bluuebunny/crossref_metadata_2025_split huggingface dataset:
The DUSP1 on CaMKII-positive neurons in mPFC mediates adolescent cocaine exposure-induced higher sensitivity to cocaine during adulthood
Authors: Wei Xiaoyan , Chang Jiasong , Cheng Zhen , Chen Wenwen , Guo Hao , Liu Zhaoyu , Mai Yuning , Hu Tao , Zhang Yuanyuan , Cai Qinglong , Ge Feifei , Fan Yu , Guan Xiaowei 
Published: August 2022

AbstractAdolescent cocaine abuse increases the risk for developing addiction in later life, which remains a big public health concern, but the underlying molecular mechanism is poorly understood. Here, adolescent cocaine-exposed (ACE) male mice models were established by administrating cocaine during adolescent period. When growing to adult age, mice were subjected to conditioned place preference (CPP) to evaluate the sensitivity to cocaine, then potential molecule of dual specificity phosphatase 1 (DUSP1) were screened out by transcriptomic sequencing. Subthreshold dose of cocaine (sdC), that is insufficient to produce CPP, was used to induce CPP in adulthood. The sdC treatment effectively induced CPP in ACE mice during adulthood, accompanied with the more triggered CaMKII-positive neurons, and induced higherDusp1gene, lower DUSP1 protein, lower DUSP1 activity and lower DUSP1 expression on CaMKII-positive neurons (DUSP1CaMKII) in medial prefrontal cortex (mPFC). Overexpressing DUSP1CaMKIIsuppressed CaMKII-positive neuronal activation, and ultimately blocked sdC-induced CPP in ACE mice during adulthood. While, knocking-down DUSP1CaMKIIactivated more CaMKII-positive neurons, and aggravated sdC-preferred behavior in ACE mice during adulthood. ERK1/2 might be potential subsequent signal for DUSP1 in the process. Collectively, our findings reveal a novel molecular mechanism underlying adolescent drug abuse-induced susceptibility to addiction during adulthood, and mPFC DUSP1CaMKIIis a promising pharmacological target to predict or treat addiction, especially caused by adolescent substance use.SummaryAdolescent cocaine exposure causes higher cocaine-preferred behaviors during adulthood, along with evoked mPFC activity in response to cocaine challenge. Locally overexpressing but not knocking-down the dual specificity phosphatase 1 (DUSP1) on CaMKII-positive neurons (DUSP1CaMKII) suppresses mPFC activation, and ultimately rescues the higher sensitivity to cocaine during adulthood.
Anti-tumour efficacy of Musa paradisiaca flower extracts on DMBA induced Mammary carcinogenesis in female Wistar rats
Authors: Lavudi Kousalya , S Hemalatha , Kokkanti Rekha Rani , G.V. S Harika , Patnaik Srinivas , Penchalaneni Josthna 
Published: August 2022

AbstractBackgroundSeveral reports have shown the beneficial advantages of Musa paradisiaca in wound healing activities and other ailments. Previously, our in vitro studies validated the anti-cancer activities of Musa flower extracts and confirmed the potential. This thread has led to our current investigation to explore the anticancer potential in vivo.PurposeThis study focused on the efficacy of banana florets on DMBA induced breast cancer in female wistar rats.MethodsInduction of tumour using Dimethylbenzanthracene (DMBA) in female wistar rats. Hormonal, antioxidant and anticarcinogenic studies were performed in vivo.ResultsIn our current study, we investigated that tumour induction has an effect in disrupting the estrous cycle in mice which may result by hormonal fluctuation levels. Antioxidant and hormonal analysis in vivo revealed the imbalance in estrogen and progesterone levels in untreated group compared to the treated ones. Floral crude extract treatment in vivo has shrunken the tumour volume in flower extract treatment group as well as in standard drug compared to the control. Histopathological staining confirms the disruption of epithelial tissues in tumour induced groups compared to the treated ones. Moreover, Musa floral treatment has shown to revert the damaged tissue morphology in the treated groups compared to the saline treated one. In-vitro studies in MCF-7 and MDA-MB-231 breast cancer cell lines has shown the potent anti-tumorigenic activity using Musa floral extracts.ConclusionTaken together, our finding confirmed that banana flower extracts showcase anti-carcinogenic activity against breast cancer both in vitro and in vivo. Tumour induction in mice has an effect in showing the disruption of estrous cycles.HighlightsMusa paradisiaca crude ethanolic flower extracts have a potential in reducing the tumour growth.DMBA induced cancer has a deleterious effect on estrogen cycles in female wistar rats.Disruption of epithelial morphology was observed in tumour induced wistar rats.Treatment with crude Musa flower extracts on cancer induced rats shows the reduced level of damage and oxidative stress compared to the no treatment group.
Uman Type NF-L Antibodies Are Effective Reagents for the Imaging of Neurodegeneration
Authors: Shaw Gerry , Madorsky Irina , Li Ying , Wang YongSheng , Rana Sabhya , Fuller David D. 
Published: August 2022

AbstractRecent work shows that certain immunological assays for the neurofilament light chain NF-L detect informative signals in the CSF and blood of human and animals affected by a variety of CNS injury and disease states. Much of this work has been performed using two mouse monoclonal antibodies to NF-L, UD1 and UD2, also known as 2.1 and 47.3 respectively. These are the essential components of the Uman Diagnostics NF-Light™ ELISA kit, the Quanterix Simoa™ bead based NF-L assay and others. We show here that the antibodies bind to neighboring epitopes in a short, conserved and unusual peptide in the NF-L “rod” Coil 2 region. We also describe a surprising and useful feature of Uman and similar reagents. While other well characterized NF-L antibodies show robust staining of countless cells and processes in CNS sections from healthy rats, both Uman antibodies reveal only a minor subset of presumably spontaneously degenerating or degenerated neurons and their processes. However following experimental mid-cervical injuries to rat spinal cord both Uman antibodies recognize numerous profiles in tissue sections. The Uman positive material was associated with fiber tracts expected to be damaged by the injury administered and the profiles had the swollen, beaded, discontinuous and sinusoidal morphology expected for degenerating and degenerated processes. We also found that several antibodies to the C terminal “tail” region of NF-L stain undamaged axonal profiles but fail to recognize the Uman positive material. The unmasking of the Uman epitopes and the loss of the NF-L tail epitopes can be mimicked by treating sections from healthy animals with proteases suggesting that the immunological changes we have discovered are due to neurodegeneration induced proteolysis. We have also generated a novel panel of monoclonal and polyclonal antibody reagents directed against the region of NF-L including the Uman epitopes which have staining properties identical to the Uman reagents. Using these we show that the NF-L region to which the Uman reagents bind contains further hidden epitopes distinct from those recognized by the two Uman reagents. We speculate that the Uman type epitopes are part of a binding region important for higher order neurofilament assembly. The work provides important insights into the properties of the NF-L biomarker, describes novel and useful properties of Uman type and NF-L tail binding antibodies and provides a hypothesis relevant to further understanding of neurofilament assembly.
Rational engineering of a β-glucosidase (H0HC94) from glycosyl family I (GH1) to improve catalytic performance on cellobiose
Authors: Sengupta Sauratej , Chanda Pinaki , Manna Bharat , Datta Supratim 
Published: August 2022

AbstractThe conversion of lignocellulosic feedstocks by cellulases to glucose is a critical step in biofuel production. β-glucosidases catalyze the final step in cellulose breakdown, producing glucose, and is often the rate-limiting step in biomass hydrolysis. Rationally engineering previously characterized enzymes may be one strategy to increase catalytic activity and the efficiency of cellulose hydrolysis. The specific activity of most natural and engineered β-glucosidase is higher on the artificial substrate p-Nitrophenyl β-D-glucopyranoside (pNPGlc) than on the natural substrate, cellobiose. Based on our hypothesis of increasing catalytic activity by reducing the interaction of residues present near the active site tunnel entrance with glucose without disturbing any existing interactions with cellobiose, we report an engineered β-glucosidase (Q319A H0HC94) with a 1.8-fold specific activity increase (366.3 ± 36 µmol/min/mg), an almost 1.5-fold increase in kcat (340.8 ± 27 s-1), and a 3-fold increase in Q319A H0HC94 cellobiose specificity (236.65 mM-1 s-1) over HOHC94. Molecular dynamic simulations and protein structure network analysis indicate that Q319A significantly increased the dynamically stable communities and hub residues, leading to a change in enzyme conformation and higher enzymatic activity. This study shows the impact of rational engineering of non-conserved residue to increase β-glucosidase substrate accessibility and enzyme specificity.TOCA rationally engineered β-glucosidase with a 1.5-fold increase in kcat, and a 3-fold increase in cellobiose specificity over the wild-type
Intrinsic neural excitability induces time-dependent overlap of memory engrams
Authors: Delamare Geoffroy , Feitosa Tomé Douglas , Clopath Claudia 
Published: August 2022

AbstractMemories are thought to be stored in neural ensembles known as engrams that are specifically reactivated during memory recall. Recent studies have found that memory engrams of two events that happened close in time tend to overlap in the hippocampus and the amygdala, and these overlaps have been shown to support memory linking. It has been hypothesised that engram overlaps arise from the mechanisms that regulate memory allocation itself, involving neural excitability, but the exact process remains unclear. Indeed, most theoretical studies focus on synaptic plasticity and little is known about the role of intrinsic plasticity, which could be mediated by neural excitability and serve as a complementary mechanism for forming memory engrams. Here, we developed a rate-based recurrent neural network that includes both synaptic plasticity and neural excitability. We obtained structural and functional overlap of memory engrams for contexts that are presented close in time, consistent with experimental studies. Moreover, we showed that enhancing the initial excitability of a subset of neurons just before presenting a context biases the memory allocation to these neurons. We then explored the role of inhibition as a way of controlling competition among neurons from two ensembles. This work suggests mechanisms underlying the role of intrinsic excitability in memory allocation and linking, and yields predictions regarding the dynamics of memory engrams.
CRISPR-Cas-based Microhomology-Mediated End Joining for Precise Gene Replacement in Plant
Authors: Vu Tien Van , Lim Gah-Hyun , Choi Seung Hee , Moon Ju Yeon , Nguyen Ngan Thi , Das Swati , Tran Mil Thi , Sung Yeon Woo , Kim Jihae , Song Young Jong , Kim Suk Weon , Jeong Jae Cheol , Kim Jae-Yean 
Published: August 2022

AbstractPrecise gene or allele replacement is a desirable technology, but implementing it in plants remains challenging. CRISPR-Cas-based approaches, such as gene targeting (GT) and prime editing (PE), have opened up new possibilities for precise gene replacement in plants. However, their editing size and efficiency still need improvement. Recently, strategies using canonical nonhomologous end-joining (cNHEJ) and microhomology-mediated end joining (MMEJ) have been considered promising alternatives for precise gene replacement in yeast and mammals. However, these approaches have not been extensively explored and applied to plants. Here, we proposed and tested a CRISPR-Cas-based tool, termed PREMJ (precision genereplacement viamicrohomology-mediated end joining), for precision gene replacement in plants. The PREMJ strategy employing 20-bp microhomology MMEJ donors (∼100 bp lengths) and a canonical nonhomologous end-joining (cNHEJ) inhibitor, NU7441, produced high targeted gene replacement efficiencies, up to 1.60 ± 0.14, 4.47 ± 1.98, and 8.98 ± 4.73 % in protoplasts of tomato, lettuce, and cabbage, respectively. Our data also revealed the critical impacts of the microhomology length and NU7441 concentration on PREMJ-based precision gene editing in plants. Although obtaining edited plants remains challenging due to inefficient protoplast regenerations andAgrobacterium-mediated delivery, PREMJ may significantly contribute to precision gene editing in plants competent to PREMJ complex delivery and plant regeneration.Key MessageWe designed and tested a method, termed PREMJ, for precise gene replacement using the CRISPR-Cas-mediated double-stranded break (DSB) formation and repairing the DSBs via microhomology-mediated end joining (MMEJ) with MMEJ donor template carrying desired base changes and microhomologies flanking the DSB ends. PREMJ showed feasibility in precise gene replacement in protoplasts of tomatoes, lettuce, and cabbage, albeit its efficacy inAgrobacterium-mediated plant transformation requires further optimization.
High sensitivity single cell RNA sequencing with split pool barcoding
Authors: Tran Vuong , Papalexi Efthymia , Schroeder Sarah , Kim Grace , Sapre Ajay , Pangallo Joey , Sova Alex , Matulich Peter , Kenyon Lauren , Sayar Zeynep , Koehler Ryan , Diaz Daniel , Gadkari Archita , Howitz Kamy , Nigos Maria , Roco Charles M. , Rosenberg Alexander B. 
Published: August 2022

AbstractSingle cell RNA sequencing (scRNA-seq) has become a core tool for researchers to understand biology. As scRNA-seq has become more ubiquitous, many applications demand higher scalability and sensitivity. Split-pool combinatorial barcoding makes it possible to scale projects to hundreds of samples and millions of cells, overcoming limitations of previous droplet based technologies. However, there is still a need for increased sensitivity for both droplet and combinatorial barcoding based scRNA-seq technologies. To meet this need, here we introduce an updated combinatorial barcoding method for scRNA-seq with dramatically improved sensitivity. To assess performance, we profile a variety of sample types, including cell lines, human peripheral blood mononuclear cells (PBMCs), mouse brain nuclei, and mouse liver nuclei. When compared to the previously best performing approach, we find up to a 2.6-fold increase in unique transcripts detected per cell and up to a 1.8-fold increase in genes detected per cell. These improvements to transcript and gene detection increase the resolution of the resulting data, making it easier to distinguish cell types and states in heterogeneous samples. Split-pool combinatorial barcoding already enables scaling to millions of cells, the ability to perform scRNA-seq on previously fixed and frozen samples, and access to scRNA-seq without the need to purchase specialized lab equipment. Our hope is that by combining these previous advantages with the dramatic improvements to sensitivity presented here, we will elevate the standards and capabilities of scRNA-seq for the broader community.
Identification of differentially expressed pyroptosis-related genes in LUAD
Authors: Qian Bao , Jiang Jiuzhou 
Published: August 2022

AbstractBackgroundLung cancer has the highest mortality rate among malignant tumors in the world, and adenocarcinoma, the most important pathological type of lung cancer, accounts for 80%-85% of all lung cancers, causing a significant burden of disease. Pyroptosis is a newly recognized form of programmed cell death (PCD).Methods288 normal tissue data from The Genotype-Tissue Expression (GTEx) database and 501 tumor tissue data from The Cancer Genome Atlas (TCGA) database were selected. Differentially expressed genes were identified between normal and LUAD patients.Results and ConclusionsWith a consensus cluster analysis, 501 LUAD patients were divided into two clusters, and there was a significant difference in survival time between the two clusters. Ten differentially expressed genes were identified, with four up-regulated and six down-regulated. Pyroptosis is closely related to LUAD.
A closed translocation channel in the substrate-free AAA+ ClpXP protease diminishes rogue degradation
Authors: Ghanbarpour Alireza , Cohen Steven E. , Fei Xue , Bell Tristan A. , Baker Tania A. , Davis Joseph H. , Sauer Robert T. 
Published: August 2022

ABSTRACTIntracellular proteases must be specific to avoid degrading the wrong proteins. Here, we present cryo-EM structures of E. coli ClpXP, a AAA+ protease, which reveal that the axial channel of ClpX is closed prior to the binding and subsequent translocation of a protein substrate. An open-channel ClpX mutation stimulates degradation of casein, a non-specific substrate, indicating that channel closure contributes to increased degradation specificity. We demonstrate that ClpX activates ClpP cleavage of a degron-free decapeptide by a channel-independent mechanism, in which the peptide substrate appears to pass through a symmetry mismatched gap in the interface between ClpX and ClpP before entering the degradation chamber via the axial portal of ClpP. The peptide products of ClpXP protein degradation are likely to exit the chamber by the reverse route.
Highly precise genome editing using enhanced CRISPR-Cas12a nickase module
Authors: Kim Chan Hyoung , Kim Hanseop , Lee Youngjeon , Lee Hyomin , Lim Kyung-Seob , Park Sang Je , Huh Jae-Won , Kim Young-Hyun , Lee Dong-Seok , Kim Kyoung Mi , Hur Junho K. , Lee Seung Hwan 
Published: August 2022

AbstractThe authors have withdrawn their manuscript owing to significant changes in content. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Changes of urinary proteome in high-fat dietApoE-/-mice
Authors: Yuanrui Hua , Wenshu Meng , Jing Wei , Yongtao Liu , Youhe Gao 
Published: August 2022

AbstractCardiovascular disease is currently the leading cause of death worldwide. Atherosclerosis is an important pathological basis of cardiovascular disease, and its early diagnosis is of great significance. Urine is more conducive in the accumulation and response of changes in the physiological state of the body and is not regulated by homeostasis mechanisms, so it is a good source of biomarkers in the early stage of disease. In this study,ApoE-/-mice were fed with a high-fat diet for 5 months. Urine samples from the experimental group and control group, which were C57BL/6 mice fed a normal diet, were collected at seven time points. Proteomic analysis was used for internalcontrol and intergroup control. Internal control results showed a significant difference in the urinary proteome before and after a 1-week high-fat diet, and several differential proteins have been reported to be associated with atherosclerosis or for use as candidate biomarkers. The results of the intergroup control indicated that the biological process enriched by the GO analysis of the differential proteins corresponded to the progression of atherosclerosis. Differences in chemical modifications of urinary proteins have also been reported to be associated with the disease. This study demonstrates that urinary proteomics has the potential to monitor changes in the body sensitively and provides the possibility of identifying early biomarkers of atherosclerosis.
Structural analysis of the macrocyclic inhibitor BI-4020 binding to EGFR kinase
Authors: Beyett Tyler S. , Rana Jaimin K. , Schaeffner Ilse K. , Heppner David E. , Eck Michael J. 
Published: August 2022

AbstractA novel macrocyclic inhibitor of mutant EGFR (BI-4020) has shown promise in pre-clinical studies of T790M and C797S drug-resistant non-small cell lung cancer. To better understand the molecular basis for BI-4020 selectivity and potency, we have carried out biochemical activity assays and structural analysis with X-ray crystallography. Biochemical potencies agree with previous studies indicating that BI-4020 is uniquely potent against drug-resistant L858R/T790M and L858R/T790M/C797S variants. Structures show that BI-4020 is likely rendered selective due to interactions with the kinase domain hinge region as well as T790M, akin to Osimertinib. Additionally, BI-4020 is also rendered more potent due to its constrained macrocycle geometry as well as additional H-bonds to conserved K745 and T845 residues in both active and inactive conformations. These findings taken together show how this novel macrocyclic inhibitor is both highly potent and selective for mutant EGFR in a reversible mechanism and motivate structure-inspired approaches to developing targeted therapies in medicinal oncology.
Genome assembly of the acoel flatworm Symsagittifera roscoffensis, a model for research on photosymbiosis
Authors: Martinez Pedro , Ustyantsev Kirill , Biryukov Mikhail , Mouton Stijn , Glasenburg Liza , Sprecher Simon G. , Bailly Xavier , Berezikov Eugene 
Published: August 2022

AbstractSymsagittifera roscoffensis is a well-known member of the order Acoela that lives in symbiosis with the algae Tetraselmis convolutae during its adult stage. Its natural habitat is the eastern coast of the Atlantic, where at specific locations thousands of individuals can be found lying in large pools on the surface of sand at low tide and in the sandy interstitial web at high tide. As a member of the Acoela it has been used as a proxy for early bilaterian animals; however, its phylogenetic position remains debated. In order to understand the basic structural characteristics of the acoel genome, we sequenced and assembled the genome of aposymbiotic S. roscoffensis. The size of S. roscoffensis genome was measured to be in range 910 - 940 Mb. Sequencing of the genome was performed using PacBio Hi-Fi technology. Hi-C and RNA-seq data were also generated to scaffold and annotate the genome. The resulting assembly is 1.1 Gb large (covering 118% of the estimated genome size) and highly continuous, with N50 scaffold size of 1.04 Mb. The repetitive fraction of the genome is 61%, of which 85% (half of the genome) are LTR retrotransposons. Genome-guided transcriptome assembly identified 34,493 genes, of which 29,351 are protein coding (BUSCO score 97.6%), and 30.2% of genes are spliced leader (SL) trans-spliced. The completeness of this genome suggests that it can be used extensively to characterize gene families and conduct accurate phylogenomic reconstructions.SignificanceSymsagittifera is a representative of the phylum Acoela, the first offshoot of bilaterian animals. This key phylogenetic position adds an extra value to the knowledge of its genome, since it will inform us on how the genome of a bilaterian ancestor might have looked like. Moreover, Symsagittifera roscoffensis is a model organism used in symbiogenesis research. Host and algae can be cultured independently and, after mixing, the symbiosis can be followed. Symbiogenesis was established early on during the evolution of Metazoa. In spite of its biological relevance, very little is known on the molecular mechanisms that control it. Here the genome of the acoel host should provide us with insights on the first adaptations to symbiogenesis occurring in bilateral animals.