Introgressed DNA within a Zea mays near-isogenic line displays lower levels of 24nt sRNA expression than the homologous region from the recurrent parent.

Near-isogenic lines (NILs) are classical genetic tools used to dissect the actions of an allele when placed in a uniform genetic background. Although the goal of NIL creation is to examine the effects of a single allele in isolation, DNA linked to the allele is invariably retained and can confound any allele-specific effects. In addition to genetic variation, highly polymorphic species such as Zea mays will contain introgressed polymorphisms encompassing transposable elements (TEs) and the cis-acting small RNA (sRNA) that represses them. Through transcriptomics, we described the differences in sRNA and TE transcriptional expression between a W22-derived introgression and its homologous B73 region. As anticipated, many differences in sRNA expression were observed. Unexpectedly, however, 24nt sRNA expression over the introgressed region was low overall compared to both the homologous B73 region and the rest of the genome. Across the introgression, low sRNA expression was accompanied by increased TE transcription. Possible explanations for the observed trends in sRNA and TE expression across the introgression region are discussed. These findings support the notion that any introgressed allele is in an epigenetic environment distinct from that found at the allele from the recurrent parent. Additionally, these results suggest that further study of sRNA expression levels during the introgression process is warranted.

Shared and genetically distinct Zea mays transcriptome responses to ongoing and past low temperature exposure.

BACKGROUND: Cold temperatures and their alleviation affect many plant traits including the abundance of protein coding gene transcripts. Transcript level changes that occur in response to cold temperatures and their alleviation are shared or vary across genotypes. In this study we identify individual transcripts and groups of functionally related transcripts that consistently respond to cold and its alleviation. Genes that respond differently to temperature changes across genotypes may have limited functional importance. We investigate if these genes share functions, and if their genotype-specific gene expression levels change in magnitude or rank across temperatures. RESULTS: We estimate transcript abundances from over 22,000 genes in two unrelated Zea mays inbred lines during and after cold temperature exposure. Genotype and temperature contribute to many genes' abundances. Past cold exposure affects many fewer genes. Genes up-regulated in cold encode many cytokinin glucoside biosynthesis enzymes, transcription factors, signalling molecules, and proteins involved in diverse environmental responses. After cold exposure, protease inhibitors and cuticular wax genes are newly up-regulated, and environmentally responsive genes continue to be up-regulated. Genes down-regulated in response to cold include many photosynthesis, translation, and DNA replication associated genes. After cold exposure, DNA replication and translation genes are still preferentially downregulated. Lignin and suberin biosynthesis are newly down-regulated. DNA replication, reactive oxygen species response, and anthocyanin biosynthesis genes have strong, genotype-specific temperature responses. The ranks of genotypes' transcript abundances often change across temperatures. CONCLUSIONS: We report a large, core transcriptome response to cold and the alleviation of cold. In cold, many of the core suite of genes are up or downregulated to control plant growth and photosynthesis and limit cellular damage. In recovery, core responses are in part to prepare for future stress. Functionally related genes are consistently and greatly up-regulated in a single genotype in response to cold or its alleviation, suggesting positive selection has driven genotype-specific temperature responses in maize.

Distinct gene networks modulate floral induction of autonomous maize and photoperiod-dependent teosinte.

Temperate maize was domesticated from its tropical ancestor, teosinte. Whereas temperate maize is an autonomous day-neutral plant, teosinte is an obligate short-day plant that requires uninterrupted long nights to induce flowering. Leaf-derived florigenic signals trigger reproductive growth in both teosinte and temperate maize. To study the genetic mechanisms underlying floral inductive pathways in maize and teosinte, mRNA and small RNA genome-wide expression analyses were conducted on leaf tissue from plants that were induced or not induced to flower. Transcriptome profiles reveal common differentially expressed genes during floral induction, but a comparison of candidate flowering time genes indicates that photoperiod and autonomous pathways act independently. Expression differences in teosinte are consistent with the current paradigm for photoperiod-induced flowering, where changes in circadian clock output trigger florigen production. Conversely, differentially expressed genes in temperate maize link carbon partitioning and flowering, but also show altered expression of circadian clock genes that are distinct from those altered upon photoperiodic induction in teosinte. Altered miRNA399 levels in both teosinte and maize suggest a novel common connection between flowering and phosphorus perception. These findings provide insights into the molecular mechanisms underlying a strengthened autonomous pathway that enabled maize growth throughout temperate regions.

Brevis plant1, a putative inositol polyphosphate 5-phosphatase, is required for internode elongation in maize.

In maize (Zea mays L.), as in other grass species, stem elongation occurs during growth and most noticeably upon the transition to flowering. Genes that reduce stem elongation have been important to reduce stem breakage, or lodging. Stem elongation has been mediated by dwarf and brachytic/brevis plant mutants that affect giberellic acid and auxin pathways, respectively. Maize brevis plant1 (bv1) mutants, first identified over 80 years ago, strongly resemble brachytic2 mutants that have shortened internodes, short internode cells, and are deficient in auxin transport. Here, we characterized two novel bv1 maize mutants. We found that an inositol polyphosphate 5-phosphatase orthologue of the rice gene dwarf50 was the molecular basis for the bv1 phenotype, implicating auxin-mediated inositol polyphosphate and/or phosphoinositide signalling in stem elongation. We suggest that auxin-mediated internode elongation involves processes that also contribute to stem gravitropism. Genes misregulated in bv1 mutants included genes important for cell wall synthesis, transmembrane transport, and cytoskeletal function. Mutant and wild-type plants were indistinguishable early in development, responded similarly to changes in light quality, had unaltered flowering times, and had normal flower development. These attributes suggest that breeding could utilize bv1 alleles to increase crop grain yields.

Analysis of Survival Modification by Furosemide Use in a Cohort of Hospitalized COVID-19 Patients with Severe or Critical Disease in Mexico: Due to Its Chemical Structure, Furosemide Is More than Just a Diuretic.

In the ongoing fight against Coronavirus Disease 2019 (COVID-19), researchers are exploring potential treatments to improve outcomes, especially in severe cases. This includes investigating the repurposing of existing medications, such as furosemide, which is widely available. This study aimed to evaluate the impact of furosemide on mortality rates among COVID-19 patients with severe or critical illness. We assessed a cohort of 515 hospitalized adults who experienced a high mortality rate of 43.9%. Using a multivariate analysis with adjusted risk ratios (AdRRs), factors like smoking (AdRR 2.48, 95% CI 1.53-4.01, p < 0.001), a high Pneumonia Severity Index (PSI) score (AdRR 7.89, 95% CI 5.82-10.70, p < 0.001), mechanical ventilation (AdRR 23.12, 95% CI 17.28-30.92, p < 0.001), neutrophilia (AdRR 2.12, 95% CI 1.52-2.95, p < 0.001), and an elevated neutrophil-to-lymphocyte ratio (NLR) (AdRR 2.39, 95% CI 1.72-3.32, p < 0.001) were found to increase mortality risk. In contrast, vaccination and furosemide use were associated with reduced mortality risk (AdRR 0.58, p = 0.001 and 0.60, p = 0.008; respectively). Furosemide showed a pronounced survival benefit in patients with less severe disease (PSI < 120) and those not on hemodialysis, with mortality rates significantly lower in furosemide users (3.7% vs. 25.7%). A Kaplan-Meier analysis confirmed longer survival and better oxygenation levels in patients treated with furosemide. Furthermore, a Structure-Activity Relationship analysis revealed that furosemide's sulfonamide groups may interact with cytokine sites such as tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6), potentially explaining its beneficial effects in COVID-19 management. These findings suggest that furosemide could be a beneficial treatment option in certain COVID-19 patient groups, enhancing survival and improving oxygenation.

Maternal admixture and population structure in Mexican-Mestizos based on mtDNA haplogroups.

The maternal ancestry (mtDNA) has important applications in different research fields, such as evolution, epidemiology, identification, and human population history. This is particularly interesting in Mestizos, which constitute the main population in Mexico (∼93%) resulting from post-Columbian admixture between Spaniards, Amerindians, and African slaves, principally. Consequently, we conducted minisequencing analysis (SNaPshot) of 11 mitochondrial single-nucleotide polymorphisms in 742 Mestizos of 10 populations from different regions in Mexico. The predominant maternal ancestry was Native American (92.9%), including Haplogroups A, B, C, and D (47, 23.7, 15.9, and 6.2%, respectively). Conversely, European and African ancestries were less frequent (5.3 and 1.9%, respectively). The main characteristics of the maternal lineages observed in Mexican-Mestizos comprised the following: 1) contrasting geographic gradient of Haplogroups A and C; 2) increase of European lineages toward the Northwest; 3) low or absent, but homogeneous, African ancestry throughout the Mexican territory; 4) maternal lineages in Mestizos roughly represent the genetic makeup of the surrounding Amerindian groups, particularly toward the Southeast, but not in the North and West; 5) continuity over time of the geographic distribution of Amerindian lineages in Mayas; and 6) low but significant maternal population structure (FST = 2.8%; P = 0.0000). The average ancestry obtained from uniparental systems (mtDNA and Y-chromosome) in Mexican-Mestizos was correlated with previous ancestry estimates based on autosomal systems (genome-wide single-nucleotide polymorphisms and short tandem repeats). Finally, the comparison of paternal and maternal lineages provided additional information concerning the gender bias admixture, mating patterns, and population structure in Mestizos throughout the Mexican territory.

Using Artificial Intelligence to Develop a Multivariate Model with a Machine Learning Model to Predict Complications in Mexican Diabetic Patients without Arterial Hypertension (National Nested Case-Control Study): Metformin and Elevated Normal Blood Pressure Are Risk Factors, and Obesity Is Protective.

Diabetes mellitus is a disease with no cure that can cause complications and even death. Moreover, over time, it will lead to chronic complications. Predictive models have been used to identify people with a tendency to develop diabetes mellitus. At the same time, there is limited information regarding the chronic complications of patients with diabetes. Our study is aimed at creating a machine-learning model that will be able to identify the risk factors of a diabetic patient developing chronic complications such as amputations, myocardial infarction, stroke, nephropathy, and retinopathy. The design is a national nested case-control study with 63,776 patients and 215 predictors with four years of data. Using an XGBoost model, the prediction of chronic complications has an AUC of 84%, and the model has identified the risk factors for chronic complications in patients with diabetes. According to the analysis, the most crucial risk factors based on SHAP values (Shapley additive explanations) are continued management, metformin treatment, age between 68 and 104 years, nutrition consultation, and treatment adherence. But we highlight two exciting findings. The first is a reaffirmation that high blood pressure figures across patients with diabetes without hypertension become a significant risk factor at diastolic > 70 mmHg (OR: 1.095, 95% CI: 1.078-1.113) or systolic > 120 mmHg (OR: 1.147, 95% CI: 1.124-1.171). Furthermore, people with diabetes with a BMI > 32 (overall obesity) (OR: 0.816, 95% CI: 0.8-0.833) have a statistically significant protective factor, which the paradox of obesity may explain. In conclusion, the results we have obtained show that artificial intelligence is a powerful and feasible tool to use for this type of study. However, we suggest that more studies be conducted to verify and elaborate upon our findings.

[The effect of MTHFR polymorphisms, pregnancy and first intercourse on cervical cancer in a population from the Northeastern Mexico]. / Interacciones entre polimorfismos del gen MTHFR, gestaciones e inicio de vida sexual modifican el riesgo para cáncer cérvico-uterino en una población del noreste de México.

OBJECTIVE: To investigate the possible association among MTHFR polymorfhisms, environmental factors and cervical cancer (CC) in the Mexican population. METHODS: Seventy patients with CC and 89 control women were questioned about clinical data and their 677 and 1298 genotypes of MTHFR gene were analized. RESULTS: Multipregnancies (0-2 vs. > or = 3, OR 2.1), an early age of first intercourse (IVS) (17 < or = vs. > or = 18 years, OR 4.3) or both factors (OR 3.5) were significantly associated with CC. MTHFR 677, 1298 polymorphisms and their combinations were not different between cases and controls. However, a significant association between pregnancies, IVS and MTHFR polymorphisms (presence of 1298C allele or 677TT genotype) was observed. The 1298C allele plus multipregnancies and IVS < or = 17 years, or both factors, increased 4.3, 5.3, and 11.8 times the risk for CC, respectively, while 677TT genotype changed the risk 2.0, 1.9, and 4.2 times, respectively. CONCLUSION: The 1298C allele increases the risk of CC strongly in women with multipregnancies and early age of IVS, while 677TT genotype has a lower risk without becoming a protection factor.

[Fibrinogen. Cardiovascular risk factor or marker?]. / Fibrinógeno. Factor o indicador de riesgo cardiovascular?

UNLABELLED: Endothelial dysfunction and inflammation play a crucial role in all stages of atherosclerosis, from the beginning, during progression, and, finally, in its highest clinical expression: acute coronary syndromes. In this process, fibrinogen, an acute phase reactant with active participation in endothelial function, thrombosis and inflammation has proved to be an independent variable to cardiovascular risk together with its participation in resistance phenomena to different antithrombotic approaches. The reasons by which fibrinogen is elevated in cardiovascular disease and atherosclerosis are, in general, only incompletely understood; but all cells involved in the atherogenetic process are able to produce cytokines, which induce an acute phase reaction that increases fibrinogen levels in plasma. The potential pathophysiological mechanisms by which elevated fibrinogen levels mediate cardiovascular risk are multiple. Fibrinogen forms the substrate for thrombin an represents the final step in the coagulation cascade, it is essential for platelet aggregation, it modulates endothelial function, it promotes smooth muscle cell proliferation and migration, it interacts with the binding of plasmin with its receptor and, finally, it represents a major acute phase protein. Epidemiological studies have established sufficient evidence to consider fibrinogen as a strong, consistent, and independent cardiovascular risk marker or factor. Based on all these implications, the target of this review is an analysis of physiopathogenic and epidemiologic evidence searching for guidelines to establish whether fibrinogen as a risk factor or marker is the lost link between cardiovascular disease and classic risk factors. CONCLUSION: Analyses of the respective studies suggest that fibrinogen is an important and independent cardiovascular risk factor, clearly associated with conventional risk factors and genetic polymorphisms. Whether or not fibrinogen is causally involved in atherothrombogenesis still remains to be determined and despite of unsolved issues that are waiting conclusive answers, fibrinogen has emerged as an important additional marker of cardiovascular risk.

A PCR-RFLP method for typing human papillomavirus type 16 variants.

Infection with some types of human papillomavirus (HPV) is required for cervical cancer development, being HPV type 16 (HPV 16) the most common type in premalignant and malignant cervical lesions. DNA sequencing has revealed the existence of intratypic variants of HPV 16 whose genotyping is clinically useful for distinguishing between persistent and recurrent infections. From the epidemiological perspective, the frequency of diverse HPV 16 variants in several populations could correlate with the presence of precursor high-risk lesions in different anatomical locations. Currently, the "gold standard" method for identifying HPV 16 variants involves the sequencing of genomic regions to identify characteristic polymorphic sites. Although some other methods have been described, they require specialized or high-cost equipment. In this study, a robust and low cost procedure is described for HPV 16 variant typing, based on the long control region of the virus.

Fibrinógeno. Factor o indicador de riesgo cardiovascular? / Fibrinogen. Cardiovascular risk factor or marker?

Endothelial dysfunction and inflammation play a crucial role in all stages of atherosclerosis, from the beginning, during progression, and, finally, in its highest clinical expression: acute coronary syndromes. In this process, fibrinogen, an acute phase reactant with active participation in endothelial function, thrombosis and inflammation has proved to be an independent variable to cardiovascular risk together with its participation in resistance phenomena to different antithrombotic approaches. The reasons by which fibrinogen is elevated in cardiovascular disease and atherosclerosis are, in general, only incompletely understood; but all cells involved in the atherogenetic process are able to produce cytokines, which induce an acute phase reaction that increases fibrinogen levels in plasma. The potential pathophysiological mechanisms by which elevated fibrinogen levels mediate cardiovascular risk are multiple. Fibrinogen forms the substrate for thrombin an represents the final step in the coagulation cascade, it is essential for platelet aggregation, it modulates endothelial function, it promotes smooth muscle cell proliferation and migration, it interacts with the binding of plasmin with its receptor and, finally, it represents a major acute phase protein. Epidemiological studies have established sufficient evidence to consider fibrinogen as a strong, consistent, and independent cardiovascular risk marker or factor. Based on all these implications, the target of this review is an analysis of physiopathogenic and epidemiologic evidence searching for guidelines to establish whether fibrinogen as a risk factor or marker is the lost link between cardiovascular disease and classic risk factors. CONCLUSION: Analyses of the respective studies suggest that fibrinogen is an important and independent cardiovascular risk factor, clearly associated with conventional risk factors and genetic polymorphisms. Whether or not fibrinogen is causally involved in atherothrombogenesis still remains to be determined and despite of unsolved issues that are waiting conclusive answers, fibrinogen has emerged as an important additional marker of cardiovascular risk.

Interacciones entre polimorfismos del gen MTHFR, gestaciones e inicio de vida sexual modifican el riesgo para cáncer cérvico-uterino en una población del noreste de México / The effect of MTHFR polymorphisms, pregnancy and first intercourse on cervical cancer in a population from the Northeastern Mexico

Objective. To investigate the possible association among MTHFR polymorfhisms, environmental factors and cervical cancer (CC) in the Mexican population. Methods. Seventy patients with CC and 89 control women were questioned about clinical data and their 677 and 1298 genotypes of MTHFR gene were analized. Results. Multipregnancies (0-2 vs. > 3, OR 2.1), an early age of first intercourse (IVS) (17 < vs. > 18 years, OR 4.3) or both factors (OR 3.5) were significantly associated with CC. MTHFR 677, 1298 polymorphisms and their combinations were not different between cases and controls. However, a significant association between pregnancies, TVS and MTHFR polymorphisms (presence of 1298C allele or 677TT genotype) was observed. The 1298C allele plus multipregnancies and IVS < 17 years, or both factors, increased 4.3, 5.3, and 11.8 times the risk for CC, respectively, while 677TT genotype changed the risk 2.0, 1.9, and 4.2 times, respectively. Conclusion. The 1298C allele increases the risk of CC strongly in women with multipregnancies and early age of IVS, while 677TT genotype has a lower risk without becoming a protection factor.

Objetivo. Buscar la asociación entre polimorfismos de la enzima metilentetrahidrofolato reductasa (MTHFR), factores ambientales y cáncer cérvico-uterino (CaCU) en mujeres del noreste de México. Métodos. Setenta pacientes con CaCU y 89 mujeres controles se sometieron a un interrogatorio clínico y a genotipificación de los polimorfismos 677C -> T y 1298A -> C del gen MTHFR. Resultados. La multigestación (0-2 vs.> 3, OR 2.1), un temprano inicio de vida sexual (IVS) (17 < vs. > 18 años, OR 4.3) o la combinación de ambos factores (OR 3.5), estuvieron asociados significativamente al CaCU. Los polimorfismos de MTHFR 677, 1298 y sus combinaciones no fueron diferentes entre casos y controles. Sin embargo, se observó una interacción significativa entre las gestaciones, el IVS y los polimorfismos de MTHFR (presencia del alelo 1298C o del genotipo 677TT). El alelo 1298C combinado con multigestación, con un IVS < 17 años, o con ambos factores, incrementó el riesgo para CaCU en 4.3, 5.3 y 11.8 veces, respectivamente, en tanto que el genotipo 677TT modificó este riesgo a 2.0, 1.9, y 4.2 veces, respectivamente. Conclusión. El alelo 1298C incrementa considerablemente el riesgo para CaCU en mujeres multigestas y con un IVS temprano, en tanto que el genotipo 677TT disminuye este riesgo, pero sin llegar a convertirse en un factor protector.