Protein Modification Process Research Articles

Computational Network Analysis Identifies Evolutionarily Conserved miRNA Gene Interactions Potentially Regulating Immune Response in Bovine Trypanosomosis.

Bovine trypanosomosis is a devastating disease that causes huge economic loss to the global cattle industry on a yearly basis. Selection of accurate biomarkers are important in early disease diagnosis and treatment. Of late, micro-RNAs (miRNAs) are becoming the most useful biomarkers for both infectious and non-infectious diseases in humans, but this is not the case in animals. miRNAs are non-coding RNAs that regulate gene expression through binding to the 3′-, 5′-untranslated regions (UTR) or coding sequence (CDS) region of one or more target genes. The molecular identification of miRNAs that regulates the expression of immune genes responding to bovine trypanosomosis is poorly defined, as is the possibility that these miRNAs could serve as potential biomarkers for disease diagnosis and treatment currently unknown. To this end, we utilized in silico tools to elucidate conserved miRNAs regulating immune response genes during infection, in addition to cataloging significant genes. Based on the p value of 1.77E-32, we selected 25 significantly expressed immune genes. Using prediction analysis, we identified a total of 4,251 bovine miRNAs targeting these selected genes across the 3′UTR, 5′UTR and CDS regions. Thereafter, we identified candidate miRNAs based on the number of gene targets and their abundance at the three regions. In all, we found the top 13 miRNAs that are significantly conserved targeting 7 innate immune response genes, including bta-mir-2460, bta-mir-193a, bta-mir-2316, and bta-mir-2456. Our gene ontology analysis suggests that these miRNAs are involved in gene silencing, cellular protein modification process, RNA-induced silencing complex, regulation of humoral immune response mediated by circulating immunoglobulin and negative regulation of chronic inflammatory response, among others. In conclusion, this study identifies specific miRNAs that may be involved in the regulation of gene expression during bovine trypanosomosis. These miRNAs have the potential to be used as biomarkers in the animal and veterinary research community to facilitate the development of tools for early disease diagnosis/detection, drug targeting, and the rational design of drugs to facilitate disease treatment.

Effect of ACSL3 Expression Levels on Preadipocyte Differentiation in Chinese Red Steppe Cattle

Domestic cattle are an important type of livestock, with beef production playing a major role in the agricultural economy. Adipocyte levels and fat content are interrelated, with meat quality being highly dependent on its fat content and distribution. Acyl-CoA synthetases of long-chain (ACSL) fatty acids (FAs) play an integral role in virtually every metabolic pathway in mammalian biochemistry, including complex lipid biosynthesis, protein modification, and β-oxidation processes. ACSL3 activity is also known to be associated with adipocyte differentiation; however, its biological mechanism of action is currently unclear. Gene expression in subcutaneous preadipocytes isolated from subcutaneous deposits of Chinese Red Steppe cattle has been studied using in vitro cell transfection, real-time polymerase chain reaction and western blot analysis. The lipid and triglyceride contents of lipid droplets have also been measured to verify the levels of gene expression. These combined studies show that ACSL3 is induced during adipocyte differentiation, with its overexpression promoting an increase in the triglyceride content of lipid droplets. Furthermore, mRNA and protein expression levels for adipocyte differentiation marker genes, such as peroxisome proliferator-activated receptor gamma (PPARγ) and CCAAT/enhancer-binding protein alpha (C/EBPα), were markedly increased during mature adipocyte cell differentiation. Knockdown of ACSL3 expression using ACSL3 small interfering RNAs (siRNAs) resulted in a decrease in lipid content of cattle adipocytes, providing further evidence that ACSL3 plays a key role in the differentiation process.

Differential regulation of mycelial growth and aflatoxin biosynthesis by Aspergillus flavus under different temperatures as revealed by strand-specific RNA-Seq.

Although several regulatory pathways have been reported for Aspergillus flavus, the regulation of aflatoxin production and mycelial growth under different temperatures remains unclear. In this study, A. flavus differentially expressed genes (DEGs) and regulatory pathways were analyzed under three temperatures, by strand‐specific RNA‐Seq. Results show that a total of 2,428 and 1,474 DEGs were identified in fungal mycelia cultured at 20°C and 37°C, respectively, as compared with the control (28°C). Approximately ~ 79% of DEGs in the 37°C samples were up‐regulated genes, while ~ 63% of DEGs in the 20°C samples were down‐regulated genes. Most of the DEG pathways enriched by lower temperatures differed from those enriched by higher temperatures, while only a small portion of the pathways were shared by A. flavus grown under different temperatures. Aflatoxin biosynthesis, Butanoate metabolism, oxidation–reduction process, and benzene‐containing compound metabolic process were the shared down‐regulated pathways, while steroid biosynthesis, oxidoreductase activity, cellular protein modification process, DNA binding, protein complex were the shared up‐regulated pathways between lower and higher temperatures. The shared genes and pathways are the key regulatory candidates for aflatoxin biosynthesis with changes of temperature. In addition, the identification of both up‐regulated and down‐regulated genes provides a useful gene set for further investigation of the aflatoxin biosynthesis among Aspergillus.

Potential effect of carnosine encapsulated niosomes in bovine serum albumin modifications

Protein modification and alteration are important factors in many age-related diseases such as diabetes and Alzheimer's disease. Modifications like the formation of advanced glycation end-products (AGE) and advanced oxidation protein products (AOPP) can cause harm to the organism and may contribute to protein aggregation and amyloid fibrils formation. Carnosine was used as a potential solution for protein modification complications. Furthermore, some organs like the brain are difficult to reach due to the blood-brain barrier. As such, new nano-engineered formulations were sought to bypass unwanted interactions and degradation. Thus, we propose the encapsulation of carnosine in niosomes as a potential solution. Initially, carnosine niosomes were synthesized and characterized. Then, modifications of bovine serum albumin (glycation, oxidation, and aggregation) were induced in vitro where carnosine and carnosine niosomes were added at different concentrations (2.5, 5, and 10 mM) to the reactions. In addition, biocomputational and docking studies were performed to elucidate the potential interactions. Data showed a dose-dependent inhibition of AGE, AOPP, and aggregation for both carnosine and niosome carnosine. Furthermore, the results suggest that carnosine interacts with specific amino acids implicated in the protein modification process. Carnosine nano-formulation shows promising potential in age-related protein modification and needs further exploration of its mechanisms.

Analysis of gene expression of Tetrahymena thermophila treated with Panax japonicas

Panax japonicus is a traditional Chinese medicine,and its principle components have shown certain pharmacological activities for cell damage,aging and cell apoptosis. In order to clarify the pharmacological mechanism and involved metabolic pathways of P. japonicas,the gene expression of Tetrahymena thermophila under P. japonicus treatment was analyzed through high-throughput transcriptome sequencing in this study. Based on the transcriptome analysis,3 544 differentially expressed genes were identified in control group,of which 1 945 genes showed up-regulated expression and 1 599 genes showed down-regulated expression. Under P. japonicas treatment in the experiment group,3 312 differentially expressed genes were screened,of which 1 `493 genes showed up-regulated expression and 1 819 genes showed down-regulated expression. GO enrichment analysis indicated that in control group,the genes in the cells in a series of fundamental biological process were down-regulated,such as DNA replication and protein synthesis; while the signal transduction process and fatty acids oxidizing process were enriched. Whereas in the experiment group,down-regulated genes were mainly enriched in oxidation-reduction,cofactor metabolic process and vitamin metabolic process; up-regulated genes were enriched in signal transduction process and protein modification process. In the analysis using KEGG database,cell cycle pathway was enhanced and autophagy pathway was inhibited under the condition of P. japonicas treatment. Real-time quantitative polymerase chain reaction( RT-qPCR) was used to detect the expression differences between 6 up-regulated and 4 down-regulated genes in related metabolic pathways. The RT-q PCR results and RNA-Seq data were highly correlated and consistent with each other. This study could provide important direction and basis for further study on the mechanism of cell growth regulation with the treatment of P. japonica.

KEGG-expressed genes and pathways in intervertebral disc degeneration: Protocol for a systematic review and data mining.

miRNAs and genes play significant roles in the etiology and pathogenesis of intervertebral disc degeneration (IDD). This study aimed to identify aberrantly expressed miRNAs, genes, and pathways in IDD through a comprehensive bioinformatics analysis.Data of miRNAs expression microarrays (GSE63492) and genes microarrays (GSE23130) were obtained from GEO database. Similarly, aberrantly expressed miRNAs and genes were obtained using GEO2R. In addition, functional and enrichment analyses of selected miRNAs and genes were performed using the DAVID database. Meanwhile, protein–protein interaction (PPI) network was constructed using STRING, and then visualized in Cytoscape.A total of 98 upregulated miRNAs were identified. They were enriched in biological processes of response to organelle, ion binding, cellular nitrogen compound metabolic process, biosynthetic process, small molecule metabolic process, cellular protein modification process, catabolic process, molecular function, neurotrophin TRK receptor signaling pathway, and protein complex. In addition, 1405 high expression protein genes were detected. It indicated enrichment in biological processes, such as translational initiation, nonsense-mediated decay, viral transcription, cell–cell adhesion, rRNA processing, translation, RP-dependent cotranslational protein targeting to membrane, nuclear-transcribed mRNA catabolic process, regulation of mRNA stability, and mRNA splicing via spliceosome and extracellular matrix organization. In addition, pathway analysis exhibited the common enrichment in focal adhesion, Hippo signaling pathway, ECM-receptor interaction, Wnt signaling pathway, PI3K-Akt signaling pathway, endocytosis, proteoglycans in cancer, and so on. The top 10 central genes of PPI network were POTEE, PPP2CA, RPL17, HSP90AA1, POTEF, RPL13A, ACTB, RPL18, RPS24, and HSPA1A.In conclusion, our research proposed abnormally expressed miRNAs, genes, and pathways in IDD through bioinformatics methods, which may provide new insights into the pathogenesis of IDD. Thus, the Hub gene involving POTEE, PPP2CA, RPL17, HSP90AA1, POTEF, RPL13A, ACTB, RPL18, RPS24, and HSPA1A may be biomarkers for accurate diagnosis and treatment of IDD in the future.

Transcriptome analysis to identify long non coding RNA (lncRNA) and characterize their functional role in back fat tissue of pig

Long non coding RNAs (lncRNA) have been previously found to be involved in important cellular activities like epigenetics, implantation, cell growth etc. in pigs. However, comprehensive analysis of lncRNA in back fat tissues at different developmental stages in pigs is still lacking. In this study we conducted transcriptome analysis in the back fat tissue of a F1 crossbred Korean Native Pig (KNP) × Yorkshire Pig to identify lncRNA. We investigated their role in 16 pigs at two different growth stages; stage 1 (10 weeks, n = 8) and stage 2 (26 weeks, n = 8). After quality assessment of sequencing reads, we got a total of 1,641,165 assembled transcripts out of eight paired end read from each stage. Among them, 6808 lncRNA transcripts were identified by filtering on the basis of multiple parameters like read length ≥ 200 nucleotides, exon numbers ≥2, FPKM ≥0.5, coding potential score < 0 etc. PFAM and RFAM were used to filter out all possible protein coding genes and housekeeping RNAs respectively. A total of 103 lncRNAs and 1057 mRNAs were found to be differentially expressed (DE) between the two stages (|log2FC| > 2, q < 0.05). We also identified 306 genes located around 100 kb upstream and 234 genes downstream around these DE lncRNA transcripts. The expression of top eleven DE lncRNAs (COL4A6, LY7S, MYH2, OXCT1, SMPDL3A, TMEM182, TTC36, RFOOOO4, RFOOO15, RFOOO45, CADM2) had been validating by qRT-PCR. Pathway and GO terms analysis showed that, positive regulation of biosynthetic process, Wnt signaling pathway, cellular protein modification process, and positive regulation of nitrogen compound were differentially enriched. Our results suggested that, KEGG pathways such as protein digestion and absorption, Arrhythmogenic right ventricular cardiomyopathy (ARVC) to be significantly enriched in both DE lncRNAs as well as DE mRNAs and involved in back fat tissues development. It also suggests that, identified lncRNAs are involved in regulation of important adipose tissues development pathways.

Identifying de-NEDDylation inhibitors: Virtual high-throughput screens targeting SENP8.

Protein modification can have far-reaching effects. NEDDylation, a protein modification process with the protein NEDD8, stabilizes and modifies how the targeted protein interacts with other proteins. Its role in system regulation makes it a prime therapeutic target, and virtual high-throughput screening has already identified new NEDD8 inhibitors. SENP8 matures the NEDD8 proenzyme into the active form and regulates NEDDylation by removing NEDD8 from over-NEDDylated proteins. In this work, SENP8 inhibitor candidates were identified in two rounds of virtual high-throughput screening. Of the ten candidates identified in the first round of screening, four were active in validation experiments to yield an experimental hit rate of 40%. Of the five candidates identified in the second round of screening, one was active in validation experiments to yield an experimental hit rate of 20%. Results indicate virtual high-throughput screening improved hit rates over traditional high-throughput screening. The SENP8 inhibitor candidates can be used to interrogate the NEDDylation regulation mechanism.

Global Phosphoproteomic Analysis Reveals the Defense and Response Mechanisms of Jatropha Curcas Seedling under Chilling Stress.

As a promising energy plant for biodiesel, Jatropha curcas is a tropical and subtropical shrub and its growth is affected by one of major abiotic stress, chilling. Therefore, we adopt the phosphoproteomic analysis, physiological measurement and ultrastructure observation to illustrate the responsive mechanism of J. curcas seedling under chilling (4 °C) stress. After chilling for 6 h, 308 significantly changed phosphoproteins were detected. Prolonged the chilling treatment for 24 h, obvious physiological injury can be observed and a total of 332 phosphoproteins were examined to be significantly changed. After recovery (28 °C) for 24 h, 291 phosphoproteins were varied at the phosphorylation level. GO analysis showed that significantly changed phosphoproteins were mainly responsible for cellular protein modification process, transport, cellular component organization and signal transduction at the chilling and recovery periods. On the basis of protein-protein interaction network analysis, phosphorylation of several protein kinases, such as SnRK2, MEKK1, EDR1, CDPK, EIN2, EIN4, PI4K and 14-3-3 were possibly responsible for cross-talk between ABA, Ca2+, ethylene and phosphoinositide mediated signaling pathways. We also highlighted the phosphorylation of HOS1, APX and PIP2 might be associated with response to chilling stress in J. curcas seedling. These results will be valuable for further study from the molecular breeding perspective.

Quantitative Proteomics of Potato Leaves Infected with Phytophthora infestans Provides Insights into Coordinated and Altered Protein Expression during Early and Late Disease Stages.

In order to get a better understanding of protein association during Solanum tuberosum (cv. Sarpo Mira)–Phytophthora infestans incompatible interaction, we investigated the proteome dynamics of cv. Sarpo Mira, after foliar application of zoospore suspension from P. infestans isolate, at three key time-points: zero hours post inoculation (hpi) (Control), 48 hpi (EI), and 120 hpi (LI); divided into early and late disease stages by the tandem mass tagging (TMT) method. A total of 1229 differentially-expressed proteins (DEPs) were identified in cv. Sarpo Mira in a pairwise comparison of the two disease stages, including commonly shared DEPs, specific DEPs in early and late disease stages, respectively. Over 80% of the changes in protein abundance were up-regulated in the early stages of infection, whereas more DEPs (61%) were down-regulated in the later disease stage. Expression patterns, functional category, and enrichment tests highlighted significant coordination and enrichment of cell wall-associated defense response proteins during the early stage of infection. The late stage was characterized by a cellular protein modification process, membrane protein complex formation, and cell death induction. These results, together with phenotypic observations, provide further insight into the molecular mechanism of P. infestans resistance in potatos.

Proteomic Analysis of Plasma Membrane Proteins of Antler Stem Cells Using Label-Free LC⁻MS/MS.

Deer antlers are unusual mammalian organs that can fully regenerate after annual shedding. Stem cells resident in the pedicle periosteum (PPCs) provide the main cell source for antler regeneration. Central to various cellular processes are plasma membrane proteins, but the expression of these proteins has not been well documented in antler regeneration. In the present study, plasma membrane proteins of PPCs and facial periosteal cells (FPCs) were analyzed using label-free liquid chromatography–mass spetrometry (LC–MS/MS). A total of 1739 proteins were identified. Of these proteins, 53 were found solely in the PPCs, 100 solely in the FPCs, and 1576 co-existed in both PPCs and FPCs; and 39 were significantly up-regulated in PPCs and 49 up-regulated in FPCs. In total, 226 gene ontology (GO) terms were significantly enriched from the differentially expressed proteins (DEPs). Five clusters of biological processes from these GO terms comprised responses to external stimuli, signal transduction, membrane transport, regulation of tissue regeneration, and protein modification processes. Further studies are required to demonstrate the relevancy of these DEPs in antler stem cell biology and antler regeneration.

Transcriptome responses in wheat roots to colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis.

The influence of arbuscular mycorrhizal (AM) colonization on the expression of genes in the roots of wheat (Triticum aestivum L.) at the transcriptome level is largely unknown. A pot experiment was established to study the responses of the transcriptome profile in the roots of wheat to colonization by the AM fungus Rhizophagus irregularis using high through-put sequencing methods. The results indicated that the expression of 11,746 genes was regulated by AM colonization, and 64.7% of them were up-regulated genes. 1106 genes were only expressed in roots colonized by AM fungi, and 108 genes were only expressed in non-mycorrhizal roots. The differentially expressed genes (DEGs) were primarily distributed on the 2B, 3B, 2A, 2D, and 5B chromosomes of wheat. The DEGs (including both up- and down- regulated) mainly located on membranes, and functioned in nucleotide binding and transferase activity during cellular protein modification and biosynthetic processes. The data revealed that AM colonization up-regulated genes involved in the phenylpropanoid biosynthesis pathway and transcription factors which play vital roles in protecting plants from biotic or abiotic stresses. A number of key genes involved in molecular signal biosynthesis and recognition, epidermal cell colonization and arbuscule formation, carbon and nutrients exchange during AM symbiosis were found. All the ammonium transporter (AMT), iron-phytosiderophore transporter, boron, zinc, and magnesium transporter genes found in our study were up-regulated DEGs. One new AM-specific induced AMT and three new AM-specific induced nitrate transporter (NRT) genes were found in the roots of wheat colonized by AM fungi, even though a negative growth response of wheat to AM colonization occurred. The present study provided new information which is important for understanding the mechanisms behind the development and function of the symbiosis between wheat and AM fungi.

Transcriptomic profiling of skeletal muscle from the Ts1Cje mouse model of Down syndrome suggests dysregulation of trisomic genes associated with neuromuscular junction signaling, oxidative stress and chronic inflammation

Ts1Cje is a mouse model of Down syndrome (DS) with partial triplication of chromosome 16, which encompasses a high number of human chromosome 21 (HSA21) orthologous genes. The mouse model exhibits muscle weakness resembling hypotonia in DS individuals. The effect of extra gene dosages on muscle weakness or hypotonia in Ts1Cje and DS individuals remains unknown. To identify molecular dysregulation of the skeletal muscle, we compared the transcriptomic signatures of soleus and extensor digitorum longus (EDL) muscles between the adult Ts1Cje and disomic littermates. A total of 166 and 262 differentially expressed protein-coding genes (DEGs) were identified in the soleus and EDL muscles, respectively. The partial trisomy of MMU16 in Ts1Cje mice has a greater effect on gene expression in EDL. Top-down clustering analysis of all DEGs for represented functional ontologies revealed 5 functional clusters in soleus associated with signal transduction, development of reproductive system, nucleic acid biosynthesis, protein modification and metabolism as well as regulation of gene expression. On the other hand, only 3 functional clusters were observed for EDL namely neuron and cell development, protein modification and metabolic processes as well as ion transport. A total of 11 selected DEGs were validated using qPCR (disomic DEGs: Mansc1; trisomic DEGs: Itsn1, Rcan1, Synj1, Donson, Dyrk1a, Ifnar1, Ifnar2, Runx1, Sod1 and Tmem50b). The validated DEGs were implicated in neuromuscular junction signalling (Itsn1, Syn1), oxidative stress (Sod1, Runx1) and chronic inflammation processes (Runx1, Rcan1, Ifnar1, Ifnar2). Other validated DEGs have not been well-documented as involved in the skeletal muscle development or function, thus serve as interesting novel candidates for future investigations. To our knowledge, the study was the first attempt to determine the transcriptomic profiles of both soleus and EDL muscles in Ts1Cje mice. It provides new insights on the possible disrupted molecular pathways associated with hypotonia in DS individuals.

Effects of ketamine on the fetal transcriptomic response to umbilical cord occlusion: comparison with hypoxic hypoxia in the cerebral cortex.

The cerebral response to fetal asphyxia is characterized by an upregulation of nucleic acid and chromatin modification processes, as well as a downregulation of metabolic processes at 1h post-umbilical cord occlusion (UCO). Twenty-four hours post UCO, there was an upregulation of metabolic processes and protein modifications. UCO did not alter bacterial gene expression levels, nor did it produce a robust inflammatory response compared to maternal hypoxia. The administration of ketamine produced minimal effects on the fetal response to UCO in the cerebral cortex. Umbilical cord occlusion (UCO) is known to cause neurological disorders in the neonate. Previously, we have reported that hypoxic hypoxia (HH) stimulates the appearance of bacteria in the fetal brain and upregulates the expression of inflammatory markers in fetal cerebral cortex (CTX) and also that ketamine attenuates these responses. In the present study, we aimed to test the hypothesis that UCO, similar to HH, produces an inflammatory response in the fetal CTX and also that treatment with ketamine reduces these effects. In chronically instrumented fetal sheep (∼125days), 30min of partial UCO decreased fetal levels by ∼50%. Half of the fetuses received ketamine (3mgkg-1 ) 10min prior to UCO (n=4 per group). Fetal brains were collected 1 and 24h after the experiment and mRNA was extracted and hybridized for microarray analyses. Differentially-expressed genes were analysed for significant association with gene ontologies and pathways. After 1h, UCO upregulated nucleic acid processing and chromatin modification and downregulated metabolic processes compared to control. After 24h, UCO upregulated metabolic and protein modification processes. Ketamine produced minimal effects. UCO did not alter the abundance of bacterial DNA in fetal brain, nor did it upregulate inflammation pathways compared to HH. We conclude that UCO produced time-dependent responses that did not include bacterial invasion or upregulation of inflammation pathways in fetal CTX. This contrasts with the response to HH, which resulted in the appearance of bacteria in the CTX and upregulated inflammation pathways. These responses in fetal CTX to oxygen deprivation are therefore modified by the maternal or placental response to the stimulus.

Genomic Cloning and Sequence Analysis of Trypanosoma brucei rhodesiense gene Encoding Putative N-glycosylation Enzyme

Background: Trypanosoma brucei rhodesiense is a haemoflagellate parasite of zoonotic significance. Aside from its public health importance, this parasite subspecies gained notoriety because of their effective system to circumvent the immune response of vertebrate host. The parasite cell surface is covered with millions of VSG dimers, which serve as an almost infinite repertoire of biomolecules needed for evasion of host immune system. Around two decades ago, it was resolved that all trypanosome VSG is associated with one or more N-linked oligosaccharides, with a range of structures including high mannose and complex types. This complex process of protein modification known as N-linked glycosylation is catalyzed by oligosaccharyl transferase (OST). In general, the incorporation of glycan structures can alter protein’s antigenic properties and recently it was established that glycan molecules associated with VSG were found to be important in several aspects of trypanosome-host interaction, especially during parasite evasion of the host defense mechanisms. Therefore, our major interest is to clone and characterize the trypanosome OST. Materials, Methods & Results: The template genomic DNA for PCR amplification was extracted as described previously. In an attempt to clone Trypanosoma brucei rhodesiense putative oligosaccharyl transferase, an amplicon of ~2000 bp was obtained having an open reading frame of 2057 bp and deduced primary structure composed of 685 amino acid residues (TbrOST II). Comparison of TbrOST II ORF with annotated putative oligosaccharyl transferase in the genome of other organisms revealed sequence identity to other kinetoplastid. TbrOST II had high nucleotide (Ns) and amino acid (As) sequence similarity with the genomes of T. brucei gambiense (Ns:99%; As:78%) and T. brucei (Ns:95-98%; As:77%-98%). There was also significant nucleotide and amino acid sequence identity in the genomes of T. cruzi (Ns:74%; As:63%), Leishmania infantum (Ns:70-83%; As:46-57%), L. braziliensis (Ns:69-81%; As:46-55%) and L. major (Ns:69-80%; As:46-57%). Sequence similarity (71-77%) from other origins was also exhibited. The nucleotide sequence alignments and analysis were performed using the Oxford University Mac Vector 6.5 sequence analysis software and CLC Workbench 5.6 software. Discussion: The nucleotide BLAST results indicate that sequence identity is higher between species of the same genus rather than of the same family. It is known that T. brucei, T. gambiense and T. rhodesiense are members of the Brucei-complex or Brucei group. Although T. brucei brucei has more similarities with T. brucei rhodesiense than T. brucei gambiense, these parasites are morphologically indistinguishable. This is the probable reason why high sequence identity was displayed by other subspecies of the Brucei group. In addition, the high percent identity possessed by TbrOST II with other trypansomatids agrees with the evolutionarily conserved characteristics of the established OST. The DNA sequence data of TbrOST II showing similar sequences in the genome of other organisms further corroborate the previous reports regarding the ubiquitous nature of OST in other life forms. Based on the size of the amplicon and significant percentage of nucleotide and amino acid sequence identity to homologues within the genome of related species and various organisms, the results strongly indicate that TbrOST II is a trypanosome oligosaccharyl transferase gene candidate that should be fully characterized and subjected to functional genomic studies. The study reports the molecular cloning and sequencing of a potential oligosaccharyl transferase gene in T. brucei rhodesiense (TbrOST II). The sequence data has been deposited in the GenBank with accession number GU475126.

Addicted to sugar: roles of glycans in the order Mononegavirales.

Glycosylation is a biologically important protein modification process by which a carbohydrate chain is enzymatically added to a protein at a specific amino acid residue. This process plays roles in many cellular functions, including intracellular trafficking, cell–cell signaling, protein folding and receptor binding. While glycosylation is a common host cell process, it is utilized by many pathogens as well. Protein glycosylation is widely employed by viruses for both host invasion and evasion of host immune responses. Thus better understanding of viral glycosylation functions has potential applications for improved antiviral therapeutic and vaccine development. Here, we summarize our current knowledge on the broad biological functions of glycans for the Mononegavirales, an order of enveloped negative-sense single-stranded RNA viruses of high medical importance that includes Ebola, rabies, measles and Nipah viruses. We discuss glycobiological findings by genera in alphabetical order within each of eight Mononegavirales families, namely, the bornaviruses, filoviruses, mymonaviruses, nyamiviruses, paramyxoviruses, pneumoviruses, rhabdoviruses and sunviruses.

HISTOCHEMICAL PECULIARITIES OF LIMITED PROTEOLYSIS AND OXIDATIVE PROTEIN MODIFICATION IN THE PLACENTAL TROPHOBLAST ASSOCIATED WITH PREMATURE TERM OF THE CHORIONIC TREE AND IRON DEFICIENCY ANEMIA OF PREGNANCY

Introduction. Assessment of the processes of limited proteolysis and oxidative protein modification is necessary to specify the mechanisms of preterm maturation of the placental chorionic tree and preterm labour. The study was first carried out in association with iron deficiency anemia of pregnancy.Objective: to determine peculiarities of the limited proteolysis and oxidative protein modification in the trophoblast of the placental chorionic tree in case of preterm maturation of the chorionic tree associated with iron deficiency anemia of pregnancy during two different periods of gestation – 29-32 and 33-36 weeks of gestation.Material and methods. 182 placentas were examined. The design of the study assumed isolation of two main groups of the above mentioned terms of gestation and three groups of comparison. The technique for free amino groups of proteins by A.Yasuma and T.Ichikava method and the method for “acid” and “basic” proteins in Mikel Calvo modification were applied.Results. Average indices concerning the processes of limited proteolysis and oxidative protein modification in the trophoblast of the placental chorionic tree were determined in all the groups under study. The main results of quantitative staining assessment are presented in the conclusions.Conclusions. The highest level of limited proteolysis and oxidative protein modification in the trophoblast cytoplasm of the placental chorionic tree was found in case of preterm maturation of the chorionic tree associated with iron deficiency anemia.

"NO" to Autophagy: Fat Does the Trick for Diabetes.

During the progression from obesity to diabetes, a critical attribute is inability to maintain metabolic homeostasis under excessive energy and nutrient exposure, which triggers insulin resistance. Intensive research efforts have linked chronic inflammation, redox changes, and intracellular stress responses to dysregulated energy metabolism, particularly insulin resistance (1). Autophagy, a lysosomal degradation pathway for damaged organelles or long-lived proteins, was recently identified as a key regulatory pathway to preserve lipid homeostasis and insulin sensitivity under metabolic stress conditions (2–4). Dysfunction of autophagy is associated with obesity and type 2 diabetes. However, the mechanisms underlying the cause of autophagic defect in metabolic disorders remain elusive. In this issue of Diabetes , a study conducted by Qian et al. (5) revealed a mechanism by which obesity cripples autophagy in the liver through S -nitrosylation, an inhibitory protein modification process induced by nitric oxide (NO). Their data argue that in obese animals, NO-induced repression of hepatic autophagy causes hepatic steatosis, impairs hepatic insulin signaling, and eventually contributes to the progression of type 2 diabetes (Fig. 1). Figure 1 Proposed model of impairment of hepatic autophagy and insulin action by GSNOR deficiency and nitrosative stress in obesity. Obesity decreases the activity of the denitrosylation enzyme GSNOR, causing nitosative stress and S -nitrosylation of the lysosomal enzymes HexB and CTSB. This leads to hepatic autophagic defect and insulin resistance. The “?” markers indicate the uncharacterized links between metabolic …

In vitro Analysis of Ubiquitin-like Protein Modification in Archaea.

The ubiquitin-like (Ubl) protein is widely distributed in Archaea and involved in many cellular pathways. A well-established method to reconstitute archaeal Ubl protein conjugation in vitro is important to better understand the process of archaeal Ubl protein modification. This protocol describes the in vitro reconstitution of Ubl protein modification and following analysis of this modification in Haloferax volcanii, a halophilic archaeon serving as the model organism.

Association of Genetic Variants of Small Non-Coding RNAs with Survival in Colorectal Cancer.

Background: Single nucleotide polymorphisms (SNPs) of small non-coding RNAs (sncRNAs) can influence sncRNA function and target gene expression to mediate the risk of certain diseases. The aim of the present study was to evaluate the prognostic relevance of sncRNA SNPs for colorectal cancer, which has not been well characterized to date.Methods: We comprehensively examined 31 common SNPs of sncRNAs, and assessed the impact of these variants on survival in a cohort of 188 patients with colorectal cancer.Results: Three SNPs were significantly associated with survival of patients with colorectal cancer after correction for multiple testing, and two of the SNPs (hsa-mir-196a-2 rs11614913 and U85 rs714775) remained significant in multivariate analyses. Additional in silico analysis provided further evidence of this association, since the expression levels of the target genes of the hsa-miR-196a (HOXA7, HOXB8, and AKT1) were significantly correlated with colorectal cancer progression. Furthermore, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that hsa-miR-196a is associated with well-known oncogenic pathways, including cellular protein modification process, mitotic cell cycle, adherens junction, and extracellular matrix receptor interaction pathways.Conclusion: Our results suggest that SNPs of sncRNAs could play a critical role in cancer progression, and that hsa-miR-196a might be a valuable biomarker or therapeutic target for colorectal cancer patients.