Advanced Oxidative Protein Products Had a Diagnostic Accuracy for Identifying Chronic Kidney Disease in Adult Population.

Chronic Kidney Disease (CKD) is a serious public health problem. Hyperglycemia stimulates the production of reactive oxygen species that cause oxidative damage to proteins. AOPPs constitute a group of oxidized dityrosine-containing proteins that are generated during periods of oxidative stress. They have proved to be a valuable early marker of oxidative tissue damage and active mediators of inflammation associated with the uremic state. To analyze if advanced oxidative protein products (AOPPs) have diagnostic accuracy for identifying chronic kidney disease (CKD) in the adult population. We conducted a diagnostic test validation study in 302 adults ≥20 years old, of both sexes, with and without T2D. After obtaining informed consent, a comprehensive clinical history, anthropometric measurements (weight, BMI) and blood pressure were recorded. Glucose, cholesterol, triglyceride, HDL-c, LDL-c and AOPPs were determinates. Glomerular filtration rate (GFR) was calculated using Cockcroft-Gault (C-G) corrected by body surface area (BSA, mL/min/1.73 m2), CKD-EPI and MDRD equations to identify five stages of CKD. This study follows the Standards for Reporting Diagnostic Accuracy Studies (STARD). The median value of AOPPs was 198.32 µmol/L (minimum-maximum value: 113.48-522.42 µmol/L). The group with patients diagnosed with T2D exhibited higher concentrations (median: 487.39 µmol/L) compared to the non-diabetic group (median: 158.50 µmol/L, p = 0.0001). The selected cut-off point was ≥200 µmol/L using the closest to the median value of AOPPs with sensitivity and specificity as follows: C-G: sensitivity 96.58%; specificity 80%; likelihood ratio: 4.83; CKD-EPI: sensitivity 95.76%; specificity 79.89%; likelihood ratio: 4.76; MDRD: sensitivity 86.55%; specificity: 73.22%; likelihood ratio: 3.23. A difference was observed between AOPPs and chronic kidney disease stage. This study provides evidence that AOPPs ≥ 200 µmol/L have diagnostic accuracy in identifying stage 4-5 CKD by C-G, MDRD and CKD-EPI equations in adults with and without T2D.

STIGMA: Single-cell tissue-specific gene prioritization using machine learning.

Clinical exome and genome sequencing have revolutionized the understanding of human disease genetics. Yet many genes remain functionally uncharacterized, complicating the establishment of causal disease links for genetic variants. While several scoring methods have been devised to prioritize these candidate genes, these methods fall short of capturing the expression heterogeneity across cell subpopulations within tissues. Here, we introduce single-cell tissue-specific gene prioritization using machine learning (STIGMA), an approach that leverages single-cell RNA-seq (scRNA-seq) data to prioritize candidate genes associated with rare congenital diseases. STIGMA prioritizes genes by learning the temporal dynamics of gene expression across cell types during healthy organogenesis. To assess the efficacy of our framework, we applied STIGMA to mouse limb and human fetal heart scRNA-seq datasets. In a cohort of individuals with congenital limb malformation, STIGMA prioritized 469 variants in 345 genes, with UBA2 as a notable example. For congenital heart defects, we detected 34 genes harboring nonsynonymous de novo variants (nsDNVs) in two or more individuals from a set of 7,958 individuals, including the ortholog of Prdm1, which is associated with hypoplastic left ventricle and hypoplastic aortic arch. Overall, our findings demonstrate that STIGMA effectively prioritizes tissue-specific candidate genes by utilizing single-cell transcriptome data. The ability to capture the heterogeneity of gene expression across cell populations makes STIGMA a powerful tool for the discovery of disease-associated genes and facilitates the identification of causal variants underlying human genetic disorders.

Evaluation of long acting GLP1R/GCGR agonist in a DIO and biopsy-confirmed mouse model of NASH suggest a beneficial role of GLP-1/glucagon agonism in NASH patients.

OBJECTIVE: The metabolic benefits of GLP-1 receptor (GLP-1R) agonists on glycemic and weight control are well established as therapy for type 2 diabetes and obesity. Glucagon's ability to increase energy expenditure is well described, and the combination of these mechanisms-of-actions has the potential to further lower hepatic steatosis in metabolic disorders and could therefore be attractive for the treatment for non-alcoholic steatohepatitis (NASH). Here, we have investigated the effects of a dual GLP-1/glucagon receptor agonist NN1177 on hepatic steatosis, fibrosis, and inflammation in a preclinical mouse model of NASH. Having observed strong effects on body weight loss in a pilot study with NN1177, we hypothesized that direct engagement of the hepatic glucagon receptor (GCGR) would result in a superior effect on steatosis and other liver related parameters as compared to the GLP-1R agonist semaglutide at equal body weight. METHODS: Male C57Bl/6 mice were fed a diet high in trans-fat, fructose, and cholesterol (Diet-Induced Obese (DIO)-NASH) for 36 weeks. Following randomization based on the degree of fibrosis at baseline, mice were treated once daily with subcutaneous administration of a vehicle or three different doses of NN1177 or semaglutide for 8 weeks. Hepatic steatosis, inflammation and fibrosis were assessed by immunohistochemistry and morphometric analyses. Plasma levels of lipids and liver enzymes were determined, and hepatic gene expression was analyzed by RNA sequencing. RESULTS: NN1177 dose-dependently reduced body weight up to 22% compared to vehicle treatment. Plasma levels of ALT, a measure of liver injury, were reduced in all treatment groups with body weight loss. The dual agonist reduced hepatic steatosis to a greater extent than semaglutide at equal body weight loss, as demonstrated by three independent methods. Both the co-agonist and semaglutide significantly decreased histological markers of inflammation such as CD11b and Galectin-3, in addition to markers of hepatic stellate activation (αSMA) and fibrosis (Collagen I). Interestingly, the maximal beneficial effects on above mentioned clinically relevant endpoints of NN1177 treatment on hepatic health appear to be achieved with the middle dose tested. Administering the highest dose resulted in a further reduction of liver fat and accompanied by a massive induction in genes involved in oxidative phosphorylation and resulted in exaggerated body weight loss and a downregulation of a module of co-expressed genes involved in steroid hormone biology, bile secretion, and retinol and linoleic acid metabolism that are also downregulated due to NASH itself. CONCLUSIONS: These results indicate that, in a setting of overnutrition, the liver health benefits of activating the fasting-related metabolic pathways controlled by the glucagon receptor displays a bell-shaped curve. This observation is of interest to the scientific community, due to the high number of ongoing clinical trials attempting to leverage the positive effects of glucagon biology to improve metabolic health.

Profiling the genome and proteome of metabolic dysfunction-associated steatotic liver disease identifies potential therapeutic targets.

BACKGROUND & AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) affects over 25% of the population and currently has no effective treatments. Plasma proteins with causal evidence may represent promising drug targets. We aimed to identify plasma proteins in the causal pathway of MASLD and explore their interaction with obesity. METHODS: We analysed 2,941 plasma proteins in 43,978 European participants from UK Biobank. We performed genome-wide association study (GWAS) for all MASLD-associated proteins and created the largest MASLD GWAS (109,885 cases/1,014,923 controls). We performed Mendelian Randomization (MR) and integrated proteins and their encoding genes in MASLD ranges to identify candidate causal proteins. We then validated them through independent replication, exome sequencing, liver imaging, bulk and single-cell gene expression, liver biopsies, pathway, and phenome-wide data. We explored the role of obesity by MR and multivariable MR across proteins, body mass index, and MASLD. RESULTS: We found 929 proteins associated with MASLD, reported five novel genetic loci associated with MASLD, and identified 17 candidate MASLD protein targets. We identified four novel targets for MASLD (CD33, GRHPR, HMOX2, and SCG3), provided protein evidence supporting roles of AHCY, FCGR2B, ORM1, and RBKS in MASLD, and validated nine previously known targets. We found that CD33, FCGR2B, ORM1, RBKS, and SCG3 mediated the association of obesity and MASLD, and HMOX2, ORM1, and RBKS had effect on MASLD independent of obesity. CONCLUSIONS: This study identified new protein targets in the causal pathway of MASLD, providing new insights into the multi-omics architecture and pathophysiology of MASLD. These findings advise further therapeutic interventions for MASLD.

Prebiotics in Global and Mexican Fish Aquaculture: A Review.

Continued human population growth has resulted in increased demand for products, including those derived from aquaculture. The main challenge in aquaculture is producing more every year. In recent years, environmentally friendly supplements that provide the necessary pathways for optimal production have been emphasized. One of them is prebiotics, selectively utilized substrates by host microorganisms conferring a health benefit. Interest in applying prebiotics in global fish farming has increased in recent years as it has been shown to improve growth, boost the immune system, resist stress conditions, and cause the modulation of digestive enzymes. These effects reflect reduced production and disease costs. However, in Latin American countries such as Mexico, large-scale use of these food supplements is needed as a sustainable alternative to improve fish production. This paper gives a review of the current advances obtained with the application of prebiotics in commercially farmed fish worldwide, mentions the prebiotics to use in the aquaculture industry, and updates the status of studies about the used prebiotics in global commercial fish cultivated in Mexico, as well as freshwater and marine endemic fish in this country. Also, the limitations of prebiotics application in terms of their use and legislation are analyzed.

Assessment of carbon, oxygen, strontium, and lead isotopic variation in modern Colombian teeth: An application to human identification.

Colombia faces the complex humanitarian challenges of locating approximately 100,000 missing persons and identifying thousands who are deceased. Identification is a difficult task in many cases, because the skeletonized bodies are deteriorated, missing person data are unavailable for comparison, and the provenance of the remains is often totally unknown. Isotopic analysis of human tissues (e.g., bone, hair, nails, and teeth) aid in the identification process of unknown individuals because they can provide valuable information on possible geographic origin. This project evaluated the isotopic variability of carbon (C), oxygen (O), strontium (Sr), and lead (Pb) in modern Colombian teeth according to city, department (a political designation similar to "state" in the US or Mexico), and one of four geographically determined regions of origin; and assessed its utility for human identification in Colombia. Isotopic data (O-C-Sr-Pb) were analyzed from modern Colombians originating from the cities of Bogotá, Cali, and Neiva (n = 95); and these data were compiled with published Colombian data of individuals mainly from the city of Medellín (n = 61). Results indicate a wide range and overlap of O-C-Sr-Pb isotopic distribution according to the defined categories. However, differences between coastal and lowland individuals are observed when using δ18 O values, and differences between mountainous regions are observed when using 87 Sr/86 Sr values. In addition, this study suggests that the usefulness of isotopic analysis for unidentified individuals in Colombia would be with assigning them geographically using the designations of North, Central Andes, Eastern Andes, or Southwest Andes versus making classifications at a city or department level.

The Influence of Recycled Cement, Fly Ash, and Magnesium Oxide on the Mechanical Performance of Sustainable Cementitious Materials.

In the construction industry, cement is the most widely used material. So, to achieve greater sustainability in this industry, it is imperative to improve the sustainability of this material. One way to reduce the ecological footprint of cement is to replace it, even if partially, with other more sustainable materials that can act as binders. This paper analyses the mechanical properties of more sustainable mortars containing recycled cement (RC), fly ash (FA), and magnesium oxide (MgO). Different types of binary, ternary, and quaternary mortars were used: containing recycled cement (5% and 10%), fly ash (10% and 20%), and MgO (7.5% and 15%). An experimental campaign was carried out analysing air content, density, compressive and flexural strengths, modulus of elasticity, and ultrasonic pulse velocity. The ternary mortars showed decreases between 0.4% (M-5RC10FA) and 35.3% (M-10RC15Mg) in terms of compressive strength at 365 days (compared to RM), when the theoretically expected decrease (the sum of the decreases obtained with the individual incorporation of these materials) would be between 16.6% and 41.5%, respectively. The results obtained allow for concluding that the joint use of these materials in ternary mortars improves the mechanical capacity, relative to the individual incorporation of each material in binary mortars.

Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation.

Heterotopic ossification is a disorder caused by abnormal mineralization of soft tissues in which signaling pathways such as BMP, TGFß and WNT are known key players in driving ectopic bone formation. Identifying novel genes and pathways related to the mineralization process are important steps for future gene therapy in bone disorders. In this study, we detect an inter-chromosomal insertional duplication in a female proband disrupting a topologically associating domain and causing an ultra-rare progressive form of heterotopic ossification. This structural variant lead to enhancer hijacking and misexpression of ARHGAP36 in fibroblasts, validated here by orthogonal in vitro studies. In addition, ARHGAP36 overexpression inhibits TGFß, and activates hedgehog signaling and genes/proteins related to extracellular matrix production. Our work on the genetic cause of this heterotopic ossification case has revealed that ARHGAP36 plays a role in bone formation and metabolism, outlining first details of this gene contributing to bone-formation and -disease.

Identification of genetic loci associated with five agronomic traits in alfalfa using multi-environment trials.

KEY MESSAGE: The use of multi-environment trials to test yield-related traits in a diverse alfalfa panel allowed to find multiple molecular markers associated with complex agronomic traits. Yield is one of the most important target traits in alfalfa breeding; however, yield is a complex trait affected by genetic and environmental factors. In this study, we used multi-environment trials to test yield-related traits in a diverse panel composed of 200 alfalfa accessions and varieties. Phenotypic data of maturity stage measured as mean stage by count (MSC), dry matter content, plant height (PH), biomass yield (Yi), and fall dormancy (FD) were collected in three locations in Idaho, Oregon, and Washington from 2018 to 2020. Single-trial and stagewise analyses were used to obtain estimated trait means of entries by environment. The plants were genotyped using a genotyping by sequencing approach and obtained a genotypic matrix with 97,345 single nucleotide polymorphisms. Genome-wide association studies identified a total of 84 markers associated with the traits analyzed. Of those, 29 markers were in noncoding regions and 55 markers were in coding regions. Ten significant SNPs at the same locus were associated with FD and they were linked to a gene annotated as a nuclear fusion defective 4-like (NFD4). Additional SNPs associated with MSC, PH, and Yi were annotated as transcription factors such as Cysteine3Histidine (C3H), Hap3/NF-YB family, and serine/threonine-protein phosphatase 7 proteins, respectively. Our results provide insight into the genetic factors that influence alfalfa maturity, yield, and dormancy, which is helpful to speed up the genetic gain toward alfalfa yield improvement.

Nuevos registros de murciélagos para el Perú

Presentamos el primer registro de tres mamíferos pequeños voladores para el Perú en base a especímenes colectados entre 2007 y 2014. Estos son: Eumops glaucinus, en la selva baja del centro del Perú; Molossus bondae en el bosque tropical del Pacífico, y Promops nasutus en bosques montanos del sureste. Los nuevos registros incrementan la diversidad de mamíferos del Perú a 579 especies.

We presented the first record of three species bats for Peru based on specimens collected between 2007 and 2014. These are Eumops glaucinus, captured in the rainforest from the center of Peru, Molossus bondae captured in the Pacifico rainforest, and Promops nasutus, captured in the montane forests from southeastern. The new records increase the mammal diversity of Peru to 579 species.

Lesión autoinfligida y absceso cerebral secundario en un paciente con esquizofrenia / Self-inflicted injury and secondary cerebral abscess in a patient with schizophrenia

RESUMEN La lesión autoinfligida es un acto intencional de hacerse daño sin propósito suicida. El presente caso describe a un paciente esquizofrénico de 37 años de edad, que ha padecido 20 años con la enfermedad, y síntomas recientes de irritabilidad, agresividad, aislamiento, ideas de perjuicio y contaminación («tengo un estafilococo en mi cabeza¼). Durante 10 años utilizaba varios objetos, incluido un bisturí con el que llegó a remover (extirpar) parte de la calota, ocasionando un edema vasogénico en la región córtico-fronto-parietal izquierda que produjo hemiparesia braquiocrural derecha y motivó su admisión. Luego de descartarse un accidente cerebrovascular o tumor cerebral, fue intervenido quirúrgicamente para la extracción de un absceso cerebral. Recibió varios fármacos antipsicóticos con respuesta parcial, y más tarde mejoró con la administración de paliperidona. En casos como este, es necesario un tamizaje, diagnóstico y tratamiento oportunos para evitar evolución y pronóstico tórpidos en pacientes esquizofrénicos con lesiones autoinfligidas y con historia de pobre respuesta y adherencia al tratamiento.

ABSTRACT Self-injury is the intentional act of causing harm to oneself, without suicidal purposes. This case report describes a 37-year-old schizophrenic patient, with a history of 20 years, and recent symptoms of irritability, aggressiveness, isolation, self-harm and contamination ideas ("I have a staphylococcus in my head"). For 10 years, he used a variety of objects to manipulate himself, among them a scalpel with which he extirpated part of the calotte, causing a vasogenic edema in the left cortico-fronto-parietal region that produced a right brachio-crural haemiparesis, the reason for his admission. After ruling out a stroke or a brain tumor, he underwent surgery for the removal of a brain abscess; he received several antipsychotic agents with only a partial response that later improved after being switched to paliperidone. In cases like this, it is necessary to conduct a timely screening, diagnosis and treatment in order to avoid a torpid evolution and prognosis in schizophrenic patients with long-standing self-inflicted injuries and a history of poor adherence and response to treatment.

Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve split-hand/foot malformation type 3.

Split-Hand/Foot Malformation type 3 (SHFM3) is a congenital limb malformation associated with tandem duplications at the LBX1/FGF8 locus. Yet, the disease patho-mechanism remains unsolved. Here we investigate the functional consequences of SHFM3-associated rearrangements on chromatin conformation and gene expression in vivo in transgenic mice. We show that the Lbx1/Fgf8 locus consists of two separate, but interacting, regulatory domains. Re-engineering of a SHFM3-associated duplication and a newly reported inversion in mice results in restructuring of the chromatin architecture. This leads to ectopic activation of the Lbx1 and Btrc genes in the apical ectodermal ridge (AER) in an Fgf8-like pattern induced by AER-specific enhancers of Fgf8. We provide evidence that the SHFM3 phenotype is the result of a combinatorial effect on gene misexpression in the developing limb. Our results reveal insights into the molecular mechanism underlying SHFM3 and provide conceptual framework for how genomic rearrangements can cause gene misexpression and disease.

Systematics and diversification of the Ichthyomyini (Cricetidae, Sigmodontinae) revisited: evidence from molecular, morphological, and combined approaches.

Ichthyomyini, a morphologically distinctive group of Neotropical cricetid rodents, lacks an integrative study of its systematics and biogeography. Since this tribe is a crucial element of the Sigmodontinae, the most speciose subfamily of the Cricetidae, we conducted a study that includes most of its recognized diversity (five genera and 19 species distributed from southern Mexico to northern Bolivia). For this report we analyzed a combined matrix composed of four molecular markers (RBP3, GHR, RAG1, Cytb) and 56 morphological traits, the latter including 15 external, 14 cranial, 19 dental, five soft-anatomical and three postcranial features. A variety of results were obtained, some of which are inconsistent with the currently accepted classification and understanding of the tribe. Ichthyomyini is retrieved as monophyletic, and it is divided into two main clades that are here recognized as subtribes: one to contain the genus Anotomys and the other composed by the remaining genera. Neusticomys (as currently recognized) was found to consist of two well supported clades, one of which corresponds to the original concept of Daptomys. Accordingly, we propose the resurrection of the latter as a valid genus to include several species from low to middle elevations and restrict Neusticomys to several highland forms. Numerous other revisions are necessary to reconcile the alpha taxonomy of ichthyomyines with our phylogenetic results, including placement of the Cajas Plateau water rat (formerly Chibchanomys orcesi) in the genus Neusticomys (sensu stricto), and the recognition of at least two new species (one in Neusticomys, one in Daptomys). Additional work is necessary to confirm other unanticipated results, such as the non-monophyletic nature of Rheomys and the presence of a possible new genus and species from Peru. Our results also suggest that ichthyomyines are one of the main Andean radiations of sigmodontine cricetids, with an evolutionary history dating to the Late Miocene and subsequent cladogenesis during the Pleistocene.

Genetic Mapping of Tolerance to Bacterial Stem Blight Caused by Pseudomonas syringae pv. syringae in Alfalfa (Medicago sativa L.).

The bacterial stem blight of alfalfa (Medicago sativa L.), first reported in the United States in 1904, has emerged recently as a serious disease problem in the western states. The causal agent, Pseudomonas syringae pv. syringae, promotes frost damage and disease that can reduce first harvest yields by 50%. Resistant cultivars and an understanding of host-pathogen interactions are lacking in this pathosystem. With the goal of identifying DNA markers associated with disease resistance, we developed biparental F1 mapping populations using plants from the cultivar ZG9830. Leaflets of plants in the mapping populations were inoculated with a bacterial suspension using a needleless syringe and scored for disease symptoms. Bacterial populations were measured by culture plating and using a quantitative PCR assay. Surprisingly, leaflets with few to no symptoms had bacterial loads similar to leaflets with severe disease symptoms, indicating that plants without symptoms were tolerant to the bacterium. Genotyping-by-sequencing identified 11 significant SNP markers associated with the tolerance phenotype. This is the first study to identify DNA markers associated with tolerance to P. syringae. These results provide insight into host responses and provide markers that can be used in alfalfa breeding programs to develop improved cultivars to manage the bacterial stem blight of alfalfa.

Role of the Spore Coat Proteins CotA and CotB, and the Spore Surface Protein CDIF630_02480, on the Surface Distribution of Exosporium Proteins in Clostridioides difficile 630 Spores.

Clostridioides difficile is Gram-positive spore-former bacterium and the leading cause of nosocomial antibiotic-associated diarrhea. During disease, C. difficile forms metabolically dormant spores that persist in the host and contribute to recurrence of the disease. The outermost surface of C. difficile spores, termed the exosporium, plays an essential role in interactions with host surfaces and the immune system. The main exosporium proteins identified to date include three orthologues of the BclA family of collagen-like proteins, and three cysteine-rich proteins. However, how the underlying spore coat influences exosporium assembly remains unclear. In this work, we explore the contribution of spore coat proteins cotA and cotB, and the spore surface protein, CDIF630_02480, to the exosporium ultrastructure, formation of the polar appendage and the surface accessibility of exosporium proteins. Transmission electron micrographs of spores of insertional inactivation mutants demonstrate that while cotB contributes to the formation of thick-exosporium spores, cotA and CDIF630_02480 contribute to maintain proper thickness of the spore coat and exosporium layers, respectively. The effect of the absence of cotA, cotB and CDIF630_02480 on the surface accessibility of the exosporium proteins CdeA, CdeC, CdeM, BclA2 and BclA3 to antibodies was affected by the presence of the spore appendage, suggesting that different mechanisms of assembly of the exosporium layer might be implicated in each spore phenotype. Collectively, this work contributes to our understanding of the associations between spore coat and exosporium proteins, and how these associations affect the assembly of the spore outer layers. These results have implications for the development of anti-infecting agents targeting C. difficile spores.

Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes.

Regulatory landscapes drive complex developmental gene expression, but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1's intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42's unresponsiveness. Rather, Zfp42's promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome wide, most TADs contain multiple independently expressed genes.