bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microhomology-Mediated Circular DNA Formation from Oligonucleosomal Fragments During Spermatogenesis
Authors: Hu Jun , Zhang Zhe , Xiao Sai , Cao Yalei , Chen Yinghong , Weng Jiaming , Jiang Hui , Li Wei , Chen Jia-Yu , Liu Chao 
Published: March 2023

AbstractThe landscape of extrachromosomal circular DNA (eccDNA) during mammalian spermatogenesis, as well as the biogenesis mechanism remains to be explored. Here, we revealed widespread eccDNA formation in human sperms and mouse spermatogenesis. We noted that germline eccDNAs are derived from oligonucleosomal DNA fragmentation in cells likely undergoing cell death, providing a potential new way for quality assessment of human sperms. Interestingly, small-sized eccDNAs are associated with euchromatin, while large-sized ones are preferentially generated from heterochromatin. By comparing sperm eccDNAs with meiotic recombination hotspots and structural variations, we found that they are barely associated withde novogermline deletions. We further developed a bioinformatics pipeline to achieve nucleotide-resolution eccDNA detection even with the presence of microhomologous sequences that interfere with precise break-point identification. Empowered by our method, we provided strong evidence to show that microhomology-mediated end joining is the major eccDNA biogenesis mechanism. Together, our results shed lights on eccDNA biogenesis mechanism in mammalian germline cells.
Elucidating Molecular Mechanisms of Protoxin-2 State-specific Binding to the Human NaV1.7 Channel
Authors: Ngo Khoa , Mateos Diego Lopez , Han Yanxiao , Rouen Kyle C. , Ahn Surl-Hee , Wulff Heike , Clancy Colleen E. , Yarov-Yarovoy Vladimir , Vorobyov Igor 
Published: March 2023

AbstractHuman voltage-gated sodium (hNaV) channels are responsible for initiating and propagating action potentials in excitable cells and mutations have been associated with numerous cardiac and neurological disorders. hNaV1.7 channels are expressed in peripheral neurons and are promising targets for pain therapy. The tarantula venom peptide protoxin-2 (PTx2) has high selectivity for hNaV1.7 and serves as a valuable scaffold to design novel therapeutics to treat pain. Here, we used computational modeling to study the molecular mechanisms of the state-dependent binding of PTx2 to hNaV1.7 voltage-sensing domains (VSDs). Using Rosetta structural modeling methods, we constructed atomistic models of the hNaV1.7 VSD II and IV in the activated and deactivated states with docked PTx2. We then performed microsecond-long all-atom molecular dynamics (MD) simulations of the systems in hydrated lipid bilayers. Our simulations revealed that PTx2 binds most favorably to the deactivated VSD II and activated VSD IV. These state-specific interactions are mediated primarily by PTx2’s residues R22, K26, K27, K28, and W30 with VSD as well as the surrounding membrane lipids. Our work revealed important protein-protein and protein-lipid contacts that contribute to high-affinity state-dependent toxin interaction with the channel. The workflow presented will prove useful for designing novel peptides with improved selectivity and potency for more effective and safe treatment of pain.SummaryNaV1.7, a voltage-gated sodium channel, plays a crucial role in pain perception and is specifically targeted by PTx2, which serves as a template for designing pain therapeutics. In this study,Ngo et al.employed computational modeling to evaluate the state-dependent binding of PTx2 to NaV1.7.
Substrate stiffness facilitates improved induced pluripotent stem cell production through modulation of both early and late phases of cell reprogramming
Authors: Chowdhury Mohammad Mahfuz , Zimmerman Samuel , Leeson Hannah , Nefzger Christian Maximilian , Mar Jessica Cara , Laslett Andrew , Polo Jose Maria , Wolvetang Ernst , Cooper-White Justin John 
Published: March 2023

AbstractCell reprogramming involves time-intensive, costly processes that ultimately produce low numbers of reprogrammed cells of variable quality. By screening a range of polyacrylamide hydrogels (pAAm gels) of varying stiffness (1 kPA – 1.3 MPa) we found that a gel of medium stiffness significantly increases the overall number of reprogrammed cells by up to ten-fold with accelerated reprogramming kinetics, as compared to the standard Tissue Culture PolyStyrene (TCPS)-based protocol. We observe that though the gel improves both early and late phases of reprogramming, improvement in the late (reprogramming prone population maturation) phase is more pronounced and produces iPSCs having different characteristics and lower remnant transgene expression than those produced on TCPS. Comparative RNA-Seq analyses coupled with experimental validation reveals that modulation of Bone Morphogenic Protein (BMP) signalling by a novel reprogramming regulator, Phactr3, upregulated in the gel at an earliest time-point without the influence of transcription factors used for reprogramming, plays a crucial role in the improvement in the early reprogramming kinetics and overall reprogramming outcomes. This study provides new insights into the mechanism via which substrate stiffness modulates reprogramming kinetics and iPSC quality outcomes, opening new avenues for producing higher numbers of quality iPSCs or other reprogrammed cells at shorter timescales.
A survey and antibody test following the surge of SARS-CoV-2 Omicron infection in China
Authors: Yao Yichuan , Yang Yunru , Wu Qiqin , Liu Mengyao , Bao Wei , Wang Qiutong , Cheng Meijun , Chen Yunuo , Cai Yuan , Zhang Mei , Yao Jingxue , He Hongliang , Jin Changjiang , Xue Tian , Zheng Changcheng , Jin Tengchuan , Tong Dali 
Published: March 2023

AbstractThe surge of SARS-CoV-2 Omicron infection in most Chinese residents at the end of 2022 provided a unique opportunity to understand how the immune system responds to the Omicron infection in a population with limited contact to prior SARS-CoV-2 variants. Moreover, whether the prototype SARS-CoV-2 booster vaccination could help induce the antibody against Omicron variants? Here, we tested the level of IgG, IgA, and IgM specific to the prototype SARS-CoV-2 spike RBD (Receptor Binding Domain) from the collected blood samples from 636 individuals. Sequential inoculation of different vaccines showed higher IgG levels after infection. As the antibody level against Omicron BA.5, BF.7, and XBB 1.5 of the individuals has highly positive correlation with the antibody level against prototype SARS-CoV2, the IgG level specific to the prototype SARS-CoV-2 spike RBD could also represent the IgG level against Omicron variants. Furthermore, the 4thbooster vaccination could induce a comparable antibody level against prototype, Omicron BA.5, BF.7, and XBB 1.5 variants in the patients with 2 or 3-dose vaccination and protect people from being infected. In conclusion, these data suggest that the prototype SARS-CoV-2 booster vaccination helps induce a high level of antibody against prototype, BA.5, BF.7, and XBB 1.5 variants after Omicron infection.
A biologically plausible decision-making model based on interacting neural populations
Authors: Baspinar Emre , Cecchini Gloria , DePass Michael , Andujar Marta , Pani Pierpaolo , Ferraina Stefano , Moreno-Bote Rubén , Cos Ignasi , Destexhe Alain 
Published: March 2023

AbstractWe present a novel decision-making model with two populations. Each population is composed of Regularly Spiking (excitatory) and Fast Spiking (inhibitory) cells in cortical layer 2/3. Each population votes for one of the two visual alternatives shown on a monitor in human and macaque experiments. The model is biophysically plausible since it is based on long-range cortico-cortical connections between the layer 2/3 populations. These connections are excitatory. They contact both Regularly Spiking and Fast Spiking cells. This long-range excitation is conflicted by an inhibition based on local connections within the populations. This configuration introduces a competition between the layer 2/3 populations, sufficient for making a decision to choose between two alternatives shown on the monitor. We integrate the model with a reward-driven learning mechanism. This allows the model to learn the optimal strategy maximizing the cumulative reward in the long term. We test the model on two decision-making tasks applied on human and macaque. This model elaborates certain biophysical details which were not considered by simpler phenomenological models proposed for similar decision-making tasks. Finally, the model can be embedded in a brain simulator such as The Virtual Brain to study decision-making in terms of large-scale brain dynamics.
Single-cell RNA sequencing identifies KSHV-infected Mesenchymal stem cell subpopulations precursors of Kaposi’s Sarcoma
Authors: Lacunza Ezequiel , Ahuja Anuj , Coso Omar A. , Abba Martin , Mesri Enrique , Naipauer Julian 
Published: March 2023

ABSTRACTKaposi’s sarcoma (KS) may derive from Kaposi’s Sarcoma Herpesvirus (KSHV)-infected human Mesenchymal Stem Cells (hMSCs) migrating into an inflammatory and angiogenic site, enhancing KS initiation. KSHV infection of primary hMSCs uncovers specific cell subpopulations, mechanisms, and conditions involved in the first steps of the KSHV-induced transformation and reprogramming process toward KS progenitor cells. The pro-angiogenic environmental conditions allowed KSHV to reprogram hMSCs closer to KS gene expression profiles and points to KSHV infection as an important factor inducing the Mesenchymal-to-Endothelial (MEndT) transition of hMSC. Single-cell RNA-sequencing analysis revealed a subpopulation of infected cells growing in a pro-angiogenic environment with both viral and host oncogenes upregulation. This highlights the importance of this condition in boosting the KSHV-induced transformation and reprogramming of hMSC towards MEndT and closer to KS gene expression profiles, reinforcing the notion of these cell subpopulations as KS precursors.
Photoreceptor genes in a trechine beetle,Trechiama kuznetsovi, living in the upper hypogean zone
Authors: Niida Takuma , Terashima Yuto , Aonuma Hitoshi , Koshikawa Shigeyuki 
Published: March 2023

AbstractTo address how organisms adapt to a new environment, subterranean organisms whose ancestors colonized subterranean habitats from surface habitats have been studied. Photoreception abilities have been shown to have degenerated in organisms living in caves and calcrete aquifers. Meanwhile, the organisms living in a shallow subterranean environment, which are inferred to reflect an intermediate stage in an evolutionary pathway to colonization of a deeper subterranean environment, have not been studied well. In the present study, we examined the photoreception ability in a trechine beetle,Trechiama kuznetsovi, which inhabits the upper hypogean zone and has a vestigial compound eye. Byde novoassembly of genome and transcript sequences, we were able to identify photoreceptor genes and phototransduction genes. Specifically, we focused onopsingenes, where onelong wavelength opsingene and oneultraviolet opsingene were identified. The encoded amino acid sequences had neither a premature stop codon nor a frameshift mutation, and appeared to be subject to purifying selection. Subsequently, we examined the internal structure of the compound eye and nerve tissue in the adult head, and found potential photoreceptor cells in the compound eye and nerve bundle connected to the brain. The present findings suggest thatT. kuznetsovihas retained the ability of photoreception. This species represents a transitional stage of vision, in which the compound eye regresses, but it may retains the ability of photoreception using the vestigial eye.
Mechanism of barotaxis in marine zooplankton
Authors: Calderón Luis Alberto Bezares , Shahidi Réza , Jékely Gáspár 
Published: March 2023

AbstractHydrostatic pressure is a dominant environmental cue for vertically migrating marine organisms but the physiological mechanisms of responding to pressure changes remain unclear. Here we uncovered the cellular and circuit bases of a barokinetic response in the planktonic larva of the marine annelidPlatynereis dumerilii. Increased pressure induced a rapid, graded and adapting upward swimming response due to the faster beating of cilia in the head multiciliary band. By calcium imaging, we found that brain ciliary photoreceptors showed a graded response to pressure changes. The photoreceptors in animals mutant forciliary opsin-1had a smaller sensory compartment and mutant larvae showed diminished pressure responses. The ciliary photoreceptors synaptically connect to the head multiciliary band via serotonergic motoneurons. Genetic inhibition of the serotonergic cells blocked pressure-dependent increases in ciliary beating. We conclude that ciliary photoreceptors function as pressure sensors and activate ciliary beating through serotonergic signalling during barokinesis.
Tracking the progression of Alzheimer’s disease with peripheral blood monocytes
Authors: Bavykina Viktoriia , Avino Mariano , Husain Mohammed Amir , Zimmer Adrien , Parent-Roberge Hugo , Khalil Abdelouahed , Brunet Marie A. , Fülöp Tamas , Laurent Benoit 
Published: March 2023

AbstractBackgroundAlzheimer’s disease (AD) is the most common form of dementia with the symptoms gradually worsening over the years. However, the driving pathological processes occur well before the appearance of symptoms. AD patients display signs of systemic inflammation, suggesting that it could precede the well-established AD hallmarks. We recently showed that the innate immune response in the form of monocyte activation is detectable at the pre-clinical stage.ObjectivesOur goal here is to characterize changes of gene expression in peripheral blood monocytes from patients at different stages of AD progression and validate potential biomarkers for a better prognosis and diagnosis of AD clinical spectrum.ResultsWe performed a whole transcriptome analysis on monocytes purified from healthy subjects, Mild Cognitive Impairment (MCI) and AD patients, and established the list of genes differentially expressed in monocytes during the disease evolution. We observed that, in the top 500 genes differentially expressed, a majority of these genes were upregulated (65%) during AD progression. These genes are mainly involved in chemokine/cytokine-mediated signaling pathways. We further confirmed several biomarkers by quantitative PCR and immunoblotting and showed that they are often deregulated at pre-clinical stages of the disease (MCI stage), supporting the hyperactivation of monocytes in MCI patients.PerspectivesOur findings provide evidence that the pre-clinical stage of AD can be detected in monocytes using a specific set of biomarkers, highlighting the importance to study the early innate immune response in AD. Our results open the possibility to use these biomarkers with different diagnostic methodologies to better predict and efficiently treat AD.
Discovery of decreased ferroptosis in male colorectal cancer patients with KRAS mutations
Authors: Yan Hong , Talty Ronan , Jain Abhishek , Cai Yuping , Zheng Jie , Shen Xinyi , Muca Engjel , Paty Philip B. , Bosenberg Marcus W. , Khan Sajid A. , Johnson Caroline H. 
Published: March 2023

AbstractAberrant tumor metabolism is a hallmark of cancer in which metabolic rewiring can support tumor growth under nutrient deficient conditions. KRAS mutations occur in 35-45% of all colorectal cancer (CRC) cases and are difficult to treat. The relationship between mutant KRAS and aberrant metabolism in CRCs has not been fully explored and could be a target for intervention. We previously acquired non-targeted metabolomics data from 161 tumor tissues and 39 normal colon tissues from stage I-III chemotherapy naïve CRC patients. In this study, we revealed that tumors from male patients with KRAS mutations only, had several altered pathways that suppress ferroptosis, including glutathione biosynthesis, transsulfuration activity, and methionine metabolism. To validate this phenotype, MC38 CRC cells (KRASG13R) were treated with a ferroptosis inducer; RAS-selected lethal (RSL3). RSL3 altered metabolic pathways in the opposite direction to that seen in KRAS mutant tumors from male patients confirming a suppressed ferroptosis metabolic phenotype in these patients. We further validated gene expression data from an additional CRC patient cohort (Gene Expression Omnibus (GEO), and similarly observed differences in ferroptosis-related genes by sex and KRAS status. Further examination of the relationship between these genes and overall survival (OS) in the GEO cohort showed that KRAS mutant tumors are associated with poorer 5-year OS compared to KRAS wild type tumors, and only in male patients. Additionally, high compared to low expression ofGPX4, FTH1, FTL, which suppressed ferroptosis, were associated with poorer 5-year OS only in KRAS mutant tumors from male CRC patients. Low compared to high expression ofACSL4was associated with poorer OS for this group. Our results show that KRAS mutant tumors from male CRC patients have suppressed ferroptosis, and gene expression changes that suppress ferroptosis associate with adverse outcomes for these patients, revealing a novel potential avenue for therapeutic approaches.
Development and validation of an experimental life support system to study the impact of ultraviolet B radiation and temperature on coral reef microbial communities
Authors: Stuij T.M. , Cleary D.F.R. , Rocha R.J.M. , Polonia A.R.M. , Silva D.A.M. , Frommlet J.C. , Louvado A. , Huang Y. M. , Van der Windt N. , De Voogd N.J. , Gomes N.C.M. 
Published: March 2023

AbstractIn the present study, we developed and validated an experimental life support system (ELSS) designed to investigate the response of coral reef associated bacterial communities to increases in temperature and UVB intensity. The ELSS consisted of 32 independent microcosms, which enables researchers to study the individual and interactive effects of up to three factors using a full factorial experimental design. Temperature can be controlled using water-baths. UV exposure was introduced to the system using UV fluorescent lights. Individual UVB-opaque polyester films were added to the microcosms using a random design. In the validation experiment (stable temperature and no UVB), a coral reef environment was simulated using a layer of coral reef sediment, synthetic seawater, and specimens from five benthic reef species. The species used were two hard coralsMontipora digitataandMontipora capricornis, a soft coralSarcophyton glaucum, a zoanthidZoanthussp., and a spongeChondrillasp.. To validate the system, we assessed physical and chemical parameters and characterised host and free-living bacterial communities of the ELSS over 34 days and compared these data to those observed in natural reef ecosystems. Water temperature, dissolved oxygen, pH, salinity and dissolved nutrients in the ELSS were similar to those at shallow coral reef sites. Sediment bacterial diversity and composition were more similar to natural-type communities at day 29 and 34 than at day 8 after transfer to the microcosms, indicating a return to natural-type conditions following an initial, apparent perturbation phase. Transplantation significantly altered the bacterial community composition ofM. digitataandChondrillasp. and increased coral photosynthetic efficiency compared to before transplantation. These results highlight the importance ofM. digitataandChondrillasp. microbiomes to host adaptation following potential stress events.. Altogether, our results validated the suitability of the ELLS developed in this study as a model system to investigate the responses of coral reef associated bacterial communities to shifts of temperature and UVB radiation and potentially other environmental conditions (e.g., environmental pollution).
Rapid molecular phenotypic antimicrobial susceptibility test forNeisseria gonorrhoeaebased on propidium monoazide viability PCR
Authors: Tjandra Kristel C. , Ram-Mohan Nikhil , Abe Ryuichiro , Wang Tza-Huei , Yang Samuel 
Published: March 2023

AbstractNeisseria gonorrhoeae(NG) is an urgent threat to antimicrobial resistance (AMR) worldwide. NG has acquired rapid resistance to all previously recommended treatments leaving ceftriaxone monotherapy as the first and last line of therapy for uncomplicated NG. The ability to rapidly determine susceptibility, which is currently nonexistent for NG, has been proposed as a strategy to preserve ceftriaxone by using alternative treatments. Herein, we used a DNA-intercalating dye in combination with NG-specific primers/probes to generate qPCR cycle threshold (Ct) values at different concentrations of 2 NG-relevant antimicrobials. Our proof of concept dual-antimicrobial logistic regression model based on the differential Ct measurements achieved an AUC of 0.93 with a categorical agreement for susceptibility of 84.6%. When surveying the performance against each antimicrobial separately, the model predicted 90% and 75% susceptible and resistant strains respectively to ceftriaxone and 66.7% and 83.3% susceptible and resistant strains respectively to ciprofloxacin. We further validated the model against the individual replicates and determined the accuracy of the model in classifying susceptibility agnostic of the inoculum size. We demonstrated a novel PCR-based approach to determine phenotypic ciprofloxacin and ceftriaxone susceptibility information for NG with reasonable accuracy in under 30 min, a significant improvement compared to the conventional method which takes 3 days.Table of Content Graphic
Repurposing host-guest chemistry to sequester virulence and eradicate biofilms in multidrug resistantPseudomonas aeruginosaandAcinetobacter baumannii
Authors: Jonkergouw Christopher , Beyeh Ngong Kodiah , Osmekhina Ekaterina , Leskinen Katarzyna , Taimoory S. Maryamdokht , Federov Dmitrii , Anaya-Plaza Eduardo , Kostiainen Mauri A. , Trant John F. , Ras Robin H. A. , Saavalainen Päivi , Linder Markus B. 
Published: March 2023

AbstractThe limited diversity in targets of available antibiotic therapies has put tremendous pressure on the treatment of bacterial pathogens, where numerous resistance mechanisms that counteract their function are becoming increasingly prevalent. Here, we utilize an unconventional anti-virulence screen of host-guest interacting macrocycles, and identify a water-soluble synthetic macrocycle, Pillar[5]arene, that is non-bactericidal/bacteriostatic and has a mechanism of action that involves binding to both homoserine lactones and lipopolysaccharides, key virulence factors in Gram-negative pathogens. Pillar[5]arene is active against Top Priority carbapenem- and third/fourth-generation cephalosporin-resistantPseudomonas aeruginosaandAcinetobacter baumannii, suppressing toxins and biofilms and increasing the penetration and efficacy of standard-of-care antibiotics in combined administrations. The binding of homoserine lactones and lipopolysaccharides also sequesters their direct effects as toxins on eukatryotic membranes, neutralizing key tools that promote bacterial colonization and impede immune defenses, bothin vitroandin vivo. Pillar[5]arene evades both existing antibiotic resistance mechanisms, as well as the build-up of rapid tolerance/resistance. The versatility of macrocyclic host-guest chemistry provides ample strategies for tailored targeting of virulence in a wide range of Gram-negative infectious diseases.