bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sodium regulates PLC and IP3R-mediated calcium signalling in invasive breast cancer cells
Authors: James Andrew D. , Unthank Katherine P. , Jones Isobel , Sajjaboontawee Nattanan , Sizer Rebecca E. , Chawla Sangeeta , Evans Gareth J.O. , Brackenbury William J. 
Published: August 2022

AbstractIntracellular Ca2+signalling and Na+homeostasis are inextricably linked via ion channels and co-transporters, with alterations in the concentration of one ion having profound effects on the other. Evidence indicates that intracellular Na+concentration ([Na+]i) is elevated in breast tumours, and that aberrant Ca2+signalling regulates numerous key cancer hallmark processes. The present study therefore aimed to determine the effects of Na+depletion on intracellular Ca2+handling in metastatic breast cancer cell lines. The relationship between Na+and Ca2+was probed using fura-2 and SBFI fluorescence imaging and replacement of extracellular Na+with equimolar N-methyl-D-glucamine (0Na+/NMDG) or choline chloride (0Na+/ChoCl). In triple-negative MDA-MB-231 and MDA-MB-468 cells and Her2+ SKBR3 cells, but not ER+ MCF-7 cells, 0Na+/NMDG and 0Na+/ChoCl resulted in a slow, sustained depletion in [Na+]ithat was accompanied by a rapid and sustained increase in intracellular Ca2+concentration ([Ca2+]i). Application of La3+in nominal Ca2+-free conditions had no effect on this response, ruling out reverse-mode NCX activity and Ca2+entry channels. Moreover, the Na+-linked [Ca2+]iincrease was independent of membrane potential hyperpolarisation (NS-1619), but was inhibited by pharmacological blockade of IP3receptors (2-APB), phospholipase C (PLC, U73122) or following depletion of endoplasmic reticulum Ca2+stores (cyclopiazonic acid). Thus, Na+is linked to PLC/IP3-mediated activation of endoplasmic reticulum Ca2+release in metastatic breast cancer cells and this may have an important role in breast tumours where [Na+]iis perturbed.
Reduced glucosinolate content in oilseed rape (Brassica napus L.) by random mutagenesis of BnMYB28 and BnCYP79F1 genes
Authors: Jhingan Srijan , Harloff Hans-Joachim , Abbadi Amine , Welsch Claudia , Blümel Martina , Tasdemir Deniz , Jung Christian 
Published: August 2022

AbstractThe presence of anti-nutritive compounds like glucosinolates (GSLs) in the rapeseed meal severely restricts its utilization as animal feed. Therefore, reducing the GSL content to <18 µmol/g dry weight in the seeds is a major breeding target. While candidate genes involved in the biosynthesis of GSLs have been described in rapeseed, comprehensive functional analyses are missing. By knocking out the aliphatic GSL biosynthesis genes BnMYB28 and BnCYP79F1 encoding an R2R3 MYB transcription factor and a cytochrome P450 enzyme, respectively, we aimed to reduce the seed GSL content in rapeseed. After expression analyses on single paralogs, we used an ethyl methanesulfonate (EMS) treated population of the inbred winter rapeseed ‘Express617’ to detect functional mutations in the two gene families. Our results provide the first functional analysis by knock-out for the two GSL biosynthesis genes in winter rapeseed. We demonstrate that independent knock-out mutants of the two genes possessed significantly reduced seed aliphatic GSLs, primarily progoitrin. Compared to the wildtype Express617 control plants (36.3 µmol/g DW), progoitrin levels were decreased by 55.3% and 32.4% in functional mutants of BnMYB28 (16.20 µmol/g DW) and BnCYP79F1 (24.5 µmol/g DW), respectively. Our study provides a strong basis for breeding rapeseed with improved meal quality in the future.
A low-cost, thermostable, cell-free protein synthesis platform for on demand production of conjugate vaccines
Authors: Warfel Katherine F. , Williams Asher , Wong Derek A. , Sobol Sarah E. , Desai Primit , Li Jie , Chang Yung-Fu , DeLisa Matthew P. , Karim Ashty S. , Jewett Michael C. 
Published: August 2022

AbstractCell-free protein synthesis systems that can be lyophilized for long-term, nonrefrigerated storage and transportation have the potential to enable decentralized biomanufacturing. However, increased thermostability and decreased reaction cost are necessary for further technology adoption. Here, we identify maltodextrin as an additive to cell-free reactions that can act as both a lyoprotectant to increase thermostability, as well as a lowcost energy substrate. As a model, we apply optimized formulations to produce conjugate vaccines for ~$0.50 per dose after storage at room temperature or 37 °C for up to 4 weeks and ~$1.00 per dose after storage at 50 °C for up to 4 weeks. We show that these conjugates generate bactericidal antibodies against enterotoxigenic E. coli (ETEC) O78 O-polysaccharide, a pathogen responsible for diarrheal disease, in immunized mice. We anticipate that our lowcost, thermostable cell-free glycoprotein synthesis system will enable new models of medicine biosynthesis and distribution that bypass cold-chain requirements.
Protein engineering via Bayesian optimization-guided evolutionary algorithm and robotic experiments
Authors: Hu Ruyun , Fu Lihao , Chen Yongcan , Chen Junyu , Qiao Yu , Si Tong 
Published: August 2022

ABSTRACTProtein engineering aims to find top functional sequences in a vast design space. For such an expensive “black-box” function optimization problem, Bayesian optimization is a principled sample-efficient approach, which is guided by a surrogate model of the objective function. Unfortunately, Bayesian optimization is computationally intractable with the vast search space. Even worse, it proposes sequences sequentially, making it incompatible with batched wet-lab measurement. Here, we report a scalable and batched method, Bayesian Optimization-guided EVOlutionary (BO-EVO) algorithm, to guide multiple rounds of robotic experiments to explore protein fitness landscapes of combinatorial mutagenesis libraries. We first examined various design specifications based on an empirical landscape of protein G domain B1. Then, BO-EVO was successfully generalized to another empirical landscape of an Escherichia coli kinase PhoQ, as well as simulated NK landscapes with up to moderate epistasis. This approach was then applied to guide robotic library creation and screening to engineer enzyme specificity of RhlA, a key biosynthetic enzyme for rhamnolipid biosurfactants. A 4.8-fold improvement in producing a target rhamnolipid congener was achieved after examining less than 1% of all possible mutants after 4 iterations. Overall, BO-EVO proves to be an efficient and general approach to guide combinatorial protein engineering without prior knowledge.
Npas4-mediated dopaminergic regulation of fear memory states
Authors: Ko BumJin , Yoo Jong-Yeon , Choi Woochul , Dogan Rumeysa , Sung Kibong , Lee Sangjun , Um Dahun , Lee Su Been , Yoo Taesik , Kim Hyun Jin , Beak Seung Tae , Park Sang Ki , Paik Se-Bum , Kim Tae-Kyung , Kim Joung-Hun 
Published: August 2022

AbstractAmygdala circuitry encodes associations between conditioned stimuli and aversive unconditioned stimuli, and also controls fear expression (Pape and Pare, 2010). However, whether and how irrelevant information for unpaired conditioned stimuli (CS-) is discretely processed, and how it was influenced by stress remain unknown. CS- memory is retrievable immediately after fear conditioning, but then becomes silent after memory consolidation in mice. Synaptic pathway from the lateral to the anterior basal amygdala gates the expression of CS- memory, depending upon Npas4-mediated Drd4 synthesis. The upregulation of Npas4-Drd4 axis, which is precluded by corticosterone, shifts functional states of neural engrams for CS- memory toward silent states and limits its retrievability. In here, we demonstrate the cellular and molecular mechanisms regulating the functional states of neural engrams, which can be switched or maintained, supporting discriminative memory.
The transcriptional regulator JAZ8 interacts with the C2 protein from geminiviruses and limits the viral infection in Arabidopsis
Authors: Rosas-Diaz Tabata , Cana-Quijada Pepe , Wu Mengshi , Du Hui , Fernandez-Barbero Gemma , Macho Alberto P. , Solano Roberto , Castillo Araceli G. , Wang Xiao-Wei , Lozano-Duran Rosa , Bejarano Eduardo R. 
Published: August 2022

ABSTRACTJasmonates (JAs) are phytohormones that finely regulate critical biological processes, including plant development and defense. JASMONATE ZIM-DOMAIN (JAZ) proteins are crucial keeping JA-responsive genes in a repressed state. In the presence of JA-Ile, JAZ repressors are ubiquitinated and targeted for degradation by the ubiquitin/proteasome system, allowing the activation of the downstream transcription factors and, consequently, the activation of JA-responsive genes. A growing body of evidence has shown that JA signalling is crucial in defending against plant viruses and their insect vectors. Here, we describe the interaction of C2 proteins from two geminiviruses from the genus Begomovirus, tomato yellow curl Sardinia virus (TYLCSaV) and tomato yellow leaf curl virus (TYLCV), with the transcriptional repressor JAZ8 from Arabidopsis thaliana and its closest orthologue in tomato, SlJAZ9. Both JAZ and C2 proteins colocalize in the nucleus, forming discrete nuclear speckles. Overexpression of JAZ8 did not lead to altered responses to TYLCV infection; however, knock-down of JAZ8 favours the geminiviral infection in plants. Low levels of JAZ8 likely affect the viral infection specifically since JAZ8-silenced plants do not display developmental phenotypes nor present differences in their interaction with the viral insect vector. Our results show that JAZ8 interacts with geminiviral C2 proteins and exerts an anti-geminiviral effect.
Cryo-ET of infected cells reveals that a succession of two lattices drives vaccinia virus assembly
Authors: Hernandez-Gonzalez Miguel , Calcraft Thomas , Nans Andrea , Rosenthal Peter B , Way Michael 
Published: August 2022

AbstractDuring its cytoplasmic replication, vaccinia virus assembles non-infectious spherical immature virions (IV) coated by a viral D13 lattice. Subsequently, IV mature into infectious brick-shaped intracellular mature virus (IMV) that lack D13. Here, we performed cryo-electron tomography of frozen-hydrated vaccinia-infected cells to structurally characterise the maturation process in situ. During IMV formation a new viral core forms inside IV with a wall consisting of trimeric pillars arranged in a new pseudohexagonal lattice. This lattice appears as a palisade in cross-section. During maturation, which involves a 50% reduction in virion volume, the viral membrane becomes corrugated as it adapts to the newly formed viral core in a process that does not appear to require membrane removal. Our study suggests that the length of this core is determined by the D13 lattice and that the consecutive D13 and palisade lattices control virion shape and dimensions during vaccinia assembly and maturation.
A lncRNA identifiesIRF8enhancer element in negative feedback control of dendritic cell differentiation
Authors: Xu Huaming , Li Zhijian , Kuo Chao-Chung , Götz Katrin , Look Thomas , de Toledo Marcelo Augusto Szymanski , Seré Kristin , Costa Ivan G. , Zenke Martin 
Published: August 2022

AbstractTranscription factors play a determining role in lineage commitment and cell differentiation. Interferon regulatory factor 8 (IRF8), a hematopoietic transcription factor, is prominently upregulated in dendritic cells (DC) by autoactivation and controls DC differentiation and function. However, it is unclear howIRF8autoactivation is controlled and eventually limited. Here we identified a novel long non-coding RNA transcribed from the +32 kb enhancer downstream ofIRF8transcription start site and expressed specifically in plasmacytoid DC (pDC), referred to aslncIRF8. A sequence element of thelncIRF8promoter, but notlncIRF8itself, is crucial for pDC and classical DC type 1 (cDC1) differentiation. In DC developmentIRF8autoactivation is first initiated by flanking enhancers and then second controlled by feedback inhibition through thelncIRF8promoter element in the +32 kb enhancer. Our work reveals a previously unrecognized negative feedback loop ofIRF8that orchestrates its own expression and thereby controls DC differentiation.
Lipidomic analysis reveals differences inBacteroidesspecies driven largely by plasmalogens, glycerophosphoinositols and certain sphingolipids
Authors: Ryan Eileen , Gonzales Pastor Belén , Gethings Lee A. , Clarke David J. , Joyce Susan A. 
Published: August 2022

AbstractThere has been increasing interest in bacterial lipids in recent years due, in part, to their emerging role as molecular signalling molecules.Bacteroides thetaiotaomicronis an important member of the mammalian gut microbiota that has been shown to produce sphingolipids (SP) that pass through the gut epithelial barrier to impact host SP metabolism and signal into host inflammation pathways.B. thetaiotaomicronalso produces a novel family of N-acyl amines (called glycine lipids) that are potent ligands of host Toll-like receptor 2 (TLR2). Here, we specifically examine the lipid signatures of 4 species of gut associatedBacteroides. In total we identify 170 different lipids and we report that the range and diversity ofBacteroideslipids is species-specific. Multi-variate analysis reveals that the differences in the lipid signatures are largely driven by the presence/absence of plasmalogens, glycerophosphoinositols and certain SP. Moreover, we show that, inB. thetaiotaomicron, mutations altering either SP or glycine lipid biosynthesis results in significant changes in the levels of other lipids suggesting the existence of compensatory mechanisms required to maintain the functionality of the bacterial membrane.ImportanceBacteroidesare important beneficial members of the gut microbiome that produce lipids that can function as cross-kingdom signalling molecules. We describe, for the first time, a comprehensive and qualitative comparison of the lipid signatures of 4 importantBacteroidesspecies. We identify a group ofBacteroidescore lipids and uncover species-specific differences in plasmalogen, glycerophospholipid and SP metabolism with more subtle differences observed in glycine lipid production. This data will provide a useful platform for the further characterisation of the lipid-based host-microbe dialogue and the influence of microbial lipids on host health and disease states.
A multiplexed, confinable CRISPR/Cas9 gene drive propagates in caged Aedes aegypti populations
Authors: Anderson Michelle A.E. , Gonzalez Estela , Edgington Matthew P. , Ang Joshua X. D. , Purusothaman Deepak-Kumar , Shackleford Lewis , Nevard Katherine , Verkuijl Sebald A. N. , Harvey-Samuel Tim , Leftwich Philip T. , Esvelt Kevin , Alphey Luke 
Published: August 2022

AbstractAedes aegypti, the yellow fever mosquito, is the main vector of several major pathogens including yellow fever, dengue, Zika and chikungunya viruses. Classical mosquito control strategies, mainly utilizing insecticides, have had success in controlling other mosquito vectors in recent years, but are much less useful against Ae. aegypti, and even these methods are threatened by rising insecticide resistance. This has stimulated interest in new mosquito control mechanisms, notably genetic systems such as gene drives. However, the development of CRISPR/Cas9 gene drive systems has faced challenges such as low inheritance biasing rate, the emergence of resistance alleles, and the possibility of spreading beyond the intended population. Here, we test the regulatory sequences from the Ae. aegypti benign gonial cell neoplasm (bgcn) homolog to express Cas9 in the germline to find an expression timing more conducive to homing. We also created a separate multiplexing (targeting multiple different sites within the target gene) sgRNA-expressing homing cassette inserted into the Ae. aegypti kynurenine 3-monooxygenase (kmo) gene to limit the consequences of resistance alleles. This creates a ‘split’ gene drive such that one part does not drive, allowing control over geographic spread and temporal persistence. When combined, these two elements provide highly effective germline cutting at the kmo locus and act as a gene drive. Our target genetic element was driven through a cage trial population such that carrier frequency of the element increased from 50% to up to 89% of the population despite significant fitness costs to kmo insertions. Deep sequencing suggests that the multiplexing design could mitigate resistance allele formation in our gene drive system.Significance statementMosquito-borne diseases affect millions of people worldwide, with the yellow fever mosquito (Aedes aegypti) being the principal vector of many viral diseases. Effective measures for controlling this mosquito are sorely needed. Gene drive systems have arisen as a potential tool for mosquito control due to their ability of biasing inheritance of a trait into a target population. Here, we assess a split gene drive, based on CRISPR/Cas9 endonuclease technology driving a target element into the mosquito population. Evaluated over successive generations in a replicated cage trial, the drive successfully biased its inheritance, increasing in frequency from 50% to up to 89%. Our results are encouraging for the potential use of this type of contained gene drive system for mosquito control in endemic areas.
Optogenetic control of cell signaling with red/far-red light-responsive optogenetic tools in Caenorhabditis elegans
Authors: Oda Shigekazu , Sato-Ebine Emi , Nakamura Akinobu , Kimura Koutarou D. , Aoki Kazuhiro 
Published: August 2022

AbstractOptogenetic techniques have been intensively applied to the nematode Caenorhabditis elegans to investigate its neural functions. However, as most of these optogenetics are responsive to blue light and the animals exhibits avoidance behavior to blue light, the application of optogenetic tools responsive to longer wavelength light has been eagerly anticipated. In this study, we report the implementation in C. elegans of a phytochrome-based optogenetic tool that responds to red/near-infrared light and manipulates cell signaling. We first introduced the SynPCB system, which enabled us to synthesize phycocyanobilin (PCB), a chromophore for phytochrome, and confirmed the biosynthesis of PCB in neurons, muscles, and intestinal cells. We further confirmed that the amount of PCBs synthesized by the SynPCB system was sufficient for photoswitching of phytochrome B (PhyB)-phytochrome interacting factor 3 (PIF3). In addition, optogenetic elevation of intracellular Ca2+ levels in intestinal cells induced a defecation motor program. These SynPCB system and phytochrome-based optogenetic techniques would be of great value in elucidating the molecular mechanisms underlying C. elegans behaviors.
Towards unified management of software capstone projects in Saudi universities: a survey-based study
Authors: Ahmad Ehsan , Alammary Ali 
Published: August 2022

PurposeSaudi universities have incorporated capstone projects in the final year of an undergraduate study. Although universities are following recommendations of the National Commission for National Commission for Academic Accreditation and Assessment (NCAAA) and Accreditation Board for Engineering and Technology (ABET), no detailed guidelines for management and assessment of capstone projects are provided by these accreditation bodies. Variation in the management and assessment practices of capstone project courses and analysis of the students' capabilities to align with industry demands, to realize Vision 2030, is challenging. This study investigates the current practices for structure definition, management and assessment criteria used for capstone project courses at undergraduate level for information technology (IT) programs at Saudi universities.Design/methodology/approachA web-based questionnaire is administered using a web service commonly used for questionnaires and polls to investigate the structure, management and assessment of capstone projects at the undergraduate level offering software engineering, computer science and information technology (SECSIT) programs. In total, 42 faculty members (with range of experience of managing/advising capstone projects from 1 to more than 10 years) from 22 Saudi universities (out of more than 30 universities offering SECSIT undergraduate programs) participated in the study.FindingsThe authors have identified that Saudi universities are facing challenges in the utilized process model, the distribution of work and marks, the knowledge sharing approach and the assessment scheme. To cope with these challenges, the authors recommend the use of an incremental development process, the utilization of a project-driven approach, the development of a national level digital archive and the implementation of homogeneous assessment scheme.Social implicationsTo contribute to the national growth and to fulfill the market demand, universities are recommended to align the capstone project courses with latest technology trends. Universities must collaborate with the industry and update the structure and requirements of capstone project courses accordingly. This will further facilitate to bridge the gap between industry and academia and will develop a win–win scenario for all the stakeholders.Originality/valueAlthough universities are committed to increase innovative capacities of their students for enabling them to contribute to economic and social growth, it is still hard to know the knowledge creation and sharing at national level. Variations in the management and assessment practices for capstone projects further intensify this challenge. Hence, there is a need of smart assessment and management of software capstone projects being developed in Saudi universities. Incorporating latest technologies, such unified management can facilitate discovering the trends and patterns related to the domain and complexity.
Impact of lockdown and government subsidies on rural households at early COVID-19 pandemic in China
Authors: Li Nan , Chen Muzi , Gao Haoyu , Huang Difang , Yang Xiaoguang 
Published: August 2022

PurposeGiven the scarcity of data during the early stages of the COVID-19 pandemic in China, the decision-making for non-pharmaceutical policies was mostly based on insufficient evidence. The purpose of this study is to assess the effectiveness of these policies, such as lockdown and government subsidies, on rural households and identify policy implications for China and other countries in dealing with pandemics.Design/methodology/approachThe authors survey 2,408 rural households by telephone from 101 counties across 17 provinces in China during the first stage of the pandemic (March 2020). The authors use the ordered probit model and linear regression model to study the overall impact of policies and then use the quantile regression model and sub-sample regression method to study the heterogeneity of the effects of government policies.FindingsThe authors find that logistics disruption due to lockdown negatively affected rural households. Obstructed logistics is associated with a more significant loss for high-income households, while its impact on the loss expectation of low-income households is more severe. Breeding and other industries such as transport and sales suffer more from logistics than cultivation. The impact of logistics on intensive agricultural entities is more serious than that on professional farms. The government subsidy is more effective at reducing loss for low-income households. Lockdown and government subsidies have shown heterogeneous impacts on rural households.Practical implicationsThe overall economic losses experienced by rural households in the early stages of the pandemic are controllable. The government policies of logistics and subsidies should target specific groups.Originality/valueThe authors evaluate the economic impacts of lockdown and government subsidies on rural households and show their heterogeneity among different groups. The authors further demonstrate the policy effectiveness in supporting rural households during the early stages of the pandemic and provide future policy guidance on major public health event.