Association of genes of different functional classes with type 1 diabetes

The genetic structure of susceptibility to type 1 diabetes (T1D) in the population of Tomsk was studied. We had a group of T1D patients (N = 285) and a population sample (N = 300) and we studied 58 SNPs localized in the 47 genes which products are involved in various metabolic pathways and processes as fibrogenesis, endothelial dysfunction, and inflammation. Genotyping was performed by mass spectrometry using the Sequenom MassARRAY system (United States). We compared the group of T1D patients and the population sample and found an association with the predisposition to disease for seven markers: rs3765124 of the ADAMDEC1 gene, genotype AA (p = 0.004), allele A (p = 0.033); rs1007856 of the ITGB5 gene, genotype TT (p = 0.015), allele T (p = 0.036); rs20579 of the LIG1 gene, genotype CC (p = 0.004), allele C (p = 0.002); rs12980602 of the IFNL2 gene, allele C (p = 0.029); rs4986819 of the PARP4 gene, allele C (p = 0.044); rs1143674 of the ITGA4 gene genotype GG (p = 0.002); rs679620 of the MMP3 gene, genotype AA (p = 0.008). Thus, the products of genes associated with T1D belong to different molecular classes: metalloproteases (ADAMDEC1, MMP3), cytokines (IL28A), cell surface receptors (ITGA4), adhesion molecules (ITGB5), DNA ligases (LIG1), and ribosyltransferase enzymes (PARP4). The ADAMDEC1, ITGA4, and ITGB5 genes belong to two biological processes: cell communication and signal transduction. The LIG1 and PARP4 genes regulate the metabolism of nucleic acids, MMP3 is involved in the regulation of protein metabolism, and the IFNL2 is involved in the immune response.     

Insight into the molecular mechanism of the sulfur oxidation process by reverse sulfite reductase (rSiR) from sulfur oxidizer <Emphasis Type="Italic">Allochromatium vinosum</Emphasis>

Sulfur metabolism is one of the oldest known biochemical processes. Chemotrophic or phototrophic proteobacteria, through the dissimilatory pathway, use sulfate, sulfide, sulfite, thiosulfate or elementary sulfur by either reductive or oxidative mechanisms. During anoxygenic photosynthesis, anaerobic sulfur oxidizer Allochromatium vinosum forms sulfur globules that are further oxidized by dsr operon. One of the key redox enzymes in reductive or oxidative sulfur metabolic pathways is the DsrAB protein complex. However, there are practically no reports to elucidate the molecular mechanism of the sulfur oxidation process by the DsrAB protein complex from sulfur oxidizer Allochromatium vinosum. In the present context, we tried to analyze the structural details of the DsrAB protein complex from sulfur oxidizer Allochromatium vinosum by molecular dynamics simulations. The molecular dynamics simulation results revealed the various types of molecular interactions between DsrA and DsrB proteins during the formation of DsrAB protein complex. We, for the first time, predicted the mode of binding interactions between the co-factor and DsrAB protein complex from Allochromatium vinosum. We also compared the binding interfaces of DsrAB from sulfur oxidizer Allochromatium vinosum and sulfate reducer Desulfovibrio vulgaris. This study is the first to provide a comparative aspect of binding modes of sulfur oxidizer Allochromatium vinosum and sulfate reducer Desulfovibrio vulgaris.     

Adherence to Mediterranean diet is associated with methylation changes in inflammation-related genes in peripheral blood cells

Epigenetic processes, including DNA methylation, might be modulated by environmental factors such as the diet, which in turn have been associated with the onset of several diseases such as obesity or cardiovascular events. Meanwhile, Mediterranean diet (MedDiet) has demonstrated favourable effects on cardiovascular risk, blood pressure, inflammation and other complications related to excessive adiposity. Some of these effects could be mediated by epigenetic modifications. Therefore, the objective of this study was to investigate whether the adherence to MedDiet is associated with changes in the methylation status from peripheral blood cells. A subset of 36 individuals was selected within the Prevención con Dieta Mediterránea (PREDIMED)-Navarra study, a randomised, controlled, parallel trial with three groups of intervention in high cardiovascular risk volunteers, two with a MedDiet and one low-fat control group. Changes in methylation between baseline and 5 years were studied. DNA methylation arrays were analysed by several robust statistical tests and functional classifications. Eight genes related to inflammation and immunocompetence (EEF2, COL18A1, IL4I1, LEPR, PLAGL1, IFRD1, MAPKAPK2, PPARGC1B) were finally selected as changes in their methylation levels correlated with adherence to MedDiet and because they presented sensitivity related to a high variability in methylation changes. Additionally, EEF2 methylation levels positively correlated with concentrations of TNF-α and CRP. This report is apparently the first showing that adherence to MedDiet is associated with the methylation of the reported genes related to inflammation with a potential regulatory impact.     

Isolation and Expression Analysis of <Emphasis Type="Italic">PeDWF1</Emphasis> in <Emphasis Type="Italic">Phyllostachys edulis</Emphasis>

Brassinosteroids (BRs) are steroidal hormones that play crucial roles in various processes of plant growth and development. DWF1 encodes a delta(24)-sterol reductase that participates in one of the early stage in the brassinosteroids’ biosynthetic pathway: the conversion of 24-methylenecholesterol to campesterol. Here we report the isolation and expression of one DWF1 homologous gene, PeDWF1, in moso bamboo (Phyllostachys edulis (Carrière) J. Houz.). Sequence analysis revealed that the open reading frame of PeDWF1 was 1686-bp encoding a protein composed of 561 amino acid residues with a calculated molecular weight of 65.1 kD and a theoretic isoelectric point of 8.32. Phylogenetic analysis indicated that PeDWF1 was very close to the cell elongation protein Dwarf1 in rice (Oryza sativa). Furthermore, transient expression of a PeDWF1::GFP fusion protein showed that PeDWF1 was an integral membrane protein most probably associated with the endoplasmic reticulum similar to Dwarf1. Tissue specific expression analysis showed that PeDWF1 was constitutively expressed in moso bamboo with the highest level in shoots and the lowest level in mature leaves. In the early growing stage of shoots, the expression level of PeDWF1 had a rising trend with the increasing height of shoots. These results indicated that PeDWF1 might be involved in the regulation of shoot development by participating in BRs biosynthesis. Moreover, PeDWF1 was heterologously expressed in Escherichia coli and the recombinant protein was about 65 kD, which facilitated further study on the gene function of PeDWF1 in bamboo.     

<Emphasis Type="Italic">SOC1</Emphasis> and <Emphasis Type="Italic">AGL24</Emphasis> interact with AGL18-1, not the other family members AGL18-2 and AGL18-3 in <Emphasis Type="Italic">Brassica juncea</Emphasis>

Many MCM1-AGAMOUS-DEFICIENS-SRF (MADS) genes have been proved to play an important role in the flowering time regulation of plants. The flowering-inhibiting factor AGAMOUS-LIKE 18 (AGL18) integrates into the two flowering-activating factors SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and AGAMOUS-LIKE 24 (AGL24), which play an important role during the plant developmental stages of the flowering pathway. However, it remains unknown whether and how the AGL18 protein directly interacts with SOC1 and/or AGL24 genes to regulate flowering time in Brassica juncea. In this study, three members (AGL18-1 in florescence, AGL18-2 and AGL18-3 in young seedlings) of the AGL18 family, and SOC1 and AGL24 in florescence were cloned in Brassica juncea. Yeast One-Hybrid assays and Dual-Glo^® Luciferase assays showed that the SOC1 and AGL24 promoters interacted only with AGL18-1 protein, not AGL18-2 and AGL18-3. The typical conserved structure of the M-domain of AGL18-1 was the key region that mediated the interaction between the AGL18-1 protein and SOC1 promoter, and the I-domain, K-domain and C-domain did not regulate the interaction of AGL18-1/SOC1. In contrast, the K-domain and M-domain in AGL18-1 could mediate the interaction between the AGL18-1 protein and AGL24 promoter. This indicated that the AGL18-1 protein must have its unique functions that differed from AGL18-2 and AGL18-3. This work provides valuable information for in-depth studies into the molecular mechanisms of the AGL18 protein with SOC1 and AGL24 for flowering time control of Brassica juncea.     

Transcriptome and physiological analyses reveal that AM1 as an ABA-mimicking ligand improves drought resistance in <Emphasis Type="Italic">Brassica napus</Emphasis>

Abscisic acid (ABA) is the most important stress hormone in the regulation of plant adaptation to drought. Owing to the chemical instability and rapid catabolism of ABA, ABA mimic 1 (AM1) is frequently applied to enhance drought resistance in plants, but the molecular mechanisms governed by AM1 on improving drought resistance in Brassica napus are not entirely understood. To investigate the effect of AM1 on drought resistance at the physiological and molecular levels, exogenous ABA and AM1 were applied to the leaves of two B. napus genotypes (Q2 and Qinyou 8) given progressive drought stress. The results showed that the leaves of 50 µM ABA- and AM1-treated plants shared over 60% differential expressed genes and 90% of the enriched functional pathways in Qinyou 8 under drought. AM1 affected the expression of the genes involved in ABA signaling; they down-regulated pyrabactin resistance/PYR1-like (PYR/PYLs), up-regulated type 2C protein phosphatases (PP2Cs), partially up-regulated sucrose non-fermenting 1-related protein kinase 2s (SnRK2s), and down-regulated ABA-responsive element (ABRE)-binding protein/ABRE-binding factors (AREB/ABFs). Additionally, AM1 treatment repressed the expression of photosynthesis-related genes, those mainly associated with the light reaction process. Moreover, AM1 decreased the stomatal conductance, the net photosynthetic rate, and the transpiration rate, but increased the relative water content in leaves and increased survival rates of two genotypes under drought stress. Our findings suggest that AM1 has a potential to improve drought resistance in B. napus by triggering molecular and physiological responses to reduce water loss and impair growth, leading to increased survival rates.     

Expression of iron-regulators in the bone tissue of rats with and without iron overload

Recently, more and more studies indicate that iron overload would cause osteopenia or osteoporosis. However, the molecular mechanism of it remains unclear. Moreover, very little is known about the iron metabolism in bone tissue at present. Therefore, the mRNA expression of iron-regulators, transferrin receptor1 (Tfr1), divalent metal transporter1 (Dmt1?+?IRE and Dmt1???IRE), ferritin (FtH and FtL), and ferroportin1 (Ireg1), and the localization of ferroportin1 protein were examined in the bone tissue of rats. In addition, the mRNA expression of each gene was compared between groups of rats with and without iron overload. The results showed that ferroportin1 protein was localized in the cytoplasm of osteoblast, osteocyte, chondrocyte and osteoclast of rats’ femur. The six iron-regulatory genes, Tfr1, ferritin (FtH and FtL), (Dmt1?+?IRE and Dmt1???IRE) and ferroportin1 (Ireg1), were found in femurs of rats. In addition, significantly up-regulated expression of FtH and FtL mRNA, and markedly down-regulated expression of Tfr1, Dmt1?+?IRE and Ireg1 mRNA, were observed in the iron overload group compared with the control group. The result indicates that ferroportin1 protein is localized in the cytoplasm of bone cells of rats. Tfr1, Dmt1, ferritin and ferroportin1 exist in bone tissue of rats, and they may be involved in the pathological process of iron overload-induced bone lesion.     

Chaotic Dynamics of Neuromuscular System Parameters and the Problems of the Evolution of Complexity

The evolution rate v(t) varies among diverse biosystems, but a general theory can be formulated when the dynamics of the biosystem stater x = x(t) = (x₁, x₂, x _m ) ^T is considered in the m-dimensional space of states. A mathematical approach is proposed for evaluating such processes and describes the processes in terms of particular chaos of the statistical distribution functions f(x). In the case of complex multicomponent systems with a high dimension number m (m ?1) of the phase space of states, we propose using pairwise comparison matrices of samples x(t) when homeostasis is constant and calculating the parameters of quasiattractors. The Glensdorff–Prigogine thermodynamic approach to estimating evolution is inefficient in assessing the third-type systems, while it is applicable and the Prigogine theorem works at the level of molecular systems. Alterations in the state of the human neuromuscular system were found to lead to chaotic changes in the statistical functions f(x) in tremor recording samples, while quasiattractor parameters demonstrate a certain regularity.     

The promoter of filamentation (POF1) protein from <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> is an ATPase involved in the protein quality control process

Background

The gene YCL047C, which has been renamed promoter of filamentation gene (POF1), has recently been described as a cell component involved in yeast filamentous growth. The objective of this work is to understand the molecular and biological function of this gene.

Results

Here, we report that the protein encoded by the POF1 gene, Pof1p, is an ATPase that may be part of the Saccharomyces cerevisiae protein quality control pathway. According to the results, Δpof1 cells showed increased sensitivity to hydrogen peroxide, tert-butyl hydroperoxide, heat shock and protein unfolding agents, such as dithiothreitol and tunicamycin. Besides, the overexpression of POF1 suppressed the sensitivity of Δpct1, a strain that lacks a gene that encodes a phosphocholine cytidylyltransferase, to heat shock. In vitro analysis showed, however, that the purified Pof1p enzyme had no cytidylyltransferase activity but does have ATPase activity, with catalytic efficiency comparable to other ATPases involved in endoplasmic reticulum-associated degradation of proteins (ERAD). Supporting these findings, co-immunoprecipitation experiments showed a physical interaction between Pof1p and Ubc7p (an ubiquitin conjugating enzyme) in vivo.

Conclusions

Taken together, the results strongly suggest that the biological function of Pof1p is related to the regulation of protein degradation.

     

Mutations in <Emphasis Type="Italic">CsPID</Emphasis> encoding a Ser/Thr protein kinase are responsible for round leaf shape in cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.)

Key message

Two round-leaf mutants, rl-1 and rl-2, were identified from EMS-induced mutagenesis. High throughput sequencing and map-based cloning suggested CsPID encoding a Ser/Thr protein kinase as the most possible candidate for rl-1. Rl-2 was allelic to Rl-1.

Abstract

Leaf shape is an important plant architecture trait that is affected by plant hormones, especially auxin. In Arabidopsis, PINOID (PID), a regulator for the auxin polar transporter PIN (PIN-FORMED) affects leaf shape formation, but this function of PID in crop plants has not been well studied. From an EMS mutagenesis population, we identified two round-leaf (rl) mutants, C356 and C949. Segregation analysis suggested that both mutations were controlled by single recessive genes, rl-1 and rl-2, respectively. With map-based cloning, we show that CsPID as the candidate gene of rl-1; a non-synonymous SNP in the second exon of CsPID resulted in an amino acid substitution and the round leaf phenotype. As compared in the wild type plant, CsPID had significantly lower expression in the root, leaf and female flowers in C356, which may result in the less developed roots, round leaves and abnormal female flowers, respectively in the rl-1 mutant. Among the three copies of PID genes, CsPID, CsPID2 and CSPID2L (CsPID2-like) in the cucumber genome, CsPID was the only one with significantly differential expression in adult leaves between WT and C356 suggesting CsPID plays a main role in leaf shape formation. The rl-2 mutation in C949 was also cloned, which was due to another SNP in a nearby location of rl-1 in the same CsPID gene. The two round leaf mutants and the work presented herein provide a good foundation for understanding the molecular mechanisms of CsPID in cucumber leaf development.