19 pandemic had the greatest impact on increased stress levels and depressive symptoms.

Conclusions

This population-based longitudinal study showed that Covid-19 related measures had significant impact on mental health in a general population with the feeling of loneliness identified as the biggest risk factor. This impact indicates the need of timely and tailored treatment of mental health disorders and integration of preventive mental health measures into global public health policies to protect mental health during future pandemics.
Evaluation of a SARS-CoV-2 surrogate virus neutralization test for detection of antibody in human, canine, cat and hamster sera
Authors: Perera Ranawaka APM , Ko Ronald , Tsang Owen TY , Brackman Christopher J , To Esther M. W. , Yen Hui-ling , Leung Kathy , Cheng Samuel MS , Chan Kin Ho , Chan Karl CK , Li Ka-Chi , Saif Linda , Barrs Vanessa R. , Wu Joseph T , Sit Thomas H. C. , Poon Leo LM , Peiris Malik
Published: July 2020

Surrogate neutralization assays for SARS-CoV-2 that can be done without biosafety-level-3 containment and across multiple species are desirable. We evaluate a recently developed surrogate virus neutralization test (sVNT) in comparison to 90% plaque reduction neutralization tests (PRNT90) in human, canine, cat and hamster sera and found excellent concordance between the two assays. Using a panel of immune sera to other coronaviruses, we confirm the lack of cross reactivity in sVNT and PRNT90 assays.
Comparative Analysis of Human Coronaviruses Focusing on Nucleotide Variability and Synonymous Codon Usage Pattern
Authors: Das Jayanta Kumar , Roy Swarup
Published: July 2020

Prevailing pandemic across the world due to SARSCoV-2 drawing great attention towards discovering its evolutionary origin. We perform an exploratory study to understand the variability of the whole coding region of possible proximal evolutionary neighbours of SARSCoV-2. We consider seven (07) human coronavirus strains from six different species as a candidate for our study.

First, we observe a good variability of nucleotides across candidate strains. We did not find a significant variation of GC content across the strains for codon position first and second. However, we interestingly see huge variability of GC-content in codon position 3rd (GC3), and pairwise mean GC-content (SARSCoV, MERSCoV), and (SARSCoV-2, hCoV229E) are quite closer. While observing the relative abundance of dinucleotide feature, we find a shared typical genetic pattern, i.e., high usage of GC and CT nucleotide pair at the first two positions (P12) of codons and the last two positions (P23) of codons, respectively. We also observe a low abundance of CG pair that might help in their evolution bio-process. Secondly, Considering RSCU score, we find a substantial similarity for mild class coronaviruses, i.e., hCoVOC43, hCoVHKU1, and hCoVNL63 based on their codon hit with high RSCU value (≥ 1.5), and minim number of codons hit (count-9) is observed for MERSCoV. We see seven codons ATT, ACT, TCT, CCT, GTT, GCT and GGT with high RSCU value, which are common in all seven strains. These codons are mostly from Aliphatic and Hydroxyl amino acid group. A phylogenetic tree built using RSCU feature reveals proximity among hCoVOC43 and hCoV229E (mild). Thirdly, we perform linear regression analysis among GC content in different codon position and ENC value. We observe a strong correlation (significant p-value) between GC2 and GC3 for SARSCoV-2, hCoV229E and hCoVNL63, and between GC1 and GC3 for hCoV229E, hCoVNL63, SARSCoV. We believe that our findings will help in understanding the mechanism of human coronavirus.
Disentangling Conditional Effects of Multiple Regime Shifts on Atlantic Cod Productivity
Authors: Perälä Tommi , Olsen Esben M. , Hutchings Jeffrey A.
Published: July 2020

Regime shifts are increasingly prevalent in the ecological literature. However, definitions vary, and many detection methods are subjective. Here, we employ an operationally objective means of identifying regime shifts, using a Bayesian online change-point detection algorithm able to simultaneously identify shifts in the mean and(or) variance of time series data. We detected multiple regime shifts in long-term (59-154 years) patterns of coastal Norwegian Atlantic cod (>70% decline) and putative drivers of cod productivity: North Atlantic Oscillation (NAO); sea-surface temperature; zooplankton abundance; fishing mortality (F). The consequences of an environmental or climate-related regime shift on cod productivity are accentuated when regime shifts coincide, fishing mortality is high, and populations are small. The analyses suggest that increasingFincreasingly sensitized cod in the mid 1970s and late 1990s to regime shifts in NAO, zooplankton abundance, and water temperature. Our work underscores the necessity of accounting for human-induced mortality in regime shift analyses of marine ecosystems.
The impact of different negative training data on regulatory sequence predictions
Authors: Krützfeldt Louisa-Marie , Schubach Max , Kircher Martin
Published: July 2020

Regulatory regions, like promoters and enhancers, cover an estimated 5-15% of the human genome. Changes to these sequences are thought to underlie much of human phenotypic variation and a substantial proportion of genetic causes of disease. However, our understanding of their functional encoding in DNA is still very limited. Applying machine or deep learning methods can shed light on this encoding and gapped k-mer support vector machines (gkm-SVMs) or convolutional neural networks (CNNs) are commonly trained on putative regulatory sequences.

Here, we investigate the impact of negative sequence selection on model performance. By training gkm-SVM and CNN models on open chromatin data and corresponding negative training dataset, both learners and two approaches for negative training data are compared. Negative sets use either genomic background sequences or sequence shuffles of the positive sequences. Model performance was evaluated on three different tasks: predicting elements active in a cell-type, predicting cell-type specific elements, and predicting elements’ relative activity as measured from independent experimental data.

Our results indicate strong effects of the negative training data, with genomic backgrounds showing overall best results. Specifically, models trained on highly shuffled sequences perform worse on the complex tasks of tissue-specific activity and quantitative activity prediction, and seem to learn features of artificial sequences rather than regulatory activity. Further, we observe that insufficient matching of genomic background sequences results in model biases. While CNNs achieved and exceeded the performance of gkm-SVMs for larger training datasets, gkm-SVMs gave robust and best results for typical training dataset sizes without the need of hyperparameter optimization.
Crystal structure of schizorhodopsin reveals mechanism of inward proton pumping
Authors: Higuchi Akimitsu , Shihoya Wataru , Konno Masae , Ikuta Tatsuya , Kandori Hideki , Inoue Keiichi , Nureki Osamu
Published: July 2020

Schizorhodopsins (SzRs), a new rhodopsin family identified in Asgard archaea, are phylogenetically located at an intermediate position between type-1 microbial rhodopsins and heliorhodopsins. SzRs reportedly work as light-driven inward H+pumps, as xenorhodopsin. Here we report the crystal structure of SzR AM_5_00977 at 2.1 Å resolution. The SzR structure superimposes well on that of bacteriorhodopsin rather than heliorhodopsin, suggesting that SzRs are classified with type-1 rhodopsins. The structure-based mutagenesis study demonstrated that the residues N100 and V103 are essential for color tuning in SzRs. The cytoplasmic parts of transmembrane helices 2, 6, and 7 in SzR are shorter than those in the other microbial rhodopsins. Thus, E81 is located near the cytosol, playing a critical role in the inward H+release. We suggested the H+is not metastably trapped in E81 and released through the water-mediated transport network from the retinal Schiff base to the cytosol. Moreover, most residues on the H+transport pathway are not conserved between SzRs and xenorhodopsins, suggesting that they have entirely different inward H+release mechanisms.
Leveraging phenotypic variability to identify genetic interactions in human phenotypes
Authors: Marderstein Andrew R. , Davenport Emily , Kulm Scott , Van Hout Cristopher V. , Elemento Olivier , Clark Andrew G.
Published: July 2020

While thousands of loci have been associated with human phenotypes, the role of gene-environment (GxE) interactions in determining individual risk of human diseases remains unclear. This is partly due to the severe erosion of statistical power resulting from the massive number of statistical tests required to detect such interactions. Here, we focus on improving the power of GxE tests by developing a statistical framework for assessing quantitative trait loci (QTLs) associated with the trait means and/or trait variances. When applying this framework to body mass index (BMI), we find that GxE discovery and replication rates are significantly higher when prioritizing genetic variants associated with the variance of the phenotype (vQTLs) compared to assessing all genetic variants. Moreover, we find that vQTLs are enriched for associations with other non-BMI phenotypes having strong environmental influences, such as diabetes or ulcerative colitis. We show that GxE effects first identified in quantitative traits such as BMI can be used for GxE discovery in disease phenotypes such as diabetes. A clear conclusion is that strong GxE interactions mediate the genetic contribution to body weight and diabetes risk.
The multicomparative 2-n-way genome suite
Authors: Churakov Gennady , Zhang Fengjun , Grundmann Norbert , Makalowski Wojciech , Noll Angela , Doronina Liliya , Schmitz Jürgen
Published: July 2020

To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the “2-n-way” software suite to provide a fundamental and innovative processing framework for revealing and comparing inserted elements among various genomes. The suite comprises two user-friendly web-based modules. The 2-way module generates pairwise whole-genome alignments of target and query species. The resulting genome coordinates of blocks (matching sequences) and gaps (missing sequences) from multiple 2-ways are then transferred to the n-way module and sorted into projects, in which user-defined coordinates from reference species are projected to the block/gap coordinates of orthologous loci in query species to provide comparative information about presence (blocks) or absence (gaps) patterns of targeted elements over many entire genomes and phylogroups. Thus, the 2-n-way software suite is ideal for performing multidirectional, non-ascertainment-biased screenings to extract all possible presence/absence data of user-relevant elements in orthologous sequences. To highlight its applicability and versatility, we used 2-n-way to expose approximately 100 lost introns in vertebrates, analyzed thousands of potential phylogenetically informative bat and whale retrotransposons, and novel human exons as well as thousands of human polymorphic retrotransposons.
A limited set of transcriptional programs define major cell types
Authors: Breschi Alessandra , Muñoz-Aguirre Manuel , Wucher Valentin , Davis Carrie A. , Garrido-Martín Diego , Djebali Sarah , Gillis Jesse , Pervouchine Dmitri D. , Vlasova Anna , Dobin Alexander , Zaleski Chris , Drenkow Jorg , Danyko Cassidy , Scavelli Alexandra , Reverter Ferran , Snyder Michael P. , Gingeras Thomas R. , Guigó Roderic
Published: July 2020

We have produced RNA sequencing data for 53 primary cells from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, which define five major cell types: epithelial, endothelial, mesenchymal, neural, and blood cells. These act as basic components of many tissues and organs. Based on gene expression, these cell types redefine the basic histological types by which tissues have been traditionally classified. We identified genes whose expression is specific to these cell types, and from these genes, we estimated the contribution of the major cell types to the composition of human tissues. We found this cellular composition to be a characteristic signature of tissues and to reflect tissue morphological heterogeneity and histology. We identified changes in cellular composition in different tissues associated with age and sex, and found that departures from the normal cellular composition correlate with histological phenotypes associated with disease.
Structural characterization of three noncanonical NTF2-like superfamily proteins: implications for polyketide biosynthesis
Authors: Vuksanovic Nemanja , Zhu Xuechen , Serrano Dante A. , Siitonen Vilja , Metsä-Ketelä Mikko , Melançon Charles E. , Silvaggi Nicholas R.
Published: July 2020

Proteins belonging to the NTF2-like superfamily are present in the biosynthetic pathways of numerous polyketide natural products, such as anthracyclins and benzoisochromanequinones. Some have been found to bebona fidepolyketide cyclases, but many of them have roles that are currently unknown. Here, the X-ray crystal structures of three NTF2-like proteins of unknown function are reported: those of ActVI-ORFA fromStreptomyces coelicolorA3(2) and its homologs Caci_6494, a protein from an uncharacterized biosynthetic cluster inCatenulispora acidiphila, and Aln2 fromStreptomycessp. CM020, a protein in the biosynthetic pathway of alnumycin. The presence of a solvent-accessible cavity and the conservation of the His/Asp dyad that is characteristic of many polyketide cyclases suggest a potential enzymatic role for these enzymes in polyketide biosynthesis.
How are research data governed at Japanese repositories? A knowledge commons perspective
Authors: Nishikawa Kai
Published: July 2020

Purpose

The purpose of this paper is to survey how research data are governed at repositories in Japan by deductively establishing a governance typology based on the concept of openness in the context of knowledge commons and empirically assessing the conformity of repositories to each type.

Design/methodology/approach

The fuzzy-set ideal type analysis (FSITA) was adopted. For data collection, a manual assessment was conducted with all Japanese research data repositories registered on re3data.org.

Findings

The typology constructed in this paper consists of three dimensions: openness to resources (here equal to research data), openness to a community and openness to infrastructure provision. This paper found that there is no case where all dimensions are open, and there are several cases where the resources are closed despite research data repositories being positioned as a basis for open science in Japanese science and technology policy.

Originality/value

This is likely the first construction of the typology and application of FSITA to the study of research data governance based on knowledge commons. The findings of this paper provide practitioners insight into how to govern research data at repositories. The typology serves as a first step for future research on knowledge commons, for example, as a criterion of case selection in conducting in-depth case studies.
Prioritization of dimensions of visual merchandising for apparel retailers using FAHP
Authors: Jakhar Riju , Verma Deepak , Rathore Ajay Pal Singh , Kumar Divesh
Published: July 2020

Purpose

Visual merchandising has a direct impact on shopping experience, making it pertinent for the retailers to ensure that their store environment has an effective design. This study blends fuzzy numbers and Analytical Hierarchy Process to create a fuzzy evaluation model prioritizing the relative weights of visual merchandising dimensions of online fashion apparel store. This study will help the fashion retailers in creating more engaging and informative online stores leading to subsequent increase in online retail sales.

Design/methodology/approach

Visual merchandising dimensions and sub dimensions used by retailers for online stores were identified through review of literature and discussion with experts. Twenty experts were interviewed and their responses captured. The responses were analyzed using Fuzzy AHP technique resulting in prioritizing the dimensions according to the weight. For testing the stability of the results, sensitivity analysis was conducted.

Findings

Four key dimensions and sixteen sub dimensions were extracted. Weights were calculated using FAHP. “Pictorial Presentation” has the highest weight followed closely by “Product Information” dimension. Amongst the sub-dimensions “Number of Product Images” scored highest followed by “Product Presentation mode”. “Alterable Background” scored the least weight.

Originality/value

Previous studies have identified Online Visual Merchandising dimensions and have also studied the impact of some of these dimensions on consumer buying behavior, but the relative significance has not been determined yet. This study fills the gap.
Digital transformation of regional industries through asset modification
Authors: Isaksen Arne , Trippl Michaela , Kyllingstad Nina , Rypestøl Jan Ole
Published: July 2020

Purpose

This paper aims to develop a conceptual framework for analysing wide-ranging digital transformation processes of industries in regional contexts.

Design/methodology/approach

The paper includes theoretical work to create a conceptual framework. The paper illustrates and advances the framework by analysing examples from two clusters, one focused on the production of digital products and services and one centred on applying digital tools to make firms’ existing activities more efficient.

Findings

The paper distinguishes between three main and interlinked categories of digitalisation; development of scientific principles that form the basis for developing digital technologies; making of digital products and services; and application of these in production and work processes. Digital transformation of industries located in particular regions relate to changes of (regional) innovation systems. The authors interpret this as processes of asset modification, distinguishing between re-use of existing assets, creation of new assets and (strategic) destruction of outdated assets. Digital transformation may lead to various forms of innovation and path development activities in regional economies.

Practical implications

The paper highlights the importance of modification of assets in organisations and at the level of regional innovation systems to support digitalisation. Organisations need to build absorptive capacity for digitalisation. Regional innovation systems face the challenge to build relevant common assets.

Originality/value

The paper advocates a comprehensive framework to better understand how digital transformation unfolds. It challenges established economic geography approaches, which propagate firm-based views and centre stage skill and technological relatedness. An alternative conceptual framework for scrutinising digital transformation processes in industries in regional contexts is presented.
Does participation in case competitions improve career decision-making self-efficacy of university students?
Authors: Plakhotnik Maria S. , Krylova Anastasiia V. , Maslikova Anna D.
Published: July 2020

Purpose

The purpose of this study was to explore the relationship between participation in case competitions and career decision-making self-efficacy (CDMSE) of university students.

Design/methodology/approach

The sample included 273 Russian university students; 109 (40%) of them had never participated in case competitions, whereas 164 (60%) participated at least once in case competitions related to business, management and economics. Data were collected via an online survey that included the CDMSE scale–short form. Descriptive, correlation and linear regression analyses of data were conducted to test five hypotheses.

Findings

The research study showed a significant difference in CDMSE between those who had never participated in case competitions and those who had participated at least once. However, the study did not show a significant influence of participation in case competitions on the level of CDMSE. The results also indicated that the level of CDMSE could be explained by the participants' work experience, career choice status and age, as well as the highest level achieved during participation in case competitions.

Research limitations/implications

The study provides limitations and implications for future research as well as practice, including career centers and career counselors, university faculty, organizers of case competitions and recruitment specialists in organizations.

Originality/value

Prior research suggests that participation in case competitions helps students’ transition into the workplace. Despite their global popularity, empirical research on case competitions is very limited and focused primarily on skill development. This study contributes to the knowledge base by exploring links between case participation and CDMSE.
Integrated management systems as a driver of sustainability performance: exploring evidence from multiple-case studies
Authors: de Nadae Jeniffer , Carvalho Marly M. , Vieira Darli Rodrigues
Published: July 2020

Purpose

The purpose of this paper is to analyze the impact of integrated management systems (IMSs) on sustainability (based on the triple bottom line (TBL) concept). To accomplish this objective, this paper seeks to answer the following research questions: How can IMS impact organizational sustainability performance? And, how the key challenges of IMS can influence companies in practice?

Design/methodology/approach

A case-based approach is used based on the following four cases from different sectors: an electric power distributor; an environmental consulting firm; a public transport firm; and a firm with a broad portfolio of equipment, products and provisions for industrial services in different markets.

Findings

The results show that the integration of management systems was driven by the companies' strategies toward sustainability. The stakeholders' perception is that a firm's image as a sustainable company also enhances environmental and social performance. The economic performance was not emphasized. Companies noted that the main challenge was motivating and engaging human resources.

Originality/value

This paper shows that sustainability was not a motivation for implementing an IMS. But, implementing an IMS was a driver of sustainability performance. Also, the relationship between IMS and organizational performance can be presented based on TBL perspectives, and implementing an IMS can be challenging in practice.
The human capital–economic growth nexus in SSA countries: what can strengthen the relationship?
Authors: Karambakuwa Roseline Tapuwa , Ncwadi Ronney , Phiri Andrew
Published: July 2020

Purpose

The purpose of this study is to examine the impact of human capital on economic growth for a selected sample of nine SSA countries between 1980 and 2014 using a panel econometric approach.

Design/methodology/approach

The authors estimate a log-linearized endogenous using the fully modified ordinary least squares (FMOLS) and the dynamic ordinary least squares (POLS) applied to our panel data time series.

Findings

The empirical analysis shows an insignificant effect of human capital on economic growth for our selected sample. These findings remain unchanged even after adding interactive terms to human capital, which are representatives of government spending as well as foreign direct investment. Nevertheless, the authors establish a positive and significant effect of the interactive term between urbanization and human capital on economic growth.

Practical implications

The results emphasize the need for African policymakers to develop urbanized, “smart”, technologically driven cities within the SSA region as a platform toward strengthening the impact of human capital-economic growth relationship.

Originality/value

This study becomes the first in the literature to validate the human capital–urbanization–growth relationship for African countries.