Miracle-dz/UniFAR-FTUs huggingface dataset:
CryoGAN: A New Reconstruction Paradigm for Single-Particle Cryo-EM via Deep Adversarial Learning

We present CryoGAN, a new paradigm for single-particle cryo-EM reconstruction based on unsupervised deep adversarial learning. The major challenge in single-particle cryo-EM is that the imaged particles have unknown poses. Current reconstruction techniques are based on a marginalized maximum-likelihood formulation that requires calculations over the set of all possible poses for each projection image, a computationally demanding procedure. CryoGAN sidesteps this problem by using a generative adversarial network (GAN) to learn the 3D structure that has simulated projections that most closely match the real data in a distributional sense. The architecture of CryoGAN resembles that of standard GAN, with the twist that the generator network is replaced by a model of the cryo-EM image acquisition process. CryoGAN is an unsupervised algorithm that only demands projection images and an estimate of the contrast transfer function parameters. No initial volume estimate or prior training is needed. Moreover, CryoGAN requires minimal user interaction and can provide reconstructions in a matter of hours on a high-end GPU. In addition, we provide sound mathematical guarantees on the recovery of the correct structure. CryoGAN currently achieves a 8.6 Å resolution on a realistic synthetic dataset. Preliminary results on real β-galactosidase data demonstrate CryoGAN’s ability to exploit data statistics under standard experimental imaging conditions. We believe that this paradigm opens the door to a family of novel likelihood-free algorithms for cryo-EM reconstruction.
JNK pathway restricts DENV, ZIKV and CHIKV infection by activating complement and apoptosis in mosquito salivary glands

Arbovirus infection of Aedes aegypti salivary glands (SGs) determines transmission. However, there is a dearth of knowledge on SG immunity. Here, we characterized SG immune response to dengue, Zika and chikungunya viruses using high-throughput transcriptomics. The three viruses regulate components of Toll, IMD and JNK pathways. However, silencing of Toll and IMD components showed variable effects on SG infection by each virus. In contrast, regulation of JNK pathway produced consistent responses. Virus infection increased with depletion of component Kayak and decreased with depletion of negative regulator Puckered. Virus-induced JNK pathway regulates complement and apoptosis in SGs via TEP20 and Dronc, respectively. Individual and co-silencing of these genes demonstrate their antiviral effects and that both may function together. Co-silencing either TEP20 or Dronc with Puckered annihilates JNK pathway antiviral effect. We identified and characterized the broad antiviral function of JNK pathway in SGs, expanding the immune arsenal that blocks arbovirus transmission.
IMPLICON: an ultra-deep sequencing method to uncover DNA methylation at imprinted regions

Genomic imprinting is an epigenetic phenomenon leading to parental allele-specific expression. Dosage of imprinted genes is crucial for normal development and its dysregulation accounts for several human disorders. This unusual expression pattern is mostly dictated by differences in DNA methylation between parental alleles at specific regulatory elements known as imprinting control regions (ICRs). Although several approaches can be used for methylation inspection, we lack an easy and cost-effective method to simultaneously measure DNA methylation at multiple imprinted regions. Here, we present IMPLICON, a new high-throughput method measuring DNA methylation levels at imprinted regions with base-pair resolution and over 1000-fold coverage. We initially designed IMPLICON to look at ICRs in adult tissues of inbred mice. Then, we validated it in hybrid mice from reciprocal crosses for which we could discriminate methylation profiles in the two parental alleles. Lastly, we developed a human version of IMPLICON and detected imprinting errors in embryonic and induced pluripotent stem cells. We also provide rules and guidelines to adapt this method for investigating the DNA methylation landscape of any set of genomic regions. In summary, IMPLICON is a rapid, cost-effective and scalable method, which could become the gold standard in both imprinting research and diagnostics.
Community-level impacts of spatial repellents for control of diseases vectored by Aedes aegypti mosquitoes

Spatial repellents (SRs) reduce human-mosquito contact by preventing mosquito entrance into human-occupied spaces and interfering with host seeking and blood-feeding. A new model to synthesize experimental data on the effects of transfluthrin on Aedes aegypti explores how SR effects interact to impact the epidemiology of diseases vectored by these mosquitoes. Our results indicate that the greatest impact on force of infection is expected to derive from the chemical’s lethal effect but delayed biting and associated negative feedbacks on the vector population could elicit substantial impact in the absence of lethality. The relative contributions of these effects depend on coverage, chemical dose, mechanism of action, and housing density. We also demonstrate potential adverse impacts of increased partial blood-feeding and reduced exiting, which could offset gains achieved by other effects. Our analysis demonstrates how small-scale experimental data can be leveraged to derive expectations of epidemiological impact of SRs deployed at larger scales.
A Multiplex Autoantibody Panel for Early Detection of Autoimmune Disease Activity

Background: Detection of autoantibodies has played a consolidate role in diagnosis of systemic autoimmune disorders. A cascade autoantibody testing is usually performed by employing antinuclear antibodies (ANA) test as a first screening test and the other tests as second level determinations. Here, we present that supplementing extractable nuclear antigens (ENA) tests to the ANA test may capture more autoimmunity and provide critical medical information at an early stage. In this study, we evaluated the clinical significance of a multiplex ANA + ENA panel. Methods: A cohort of 110 subjects, identified as ANA negative but ENA positive, were followed up for two years. The detection of their ANA and anti-ENA autoantibodies was assessed with a multiplex ANA + ENA panel at Vibrant America Clinical Laboratory. Results: During two years of multi-visit follow-up, 23 out of 110 subjects (20.9%) were found to become ANA positive within an average of 385 (±144) days. Histone (50/110, 45.5%) and Chromatin (25/110, 22.7%) antibodies were the most frequently found antibodies at their first visits. The subjects who were positive for RNP (5/8, 62.5%) and SSA (Ro) (10/22, 45.5%) have the highest ratio of conversion to positive ANA. No significant correlation was observed between the conversion frequency and the number of anti-ENA antibodies being carried. Conclusion: This study, which followed up on the subjects who had disparate ANA and ENA test results, showed that anti-ENA antibodies may exist years earlier than ANA. Combining ENA tests with ANA screening may reduce false negatives and improve sensitivity.
Comparative Pathogenesis Of COVID-19, MERS And SARS In A Non-Human Primate Model

A novel coronavirus, SARS-CoV-2, was recently identified in patients with an acute respiratory syndrome, COVID-19. To compare its pathogenesis with that of previously emerging coronaviruses, we inoculated cynomolgus macaques with SARS-CoV-2 or MERS-CoV and compared with historical SARS-CoV infections. In SARS-CoV-2-infected macaques, virus was excreted from nose and throat in absence of clinical signs, and detected in type I and II pneumocytes in foci of diffuse alveolar damage and mucous glands of the nasal cavity. In SARS-CoV-infection, lung lesions were typically more severe, while they were milder in MERS-CoV infection, where virus was detected mainly in type II pneumocytes. These data show that SARS-CoV-2 can cause a COVID-19-like disease, and suggest that the severity of SARS-CoV-2 infection is intermediate between that of SARS-CoV and MERS-CoV. One Sentence Summary SARS-CoV-2 infection in macaques results in COVID-19-like disease with prolonged virus excretion from nose and throat in absence of clinical signs.
Summary statistic analyses do not correct confounding bias

LD SCore regression (LDSC) has become a popular approach to estimate confounding bias, heritability and genetic correlation using only genome wide association study (GWAS) test statistics. SumHer is a newly-introduced alternative with similar aims. We show using theory and simulations that both approaches fail to adequately account for confounding bias, even when the assumed heritability model is correct. Consequently, these methods may estimate heritability poorly if there was inadequate adjustment for confounding in the original GWAS analysis. We also show that choice of summary statistic for use in LDSC or SumHer can have a large impact on resulting inferences. Further, covariate adjustments in the original GWAS can alter the target of heritability estimation, which can be problematic when LDSC or SumHer is applied to test statistics from a meta-analysis of GWAS with different covariate adjustments.
Controlling minimal and maximal hook-length of the bacterial flagellum

Hook-length control is a central checkpoint during assembly of the bacterial flagellum. During hook growth, a 405 amino acids (aa) protein, FliK, is intermittently secreted and thought to function as a molecular measuring tape that, in Salmonella, controls hook-length to 55 nm ± 6 nm. The underlying mechanism involves interactions of both the α-helical, N-terminal domain of FliK (FliKN) with the hook and hook cap, and of its C-terminal domain with a component of the export apparatus. However, various deletion mutants of FliKN display uncontrolled hook-length, which is not consistent with a ruler mechanism. Here, we carried out an extensive deletion analysis of FliKN to investigate its contribution in the hook-length control mechanism. We identified FliKN mutants deleted for up to 80 aa that retained wildtype motility. However, the short FliK variants did not produce shorter hook-lengths as expected from a physical ruler. Rather, the minimal length of the hook depends on the level of hook protein production and secretion. Our results thus support a model in which FliK functions as a hook growth terminator protein that limits the maximal length of the hook, and not as a molecular ruler that physically measures hook-length.
HIV and Depression: A Potential Role for Attention Training in Prevention and Treatment

Much research indicates a strong relationship between depressive symptoms and poor health behaviors, including those key to HIV infection and unfavorable treatment outcomes. Given the role of attention bias for negative stimuli in the development and maintenance of depressive symptoms, attention bias modification (ABM) training has gained growing support as a promising clinical approach. ABM is a computerized treatment designed to induce changes in mood and behavior by retraining an individual’s attentional focus. Using explicit instructions and trial-by-trial feedback, this preliminary study explored the potential utility of a single session of ABM training in addressing depressive symptoms among individuals at heightened vulnerability for poor HIV-related health behaviors. The sample, recruited from a clinic that provides services to residents of a Los Angeles community impacted by high HIV infection rates, consisted of 14 African American men who have sex with men (MSM). Participants exhibited a significant reduction in attention bias for negative emotional stimuli following a single session of attention training. Engagement with negative stimuli was lower after training than before training regardless of trial type. This study suggests that brief attention training sessions using novel procedures designed to enhance the learning experience of participants could be employed to address depressive symptoms among individuals at risk for poor HIV-related health behaviors. Future studies should employ these procedures as part of multisession attention trainings with repeated measures of attention bias and depressive symptoms.
An agent-based model of dengue virus transmission shows how multiple uncertainties about vaccine efficacy influence public health impact projections

Given the limited effectiveness of strategies based solely on vector control to reduce dengue virus (DENV) transmission, it is expected that an effective vaccine could play a pivotal role in reducing the global disease burden of dengue. Of several dengue vaccines under development, Dengvaxia® from Sanofi Pasteur recently became the first to become licensed in select countries and to achieve WHO recommendation for use in certain settings, despite the fact that a number of uncertainties about its profile complicate projections of its public health impact. We used a stochastic, agent-based model for DENV transmission to perform simulations of the public health impact of dengue vaccines in light of two key uncertainties: (1) “statistical uncertainty” about the numerical value of the vaccine’s efficacy against disease, and (2) “biological uncertainty” about the extent to which its efficacy against disease derives from the amelioration of symptoms, blocking of DENV infection, or some combination thereof. Simulations of a generic dengue vaccine showed that the proportion of disease episodes averted following 20 years of routine vaccination of nine-year olds at 80% coverage was sensitive to both the numerical value of vaccine efficacy and to the extent to which efficacy derives from blocking of DENV infection. Simulations of a vaccine resembling Dengvaxia® took into account that vaccine trial results substantially reduced statistical uncertainty but did not address biological uncertainty, resulting in the proportion of disease episodes averted being more sensitive to biological uncertainty than to statistical uncertainty. Taken together, our results indicate limitations associated with the use of symptomatic disease as the primary endpoint of dengue vaccine trials and highlight the importance of considering multiple forms of uncertainty in projections of a vaccine’s public health impact.
Poly(ADP-ribose) glycohydrolase promotes formation and homology-directed repair of meiotic DNA double-strand breaks independent of its catalytic activity

Poly(ADP-ribosyl)ation is a reversible post-translational modification synthetized by ADP-ribose transferases and removed by poly(ADP-ribose) glycohydrolase (PARG), which plays important roles in DNA damage repair. While well-studied in somatic tissues, much less is known about poly(ADP-ribosyl)ation in the germline, where DNA double-strand breaks are introduced by a regulated program and repaired by crossover recombination to establish a tether between homologous chromosomes. The interaction between the parental chromosomes is facilitated by meiotic specific adaptation of the chromosome axes and cohesins, and reinforced by the synaptonemal complex. Here, we uncover an unexpected role for PARG in promoting the induction of meiotic DNA breaks and their homologous recombination-mediated repair in Caenorhabditis elegans. PARG-1/PARG interacts with both axial and central elements of the synaptonemal complex, REC-8/Rec8 and the MRN/X complex. PARG-1 shapes the recombination landscape and reinforces the tightly regulated control of crossover numbers without requiring its catalytic activity. We unravel roles in regulating meiosis, beyond its enzymatic activity in poly(ADP-ribose) catabolism.
YAP Orchestrates Heterotypic Endothelial Cell Communication via HGF/c-MET Signaling in Liver Tumorigenesis

YAP-dependent changes of the liver vascular niche comprise the formation of heterologous communication hubs in which tumor cell-derived factors modify the cross-talk between EC subpopulations. The oncogene yes-associated protein (YAP) controls liver tumor initiation and progression via cell extrinsic functions by creating a tumor-supporting environment in conjunction with cell autonomous mechanisms. However, how YAP controls organization of the microenvironment and in particular the vascular niche, which contributes to liver disease and hepatocarcinogenesis, is poorly understood. To investigate heterotypic cell communication, we dissected murine and human liver endothelial cell (EC) populations into liver sinusoidal endothelial cells (LSEC) and continuous endothelial cells (CEC) through histomorphological and molecular characterization. In YAPS127A-induced tumorigenesis, a gradual replacement of LSECs by CECs was associated with dynamic changes in the expression of genes involved in paracrine communication. The formation of new communication hubs connecting CECs and LSECs included the hepatocyte growth factor (Hgf)/c-Met signaling pathway. In hepatocytes and tumor cells, YAP/TEA domain transcription factor 4 (TEAD4)–dependent transcriptional induction of osteopontin (Opn) stimulated c-Met expression in EC with CEC phenotype, which sensitized these cells to the promigratory effects of LSEC-derived Hgf. In human hepatocellular carcinoma, the presence of a migration-associated tip-cell signature correlated with poor clinical outcome and the loss of LSEC marker gene expression. The occurrence of c-MET–expressing CECs in human liver cancer samples was confirmed at the single-cell level. In summary, YAP-dependent changes of the liver vascular niche comprise the formation of heterologous communication hubs in which tumor cell–derived factors modify the cross-talk between LSECs and CECs via the HGF/c-MET axis. Significance: YAP-dependent changes of the liver vascular niche comprise the formation of heterologous communication hubs in which tumor cell-derived factors modify the cross-talk between EC subpopulations. Graphical Abstract: http://cancerres.aacrjournals. org/content/canres/80/24/5502/F1.large. jpg. Graphical Abstract
The Length of Lipoteichoic Acid Polymers Controls Staphylococcus aureus Cell Size and Envelope Integrity

Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of community- and hospital-acquired infections and is responsible for a large fraction of deaths caused by antibiotic-resistant bacteria. S. aureus is surrounded by a complex cell envelope that protects it from antimicrobial compounds and other stresses. Here, we show that controlling the length of an essential cell envelope polymer, lipoteichoic acid, is critical for controlling S. aureus cell size and cell envelope integrity. We also show that genes involved in LTA length regulation are required for resistance to beta-lactam antibiotics in MRSA. The proteins encoded by these genes may be targets for combination therapy with an appropriate beta-lactam. ABSTRACT The opportunistic pathogen Staphylococcus aureus is protected by a cell envelope that is crucial for viability. In addition to peptidoglycan, lipoteichoic acid (LTA) is an especially important component of the S. aureus cell envelope. LTA is an anionic polymer anchored to a glycolipid in the outer leaflet of the cell membrane. It was known that deleting the gene for UgtP, the enzyme that makes this glycolipid anchor, causes cell growth and division defects. In Bacillus subtilis, growth abnormalities from the loss of ugtP have been attributed to both the absence of the encoded protein and the loss of its products. Here, we show that growth defects in S. aureus ugtP deletion mutants are due to the long, abnormal LTA polymer that is produced when the glycolipid anchor is missing from the outer leaflet of the membrane. Dysregulated cell growth leads to defective cell division, and these phenotypes are corrected by mutations in the LTA polymerase gene, ltaS, that reduce polymer length. We also show that S. aureus mutants with long LTA are sensitized to cell wall hydrolases, beta-lactam antibiotics, and compounds that target other cell envelope pathways. We conclude that control of LTA polymer length is important for S. aureus physiology and promotes survival under stressful conditions, including antibiotic stress. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of community- and hospital-acquired infections and is responsible for a large fraction of deaths caused by antibiotic-resistant bacteria. S. aureus is surrounded by a complex cell envelope that protects it from antimicrobial compounds and other stresses. Here, we show that controlling the length of an essential cell envelope polymer, lipoteichoic acid, is critical for controlling S. aureus cell size and cell envelope integrity. We also show that genes involved in LTA length regulation are required for resistance to beta-lactam antibiotics in MRSA. The proteins encoded by these genes may be targets for combination therapy with an appropriate beta-lactam.
Proteomics of osmoregulatory responses in threespine stickleback gills

The gill proteome of threespine sticklebacks (Gasterosteus aculeatus) differs greatly in populations that inhabit diverse environments characterized by different temperature, salinity, food availability, parasites, and other parameters. To assess the contribution of a specific environmental parameter to such differences it is necessary to isolate its effects from those of other parameters. In this study the effect of environmental salinity on the gill proteome of G. aculeatus was isolated in controlled mesocosm experiments. Salinity-dependent changes in the gill proteome were analyzed by LC/MSMS data-independent acquisition (DIA) and Skyline. Relative abundances of 1691 proteins representing the molecular phenotype of stickleback gills were quantified using previously developed MSMS spectral and assay libraries in combination with DIA quantitative proteomics. General stress responses were distinguished from osmoregulatory protein abundance changes by their consistent occurrence during both hypo- and hyper-osmotic salinity stress in six separate mesocosm experiments. If the abundance of a protein was consistently regulated in opposite directions by hyper- versus hypo-osmotic salinity stress, then it was considered an osmoregulatory protein. In contrast, if protein abundance was consistently increased irrespective of whether salinity was increased or decreased, then it was considered a general stress response protein. KEGG pathway analysis revealed that the salivary secretion, inositol phosphate metabolism, valine, leucine and isoleucine degradation, citrate cycle, oxidative phosphorylation, and corresponding endocrine and extracellular signaling pathways contain most of the osmoregulatory gill proteins whose abundance is directly proportional to environmental salinity. Most proteins that were inversely correlated with salinity map to KEGG pathways that represent proteostasis, immunity, and related intracellular signaling processes. General stress response proteins represent fatty and amino acid degradation, purine metabolism, focal adhesion, mRNA surveillance, phagosome, endocytosis, and associated intracellular signaling KEGG pathways. These results demonstrate that G. aculeatus responds to salinity changes by adjusting osmoregulatory mechanisms that are distinct from transient general stress responses to control compatible osmolyte synthesis, transepithelial ion transport, and oxidative energy metabolism. Furthermore, this study establishes salinity as a key factor for causing the regulation of numerous proteins and KEGG pathways with established functions in proteostasis, immunity, and tissue remodeling. We conclude that the corresponding osmoregulatory gill proteins and KEGG pathways represent molecular phenotypes that promote transepithelial ion transport, cellular osmoregulation, and gill epithelial remodeling to adjust gill function to environmental salinity.