bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ginsentide TP1 Protects Hypoxia-Induced Dysfunction and ER Stress-Linked Apoptosis
Authors: Dutta Bamaprasad , Loo Shining , Kam Antony , Sze Siu Kwan , Tam James P. 
Published: April 2023

AbstractHypoxia-induced vascular endothelial dysfunction (VED) is a significant contributor to several severe human conditions, including heart disease, stroke, dementia, and cancer. However, current treatment options for VED are limited due to a lack of understanding of the underlying disease mechanisms and therapeutic leads. We recently discovered a heat-stable microprotein in ginseng, known as ginsentide TP1 that has been shown to reduce vascular dysfunction in cardiovascular disease models. In this study, we use a combination of functional assays and quantitative pulsed SILAC proteomics to determine new proteins synthesized in hypoxia and to show that ginsentide TP1 provides protection for human endothelial cells against hypoxia and ER stress. We found that hypoxia activates various pathways related to endothelium activation and monocyte adhesion, which in turn, impairs nitric oxide (NO) synthase activity, reduces NO bioavailability, and increases the production of reactive oxygen species that contribute to VED. Additionally, hypoxia triggers endoplasmic reticulum stress and initiates apoptotic signaling pathways associated with cardiovascular pathology. Treatment with ginsentide TP1 reduced surface adhesion molecule expression prevented activation of the endothelium and leukocyte adhesion, restored protein hemostasis, and reduced ER stress to protect against hypoxia-induced cell death. Ginsentide TP1 also restored NO signaling and bioavailability, reduced oxidative stress, and protected endothelial cells from endothelium dysfunction. In conclusion, this study shows that the molecular pathogenesis of VED induced by hypoxia can be mitigated by treatment with ginsentide TP1, which could be one of the key bioactive compounds responsible for the “cure-all” effect of ginseng. This research may lead to the development of new therapies for cardiovascular disorders.
The Impact of Chronic Phthalate Exposure on Rodent Anxiety and Cognition
Authors: Yu Zhe , Iyer Laxmi , Swiercz Adam P. , Paronett Elizabeth , Ramadan Manelle , Marvar Paul J. , Posnack Nikki Gillum 
Published: April 2023

AbstractThere is a growing importance for environmental contributions to psychiatric disorders and understanding the impact of the exposome (i.e., pollutants and toxins). Increased biomonitoring and epidemiological studies, for example, suggest that daily phthalate chemical exposure contribute to neurological and behavioral abnormalities, however these mechanisms remain poorly understood. The current study therefore aimed to examine the effects of chronic phthalate exposure on rodent anxiety behaviors, cognition, and the impact on hypothalamic-pituitary­ adrenal (HPA)-axis function. Adult male mice (C57BL6/J) were administered mono-2-ethylhexyl phthalate (MEHP) via drinking water (1 mg/ml), and anxiety-like behavior, cognition combined with HPA- axis and inflammatory assays were assessed after 3 weeks of MEHP exposure. MEHP-treated mice exhibited enhanced generalized anxiety-like behaviors, as demonstrated by reduced time spent in the open-arm of the elevated plus maze (EPM) and center exploration in the open field (OF). Tests of spatial, cognition and memory function were unchanged. Following MEHP administration, circulating levels of corticosterone and pro­ inflammatory cytokines were significantly increased, while at the tissue level, MEHP-dependent reductions in glucocorticoid metabolism genes 11β-hydroxysteroid dehydrogenase (11β-HSD) 1 and 2. These data suggest that chronic MEHP exposure leads to enhanced generalized-anxiety behaviors independent of rodent measures of cognition and memory, which maybe driven by MEHP-dependent effects on HPA-axis and peripheral glucocorticoid metabolism function.
An integrated single-cell RNA-seq map of human neuroblastoma tumors and preclinical models uncovers divergent mesenchymal-like gene expression programs
Authors: Chapple Richard H. , Liu Xueying , Natarajan Sivaraman , Alexander Margaret I.M. , Kim Yuna , Patel Anand G. , LaFlamme Christy W. , Pan Min , Wright William C. , Lee Hyeong-Min , Zhang Yinwen , Lu Meifen , Koo Selene C. , Long Courtney , Harper John , Savage Chandra , Johnson Melissa D. , Confer Thomas , Akers Walter J. , Dyer Michael A. , Sheppard Heather , Easton John , Geeleher Paul 
Published: April 2023

ABSTRACTNeuroblastoma is a common pediatric cancer, where preclinical studies suggest that a mesenchymal-like gene expression program contributes to chemotherapy resistance. However, clinical outcomes remain poor, implying we need a better understanding of the relationship between patient tumor heterogeneity and preclinical models. Here, we generated single-cell RNA-seq maps of neuroblastoma cell lines, patient-derived xenograft models (PDX), and a genetically engineered mouse model (GEMM). We developed an unsupervised machine learning approach (‘automatic consensus nonnegative matrix factorization’ (acNMF)) to compare the gene expression programs found in preclinical models to a large cohort of patient tumors. We confirmed a weakly expressed, mesenchymal-like program in otherwise adrenergic cancer cells in some pre-treated high-risk patient tumors, but this appears distinct from the presumptive drug-resistance mesenchymal programs evident in cell lines. Surprisingly however, this weak-mesenchymal-like program was maintained in PDX and could be chemotherapy-induced in our GEMM after only 24 hours, suggesting an uncharacterized therapy-escape mechanism. Collectively, our findings improve the understanding of how neuroblastoma patient tumor heterogeneity is reflected in preclinical models, provides a comprehensive integrated resource, and a generalizable set of computational methodologies for the joint analysis of clinical and pre-clinical single-cell RNA-seq datasets.
Identification of Mirror Repeats in Viral Genomes using FPCB Analysis
Authors: Yadav Pooja , Kumari Jyoti , Yadav Priyanka , Yadav Rachna , Yadav Shivani , Sharma Dinesh , Singh Amrita , Sehrawat Barkha , Yadav Manisha , Yadav Sandeep 
Published: April 2023

AbstractThe majority of living domains consist of DNA as genetic material with the minor exception of viruses. The unique nature of every species determines by its unique pattern of genome or gene products. The genomic features become an evident example of evolutionary study also. Different types of repeat patterns are observed in genomes of living domains including human beings whose two third portion of the genome is repetitive. Among the varied type of repeat sequences Mirror Repeats (MR) play crucial roles at the genetic level in every species. The major focus of our research is on identification & to check the distribution of mirror repeat. For this, we employed a bioinformatics-based approach refer as FASTA PARALLEL COMPLEMENT BLAST (FPCB) to identify unique mirror repeat (MR) sequences in some selected viral genomes from three different categories (Animal, Plant & Human). The identified repeats vary in their length as well as found to be distributed throughout the selected viral genomes. The maximum no of MR were reported in the case of Dengue virus (229) & minimum is in the case of TMV (97). In the remaining selected viruses - HCV, HPV, HTLV-1, PVY, Rabies virus 178, 156, 175, 203 & 204 MR sequences were reported. These sequences can be utilized in many ways like in molecular diagnosis, drug delivery target as well as evolutionary study, etc. The present research also helps in the development of novel tools of bioinformatics to study mirror repeats and their functional perspective in the context of their occurrence in all domains.
A cell-free strategy for profiling intracellular antibiotic sensitivity and resistance
Authors: Chengan Kameshwari , Hind Charlotte , Nagappa Lakshmeesha , Wand Matthew E. , Hanson Tanith , Escolano Ruben Martin , Tsaousis Anastasios , Bengoechea José A , Mark Sutton J. , Smales Christopher M , Moore Simon J 
Published: April 2023

AbstractAntimicrobial resistance (AMR) is a pandemic spread across multiple priority infectious disease threats. While the cell envelope plays a key role in AMR, this also makes it challenging to study how antibiotics function inside the cell. Herein, we present aKlebsiella pneumoniaecell-free gene expression (CFE) platform for the rapid profiling of intracellular antibiotic sensitivity and resistance. This cell-free approach provides the unique macromolecular and metabolite components from this microbe, which include multiple antibiotic targets from transcription, translation, and metabolic processes. First, we compare theK. pneumoniaeCFE system to whole cell antimicrobial assays. We find that several antibiotic classes show higher sensitivity in the CFE system, suggesting limitations in antibiotic transport in the whole cell assay. Next, we evolvedK. pneumoniaestrains with resistance to specific antibiotics and use whole genome sequencing analysis for genotyping. As an exemplary case, we show that a single RNA polymerase beta subunit variant H526L (also frequently found in multidrug resistantMycobacterium tuberculosis) confers a 58-fold increase in CFE resistance to rifampicin. Overall, we describe a safe (i.e., non-living, non-pathogenic) platform suitable for studying an infectious disease model in a Containment Level 1 laboratory. Our CFE strategy is generalisable to laboratory and clinicalK. pneumoniaestrains and provides a new experimental tool to profile intracellular AMR variants. In conclusion, our CFE tool provides a significant advance towards understanding AMR and complements wider infectious disease studies.
Pan-cancer analysis reveals tumor microbiome associations with host molecular aberrations
Authors: Ma Chenchen , Su Changxing , Li Jiaxuan , Qu Jiuxin , Shuai Shimin 
Published: April 2023

AbstractHost-microbiome interaction is known to play a pivotal role in the cancer ecosystem, yet the associations have not been systematically investigated at the pan-cancer and the multi-omics level. Here, we evaluated nearly 10,000 samples across 32 cancer types collected from The Cancer Genome Atlas (TCGA), to investigate the association between the tumor microbiome (taxa, n=1,630) and tumor microenvironment composition (cell types, n=20), epigenome (CpG island methylation, n=30,716), transcriptome (gene expression, n=10,216) and proteome (protein expression, n=193). We identified 836,738 candidate associations between the tumor microbiome and host molecular aberrations across multiple cancers. Besides cancer-specific associations, we also revealed recurrent pan-cancer associations between microbes (Lachnoclostridium,Flammeovirga,TerrabacterandCampylobacter) and immune cells, as well as between microbes (CollimonasandSutterella) and fibroblasts, which were further validated by cell type estimations derived from pathological images and methylation data. We also identified several potential microbe and gene/protein expression associations mediated by DNA methylation using the sequential mediation analysis. Furthermore, our survival analysis demonstrated that tumor microbes may affect the patient’s overall survival and progression-free survival. Finally, a user-friendly web portal, Multi-Omics and Microbiome Associations in Cancer (MOMAC) was constructed for users to explore potential host-microbe interactions in cancer.Graphical abstract
What is a rhythm for the brain? The impact of contextual temporal variability on auditory perception
Authors: Bonnet Pierre A , Bonnefond Mathilde , Kösem Anne 
Published: April 2023

AbstractTemporal predictions can be formed and impact perception when sensory timing is fully predictable: for instance, the detection of a target sound is enhanced if it is presented on the beat of an isochronous rhythm. However, natural sensory stimuli, like speech or music, are not entirely predictable, but still possess statistical temporal regularities. We investigated whether temporal expectations can be formed in non-fully predictable contexts, and how the temporal variability of sensory contexts affects auditory perception. Specifically, we asked how “rhythmic” an auditory stimulation needs to be in order to observe temporal predictions effects on auditory discrimination performances. In this behavioral auditory oddball experiment, participants listened to auditory sound sequences where the temporal interval between each sound was drawn from gaussian distributions with distinct standard deviations. Participants were asked to discriminate sounds with a deviant pitch in the sequences. Auditory discrimination performances, as measured with deviant sound discrimination accuracy and response times, progressively declined as the temporal variability of the sound sequence increased. Temporal predictability effects ceased to be observed only for the more variable contexts. Moreover, both global and local temporal statistics impacted auditory perception, suggesting that temporal statistics are promptly integrated to optimize perception. Altogether, these results suggests that temporal predictions can be set up quickly based on the temporal statistics of past sensory events and are robust to a certain amount of temporal variability. Therefore, temporal predictions can be built on sensory stimulations that are not purely periodic nor temporally deterministic.Significance statementThe perception of sensory events is known to be enhanced when their timing is fully predictable. However, it is unclear whether temporal predictions are robust to temporal variability, which is naturally present in many auditory signals such as speech and music. In this behavioral experiment, participants listened to auditory sound sequences where the timing between each sound was drawn from distinct gaussian distributions. Participant’s ability to discriminate deviant sounds in the sequences was function of the temporal statistics of past events: auditory deviant discrimination progressively declined as the temporal variability of the sound sequence increased. Results therefore suggest that auditory perception is sensitive to prediction mechanisms that are involved even if temporal information is not totally predictable.
Biomechanics Characterization of Autonomic and Somatic Nerves by High Dynamic Closed-Loop MEMS force sensing
Authors: González-González María Alejandra , Alemansour Hammed , Maroufi Mohammad , Coskun Mustafa Bulut , Lloyd David , Moheimani S. O. Reza , Romero-Ortega Mario I. 
Published: April 2023

AbstractThe biomechanics of peripheral nerves are determined by the blood-nerve barrier (BNB), together with the epineural barrier, extracellular matrix, and axonal composition, which maintain structural and functional stability. These elements are often ignored in the fabrication of penetrating devices, and the implant process is traumatic due to the mechanical distress, compromising the function of neuroprosthesis for sensory-motor restoration in amputees. Miniaturization of penetrating interfaces offers the unique opportunity of decoding individual nerve fibers associated to specific functions, however, a main issue for their implant is the lack of high-precision standardization of insertion forces. Current automatized electromechanical force sensors are available; however, their sensitivity and range amplitude are limited (i.e. mN), and have been tested onlyin-vitro. We previously developed a high-precision bi-directional micro-electromechanical force sensor, with a closed-loop mechanism (MEMS-CLFS), that while measuring with high-precision (−211.7μN to 211.5μN with a resolution of 4.74nN), can be used in alive animal. Our technology has an on-chip electrothermal displacement sensor with a shuttle beam displacement amplification mechanism, for large range and high-frequency resolution (dynamic range of 92.9 dB), which eliminates the adverse effect of flexural nonlinearity measurements, observed with other systems, and reduces the mechanical impact on delicate biological tissue. In this work, we use the MEMS-CLFS forin-vivobidirectional measurement of biomechanics in somatic and autonomic nerves. Furthermore we define the mechanical implications of irrigation and collagen VI in the BNB, which is different for both autonomic and somatic nerves (∼ 8.5-8.6 fold density of collagen VI and vasculature CD31+ in the VN vs ScN). This study allowed us to create a mathematical approach to predict insertion forces. Our data highlights the necessity of nerve-customization forces to prevent injury when implanting interfaces, and describes a high precision MEMS technology and mathematical model for their measurements.
Fibronectin, DHPS and SLC3A2 Signaling Cooperate to Control Tumor Spheroid Growth, Subcellular eIF5A1/2 Distribution and CDK4/6 Inhibitor Resistance
Authors: Geller Cameron , Maddela Joanna , Tuplano Ranel , Runa Farhana , Adamian Yvess , Güth Robert , Soto Gabriela Ortiz , Tomaneng Luke , Cantor Joseph , Kelber Jonathan A. 
Published: April 2023

ABSTRACTExtracellular matrix (ECM) protein expression/deposition within and stiffening of the breast cancer microenvironment facilitates disease progression and correlates with poor patient survival. However, the mechanisms by which ECM components control tumorigenic behaviors and responses to therapeutic intervention remain poorly understood. Fibronectin (FN) is a major ECM protein controlling multiple processes. In this regard, we previously reported that DHPS-dependent hypusination of eIF5A1/2 is necessary for fibronectin-mediated breast cancer metastasis and epithelial to mesenchymal transition (EMT). Here, we explored the clinical significance of an interactome generated using hypusination pathway components and markers of intratumoral heterogeneity. Solute carrier 3A2 (SLC3A2 or CD98hc) stood out as an indicator of poor overall survival among patients with basal-like breast cancers that express elevated levels of DHPS. We subsequently discovered that blockade of DHPS or SLC3A2 reduced triple negative breast cancer (TNBC) spheroid growth. Interestingly, spheroids stimulated with exogenous fibronectin were less sensitive to inhibition of either DHPS or SLC3A2 – an effect that could be abrogated by dual DHPS/SLC3A2 blockade. We further discovered that a subset of TNBC cells responded to fibronectin by increasing cytoplasmic localization of eIF5A1/2. Notably, these fibronectin-induced subcellular localization phenotypes correlated with a G0/G1 cell cycle arrest. Fibronectin-treated TNBC cells responded to dual DHPS/SLC3A2 blockade by shifting eIF5A1/2 localization back to a nucleus-dominant state, suppressing proliferation and further arresting cells in the G2/M phase of the cell cycle. Finally, we observed that dual DHPS/SLC3A2 inhibition increased the sensitivity of both Rb-negative and -positive TNBC cells to the CDK4/6 inhibitor palbociclib. Taken together, these data identify a previously unrecognized mechanism through which extracellular fibronectin controls cancer cell tumorigenicity by modulating subcellular eIF5A1/2 localization and provides prognostic/therapeutic utility for targeting the cooperative DHPS/SLC3A2 signaling axis to improve breast cancer treatment responses.
Reproducible and fully automated testing of nocifensive behavior in mice
Authors: Dedek Christopher , Azadgoleh Mehdi A. , Prescott Steven A. 
Published: April 2023

ABSTRACTPain in rodents is often inferred from their withdrawal to noxious stimulation, using the threshold stimulus intensity or response latency to quantify pain sensitivity. This usually involves applying stimuli by hand and measuring responses by eye, which limits reproducibility and throughput to the detriment of preclinical pain research. Here, we describe a device that standardizes and automates pain testing by providing computer-controlled aiming, stimulation, and response measurement. Optogenetic and thermal stimuli are applied to the hind paw using blue and infrared light, respectively. Red light delivered through the same light path assists with aiming, and changes in its reflectance off the paw are used to measure paw withdrawal latency with millisecond precision at a fraction of the cost and data processing associated with high-speed video. Using standard video, aiming was automated by training a neural network to recognize the paws and move the stimulator using motorized linear actuators. Real-time data processing allows for closed-loop control of stimulus initiation and termination. We show that stimuli delivered with this device are significantly less variable than hand-delivered stimuli, and that reducing stimulus variability is crucial for resolving stimulus-dependent variations in withdrawal. Slower stimulus waveforms whose stable delivery is made possible with this device reveal details not evident with typical photostimulus pulses. Moreover, the substage video reveals a wealth of “spontaneous” behaviors occurring before and after stimulation that can considered alongside withdrawal metrics to better assess the pain experience. Automation allows comprehensive testing to be standardized and carried out efficiently.
A time for every purpose: using time-dependent sensitivity analysis to help understand and manage dynamic ecological systems
Authors: Ng Wee Hao , Myers Christopher R. , McArt Scott , Ellner Stephen P. 
Published: April 2023

AbstractSensitivity analysis is often used to help understand and manage ecological systems, by assessing how a constant change in vital rates or other model parameters might affect the management outcome. This allows the manager to identify the most favorable course of action. However, realistic changes are often localized in time—for example, a short period of culling leads to a temporary increase in the mortality rate over the period. Hence, knowing when to act may be just as important as knowing what to act upon. In this article, we introduce the method of time-dependent sensitivity analysis (TDSA) that simultaneously addresses both questions. We illustrate TDSA using three case studies: transient dynamics in static disease transmission networks, disease dynamics in a reservoir species with seasonal life-history events, and endogenously-driven population cycles in herbivorous invertebrate forest pests. We demonstrate how TDSA often provides useful biological insights, which are understandable on hindsight but would not have been easily discovered without the help of TDSA. However, as a caution, we also show how TDSA can produce results that mainly reflect uncertain modeling choices and are therefore potentially misleading. We provide guidelines to help users maximize the utility of TDSA while avoiding pitfalls.
Benchmarking cassette-based deep mutagenesis by Golden Gate assembly
Authors: Daffern Nicolas , Francino-Urdaniz Irene , Baumer Zachary T. , Whitehead Timothy A. 
Published: April 2023

AbstractProtocols for the construction of large, deeply mutagenized protein encoding libraries via Golden Gate assembly of synthetic DNA cassettes employ disparate, system specific methodology. Here we benchmark a broadly applicable Golden Gate method for building user-defined libraries. We demonstrate that a 25 μl reaction, using 40 fmol of input DNA, can generate a library on the order of 1×106members and that reaction volume or input DNA concentration can be scaled up with no losses in transformation efficiency. Such libraries can be constructed from dsDNA cassettes generated either by degenerate oligonucleotides or oligo pools. We demonstrate its real-world effectiveness by building custom, user-defined libraries on the order of 104to 107unique protein encoding variants for two orthogonal protein engineering systems. We include a detailed protocol and provide several general-use destination vectors.