bluuebunny/crossref_metadata_2025 huggingface dataset:
Performance of large scale pooled CRISPR screens is dependent on Cas9 expression levels
Authors: Fernandes Neto João M. , Lieftink Cor , Jastrzebski Katarzyna , Krenning Lenno , Dias Matheus , Morris Ben , van der Ven Daimy , Heimans Hester , Medema René H. , Bernards René , Beijersbergen Roderick L.
Published: July 2021

Background

The widespread application of CRISPR/Cas9 technology has yielded numerous findings in biomedical research in recent years, making it an invaluable tool for gene knockout and for high-throughput screening studies. In (low-throughput) gene knockout studies, editing efficiency is not a major concern because only a few edited clones are necessary for a successful assay. However, in large scale pooled screening studies, editing efficiency is a major concern because each sgRNA has to knockout its target gene in a large cell population in a short period of time. Therefore, a thorough understanding of the role that key factors play in determining CRISPR knockout efficiency is essential to improve the performance of pooled CRISPR screening.

Methods

In this study, cell lines with different expression levels of CAS9 were generated and used to determine gene-editing efficiency. Collections of sgRNAs targeting essential genes were used to study their depletion in the different cell line models.

Results

Using cell lines with variable expression of Cas9, we confirmed that editing efficiency and speed are mostly dependent on the sgRNA sequence and Cas9 expression, respectively. Importantly, we show that the strategy employed for delivering sgRNAs and Cas9 to cells impacts the performance of high-throughput screens, which is improved in conditions with higher Cas9 expression.

Conclusions

Our findings highlight the importance of optimizing Cas9 expression levels when performing gene editing experiments and provide guidance on the necessary decisions for implementing optimal pooled CRISPR screening strategies.
Disentangling environmental effects in microbial association networks
Authors: Deutschmann Ina Maria , Lima-Mendez Gipsi , Krabberød Anders K. , Raes Jeroen , Vallina Sergio M. , Faust Karoline , Logares Ramiro
Published: July 2021

Background

Ecological interactions among microorganisms are fundamental for ecosystem function, yet they are mostly unknown or poorly understood. High-throughput-omics can indicate microbial interactions through associations across time and space, which can be represented as association networks. Associations could result from either ecological interactions between microorganisms, or from environmental selection, where the associations are environmentally-driven. Therefore, before downstream analysis and interpretation, we need to distinguish the nature of the association, particularly if it is due to environmental selection or not.

Results

We present EnDED (Environmentally-DrivenEdgeDetection), an implementation of four approaches as well as their combination to predict which links between microorganisms in an association network are environmentally-driven. The four approaches are Sign Pattern, Overlap, Interaction Information, and Data Processing Inequality. We tested EnDED on networks from simulated data of 50 microorganisms. The networks contained on average 50 nodes and 1087 edges, of which 60 were true interactions but 1026 false associations (i.e. environmentally-driven or due to chance). Applying each method individually, we detected a moderate to high number of environmentally-driven edges—87% Sign Pattern and Overlap, 67% Interaction Information, and 44% Data Processing Inequality. Combining these methods in an intersection approach resulted in retaining more interactions, both true and false (32% of environmentally-driven associations). After validation with the simulated datasets, we applied EnDED on a marine microbial network inferred from 10 years of monthly observations of microbial-plankton abundance. The intersection combination predicted that 8.3% of the associations were environmentally-driven, while individual methods predicted 24.8% (Data Processing Inequality), 25.7% (Interaction Information), and up to 84.6% (Sign Pattern as well as Overlap). The fraction of environmentally-driven edges among negative microbial associations in the real network increased rapidly with the number of environmental factors.

Conclusions

To reach accurate hypotheses about ecological interactions, it is important to determine, quantify, and remove environmentally-driven associations in marine microbial association networks. For that, EnDED offers up to four individual methods as well as their combination. However, especially for the intersection combination, we suggest using EnDED with other strategies to reduce the number of false associations and consequently the number of potential interaction hypotheses.
Binding Free energy Decomposition and Multiple Unbinding Paths of Buried Ligands in a PreQ1 Riboswitch
Authors: Hu Guodong , Zhou Huan-Xiang
Published: July 2021

Riboswitches are naturally occurring RNA elements that control bacterial gene expression by binding to specific small molecules. They serve as important models for RNA-small molecule recognition and have also become a novel class of targets for developing antibiotics. Here, we carried out conventional and enhanced-sampling molecular dynamics (MD) simulations, totaling 141.5 μs, to characterize the determinants of binding free energies and unbinding paths for the cognate and synthetic ligands of a PreQ1 riboswitch. Binding free energy analysis showed that two triplets of nucleotides U6-C15-A29 and G5-G11-C16, contribute the most to the binding of the cognate ligands, by hydrogen bonding and by base stacking, respectively. Mg2+ ions are essential in stabilizing the binding pocket. For the synthetic ligands, the hydrogen-bonding contributions of the U6-C15-A29 triplet are significantly compromised, and the bound state resembles the apo state in several respects, including the disengagement of the C15-A14-A13 and A32-G33 base stacks. The bulkier synthetic ligands lead to significantly loosening of the binding pocket, including extrusion of the C15 nucleobase and a widening of the C15-C30 groove. Enhanced-sampling simulations further revealed that the cognate and synthetic ligands unbind in almost opposite directions. Our work offers new insight for designing riboswitch ligands.
Livestock as vectors of organic matter and nutrient loading in aquatic ecosystems in African savannas
Authors: Iteba Jacob O. , Hein Thomas , Singer Gabriel A. , Masese Frank O.
Published: July 2021

Populations of large wildlife have declined in many landscapes around the world, and have been replaced or displaced by livestock. The consequences of these changes on the transfer of organic matter (OM) and nutrients from terrestrial to aquatic ecosystems are not well understood. We used behavioural data, excretion and egestion rates and C: N: P stoichiometry of dung and urine of zebu cattle, to develop a metabolism-based estimate of loading rates of OM (dung), C, N and P into the Mara River, Kenya. We also directly measured the deposition of OM and urine by cattle into the river during watering. Per head, zebu cattle excrete and/or egest 25.6 g dry matter (DM, 99.6 g wet mass; metabolism) - 27.7 g DM (direct input) of OM, 16.0-21.8 g C, 5.9-9.6 g N, and 0.3-0.5 g P per day into the river. To replace loading rates OM of an individual hippopotamus by cattle, around 100 individuals will be needed, but much less for different elements. In parts of the investigated sub-catchments loading rates by cattle were equivalent to or higher than that of the hippopotamus. The patterns of increased suspended materials and nutrients as a result of livestock activity fit into historical findings on nutrients concentrations, dissolved organic carbon and other variables in agricultural and livestock areas in the Mara River basin. Changing these patterns of OM and nutrients transport and cycling are having significant effects on the structure and functioning of both terrestrial and aquatic ecosystems.
Entangling snakebite dynamics: the spatiotemporal role of rainfall on snake envenoming in Colombia
Authors: Bravo-Vega Carlos , Santos-Vega Mauricio , Cordovez Juan Manuel
Published: July 2021

The role of climate forcing on the population dynamics of infectious diseases has typically been addressed via retrospective analyses of aggregated incidence records over whole political regions. A central question in epidemiology has been whether seasonal and interannual cycles are driven by climate variation, or instead generated by other factors such as poverty or underreporting. Here, we use process-based models to determine the role of rainfall in the dynamics of snakebite, which is one of the main neglected tropical diseases around the world. We combined space-time datasets of snakebite incidence and rainfall for Colombia in combination with stochastic epidemiological models and iterated filtering methods to show the response to rainfall forcing, specifically, modulating the encounter frequency with venomous snakes. We identified six zones with different rainfall patterns to demonstrate that the relationship between rainfall and snakebite incidence was heterogeneous. Rainfall only drives snakebite incidence in regions with marked dry seasons, where rainfall becomes the limiting resource. In addition, the encounter frequency also differs between regions, and it is higher in regions where Bothrops atrox can be found. Our results show how the heterogeneous spatial distribution of snakebite risk seasonality in the country may be related to important traits of venomous snakes’ natural history.

SIGNIFICANCE STATEMENT

The association between seasonal climatic variables and diseases’ epidemiology has helped to understand disease burden under changing environments. For example, for several tropical zoonotic diseases rainfall has been identified as a critical covariate inducing incidence seasonality. Snakebite envenoming is a disease that affects mostly economically deprived populations, and the availability of treatment is scarce. However, the role of environmental factors on snakebite is still missing in the literature. We formulated an epidemiological model to quantify the role of rainfall on snakebite seasonality throughout Colombia. We found that rainfall has a significant effect on incidence in places with a marked dry season (Caribbean and Orinoco plains), but in areas without dry season (Amazonian basin and southwestern Colombia) incidence exhibits no seasonality. This study is the first epidemiological modeling approach to snakebite and underscores the importance of rainfall as the limiting resource in this system. Thus, it is important to consider the interaction between climate forcing and venomous snakes’ ecology as determinants of envenomation risk.
When Does Mutualism Offer a Competitive Advantage? A Game-Theoretic Analysis of Host-Host Competition in Mutualism
Authors: Halloway Abdel H. , Heath Katy D. , McNickle Gordon G.
Published: July 2021

Plants due to their non-motile nature rely heavily on mutualistic interactions to obtain resources and carry out services. One key mutualism is the plant-microbial mutualism in which a plant trades away carbon to a microbial partner for nutrients like nitrogen and phosphorous. Plants show much variation in the use of this partnership from the individual level to entire lineages depending upon ecological, evolutionary, and environmental context. We sought to determine how this context dependency could result in the promotion, exclusion, or coexistence of the microbial mutualism by seeing if and when the partnership provided a competitive advantage to the plant. To that end, we created a simple 2 × 2 evolutionary game in which plants could either be a mutualist and pair with a microbe or a non-mutualist and forgo the partnership. This model included nutrients freely available to the plant, nutrients obtained only through mutualism with microbes, the cost of producing roots, the cost of trade with microbes, and the size of the local competitive neighborhood. Not surprisingly, we found that mutualism could offer a competitive advantage if its net benefit was positive. Coexistence between strategies is possible though due to competition between mutualists over the microbially obtained nutrient. In addition, the greater the size of the local competitive neighborhood, the greater the region of coexistence but only at the expense of mutualist fixation (non-mutualist fixation was unaffected). Our model, though simple, shows that plants can gain a competitive advantage from using a mutualism depending upon the context and points to basic experiments that can be done to verify the results.
Myonuclear maturation dynamics in aged and adult regenerating mouse skeletal muscle
Authors: Kurland Jesse V. , Van Deusen Ashleigh , Pawlikowski Brad , Hall Monica , Dalla Betta Nicole , Antwine Tiffany , Cutler Alicia C , Russell Alan , Allen Mary Ann , Dowell Robin , Olwin Bradley
Published: July 2021

Skeletal muscle cells are multinucleated syncytial cells arising from cell fusion, yet despite sharing a common cytoplasm individual myonuclei express distinct transcriptional programs. Whether individual myonuclei acquire heterogenous transcriptional states via differences in their progenitors, during differentiation, or once their anatomical position is acquired, is not known. We performed transcriptome and pseudotime analysis of single myogenic nuclei from uninjured and post-injury murine skeletal muscle to assess when myonuclear heterogeneity is acquired. Two distinct progenitors contribute to myonuclei, one a non-myogenic fibroblast subtype, and skeletal muscle stem cells the other. Both progenitors enter a single pseudotime trajectory that bifurcates as myonuclei mature into two branches segregated by myosin isoform expression and metabolic profiles, suggesting transcriptional heterogeneity is acquired as myonuclei mature. In aged skeletal muscle myogenic progenitor expansion is perturbed and nuclei from aged muscle display distinct pseudotemporal kinetics compared to nuclei from young mice. In aged mice, the inferred myogenic differentiation trajectory is delayed, altering the distribution of myogenic nuclei in pseudotime, suggesting that altered transcriptional dynamics in nuclei in aged mice may drive age-associated muscle deficits and bias myonuclei towards acquiring oxidative metabolic profiles.
Glutamatergic and GABAergic neurons mediate distinct neurodevelopmental phenotypes of STXBP1 encephalopathy
Authors: Kim Joo Hyun , Chen Wu , Chao Eugene S. , Chen Hongmei , Xue Mingshan
Published: July 2021

Heterozygous pathogenic variants in syntaxin-binding protein 1 (STXBP1, also known as MUNC18-1) cause STXBP1 encephalopathy and are among the most frequent causes of developmental and epileptic encephalopathies and intellectual disabilities. STXBP1 is an essential protein for presynaptic neurotransmitter release, and its haploinsufficiency impairs glutamatergic and GABAergic neurotransmission. However, the mechanism underlying the broad spectrum of neurological phenotypes is poorly understood. Here we show that glutamatergic and GABAergic neurons mediate distinct disease features with few overlaps. Glutamatergic and GABAergic neurons-specific Stxbp1 haploinsufficient mice exhibit different subsets of the cognitive and seizure phenotypes observed in the constitutive Stxbp1 haploinsufficient mice. Developmental delay and most of the motor and psychiatric phenotypes are only recapitulated by GABAergic Stxbp1 haploinsufficiency. Thus, the contrasting roles of excitatory and inhibitory signaling in STXBP1 encephalopathy identify GABAergic dysfunction as a main disease mechanism and reveal the possibility to selectively modulate disease phenotypes by targeting specific neurotransmitter systems.
Pfam domain adaptation profiles reflect plant species’ evolutionary history
Authors: Jensen Sarah E. , Buckler Edward S.
Published: July 2021

The increase in global temperatures predicted by climate change models presents a serious problem for agriculture because high temperatures reduce crop yields. Protein biochemistry is at the core of plant heat stress response, and understanding the interactions between protein biochemistry and temperature will be key to developing heat-tolerant crop varieties. Current experimental studies of proteome-wide plant thermostability are limited by the complexity of plant proteomes: evaluating function for thousands of proteins across a variety of temperatures is simply not feasible with existing technologies. In this paper, we use homologous prokaryote sequences to predict plant Pfam temperature adaptation and gain insights into how thermostability varies across the proteome for three species: maize, Arabidopsis, and poplar. We find that patterns of Pfam domain adaptation across organelles are consistent and highly significant between species, with cytosolic proteins having the largest range of predicted Pfam stabilities and a long tail of highly-stable ribosomal proteins. Pfam adaptation in leaf and root organs varies between species, and maize root proteins have more low-temperature Pfam domains than do Arabidopsis or poplar root proteins. Both poplar and maize populations have an excess of low-temperature mutations in Pfam domains, but only the mutations identified in poplar accessions have a negative effect on Pfam temperature adaptation overall. These Pfam domain adaptation profiles provide insight into how different plant structures adapt to their surrounding environment and can help inform breeding or protein editing strategies to produce heat-tolerant crops.
A genetic toolkit for investigating Clavibacter: markerless deletion, permissive site identification and an integrative plasmid
Authors: Stevens Danielle M. , Tang Andrea , Coaker Gitta
Published: July 2021

The development of knockout mutants and expression variants are critical for understanding genotype-phenotype relationships. However, advancements of these techniques in Gram-positive actinobacteria have stagnated over the last decade. Actinobacteria in the Clavibacter genus are composed of diverse crop pathogens which cause a variety of wilt and cankering diseases. Here, we present a suite of tools for genetic manipulation in the tomato pathogen C. michiganensis including a markerless deletion system, an integrative plasmid, and an R package for identification of permissive sites for plasmid integration. The vector pSelAct-KO is a recombination based, markerless knockout system that uses dual selection to engineer seamless deletions of a region of interest, providing opportunities for repeated higher-order genetic knockouts. The efficacy of pSelAct-KO was demonstrated in C. michiganensis and confirmed using whole genome sequencing. We developed permissR, an R package to identify permissive sites for chromosomal integration, which can be used in conjunction with pSelAct-Express, a non-replicating integrative plasmid that enables recombination into a permissive genomic location. Expression of eGFP by pSelAct-Express was verified in two candidate permissive regions predicted by permissR in C. michiganensis. These molecular tools are essential advancements for investigating Gram-positive actinobacteria, particularly for important pathogens in the Clavibacter genus.
Use of 1-MNA to Improve Exercise Tolerance and Fatigue in Patients After COVID-19
Authors: Chudzik Michał , Kapusta Joanna , Burzyńska Monika
Published: July 2021

Background

Coronavirus disease 2019 (COVID-19) is a serious respiratory disease that results from infection with a newly discovered coronavirus (SARS-COV-2). Unfortunately, COVID-19 is not only a short-term infection but that patients (pts) recovering from SARS-CoV2 infection complain of persisting symptoms including: fatigue, diffuse myalgia and weakness, which may lead to chronic fatigue syndrome. There is currently no evidence that nutritional supplements and/or physical exercise can assist in the recovery of pts with chronic fatigue syndrome. 1-Methylnicotinamide (1-MNA) is an endogenic substance that is produced in the liver when nicotinic acid is metabolized. 1-MNA demonstrates anti-inflammatory and anti-thrombotic properties. Therefore, we investigated whether 1-MNA supplements could improve exercise tolerance and decrease fatigue among patients recovering from SARS-CoV-2.

Methods

The study population was composed of pts after COVID-19, expressing subjective feelings of limited tolerance to exercise. The selected pts were randomized into two groups: GrM0 – without supplementation; GrM1 – with 1-MNA supplementation. At the beginning of the study (Phase 0), in both groups, a 6-minute walk test (6MWT) was carried out and fatigue assessment with Fatigue Severity Scale (FSS) was performed. After 1 month (Phase 1), a follow up FSS and 6MWT once more were performed in both groups.

Results

A significant improvement in the mean distance covered in the 6MWT was noted among the pts in GrM1, compared to those in GrM0. We also noted that in GrM1 the 6MWT distance was significantly higher after 1 month of supplementation with 1-MNA, compared to the beginning of the study (515.18 m in Phase 0 vs 557.8m in Phase 1; p = 0.000034). In GrM1, significantly more pts improved their distance in the 6MWT (23 out of 25 pts, equal to 92%), by a mean of 47 meters, compared to GrM0 (15 of 25 pts, equal to 60%) (p = 0.0061). After one month, significantly more patients in the group without 1-MNA had severe fatigue (FSS ≥ 4) compared to the group with supplementation (GrM1 = 5 pts (20%) vs GrM0 = 14pts (56%); p = 0.008).

Conclusions

1-MNA supplementation significantly improved physical performance in a 6-minute walk test and reduced the percentage of patients with severe fatigue after COVID-19. The comprehensive action of 1-MNA, including anti-inflammatory and anticoagulant effects, as well as activation of the SIRT1 enzyme, may be beneficial for the recovery of patients with persistent symptoms of fatigue and low tolerance to exercise after COVID-19.
Programmed axon death executor SARM1 is a multi-functional NAD(P)ase with prominent base exchange activity, all regulated by physiological levels of NMN, NAD, NADP and other metabolites
Authors: Angeletti Carlo , Amici Adolfo , Gilley Jonathan , Loreto Andrea , Trapanotto Antonio G. , Antoniou Christina , Coleman Michael P. , Orsomando Giuseppe
Published: July 2021

SARM1 is an NAD glycohydrolase and TLR adapter with an essential, prodegenerative role in programmed axon death (Wallerian degeneration). It has low basal NADase activity that becomes strongly activated by NAD precursor NMN. Very high levels of NAD oppose this activation, competing for the same allosteric site on SARM1’s regulatory ARM domain. Injury or diseases that deplete axons of NMNAT2, an essential enzyme converting NMN to NAD, cause SARM1 activation. The resulting NAD degradation by SARM1, combined with loss of NAD synthesis by NMNAT2, causes rapid depletion of axonal NAD. This NAD loss is widely assumed to mediate axon death and is consequently a key focus for therapeutic strategies for axonopathies. However, like other NAD(P) glycohydrolases, SARM1 has additional enzyme activities whose contributions, consequences and regulation need to be fully understood. Here, we compare the multiple actions and regulation of recombinant human SARM1 with those of two other NAD(P) glycohydrolases, human CD38 and Aplysia californica ADP ribosyl cyclase. We find that SARM1 has the highest transglycosidation (base exchange) activity of these enzymes at neutral pH and with some bases this dominates NAD(P) hydrolysis and cyclisation. Moreover, like its NADase and NADPase reactions, SARM1-mediated base exchange at neutral pH is activated by increases in the NMN:NAD ratio, which we show for the first time can act in the presence of physiological levels of both metabolites. We establish that SARM1 base exchange is the most likely physiological source of calcium mobilizing agent NaADP, and potentially of other NAD(P) analogues, which could contribute to axon and cell death. We also identify regulatory effects of free pyridine bases, of NADP and of nicotinic acid riboside (NaR) on SARM1 that represent further therapeutic opportunities. These data will help to pinpoint which of the multiple functions of SARM1 is responsible for axon degeneration and how it can be optimally targeted to block axon degeneration in disease.
RNase HI depletion strongly potentiates cell killing by rifampicin in mycobacteria
Authors: Al-Zubaidi Abeer , Cheung Chen-Yi , Cook Gregory M. , Taiaroa George , Mizrahi Valerie , Lott J. Shaun , Dawes Stephanie S.
Published: July 2021

Multidrug resistant (MDR) tuberculosis (TB) is defined by the resistance of Mycobacterium tuberculosis, the causative organism, to the first-line antibiotics rifampicin and isoniazid. Mitigating or reversing resistance to these drugs offers a means of preserving and extending their use in TB treatment. R-loops are RNA/DNA hybrids that are formed in the genome during transcription, and can be lethal to the cell if not resolved. RNase HI is an enzyme that removes R-loops, and this activity is essential in M. tuberculosis: knockouts of rnhC, the gene encoding RNase HI, are non-viable. This essentiality supports it as a candidate target for the development of new antibiotics. In the model organism Mycolicibacterium smegmatis, RNase HI activity is provided by two RNase HI enzymes, RnhA and RnhC. We show that the partial depletion of RNase HI activity in M. smegmatis, by knocking out either of the genes encoding RnhA or RnhC, led to the accumulation of R-loops. The sensitivity of the knockout strains to the antibiotics moxifloxacin, streptomycin and rifampicin was increased, with sensitivity to the transcriptional inhibitor rifampicin strikingly increased by nearly 100-fold. We also show that R-loop accumulation accompanies partial transcriptional inhibition, suggesting a mechanistic basis for the synergy between RNase HI depletion and transcriptional inhibition. A model of how transcriptional inhibition can potentiate R-loop accumulation is presented. Finally, we identified four small molecules that inhibit recombinant RnhC activity and that also potentiated rifampicin activity in whole-cell assays against M. tuberculosis, supporting an on-target mode of action, and providing the first step in developing a new class of anti-mycobacterial drug.

Importance

This study validates mycobacterial RNase HI as a druggable, vulnerable candidate for a new therapeutic treatment of M. tuberculosis with a novel mode of action. RNase HI depletion shows synergistic bacterial killing with some current first- and second-line antibiotics, suggesting that RNase HI inhibitors would combine well with these regimens, and could potentially accelerate the clearance of drug-sensitive strains. RNase HI inhibitors also have the potential to reduce the effective dose of rifampicin, with the comcommitant reduction in side effects. The potentiation of rifampicin efficacy conferred by RNase HI deficiency suggests that RNase HI inhibitors may be able to mitigate against development of rifampicin resistance. The synergy may also be able to reverse rifampicin resistance, rescuing this antibiotic for therapy. The surprising finding that low levels of transcriptional inhibition potentiate R-loop formation provides a key new insight into R-loop metabolism.
Systematic in vivo interrogation identifies novel enhancers and silencers associated to Atrial Fibrillation
Authors: Victorino Jesus , Rollan Isabel , Rouco Raquel , Adan Javier , Manzanares Miguel
Published: July 2021

Cis-regulatory elements control gene expression in time and space and their disruption can lead to pathologies. Reporter assays allow the functional validation of enhancers and other regulatory elements, and such assays by means of the generation of transgenic mice provide a powerful tool to study gene regulation in development and disease. However, these experiments are time-consuming and, thus, their performance is very limited. Here, we increase the throughput of in vivo mouse reporter assays by using a piggyBac transposon-based system, and use it to decode the regulatory landscape of atrial fibrillation, a prevalent cardiac arrhythmia. We systematically interrogated ten human loci associated to atrial fibrillation in the search for regulatory elements. We found five new cardiac-specific enhancers and implicated novel genes in arrhythmia through genome editing and three-dimensional chromatin analysis by 4C-seq. Of note, functional dissection of the 7q31 locus identified a bivalent regulatory element in the second intron of the CAV1 gene differentially acting upon four genes. Our system also detected negative regulatory elements thanks to which we identified a ubiquitous silencer in the 16q22 locus that regulates ZFHX3 and can outcompete heart enhancers. Our study characterizes the function of new genetic elements that might be of relevance for the better understanding of gene regulation in cardiac arrhythmias. Thus, we have .established a new framework for the efficient dissection of the genetic contribution to common human diseases.
The J domain of sacsin disrupts intermediate filament assembly
Authors: Dabbaghizadeh Afrooz , Paré Alexandre , Cheng-Boivin Zacharie , Dagher Robin , Minotti Sandra , Dicaire Marie-Josée , Bernard Brais , Young Jason C. , Durham Heather D. , Gentil Benoit J.
Published: July 2021

Autosomal Recessive Spastic Ataxia of the Charlevoix Saguenay (ARSACS), is caused by loss of function mutations in the SACS gene, which encodes sacsin, a giant protein of 520 kDa. A key feature of the absence of sacsin in cells is the formation of abnormal bundles of intermediate filaments (IF) including neurofilaments (NF) in neurons and vimentin IF in fibroblasts, suggesting a role of sacsin in IF homeostasis. Sacsin contains a J domain (SacsJ) homologous to Hsp40, that can interact with Hsp70 chaperones. The SacsJ domain resolved NF bundles in cultured Sacs-/- neurons, however, its mechanism is still unclear. Here, we focused on the role of SacsJ in NF assembly. We report that the SacsJ domain directly interacts with NF proteins in vitro to disassemble NFL filaments, and to inhibit their initial assembly, in the absence of Hsp70. We generated a cell-penetrating peptide derived from this domain, SacsJ-myc-TAT, which was efficient in disassembling both vimentin IF and NF in cultured fibroblasts and Sacs+/+ motor neurons as well as NF bundles in cultured Sacs-/- motor neurons. Whereas a normal NF network was restored in Sacs-/- neurons treated with the SacsJ peptide, there was some loss of IF networks in Sacs+/+ fibroblasts or neurons. These results suggest that SacsJ is a key regulator of NF and IF networks in cells, with implications for its therapeutic use.
Deep learning for improving non-destructive grain mapping in 3D
Authors: Fang H. , Hovad E. , Zhang Y. , Clemmensen L. K. H. , Ersbøll B. Kjaer , Juul Jensen D.
Published: July 2021

Laboratory X-ray diffraction contrast tomography (LabDCT) is a novel imaging technique for non-destructive 3D characterization of grain structures. An accurate grain reconstruction critically relies on precise segmentation of diffraction spots in the LabDCT images. The conventional method utilizing various filters generally satisfies segmentation of sharp spots in the images, thereby serving as a standard routine, but it also very often leads to over or under segmentation of spots, especially those with low signal-to-noise ratios and/or small sizes. The standard routine also requires a fine tuning of the filtering parameters. To overcome these challenges, a deep learning neural network is presented to efficiently and accurately clean the background noise, thereby easing the spot segmentation. The deep learning network is first trained with input images, synthesized using a forward simulation model for LabDCT in combination with a generic approach to extract features of experimental backgrounds. Then, the network is applied to remove the background noise from experimental images measured under different geometrical conditions for different samples. Comparisons of both processed images and grain reconstructions show that the deep learning method outperforms the standard routine, demonstrating significantly better grain mapping.
Conformational flexibility of EptA driven by an interdomain helix provides insights for enzyme–substrate recognition
Authors: Anandan Anandhi , Dunstan Nicholas W. , Ryan Timothy M. , Mertens Haydyn D. T. , Lim Katherine Y. L. , Evans Genevieve L. , Kahler Charlene M. , Vrielink Alice
Published: July 2021

Many pathogenic gram-negative bacteria have developed mechanisms to increase resistance to cationic antimicrobial peptides by modifying the lipid A moiety. One modification is the addition of phosphoethanolamine to lipid A by the enzyme phosphoethanolamine transferase (EptA). Previously we reported the structure of EptA from Neisseria, revealing a two-domain architecture consisting of a periplasmic facing soluble domain and a transmembrane domain, linked together by a bridging helix. Here, the conformational flexibility of EptA in different detergent environments is probed by solution scattering and intrinsic fluorescence-quenching studies. The solution scattering studies reveal the enzyme in a more compact state with the two domains positioned close together in an n-dodecyl-β-D-maltoside micelle environment and an open extended structure in an n-dodecyl-phosphocholine micelle environment. Intrinsic fluorescence quenching studies localize the domain movements to the bridging helix. These results provide important insights into substrate binding and the molecular mechanism of endotoxin modification by EptA.
How far the Indian banking sectors are efficient?: An empirical investigation
Authors: Maity Sudarshan , Sahu Tarak Nath
Published: July 2021

Purpose

Bank mobilizes savings and transforms it into credit for investments in various sectors, which helps the economy running. The purpose of this paper is to examine the efficiency of three bank groups in India with data spanning from 2009–2010 to 2018–2019.

Design/methodology/approach

The study uses data envelopment analysis for measuring the efficiency of the selected banks. It measures the efficiency both from the revenue dimension and from the supply-side dimension of financial inclusion.

Findings

The study finds that foreign banks on average are working efficiently far better than the public-sector and private-sector banks. It indicates that foreign banks in India are operating at 92.53% efficiency level, whereas private- and public-sector banks are operating at 90.20 and 86.04% efficiency levels, respectively. Further, the result of the Friedman test reveals that there is no significant difference in efficiency scores amongst these three bank groups. As major challenges, non-performing assets of the banking industry to be reduced by 15% as radial and 53.18% as slack.

Originality/value

One of the notable innovativeness of this study is that, unlike most of the previous studies that are mostly selected few banks and specific group, the present study may place itself as a unique inquiry in the domain of technical efficiency in macro concept by considering three major bank groups operating in India. An important contribution of the study is the classification of reasons behind the inefficiency, i.e. managerial or inappropriate scale size and further projections of input factors for the same level of output.
The productivity of the agricultural sector and industrial sector as a driving force of economic growth and community welfare in Indonesia
Authors: Salendu Salendu
Published: July 2021

Purpose

This study aims to examine the effect of trade liberalization on welfare, directly or indirectly, through the productivity of the agricultural sector and the productivity of the industrial sector, which affects economic growth and the welfare of the community.

Design/methodology/approach

This study is explanatory as it looks at causal relationships between one variable with another (causality relationship). The data used in this study are secondary data from various sources, such as the International Financial Statistics (IFS) from the International Monetary Fund (IMF), World Bank, Bank Indonesia reports, Central Bureau of Statistics and several other sources. All data used in this study is annual data for each research variable from 1986 to 2016.

Findings

Based on the results of the analysis, there is a significant direct and negative influence of the agricultural sector productivity on economic growth, a significant direct and negative influence of the industrial sector productivity on economic growth.

Originality/value

Considering the diverse effects of trade liberalization both on economic growth and people's welfare in developing countries, the researcher was interested in knowing how trade liberalization affects Indonesia. This study tries to observe and analyze those relations.
The critical factors shaping customer shopping experiences with innovative technologies
Authors: Ylilehto Marianne , Komulainen Hanna , Ulkuniemi Pauliina
Published: July 2021

Purpose

The purpose of this study is to explore the customer shopping experience in the innovative technology setting. Specifically, the purpose is to understand how do innovative technologies influence the customer shopping experience?

Design/methodology/approach

This qualitative, explorative study has characteristics of a phenomenological research strategy. The data were collected from four focus groups and ten in-depth interviews with consumers. Abductive approach with an implementation of content analysis was used as a method of analysis.

Findings

The results show that there are three critical factors in customer's shopping experience in the context of innovative technologies; (1) channel choice, (2) value dimensions related to convenience and enjoyment, and (3) social interaction. All factors are highly intertwined and influence each other.

Originality/value

This study contributes to customer experience literature by offering a framework for understanding customer shopping experiences in the innovative technology setting. These findings have important implications for retail managers seeking to enhance customer experience and achieve a competitive advantage by utilizing innovative technology.
Corporate governance and risk-taking of Islamic banks: evidence from OIC countries
Authors: Aslam Ejaz , Haron Razali
Published: July 2021

Purpose

This paper aims to investigate the impact of corporate governance and other related factors on the risk-taking of Islamic banks. Risk-taking is defined according to credit risk, liquidity risk and operational risk.

Design/methodology/approach

The study uses the two step system generalized method of moment (2SYS-GMM) estimation technique by using a panel data set of 129 Islamic banks (IBs) from 29 countries in the Middle East, South Asia and the Southeast Asia regions covering from 2008 to 2017. Governance variables incorporated include board size, board independence, chief executive officer (CEO) power, Shariah board and audit committee, as well as other control variables.

Findings

This study provides evidence that board size and Shariah board are positively and significantly related to credit and liquidity risk. Board independence and CEO power are negative and significantly associated with credit and liquidity risk, but the audit committee has a mixed relationship with bank risk. Male CEOs take more risk compared to the female and more board meeting has an inverse relationship with Islamic banks risk. Bank size, however, does not influence the level of risk in Islamic banks, but leverage has an inverse relationship with bank risk.

Research limitations/implications

The present study sheds light on the risk-taking behaviour of the board of IBs, particularly the board independence and CEO power reducing the level of risk in IBs thereby contributing to the agency theory. Therefore, regulators and policymakers can use the findings of this study to strengthen the internal corporate governance mechanism to protect IBs at a time of financial distress. Moreover, it increases the trust of the shareholders and stakeholders in the effectiveness of governance reforms that have been pursued to reap long-term benefits.

Originality/value

To the best of the knowledge, this research is preliminary in examining the board behaviour on risk-taking of IBs from four different regions. The results are robust and suggest that the board of directors mitigate the level of risk in IBs.
Multi-objective NSGA-II based shape optimisation of the cross-sectional shape of passively cooled heat sinks
Authors: Santhanakrishnan Mani Sekaran , Tilford Tim , Bailey Chris
Published: July 2021

Purpose

The purpose of the study is to optimise the cross-sectional shape of passively cooled horizontally mounted pin-fin heat sink for higher cooling performance and lower material usage.

Design/methodology/approach

Multi-objective shape optimisation technique is used to design the heat sink fins. Non-dominated sorting genetic algorithm (NSGA-II) is combined with a geometric module to develop the shape optimiser. High-fidelity computational fluid dynamics (CFD) is used to evaluate the design objectives. Separate optimisations are carried out to design the shape of bottom row fins and middle row fins of a pin-fin heat sink. Finally, a computational validation was conducted by generating a three-dimensional pin-fin heat sink using optimised fin cross sections and comparing its performance against the circular pin-fin heat sink with the same inter-fin spacing value.

Findings

Heat sink with optimised fin cross sections has 1.6% higher cooling effectiveness than circular pin-fin heat sink of same material volume, and has 10.3% higher cooling effectiveness than the pin-fin heat sink of same characteristics fin dimension. The special geometric features of optimised fins that resulted in superior performance are highlighted. Further, Pareto-optimal fronts for this multi-objective optimisation problem are obtained for different fin design scenarios.

Originality/value

For the first time, passively cooled heat sink’s cross-sectional shapes are optimised for different spatial arrangements, using NSGA-II-based shape optimiser, which makes use of CFD solver to evaluate the design objectives. The optimised, high-performance shapes will find direct application to cool power electronic equipment.
University–industry collaboration: constructing a business model lab for student venture creation
Authors: Hasche Nina , Linton Gabriel
Published: July 2021

Purpose

The study aims to examine the development of student venture creation in a co-curricular business model lab initiative with collaboration between students, researchers, technology transfer offices (TTO) and industry. It presents a fresh approach to the study of student venture creation by discussing a unique co-curricular case, its embeddedness in a network and drawing on the concept of tension.

Design/methodology/approach

A qualitative, case-based research design is applied containing data from interviews, observations and active participation.

Findings

The findings point to the inherent difficulties in managing and organizing student venture creation and networks surrounding the student venture creation in a co-curricular setting that can lead to several different types of tensions. Episodes where task-, role-, process-, affective- and value-related tensions arise are identified. Furthermore, the findings highlight that affective-related tension is often an outcome of other types of tensions.

Research limitations/implications

Our theoretical implications point to the importance of the context of student venture creation, but not only regarding curricular and co-curricular initiatives; depending on the context, such as if student surrogate entrepreneurship is used, different types of support structure might also be needed to enable student venture creation.

Originality/value

Research on the entrepreneurial university has mainly focused on entrepreneurship education and ventures created by researchers. This study responds to recent calls for research on the venture creation of students. The limited research conducted on student venture creation can be divided between curricular and co-curricular initiatives. Our research points out that many other contextual factors are of importance, such as the origin of ideas, student surrogate entrepreneurship, industry collaboration, team formation and expectations.
Adoption of mobile technology for mobile learning by university students during COVID-19
Authors: Zaidi Syed Faizan Hussain , Osmanaj Valmira , Ali Omar , Zaidi S.A.H.
Published: July 2021

Purpose

Due to the eruption of the COVID-19 pandemic, many universities were forced to shift from the traditional learning practices to digital learning. Hence, the purpose of this study is to evaluate the factors that affect the university student's adoption of mobile technologies for mobile learning (m-learning) in their learning process.

Design/methodology/approach

Technology acceptance model (TAM) is incorporated to study the adoption of mobile learning by university students. Quantitative research technique is used as core research approach in this study. Structural equation modelling (SEM), which is a part of quantitative research method, was employed on the congregated data via a set of questionnaire from 268 University students. SEM is used to explore the relationships among the hypothesized constructs. SPSS and AMOS software were used for the analysis of data.

Findings

This study validated the updated TAM model and assessed the students' adoption of mobile technologies for m-learning during COVID-19. All the constructs of proposed model were found to be significant with more than 50% average variance extracted. It was found that two external constructs mobile system efficacy and mobile service efficacy appended in technology acceptance model show the direct positive effect on perceived usefulness and perceived ease of use constructs. However, hypothesized relationships were found to be unsupported among perceived usefulness and perceived ease of use. Furthermore, perceived usefulness and ease of use during m-learning impact the students' usage attitude which consequently impact the students' adoption behaviour towards adoption of mobile technology.

Research limitations/implications

Six constructs were considered for this study; however, mobile information quality for mobile learning was not included which could affect students' adoption criteria. Additionally, this study is limited to a country where future study needs validation of propose constructs in different demographic settings.

Originality/value

No study allied to the students' adoption of mobile technology for m-learning has accomplished in the context of India during COVID-19. Furthermore, TAM model has been updated with regard to the students' adoption of mobile learning during COVID-19 in Indian higher education setting.