Genome-wide screen for aberrantly expressed miRNAs reveals miRNA profile signature in breast cancer

Dysregulation in the expression of miRNAs contributes to the occurrence and development of many human cancers. We herein attempted to obtain the potential association between miRNA expression profile and breast cancer by applying high-throughput sequencing technology. Small RNAs from seven paired tumor and adjacent normal tissue samples were sequenced. To determine the miRNA expression profiles in tissues and sera, another five equally pooled serum samples from 20 patients and 30 normal women were sequenced. Despite a similar number in abundantly expressed miRNAs across samples, we detected varying miRNA expression profiles. Some miRNAs showed inconsistent or opposite dysregulation trends across different tumor tissues, including some abundantly expressed miRNA gene clusters and gene families. Wilcoxon sign-rank test for paired samples analysis revealed that abnormal miRNAs showed a higher level of variation across the seven tumor samples. We also completely surveyed abnormal miRNAs expressed in tumor and serum tissues in the mixed datasets based on the relative expression levels. Most of these miRNAs were significantly down-regulated in tumor samples, but nine abnormal miRNAs (miR-18a, 19a, 20a, 30a, 103b, 126, 126*, 192, 1287) were consistently expressed in tumor tissues and serum samples. Based on experimentally validated target mRNAs, functional enrichment analysis indicated that these abnormal miRNAs and miRNA groups (miRNA gene clusters and gene families) have important roles in multiple biological processes. Dynamic miRNA expression profiles, various abnormal miRNA profiles and complexity of the miRNA regulatory network reveal that the miRNA expression profile is a potential biomarker for classifying or detecting human disease.     

Biodegradation of the neonicotinoid insecticide thiamethoxam by the nitrogen-fixing and plant-growth-promoting rhizobacterium Ensifer adhaerens strain TMX-23

Thiamethoxam (THIA), a second generation neonicotinoid insecticide in the thianicotinyl subclass, is used worldwide. Environmental studies revealed that microbial degradation is the major mode of removal of this pesticide from soil. However, microbial transformation of THIA is poorly understood. In the present study, we isolated a bacterium able to degrade THIA from rhizosphere soil. The bacterium was identified as Ensifer adhaerens by its morphology and 16S ribosomal DNA sequence analysis. High-performance liquid chromatography and mass spectrometry analysis suggested that the major metabolic pathway of THIA in E. adhaerens TMX-23 involves the transformation of its N-nitroimino group (=N–NO₂) to N-nitrosoimino (=N–NO) and urea (=O) metabolites. E. adhaerens TMX-23 is a nitrogen-fixing bacterium harboring two types of nifH genes in its genome, one of which is 98 % identical to the nifH gene in the cyanobacterium Calothrix sp. MCC-3A. E. adhaerens TMX-23 released various plant-growth-promoting substances including indole-3-acetic acid, exopolysaccharides, ammonia, HCN, and siderophores. Inoculation of E. adhaerens TMX-23 onto soybean seeds (Glycine max L.) with NaCl at 50, 100, or 154 mmol/L increased the seed germination rate by 14, 21, and 30 %, respectively. THIA at 10 mg/L had beneficial effects on E. adhaerens TMX-23, enhancing growth of the bacterium and its production of salicylic acid, an important plant phytohormone associated with plant defense responses against abiotic stress. The nitrogen-fixing and plant-growth-promoting rhizobacterium E. adhaerens TMX-23, which is able to degrade THIA, has the potential for bioaugmentation as well as to promote growth of field crops in THIA-contaminated soil.     

Different utilizable substrates have different effects on cometabolic fate of imidacloprid in Stenotrophomonas maltophilia

Imidacloprid, the largest selling insecticide in the world, is more stable in soil, and its environmental residue and effects are attracting people's close attention. One of imidacloprid metabolism pathways was degraded to CO₂ through olefin imidacloprid pathway. Here, we report that sucrose as a utilizable substrate enhanced the cometabolism of imidacloprid by Stenotrophomonas maltophilia CGMCC 1.1788 to produce 5-hydroxy imidacloprid, whereas when succinate was used as a utilizable substrate, 5-hydroxy imidacloprid from imidacloprid was transformed to olefin imidacloprid, and the latter was further degraded. The hydroxylation of imidacloprid required NAD(P)H, whereas the dehydration of 5-hydroxy imidacloprid to form olefin imidacloprid required succinate rather than NAD(P)H. NADPH greatly favored the hydroxylation of imidacloprid more than NADH, and NADPH inhibited the dehydration of 5-hydroxy imidacloprid to olefin imidacloprid, but NADH did not. Therefore, sucrose may be metabolized through hexose monophosphate pathway to produce mainly NADPH which participated in the hydroxylation of imidacloprid to 5-hydroxy imidacloprid and meanwhile inhibited the dehydration of 5-hydroxy imidacloprid to olefin imidacloprid, whereas succinate may be metabolized mainly through the tricarboxylic acid cycle to produce NADH which was involved in hydroxylation of imidacloprid to 5-hydroxy imidacloprid but did not inhibit the dehydration of 5-hydroxy imidacloprid to olefin imidacloprid. Our results have a significant meaning in further understanding the influence of different utilizable substrates on the cometabolic pathways and the fate of environmental imidacloprid.     

Arginine vasopressin does not mediate heat loss in the tail of the rat

It has been reported that hypothermia induced by arginine vasopressin (AVP) is brought about by a coordinated response of reduced thermogenesis in brown adipose tissue (BAT) and increased heat loss through the tail of rats. However, it is well known that AVP is one of the strongest peripheral vasoconstrictors. Whether the AVP-induced hypothermia is associated with an increase in heat loss through the tail is questionable. Therefore, the present study assessed the relationship between the effects of AVP on tail skin temperature and the induced hypothermic response, and to determine if peripheral AVP administration increases heat loss from the tail. Core, BAT and tail skin temperature were monitored by telemetry in male Sprague–Dawley rats before and after intraperitoneal administration of AVP or vasopressin receptor antagonist. We also analyzed simultaneously of the time-course of AVP-induced hypothermic response and its relationship with changes in BAT temperature, and effect of AVP on grooming behavior. The key observations in this study were: (1) rats dosed with AVP induced a decrease in heat production (i.e., a reduction of BAT thermogenesis) and an increase of saliva spreading for evaporative heat loss (i.e., grooming behavior); (2) AVP caused a marked decrease in tail skin temperature and this effect was prevented by the peripheral administration of the vasopressin V1a receptor antagonist, suggesting that exogenous AVP does not increase heat loss in the tail of rats; (3) the vasopressin V1a receptor antagonist could elevate core temperature without affecting tail skin temperature, suggesting that endogenous AVP is involved in suppression of thermogenesis, but not mediates heat loss in the tail of rats. Overall, the present study does not support the conclusion of previous reports that AVP increased tail heat loss in rats, because AVP-induced hypothermia in the rat is accompanied by a decrease in tail skin temperature. The data indicate that exogenous AVP-induced hypothermia attributed to the suppression of thermoregulatory heat production and the increase of saliva spreading for evaporative heat loss.     

miR‐10a restores human mesenchymal stem cell differentiation by repressing KLF4

miRNAs have recently been shown to play a significant role in human aging. However, data demonstrating the effects of aging‐related miRNAs in human mesenchymal stem cells (hMSCs) are limited. We observed that hMSC differentiation decreased with aging. We also identified that miR‐10a expression was significantly decreased with age by comparing the miRNA expression of hMSCs derived from young and aged individuals. Therefore, we hypothesized that the downregulation of miR‐10a may be associated with the decreased differentiation capability of hMSCs from aged individuals. Lentiviral constructs were used to up‐ or downregulate miR‐10a in young and old hMSCs. Upregulation of miR‐10a resulted in increased differentiation to adipogenic, osteogenic, and chondrogenic lineages and in reduced cell senescence. Conversely, downregulation of miR‐10a resulted in decreased cell differentiation and increased cell senescence. A chimeric luciferase reporter system was generated, tagged with the full‐length 3′‐UTR region of KLF4 harboring the seed‐matched sequence with or without four nucleotide mutations. These constructs were cotransfected with the miR‐10a mimic into cells. The luciferase activity was significantly repressed by the miR‐10a mimic, proving the direct binding of miR‐10a to the 3′‐UTR of KLF4. Direct suppression of KLF4 in aged hMSCs increased cell differentiation and decreased cell senescence. In conclusion, miR‐10a restores the differentiation capability of aged hMSCs through repression of KLF4. Aging‐related miRNAs may have broad applications in the restoration of cell dysfunction caused by aging. J. Cell. Physiol. 228: 2324–2336, 2013. © The Authors. Published by Wiley Periodicals, Inc.     

Novel technique for internal structure and elemental distribution analyses of granular sludge from reactors for wastewater treatment

A novel technique for internal structure and elemental distribution analyses of granular sludge is presented. Sludge samples were freeze-dried and embedded in epoxy resin to form a module, which were then ground and polished to obtain sequential cross-sections. The cross-sections were analyzed by scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDX). SEM observations showed that one granule was formed having several cores with different inorganic minerals, rather than a single core. EDX results indicate that the main elements of the granules are O, Ca, Mg, and P. In addition, the distribution areas of calcium and magnesium in the granule do not coincide.     

Differences in capacities of in vitro organ regeneration between two Arabidopsis ecotypes Wassilewskija and Columbia

In vitro organogenesis is well-controlled and thus provides an ideal system to study mechanisms of plant organ development. Although it has been well investigated for a long time that exogenous hormones play important roles in determining the types of organs regenerated in vitro, there is currently limited information available for other key factors that mediate de novo organ regeneration. Here, we reported simple and efficient one-step processes for evaluating capacities of inflorescence stem-derived in vitro organogenesis between two different ecotypes in Arabidopsis. Different types of organs, including shoots and roots were initiated from inflorescence stem explants cultured on the media containing 216 combinations of exogenous auxin and cytokinin. Further, we showed that Wassilewskija ecotype had the much higher shoot regeneration capacity than Columbia with different combinations of hormones, indicating that the ecotype is an essential factor determining de novo organogenesis. Our results also suggested that the defined expression patterns of genes involved in auxin and cytokinin biosynthesis were correlated with the variations in organogenesis capacities between the two ecotypes. Thus, in vitro organogenesis is likely regulated by ecotypes through mediating endogenous hormonal biosynthesis.     

Abscisic acid is required for somatic embryo initiation through mediating spatial auxin response in Arabidopsis

Abscisic acid (ABA) regulates many aspects of plant development, including somatic embryo (SE) initiation. However, mechanisms of ABA functions on SE initiation have remained to be investigated. In this study, we examined the endogenous ABA contents of calli in Arabidopsis during the SE inductive process. We further found that the capacity for SE initiation was strongly impaired by treatment of fluridone, a potent inhibitor of ABA biosynthesis, as well as by mutation of ABA biosynthetic gene ABA2, suggesting that ABA is required for SE initiation. Furthermore, treatment of fluridone inhibited local auxin biosynthesis and auxin polar transport in the embryonic calli, resulting in the disturbance of auxin response pattern and the decreased regeneration frequency of SEs. However, application of exogenous ABA in the medium almost recovered patterns of auxin response and SE initiation. Thus, the results suggest that ABA functions on SE initiation through mediating both auxin biosynthesis and polar transport for establishment of auxin response pattern in callus. Our study provides new information for understanding mechanisms of SE initiation.     

Genetic diversity of Bartonella quintana in macaques suggests zoonotic origin of trench fever

Bartonella quintana is a bacterium that causes a broad spectrum of diseases in humans including trench fever. Humans were previously considered to be the primary, if not the only, reservoir hosts for B. quintana. To identify the animal reservoir and extend our understanding of the ecological and evolutionary history of B. quintana, we examined blood samples from macaques and performed multilocus sequence typing (MLST) analysis. We demonstrated the prevalence of B. quintana infection was common in macaques from main primate centres in mainland China. Overall, 18.0% (59/328) of rhesus macaques and 12.7% (39/308) of cynomolgus macaques were found to be infected with B. quintana by blood culture and/or polymerase chain reaction. The infection was more frequently identified in juvenile and young monkeys compared with adult animals. In contrast with the relatively low level of sequence divergence of B. quintana reported in humans, our investigation revealed much higher genetic diversity in nonhuman primates. We identified 44 new nucleotide variable sites and 14 novel sequence types (STs) among the B. quintana isolates by MLST analysis. Some STs were found only in cynomolgus macaques, while some others were detected only in rhesus macaques, suggesting evidence of host‐cospeciation, which were further confirmed by phylogenetic analysis and Splits decomposition analysis. Our findings suggest that trench fever may primarily be a zoonotic disease with macaques as the natural hosts.