bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative and temporal measurement of dynamic autophagy rates
Authors: Beesabathuni Nitin Sai , Shah Priya S. 
Published: December 2021

AbstractAutophagy is a multistep degradative process that is essential for maintaining cellular homeostasis. Systematically quantifying flux through this pathway is critical for gaining fundamental insights and effectively modulating this process that is dysregulated during many diseases. Established methods to quantify flux use steady state measurements, which provide limited information about the perturbation and the cellular response. We present a theoretical and experimental framework to measure autophagic steps in the form of rates under non-steady state conditions. We use this approach to measure temporal responses to rapamycin and wortmannin treatments, two commonly used autophagy modulators. We quantified changes in autophagy rates in as little as 10 minutes, which can establish direct mechanisms for autophagy perturbation before feedback begins. We identified concentration-dependent effects of rapamycin on the initial and temporal progression of autophagy rates. We also found variable recovery time from wortmannin’s inhibition of autophagy, which is further accelerated by rapamycin. In summary, this new approach enables the quantification of autophagy flux with high sensitivity and temporal resolution and facilitates a comprehensive understanding of this process.
Validating EEG, MEG and combined MEG and EEG beamforming for an estimation of the epileptogenic zone in focal cortical dysplasia
Authors: Neugebauer Frank , Antonakakis Marios , Unnwongse Kanjana , Parpaley Yaroslav , Wellmer Jörg , Rampp Stefan , Wolters Carsten H. 
Published: December 2021

AbstractMEG and EEG source analysis is frequently used for the presurgical evaluation of pharma-coresistant epilepsy patients. The source localization of the epileptogenic zone depends, among other aspects, on the selected inverse and forward approaches and their respective parameter choices. In this validation study, we compare for the inverse problem the standard dipole scanning method with two beamformer approaches and we investigate the influence of the covariance estimation method and the strength of regularization on the localization performance for EEG, MEG and combined EEG and MEG. For forward modeling, we investigate the difference between calibrated six-compartment and standard three-compartment head modeling. In a retrospective study of two patients with focal epilepsy due to focal cortical dysplasia type IIb and seizure-freedom following lesionectomy or radiofrequency-guided thermocoagulation, we used the distance of the localization of interictal epileptic spikes to the resection cavity resp. rediofrequency lesion as reference for good localization. We found that beamformer localization can be sensitive to the choice of the regularization parameter, which has to be individually optimized. Estimation of the covariance matrix with averaged spike data yielded more robust results across the modalities. MEG was the dominant modality and provided a good localization in one case, while it was EEG for the other. When combining the modalities, the good results of the dominant modality were mostly not spoiled by the weaker modality. For appropriate regularization parameter choices, the beamformer localized better than the standard dipole scan. Compared to the importance of an appropriate regularization, the sensitivity of the localization to the head modeling was smaller, due to similar skull conductivity modeling and the fixed source space without orientation constraint.
In-hospital mortality due to breakthrough COVID-19 among recipients of COVISHIELD (ChAdOx nCoV-19) and COVAXIN (BBV152)
Authors: Suri Tejas M , Ghosh Tamoghna , Arunachalam M , Vadala Rohit , Vig Saurabh , Bhatnagar Sushma , Mohan Anant 
Published: December 2021

AbstractBackgroundMultiple vaccines have received emergency-use authorization in different countries in the fight against the COVID-19 pandemic. India had started its vaccination campaign using the COVISHIELD (ChAdOx nCoV-19) and the COVAXIN (BBV152) vaccines. However, there is a lack of head-to-head comparisons of the different vaccines.MethodsWe performed a retrospective cohort study during the second wave of the pandemic in India with predominant circulation of the delta strain of SARS-CoV-2. We enrolled adult patients who were hospitalized with breakthrough COVID-19 infection after vaccination. We compared in-hospital outcomes between patients who had received the COVISHIELD (n=181) or COVAXIN vaccines.ResultsBetween April and June 2021, a total of 353 patients were enrolled, among whom 181 (51.3%) received COVAXIN (156 partially vaccinated and 25 fully vaccinated) and 172 (48.7%) received COVISHIELD (155 partially vaccinated and 17 fully vaccinated). The in-hospital mortality did not differ between the recipients of COVISHIELD or COVAXIN in either the fully vaccinated [2 deaths (11.8%) vs 0 deaths (0%), respectively p=0.08] or the partially vaccinated cohorts [31 deaths (20%) vs 28 deaths (17.9%), respectively, p=0.65].ConclusionsPatients who are hospitalized with breakthrough COVID-19 had similar in-hospital outcome irrespective of whether they received COVISHIELD or COVAXIN.
Impaired LAIR-1-mediated immune control due to collagen degradation in fibrosis
Authors: Carvalheiro Tiago , Marut Wioleta , Pascoal Ramos M. Inês , García Samuel , Fleury Devan , Affandi Alsya J. , Meijers Aniek S. , Giovannone Barbara , Tieland Ralph G. , Elshof Eline , Ottria Andrea , Cossu Marta , Meizlish Matthew L. , Veenendaal Tineke , Ramanujam Meera , Moreno-García Miguel E. , Klumperman Judith , Liv Nalan , Radstake Timothy R.D.J. , Meyaard Linde 
Published: December 2021

AbstractTissue repair is disturbed in fibrotic diseases like systemic sclerosis (SSc), where the deposition of large amounts of extracellular matrix components such as collagen interferes with organ function. LAIR-1 is an inhibitory collagen receptor highly expressed on tissue immune cells. We questioned whether in SSc, impaired LAIR-1-collagen interaction is contributing to the ongoing inflammation and fibrosis.We found that SSc patients do not have an intrinsic defect in LAIR-1 expression or function. Instead, fibroblasts from SSc patients deposit disorganized collagen productsin vitro, which are dysfunctional LAIR-1 ligands. This can be mimicked in healthy fibroblasts stimulated by soluble factors that drive inflammation and fibrosis in SSc and is dependent of matrix metalloproteinases and platelet-derived growth factor receptor signaling.In support of a non-redundant role of LAIR-1 in the control of fibrosis, we found that LAIR-1-deficient mice have increased skin fibrosis in response to repeated injury and in the bleomycin mouse model for SSc. Thus, LAIR-1 represents an essential control mechanism for tissue repair. In fibrotic disease, excessive collagen degradation may lead to a disturbed feedback loop. The presence of functional LAIR-1 in patients provides a therapeutic opportunity to reactivate this intrinsic negative feedback mechanism in fibrotic diseases.
Decoupling growth and production by removing the origin of replication from a bacterial chromosome
Authors: Kasari Marje , Kasari Villu , Kärmas Mirjam , Jõers Arvi 
Published: December 2021

AbstractEfficient production of biochemicals and proteins in cell factories frequently benefits from a two-stage bioprocess in which growth and production phases are decoupled. Here we describe a novel growth switch based on the permanent removal of the origin of replication (oriC) from the Escherichia coli chromosome. Without oriC, cells cannot initiate a new round of replication and they stop growing while their metabolism remains active. Our system relies on a serine recombinase from bacteriophage phiC31 whose expression is controlled by the temperature-sensitive cI857 repressor from phage lambda. Reporter protein expression in switched cells continues after cessation of growth, leading to protein levels up to five times higher compared to non-switching cells. Switching induces a unique physiological state that is different from both normal exponential and stationary phases. Switched cells remain in this state even when not growing, retain their protein synthesis capacity, and do not induce proteins associated with the stationary phase. Our switcher technology is potentially useful for a range of products and applicable in many bacterial species for decoupling growth and production.
A single nucleotide variant in the PPARγ-homologEip75Baffects fecundity inDrosophila
Authors: Hoedjes Katja M , Kostic Hristina , Flatt Thomas , Keller Laurent 
Published: December 2021

ABSTRACTSingle nucleotide polymorphisms are the most common type of genetic variation, but how these variants contribute to the evolutionary adaptation of complex phenotypes is largely unknown. Experimental evolution and genome-wide association studies have demonstrated that variation in the PPARg-homologEip75Bis associated with longevity and life-history differences in the fruit flyDrosophila melanogaster. Using RNAi knockdown, we first demonstrate that reduced expression ofEip75Bin adults affects lifespan, egg-laying rate and egg volume. We then tested the effect of a naturally occurring SNP variant within a cis-regulatory domain ofEip75Bby applying two complementary approaches: a Mendelian randomization approach using lines of theDrosophilaGenetic Reference Panel, and allelic replacement using precise CRISPR/Cas9-induced genome editing. Our experiments reveal that this natural polymorphism has a significant pleiotropic effect on fecundity and egg-to-adult viability, but not on longevity or other life-history traits. These results provide a rare functional validation at the nucleotide level and identify a natural allelic variant affecting fitness and life-history adaptation.
Design of aStreptococcus pyogenesM protein immunogen to elicit M type cross-reactivity
Authors: Wang Kuei-Chen , Kuliyev Eziz , Nizet Victor , Ghosh Partho 
Published: December 2021

AbstractCoiled coil-forming M proteins of the widespread and potentially deadly bacterial pathogenStreptococcus pyogenes(Strep A) are immunodominant targets of opsonizing antibodies. However, antigenic sequence variability into >220 M types, as defined by the M protein hypervariable region (HVR), has been considered to limit its utility as a vaccine immunogen due to type-specificity in the antibody response. Surprisingly, a multi-HVR immunogen in clinical vaccine trials elicited M type cross-reactivity. The basis for this cross-reactivity is unknown but may be due in part to antibody recognition of a three-dimensional (3D) pattern conserved in many M protein HVRs that confers binding to human C4b-binding protein (C4BP). To test this hypothesis, we asked whether a single M protein immunogen carrying the 3D pattern would elicit cross-reactivity against other M types carrying the 3D pattern. We found that a 34-amino acid sequence of M2 protein bearing the 3D pattern retained full C4BP-binding capacity when fused to a coiled coil-stabilizing sequence from GCN4. This immunogen, called M2G, elicited cross-reactive antibodies against a number of M types that carry the 3D pattern but not against those that lack the 3D pattern. The M2G antiserum recognized M proteins as displayed natively on the Strep A surface, and promoted the opsonophagocytic killing of Strep A strains expressing these M proteins. As C4BP-binding is a conserved virulence trait of Strep A, targeting the 3D pattern may prove advantageous in vaccine design.
From STRs to SNPs via ddRAD-seq: geographic assignment of confiscated tortoises at reduced costs
Authors: Biello Roberto , Zampiglia Mauro , Fuselli Silvia , Fabbri Giulia , Bisconti Roberta , Chiocchio Andrea , Trucchi Emiliano , Canestrelli Daniele , Bertorelle Giorgio 
Published: December 2021

ABSTRACTAssigning individuals to their source populations is crucial for conservation research, especially for endangered species threatened by illegal trade and translocations. Genetic assignment can be achieved with different types of molecular markers, but technical advantages and cost saving are recently promoting the shift from short tandem repeats (STRs) to single nucleotide polymorphisms (SNPs). Here, we designed, developed, and tested a small panel of SNPs for cost-effective geographic assignment of individuals with unknown origin of the endangered Mediterranean tortoise Testudo hermanni. We started by performing a ddRAD-seq experiment on 70 wild individuals of T. hermanni from 38 locations. Results obtained using 3,182 SNPs are comparable to those previously obtained using STR markers in terms of genetic structure and power to identify the macro-area of origin. However, our SNPs revealed further insights into the substructure in Western populations, especially in Southern Italy. A small panel of highly informative SNPs was then selected and tested by genotyping 190 individuals using the KASP genotyping chemistry. All the samples from wild populations of known geographic origin were genetically re-assigned with high accuracy to the original population. This reduced SNPs panel represents an efficient molecular tool that enables individuals to be genotyped at low cost (less than €15 per sample) for geographical assignment and identification of hybrids. This information is crucial for the management in-situ of confiscated animals and their possible re-allocation in the wild. Our methodological pipeline can easily be extended to other species.
Inhibiting Host Protein Deposition on Urinary Catheters Reduces Urinary Tract Infections
Authors: Andersen Marissa Jeme , Fong ChunKi , La Bella Alyssa Ann , Molesan Alex , Champion Matthew M. , Howell Caitlin , Flores-Mireles Ana L. 
Published: December 2021

SummaryMicrobial adhesion to medical devices is common for hospital-acquired infections, particularly for urinary catheters. If not properly treated these infections cause complications and exacerbate antimicrobial resistance. Catheter use elicits bladder inflammation, releasing host serum-proteins, including fibrinogen, into the bladder, which deposit on the urinary catheter. Enterococcus faecalis uses fibrinogen as a scaffold to bind and persist in the bladder despite antibiotic treatments. Inhibition of fibrinogen-pathogen interaction significantly reduces infection. Here, we show deposited fibrinogen is advantageous for uropathogens, suggesting that targeting catheter protein deposition may reduce colonization creating an effective intervention. Hostprotein deposition was reduced, using liquid-infused catheters, resulting in decreased colonization on catheters, in bladders, and dissemination in vivo. Furthermore, proteomics revealed a significant decrease in deposition of host-secreted proteins on liquid-infused catheter surfaces. Our findings suggest targeting microbial binding scaffolds may be an effective antibiotic-sparing intervention for use against catheter-associated urinary tract infections and other medical device infections.
Pre-meiotic pairing of homologous chromosomes during Drosophila male meiosis
Authors: Rubin Thomas , Macaisne Nicolas , Vallés Ana Maria , Guilleman Clara , Gaugué Isabelle , Huynh Jean-René 
Published: December 2021

ABSTRACTIn the early stages of meiosis, maternal and paternal chromosomes pair with their homologous partner and recombine to ensure exchange of genetic information and proper segregation. These events can vary drastically between species and between males and females of the same species. In Drosophila, in contrast to females, males do not form synaptonemal complexes (SCs), do not recombine and have no crossing-over; yet, males are able to segregate their chromosomes properly. Here, we investigated the early steps of homologues pairing in Drosophila males. We found that homologues are not paired in germline stem cells (GSCs) and become paired in the mitotic region before meiotic entry, similarly to females. Surprisingly, male germline cells express SC proteins, which localize to centromeres and promote pairing. We further found that the SUN/KASH (LINC) complex and microtubules are required for homologues pairing as in females. Chromosome movements are however much slower than in females and we demonstrate that this slow dynamic is compensated in males by having longer cell cycles. In agreement, slowing down cell cycles was sufficient to rescue pairing-defective mutants in female meiosis. Our results demonstrate that although meiosis differs significantly between males and females, sex-specific cell cycle kinetics are integrated with similar molecular mechanisms to achieve proper homologues pairing.
Integrin-driven Axon Regeneration in the Spinal Cord Activates a Distinctive CNS Regeneration Program
Authors: Cheah Menghon , Cheng Yuyan , Petrova Veselina , Cimpean Anda , Jendelova Pavla , Swarup Vivek , Woolf Clifford J. , Geschwind Daniel H. , Fawcett James W. 
Published: December 2021

ABSTRACTThe peripheral branch of sensory dorsal root ganglion (DRG) neurons regenerates readily after injury unlike their central branch in the spinal cord. However extensive regeneration and reconnection of sensory axons in the spinal cord can be driven by the expression of α9 integrin and its activator kindlin- 1(α9k1), which enable axons to interact with tenascin-C. To elucidate the mechanisms and downstream pathways affected by activated integrin expression and central regeneration, we conducted transcriptomic analyses of DRG sensory neurons transduced with α9k1, and controls, with and without axotomy of the central branch. Expression of α9k1 without the central axotomy led to upregulation of a known PNS regeneration program, including many genes associated with peripheral nerve regeneration. Coupling α9k1 treatment with dorsal root axotomy led to extensive central axonal regeneration and caused expression of a distinctive CNS regeneration program, including genes associated with ubiquitination, autophagy, endoplasmic reticulum, trafficking, and signalling. Pharmacological inhibition of these processes blocked the regeneration of axons from DRGs and human iPS-derived sensory neurons, validating their causal contributions. This CNS regeneration- associated program showed little correlation with either embryonic development or PNS regeneration programs. Potential transcriptional drivers of this CNS program coupled to regeneration include Mef2a, Runx3, E2f4, Tfeb, Yy1. Signalling from integrins primes sensory neurons for regeneration, but their axon growth in the CNS is associated with a distinctive program that differs from that involved in PNS regeneration.
Zebrafish xenografts to isolate unique human breast cancer metastatic cell populations
Authors: Xiao Jerry , McGill Joseph R. , Nasir Apsra , Lekan Alexander , Johnson Bailey , Wilkins Devan J. , Pearson Gray W. , Tanner Kandice , Goodarzi Hani , Glasgow Eric , Schlegel Richard , Agarwal Seema 
Published: December 2021

AbstractCancer metastasis is a critical culprit frequently blamed for treatment failure, drug resistance, poor prognosis, and high mortality rate among all human cancers. Laboratory efforts to isolate metastatic cell populations have typically been confined to mouse models, which are time-consuming and expensive. Here, we present a model system based on xenografting zebrafish embryos to select for cells that are predisposed to progress through the early stages of metastasis. This model requires only 3-5 days to achieve distinct intravasation to the zebrafish circulatory system. The metastatic cells are easily tracked in real-time as they migrate, as well as isolated and propagatedin vitro. Once expanded, molecular characterization of the serially derived invasive cell populations from the tails of the zebrafish accurately predicts genes, signaling pathways, protein-protein interactions, and differential splicing products that are important for an invasive phenotype. This zebrafish model therefore offers a high-throughput and robust method for identifying gene targets critical for cancer metastasis.
Chemical, molecular, and single cell analysis reveal chondroitin sulfate proteoglycan aberrancy in fibrolamellar carcinoma
Authors: Francisco Adam B. , Li Jine , Farghli Alaa R. , Kanke Matt , Shui Bo , Soloway Paul D. , Wang Zhangjie , Reid Lola M. , Liu Jian , Sethupathy Praveen 
Published: December 2021

AbstractFibrolamellar carcinoma (FLC) is an aggressive liver cancer with no effective therapeutic options. The extracellular environment of FLC tumors is poorly characterized and may contribute to cancer growth and/or metastasis. To bridge this knowledge gap, we assessed pathways relevant to proteoglycans, a major component of the extracellular matrix. We first analyzed gene expression data from FLC and non-malignant liver tissue (n=27) to identify changes in glycosaminoglycan (GAG) biosynthesis pathways and found that genes associated with production of chondroitin sulfate, but not other GAGs, are significantly increased by 8-fold. We then implemented a novel LC-MS/MS based method to quantify the abundance of different types of GAGs in patient tumors (n=16) and found that chondroitin sulfate is significantly more abundant in FLC tumors by 6-fold. Upon further analysis of GAG-associated proteins we found that versican (VCAN) expression is significantly up-regulated at the mRNA and protein levels, the latter of which was validated by immunohistochemistry. Finally, we performed single-cell assay for transposon-accessible chromatin-sequencing on FLC tumors (n=3), which revealed for the first time the different cell types in FLC tumors and also showed that VCAN is likely produced not only from FLC tumor epithelial cells but also activated stellate cells. Our results reveal a pathologic aberrancy in chondroitin (but not heparan) sulfate proteoglycans in FLC and highlight a potential role for activated stellate cells.SignificanceThis study leverages a multi-disciplinary approach, including state-of-the-art chemical analyses and cutting-edge single-cell genomic technologies, to identify for the first time a marked chondroitin sulfate aberrancy in fibrolamellar carcinoma (FLC) that could open novel therapeutic avenues in the future.
The oscillation of mitotic kinase governs cell cycle latches
Authors: Novak Bela , Tyson John J 
Published: December 2021

SummaryIn order to transmit a eukaryotic cell’s genome accurately from mother cell to daughter cells, it is essential that the basic events of the cell division cycle (DNA synthesis and mitosis) occur once and only once per cycle, i.e., that a cell progresses irreversibly from G1 to S to G2 to M and back to G1. Irreversible progression through the cell cycle is assured by a sequence of ‘latching’ molecular switches, based on molecular interactions among cyclin-dependent kinases and their auxiliary partners. Positive feedback loops (++ or −−) create bistable switches with latching properties, and negative feedback loops drive progression from one stage to the next. In budding yeast (Saccharomyces cerevisiae) these events are coordinated by double-negative feedback loops between Clb-dependent kinases (Clb1-6) and their antagonists (APC:Cdh1 and Sic1). If the coordinating signal is compromised, either by deletion of Clb1-5 proteins or expression of non-degradable Clb2, then irreversibility is lost and yeast cells exhibit multiple rounds of DNA replication or mitotic exit events (Cdc14 endocycles). Using mathematical modelling of a stripped-down control network, we show how endocycles arise because the switches fail to latch, and the gates swing back and forth by the action of the negative feedback loops.