A naturally occurring variant of MBD4 causes maternal germline hypermutation in primates.

As part of an ongoing genome sequencing project at the Oregon National Primate Research Center, we identified a rhesus macaque with a rare homozygous frameshift mutation in the gene methyl-CpG binding domain 4, DNA glycosylase (MBD4). MBD4 is responsible for the repair of C > T deamination mutations at CpG dinucleotides and has been linked to somatic hypermutation and cancer predisposition in humans. We show here that MBD4-associated hypermutation also affects the germline: The six offspring of the MBD4-null dam have a fourfold to sixfold increase in de novo mutation burden. This excess burden was predominantly C > T mutations at CpG dinucleotides consistent with MBD4 loss of function in the dam. There was also a significant excess of C > T at CpA sites, indicating an important, unappreciated role for MBD4 to repair deamination in CpA contexts. The MBD4-null dam developed sustained eosinophilia later in life, but we saw no other signs of neoplastic processes associated with MBD4 loss of function in humans nor any obvious disease in the hypermutated offspring. This work provides the first evidence for a genetic factor causing hypermutation in the maternal germline of a mammal and adds to the very small list of naturally occurring variants known to modulate germline mutation rates in mammals.

Comparative single-cell analysis of biopsies clarifies pathogenic mechanisms in Klinefelter syndrome.

Klinefelter syndrome (KS), also known as 47, XXY, is characterized by a distinct set of physiological abnormalities, commonly including infertility. The molecular basis for Klinefelter-related infertility is still unclear, largely because of the cellular complexity of the testis and the intricate endocrine and paracrine signaling that regulates spermatogenesis. Here, we demonstrate an analysis framework for dissecting human testis pathology that uses comparative analysis of single-cell RNA-sequencing data from the biopsies of 12 human donors. By comparing donors from a range of ages and forms of infertility, we generate gene expression signatures that characterize normal testicular function and distinguish clinically distinct forms of male infertility. Unexpectedly, we identified a subpopulation of Sertoli cells within multiple individuals with KS that lack transcription from the XIST locus, and the consequence of this is increased X-linked gene expression compared to all other KS cell populations. By systematic assessment of known cell signaling pathways, we identify 72 pathways potentially active in testis, dozens of which appear upregulated in KS. Altogether our data support a model of pathogenic changes in interstitial cells cascading from loss of X inactivation in pubertal Sertoli cells and nominate dosage-sensitive factors secreted by Sertoli cells that may contribute to the process. Our findings demonstrate the value of comparative patient analysis in mapping genetic mechanisms of disease and identify an epigenetic phenomenon in KS Sertoli cells that may prove important for understanding causes of infertility and sex chromosome evolution.

SATINN: an automated neural network-based classification of testicular sections allows for high-throughput histopathology of mouse mutants.

MOTIVATION: The mammalian testis is a complex organ with a cellular composition that changes smoothly and cyclically in normal adults. While testis histology is already an invaluable tool for identifying and describing developmental differences in evolution and disease, methods for standardized, digital image analysis of testis are needed to expand the utility of this approach. RESULTS: We developed SATINN (Software for Analysis of Testis Images with Neural Networks), a multi-level framework for automated analysis of multiplexed immunofluorescence images from mouse testis. This approach uses residual learning to train convolutional neural networks (CNNs) to classify nuclei from seminiferous tubules into seven distinct cell types with an accuracy of 81.7%. These cell classifications are then used in a second-level tubule CNN, which places seminiferous tubules into one of 12 distinct tubule stages with 57.3% direct accuracy and 94.9% within ±1 stage. We further describe numerous cell- and tubule-level statistics that can be derived from wild-type testis. Finally, we demonstrate how the classifiers and derived statistics can be used to rapidly and precisely describe pathology by applying our methods to image data from two mutant mouse lines. Our results demonstrate the feasibility and potential of using computer-assisted analysis for testis histology, an area poised to evolve rapidly on the back of emerging, spatially resolved genomic and proteomic technologies. AVAILABILITY AND IMPLEMENTATION: The source code to reproduce the results described here and a SATINN standalone application with graphic-user interface are available from http://github.com/conradlab/SATINN. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Expansion of the area of occurrence of the genus Anochetus Mayr 1861 (Hymenoptera: Formicidae).

The study was carried out on an agroecological property located in Cologne São Manoel, 8th district of Pelotas, RS, Brazil. Anochetus neglectus Emery, 1894 was collected in an area of peach orchard that has been under an agroecological system for 18 years. This record expands the area of ​​occurrence and distribution of this rare species in the Neotropical Region.

What is the influence of agroecological and conventional crops under ant assemblages?

The objective of the study was to compare the richness and diversity of ant assemblages in an agroecological system under peach orchard, conventional system under peach orchard cultivation and native vegetation in rural properties located in a Pampa Biome. The study was conducted in four samplings in 2017: 1st and 09th March (summer); 24th and 31st July (winter); and four samplings in 2018: 23rd and 30th January (summer); 31st July and 07th August (winter). Pitfall traps were used. The assemblages were characterized and compared using richness, number of occurrences of ants, Shannon diversity (H'), equitability, rarefaction analysis and Chao 1. The association of the species with the samples was evaluated by a Principal Component Analysis (PCA). The agroecological system had the highest number of occurrences, while the conventional orchard the lowest number. Richness and abundance were greatest during the summer. The conventional peach orchard obtained the lowest H' for both seasons when compared to the agroecological orchard and native vegetation. The PCA explained 77.40% of the occurrence of ants in the environments and in the seasons. The results found demonstrated that conservationist systems tend to harbor greater wealth and diversity of ant assemblages, as well as occurring in native áreas.

Effects of additives in wet brewery residue silage on lamb carcass traits and meat quality.

The objective was to evaluate the use of wet brewery residue (WBR) silage additives on carcass characteristics and sheep meat quality. Thirty-two Santa Inês male sheep uncastrated with initial body weight of 22.61 ± 7.2 kg were allocated to a completely randomized design with four treatments: (1) WBR silage without additive (WBRS), (2) WBR silage with milled corn (WBRS + MC), (3) WBR silage with wheat bran (WBRS + WB), and (4) WBR silage with cassava flour (WBRS + CF) and eight replicates. WBRS + WB resulted in lower cold carcass weight than WBRS + CF; however, this reduction was not sufficient to alter the carcass commercial yield or loin-eye area. The leg cut of animals fed WBRS + WB showed less value than those animals fed with WBRS + CS. The meat lightness of WBRS was higher that of WBRS + MC, WBRS + WB, and WBRS + CF. The cooking loss for WBRS + WB was less than those animals fed with WBRS + CS. However, meat protein, meat cholesterol, and shear force were similar among treatments (17.69%, 42.46 mg/100 g of meat, and 2.48 kgf/cm2, respectively). The use of additives in wet brewery residue silage does not improve carcass characteristics or the quality of sheep meat, and it is therefore recommended to use WBR silage without additives.

Commercially Relevant Orthogonal Multi-Component Supramolecular Hydrogels for Programmed Cell Growth.

This study reports the ability of synthetically simple, commercially viable sugar-derived 1,3:2,4-dibenzylidenesorbitol-4',4"-diacylhydrazide (DBS-CONHNH2 ) to support cell growth. Simple mixing and orthogonal self-sorting can formulate heparin, agarose, and heparin-binding micelles into these gels-easily incorporating additional function. Interestingly, the components used in the gel formulation, direct the ability of cells to grow, meaning the chemical programming of these multi-component gels is directly translated to the biological systems in contact with them. This simple approach has potential for future development in regenerative medicine.

Multispecies Purification of Testicular Germ Cells.

Advanced methods of cellular purification are required to apply genome technology to the study of spermatogenesis. One approach, based on flow cytometry of murine testicular cells stained with Hoechst-33342 (Ho-FACS), has been extensively optimized and currently allows the isolation of 9 germ cell types. This staining technique is straightforward to implement, highly effective at purifying specific germ cell types and yields sufficient cell numbers for high throughput studies. Ho-FACS is a technique that does not require species-specific markers, but whose applicability to other species is largely unexplored. We hypothesized that, due to the similar cell physiology of spermatogenesis across mammals, Ho-FACS could be used to produce highly purified subpopulations of germ cells in mammals other than mouse. To test this hypothesis, we applied Ho-FACS to 4 mammalian species that are widely used in testis research - Rattus norvegicus, Cavia porcellus, Canis familiaris and Sus scrofa domesticus We successfully isolated 4 germ cell populations from these species with average purity of 79% for spermatocytes, and 90% for spermatids and 66% for spermatogonia. Additionally, we compare the performance of mechanical and chemical dissociation for each species, and propose an optimized gating strategy to better discriminate round and elongating spermatids in the mouse, which can potentially be applied to other species. Our work indicates that spermatogenesis may be uniquely accessible among mammalian developmental systems, as a single set of reagents may be sufficient to isolate germ cell populations from many different mammalian species, opening new avenues in the fields of development and male reproductive biology.

Social and health dimensions of climate change in the Amazon.

CONTEXT: The Amazon region has been part of climate change debates for decades, yet attention to its social and health dimensions has been limited. OBJECTIVE: This paper assesses literature on the social and health dimensions of climate change in the Amazon. A conceptual framework underscores multiple stresses and exposures created by interactions between climate change and local social-environmental conditions. METHODS: Using the Thomson-Reuter Web of Science, this study bibliometrically assessed the overall literature on climate change in the Amazon, including Physical Sciences, Social Sciences, Anthropology, Environmental Science/Ecology and Public, Environmental/Occupational Health. From this assessment, a relevant sub-sample was selected and complemented with literature from the Brazilian database SciELO. RESULTS: This sample discusses three dimensions of climate change impacts in the region: livelihood changes, vector-borne diseases and microbial proliferation, and respiratory diseases. This analysis elucidates imbalance and disconnect between ecological, physical and social and health dimensions of climate change and between continental and regional climate analysis, and sub-regional and local levels. CONCLUSION: Work on the social and health implications of climate change in the Amazon falls significantly behind other research areas, limiting reliable information for analytical models and for Amazonian policy-makers and society at large. Collaborative research is called for.

The mutational spectrum of WT1 in male infertility.

PURPOSE: We evaluated the impact of WT1 mutations in isolated severe spermatogenic impairment in a population of European ancestry. WT1 was first identified as the gene responsible for Wilms tumor. It was later associated with a plethora of clinical phenotypes often accompanied by urogenital defects and male infertility. The recent finding of WT1 missense mutations in Chinese azoospermic males without major gonadal malformations broadened the phenotypic spectrum of WT1 defects and motivated this study. MATERIALS AND METHODS: We analyzed the WT1 coding region in a cohort of 194 Portuguese patients with nonobstructive azoospermia and in 188 with severe oligozoospermia with increased depth for the exons encoding the regulatory region of the protein. We also analyzed a group of 31 infertile males with a clinical history of unilateral or bilateral cryptorchidism and 1 patient with anorchia. RESULTS: We found 2 WT1 missense substitutions at higher frequency in patients than in controls. 1) A novel variant in exon 1 (p.Pro130Leu) that disrupted a mammalian specific polyproline stretch in the self-association domain was more frequent in azoospermia cases (0.27% vs 0.13%, p = 0.549). 2) A rare variant in a conserved residue in close proximity to the first zinc finger (pCys350Arg) was more frequent in severe oligozoospermia cases (0.80% vs 0.13%, p = 0.113). CONCLUSIONS: Results suggest a role for rare WT1 damaging variants in severe spermatogenic failure in populations of European ancestry. Large multicenter studies are needed to fully assess the contribution of WT1 genetic alterations to male infertility in the absence of other disease phenotypes.

The human infertility single-cell testis atlas (HISTA): an interactive molecular scRNA-Seq reference of the human testis.

BACKGROUND: Single-cell RNA-seq (scRNA-Seq) has been widely adopted to study gene expression of the human testis. Several datasets of scRNA-Seq from human testis have been generated from different groups processed with different informatics pipelines. An integrated atlas of scRNA-Seq expression constructed from multiple donors, developmental ages, and fertility states would be widely useful for the testis research community. OBJECTIVE: To describe the generation and use of the human infertility single-cell testis atlas (HISTA), an interactive web tool for understanding human spermatogenesis through scRNA-Seq analysis. METHODS: We obtained scRNA-Seq datasets derived from 12 donors, including healthy adult controls, juveniles, and several infertility cases, and reprocessed these data using methods to remove batch effects. Using Shiny, an open-source environment for data visualization, we created numerous interactive tools for exploring the data, some of which support simple statistical hypothesis testing. We used the resulting HISTA browser and its underlying data to demonstrate HISTA's value for testis researchers. RESULTS: A primary application of HISTA is to search by a single gene or a set of genes; thus, we present various analyses that quantify and visualize gene expression across the testis cells and pathology. HISTA also contains machine-learning-derived gene modules ("components") that capture the entire transcriptional landscape of the testis tissue. We show how the use of these components can simplify the highly complex data in HISTA and assist with the interpretation of genes with unknown functions. Finally, we demonstrate the diverse ways HISTA can be used for new data analysis, including hypothesis testing. DISCUSSION AND CONCLUSIONS: HISTA is a research environment that can help scientists organize and understand the high-dimensional transcriptional landscape of the human testis. HISTA has already contributed to published testis research and can be updated as needed with input from the research community or downloaded and modified for individual needs.

Detection of anti-Mycoplasma hyopneumoniae antibodies in backyard pigs in the state of Paraná, Brazil.

Mycoplasma hyopneumoniae is the causative bacterium of porcine enzootic pneumonia and one of the primary etiologic agents of the porcine respiratory disease complex. Most Brazilian commercial pig farms are positive for this pathogen. However, the prevalence of the pathogen in backyard pig farms has not been described, to our knowledge. Therefore, we aimed to determine the prevalence of M. hyopneumoniae in backyard pig farms in the state of Paraná, Brazil. In January-March 2020, we collected 585 serum samples from pigs in 187 non-vaccinated herds. We tested the sera with an indirect ELISA for anti-M. hyopneumoniae antibodies and found that 182 of 585 (31.1%) samples were positive, and were found in 109 of 187 (58.3%) herds assessed.

Deletion of an evolutionarily conserved TAD boundary compromises spermatogenesis in mice.

Spermatogenesis is a complex process that can be disrupted by genetic and epigenetic changes, potentially leading to male infertility. Recent research has rapidly increased the number of protein coding mutations causally linked to impaired spermatogenesis in humans and mice. However, the role of non-coding mutations remains largely unexplored. As a case study to evaluate the effects of non-coding mutations on spermatogenesis, we first identified an evolutionarily conserved topologically associated domain (TAD) boundary near two genes with important roles in mammalian testis function: Dmrtb1 and Lrp8 . We then used CRISPR-Cas9 to generate a mouse line where 26kb of the boundary was removed including a strong and evolutionarily conserved CTCF binding site. ChIP-seq and Hi-C experiments confirmed the removal of the CTCF site and a resulting increase in the DNA-DNA interactions across the domain boundary. Mutant mice displayed significant changes in testis gene expression, abnormal testis histology, a 35% drop in the estimated efficiency of spermatogenesis and a 28% decrease in daily sperm production compared to littermate controls. Despite these quantitative changes in testis function, mutant mice show no significant changes in fertility. This suggests that non-coding deletions affecting testis gene regulation may have smaller effects on fertility compared to coding mutations of the same genes. Our results demonstrate that disruption of a TAD boundary can have a negative impact on sperm production and highlight the importance of considering non-coding mutations in the analysis of patients with male infertility.

TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function.

Topological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species, and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. We find that only 14% of all human TAD boundaries are shared among all eight species (ultraconserved), while 15% are human-specific. Ultraconserved TAD boundaries have stronger insulation strength, CTCF binding, and enrichment of older retrotransposons, compared to species-specific boundaries. CRISPR-Cas9 knockouts of two ultraconserved boundaries in mouse models leads to tissue-specific gene expression changes and morphological phenotypes. Deletion of a human-specific boundary near the autism-related AUTS2 gene results in upregulation of this gene in neurons. Overall, our study provides pertinent TAD boundary evolutionary conservation annotations, and showcase the functional importance of TAD evolution.

TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function.

Topological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. We find 14% of all human TAD boundaries to be shared among all eight species (ultraconserved), while 15% are human-specific. Ultraconserved TAD boundaries have stronger insulation strength, CTCF binding, and enrichment of older retrotransposons compared to species-specific boundaries. CRISPR-Cas9 knockouts of an ultraconserved boundary in a mouse model lead to tissue-specific gene expression changes and morphological phenotypes. Deletion of a human-specific boundary near the autism-related AUTS2 gene results in the upregulation of this gene in neurons. Overall, our study provides pertinent TAD boundary evolutionary conservation annotations and showcases the functional importance of TAD evolution.

Superstructure based on ß-CD self-assembly induced by a small guest molecule.

The size, shape and surface chemistry of nanoparticles play an important role in cellular interaction. Thus, the main objective of the present study was the determination of the ß-cyclodextrin (ß-CD) self-assembly thermodynamic parameters and its structure, aiming to use these assemblies as a possible controlled drug release system. Light scattering measurements led us to obtain the ß-CD's critical aggregation concentration (cac) values, and consequently the thermodynamic parameters of the ß-CD spontaneous self-assembly in aqueous solution: Δ(agg)G(o) = -16.31 kJ mol(-1), Δ(agg)H(o) = -26.48 kJ mol(-1) and TΔ(agg)S(o) = -10.53 kJ mol(-1) at 298.15 K. Size distribution of the self-assembled nanoparticles below and above cac was 1.5 nm and 60-120 nm, respectively. The number of ß-CD molecules per cluster and the second virial coefficient were identified through Debye's plot and molecular dynamic simulations proposed the three-fold assembly for this system below cac. Ampicillin (AMP) was used as a drug model in order to investigate the key role of the guest molecule in the self-assembly process and the ß-CD:AMP supramolecular system was studied in solution, aiming to determine the structure of the supramolecular aggregate. Results obtained in solution indicated that the ß-CD's cac was not affected by adding AMP. Moreover, different complex stoichiometries were identified by nuclear magnetic resonance and isothermal titration calorimetry experiments.

Precision biomaterials in cancer theranostics and modelling.

Despite significant achievements in the understanding and treatment of cancer, it remains a major burden. Traditional therapeutic approaches based on the 'one-size-fits-all' paradigm are becoming obsolete, as demonstrated by the increasing number of patients failing to respond to treatments. In contrast, more precise approaches based on individualized genetic profiling of tumors have already demonstrated their potential. However, even more personalized treatments display shortcomings mainly associated with systemic delivery, such as low local drug efficacy or specificity. A large amount of effort is currently being invested in developing precision medicine-based strategies for improving the efficiency of cancer theranostics and modelling, which are envisioned to be more accurate, standardized, localized, and less expensive. To this end, interdisciplinary research fields, such as biomedicine, material sciences, pharmacology, chemistry, tissue engineering, and nanotechnology, must converge for boosting the precision cancer ecosystem. In this regard, precision biomaterials have emerged as a promising strategy to detect, model, and treat cancer more efficiently. These are defined as those biomaterials precisely engineered with specific theranostic functions and bioactive components, with the possibility to be tailored to the cancer patient needs, thus having a vast potential in the increasing demand for more efficient treatments. In this review, we discuss the latest advances in the field of precision biomaterials in cancer research, which are expected to revolutionize disease management, focusing on their uses for cancer modelling, detection, and therapeutic applications. We finally comment on the needed requirements to accelerate their application in the clinic to improve cancer patient prognosis.

Microfluidic-assisted electrospinning, an alternative to coaxial, as a controlled dual drug release system to treat inflammatory arthritic diseases.

Inflammatory arthritic diseases are characterized by a persistent inflammation of the synovial tissues where tumor necrosis factor alpha (TNFα) and interleukin-6 (IL-6) pro-inflammatory cytokines are over-expressed, leading to progressive musculoskeletal disability. Methotrexate (MTX), a disease-modifying-anti-rheumatic drug (DMARD) commonly applied in their treatment, can be used in combination with biological-DMARDs as anti-TNFα antibody to improve the treatments efficacy. However, their systemic administration comes with severe side-effects and limited therapeutic efficacy due to their off-target distribution and short half-life. To overcome such limitations, encapsulation of clinically relevant concentrations of MTX and anti-TNFα antibody into polycaprolactone (PCL) or poly(vinyl-alcohol) (PVA) microfluidic-assisted or coaxial electrospun fibrous meshes is proposed as local controlled dual drug release systems. Release studies show that microfluidic-assisted electrospinning meshes encapsulating both drugs achieved higher concentrations than coaxials. Biological assays using human articular chondrocytes (hACs) and monocytic cells (THP-1 cell line) demonstrate that fibrous meshes encapsulating the drugs are non-toxic. The systems' efficacy is proved by a significant decrease of TNFα and IL-6 concentrations in conditioned medium of lipopolysaccharide (LPS)-stimulated THP-1 cells, especially in the presence of microfluidic-assisted electrospun meshes, when compared with THP-1 conditioned medium (59.5% and 83.9% less, respectively). Therefore, microfluidic-assisted electrospinning fibrous meshes with encapsulating drugs represent an alternative to coaxial, as a local therapy for inflammatory arthritis diseases.