Miracle-dz/UniFAR-FTUs huggingface dataset:
CDK2 Is Required for the DNA Damage Response During Porcine Early Embryonic Development1

ABSTRACT Cyclin-dependent kinase (CDK) 2 inhibition plays a central role in DNA damage-induced cell cycle arrest and DNA repair. However, whether CDK2 also influences early porcine embryo development is unknown. In this study, we examined whether CDK2 is involved in the regulation of oocyte meiosis and early embryonic development of porcine embryos. We found that disrupting CDK2 activity with RNAi or an inhibitor did not affect meiotic resumption or meiosis II arrest. However, CDK2 inhibitor-treated embryos showed delayed cleavage and ceased development before the blastocyst stage. Disrupting CDK2 activity is able to induce sustained DNA damage, as demonstrated by the formation of distinct gammaH2AX foci in nuclei of Day-3 and Day-5 embryos. Inhibiting CDK2 triggers a DNA damage checkpoint by activation of the ataxia telangiectasia mutated (ATM)-P53-P21 pathway. However, the mRNA expression of genes involved in nonhomologous end joining or homologous recombination pathways for double-strand break repair were reduced after administering CDK2 inhibitor to 5-day-old embryos. Furthermore, CDK2 inhibition caused apoptosis in Day-7 blastocysts. Thus, our results indicate that an ATM-P53-P21 DNA damage checkpoint is intact in the absence of CDK2; however, CDK2 is important for proper repair of the damaged DNA by either directly or indirectly influencing DNA repair-related gene expression.
Clinical Investigation : Breast Cancer Preradiotherapy Calcium Scores of the Coronary Arteries in a Cohort of Women With Early-Stage Breast Cancer : A Comparison With a Cohort of Healthy Women

Preradiotherapy Calcium Scores of the Coronary Arteries in a Cohort of Women With Early-Stage Breast Cancer: A Comparison With a Cohort of Healthy Women Mirjam E. Mast, M.Sc.,* Mark W. Heijenbrok, M.D.,y Anna L. Petoukhova, Ph.D.,* Astrid N. Scholten, M.D., Ph.D.,z Joop H.M. Schreur, M.D., Ph.D.,x and Henk Struikmans, M.D., Ph.D.*,z *Radiotherapy Centre West, The Hague, The Netherlands; yDepartment of Radiology, Medical Center Haaglanden, The Hague, The Netherlands; zDepartment of Clinical Oncology, Leiden University Medical Centre, Leiden, The Netherlands; and Department of Cardiology, xMedical Center Haaglanden, The Hague, The Netherlands
Rothamsted Repository Download

, , Mosquitoes infected with malaria parasites have demonstrated altered behaviour that may increase the probability of parasite transmission. Here, we examine the responses of the olfactory system in Plasmodium falciparum infected Anopheles gambiae , Plasmodium berghei infected Anopheles stephensi , and P . berghei infected An . gambiae . Infected and uninfected mosquitoes showed differential responses to compounds in human odour using electroantennography coupled with gas chromatography (GC-EAG), with 16 peaks triggering responses only in malaria-infected mosquitoes (at oocyst, sporozoite or both stages). A selection of key compounds were examined with EAG, and responses showed differences in the detection thresholds of infected and uninfected mosquitoes to compounds including lactic acid, tetradecanoic acid and benzothiazole, suggesting that the changes in sensitivity may be the reason for differential attraction and biting at the oocyst and sporozoite stages. Importantly, the different cross-species comparisons showed varying sensitivities to compounds, with P . falciparum infected An . gambiae differing from P . berghei infected An . stephensi , and P . berghei infected An . gambiae more similar to the P . berghei infected An . stephensi . These differences in sensitivity may reflect long-standing evolutionary relationships between specific Plasmodium and Anopheles
Expression analysis of growth differentiation factor 9 (Gdf9/gdf9), anti-muüllerian hormone (Amh/amh) and aromatase (Cyp19a1a/cyp19a1a) during gonadal differentiation of the zebrafish, Danio rerio†

Abstract In the zebrafish, no sex-determining gene has been identified, while some sex-related genes, such as cyp19a1a and amh, show sexually dimorphic expression. Interestingly, most of these genes are expressed in the somatic cells. With increasing evidence suggesting roles of germ cells in gonadal differentiation, there is an increasing interest in the factors released by the germ cells for the bidirectional communication between the two compartments. We have reported that Gdf9/gdf9 is an oocyte-specific factor in the zebrafish, similar to that of mammals. Whether and how Gdf9 is involved in gonadal differentiation is unknown. In this study, we compared the expression levels of gdf9, cyp19a1a, and amh among several other sex-related genes in the gonads before, during, and after sex differentiation. The expression of gdf9 started in the gonads before sex differentiation, and its level surged in the differentiated ovary. Its expression pattern was similar to that of cyp19a1a, but reciprocal to amh expression. Using recombinant zebrafish Gdf9 (rzfGdf9), we further showed that Gdf9 significantly suppressed the expression of amh while increased that of activin beta subunits (inhbaa and inhbb) in vitro. Although gdf9 and cyp19a1a showed co-expression during gonadal differentiation, we only observed a slight but not significant response of cyp19a1a to rzfGdf9. Knocking down the expression of gdf9 and cyp19a1a with vivo-morpholinos caused a male-skewed sex ratio. Our data suggested that Gdf9 is likely involved in promoting oocyte/ovary differentiation in the zebrafish and it may act by suppressing amh expression, at least partly, in the somatic cells. Summary Sentence Oocytes may influence gonadal differentiation by releasing growth differentiation factor 9.
Bile acid transport across the hepatocyte cánalicular membrane

Transport of bile acids across the canalicular membrane of the hepatocyte provides the primary motive force for generation of bile flow and is rate limiting in the vectorial movement of bile acids from blood to bile. Several distinct carriers for bile acids have been defined based on physiological studies in isolated hepatocytes, membrane vesicles, hepatocyte couplets, and the perfused rat liver including membrane potential‐driven and ATP‐dependent mechanisms. Several groups have isolated and functionally reconstituted a canalicular bile acid transport protein of Mr ~ 110 kDa. The ATP‐dependent mechanism for secretion of monovalent bile acids appears to be mediated by a yet to be identified protein of the ATP binding cassette family of transporters. However, it remains conjectural whether the ATP‐dependent and membrane potential‐driven components of canalicular bile acid transport are mediated by one or more transport porteins. Bile acid sulfates and glucuronides are substrates for the canalicular multispecific organic anion transporter whose activity has recently been associated with the multidrug resistance‐associated protein. —Suchy, F. J., Sippel, C. J., Ananthanarayanan, M. Bile acid transport across the hepatocyte canalicular membrane. FASEB J. 11, 199‐205 (1997)
An inducible amphipathic helix within the intrinsically disordered C terminus can participate in membrane curvature generation by peripherin-2/rds

Peripherin-2/rds is required for biogenesis of vertebrate photoreceptor outer segment organelles. Its localization at the high-curvature rim domains of outer segment disk membranes suggests that it may act to shape these structures; however, the molecular function of this protein is not yet resolved. Here, we apply biochemical, biophysical, and imaging techniques to elucidate the role(s) played by the protein's intrinsically disordered C-terminal domain and an incipient amphipathic α-helix contained within it. We investigated a deletion mutant lacking only this α-helix in stable cell lines and Xenopus laevis photoreceptors. We also studied a soluble form of the full-length ∼7-kDa cytoplasmic C terminus in cultured cells and purified from Escherichia coli. The α-helical motif was not required for protein biosynthesis, tetrameric subunit assembly, tetramer polymerization, localization at disk rims, interaction with GARP2, or the generation of membrane curvature. Interestingly, however, loss of the helical motif up-regulated membrane curvature generation in cellulo, introducing the possibility that it may regulate this activity in photoreceptors. Furthermore, the incipient α-helix (within the purified soluble C terminus) partitioned into membranes only when its acidic residues were neutralized by protonation. This suggests that within the context of full-length peripherin-2/rds, partitioning would most likely occur at a bilayer interfacial region, potentially adjacent to the protein's transmembrane domains. In sum, this study significantly strengthens the evidence that peripherin-2/rds functions directly to shape the high-curvature rim domains of the outer segment disk and suggests that the protein's C terminus may modulate membrane curvature-generating activity present in other protein domains.
The cytoplasmic tail of L-selectin interacts with the adaptor-protein complex AP-1 subunit μ1A via a novel basic binding motif

L-selectin regulates leukocyte adhesion and rolling along the endothelium. Proteins binding to the cytoplasmic tail of L-selectin regulate L-selectin functions. We used L-selectin cytoplasmic tail peptide pulldown assays combined with high sensitivity liquid chromatography/mass spectrometry to identify novel L-selectin tail-binding proteins. Incubation of the L-selectin tail with cell extracts from phorbol 12-myristate 13-acetate-stimulated Raw 264.7 macrophages resulted in the binding of μ1A of the clathrin-coated vesicle AP-1 complex. Furthermore, full-length GST-μ1A and the GST-μ1A C-terminal domain, but not the GST-μ1A N-terminal domain, bind to L-selectin tail peptide, and the intracellular pool of L-selectin colocalizes with AP-1 at the trans-Golgi network. We identified a novel basic protein motif consisting of a cluster of three dibasic residues (356RR357, 359KK360, and 362KK363) in the membrane-proximal domain of the L-selectin tail as well as a doublet of aspartic acid residues (369DD370) in the membrane-distal end of the L-selectin tail involved in μ1A binding. Stimulation of Raw 264.7 macrophages with PMA augmented the amount of μ1A associated with anti-L-selectin immunoprecipitates. However, full-length GST-μ1A did not bind to the phospho-L-selectin tail or phospho-mimetic S364D L-selectin tail. Accordingly, we propose that phosphorylation of μ1A is required for interaction with the L-selectin tail and that L-selectin tail phosphorylation may regulate this interaction in vivo. Molecular docking of the L-selectin tail to μ1A was used to identify the μ1A surface domain binding the L-selectin tail and to explain how phosphorylation of the L-selectin tail abrogates μ1A interaction. Our findings indicate that L-selectin is transported constitutively by the AP-1 complex, leading to the formation of a trans-Golgi network reserve pool and that phosphorylation of the L-selectin tail blocks AP-1-dependent retrograde transport of L-selectin.
Structural basis of apoptosis inhibition by the fowlpox virus protein FPV039

Programmed cell death or apoptosis of infected host cells is an important defense mechanism in response to viral infections. This process is regulated by proapoptotic and prosurvival members of the B-cell lymphoma 2 (Bcl-2) protein family. To counter premature death of a virus-infected cell, poxviruses use a range of different molecular strategies including the mimicry of prosurvival Bcl-2 proteins. One such viral prosurvival protein is the fowlpox virus protein FPV039, which is a potent apoptosis inhibitor, but the precise molecular mechanism by which FPV039 inhibits apoptosis is unknown. To understand how fowlpox virus inhibits apoptosis, we examined FPV039 using isothermal titration calorimetry, small-angle X-ray scattering, and X-ray crystallography. Here, we report that the fowlpox virus prosurvival protein FPV039 promiscuously binds to cellular proapoptotic Bcl-2 and engages all major proapoptotic Bcl-2 proteins. Unlike other identified viral Bcl-2 proteins to date, FPV039 engaged with cellular proapoptotic Bcl-2 with affinities comparable with those of Bcl-2's endogenous cellular counterparts. Structural studies revealed that FPV039 adopts the conserved Bcl-2 fold observed in cellular prosurvival Bcl-2 proteins and closely mimics the structure of the prosurvival Bcl-2 family protein Mcl-1. Our findings suggest that FPV039 is a pan-Bcl-2 protein inhibitor that can engage all host BH3-only proteins, as well as Bcl-2-associated X, apoptosis regulator (Bax) and Bcl-2 antagonist/killer (Bak) proteins to inhibit premature apoptosis of an infected host cell. This work therefore provides a mechanistic platform to better understand FPV039-mediated apoptosis inhibition.
Meta-Dataset: A Dataset of Datasets for Learning to Learn from Few Examples

Few-shot classification refers to learning a classifier for new classes given only a few examples. While a plethora of models have emerged to tackle it, we find the procedure and datasets that are used to assess their progress lacking. To address this limitation, we propose Meta-Dataset: a new benchmark for training and evaluating models that is large-scale, consists of diverse datasets, and presents more realistic tasks. We experiment with popular baselines and meta-learners on Meta-Dataset, along with a competitive method that we propose. We analyze performance as a function of various characteristics of test tasks and examine the models' ability to leverage diverse training sources for improving their generalization. We also propose a new set of baselines for quantifying the benefit of meta-learning in Meta-Dataset. Our extensive experimentation has uncovered important research challenges and we hope to inspire work in these directions.
Respiratory chain dysfunction and oxidative stress correlate with severity of primary CoQ10 deficiency

Coenzyme Q10 (CoQ10) is essential for electron transport in the mitochondrial respiratory chain and antioxidant defense. Last year, we re ported the first mutations in CoQ10 biosynthetic genes, COQ2, which encodes 4‐parahydroxybenzoate: polyprenyl transferase;and PDSS2, which encodes subunit 2 of decaprenyl diphosphate synthase. How ever, the pathogenic mechanisms of primary CoQ10deficiency have not been well characterized. In this study, we investigated the consequence of severe CoQ10 deficiency on bioenergetics, oxidative stress, and antioxidant defenses in cultured skin fibroblasts harboring COQ2 and PDSS2 mutations. Defects in the first two committed steps of the CoQ10 biosynthetic pathway produce different biochemical alterations. PDSS2 mutant fibroblasts have 12% CoQ10 relative to control cells and markedly reduced ATP synthesis, but do not show increased reactive oxygen species (ROS) production, signs of oxidative stress, or in creased antioxidant defense markers. In contrast, COQ2 mutant fibroblasts have 30% CoQ10 with par tial defect in ATP synthesis, as well as significantly increased ROS production and oxidation of lipids and proteins. On the basis of a small number of cell lines, our results suggest that primary CoQ10 defi ciencies cause variable defects of ATP synthesis and oxidative stress, which may explain the different clinical features and may lead to more rational therapeutic strategies. — Quinzii, C. M. , López, L. C. , Von‐Moltke, J., Naini, A. , Krishna, S. , Schuelke, M. , Salviati, L. , Navas, P., DiMauro, S. , Hirano, M. Respiratory chain dysfunction and oxidative stress correlate with severity of primary CoQ10 deficiency. FASEB J. 22, 1874–1885 (2008)
Clinical Investigation : Lymphoma Dosimetric and Clinical Outcomes of Involved-Field Intensity-Modulated Radiotherapy After Chemotherapy for Early-Stage Hodgkin ’ s Lymphoma With Mediastinal Involvement

This study reports the dosimetric parameters and clinical outcomes of involved-field intensitymodulated radiotherapy (IF-IMRT) following chemotherapy for patients with early stage mediastinum-involved Hodgkin’s lymphoma. Even with larger clinical target volume (CTV), IF-IMRT could yield perfect target volume coverage and sparing of normal tissue. Chemotherapy and IF-IMRT resulted in a favorable outcome and
Growth, reproductive traits and habitat patterns of Unio ravoisieri (Mollusca: Bivalvia) from Ichkeul Lake tributaries (Northern Tunisia)

Habitat patterns, growth and reproductive traits of the freshwater mussel Unio ravoisieri were investigated for the first time in two streams (Sejenane and Elmaleh) of the Ichkeul Lake basin (northern Tunisia) over the course of a year. A very similar profile was observed for the two studied populations. The median age class dominated in the age structure, indicating good recruitment and viability. The reproductive period lasted approximately 10 months (from September to June). Females at different gametogenesis stages were found during autumn, winter and spring. Gravid females were sampled during winter and spring, and larval release occurred from early spring to early summer. The number of embryos produced per female reached 84,000 per year. In Elmaleh stream, characterized by high salinity, reproduction of the mussel took place slightly earlier than in the other habitat (Sejenane). However, the variation in reproduction traits between the two populations was not significant (p > 0.05). Similar patterns, but with a difference in the timing of the breeding season, were recorded for Spanish populations. The results highlight a reproductive plasticity of U. ravoisieri and an ability to tolerate harsh abiotic conditions. Nevertheless, salinity and temperature seem to have a stressful effect on different reproductive stages, mainly during the brooding period; negative correlation was found between condition index and the two parameters: Pearson’s r = 0.4–0.8; p < 0.05. To avoid their adverse effects, U. ravoisieri appears to be able to adjust its reproductive cycle to the wet season when these parameters are moderate.
Normalization of Hepatic Homeostasis in the Npc1nmf164 Mouse Model of Niemann-Pick Type C Disease Treated with the Histone Deacetylase Inhibitor Vorinostat*

Niemann-Pick type C (NP-C) disease is a fatal genetic lipidosis for which there is no Food and Drug Administration (FDA)-approved therapy. Vorinostat, an FDA-approved inhibitor of histone deacetylases, ameliorates lysosomal lipid accumulation in cultured NP-C patient fibroblasts. To assess the therapeutic potential of histone deacetylase inhibition, we pursued these in vitro observations in two murine models of NP-C disease. Npc1nmf164 mice, which express a missense mutation in the Npc1 gene, were treated intraperitoneally, from weaning, with the maximum tolerated dose of vorinostat (150 mg/kg, 5 days/week). Disease progression was measured via gene expression, liver function and pathology, serum and tissue lipid levels, body weight, and life span. Transcriptome analyses of treated livers indicated multiple changes consistent with reversal of liver dysfunction that typifies NP-C disease. Significant improvements in liver pathology and function were achieved by this treatment regimen; however, NPC1 protein maturation and levels, disease progression, weight loss, and animal morbidity were not detectably altered. Vorinostat concentrations were >200 μm in the plasma compartment of treated animals but were almost 100-fold lower in brain tissue. Apolipoprotein B metabolism and the expression of key components of lipid homeostasis in primary hepatocytes from null (Npc1−/−) and missense (Npc1nmf164) mutant mice were altered by vorinostat treatment, consistent with a response by these cells independent of the status of the Npc1 locus. These results suggest that HDAC inhibitors have utility to treat visceral NP-C disease. However, it is clear that improved blood-brain barrier penetration will be required to alleviate the neurological symptoms of human NP-C disease.
Metabolic Alterations Contribute to Enhanced Inflammatory Cytokine Production in Irgm1-deficient Macrophages*

The immunity-related GTPases (IRGs) are a family of proteins that are induced by interferon (IFN)-γ and play pivotal roles in immune and inflammatory responses. IRGs ostensibly function as dynamin-like proteins that bind to intracellular membranes and promote remodeling and trafficking of those membranes. Prior studies have shown that loss of Irgm1 in mice leads to increased lethality to bacterial infections as well as enhanced inflammation to non-infectious stimuli; however, the mechanisms underlying these phenotypes are unclear. In the studies reported here, we found that uninfected Irgm1-deficient mice displayed high levels of serum cytokines typifying profound autoinflammation. Similar increases in cytokine production were also seen in cultured, IFN-γ-primed macrophages that lacked Irgm1. A series of metabolic studies indicated that the enhanced cytokine production was associated with marked metabolic changes in the Irgm1-deficient macrophages, including increased glycolysis and an accumulation of long chain acylcarnitines. Cells were exposed to the glycolytic inhibitor, 2-deoxyglucose, or fatty acid synthase inhibitors to perturb the metabolic alterations, which resulted in dampening of the excessive cytokine production. These results suggest that Irgm1 deficiency drives metabolic dysfunction in macrophages in a manner that is cell-autonomous and independent of infectious triggers. This may be a significant contributor to excessive inflammation seen in Irgm1-deficient mice in different contexts.
Induction of cell death and gain-of-function properties of connexin26 mutants predict severity of skin disorders and hearing loss

Connexin26 (Cx26) is a gap junction protein that oligomerizes in the cell to form hexameric transmembrane channels called connexons. Cell surface connexons dock between adjacent cells to allow for gap junctional intercellular communication. Numerous autosomal dominant mutations in the Cx26-encoding GJB2 gene lead to many skin disorders and sensorineural hearing loss. Although some insights have been gained into the pathogenesis of these diseases, it is not fully understood how distinct GJB2 mutations result in hearing loss alone or in skin pathologies with comorbid hearing loss. Here we investigated five autosomal dominant Cx26 mutants (N14K, D50N, N54K, M163V, and S183F) linked to various syndromic or nonsyndromic diseases to uncover the molecular mechanisms underpinning these disease links. We demonstrated that when gap junction-deficient HeLa cells expressed the N14K and D50N mutants, they undergo cell death. The N54K mutant was retained primarily within intracellular compartments and displayed dominant or transdominant properties on wild-type Cx26 and coexpressed Cx30 and Cx43. The S183F mutant formed some gap junction plaques but was largely retained within the cell and exhibited only a mild transdominant reduction in gap junction communication when co-expressed with Cx30. The M163V mutant, which causes only hearing loss, exhibited impaired gap junction function and showed no transdominant interactions. These findings suggest that Cx26 mutants that promote cell death or exert transdominant effects on other connexins in keratinocytes will lead to skin diseases and hearing loss, whereas mutants having reduced channel function but exhibiting no aberrant effects on coexpressed connexins cause only hearing loss. Moreover, cell death-inducing GJB2 mutations lead to more severe syndromic disease.
Theme 5 Epidemiology and informatics

Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom, The Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, United Kingdom, The Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, United Kingdom, Department of Clinical Neurosciences, NHS Lothian, Edinburgh, United Kingdom, Institute of Neurosciences, NHS Greater Glasgow and Clyde, Glagow, United Kingdom, Department of Neurology, NHS Tayside, Dundee, United Kingdom