Miracle-dz/UniFAR-FTUs huggingface dataset:
Localization of infection in neonatal rhesus macaques after oral viral challenge

While vertical transmission of human immunodeficiency virus (HIV) can occur in utero and during delivery and through breastfeeding. We utilized Positron Emission Tomography (PET) imaging coupled with fluorescent microscopy of 64Cu-labeled photoactivatable-GFP-HIV (PA-GFP-BaL) to determine how HIV virions distribute and localize in neonatal rhesus macaques two and four hours after oral viral challenge. Our results show that by four hours after oral viral exposure, HIV virions localize to and penetrate the rectal mucosa. We also used a dual viral challenge with a non-replicative viral vector and a replication competent SHIV-1157ipd3N4 to examine viral transduction and dissemination at 96 hours. Our data show that while SHIV-1157ipd3N4 infection can be found in the oral cavity and upper gastrointestinal (GI) tract, the small and large intestine contained the largest number of infected cells. Moreover, we found that T cells were the biggest population of infected immune cells. Thus, thanks to these novel technologies, we are able to visualize and delineate of viral distribution and infection throughout the entire neonatal GI tract during acute viral infection. Author Summary Approximately 1.8 million children are currently living with human immunodeficiency virus (HIV). While mother-to-child HIV transmission can occur in utero and during delivery, it most commonly occurs through breastfeeding, creating the need to understand how the virus moves throughout the body and infects the infant once breast milk is consumed. Here, we used multiple imaging techniques and PCR to determine how HIV distributes throughout the gastrointestinal tract after oral viral exposure and in which tissues and cell types become acutely infected. We found that HIV rapidly spreads throughout and penetrates the entire gastrointestinal tract as early as four hours after exposure. We also found that the intestine contained the largest number of infected cells at 96 hours and that most cells infected were T cells. Our study shows that these imaging technologies allow for the examination of viral distribution and infection in a rhesus macaque model.
Evolution of protection after maternal immunization for respiratory syncytial virus in cotton rats

Maternal anti-respiratory syncytial virus (RSV) antibodies acquired by the fetus through the placenta protect neonates from RSV disease through the first weeks of life. In the cotton rat model of RSV infections, we previously reported that immunization of dams during pregnancy with virus-like particles assembled with mutation stabilized pre-fusion F protein as well as the wild type G protein resulted in robust protection of their offspring from RSV challenge (Blanco, et al Journal of Virology 93: e00914-19, https://doi.org/10.1128/JVI.00914-19). Here we describe the durability of those protective responses in dams, the durability of protection in offspring, and the transfer of that protection to offspring of two consecutive pregnancies without a second boost immunization. We report that four weeks after birth, offspring of the first pregnancy were significantly protected from RSV replication in both lungs and nasal tissues after RSV challenge, but protection was reduced in pups at 6 weeks after birth. However, the overall protection of offspring of the second pregnancy was considerably reduced, even at four weeks of age. This drop in protection occurred even though the levels of total anti-pre-F IgG and neutralizing antibody titers in dams remained at similar, high levels before and after the second pregnancy. The results are consistent with an evolution of antibody properties in dams to populations less efficiently transferred to offspring or the less efficient transfer of antibodies in elderly dams. Author Summary Respiratory syncytial virus (RSV) is a major cause of acute lower respiratory tract infection of infants. Because there is no licensed vaccine for RSV as well as potential safety issues with any new vaccine, protection of infants from RSV is problematic. A possible safe approach for infant protection is the transfer of maternal anti-RSV antibodies, induced by immunization, across the placenta to the fetus serving to protect the newborn for months after birth. In a cotton rat model, we have previously shown that maternal immunization with virus-like particles assembled with the RSV F and G proteins protects offspring from RSV infection. Here we describe protection of offspring, following a single immunization, through two pregnancies showing that offspring of the first were well protected from RSV challenge. However, offspring of the second pregnancy were very weakly protected although the levels of total anti-pre-F antibodies and neutralizing antibody titers in the dams remained at constant and high levels before and after the second pregnancy. This result is consistent with an evolution of antibody properties in the dams to those less efficiently transferred to offspring and highlights the importance of appropriate strategies for maternal immunization, such as immunization during each pregnancy.
Functional connectomics spanning multiple areas of mouse visual cortex

To understand the brain we must relate neurons’ functional responses to the circuit architecture that shapes them. Here, we present a large functional connectomics dataset with dense calcium imaging of a millimeter scale volume. We recorded activity from approximately 75,000 neurons in primary visual cortex (VISp) and three higher visual areas (VISrl, VISal and VISlm) in an awake mouse viewing natural movies and synthetic stimuli. The functional data were co-registered with a volumetric electron microscopy (EM) reconstruction containing more than 200,000 cells and 0.5 billion synapses. Subsequent proofreading of a subset of neurons in this volume yielded reconstructions that include complete dendritic trees as well the local and inter-areal axonal projections that map up to thousands of cell-to-cell connections per neuron. Here, we release this dataset as an open-access resource to the scientific community including a set of tools that facilitate data retrieval and downstream analysis. In accompanying papers we describe our findings using the dataset to provide a comprehensive structural characterization of cortical cell types1–3 and the most detailed synaptic level connectivity diagram of a cortical column to date2, uncovering unique cell-type specific inhibitory motifs that can be linked to gene expression data4. Functionally, we identify new computational principles of how information is integrated across visual space5, characterize novel types of neuronal invariances6 and bring structure and function together to decipher a general principle that wires excitatory neurons within and across areas7, 8.
Control of neurotransmitter release and presynaptic plasticity by re-orientation of membrane-bound Munc13-1

Munc13-1 plays a central role in neurotransmitter release through its conserved C-terminal region, which includes a diacyglycerol (DAG)-binding C1 domain, a Ca2+/PIP2-binding C2B domain, a MUN domain and a C2C domain. Munc13-1 was proposed to bridge synaptic vesicles to the plasma membrane in two different orientations mediated by distinct interactions of the C1C2B region with the plasma membrane: i) one involving a polybasic face that yields a perpendicular orientation of Munc13-1 and hinders release; and ii) another involving the DAG-Ca2+-PIP2-binding face that induces a slanted orientation and facilitates release. Here we have tested this model and investigated the role of the C1C2B region in neurotransmitter release. We find that K603E or R769E point mutations in the polybasic face severely impair synaptic vesicle priming in primary murine hippocampal cultures, and Ca2+-independent liposome bridging and fusion in in vitro reconstitution assays. A K720E mutation in the polybasic face and a K706E mutation in the C2B domain Ca2+-binding loops have milder effects in reconstitution assays and do not affect vesicle priming, but enhance or impair Ca2+-evoked release, respectively. The phenotypes caused by combining these mutations are dominated by the K603E and R769E mutations. Our results show that the C1-C2B region of Munc13-1 plays a central role in vesicle priming and support the notion that re-orientation of Munc13-1 controls neurotransmitter release and short-term presynaptic plasticity.
Species-wide phylogenomics of the Staphylococcus aureus agr operon reveals convergent evolution of frameshift mutations

Staphylococcus aureus is a prominent nosocomial pathogen that causes several life-threatening diseases such as pneumonia and bacteremia. S. aureus modulates expression of its arsenal of virulence factors through sensing and integrating responses to environmental signals. The agr (accessory gene regulator) quorum sensing (QS) system is a major regulator of virulence phenotypes in S. aureus. There are four agr specificity groups each with a different autoinducer peptide sequence (encoded by the agrD gene). Though agr is critical for expression of many toxins, paradoxically, S. aureus strains often have non-functional agr activity due to loss-of-function mutations in the four-gene agr operon. To understand patterns in agr variability across S. aureus, we undertook a species-wide genomic investigation. We developed a software tool (AgrVATE; https://github.com/VishnuRaghuram94/AgrVATE) for typing and detecting frameshift mutations in the agr operon. In an analysis of over 40,000 S. aureus genomes, we showed close association between agr type and S. aureus clonal complex. We also found strong linkage between agrBDC alleles (encoding the peptidase, the autoinducing peptide itself, and the peptide sensor respectively) but not agrA (encoding the -response regulator). More than five percent of genomes were found to have frameshift mutations in the agr operon. Though most mutations occur only once in the entire species, we observed a small number of recurring mutations evolving convergently across different clonal lineages. Phylogenetic patterns suggested that strains with agr frameshifts were evolutionary dead ends. Overall, genomic analysis of agr operon suggests evolution through multiple processes with functional consequences that are not fully understood. Importance Staphylococcus aureus is a globally pervasive pathogen that produces a plethora of toxic molecules that can degrade, evade, or inhibit the host immune cells. Production of these toxins is mainly controlled by an active agr quorum sensing system, which senses and responds to bacterial cell density. However, there are many reports of S. aureus strains with genetic changes leading to impaired agr activity, often found during chronic bloodstream infections, and may be associated with increased disease severity. We developed an open-source software called AgrVATE to type agr systems and identify putative frameshifts. We used AgrVATE for a species-wide genomic survey of S. aureus, finding that more than 5 % of strains in the public database had non-functional agr systems. We also provide new insights into the evolution of these genetic mutations in the agr system. Overall, this study contributes to our understanding of a common but relatively understudied means of virulence regulation in S. aureus.
METTL18-mediated histidine methylation of RPL3 modulates translation elongation for proteostasis maintenance

Protein methylation occurs predominantly on lysine and arginine residues, but histidine also serves as a substrate for the modification. However, a limited number of enzymes responsible for this modification have been reported. Moreover, the biological role of histidine methylation has remained poorly understood. Here, we report that human METTL18 is a histidine methyltransferase for the ribosomal protein RPL3 and that the modification specifically slows ribosome traverse on tyrosine codons, allowing the proper folding of synthesized proteins. By performing an in vitro methylation assay with a methyl donor analog and quantitative mass spectrometry, we found that His245 of RPL3 is methylated at the τ-N position by METTL18. Structural comparison of the modified and unmodified ribosomes showed stoichiometric modification and suggested a role in translation tuning. Indeed, genome-wide ribosome profiling revealed suppressed ribosomal translocation at tyrosine codons by RPL3 methylation. Because the slower elongation provides enough time for nascent protein folding, RPL3 methylation protects cells from the cellular aggregation of Tyr-rich proteins. Our results reveal histidine methylation as an example of a “ribosome code” that ensures proteome integrity in cells.
A new paradigm for leprosy diagnosis based on host gene expression

Transcriptional profiling is a powerful tool to investigate and detect human diseases. In this study, we used bulk RNA-sequencing (RNA-Seq) to compare the transcriptomes in skin lesions of leprosy patients or controls affected by other dermal conditions such as granuloma annulare, a confounder for paucibacillary leprosy. We identified five genes capable of accurately distinguishing multibacillary and paucibacillary leprosy from other skin conditions. Indoleamine 2,3-dioxygenase 1 (IDO1) expression alone was highly discriminatory, followed by TLR10, BLK, CD38, and SLAMF7, whereas the HS3ST2 and CD40LG mRNA separated multi- and paucibacillary leprosy. Finally, from the main differentially expressed genes (DEG) and enriched pathways, we conclude that paucibacillary disease is characterized by epithelioid transformation and granuloma formation, with an exacerbated cellular immune response, while multibacillary leprosy features epithelial-mesenchymal transition with phagocytic and lipid biogenesis patterns in the skin. These findings will help catalyze the development of better diagnostic tools and potential host-based therapeutic interventions. Finally, our data may help elucidate host-pathogen interplay driving disease clinical manifestations. Author Summary Despite effective treatment, leprosy is still a significant public health issue in more than 120 countries, with more than 200 000 new cases yearly. The disease is caused mainly by Mycobacterium leprae, a slow-growing bacillus still uncultivable in axenic media. This limitation has hampered basic research into host-pathogen interaction and the development of new diagnostic assays. Currently, leprosy is diagnosed clinically, with no standalone diagnostic assay accurate enough for all clinical forms. Here, we use RNA-seq transcriptome profiling in leprosy lesions and granuloma annulare to identify mRNA biomarkers with potential diagnostic applications. Also, we explored new pathways that can be useful in further understanding the host-pathogen interaction and how the bacteria bypass host immune defenses. We found that IDO1, a gene involved with tryptophan catabolism, is an excellent candidate for distinguishing leprosy lesions from other dermatoses. Additionally, we observed that a previous signature of keratinocyte development and cornification negatively correlates with epithelial-mesenchymal transition genes in the skin, suggesting new ways in which the pathogen may subvert its host to survive and spread throughout the body. Our study identifies new mRNA biomarkers that can improve leprosy diagnostics and describe new insights about host-pathogen interactions in human skin.
Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin

Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically required for small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin.
Is There Any Association Between Chronic Periodontitis and Anxiety in Adults? A Systematic Review

Periodontitis is a multifactorial disease triggered by dysbiotic biofilms, involving the host's immune response, systemic and behavioral factors, including psychosocial conditions. This systematic review aimed to investigate the possible association between periodontitis and anxiety in adults. Searches were performed in PubMed, Scopus, Web of Science, Lilacs, Cochrane, and OpenGrey databases, without language restrictions, considering studies in adults (P-Participants), with (E-Exposure) and without periodontitis (C- Comparison) in an outcome of association with anxiety (O-outcome). Methodological quality assessment was carried out using the Newcastle-Ottawa protocol for case-control and cross-sectional studies, followed by an analysis of the level of evidence using the GRADE tool. Metanalysis was not performed due to several differences in methods applied by authors in primary studies. Eleven observational studies were selected according to the inclusion criteria from the total of 6,380 studies retrieved from databases. Eight studies demonstrated higher anxiety levels in subjects with periodontitis, among which only one study presented a high risk of bias. The GRADE tool revealed a low level of evidence for the anxiety outcome measured by the State-Trait Anxiety Inventory (STAI), both for case-control and cross-sectional studies. However, since anxiety may affect the quality of life of many subjects, it reinforces the need for further studies that evaluate this association for more extended periods. Clinical Trial Registration:PROSPERO-CRD42020190445.
Agreement of Bioreactance Cardiac Output Monitoring With Thermodilution in Healthy Standing Horses

Bioreactance is the continuous analysis of transthoracic voltage variation in response to an applied high frequency transthoracic current and was recently introduced for non-invasive cardiac output measurement (NICOM). We evaluated NICOM compared to thermodilution (TD) in adult horses. Six healthy horses were used for this prospective, blinded, experimental study. Cardiac output (CO) measurements were performed simultaneously using TD and the bioreactance method. Different cardiac output scenarios were established using xylazine (0.5 mg/kg IV) and dobutamine (1.5–3 mcg/kg/min). Statistical analysis was performed by calculating the concordance rate, performing a regression analysis, Pearson correlation, and Bland Altman. The TD-based CO and NICOM values were highly correlated for low, normal and high CO values with an overall correlation coefficient. A 4-quadrant plot showed an 89% rate of concordance. The linear regression calculated a relationship between NICOM and TDCO of Y = 0.4874 · X + 0.5936. For the corrected Bland Altman agreement, the mean bias and lower/upper limits of agreement were −0.26 and −3.88 to 3.41 L/min, respectively. Compared to TD, bioreactance- based NICOM showed good accuracy at induced low, normal, and high CO states in normal horses. Future studies performed under more clinical conditions will show if this monitor can help to assess hemodynamic status and guide therapy in horses in ICU settings and under general anesthesia.
Isolation and Genetic Characterization of Canine Parvovirus in a Malayan Tiger

Naïve Felidae in the wild may harbor infectious viruses of importance due to cross-species transmission between the domesticated animals or human–wildlife contact. However, limited information is available on virus shedding or viremia in the captive wild felids, especially in Malaysia. Four infectious viruses of cat, feline herpesvirus (FHV), feline calicivirus (FCV), canine distemper virus (CDV), and canine parvovirus (CPV), were screened in leopards, feral cats, and tigers in Malaysia based on virus isolation in Crandell-Rees feline kidney (CRFK) cells, PCR/RT-PCR, and whole-genome sequencing analysis of the positive isolate. From a total of 36 sera collected, 11 samples showed three consecutive cytopathic effects in the cell culture and were subjected to PCR using specific primers for FHV, FCV, CDV, and CPV. Only one sample from a Malayan tiger was detected positive for CPV. The entire viral genome of CPV (UPM-CPV15/P. tigris jacksoni; GenBank Accession number MW380384) was amplified using the Sanger sequencing approach. Genome sequencing of the isolate revealed 99.13, 98.65, and 98.40% close similarity to CPV-31, CPV-d Cornell #320, and CPV-15 strains, respectively, and classified as CPV-2a. Time-scaled Bayesian Maximum Clade Credibility tree for the non-structural (NS) genes of CPV showed a close relationship to the isolates CPV-CN SD6_2014 and KSU7-SD_2004 from China and USA, respectively, while the capsid gene showed the same ancestor as the FPV-BJ04 strain from China. The higher evolution rate of the capsid protein (CP) (VP 1 and VP2) [1.649 × 10−5 (95% HPD: 7.626 × 10−3 to 7.440 × 10−3)] as compared to the NS gene [1.203 × 10−4 (95% HPD: 6.663 × 10−3 to 6.593 × 10−3)] was observed in the CPV from this study, and fairly higher than other parvovirus species from the Protoparvovirus genus. Genome sequencing of the isolated CPV from a Malayan tiger in the present study provides valuable information about the genomic characteristics of captive wild felids, which may add information on the presence of CPV in species other than dogs.
The Small Protein YmoA Controls the Csr System and Adjusts Expression of Virulence-Relevant Traits of Yersinia pseudotuberculosis

Virulence gene expression of Yersinia pseudotuberculosis changes during the different stages of infection and this is tightly controlled by environmental cues. In this study, we show that the small protein YmoA, a member of the Hha family, is part of this process. It controls temperature- and nutrient-dependent early and later stage virulence genes in an opposing manner and co-regulates bacterial stress responses and metabolic functions. Our analysis further revealed that YmoA exerts this function by modulating the global post-transcriptional regulatory Csr system. YmoA pre-dominantly enhances the stability of the regulatory RNA CsrC. This involves a stabilizing stem-loop structure within the 5′-region of CsrC. YmoA-mediated CsrC stabilization depends on H-NS, but not on the RNA chaperone Hfq. YmoA-promoted reprogramming of the Csr system has severe consequences for the cell: we found that a mutant deficient of ymoA is strongly reduced in its ability to enter host cells and to disseminate to the Peyer’s patches, mesenteric lymph nodes, liver and spleen in mice. We propose a model in which YmoA controls transition from the initial colonization phase in the intestine toward the host defense phase important for the long-term establishment of the infection in underlying tissues.