Gene expression analysis reveals diabetes-related gene signatures

BACKGROUND

Diabetes is a spectrum of metabolic diseases affecting millions of people worldwide. The loss of pancreatic β-cell mass by either autoimmune destruction or apoptosis, in type 1-diabetes (T1D) and type 2-diabetes (T2D), respectively, represents a pathophysiological process leading to insulin deficiency. Therefore, therapeutic strategies focusing on restoring β-cell mass and β-cell insulin secretory capacity may impact disease management. This study took advantage of powerful integrative bioinformatic tools to scrutinize publicly available diabetes-associated gene expression data to unveil novel potential molecular targets associated with β-cell dysfunction.

METHODS

A comprehensive literature search for human studies on gene expression alterations in the pancreas associated with T1D and T2D was performed. A total of 6 studies were selected for data extraction and for bioinformatic analysis. Pathway enrichment analyses of differentially expressed genes (DEGs) were conducted, together with protein-protein interaction networks and the identification of potential transcription factors (TFs). For noncoding differentially expressed RNAs, microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), which exert regulatory activities associated with diabetes, identifying target genes and pathways regulated by these RNAs is fundamental for establishing a robust regulatory network.

RESULTS

Comparisons of DEGs among the 6 studies showed 59 genes in common among 4 or more studies. Besides alterations in mRNA, it was possible to identify differentially expressed miRNA and lncRNA. Among the top transcription factors (TFs), HIPK2, KLF5, STAT1 and STAT3 emerged as potential regulators of the altered gene expression. Integrated analysis of protein-coding genes, miRNAs, and lncRNAs pointed out several pathways involved in metabolism, cell signaling, the immune system, cell adhesion, and interactions. Interestingly, the GABAergic synapse pathway emerged as the only common pathway to all datasets.

CONCLUSIONS

This study demonstrated the power of bioinformatics tools in scrutinizing publicly available gene expression data, thereby revealing potential therapeutic targets like the GABAergic synapse pathway, which holds promise in modulating α-cells transdifferentiation into β-cells.

Zooplankton assemblages in eutrophic reservoirs of the Brazilian semi-arid

Species composition, density, and temporal dynamics of zooplankton were studied in six reservoirs in a semi-arid region in tropical northeastern Brazil (Rio Grande do Norte state). All the reservoirs are highly eutrophic, with high contents of total nitrogen (minimum of 1200 µg.L-1) and total phosphorus (minimum of 10 µg.L-1), and extremely high algal biomass was registered (surpassing 20 µg Chl a.L-1). All the reservoirs showed an enduring condition of high turbidity and phytoplankton assemblages dominated by cyanobacteria. Zooplankton also showed quantitative patterns suggestive of eutrophic conditions, expressed by high densities, mainly in Passagem das Traíras and Sabugi reservoirs. A spatial differentiation in the composition of the zooplankton community was registered. Rotifers (especially Keratella tropica, Brachionus havanensis, and Keratella americana) were the dominant forms in the zooplankton community of Itans, Passagem das Traíras, and Sabugi reservoirs, while calanoid copepods (mainly Notodiaptomus cearensis) dominated in the Armando Ribeiro, Gargalheiras, and Parelhas systems. The existence of novel relationships in zooplankton community composition in eutrophic reservoirs in this tropical semi-arid region must be considered in designating zooplankton indicators of eutrophic conditions.

Insights from studies with oral cleft genes suggest associations between WNT-pathway genes and risk of oral cancer

Oral squamous cell carcinoma (OSCC) accounts for more than 90% of the malignant neoplasms that arise in the mucosa of the upper aerodigestive tract. Recent studies of cleft lip/palate have shown the association of genes involved in cancer. WNT pathway genes have been associated with several types of cancer and recently with cleft lip/palate. To investigate if genes associated with cleft lip/palate were also associated with oral cancer, we genotyped 188 individuals with OSCC and 225 control individuals for markers in AXIN2, AXIN1, GSK3β, WNT3A, WNT5A, WNT8A, WNT11, WNT3, and WNT9B. Statistical analysis was performed with PLINK 1.06 software to test for differences in allele frequencies of each polymorphism between cases and controls. We found association of SNPs in GSK3B (p = 0.0008) and WNT11 (p = 0.03) with OSCC. We also found overtransmission of GSK3B haplotypes in OSCC cases. Expression analyses showed up-regulation of WNT3A, GSK3B, and AXIN1 and down-regulation of WNT11 in OSCC in comparison with control tissues (P < 0.001). Additional studies should focus on the identification of potentially functional variants in these genes as contributors to human clefting and oral cancer.

Unified paradigm for interface dynamics

In this paper we develop a common theoretical framework for the dynamics of thin featureless interfaces. We explicitly demonstrate that the same phase field and velocity dependent one-scale models characterizing the dynamics of relativistic domain walls, in a cosmological context, can also successfully describe, in a friction dominated regime, the dynamics of nonrelativistic interfaces in a wide variety of material systems. We further show that a statistical version of the von Neumann's law applies in the case of scaling relativistic interface networks, implying that, although relativistic and nonrelativistic interfaces have very different dynamics, a single simulation snapshot is not able to clearly distinguish the two regimes. We highlight that crucial information is contained in the probability distribution function for the number of edges of domains bounded by the interface network and explain why laboratory tests with nonrelativistic interfaces can be used to rule out cosmological domain walls as a significant dark energy source.

Novel cleft susceptibility genes in chromosome 6q

Cleft lip/palate is a defect of craniofacial development. In previous reports, chromosome 6q has been suggested as a candidate region for cleft lip/palate. A multipoint posterior probability of linkage analysis of multiplex families from the Philippines attributed an 88% probability of harboring a cleft-susceptibility gene to a narrower region on bands 6q14.2-14.3. We genotyped 2732 individuals from families and unrelated individuals with and without clefts to investigate the existence of possible cleft-susceptibility genes in this region. We found association of PRSS35 and SNAP91 genes with cleft lip/palate in the case-control cohort and in Caucasian families. Haplotype analyses support the individual associations with PRSS35. We found Prss35 expression in the head and palate of mouse embryos at critical stages for palatogenesis, whereas Snap91 was expressed in the adult brain. We provide further evidence of the involvement of chromosome 6q in cleft lip/palate and suggest PRSS35 as a novel candidate gene.

Defining subphenotypes for oral clefts based on dental development

Individuals with clefts present considerably more dental anomalies than do individuals without clefts. We used dental development to subphenotype clefts with the goal of identifying cleft subgroups that could have specific genetic contributions. We examined 1000 individuals, 500 with clefts and 500 without. We used several clinical features, such as cleft completeness or incompleteness, laterality, and the presence of dental anomalies to assess each individual's cleft status. We performed chi-square and Fisher's exact tests to compare the frequencies of observed anomalies between individuals with and individuals without clefts, and among individuals with different cleft subphenotypes. Agenesis of the lateral incisor on the non-cleft side was the most remarkable observation, and may suggest that such cases could be considered incomplete forms of bilateral clefts of the lip.

Brain mappings of the arithmetic processing in children and adults

Despite the increasing number of experimental mapping showing that human arithmetic cognition is supported by widely spread neural circuits; the theoretical reasoning about these data remains mostly metaphorical and guided by a connectionist approach. Although neurons at distinct areas in the brain are assumed to take charge of different duties in the solution of the experimental task, the results are always discussed by hypothesizing some association between the different areas without questioning any difference of behavior at the level of the neurons at each of these areas. Here, the brain is assumed as Distributed Intelligent Processing System (DIPS) formed by collections of loosely interacting specialized agents (neurons), each agent specializing, for example, in data collection (sensors), problem solving (associative neurons), data communication (interneuronal systems) and in acting upon the surrounding environment (motorneurons). A new technique for EEG brain mapping is proposed and used to study arithmetic cognition in elementary school aged children and adults. Factor analysis showed three distinct patterns of neuronal recruitment for arithmetic calculations in all experimental groups which varied according to the type of calculation, age and sex.

New global defect structures

We investigate the presence of defects in systems described by real scalar field in (D,1) spacetime dimensions. We show that when the potential assumes specific form, there are models which support stable global defects for D arbitrary. We also show how to find first-order differential equations that solve the equations of motion, and how to solve models in D dimensions via soluble problems in D=1. We illustrate the procedure examining specific models and finding explicit solutions.

Analysis of chicken mucosal immune response to Eimeria tenella and Eimeria maxima infection by quantitative reverse transcription-PCR

The recent cloning of chicken genes coding for interleukins, chemokines, and other proteins involved in immune regulation and inflammation allowed us to analyze their expression during infection with Eimeria. The expression levels of different genes in jejunal and cecal RNA extracts isolated from uninfected chickens and chickens infected with Eimeria maxima or E. tenella were measured using a precise quantitative reverse transcription-PCR technique. Seven days after E. tenella infection, expression of the proinflammatory cytokine interleukin-1beta (IL-1beta) mRNA was increased 80-fold. Among the chemokines analyzed, the CC chemokines K203 (200-fold) and macrophage inflammatory factor 1beta (MIP-1beta) (80-fold) were strongly upregulated in the infected ceca, but the CXC chemokines IL-8 and K60 were not. However, the CXC chemokines were expressed at very high levels in uninfected cecal extracts. The levels of gamma interferon (IFN-gamma) (300-fold), inducible nitric oxide synthase (iNOS) (200-fold), and myelomonocytic growth factor (MGF) (50-fold) were also highly upregulated during infection with E. tenella, whereas cyclooxygenase 2 showed a more modest (13-fold) increase. The genes upregulated during E. tenella infection were generally also upregulated during E. maxima infection but at a lower magnitude except for those encoding MIP-1beta and MGF. For these two cytokines, no significant change in expression levels was observed after E. maxima infection. CD3+ intraepithelial lymphocytes may participate in the IFN-gamma upregulation observed after infection, since both recruitment and upregulation of the IFN-gamma mRNA level were observed in the infected jejunal mucosa. Moreover, in the chicken macrophage cell line HD-11, CC chemokines, MGF, IL-1beta, and iNOS were inducible by IFN-gamma, suggesting that macrophages may be one of the cell populations involved in the upregulation of these cytokines observed in vivo during infection with Eimeria.

A theoretical model of the evolution of virulence in sexually transmitted HIV/AIDS

INTRODUCTION

The evolution of virulence in host-parasite relationships has been the subject of several publications. In the case of HIV virulence, some authors suggest that the evolution of HIV virulence correlates with the rate of acquisition of new sexual partners. In contrast some other authors argue that the level of HIV virulence is independent of the sexual activity of the host population.

METHODS

Provide a mathematical model for the study of the potential influence of human sexual behaviour on the evolution of virulence of HIV is provided.

RESULTS

The results indicated that, when the probability of acquisition of infection is a function both of the sexual activity and of the virulence level of HIV strains, the evolution of HIV virulence correlates positively with the rate of acquisition of new sexual partners.

CONCLUSION

It is concluded that in the case of a host population with a low (high) rate of exchange of sexual partners the evolution of HIV virulence is such that the less (more) virulent strain prevails.

Prevalence of homozygosity for the deleted alleles of glutathione S-transferase mu (GSTM1) and theta (GSTT1) among distinct ethnic groups from Brazil: relevance to environmental carcinogenesis?

Environmental related diseases due to occupational carcinogens and toxic substances are a serious problem particularly in developing countries. The glutathione S-transferase system is fundamental for the detoxification of numerous carcinogens and mutagens. The individual inherited susceptibility to chemical carcinogenesis due to glutathione S-transferase mu (GSTM1) and theta (GSTT1) varies significantly among distinct ethnic groups. In this study we determined the prevalence of the null genotype of the GSTM1 and GSTT1 genes among individuals from three distinct Brazilian racial groups using a multiplex-PCR methodology. The results showed that the highest prevalence of the null genotype for the GSTM1 occurred among Caucasians (55%, allele frequency = 0.74), followed by 33% among Brazilian Black subjects (allele frequency = 0.57), and 20% among Amazonian Indians (allele frequency = 0.45). For GSTT1 a homogenous distribution of the null genotype was found among Caucasian and African descendants (18.5 and 19% homozygotes, respectively, allele frequency = 0.43), with a lower prevalence among Amazonian Indians (11% of homozygotes, allele frequency = 0.34). Whether the deficiency of the GST system contributes to a predisposition to environmental related carcinogenesis in specific populations in Brazil remains to be determined.

Prevalence of the mutation C677 --> T in the methylene tetrahydrofolate reductase gene among distinct ethnic groups in Brazil

Vascular disease is a serious public health problem in the industrialized world, and is a frequent cause of death among the adult population of Brazil. Mild hyperhomocysteinemia has been identified as a risk factor for arterial disease, venous thrombosis, and neural tube defects. Individuals homozygous for the thermolabile variant of methylenetetrahydrofolate reductase (MTHFR-T) are found in 5-15% of the general population and have significantly elevated plasma homocysteine levels which represent one of the genetic risk factors for vascular diseases. We have analyzed the prevalence of individuals homozygous for the MTHFR-T in 327 subjects representing the three distinct ethnic groups in Brazil. The prevalence of homozygotes for the mutated allele MTHFR-T was high among persons of Caucasian descent (10%) and considerably lower among Black (1.45%) and Indians persons populations (1.2%). These data suggest that screening for the MTHFR-T allele should help in identifying individuals with a high risk of vascular disease among populations with a heterogeneous background.

Key role for cyclooxygenase-2 in PGE2 and PGF2alpha receptor regulation and cerebral blood flow of the newborn

Ibuprofen, a cyclooxygenase (COX) inhibitor nonselective for either COX-1 or COX-2 isoform, upregulates cerebrovascular prostaglandin E2 (PGE2) and PGF2alpha receptors in newborn pigs. COX-2 was shown to be the predominant form of COX and the main catalyst of prostaglandin synthesis in the newborn brain. We proceeded to establish direct evidence that COX-2-generated prostaglandins govern PGE2 and PGF2alpha receptor density and function in the cerebral vasculature of the newborn. Hence, we determined PGE2 and PGF2alpha receptor density and functions in brain vasculature by using newborn pigs treated with saline, ibuprofen, COX-1 inhibitor (valerylsalicylate), or COX-2 inhibitors (DUP-697 and NS-398). Newborn brain PGE2 and PGF2alpha concentrations were significantly reduced by ibuprofen, DUP-697, and NS-398 but not by valerylsalicylate. In newborn pigs treated with DUP-697, NS-398, and ibuprofen, PGE2 and PGF2alpha receptor densities in brain microvessels were increased to adult levels; there was also a significant increase in inositol 1,4,5-trisphosphate (IP3) production and cerebral vasoconstrictor effects of 17-phenyl trinor PGE2 (EP1 receptor agonist), M&B-28767 (EP3 receptor agonist), PGF2alpha, and fenprostalene (PGF2alpha analog). Treatment with ibuprofen or DUP-697 also increased the upper blood pressure limit of cerebral cortex and periventricular blood flow autoregulation from 85 to > or = 125 mmHg (uppermost blood pressure studied). However, valerylsalicylate treatment did not affect cerebrovascular PGE2 and PGF2alpha receptors, IP3 production, or vasoconstrictor effects in newborn animals. These in vivo and in vitro observations indicate that COX-2 is mainly responsible for the regulation of PGE2 and PGF2alpha receptors and their functions in the newborn cerebral vasculature.