bluuebunny/crossref_metadata_2025_split huggingface dataset:
Somatic reversion impacts MDS/AML evolution in the short telomere syndromes
Authors: Schratz Kristen E. , Gaysinskaya Valeriya , Cosner Zoe L. , DeBoy Emily A. , Xiang Zhimin , Kasch-Semenza Laura , Florea Liliana , Shah Pali D. , Armanios Mary 
Published: May 2021

AbstractInherited mutations in telomerase and other telomere maintenance genes manifest in the premature aging short telomere syndromes. Myelodysplastic syndromes and acute myeloid leukemia (MDS/AML) account for 75% of associated malignancies, but how these cancers overcome the germline telomere defect is unknown. We used targeted ultra-deep sequencing to detect candidate somatic reversion mutations hypothesizing they may promote MDS/AML evolution. While no controls carried somatic mutations in telomere maintenance genes (0 of 28), 29% of adults with germline telomere maintenance defects carried at least one (16 of 56, P<0.001). In addition to TERT promoter mutations which were present in 19%, we identified POT1 and TERF2IP mutations in 13%. POT1 mutations impaired telomere binding and in some cases were identical to those found in familial melanoma associated with longer telomere length. Exclusively in patients with germline defects in telomerase RNA (TR), we identified somatic mutations in nuclear RNA exosome genes, RBM7, SKIV2L2, and DIS3, where loss-of-function upregulates mature TR levels. Paradoxically, somatic reversion events were more prevalent in patients who were MDS/AML-free (P=0.01, RR 5.0, 95% CI 1.4-18.9), and no MDS/AML patient had more than one mutant clone (P=0.048). Our data identify diverse somatic adaptive mechanisms in the short telomere syndromes, and raise the possibility that their presence alleviates the telomere crisis that promotes transformation to MDS/AML.
Synaptic density and neuronal metabolic function measured by PET in the unilateral 6-OHDA rat model of Parkinson’s disease
Authors: Raval Nakul Ravi , Gudmundsen Frederik , Juhl Morten , Andersen Ida Vang , Speth Nikolaj Raahauge , Videbæk Annesofie , Petersen Ida Nymann , Mikkelsen Jens Damsgaard , Fisher Patrick MacDonald , Herth Matthias Manfred , Plavén-Sigray Pontus , Knudsen Gitte Moos , Palner Mikael 
Published: May 2021

AbstractParkinson’s disease (PD) is caused by progressive neurodegeneration and characterised by motor dysfunction. Neurodegeneration of dopaminergic neurons also causes aberrations within the cortico-striato-thalamo-cortical (CSTC) circuit, which has been hypothesised to lead to non-motor symptoms such as depression. Individuals with PD have both lower synaptic density and changes in neuronal metabolic function in the basal ganglia, as measured using [11C]UCB-J and [18F]FDG positron emission tomography (PET), respectively. However, the two radioligands have not been directly compared in the same PD subject or in neurodegeneration animal models. Here, we investigate [11C]UCB-J binding and [18F]FDG uptake in the CSTC circuit following a unilateral dopaminergic lesion in rats and compare it to sham lesioned rats.Rats received either a unilateral injection of 6-hydroxydopamine (6-OHDA) or saline in the medial forebrain bundle and rostral substantia nigra (n=4/group). After three weeks, all rats underwent two PET scans using [18F]FDG, followed by [11C]UCB-J on a separate day. [18F]FDG uptake and [11C]UCB-J binding were both lower in the ipsilateral striatal regions compared to the contralateral regions. Using [11C]UCB-J, we could detect an 8.7% decrease in the ipsilateral ventral midbrain, compared to a 2.9% decrease in ventral midbrain using [18F]FDG. Differential changes between hemispheres for [11C]UCB-J and [18F]FDG outcomes were also evident in the CSTC circuit’s cortical regions, especially in the orbitofrontal cortex and medial prefrontal cortex where higher synaptic density yet lower neuronal metabolic function was observed, following lesioning.In conclusion, [11C]UCB-J and [18F]FDG PET can detect divergent changes following a dopaminergic lesion in rats, especially in cortical regions that are not directly affected by the neurotoxin. These results suggest that combined [11C]UCB-J and [18F]FDG scans could yield a better picture of the heterogeneous cerebral changes in neurodegenerative disorders.
Surveillance of in situ tumor arrays reveals early environmental control of cancer immunity
Authors: Ortiz-Muñoz Guadalupe , Brown Markus , Carbone Catherine B. , Pechuan-Jorge Joaquin , Ritter Alex T. , Orlova Darya , Mantri Shreya R. , Yang Angela , Doerr Jonas , Mariathasan Sanjeev , Wang Yulei , Turley Shannon , Gomez-Roca Carlos , de Andrea Carlos Eduardo , Spigel David , Wu Thomas , Modrusan Zora , Price Richard , Mellman Ira , Moussion Christine 
Published: May 2021

SummaryThe immune phenotype of a tumor is a key predictor of its response to immunotherapy1–4. Patients who respond to immune checkpoint blockade generally present with tumors that are infiltrated by activated T cells, a tumor-immune phenotype referred to as ‘immune inflamed’5–7. However, not all immune inflamed tumors respond to therapy, and in addition the majority of patients presents with tumors that lack T cells (‘immune desert’) or that exclude T cells in the periphery of the tumor islet (‘immune excluded’)8. Despite the importance of these tumor-immune phenotypes in patients, little is known about their development, heterogeneity or dynamics due to an inability to model these features pre-clinically.Here, we describe an approach designated STAMP (skin tumor array by micro-poration), which combines in vivo noninvasive, high-throughput time-lapse imaging with excisional biopsies and next generation sequencing to characterize the establishment of the immunological niche and follow its evolution during immunotherapy. STAMP involves the seeding of dozens to hundreds clonal tumors in the superficial dermis of a single mouse ear that can be visualized in situ over weeks to months. Using this approach, we found that genetically identical tumors could display surprisingly different immune phenotypes. Although individual tumors of the same array were populated by the same T cell clonotypes, regression or progression of individual tumors were associated with distinct patterns of spatial organization of the T cells. In situ imaging of 14K tumors revealed that immune phenotypes were not static over-time but could rather evolve with tumor growth and response to treatment. Therapy-induced or spontaneous early conversion to the immune inflamed phenotype correlated with tumor regression and enhanced cytotoxic T cell activity. Therefore, STAMP provides a flexible approach to study the relationship between tumor evolution, immune cell dynamics, and tumor microenvironment with therapeutic response.
Heligmosomoides bakeriandToxoplasma gondiico-infection leads to increased mortality associated with intestinal pathology
Authors: Szabo Edina K. , Bowhay Christina , Forrester Emma , Liu Holly , Dong Beverly , Coria Aralia Leon , Perera Shashini , Fung Beatrice , Badawadagi Namratha , Gaio Camila , Bailey Kayla , Ritz Manfred , Bowron Joel , Ariyaratne Anupama , Finney Constance A. M. 
Published: May 2021

AbstractCo-infections are a common reality but understanding how the immune system responds in this context is complex and can be unpredictable.Heligmosomoides bakeri(parasitic roundworm, previouslyHeligmosomoides polygyrus) andToxoplasma gondii(protozoan parasite) are well studied organisms that stimulate a characteristic Th2 and Th1 response, respectively. Several studies have demonstrated reduced inflammatory cytokine responses in animals co-infected with such organisms. However, while general cytokine signatures have been examined, the impact of the different cytokine producing lymphocytes on parasite control/clearance is not fully understood. We investigated five different lymphocyte populations (NK, NKT, γδ T, CD4+T and CD8+T cells), five organs (small intestine, Peyer’s patches, mesenteric lymph nodes, spleen and liver), and 4 cytokines (IFN γ, IL-4, IL-10 and IL-13) at two different time points (days 5 and 10 postT. gondiiinfection). We found that co-infected animals had significantly higher mortality than either single infection. This was accompanied by transient and local changes in parasite loads and cytokine profiles. Despite the early changes in lymphocyte and cytokine profiles, severe intestinal pathology in co-infected mice likely contributed to early mortality due to significant damage by both parasites in the small intestine. Our work demonstrates the importance of taking a broad view during infection research, studying multiple cell types, organs/tissues and time points to link and/or uncouple immunological from pathological findings. Our results provide insights into how co-infection with parasites stimulating different arms of the immune system can lead to drastic changes in infection dynamics.
ColFeatures: Automated data extraction and classification of bacterial colonies
Authors: García-Soriano Daniela A. , Andersen Frederikke Dybdahl , Nygaard Jens Vinge , Tørring Thomas 
Published: May 2021

AbstractExamining microbial colonies on agar plates have been at the core of microbiology for many decades. It is usually done manually, and therefore subject to bias besides requiring a considerable amount of time and effort. In order to optimize and standardize the identification of bacterial colonies growing on agar plates, we have developed an open access tool available on GitHub: ColFeatures. The software allows automated identification of bacterial colonies, extracts key morphological data and generate labels that ensure tracking of temporal development. We included machine learning algorithms that provide sorting of environmental isolates by using cluster methodologies. Furthermore, we show how cluster performance is evaluated using index scores (Silhouette, Calinski-Harabasz, Davies-Bouldin) to ensure the outcome of colony classification. As automation becomes more prominent in microbiology, tools as ColFeatures will assist identification of bacterial colonies on agar plates, bypassing human bias and complementing sequencing or mass spectrometry information that often comes attached with a considerable price tag.
Estradiol Influences Adenosinergic Signaling and NREM Sleep Need in Adult Female Rats
Authors: Smith Philip C. , Phillips Derrick J. , Pocivavsek Ana , Byrd Carissa A. , Viechweg Shaun S. , Hampton Brian , Mong Jessica A. 
Published: May 2021

AbstractStudies report estradiol (E2) suppresses sleep in females; however, the mechanisms of E2 action remain largely undetermined. Our previous findings suggest that the median preoptic nucleus (MnPO) is a key nexus for E2 action on sleep. Here, using behavioral, neurochemical and pharmacological approaches, we investigated whether E2 influenced the sleep homeostat as well as adenosinergic signaling in the MnPO of adult female rats. During the Light Phase, where rats accumulate the majority of sleep, E2 markedly reduced NREM-SWA (a measure of the homeostatic sleep need). Following 6-hours of sleep deprivation, levels of NREM-SWA were significantly increased compared to baseline sleep. However, the NREM-SWA levels were not different between E2 and control treatment despite a significant increase in wake at the expense of NREM sleep. Analysis of NREM-SWA differences between baseline and recovery sleep following sleep deprivation demonstrated that E2 induced a 2-fold increase in delta power compared to controls suggesting that E2 significantly expanded the dynamic range for the sleep homeostat. Correlated with E2-induced changes in physiological markers of homeostatic sleep was a marked increase in extracellular adenosine (a molecular marker of homeostatic sleep need) during unrestricted and recovery sleep following a 6-hour deprivation. Additionally, E2 blocked the ability of an adenosine A2A receptor agonist (CGS-21680) to increase NREM sleep compared to controls. Thus, taken together, the findings that E2 increased extracellular adenosine content, while blocking A2A signaling in the MnPO suggests a potential mechanism for how estrogens impact sleep in the female brain.Statement of SignificanceWhile gonadal steroids and gender are implicated as risk factors for sleep disruptions and insomnia, the relationship between ovarian steroids and sleep is poorly understood. Understanding the mechanisms through which estradiol (E2) is working to influence sleep-wake behavior is a critical first step toward a better understanding of the role of estrogens in sleep pathologies. Using a rodent model, the current study presents novel findings suggesting that estradiol (E2) is influencing adenosinergic actions in the MnPO. The ability of E2 to attenuate the local effects of the A2A receptors in the MnPO suggests that E2 modulation of A2A receptor signaling may underlie estrogenic suppression of sleep behavior as well as changes in homeostatic sleep need.
Chop-n-drop: in silico assessment of a novel single-molecule protein fingerprinting method employing fragmentation and nanopore detection
Authors: de Lannoy Carlos , Maglia Giovanni , de Ridder Dick 
Published: May 2021

AbstractThe identification of proteins at the single-molecule level would open exciting new venues in biological research and disease diagnostics. Previously we proposed a nanopore-based method for protein identification called chop-n-drop fingerprinting, in which the fragmentation pattern induced and measured by a proteasome-nanopore construct is used to identify single proteins. However whether such fragmentation patterns are sufficiently characteristic of proteins to identify them in complex samples remained unclear. In the simulation study presented here, we show that 97.9% of human proteome constituents are uniquely identified under close to ideal measuring circumstances, using a simple alignment-based classification method. We show that our method is robust against experimental error, as 78.8% can still be identified if the resolution is twice as low as currently attainable and 10% of proteasome restriction sites and protein fragments are randomly ignored. Based on these results and our experimental proof-of-concept, we argue that chop-n-drop fingerprinting has the potential to make cost-effective single-molecule protein identification feasible in the near future.
InferringMycobacterium bovistransmission between cattle and badgers using isolates from the Randomised Badger Culling Trial
Authors: van Tonder Andries J. , Thornton Mark , Conlan Andrew J.K. , Jolley Keith A. , Goolding Lee , Mitchell Andrew P. , Dale James , Palkopoulou Eleftheria , Hogarth Philip J. , Glyn Hewinson R. , Wood James L.N. , Parkhill Julian 
Published: May 2021

AbstractMycobacterium bovis(M. bovis)is a causative agent of bovine tuberculosis, a significant source of morbidity and mortality in the global cattle industry. The Randomised Badger Culling Trial was a field experiment carried out between 1998 and 2005 in the South West of England. As part of this trial,M. bovisisolates were collected from contemporaneous and overlapping populations of badgers and cattle within ten defined trial areas. We combined whole genome sequences from 1,442 isolates with location and cattle movement data, identifying transmission clusters and inferred rates and routes of transmission ofM. bovis. Most trial areas contained a single transmission cluster that had been established shortly before sampling, often contemporaneous with the expansion of bovine tuberculosis in the 1980s. The estimated rate of transmission from badger to cattle was approximately two times higher than from cattle to badger, and the rate of within-species transmission considerably exceeded these for both species. We identified long distance transmission events linked to cattle movement, recurrence of herd breakdown by infection within the same transmission clusters and superspreader events driven by cattle but not badgers. Overall, our data suggests that the transmission clusters in different parts of South West England that are still evident today were established by long-distance seeding events involving cattle movement, not by recrudescence from a long-established wildlife reservoir. Clusters are maintained primarily by within-species transmission, with less frequent spill-over both from badger to cattle and cattle to badger.
Parameterization of regulatory nodes for engineering broad host range heterologous gene expression
Authors: Nikel Pablo I. , Benedetti Ilaria , de Lorenzo Victor , Calles Belen 
Published: May 2021

ABSTRACTBy building on the SEVA (Standard European Vector Architecture) format we have refactored a number of regulatory nodes recruited from both Gram-negative and Gram-positive bacteria for rigorously comparing and parameterizing five expression devices that respond to diverse and unrelated chemical inducers, i.e. LacIq-Ptrc, XylS-Pm, AlkS-PalkB, CprK-PDB3and ChnR-PchnB. These were assembled as cargoes following the SEVA standard within exactly the same vector backbone and bearing the different functional segments arrayed in an invariable DNA scaffold. Their performance in anEscherichia colistrain of reference was then analyzed through the readout a fluorescence reporter gene that contained strictly identical translation signal elements in all cases and in the same DNA context. This study allowed us to describe and compare the cognate expression systems with unprecedented quantitative detail. The systems under scrutiny diverged considerably in their capacity, expression noise, inducibility and OFF/ON ratios. These features, along with the absence of physiological effects caused by the inducers and the lack of cross-regulation offer a panoply of choices to potential users and help interoperability of the specific constructs.
A distributed residue network permits conformational binding specificity in a conserved family of actin remodelers
Authors: Hwang Theresa , Parker Sara S , Hill Samantha M. , Ilunga Meucci W. , Grant Robert A. , Mouneimne Ghassan , Keating Amy E. 
Published: May 2021

AbstractMetazoan proteomes contain many paralogous proteins that have evolved distinct functions. The Ena/VASP family of actin regulators consists of three members that share an EVH1 interaction domain with a 100% conserved binding site. A proteome-wide screen revealed ciliary protein PCARE as a high-affinity ligand for ENAH EVH1. Here we report the surprising observation that PCARE is ~100-fold specific for ENAH over paralogs VASP and EVL and can selectively bind and inhibit ENAH-dependent adhesion in cells. Specificity arises from a mechanism whereby PCARE stabilizes a conformation of the ENAH EVH1 domain that is inaccessible to family members VASP and EVL. Structure-based modeling rapidly identified seven residues distributed throughout EVL that are sufficient to differentiate binding by ENAH vs. EVL. By exploiting the ENAH-specific conformation, we rationally designed the tightest and most selective ENAH binder to date. Our work uncovers a conformational mechanism of interaction specificity that distinguishes highly similar paralogs and establishes tools for dissecting specific Ena/VASP functions in processes including cancer cell invasion.
Unleashing a Novel Function of Endonuclease G in Mitochondrial Genome Instability
Authors: Dahal Sumedha , Siddiqua Humaira , Sharma Shivangi , Babu Ravi K. , Manjunath Meghana , Sharma Sheetal , Choudhary Bibha , Raghavan Sathees C. 
Published: May 2021

SUMMARYHaving its own genome makes mitochondria a unique and semiautonomous organelle within cells. Mammalian mitochondrial DNA (mtDNA) is double-stranded closed circular molecule of about 16 kb coding 37 genes. Mutations, including deletions in the mitochondrial genome can culminate in different human diseases. Mapping of the deletion junctions suggests that the breakpoints are generally seen at hotspots. ‘9-bp deletion’ (8271-8281), seen in the intergenic region of cytochrome c oxidase II/tRNALys, is the most common mitochondrial deletion. While it is associated with several diseases like myopathy, dystonia, and hepatocellular carcinoma, it has also been used as an evolutionary marker. However, the mechanism responsible for its fragility is unclear. In the current study, we show that Endonuclease G, a mitochondrial nuclease responsible for nonspecific cleavage of nuclear DNA during apoptosis, can induce breaks at sequences associated with ‘9-bp deletion’, when it is present on a plasmid or in the mitochondrial genome. Through a series of in vitro and intracellular studies, we show that Endonuclease G binds to G-quadruplex structures formed at the hotspot and induces DNA breaks. Besides, we reconstitute the whole process of ‘9-bp deletion’ using purified Endonuclease G to induce breaks in mtDNA, followed by mitochondrial extract-mediated DSB repair and establish that microhomology-mediated end joining is responsible for the generation of mtDNA deletion. Finally, we show that the whole process is regulated by different stress conditions, which may modulate release of Endonuclease G to the mitochondrial matrix. Therefore, we uncover a new role for Endonuclease G in generating deletions, which is dependent on the formation of G4 DNA within the mitochondrial genome. Thus, in this study we identify a novel property of Endonuclease G, besides its role in apoptosis, and the recently described ‘elimination of paternal mitochondria during fertilization.
Human HELB is a processive motor protein which catalyses RPA clearance from single-stranded DNA
Authors: Hormeno S , Wilkinson OJ , Aicart-Ramos C , Kuppa S , Antony E , Dillingham MS , Moreno-Herrero F 
Published: May 2021

SUMMARYHuman HELB is a poorly-characterised helicase suggested to play both positive and negative regulatory roles in DNA replication and recombination. In this work, we used bulk and single molecule approaches to characterise the biochemical activities of HELB protein with a particular focus on its interactions with RPA and RPA-ssDNA filaments. HELB is a monomeric protein which binds tightly to ssDNA with a site size of ∼20 nucleotides. It couples ATP hydrolysis to translocation along ssDNA in the 5′-to-3′ direction accompanied by the formation of DNA loops and with an efficiency of 1 ATP per base. HELB also displays classical helicase activity but this is very weak in the absence of an assisting force. HELB binds specifically to human RPA which enhances its ATPase and ssDNA translocase activities but inhibits DNA unwinding. Direct observation of HELB on RPA nucleoprotein filaments shows that translocating HELB concomitantly clears RPA from single-stranded DNA.
Deciphering signatures of natural selection via deep learning
Authors: Qin Xinghu , Chiang Charleston W. K. , Gaggiotti Oscar E. 
Published: May 2021

AbstractIdentifying genomic regions influenced by natural selection provides fundamental insights into the genetic basis of local adaptation. We propose a deep learning-based framework, DeepGenomeScan, that can detect signatures of local adaptation. We demonstrate that DeepGenomeScan outperformed PCA and RDA-based genome scans in identifying loci underlying quantitative traits subject to complex spatial patterns of selection. Noticeably, DeepGenomeScan increases statistical power by up to 47.25% under non-linear environmental selection patterns. We applied DeepGenomeScan to a European human genetic dataset and identified some well-known genes under selection and a substantial number of clinically important genes that were not identified using existing methods.