bluuebunny/crossref_metadata_2025 huggingface dataset:
Loop Extrusion Mediates Physiological Locus Contraction for V(D)J Recombination
Authors: Dai Hai-Qiang , Hu Hongli , Lou Jiangman , Ye Adam Yongxin , Chapdelaine-Williams Aimee M. , Kyritsis Nia , Zhang Yiwen , Manfredonia Nicole , Judson Rachael , Chen Huan , Johnson Kerstin , Lin Sherry , Ba Zhaoqing , Conte Andrea , Casellas Rafael , Lee Cheng-Sheng , Alt Frederick W.
Published: July 2020

Immunoglobulin heavy chain locus (Igh) VH, D, and JHgene segments are developmentally assembled into V(D)J exons. RAG endonuclease initiates V(D)J recombination by binding a JH-recombination signal sequence (RSS) within a chromatin-based recombination center (RC) and then, in an orientation-dependent process, scans upstream D-containing chromatin presented by cohesin-mediated loop extrusion for convergent D-RSSs to initiate DJH-RC formation1,2. In primary pro-B cells, 100s of upstream VH-associated RSSs, embedded in convergent orientation to the DJH-RC-RSS, gain proximity to the DJH-RC for VH-to-DJHjoining via a mechanistically-undefined VH-locus contraction process3-7. Here, we report that a 2.4 mega-base VHlocus inversion in primary pro-B cells nearly abrogates rearrangements of normally convergent VH-RSSs and cryptic RSSs, even though locus contractionper seis maintained. Moreover, this inversion activated rearrangement of both cryptic VH-locus RSSs normally in the opposite orientation and, unexpectedly, of normally-oriented cryptic RSSs within multiple, sequential upstream convergent-CBE domains. Primary pro-B cells had significantly reduced transcription ofWapl8, a cohesin-unloading factor, versus levels inv-Ablpro-B lines that lack marked locus contraction or distal VHrearrangements2,9-11. Correspondingly, Wapl depletion inv-Abllines activated VH-locus contraction and orientation-specific RAG-scanning across the VH-locus. Our findings indicate that locus contraction and physiological VH-to-DJHjoining both are regulated via circumvention of CBE scanning impediments.
Luteolin transforms the BMDM polarity to regulate the expression of inflammatory factors
Authors: Wang Shuxia , Xu Shuhang , Cao Meng , Zhou Jing , Mao Xiaodong , Yao Xiaoming , Liu Chao
Published: July 2020

Macrophage are indispensable regulator cells in inflammatory response. Macrophage polarization and its secreted inflammatory factors have affinity with the outcomes of inflammation. Luteolin, a flavonoid abundant in plants has anti-inflammatory activity, but whether luteolin can manipulate M1/M2 polarization of BMDM to suppress inflammation is still veiled. The purpose of this study was to observe the effects of luterolin on the polarity of BMDM derived from C57BL/6 mice and the expression of inflammatory factors, to explore the mechanism of luteolin regulating the BMDM polarity. M1-polarized BMDM were induced by LPS+IFN-γ, M2-polarization were stimulated with IL-4. BMDM morphology was observed by laser confocal microscopy; levels of BMDM differentiation and CD11c or CD206 on membrane surface were assessed by FCM; mRNA and protein of M1/M2-type inflammatory factors were performed by qPCR and ELISA, respectively; the expression of p-STAT1 and p-STAT6 protein pathways was detected by Western-blotting. The isolated mouse bone marrow cells were successfully differentiated into BMDM, LPS+IFN-γ induced BMDM M1-phenotype polarization, and IL-4 induced its M2-phenotype polarization. After M1-polarized BMDM treated with luteolin, M1-type pro-inflammatory factors including IL-6, TNF-α□iNOS, CD86 were down-regulated while M2-type anti-inflammatory factors including IL-10, Arg1, CD206 were up-regulated; the expression of M1-type surface marker CD11c decreased, nevertheless, M2-type marker CD206 increased; levels of inflammatory signaling protein p-STAT1 and p-STAT6 were attenuated and enhanced respectively. Our study suggests luteolin may transform BMDM polarity through p-STAT1/6 to regulate the expression of inflammatory mediators, thereby inhibiting inflammation. Naturally occurring luteolin hold promise as an anti-inflammatory and immunomodulatory agent.
Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean
Authors: Jabre Loay , Allen Andrew E. , McCain J. Scott P. , McCrow John P. , Tenenbaum Nancy , Spackeen Jenna L. , Sipler Rachel E. , Green Beverley R. , Bronk Deborah A. , Hutchins David A. , Bertrand Erin M.
Published: July 2020

The Southern Ocean (SO) harbours some of the most intense phytoplankton blooms on Earth. Changes in temperature and iron availability are expected to alter the intensity of SO phytoplankton blooms, but little is known about how environmental change will influence community composition and downstream biogeochemical processes. We performed experimental manipulations on surface ocean microbial communities from McMurdo Sound in the Ross Sea, with and without iron addition, at −0.5 °C, 3 °C, and 6 °C. We then examined nutrient uptake patterns as well as the growth and molecular responses of two dominant diatoms,FragilariopsisandPseudo-nitzschia, to these conditions. We found that nitrate uptake and primary productivity were elevated at increased temperature in the absence of iron addition, and were even greater at high temperature with added iron.Pseudo-nitzschiabecame more abundant under increased temperature without added iron, whileFragilariopsisrequired additional iron to benefit from warming. We attribute the apparent advantagePseudo-nitzschiashows under warming to upregulation of iron-conserving photosynthetic processes, utilization of iron-economic nitrogen assimilation mechanisms, and increased iron uptake and storage. These data identify important molecular and physiological differences between dominant diatom groups and add to the growing body of evidence forPseudo-nitzschia’s increasingly important role in warming SO ecosystems. This study also suggests that temperature-driven shifts in SO phytoplankton assemblages may increase utilization of the vast pool of excess nutrients in iron-limited SO surface waters, and thereby influence global nutrient distributions and carbon cycle.

Significance Statement

Phytoplankton assemblages contribute to the Southern Ocean’s ability to absorb atmospheric CO2, form the base of marine food webs, and shape the global distribution of macronutrients. Anthropogenic climate change is altering the SO environment, yet we do not fully understand how resident phytoplankton will react to this change. By comparing the responses of two prominent SO diatom groups to changes in temperature and iron in a natural community, we find that one group,Pseudo-nitzschia, grows better under warmer low-iron conditions by managing cellular iron demand and efficiently increasing photosynthetic capacity. This ability to grow and draw down nutrients in the face of warming, regardless of iron availability, may have major implications for ocean ecosystems and global nutrient and carbon cycles.
Pericytes Directly Communicate with Emerging Endothelial Cells During Vasculogenesis
Authors: Payne Laura Beth , Tewari Bhanu , Dunkenberger Logan , Bond Samantha , Savelli Alyssa , Darden Jordan , Zhao Huaning , Powell Michael , Oestreich Kenneth , Sontheimer Harald , Dal-Pra Sophie , Chappell John C.
Published: July 2020

Pericytes (PCs), cells that extend along capillaries to contribute stability and other critical functions to established vasculature, are attracting attention from various fields involving vascular-related pathologies. Here, we demonstrate primary evidence of PC communication with endothelial cells (ECs) prior to tube coalescence. Observations of apparent PCs during early embryogenesis urged development of a mouse embryonic stem cell line (DR-ESCs), enabling unique dual-reporter investigations into earliest PC-EC interactions. Live imaging of differentiating DR-ESCs corroborated emergence of a PC lineage, which preceded EC differentiation, and further revealed highly dynamic PC-EC interactions during coordinated vessel formation. We show direct PC-EC communication via cell microinjection and dye-transfer, and RNA-seq analysis indicates a PC-EC coupling mechanism via gap junction Connexin43 (Cx43), exclusively up-regulated throughout DR-ESC differentiation. High resolution imaging of embryonic and postnatal mouse vasculature substantiates Cx43 plaques at PC-EC borders. These findings indicate a new role for PCs during vasculogenesis via Cx43-mediated communication with ECs.
Leaf trichome distribution pattern inArabidopsisreveals gene expression variation associated with environmental adaptation
Authors: Okamoto Shotaro , Negishi Kohei , Toyama Yuko , Ushijima Takeo , Morohashi Kengo
Published: July 2020

Gene expression varies stochastically even in both heterogenous and homogeneous cell populations. This variation is not simply useless noise; rather, it is important for many biological processes. Unicellular organisms or cultured cell lines are useful for analyzing the variation in gene expression between cells; however, owing to technical challenges, the biological relevance of this variation in multicellular organisms such as higher plants remains unclear. Here, we addressed the biological relevance of this variation between cells by examining the genetic basis of trichome distribution patterns inArabidopsis thaliana. The distribution pattern of a trichome on a leaf is stochastic and can be mathematically represented using Turing’s reaction-diffusion (RD) model. We analyzed simulations based on the RD model and found that the variability in the trichome distribution pattern increased with the increase in stochastic variation in a particular gene expression. Moreover, differences in heat-dependent variability of the trichome distribution pattern between the accessions showed a strong correlation with environmental factors to which each accession was adapted. Taken together, we successfully visualized variations in gene expression by quantifying the variability in theArabidopsistrichome distribution pattern. Thus, our data provide evidence for the biological importance of variations in gene expression for environmental adaptation.
Line-FRAP, a versatile method based on fluorescence recovery after photobleaching to measure diffusion ratesin vitroandin vivo
Authors: Dey Debabrata , Marciano Shir , Schreiber Gideon
Published: July 2020

A cell is a densely packed conglomerate of macromolecules, where diffusion is essential for their function. The crowded conditions may affect diffusion both through hard (occluded space) and soft (weak, non-specific) interactions. Multiple-methods have been developed to measure diffusion rates at physiological protein concentrations within cells, however, each of them has its limitations. Here, we introduce Line-FRAP, a method based on measuring recovery of photobleaching under a confocal microscope that allows diffusion rate measurements for fast diffusing molecules to be measured in versatile environments using standard equipment. Implementation of Line mode to the classical FRAP technique greatly improves the time resolution in data acquisition, from 20-50 Hz in the classical mode to 800 Hz in the line mode. We also introduce an updated method for data analysis to obtain diffusion coefficients in various environments, with the number of pixels bleached at the first frame after bleaching being a critical parameter. We evaluated the method using different proteins either chemically labelled or by fusion to YFP. The calculated diffusion rates were comparable to literature data as measuredin vitro, in HeLa cells and inE.coli.Diffusion coefficients in HeLa was ~2.5-fold slower and inE. coli15-fold slower than measured in buffer. Moreover, we show that increasing the osmotic pressure onE.colifurther decreases diffusion, till a point where proteins stop to move. The method presented here is easy to apply on a standard confocal microscope, fits a large range of molecules with different sizes and provides robust results in any conceivable environment and protein concentration for fast diffusing molecules.
Trk Agonist Drugs Rescue Noise-Induced Hidden Hearing Loss
Authors: Fernandez Katharine A. , Watabe Takahisa , Tong Mingjie , Meng Xiankai , Tani Kohsuke , Kujawa Sharon G. , Edge Albert S. B.
Published: July 2020

TrkB agonist drugs are shown here to have a significant effect on the regeneration of afferent cochlear synapses after noise-induced synaptopathy. The effects were consistent with regeneration of cochlear synapses that we observedin vitroafter synaptic loss due to kainic acid-induced glutamate toxicity and were elicited by administration of TrkB agonists, amitriptyline and 7,8-dihydroxyflavone, directly into the cochlea via the posterior semicircular canal 48 h after exposure to noise. Synaptic counts at the inner hair cell and wave 1 amplitudes in the ABR were partially restored 2 weeks after drug treatment. Effects of amitriptyline on wave 1 amplitude and afferent auditory synapse numbers in noise-exposed ears after systemic (as opposed to local) delivery were profound and long-lasting; synapses in the treated animals remained intact one year after the treatment. However, the effect of systemically delivered amitriptyline on synaptic rescue was dependent on dose and the time window of administration: it was only effective when given before noise exposure at the highest injected dose. The long-lasting effect and the efficacy of post-exposure treatment indicate a potential broad application for the treatment of synaptopathy, which often goes undetected until well after the original damaging exposure(s).
GREATER EMPATHIC ABILITIES AND THEIR CORRELATION WITH RESTING STATE BRAIN CONNECTIVITY IN PSYCHOTHERAPISTS COMPARED TO NON-PSYCHOTHERAPISTS
Authors: Olalde-Mathieu Victor E. , Sassi Federica , Reyes-Aguilar Azalea , Mercadillo Roberto E. , Alcauter Sarael , Barrios Fernando A.
Published: July 2020

Psychotherapists constantly regulate their own perspective and emotions to better understand the “other’s” state. We compared 52 psychotherapists with 92 non-psychotherapists to characterized psychometric constructs like, Fantasy (FS) and Perspective Taking (PT), and the emotion regulation strategy of Expressive Suppression (ES), which hampers the empathic response. Psychotherapists showed greater FS, PT and lower ES scores. In a subsample (36, 18 ea.), we did a functional connectivity (FC) study. Psychotherapists showed greater FC between the left anterior insula and the dorsomedial prefrontal cortex; and less connectivity between rostral anterior cingulate cortex and the orbito prefrontal cortex. Both associations correlated with the PT scores and suggest a cognitive regulatory effect related to the empathic response. Considering, that the psychometric differences between groups were in the cognitive domain and that the FC associations are related to cognitive processes, these results suggest that psychotherapists have a greater cognitive regulation over their empathic response.
All-in-one comprehensive extraction of metabolites, proteins and ribonucleic acids for the rapid analysis of oil palm systems biology
Authors: Shahwan Syahanim , Othman Abrizah , Nurazah Zain , Rozali Nurul Liyana , Ramli Umi Salamah
Published: July 2020

Oil palm (Elaeis guineensisJacq.) systems biology offers a comprehensive view of the plant system by employing a holistic multi-omics approach encompassing the molecular data at various hierarchical levels. Sample limitation and the importance of integrating all molecular data with minimal variation, led to the development of sequential extraction of biomolecule fractions from a single undivided biological sample. This article describes a workflow for the comprehensive isolation of metabolites, proteins and ribonucleic acids from oil palm root. Samples were subjected to solvent extraction with methanol-chloroform-water to recover metabolites of diverse polarity. The resultant pellet was subjected to buffer and solvent partitioning to obtain RNA and proteins. RNA extracted from the oil palm root showed a recovery of 180.25 ng mg-1, with a A260:A280 ratio ranging between1.9-2.0 and a RIN value of 6.7. Co-extracted proteins resulted in a recovery of 29.28 μg mg-1and revealed a total of 1852 identified proteins. Polar metabolites revealed approximately 40 metabolite peaks, and non-polar metabolites with two major fatty acid groups i.e. saturated and unsaturated fatty acids at 55.4% and 38.6%, respectively. This protocol demonstrated an advancement of extraction protocols for oil palm root biomolecules, which will consecutively expedite the establishment of various multi-omics platforms.

Highlight

Metabolites, proteins and RNA are co-extracted from oil palm root using the all-in-one extraction protocol which provides biomolecule extracts for various omics platforms.
Desulfovibrio diazotrophicasp. nov., a sulphate reducing bacterium from the human gut capable of nitrogen fixation
Authors: Sayavedra Lizbeth , Li Tianqi , Batista Marcelo Bueno , Seah Brandon K.B. , Booth Catherine , Zhai Qixiao , Chen Wei , Narbad Arjan
Published: July 2020

Sulphate-reducing bacteria (SRB) are widespread in human guts, yet their expansion has been linked to colonic diseases. We report the isolation, genome sequencing, and physiological characterisation of a novel SRB species belonging to the classDeltaproteobacteria(QI0027T). Phylogenomic analysis revealed that the QI0027Tstrain belongs to the genusDesulfovibriowith its closest relative beingDesulfovibrio legallii. Metagenomic sequencing of stool samples from 45 individuals, as well as comparison with 1690Desulfovibrionaceaemetagenome-assembled genomes, revealed the presence of QI0027Tin at least 22 further individuals. QI0027Tencoded nitrogen fixation genes and based on the acetylene reduction assay, actively fixed nitrogen. Transcriptomics revealed that QI0027Toverexpressed 45 genes in nitrogen limiting conditions as compared to cultures supplemented with ammonia, including nitrogenases, an urea uptake system and the urease enzyme complex. To the best of our knowledge, this is the firstDesulfovibriohuman isolate for which nitrogen fixation has been demonstrated. This isolate was namedDesulfovibrio diazotrophicasp. nov., referring to its ability to fix nitrogen (‘diazotroph’).

Importance

Animals are often nitrogen limited and have evolved diverse strategies to capture biologically active nitrogen. These strategies range from amino acid transporters to stable associations with beneficial microbes that can provide fixed nitrogen. Although frequently thought as a nutrient-rich environment, nitrogen fixation can occur in the human gut of some populations, but so far it has been attributed mainly toClostridiaandKlebsiellabased on sequencing. We have cultivated a novelDesulfovibriofrom human gut origin which encoded, expressed and actively used nitrogen fixation genes, suggesting that some sulphate reducing bacteria could also play a role in the availability of nitrogen in the gut.
Retrospective Clinical Evaluation of Four Lateral Flow Assays for the Detection of SARS-CoV-2 Antibodies
Authors: McAulay Kathrine , Bryan Andrew , Greninger Alexander L. , Grill Francisca , Lake Douglas , Kaleta Erin J. , Grys Thomas E.
Published: July 2020

Coronavirus disease 2019 (COVID-19) is a potentially life-threatening respiratory infection caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), for which numerous serologic assays are available. In a CLIA laboratory setting, we used a retrospective sample set (n = 457) to evaluate two lateral flow immunoassays (LFIAs; two iterations of Rapid Response™ COVID-19 Test Cassette, BTNX Inc.) and a subset of to evaluate SARS-COV-2 IgG/IgM Rapid Test, ACON Laboratories (n = 200); and Standard Q COVID-19 IgM/IgG Duo, SD BIOSENSOR (n = 155) for their capacity to detect of SARS-CoV-2 IgG. In a cohort of primarily hospitalized patients with RT-PCR confirmed COVID-19, the BTNX assays demonstrated 95% and 92% agreement with the Abbott SARS-CoV-2 IgG assay and sensitivity was highest at ≥ 14 days from symptom onset [BTNX kit 1, 95%; BTNX kit 2, 91%]. ACON and SD assays demonstrated 99% and 100% agreement with the Abbott assay at ≥ 14 days from symptom onset. Specificity was measured using 74 specimens collected prior to SARS-CoV-2 circulation in the United States and 31 “cross-reactivity challenge” specimens, including those from patients with a history of seasonal coronavirus infection and was 98% for BTNX kit 1 and ACON and 100% for BTNX kit 2 and SD. Taken with data from EUA assays, these results suggest that LFIAs may provide adequate results for rapid detection of SARS-CoV-2. Replicating these results in fingerstick blood in outpatient populations, would further support the possibility that LFIAs may be useful to increase access to serologic testing
Accelerated aortic stiffness is associated with brain structure, perfusion and cognition in the Whitehall II Imaging Sub-study
Authors: Suri Sana , Chiesa Scott T. , Zsoldos Enikő , Mackay Clare E. , Filippini Nicola , Griffanti Ludovica , Mahmood Abda , Singh-Manoux Archana , Shipley Martin J , Brunner Eric J , Kivimäki Mika , Deanfield John E. , Ebmeier Klaus P.
Published: July 2020

Background

Aortic stiffness is closely linked with cardiovascular diseases, but recent studies suggest that it is also a risk factor for cognitive decline and dementia. However, the brain changes underlying this risk are unclear. We examined whether aortic stiffening in the transition from mid to late-life affects brain structure and cognition.

Methods and Findings

Aortic pulse wave velocity was measured in 2007-09 (Phase 9) and at a 4-year follow-up in 2012-13 (Phase 11) in the Whitehall II Imaging Sub-study cohort. Between 2012-2016 (Imaging Phase), participants received a multi-modal 3T brain magnetic resonance imaging (MRI) scans and cognitive tests. Participants were selected if they had no clinical diagnosis of dementia and no gross brain structural abnormalities. Voxel-based analyses were used to assess grey matter volume, white matter microstructure (fractional anisotropy and diffusivity), cerebral blood flow, and white matter lesions. Cognitive outcomes were performance on verbal memory, semantic fluency, working memory and executive function tests. Of 544 participants, 445 (81.8%) were men. The mean (SD) age was 63.9 (5.2) years at the baseline Phase 9 examination, 67.9 (5.3) years at Phase 11 and 69.8 (5.2) years at the Imaging Phase. Voxel-based analysis revealed that accelerated aortic stiffening in mid-to-late life was associated with poor white matter integrity, viz. lower fractional anisotropy in 4.2% of white matter and higher radial diffusivity in 6.7% of white matter, including the corpus callosum, corona radiata, superior longitudinal fasciculus and corticospinal tracts. Accelerated aortic stiffening was also related to lower cerebral perfusion in 1.1% of grey matter including the parietal, frontal, and occipital cortices. No associations with grey matter volume or white matter lesions were observed. Further, higher baseline aortic stiffness was associated with poor semantic fluency (B=-0.48, 95%CI −0.77 to −0.19, p<0.005) and verbal learning outcomes (B=-0.36, 95%CI - 0.60 to −0.13, p<0.005).

Conclusions

Faster aortic stiffening in mid-to-late life is associated with poor brain white matter microstructural integrity and reduced cerebral perfusion, likely due to increased transmission of pulsatile energy to the delicate cerebral microvasculature. Strategies to prevent arterial stiffening prior to this point may be required to offer cognitive benefit in older age.
Spatial engineering ofE. coliwith addressable phase-separated RNAs
Authors: Guo Haotian , Ryan Joseph C. , Mallet Adeline , Song Xiaohu , Pabst Victor , Decrulle Antoine , Lindner Ariel B.
Published: July 2020

Biochemical processes often require spatial regulation and specific microenvironments. The general lack of organelles in bacteria limits the potential of bioengineering complex intracellular reactions. Here we demonstrate Transcriptionally Engineered Addressable RNA Solvent droplets (TEARS) as synthetic microdomains within theEscherichia coli.TEARS are assembled from RNA-binding protein recruitment domains fused to poly-CAG repeats that spontaneously drive liquid-liquid phase separation from the bulk cytoplasm. Targeting TEARS with fluorescent proteins revealed multilayered structures and a non-equilibrium mechanism controlling their composition and reaction robustness. We show that TEARS provide organelle-like bioprocess isolation for sequestering biochemical pathways, controlling metabolic branch points, buffering mRNA translation rates and scaffolding protein-protein interactions. TEARS are a simple and versatile tool for spatially controllingE. colibiochemistry.
Reintroduced nativePopulus nigrain restored floodplain reduces spread of exotic poplar species
Authors: Broeck An Vanden , Cox Karen , Van Braeckel Alexander , Neyrinck Sabrina , De Regge Nico , Van Looy Kris
Published: July 2020

1.

ExoticPopulustaxa pose a threat to the success of riparian forest restoration in floodplain areas. We evaluated the impact of exoticPopulustaxa on softwood riparian forest development along the river Common Meuse after introducing nativePopulus nigraand after the re-establishment of the natural river dynamics. We sampled 154 poplar seedlings that spontaneously colonised restored habitat and assessed their taxonomy based on diagnostic chloroplast and nuclear microsatellite markers. Furthermore, by using a paternity analysis on 72 seedlings resulting from six open pollinatedP. nigrafemales, we investigated natural hybridization between frequently planted cultivated poplars and nativeP. nigra. The majority of the poplar seedlings from the gravel banks analyzed where identified asP. nigra; only 2% of the sampled seedlings exhibited genes of exotic poplar species. Similarly, the majority of the seedlings from the open pollinated progenies were identified asP. nigra. For three seedlings (4%), paternity was assigned to a cultivar ofP. xcanadensis. Almost two decades after reintroducingP. nigra, the constitution of the seed and pollen pools changed in the study area in favour of reproduction of the native species and at the expense of the exotic poplar species. This study indicates that, although significant gene flow form exotic poplars is observed in European floodplains, restoration programmes of the nativeP. nigracan vigorously outcompete the exotic gene flows and strongly reduce the impact of exoticPopulustaxa on the softwood riparian forest development.
High-resolution structures of malaria parasite actomyosin and actin filaments
Authors: Vahokoski Juha , Calder Lesley J. , Lopez Andrea J. , Molloy Justin E. , Rosenthal Peter B. , Kursula Inari
Published: July 2020

Malaria is responsible for half a million deaths annually and poses a huge economic burden on the developing world. The mosquito-borne parasites (Plasmodiumspp.) that cause the disease depend upon an unconventional actomyosin motor for both gliding motility and host cell invasion. The motor system, often referred to as the glideosome complex, remains to be understood in molecular terms and is an attractive target for new drugs that might block the infection pathway. Here, we present the first high-resolution structure of the actomyosin motor complex fromPlasmodium falciparum. Our structure includes the malaria parasite actin filament (PfAct1) complexed with the myosin motor (PfMyoA) and its two associated light-chains. The high-resolution core structure reveals thePfAct1:PfMyoA interface in atomic detail, while at lower-resolution, we visualize thePfMyoA light-chain binding region, including the essential light chain (PfELC) and the myosin tail interacting protein (PfMTIP). Finally, we report a barePfAct1 filament structure at an improved resolution, which gives new information about the nucleotide-binding site, including the orientation of the ATP/ADP sensor, Ser15, and the presence of a channel, which we propose as a possible phosphate exit path after ATP hydrolysis.

Significance statement

We present the first structure of the malaria parasite motor complex; actin 1 (PfAct1) and myosin A (PfMyoA) with its two light chains. We also report a high-resolution structure of filamentousPfAct1 that reveals new atomic details of the ATPase site, including a channel, which may provide an exit route for phosphate and explain why phosphate release is faster inPfAct1 compared to canonical actins.PfAct1 goes through no conformational changes uponPfMyoA binding. OurPfMyoA structure also superimposes with a recent crystal structure ofPfMyoA alone, though there are small but important conformational changes at the interface. Our structures serve as an excellent starting point for drug design against malaria, which is one of the most devastating infectious diseases.
Guide RNA categorization enables target site choice in Tn7-CRISPR-Cas transposons
Authors: Petassi Michael T. , Hsieh Shan-Chi , Peters Joseph E.
Published: July 2020

CRISPR-Cas defense systems have been coopted multiple times in nature for guide RNA-directed transposition by Tn7-like elements. Prototypic Tn7 uses dedicated proteins for two targeting pathways, one targeting a neutral and conserved attachment site in the chromosome and a second directing transposition into mobile plasmids facilitating cell-to-cell transfer. We show that Tn7-CRISPR-Cas elements evolved a system of guide RNA categorization to accomplish the same two-pathway lifestyle. Selective regulation of specialized guide RNAs allows long-term memory for access to chromosomal sites upon entry into a new host, while conventional CRISPR features maintain the ability to continually acquire guide RNAs to new plasmid and phage targets. Transposon-encoded guide RNAs are also privatized to be recognized only by the transposon-adapted system working with selective regulation to guard against toxic self-targeting by endogenous CRISPR-Cas defense systems. This information reveals new avenues to engineer guide RNAs for enhanced CRISPR-Cas functionality for genome modification.
Urine metabolomics of rats with chronic atrophic gastritis
Authors: Zu Guo-Xiu , Sun Qian-Qian , Chen Jian , Liu Xi-Jian , Sun Ke-Yun , Zhang Liang-Kun , li Ling , Han Tao , Huang Ha I-Liang
Published: July 2020

Background/Aim: To use liquid chromatography-mass spectrometry (LC-MS) to identify endogenous differential metabolites in the urine of rats with chronic atrophic gastritis (CAG). Materials and Methods: Methylnitronitrosoguanidine (MNNG) was used to produce a CAG model in Wistar rats, and HE staining was used to determine the pathological model. LC-MS was used to detect the differential metabolic profiles in rat urine. Diversified analysis was performed by the statistical method. Results: Compared with the control group, the model group had 68 differential metabolites, 25 that were upregulated and 43 that were downregulated. The main metabolic pathways were D-glutamine and D-glutamic acid metabolism, histidine metabolism and purine metabolism. Conclusion: By searching for differential metabolites and metabolic pathways in the urine of CAG rats, this study provides effective experimental data for the pathogenesis and clinical diagnosis of CAG.
Multi-ethnic transcriptome-wide association study of prostate cancer
Authors: Fiorica Peter N. , Schubert Ryan , Morris John D. , Sami Mohammed Abdul , Wheeler Heather E.
Published: July 2020

The genetic risk for prostate cancer has been governed by a few rare variants with high penetrance and over 150 commonly occurring variants with lower impact on risk; however, most of these variants have been identified in studies containing exclusively European individuals. People of non-European ancestries make up less than 15% of prostate cancer GWAS subjects. Across the globe, incidence of prostate cancer varies with population due to environmental and genetic factors. The discrepancy between disease incidence and representation in genetics highlights the need for more studies of the genetic risk for prostate cancer across diverse populations. To better understand the genetic risk for prostate cancer across diverse populations, we performed PrediXcan and GWAS in a cohort of 4,769 self-identified African American (2,463 cases and 2,306 controls), 2,199 Japanese American (1,106 cases and 1,093 controls), and 2,147 Latin American (1,081 cases and 1,066 controls) individuals from the Multiethnic Genome-wide Scan of Prostate Cancer. We used prediction models from 46 tissues in GTEx version 8 and five models from monocyte transcriptomes in the Multi-Ethnic Study of Artherosclerosis. Across the three populations, we predicted 19 gene-tissue pairs, including five unique genes, to be significantly (lfsr< 0.05) associated with prostate cancer. One of these genes,NKX3-1, replicated in a larger European cohort. At the SNP level, 110 SNPs met genome-wide significance in the African American cohort while 123 SNPs met significance in the Japanese American cohort. Fine mapping revealed three significant independent loci in the African American cohort and two significant independent loci in the Japanese American cohort. These identified loci confirm findings from previous GWAS of prostate cancer in diverse cohorts while PrediXcan-identified genes suggest potential new directions for prostate cancer research in populations across the globe.
Molecular Logic of Cellular Diversification in the Mammalian Cerebral Cortex
Authors: Di Bella Daniela J. , Habibi Ehsan , Yang Sun-Ming , Stickels Robert R. , Brown Juliana , Yadollahpour Payman , Chen Fei , Macosko Evan Z. , Regev Aviv , Arlotta Paola
Published: July 2020

The neocortex has an unparalleled diversity of cell types, which are generated during development through a series of temporally orchestrated events that are under tight evolutionary constraint and are critical for proper cortical assembly and function. However, the molecular logic that governs the establishment and organization of cortical cell types remains elusive, largely due to the large number of cell classes undergoing dynamic cell-state transitions over extended developmental timelines. Here, we have generated a comprehensive single-cell RNA-seq and single-cell ATAC-seq atlas of the developing mouse neocortex, sampled every day throughout embryonic corticogenesis. We computationally reconstruct developmental trajectories across the diversity of cortical cell classes, and infer the gene regulatory programs that accompany their lineage bifurcation decisions and their differentiation trajectories. Finally, we demonstrate how this developmental map pinpoints the origin of lineage-specific developmental abnormalities linked to aberrant corticogenesis in mutant animals. The data provides the first global picture of the regulatory mechanisms governing cellular diversification in the neocortex.
Crystal structure and site-directed mutagenesis of circular bacteriocin plantacyclin B21AG reveals cationic and aromatic residues important for antimicrobial activity
Authors: Gor Mian-Chee , Vezina Ben , McMahon Róisín M. , King Gordon J. , Panjikar Santosh , Rehm Bernd H. A. , Martin Jennifer L. , Smith Andrew T.
Published: July 2020

Plantacyclin B21AG is a circular bacteriocin produced byLactobacillus plantarumB21 which displays antimicrobial activity against various Gram-positive bacteria including foodborne pathogens,Listeria monocytogenesandClostridium perfringens. It is a 58-amino acid cyclised antimicrobial peptide, with the N and C termini covalently linked together. The circular peptide backbone contributes to remarkable stability, conferring partial proteolytic resistance and structural integrity under a wide temperature and pH range. Here, we report the first crystal structure of a circular bacteriocin from food gradeLactobacillus. The protein was crystallised using the hanging drop vapour diffusion method and the structure solved to a resolution of 1.8 Å. Sequence alignment against 17 previously characterised circular bacteriocins revealed the presence of conserved charged and aromatic residues. Alanine substitution mutagenesis validated the importance of these residues. Minimum inhibitory concentration analysis of these Ala mutants showed Phe8Ala and Trp45Ala mutants displayed a 48- and 32-fold reduction in activity, compared to wild type. Lys19Ala mutant displayed the weakest activity, with a 128-fold reduction. These experiments demonstrate the importance of aromatic and cationic residues for the antimicrobial activity of plantacyclin B21AG and by extension, other circular bacteriocins sharing these evolutionarily conserved residues.
Asymptomatic Genu Recurvatum Reshapes Lower Limb Sagittal Joint and Elevation Angles During Gait at Different Speeds
Authors: Dierick Frédéric , Schreiber Céline , Lavallée Pauline , Buisseret Fabien
Published: July 2020

Purpose

The main objective of this study is to characterize the lower limb sagittal joint and elevation angles during walking in participants with asymptomatic genu recurvatum and compare it with control participants without knee deformation. The secondary objective is to study the influence of walking speed on these kinematic variables.

Methods

The spatio-temporal parameters and kinematics of the lower limb were recorded using an optoelectronic motion capture system in 26 partici-pants (n = 13 with genu recurvatum and n = 13 controls). The participants walked on an instrumented treadmill during five minutes at three different speeds: slow, medium and fast.

Results

Participants with genu recurvatum showed several significant differences with controls: a narrower step width, a greater maximum hip joint extension angle, a greater knee joint extension angle at mid stance, a lower maximum knee joint flexion angle during the swing phase, and a greater ankle joint extension angle at the end of the gait cycle. Participants with genu recurvatum had a greater minimum thigh elevation angle, a greater maximum foot elevation angle, and a change in the orientation of the covariance plane. Walking speed had a significant effect on nearly all lower limb joint, elevation angle, and covariance plane parameters.

Conclusion

Our findings show that genu recurvatum reshapes lower limb sagittal joint and elevation angles during walking at different speeds but preserves the covariation of elevation angles along a plane during both stance and swing phases and the rotation of this plane with increasing speed.
DMT analogues: N-ethyl-N-propyltryptamine and N-allyl-N-methytryptamine as their hydrofumarate salts
Authors: Chadeayne Andrew R. , Pham Duyen N. K. , Golen James A. , Manke David R.
Published: July 2020

The solid-state structures of the hydrofumarate salts of two N,N-dialkyltryptamines, namely N-ethyl-N-propyltryptammonium (EPT) hydrofumarate {systematic name: [2-(1H-indol-3-yl)ethyl](methyl)propylazanium 3-carboxyprop-2-enoate}, C15H23N2
+·C4H3O4
−, and N-allyl-N-methyltryptammonium (MALT) hydrofumarate {systematic name: [2-(1H-indol-3-yl)ethyl](methyl)(prop-2-en-1-yl)azanium 3-carboxyprop-2-enoate}, C14H19N2
+·C4H3O4
−, are reported. Both compounds possess a protonated tryptammonium cation, and a hydrofumarate anion in the asymmetric unit. The ethyl group of the EPT cation is modeled as a two-component disorder with 50% occupancy for each component. In the extended structure, N—H...O and O—H...O hydrogen bonds generate infinite two-dimensional networks parallel to the (001) plane for both compounds.
Compact four-port vertically polarized UWB monopole antenna for MIMO communications
Authors: J. Premalatha , D. Sheela
Published: July 2020

Purpose

This paper aims to present the design of a compact vertically polarized four-element UWB antenna suitable for MIMO communications.

Design/methodology/approach

The unit cell antenna is constructed using a square ring radiator excited through a stepped impedance feed. The proposed antenna covers the Ultra-wideband (UWB) spectrum ranging from 2.2 to 12.3 GHz. The isolation between the unit cell antennas in the array is enhanced using a simple microstrip line resonator. The decoupling element is connected to the ground through a via.

Findings

The proposed scheme offers at least 16 dB improvement in the port-to-port coupling. Furthermore, the four-element antenna array is constructed using a specific interlocking scheme. The proposed antenna array’s Multiple Input Multiple Output (MIMO) performance metrics are analyzed.

Originality/value

By suitably selecting the excitation port, directional radiation patterns can be realized. The combined radiation pattern covers 360 degrees. A prototype antenna array is fabricated, and the simulation results are verified using real-time experiments. The proposed antenna is a suitable candidate for shark fin housing in automotive communications.
Leveraging social media in new product development: organisational learning processes, mechanisms and evidence from China
Authors: Zhan Yuanzhu , Tan Kim Hua , Chung Leanne , Chen Lujie , Xing Xinjie
Published: July 2020

Purpose

The main purpose of this paper is to investigate how social media can provide important platforms to facilitate organisational learning and innovation in new product development (NPD) process.

Design/methodology/approach

Using a multiple case-study approach, this study assesses qualitative data collected via 56 interviews from 13 world-leading Chinese companies in the high-technology industry.

Findings

The study identified three distinct types of organisational learning mechanisms for firms to extract potential innovation inherent in social media. It further determined various organisational enablers that facilitate the connections between these mechanisms and NPD performance.

Research limitations/implications

This research contributes to the emerging literature on digital product development and organisational learning. The cases were conducted in the Chinese context, hence, the results may not be fully generalisable to other organisations, industries and countries without appropriate re-contextualisation.

Practical implications

The empirical evidence showcases the various mechanisms adopted by managers in different NPD phases. It identifies several technological and organisational adaptations that managers can apply to smartly scale their social presence and facilitate NPD.

Originality/value

Despite the exponential growth of social media use in identifying and interacting with external stakeholders, managerial practice and academic research have paid little attention to how social media can be leveraged for NPD. The value of this research comes from applying a qualitative method to gain in-depth insights into the mechanisms for leveraging social media to facilitate innovation in NPD.
Advanced services and differentiation advantage: an empirical investigation
Authors: Sousa Rui , da Silveira Giovani J.C.
Published: July 2020

Purpose

This study theoretically articulates and empirically validates a model of relationships between market complexity (competition intensity, heterogeneity and technological change), strategic focus on product and service differentiation, ADS offerings and differentiation advantage.

Design/methodology/approach

The authors develop and test hypotheses through structural equation modeling based on data from the Sixth International Manufacturing Strategy Survey (IMSS-VI), involving 931 manufacturers from 22 countries.

Findings

The results indicate that (1) market complexity has a positive impact on strategic focus on product and service differentiation; (2) focus on product and service differentiation, but not market complexity, has a positive impact on the extent to which business units offer ADS to their customers; (3) ADS have a positive impact on service differentiation advantage, but no influence on product differentiation advantage.

Practical implications

Managers should incorporate decisions related to ADS provision as part of their manufacturing strategy formulation processes to align markets, strategic focus on product and service differentiation, and ADS provision. ADS seem an appropriate lever for market differentiation, because they appear not only to support service differentiation advantage, but also to be consistent with strategic focus on product differentiation.

Originality/value

The study provides novel insights and large-scale empirical evidence on the influence of the market environment on the offering of ADS, as well as on how relationships between the product and service activity in the manufacturing organization may affect differentiation advantage.
Improved rider optimization for optimal container resource allocation in cloud with security assurance
Authors: Vhatkar Kapil Netaji , Bhole Girish P.
Published: July 2020

Purpose

The containerization application is one among the technologies that enable microservices architectures, which is observed to be the model for operating system (OS) virtualization. Containers are the virtual instances of the OS that are structured as the isolation for the OS atmosphere and its file system, which are executed on the single kernel and a single host. Hence, every microservice application is evolved in a container without launching the total virtual machine. The system overhead is minimized in this way as the environment is maintained in a secured manner. The exploitation of a microservice is as easy to start the execution of a new container. As a result, microservices could scale up by simply generating new containers until the required scalability level is attained. This paper aims to optimize the container allocation.

Design/methodology/approach

This paper introduces a new customized rider optimization algorithm (C-ROA) for optimizing the container allocation. The proposed model also considers the impact of system performance along with its security. Moreover, a new rescaled objective function is defined in this work that considers threshold distance, balanced cluster use, system failure, total network distance and security as well. At last, the performance of proposed work is compared over other state-of-the-art models with respect to convergence and cost analysis.

Findings

For experiment 1, the implemented model at 50th iteration has achieved minimal value, which is 29.24%, 24.48% and 21.11% better from velocity updated grey wolf optimisation (VU-GWO), whale random update assisted LA (WR-LA) and rider optimization algorithm (ROA), respectively. Similarly, on considering Experiment 2, the proposed model at 100th iteration attained superior performance than conventional models such as VU-GWO, WR-LA and ROA by 3.21%, 7.18% and 10.19%, respectively. The developed model for Experiment 3 at 100th iteration is 2.23%, 5.76% and 6.56% superior to VU-GWO, WR-LA and ROA.

Originality/value

This paper presents the latest fictional optimization algorithm named ROA for optimizing the container allocation. To the best of the authors’ knowledge, this is the first study that uses the C-ROA for optimization.
Understanding consumers’ trust in social media marketing environment
Authors: Irshad Madeeha , Ahmad Muhammad Shakil , Malik Omer Farooq
Published: July 2020

Purpose

The purpose of this study was to examine the impacts of consumers’ motivations (i.e. remuneration, social, and empowerment) on online purchase intentions mediated through trust towards retailers present on social media.

Design/methodology/approach

Data were collected from consumers residing in the three metropolitan cities of Pakistan, and the research model was tested using the covariance-based structural equation modelling in Amos.

Findings

The results showed that remuneration and social motivations positively influenced consumers’ online purchase intentions directly, as well as indirectly mediated through trust. However, trust fully mediated the relationship between empowerment motivation and consumers’ online purchase intentions.

Originality/value

The existing literature reveals that only a handful of studies have endeavoured to understand consumers’ trust in the context of social media marketing, and the literature in this field is not matured yet. The novelty of this research lies in its contribution to understanding the impacts of consumers’ motives (i.e. remuneration, social, and empowerment) on trust towards retailers present on social media, which have not been explored before. In addition, it examines trust towards retailers present on social media as an underlying mechanism that affects the relationships between consumers’ motives and online purchase intentions.