bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacteria Use Structural Imperfect Mimicry To Hijack The Host Interactome
Authors: de Groot Natalia Sanchez , Burgas Marc Torrent
Published: February 2020

Bacteria use protein-protein interactions to infect their hosts and hijack fundamental pathways, which ensures their survival and proliferation. Hence, the infectious capacity of the pathogen is closely related to its ability to interact with host proteins. Here, we show that hubs in the host-pathogen interactome are isolated in the pathogen network by adapting the geometry of the interacting interfaces. An imperfect mimicry of the eukaryotic interfaces allows pathogen proteins to actively bind to the host’s target while preventing deleterious effects on the pathogen interactome. Understanding how bacteria recognize eukaryotic proteins may pave the way for the rational design of new antibiotic molecules.
Predicting antibiotic-associated virulence ofPseudomonas aeruginosausing anex-vivolung biofilm model
Authors: Hassan Marwa M. , Harrington Niamh E. , Sweeney Esther , Harrison Freya
Published: February 2020

Background

Bacterial biofilms are known to have high antibiotic tolerance which directly affects clearance of bacterial infections in people with cystic fibrosis (CF). Current antibiotic susceptibility testing methods are either based on planktonic cells or do not reflect the complexity of biofilmsin vivo. Consequently, inaccurate diagnostics affect treatment choice, preventing bacterial clearance and potentially selecting for antibiotic resistance. This leads to prolonged, ineffective treatment.

Methods

In this study, we use anex-vivolung biofilm model to study antibiotic tolerance and virulence ofPseudomonas aeruginosa. Sections of pig bronchiole were dissected, prepared and infected with clinical isolates ofP. aeruginosaand incubated in artificial sputum media to form biofilms, as previously described. Then, lung-associated biofilms were challenged with antibiotics, at therapeutically relevant concentrations, before their bacterial load and virulence were quantified and detected, respectively.

Results

The results demonstrated minimal effect on the bacterial load with therapeutically relevant concentrations of ciprofloxacin and meropenem, with the later causing an increased production of proteases and pyocyanin. A combination of meropenem and tobramycin did not show any additional decrease in bacterial load but demonstrated a slight decrease in total proteases and pyocyanin production.

Conclusions

We demonstrate a realistic model for understanding antibiotic resistance and tolerance in biofilms clinically and for molecules screening in anti-biofilm drug development.P. aeruginosashowed high levels of antibiotic tolerance, with minimal effect on bacterial load and increased proteases production, which could negatively affect lung function. This may potentially contribute to exacerbations and eventual lung failure.
Synthesis of diagnostic quality cancer pathology images
Authors: Levine Adrian B. , Peng Jason , Farnell David , Nursey Mitchell , Wang Yiping , Naso Julia R. , Ren Hezhen , Farahani Hossein , Chen Colin , Chiu Derek , Talhouk Aline , Sheffield Brandon , Riazy Maziar , Ip Philip P. , Parra-Herran Carlos , Mills Anne , Singh Naveena , Tessier-Cloutier Basile , Salisbury Taylor , Lee Jonathan , Salcudean Tim , Jones Steven J.M. , Huntsman David G. , Gilks C. Blake , Yip Stephen , Bashashati Ali
Published: February 2020

Deep learning-based computer vision methods have recently made remarkable breakthroughs in the analysis and classification of cancer pathology images. However, there has been relatively little investigation of the utility of deep neural networks to synthesize medical images. In this study, we evaluated the efficacy of generative adversarial networks (GANs) to synthesize high resolution pathology images of ten histological types of cancer, including five cancer types from The Cancer Genome Atlas (TCGA) and the five major histological subtypes of ovarian carcinoma. The quality of these images was assessed using a comprehensive survey of board-certified pathologists (n = 9) and pathology trainees (n = 6). Our results show that the real and synthetic images are classified by histotype with comparable accuracies, and the synthetic images are visually indistinguishable from real images. Furthermore, we trained deep convolutional neural networks (CNNs) to diagnose the different cancer types and determined that the synthetic images perform as well as additional real images when used to supplement a small training set. These findings have important applications in proficiency testing of medical practitioners and quality assurance in clinical laboratories. Furthermore, training of computer-aided diagnostic systems can benefit from synthetic images where labeled datasets are limited (e.g., rare cancers). We have created a publicly available website where clinicians and researchers can attempt questions from the image survey athttp://gan.aimlab.ca/.
A comprehensive influenza reporter virus panel for high-throughput deep profiling of neutralizing antibodies
Authors: Creanga Adrian , Gillespie Rebecca A. , Fisher Brian E. , Andrews Sarah F. , Hatch Liam , Stephens Tyler , Tsybovsky Yaroslav , Crank Michelle C. , McDermott Adrian B. , Mascola John R. , Graham Barney S. , Kanekiyo Masaru
Published: February 2020

A number of broadly neutralizing antibodies (bnAbs) to influenza virus have been isolated, characterized and developed as potential countermeasures for seasonal influenza epidemic and pandemic. Deep characterization of these bnAbs and polyclonal sera is critical to our understanding of influenza immunity and for desgining universal influenza vaccines. However, conventional influenza virus neutralization assays with live viruses require high-containment laboratories and are difficult to standardize and roboticize. Here, we built a panel of engineered influenza viruses carrying a fluorescent reporter gene to replace an essential viral gene. This restricts virus replication to cells expressing the missing viral genein trans, allowing it to be manipulated in a biosafety level 2 environment. Using this system, we characterize the neutralization profile of a set of published and new bnAbs with a panel consisting of 55 viruses that spans the near complete antigenic evolution of human H1N1 and H3N2 viruses, as well as pandemic viruses such as H5N1 and H7N9. Our system opens opportunities to systematically characterize influenza immunity in greater depth, including the response directed at the viral hemagglutinin stem, a major target of universal influenza vaccines.
The wiring logic of an identified serotonergic neuron that spans sensory networks
Authors: Coates Kaylynn E. , Calle-Schuler Steven A. , Helmick Levi M. , Knotts Victoria L. , Martik Brennah N. , Salman Farzaan , Warner Lauren T. , Valla Sophia V. , Bock Davi D. , Dacks Andrew M.
Published: February 2020

Serotonergic neurons modulate diverse physiological and behavioral processes in a context-dependent manner, based on their complex connectivity. However, their connectivity has not been comprehensively explored at a single-cell resolution. Using a whole-brain EM dataset we determined the wiring logic of a broadly projecting serotonergic neuron (the “CSDn”) inDrosophila. Within the antennal lobe (AL; first-order olfactory region), the CSDn receives glomerulus-specific input and preferentially targets distinct local interneuron subtypes. Furthermore, the wiring logic of the CSDn differs between olfactory regions. The CSDn innervates the AL and lateral horn (LH), yet does not maintain the same synaptic relationship with individual projection neurons that also span both regions. Consistent with this, the CSDn has more distributed connectivity in the LH relative to the AL, preferentially synapsing with principal neuron types based on presumptive transmitter content. Lastly, we identify protocerebral neurons that provide abundant synaptic input to the CSDn. Our study demonstrates how an individual modulatory neuron can interact with local networks and integrate input from non-olfactory sources.
Connectomic analysis reveals an interneuron with an integral role in the retinal circuit for night vision
Authors: Park Silvia J.H. , Lieberman Evan M. , Ke Jiang-Bin , Rho Nao , Ghorbani Padideh , Rahmani Pouyan , Jun Na Young , Lee Hae-Lim , Kim In-Jung , Briggman Kevin L. , Demb Jonathan B. , Singer Joshua H.
Published: February 2020

The mammalian rod bipolar (RB) cell pathway is perhaps the best-studied circuit in the vertebrate retina. Its synaptic interactions with other retinal circuits, however, remain unresolved. Here, we combined anatomical and physiological analyses of the mouse retina to discover that the majority of synaptic inhibition to the AII amacrine cell (AC), the central neuron in the RB pathway, is provided by a single interneuron type: a multistratified, axon-bearing GABAergic AC, with dendrites in both ON and OFF synaptic layers, but with a pure ON (depolarizing) response to light. We used the nNOS-CreER mouse retina to confirm the identity of this interneuron as the wide-field NOS-1 AC. Our study demonstrates generally that novel neural circuits can be identified from targeted connectomic analyses and specifically that the NOS-1 AC mediates long-range inhibition during night vision and is a major element of the RB pathway.
PredictingVibrio choleraeinfection and disease severity using metagenomics in a prospective cohort study
Authors: Levade Inès , Saber Morteza M. , Midani Firas , Chowdhury Fahima , Khan Ashraful I. , Begum Yasmin A. , Ryan Edward T. , David Lawrence A. , Calderwood Stephen B. , Harris Jason B. , LaRocque Regina C. , Qadri Firdausi , Shapiro B. Jesse , Weil Ana A.
Published: February 2020

Background

Susceptibility toVibrio choleraeinfection is impacted by blood group, age, and pre-existing immunity, but these factors only partially explain who becomes infected. A recent study used 16S rRNA amplicon sequencing to quantify the composition of the gut microbiome and identify predictive biomarkers of infection with limited taxonomic resolution.

Methods

To achieve increased resolution of gut microbial factors associated withV. choleraesusceptibility and identify predictors of symptomatic disease, we applied deep shotgun metagenomic sequencing to a cohort of household contacts of patients with cholera.

Results

Using machine learning, we resolved species, strains, gene families, and cellular pathways in the microbiome at the time of exposure toV. choleraeto identify markers that predict infection and symptoms. Use of metagenomic features improved the precision and accuracy of prediction relative to 16S sequencing. We also predicted disease severity, although with greater uncertainty than our infection prediction. Species within the generaPrevotellaandBifidobacteriumpredicted protection from infection, and genes involved in iron metabolism also correlated with protection.

Conclusion

Our results highlight the power of metagenomics to predict disease outcomes and suggest specific species and genes for experimental testing to investigate mechanisms of microbiome-related protection from cholera.

Cholera infection and disease severity can be predicted using metagenomic sequencing of the gut microbiome pre-infection in a prospective cohort, and suggests potentially protective bacterial species and genes.
Proteomics, lipidomics, metabolomics and 16S DNA sequencing of dental plaque from patients with diabetes and periodontal disease
Authors: Overmyer Katherine A. , Rhoads Timothy W. , Merrill Anna E , Ye Zhan , Westphall Michael S. , Acharya Amit , Shukla Sanjay K. , Coon Joshua J.
Published: February 2020

Oral microbiome influences human health, specifically pre- and type 2 diabetes (Pre-DM/DM) and periodontal diseases (PD), through complex microbial interactions. To explore these relations, we performed 16S rDNA sequencing, metabolomics, lipidomics, and proteomics analyses on supragingival dental plaque collected from individuals with Pre-DM/DM (n=39), Pre-DM/DM and PD (n=37), PD alone (n=11), or neither (n=10). We identified on average 2,790 operational taxonomic units and 2,025 microbial and host proteins per sample and quantified 110 metabolites and 415 lipids. Plaque samples from Pre-DM/DM patients contained higher abundance ofFusobacteriumandTannerellavs. plaques from metabolically healthy. Phosphatidylcholines, plasmenyl-phosphatidylcholines, ceramides containing non-OH fatty acids, and host proteins related to actin filament rearrangement were elevated in plaques from PD vs. non-PD. Cross-omic correlation analysis enabled the detection of a strong association betweenLautropiaand mono-methyl phophospotidlyethanolamine (PE-NMe), striking because synthesis of PE-NMe is uncommon in oral bacteria. Lipidomics analysis ofin vitrocultures ofLautropia mirabilisconfirmed the bacteria’s synthesis of PE-NMe. This comprehensive analysis revealed a novel microbial metabolic pathway and significant associations of host-derived proteins with PD.
Chloroplast genome of the nutmeg tree: Myristica fragrans Houtt. (Myristicaceae)
Authors: de Oliveira Sylvia Mota , Duijm Elza , Steege Hans ter
Published: February 2020

Myristica fragransHoutt. (Myristicaceae) is widely used as condiment in western countries as well as a drug in medicinal systems such as the Ayuverda and Unani. The assemblage of its chloroplast genome resulted in a total of 155,894 bp, from which 146 genes were annotated, along with 86 coding regions, 43 exons and 22 introns. This study is a step further in the species characterization and will support future phylogenetic studies within the family.
Reconstruction and dynamics of human intestinal microbiome observedin situ
Authors: Liu Xiaolin , Dai Min , Ma Yue , Zhao Na , Zhang Huijie , Xiang Liyuan , Tian He , Shui Guanghou , Zhang Faming , Wang Jun
Published: February 2020

Gut microbiome are studied primarily using fecal samples in humans and we gained vital knowledge of compositional and functional capacities of gastro-intestinal microbial communities. Yet, fecal materials limit our ability to investigate microbial dynamics in different locations along GI-tract (in situ), nor in finer temporal scales as they are infrequent. With a technology developed originally for fecal material transplantation, colonic transendoscopic enteral tubing, we were able to sample ileocecal microbiome twice daily, and carried out metagenomic as well as metatranscriptomic analyses. Ileocecal and fecal microbiome are similar in metagenomic profiling, yet their active genes (in metatranscriptomes) are highly distinct. Both were perturbed after laxatives and then became more similar to microbiome prior to treatment, demonstrating resilience as an innate property of gut microbiome. Ileocecal microbiome transcriptomes sampled during day and night revealed diurnal rhythmes exist in certain bacterial species and functional pathways, in particular those related to short-chain fatty acid production. Lastly, metabolomic analysis in fecal and urine samples mirrored the perturbance and recovery in gut microbiome, indicating crucial contribution of gut microbiome to many of the key metabolites involved in host health. Our study provides interesting novel insights into human gut microbiome, and demonstrates the inner resilience, diurnal rhythmes and potential consequences to the host.
Intravenous edaravone plus therapeutic hypothermia offers limited neuroprotection in the hypoxic-ischaemic newborn piglet
Authors: Yamato Satoshi (Hamano) , Nakamura Shinji , Htun Yinmon , Nakamura Makoto , Jinnai Wataru , Nakao Yasuhiro , Mitsuie Tsutomu , Koyano Kosuke , Wakabayashi Takayuki , Morimoto Aya (Hashimoto) , Sugino Masashiro , Iwase Takashi , Kondo Sonoko (Ijichi) , Yasuda Saneyuki , Ueno Masaki , Miki Takanori , Kusaka Takashi
Published: February 2020

Therapeutic hypothermia is a standard therapy for neonatal hypoxic-ischaemic encephalopathy. One potential additional therapy is the free radical scavenger edaravone (3-methyl-1-phenyl-2-pyrazolin-5-one). To compare the neuroprotective effects of edaravone plus therapeutic hypothermia with those of therapeutic hypothermia alone after a hypoxic-ischaemic insult in the newborn piglet, anaesthetized piglets were subjected to 40 min of hypoxia (3–5% inspired oxygen) and cerebral ischaemia was assessed by cerebral blood volume. Body temperature was maintained at 38.5 °C in the normothermia group (NT, n = 8) and at 34 °C (24 h after the insult) in the therapeutic hypothermia (TH, n = 7) and therapeutic hypothermia plus edaravone (3 mg intravenous every 12 h for 3 days after the insult; TH+EV, n = 6) groups under mechanical ventilation. Five days after the insult, the mean (standard deviation) neurological scores were 10.9 (5.7) in the NT group, 17.0 (0.4) in the TH group (p= 0.025 vs. NT) and 15.0 (3.9) in the TH+EV group. The histopathological score of the TH+EV group showed no significant improvement compared with that of the other groups. In conclusion, edaravone plus therapeutic hypothermia had no additive neuroprotective effects after hypoxia-ischaemia in neurological and histopathological assessments.
Analyzing Presymptomatic Tissue to Gain Insights into the Molecular and Mechanistic Origins of Late-Onset Degenerative Trinucleotide Repeat Disease
Authors: Chu Yongjun , Hu Jiaxin , Liang Hanquan , Kanchwala Mohammed , Xing Chao , Beebe Walter , Bowman Charles B. , Gong Xin , Corey David R. , Mootha V. Vinod
Published: February 2020

How genetic defects trigger the molecular changes that cause late-onset disease is important for understanding disease progression and therapeutic development. Fuchs’ endothelial corneal dystrophy (FECD) is an RNA-mediated disease caused by a trinucleotide CUG expansion in an intron within theTCF4gene. The mutant intronic CUG RNA is present at 1-2 copies per cell, posing a challenge to understand how a rare RNA can cause disease. Late-onset FECD is a uniquely advantageous model for studying how RNA triggers disease because; 1) Affected tissue is routinely removed during surgery; 2) The expanded CUG mutation is one of the most prevalent disease-causing mutations, making it possible to obtain pre-symptomatic tissue from eye bank donors to probe how gene expression changes precede disease; and 3) The affected tissue is a homogeneous single cell monolayer, facilitating accurate transcriptome analysis. Here we use RNA sequencing (RNAseq) to compare tissue from individuals who are pre-symptomatic (Pre_S) to tissue from patients with late stage FECD (FECD_REP). The abundance of mutant repeat intronic RNA in Pre_S and FECD_REP tissue is elevated due to increased half-life in a corneal cell-specific manner. In Pre_S tissue, changes in splicing and extracellular matrix gene expression foreshadow the changes observed in advanced disease and predict the activation of the fibrosis pathway and immune system seen in late-stage patients. The absolute magnitude of splicing changes is similar in presymptomatic and late stage tissue. Our data identify gene candidates for early drivers of disease and biomarkers that may represent diagnostic and therapeutic targets for FECD. We conclude that changes in alternative splicing and gene expression are observable decades prior to the diagnosis of late-onset trinucleotide repeat disease.
Seasonal variation in physiology and shell condition of the pteropodLimacina retroversain the Gulf of Maine relative to life cycle and carbonate chemistry
Authors: Maas Amy E. , Lawson Gareth L. , Bergan Alexander J. , Wang Zhaohui A. , Tarrant Ann M.
Published: February 2020

Natural cycles in the seawater partial pressure of carbon dioxide (CO2) in the Gulf of Maine, which vary from ∼250-550 µatm seasonally, provide an opportunity to observe how the life cycle and phenology of the shelled pteropodLimacina retroversaresponds to changing food, temperature and carbonate chemistry conditions. Distributional, hydrographic, and physiological sampling suggest that pteropod populations are located in the upper portion of the water column (0-150 m) with a maximum abundance above 50 m, allowing them to generally avoid aragonite undersaturation. Gene expression and shell condition measurements show, however, that the population already experiences biomineralization stress in the winter months even when aragonite is slightly oversaturated, reinforcing the usefulness of this organism as a bio-indicator for pelagic ecosystem response to ocean acidification. There appear to be two reproductive events per year with one pulse timed to coincide with the spring bloom, the period with highest respiration rate, fluorescence, and pH, and a second more extended pulse in the late summer and fall. During the fall there is evidence of lipid storage for overwintering, allowing the second generation to survive the period of low food and aragonite saturation state. Based on these observations we predict that in the future pteropods will likely be most vulnerable to changing CO2regionally during the fall reproductive event when CO2concentration already naturally rises and there is the added stress of generating lipid stores.
A regulatory protein that represses sporulation inClostridioides difficile
Authors: Martins Diogo , Mendes Aristides L. , Antunes Jessica , Henriques Adriano O. , Serrano Mónica
Published: February 2020

Bacteria that reside in the gastrointestinal tract of healthy humans are essential for our health, sustenance and well-being. About 50 to 60% of those bacteria have the ability to produce resilient spores, important for the life cycle in the gut and for host-to-host transmission. A genomic signature for sporulation in the human intestine was recently described, which spans both commensals and pathogens such asClostridioides difficile, and contains several genes of unknown function. We report on the characterization of a signature gene,csiA, which, as we show, is involved in the control of sporulation initiation inC. difficile. Spo0A is the main regulatory protein controlling entry into sporulation and we show that an in-frame deletion ofcsiAresults in increased sporulation, and increased expression ofspo0Aper cell. Spo0A also drives transcription of thespoIIAandspoIIGoperons, coding for the first forespore-(σF) and mother cell-specific (σE) RNA polymerase sigma factors. Strikingly, deletion ofcsiAincreases expression of thespoIIGoperon, but not that of thespoIIAoperon. Increased expression ofspoIIGresults in increased production and proteolytic activation of pro-σE, suggesting that normally, the levels of active σEare limiting for sporulation. While other regulatory proteins affect both sporulation and several processes during the transition phase of growth, including toxin production or motility, deletion of thecsiAgene does not alter the expression of the genes coding for the TcdA and TcdB cytotoxins or the genes involved in motility. Thus, our results establish that CsiA acts to modulate sporulation by reducing expression of thespo0Agene.
Regulation of NF-kappa B and cell death by bacterial gingipains
Authors: Urnowey Sonya , Ansai Toshihiro , Bitko Vira , Barik Sailen
Published: February 2020

The role of non-caspase proteases in the regulation of programmed cell death is relatively under-studied. In this short communication, we report that infection of human gingival fibroblast (HGF) cellsex vivobyPorphyromonas gingivalisrapidly activated NF-kappa B, an antiapoptotic player; PI3 kinase was also induced, and together, they inhibited apoptosis. Later, pro-apoptotic cellular genes, including caspases, were induced. Apoptosis was evidenced by the degradation of nuclear DNA and activation of caspases. Unexpectedly, aP. gingivalismutant that lacked all three major gingipain proteases was defective in promoting apoptosis, which was consistent with the cleavage of procaspase-3 to the active form by the culture supernatant of wild typeP. gingivalis, but not that of the triple protease mutant. These results suggest that cellular death in theP. gingivalis-infected gum may be orchestrated by gingipain-regulated apoptotic factors.
Identification of novel RNA Polymerase II CTD interaction sites on the mRNA Capping Enzyme
Authors: Bage Marcus G. , Almohammed Rajaei , Cowling Victoria H. , Pisliakov Andrei V.
Published: February 2020

1

Recruitment of the mRNA Capping Enzyme (CE/RNGTT) to the site of transcription is essential for the formation of the 5’ mRNA cap, which in turn ensures efficient transcription, splicing, polyadenylation, nuclear export and translation of mRNA in eukaryotic cells. The CE is recruited and activated by the Serine-5 phosphorylated carboxyl-terminal domain (CTD) of RNA polymerase II. Through the use of molecular dynamics simulations and enhanced sampling techniques, we provide a systematic and detailed characterisation of the human CE-CTD interface, describing the effect of the CTD phosphorylation state, length and orientation on this interaction. Our computational analyses identify novel CTD interaction sites on the human CE surface and quantify their relative contributions to CTD binding. We also identify differences in the CTD binding conformation when phosphorylated at either the Serine-2 or Serine-5 positions, thus providing insights into how the CE reads the CTD code. The computational findings are then validated by binding and activity assays. These novel CTD interaction sites are compared with cocrystal structures of the CE-CTD complex in different eukaryotic taxa, leading to the conclusion that this interface is considerably more conserved than previous structures have indicated.
A non-canonical histone acetyltransferase targets intragenic enhancers and regulates plant architecture
Authors: Yang Xueyong , Yan Jianbin , Zhang Zhen , Lin Tao , Xin Tongxu , Wang Bowen , Wang Shenhao , Zhao Jicheng , Zhang Zhonghua , Lucas William J. , Li Guohong , Huang Sanwen
Published: February 2020

Axillary meristem development determines both plant architecture and crop yield; this critical process is regulated by the TCP transcription factor (TF) family, including the maizeTB1and ArabidopsisBRC1. Studies have shown that both TB1 and AtBRC1 can target the gene body regions of some target genes and activate their expression; however, the regulatory mechanisms remain largely unknown. Here, we show that a cucumberCYC/TB1homologue,TEN, controls the identity and mobility of tendrils. Through its C-terminus, TEN binds at intragenic enhancers of target genes; its N-terminal domain functions as a novel, non-canonical histone acetyltransferase (HAT) to preferentially act on lysine 56 and 122, of the histone H3 globular domain. This HAT activity is responsible for chromatin loosening and host gene activation. The N-termini of all tested CYC/TB1-like proteins contain an intrinsically disordered region (IDR), and despite their sequence divergence, they have conserved HAT activity. This study discovered a non-canonical class of HATs, and as well, provides a mechanism by which modification at the H3 globular domain is integrated with the transcription process.
High-Throughput CRISPR/Cas9 Mutagenesis Streamlines Trait Gene Identification in Maize
Authors: Liu Hai-Jun , Jian Liumei , Xu Jieting , Zhang Qinghua , Zhang Maolin , Jin Minliang , Peng Yong , Yan Jiali , Han Baozhu , Liu Jie , Gao Fan , Liu Xiangguo , Huang Lei , Wei Wenjie , Ding Yunxiu , Yang Xiaofeng , Li Zhenxian , Zhang Mingliang , Sun Jiamin , Bai Minji , Song Wenhao , Chen Hanmo , Sun Xi’ang , Li Wenqiang , Lu Yuming , Liu Ya , Zhao Jiuran , Qian Yangwen , Jackson David , Fernie Alisdair R. , Yan Jianbing
Published: February 2020

Maize (Zea mays) is one of the most important crops in the world. However, few agronomically important maize genes have been cloned and used for trait improvement, due to its complex genome and genetic architecture. Here, we integrated multiplexed CRISPR/Cas9-based high-throughput targeted mutagenesis with genetic mapping and genomic approaches to successfully target 743 candidate genes corresponding to traits relevant for agronomy and nutrition. After low-cost barcode-based deep sequencing, 412 edited sequences covering 118 genes were precisely identified from individuals showing clear phenotypic changes. The profiles of the associated gene-editing events were similar to those identified in human cell lines and consequently are predictable using an existing algorithm originally designed for human studies. We observed unexpected but frequent homology-directed repair through endogenous templates that was likely caused by spatial contact between distinct chromosomes. Based on the characterization and interpretation of gene function from several examples, we demonstrate that the integration of forward and reverse genetics via a targeted mutagenesis library promises rapid validation of important agronomic genes for crops with complex genomes. Beyond specific findings, this study also guides further optimization of high-throughput CRISPR experiments in plants.
Structure of the MICU1–MICU2 heterodimer provides insights into the gatekeeping threshold shift
Authors: Park Jongseo , Lee Youngjin , Park Taein , Kang Jung Youn , Mun Sang A , Jin Minwoo , Yang Jihyeong , Eom Soo Hyun
Published: February 2020

Mitochondrial calcium uptake proteins 1 and 2 (MICU1 and MICU2) mediate mitochondrial Ca2+influx via the mitochondrial calcium uniporter (MCU). Its molecular action for Ca2+uptake is tightly controlled by the MICU1–MICU2 heterodimer, which comprises Ca2+sensing proteins which act as gatekeepers at low [Ca2+] or facilitators at high [Ca2+]. However, the mechanism underlying the regulation of the Ca2+gatekeeping threshold for mitochondrial Ca2+uptake through the MCU by the MICU1–MICU2 heterodimer remains unclear. In this study, we determined the crystal structure of the apo form of the human MICU1–MICU2 heterodimer that functions as the MCU gatekeeper. MICU1 and MICU2 assemble in the face-to-face heterodimer with salt bridges and methionine knobs stabilizing the heterodimer in an apo state. Structural analysis suggests how the heterodimer sets a higher Ca2+threshold than the MICU1 homodimer. The structure of the heterodimer in the apo state provides a framework for understanding the gatekeeping role of the MICU1–MICU2 heterodimer.
A practical overview of molecular replacement: Clostridioides difficile PilA1, a difficult case study
Authors: Crawshaw Adam D. , Baslé Arnaud , Salgado Paula S.
Published: February 2020

Many biologists are now routinely seeking to determine the three-dimensional structures of their proteins of choice, illustrating the importance of this knowledge, but also of the simplification and streamlining of structure-determination processes. Despite the fact that most software packages offer simple pipelines, for the non-expert navigating the outputs and understanding the key aspects can be daunting. Here, the structure determination of the type IV pili (TFP) protein PilA1 from Clostridioides difficile is used to illustrate the different steps involved, the key decision criteria and important considerations when using the most common pipelines and software. Molecular-replacement pipelines within CCP4i2 are presented to illustrate the more commonly used processes. Previous knowledge of the biology and structure of TFP pilins, particularly the presence of a long, N-terminal α-helix required for pilus formation, allowed informed decisions to be made during the structure-determination strategy. The PilA1 structure was finally successfully determined using ARCIMBOLDO and the ab initio MR strategy used is described.
ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation
Authors: Medina Ana , Triviño Josep , Borges Rafael J. , Millán Claudia , Usón Isabel , Sammito Massimo D.
Published: February 2020

The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where flexibility is essential in order to capture small local differences. TheALEPHsoftware is optimized for the analysis and the extraction of small protein folds by relying on their geometry rather than on their sequence. The annotation of the structural variability of a given fold provides valuable information for fragment-based molecular-replacement methods, in which testing alternative model hypotheses can succeed in solving difficult structures when no homology models are available or are successful.ARCIMBOLDO_BORGEScombines the use of composite secondary-structure elements as a search model with density modification and tracing to reveal the rest of the structure when both steps are successful. This phasing method relies on general fold libraries describing variations around a given pattern of β-sheets and helices extracted usingALEPH. The program introduces characteristic vectors defined from the main-chain atoms as a way to describe the geometrical properties of the structure.ALEPHencodes structural properties in a graph network, the exploration of which allows secondary-structure annotation, decomposition of a structure into small compact folds, generation of libraries of models representing a variation of a given fold and finally superposition of these folds onto a target structure. These functions are available through a graphical interface designed to interactively show the results of structure manipulation, annotation, fold decomposition, clustering and library generation.ALEPHcan produce pictures of the graphs, structures and folds for publication purposes.
Safe RPAS integration in non-segregated airspace
Authors: Pérez-Castán Javier A. , Gómez Comendador Fernando , Rodríguez-Sanz Álvaro , Arnaldo Valdés Rosa M. , Alonso-Alarcon Jose Felix
Published: February 2020

Purpose

This paper aims to assess the implications in safety levels by the integration of remotely piloted aircraft system (RPAS). The goal is to calculate the number of RPAS that can jointly operate with conventional aircraft regarding conflict risk, without exceeding current safety levels.

Design/methodology/approach

This approach benchmarks a calculated level of safety (CLS) with a target level of safety (TLS). Monte Carlo (MC) simulations quantify the TLS based on the current operation of conventional aircraft. Then, different experiments calculate the CLS associated with combinations of conventional aircraft and RPAS. MC simulations are performed based on probabilistic distributions of aircraft performances, entry times and geographical distribution. The safety levels are based on a conflict risk model because the safety metrics are the average number of conflicts and average conflict duration.

Findings

The results provide restrictions to the number of RPAS that can jointly operate with conventional aircraft. The TLS is quantified for four conventional aircraft. MC simulations confirm that the integration of RPAS demands a reduction in the total number of aircraft. The same number of RPAS than conventional aircraft shows an increase over 90% average number of conflicts and 300% average conflict time.

Research limitations/implications

The methodology is applied to one flight level of en-route airspace without considering climbing or descending aircraft.

Originality/value

This paper is one of the most advanced investigations performed to quantify the number of RPAS that can be safely integrated into non-segregated airspace, which is one of the challenges for the forthcoming integration of RPAS. Particularly, Europe draws to allow operating RPAS and conventional aircraft in non-segregated airspace by 2025, but this demanding perspective entails a thorough analysis of operational and safety aspects involved.
Exploring the effectiveness of maintenance and quality management strategies in Indian manufacturing enterprises
Authors: Sahoo Saumyaranjan
Published: February 2020

Purpose

The purpose of the paper is to examine the impact of human-related support practices, total productive maintenance (TPM) practices, and total quality management (TQM) practices on manufacturing performance parameters and their inter-relationship.

Design/methodology/approach

A research project was carried out in 94 Indian manufacturing companies, using the questionnaire method. The survey data was drawn from 169 respondents working in these companies. In this paper, the impact of TPM and TQM practices on manufacturing performance parameters and especially the role of support practices is investigated empirically using various structural equation models.

Findings

Two factors namely top management and leadership and human resource development categorized as support practices were found to positively influence the adoption of technical practices, i.e., TPM and TQM practices. Hence support practices were found to indirectly affect the manufacturing performance parameters via the technical factors. Also analyzing various structural equation models (SEM), shop floor implementation of TPM practices were found to be influenced (or guided) by the philosophy of TQM practices. In other words, through the proper adoption of TQM practices, the effectiveness of TPM practices gets increased.

Research limitations/implications

Because of the chosen research approach, the research results may lack generalizability. Therefore, researchers are encouraged to test the proposed propositions further using a case study approach.

Practical implications

The present study provides useful insights to practicing managers. The result of the study explaining the interrelationship between support practices (behavioral aspect) and technical practices can be used by practicing managers to develop a better understanding of the contribution of support and technical practices towards the realization of organizational objectives of growth and sustainability. In practice, TQM plays a great role in the adoption of TPM practices, which in turn helps to achieve quality in processes and therefore in products.

Originality/value

Previous research has often either concentrated on technical practices as one dimension without studying the effects of support practices on improving the adoption of technical practices. The results of the study take one step further by investigating the relationship between multiple aspects (support and technical aspects) of manufacturing practices and their impact on manufacturing performance.
Project management for social good
Authors: Goel Ashish , Ganesh L.S. , Kaur Arshinder
Published: February 2020

Purpose

Recent research on construction project management (CPM) envisions addressing wider social good while delivering value to the funding organizations. It is complemented by a growing body of knowledge on social sustainability in construction projects. These two literature streams are currently scattered and there is a lack of holistic guidance on integrating social sustainability with CPM. The current study addresses this knowledge gap through a critical review of these two bodies of literature and thereby proposing a conceptual framework for socially sustainable CPM.

Design/methodology/approach

A conceptual modelling approach, involving sequential steps of knowledge acquisition, and knowledge abstraction and representation, has been used. Knowledge acquisition was based on a systematic search and short-listing of research articles and knowledge abstraction was performed through thematic analysis of the 81 shortlisted articles. The categories abstracted through thematic analysis were integrated and presented as the framework.

Findings

A framework for socially sustainable CPM, consisting of four social sustainability characteristics and six areas of social sustainability integration in CPM (SSI-CPM), has been proposed. It presents possibilities of integrating social concerns in CPM processes at various levels – ranging from permanent firms that provide resources to the temporary (project) organization that delivers value.

Originality/value

This study seeks to bridge the gap between theory and practice of realizing social good through construction projects. To this end, a conceptual framework has been proposed along with an agenda for future research encompassing social sustainability and CPM.
Financial access, governance and insurance sector development in sub-Saharan Africa
Authors: Asongu Simplice , Odhiambo Nicholas M.
Published: February 2020

Purpose

This study investigates the role of financial access in moderating the effect of governance on insurance consumption in 42 sub-Saharan African countries using data for the period 2004–2014.

Design/methodology/approach

Two life insurance indicators are used, notably: life insurance and non-life insurance. Six governance measurements are also used, namely: political stability, ‘voice and accountability’, government effectiveness, regulation quality, corruption-control and the rule of law. The empirical evidence is based on the Generalised Method of Moments (GMM) and Least Squares Dummy Variable Corrected (LSDVC) estimators.

Findings

Estimations from the LSDVC are not significant while the following main findings are established from the GMM. First, financial access promotes life insurance through channels of political stability, ‘voice and accountability’, government effectiveness, the rule of law and corruption-control. Second, financial access also stimulates non-life insurance via governance mechanisms of political stability, ‘voice and accountability’, government effectiveness, regulation quality, the rule of law and corruption-control.

Originality/value

This research complements the sparse literature on insurance promotion in Africa by engaging the hitherto unexplored role of financial access through governance channels.
Impact of remittances on economic performance in consideration of institutional quality
Authors: Nepal Surya , Park Sae Woon , Lee Sunhae
Published: February 2020

Purpose

The purpose of this paper is to empirically assess the impact of remittances on the economic performance of the 16 Asian developing countries, taking account of their institutional qualities.

Design/methodology/approach

A panel of 16 Asian developing countries (Central Asia, South Asia, and ASEAN) over the period of 2002–2016 is employed in the analysis. To assess the impact of remittances on economic performance in consideration of institutional quality, OLS estimates as well as GMM are used.

Findings

The effect of remittances on economic growth is statistically significant. In addition, they also impact economic growth when they interact with institutional or financial development variables. For the long-run growth process of Central Asian, South Asian, and ASEAN countries, a sound and smooth institutional framework appears to be indispensable. Also, it was found that more fragile economies tend to achieve bigger growth than less fragile economies, as this kind of growth is triggered by more remittances flowing into fragile economies. However, the impact of remittances on growth does not depend on the level of ICT. FDI and financial development have positive impact on growth.

Research limitations/implications

There are limitations to this research as well. Due to the unavailability of data, several countries had to be removed from this study. The cost of sending money might be an important variable for this study. However, the data on this variable from reliable sources are almost impossible to gather. Therefore, this variable is also not included in this research. The savings from remittances when intermediated through formal financial channels will, in fact, produce a positive allocation and distribution of resources that may eventually become an important source of growth. However, one precondition for larger and greater growth is that remittances need to be well and properly utilized by the financial sector. Therefore, quality institutions should be formed first, which can facilitate investment activities and make the flow of remittances more convenient.

Originality/value

This paper exclusively considers the case of Asian developing countries (Central Asia, South Asia, and ASEAN) to assess the impact of remittances on the economic performance of these countries, with special consideration of the interaction effects of remittances and institutional quality in these emerging Asian economies. The previous studies on the effect of remittances on growth do not conform to one concrete conclusion. This study is undertaken in a bid to get the best possible result on the impact of remittances on the growth of the selected countries, majority of which attract substantial chunk of remittances into their economies.
Formation of civil servants' creativity through transformative leadership
Authors: Awang Abd Hair , Haron Maslinda , Zainuddin Rela Iskandar , Saad Suhana
Published: February 2020

Purpose

Creativity is the core of digital knowledge-based economic growth and competitiveness. Given the fact that public service is a major contributor to the country's governance system, creativity among civil servants should be enhanced. Effective leadership in public services is necessary to nurture the creativity of high-quality public services. This study aims to examine the effects of transformational leadership on civil servant's creativity.

Design/methodology/approach

This study was conducted in six selected public service agencies. A total of 214 questionnaires were distributed to civil servant offices, only 82.2 percent (176 questionnaires) were returned. Data were tested using SMART PLS to determine whether the four transformational leadership dimensions, namely, intellectual stimulation, idealized influence, individual consideration, and inspirational motivation, exhibit a significant effect on creativity of civil servant officers.

Findings

Findings showed positive effects of the four transformational leadership dimensions on the civil servant's creativity.

Research limitations/implications

With small sample size, this study can still be expanded to all available public services sector in urban and rural area to gain a wider perspective.

Practical implications

This study presents strong managerial implications that can be used by public service to evaluate the consequence of transformational leadership on the creativity of employees, particularly the young civil servants. Through transformational leadership style, public service leaders can foster and improve young civil servants' creativity and share knowledge to achieve high performance.

Originality/value

With genuine verified measurement of transformative leadership and public sector creativity, the path correlation analysis shows that intellectual stimulation, idealized influence, individual consideration, and inspirational motivation have significant direct effects on creativity of the civil servant.