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Current in vitro studies do not typically assess cellular impacts in relation to real-world atmospheric mixtures of gases. In this study, we set out to examine the feasibility of measuring biological responses at the level of gene expression in human lung cells upon direct exposures to air in the field. This study describes the successful deployment of lung cells in the heavily industrialized Houston Ship Channel. By examining messenger RNA (mRNA) levels from exposed lung cells, we identified changes in genes that play a role as inflammatory responders in the cell. The results show anticipated responses from negative and positive controls, confirming the integrity of the experimental protocol and the successful deployment of the in vitro instrument. Furthermore, exposures to ambient conditions displayed robust changes in gene expression. These results demonstrate a methodology that can produce gas-phase toxicity data in the field.

Abstract: Background: Healing of tooth extraction sockets in poorly controlled diabetic patients is often delayed and accompanied by severe infection. The exact cellular and molecular mechanisms underlying the pathogenesis of this complication are still not fully understood. Objectives: The purpose of this study was to investigate molecular changes associated with delayed oral wound healing in diabetes. Materials and methods: Six to eight weeks old male type 2 diabetes and age matched control inbred mice were used and maxillary molar tooth extractions were performed. At 4 and 7 days after tooth extraction, the edentulous mucosa of the mice were harvested, and analyzed for histology and gene expression of key wound healing factors. Results: In the diabetic model, histological analysis showed that epithelial tissue migration for wound closure was delayed after tooth extraction compared to the control. Quantitative real-time PCR revealed that expression of the TGF-β1, TGF-β2, TGF-β3, TGFβRII and TGFβRIII genes was significantly downregulated in the diabetic model at 4 and 7 days after tooth extraction. Conclusion: These results suggest that delayed wound healing of oral mucosa in diabetes may be associated with decreased expression levels of these regulatory genes which play important roles in controlling epithelial wound closure. [Copyright &y& Elsevier]

To investigate Fe deficiency tolerance in tomato cultivars, quantification of proteins and genes involved in Fe metabolism and antioxidant mechanisms were performed in "Roggusanmaru" and "Super Doterang". Fe deficiency (Moderate, low and -Fe) significantly decreased the biomass, total, and apoplastic Fe concentration of "Roggusanmaru", while a slight variation was observed in "Super Doterang" cultivar. The quantity of important photosynthetic pigments such as total chlorophyll and carotenoid contents significantly decreased in "Roggusanmaru" than "Super Doterang" cultivar. The total protein profile in leaves and roots determines that "Super Doterang" exhibited an optimal tolerance to Fe deficiency compared to "Roggusanmaru" cultivar. A reduction in expression of PSI (photosystem I), PSII (photosystem II) super-complexes and related thylakoid protein contents were detected in "Roggusanmaru" than "Super Doterang" cultivar. Moreover, the relative gene expression of SlPSI and SlPSII were well maintained in "Super Doterang" than "Roggusanmaru" cultivar. The relative expression of genes involved in Fe-transport (SlIRT1 and SlIRT2) and Fe(III) chelates reductase oxidase (SlFRO1) were relatively reduced in "Roggusanmaru", while increased in "Super Doterang" cultivar under Fe deficient conditions. The H⁺-ATPase relative gene expression (SlAHA1) in roots were maintained in "Super Doterang" compared to "Roggusanmaru". Furthermore, the gene expressions involved in antioxidant defense mechanisms (SlSOD, SlAPX and SlCAT) in leaves and roots showed that these genes were highly increased in "Super Doterang", whereas decreased in "Roggusanmaru" cultivar under Fe deficiency. The present study suggested that "Super Doterang" is better tomato cultivar than "Roggusanmaru" for calcareous soils.

This article studied the effects of platelet-rich plasma (PRP) on the potential of synovial fluid mesenchymal stem cells (SF-MSCs) to differentiate. The PRP and SF-MSCs were obtained from the blood and knees of pigs, respectively. The identification of SF-MSCs and their ability to differentiate were studied by histological and surface epitopes, respectively. The SF-MSCs can undergo trilineage mesenchymal differentiation under osteogenic, chondrogenic, and adipocyte induction. The effects of various PRP concentrations (0%, 20% and 50% PRP) on differentiation were evaluated using the SF-MSCs-alginate system, such as gene expression and DNA proliferation. A 50% PRP concentration yielded better differentiation than the 20% PRP concentration. PRP favored the chondrogenesis of SF-MSCs over their osteogenesis in a manner that depended on the ratios of type II collagen/type I collagen and aggrecan/osteopontin. Eventually, PRP promoted the proliferation of SF-MSCs and induced chondrogenic differentiation of SF-MSCs in vitro. Both PRP and SF-MSCs could be feasibly used in regenerative medicine and orthopedic surgeries.

White shrimp Litopenaeus vannamei immersed in seawater (35‰) containing Gracilaria tenuistipitata extract (GTE) at 0 (control), 400, and 600 mg/L for 3 h were exposed to 5 mg/L ammonia-N (ammonia as nitrogen), and immune parameters including hyaline cells (HCs), granular cells (GCs, including semi-granular cells), total hemocyte count (THC), phenoloxidase (PO) activity, respiratory bursts (RBs), superoxide dismutase (SOD) activity, lysozyme activity, and hemolymph protein level were examined 24~120 h post-stress. The immune parameters of shrimp immersed in 600 mg/L GTE returned to original values earlier, at 96~120 h post-stress, whereas in control shrimp they did not. In another experiment, shrimp were immersed in seawater containing GTE at 0 and 600 mg/L for 3 h and examined for transcript levels of immune-related genes at 24 h post-stress. Transcript levels of lipopolysaccharide and β-1,3-glucan binding protein (LGBP), peroxinectin (PX), cytMnSOD, mtMnSOD, and HSP70 were up-regulated at 24 h post-stress in GTE receiving shrimp. We concluded that white shrimp immersed in seawater containing GTE exhibited a capability for maintaining homeostasis by regulating cellular and humoral immunity against ammonia stress as evidenced by up-regulated gene expression and earlier recovery of immune parameters.

The mechanism of action of the potentized homeopathic drugs, particularly those diluted beyond Avogadro's limit, is still a debatable issue and various hypotheses in this regard have been advocated by many. In our studies since 1980, we found that certain ultra-highly diluted homeopathic remedies could produce ameliorative effects in various model test organisms like bacteria, fungus, mice and human beings, while the succussed alcohol (placebo) could not. These drugs could antagonize/ameliorate several types of experimentally induced tumors/cancers in mice as evident from electron microscopic studies and certain specific cancer biomarkers. They also demonstrated significant effect on cell viability and apoptotic effect (mostly mitochondria mediated) on cancer cells in culture (also in experimental mice), as revealed from various assays like AnnexinV-FITC, TUNEL, DNA fragmentation, DAPI, COMET, HOECHST 33258, Rhodamine 123 etc while the succussed alcohol ("vehicle") failed to show such effect. Expression of some key signal proteins and mRNA expressions like Bcl2 family proteins, Cytochrome c, Apaf 1, PARP, Caspase family, p53 and p38 etc in experimental mice model could be modulated by potentized homeopathic drugs. Under arsenic stress, the bacterium Escherichia coli, and the fungus Saccharomyces cerevisiae, and macrophage cells in culture responded favorably to the treatment of potentized homeopathic drug, Arsenicum Album 30C and homeopathically prepared Glucose 30C, as evident from modulation of several parameters like ROS accumulation, SOD activity, lipid peroxidation and expression level of certain relevant genes (Ars B, pts-G genes using real-time PCR) denoting detoxification, mainly via arsenic removal mechanism and suitable enzymatic modulation. Ultra-highly diluted potentized drugs (at potency 30C or above) could demonstrate protective changes simultaneously in multiple parameters (most of them under genetic control) of study, and their action continued for sometime even after the drugs were withdrawn; this indicates the ability of the drugs to trigger "gene action" involving up-regulation or down-regulation of a cascade of downstream genes, getting the recovery process into motion. The convincing evidences that support a "gene regulatory hypothesis" to explain the molecular mechanisms of action of the potentized drugs will be discussed in the light of some of our recent experimental findings on fungus, bacteria and bacteriophages. [ABSTRACT FROM AUTHOR]

Clustering has a long and rich history in a variety of scientific fields. Finding natural groupings of a data set is a hard task as attested by hundreds of clustering algorithms in the literature. Each clustering technique makes some assumptions about the underlying data set. If the assumptions hold, good clusterings can be expected. It is hard, in some cases impossible, to satisfy all the assumptions. Therefore, it is beneficial to apply different clustering methods on the same data set, or the same method with varying input parameters or both. We propose a novel method, DICLENS, which combines a set of clusterings into a final clustering having better overall quality. Our method produces the final clustering automatically and does not take any input parameters, a feature missing in many existing algorithms. Extensive experimental studies on real, artificial, and gene expression data sets demonstrate that DICLENS produces very good quality clusterings in a short amount of time. DICLENS implementation runs on standard personal computers by being scalable, and by consuming very little memory and CPU. [ABSTRACT FROM PUBLISHER]

DNase I hypersensitive sites (DHSs) mark diverse classes of cis-regulatory regions, such as promoters and enhancers. MSB-1 derived from chicken Marek's disease (MD) lymphomas is an MDV-transformed CD4+ T-cell line for MD study. Previously, DNase I HS sites were studied mainly in human cell types for mammalian. To capture the regulatory elements specific to MSB1 cells and explore the molecular mechanisms of T-cell transformation caused by MDV in MD, we generated high-quality of DHSs map and gene expression profile for functional analysis in MSB1 cell line. The total of 21,724 significant peaks of DHSs was identified from around 40 million short reads. DHSs distribution varied between chromosomes and they preferred to enrich in the gene-rich chromosomes. More interesting, DHSs enrichments appeared to be scarce on regions abundant in CpG islands. Besides, we integrated DHSs into the gene expression data and found that DHSs tended to enrich on high expressed genes throughout whole gene regions while DHSs did not show significant changes for low and silent expressed genes. Furthermore, the correlation of DHSs with lincRNAs expression was also calculated and it implied that enhancer-associated lincRNAs probably originated from enhancer-like regions of DHSs. Together, our results indicated that DNase I HS sites highly correlate with active genes expression in MSB1 cells, suggesting DHSs can be considered as markers to identify the cis-regulatory elements associated with chicken Marek's disease.

In the neural circuit functional identities of individual neurons are mainly specified by their differential gene expression patterns. Unveiling functional roles of each neuron requires cell-specific interrogation of neural circuitry in the context of gene expressions. The mRNA tagging strategy in Caenorhabditis elegans is a powerful technique, in which cell-specific transcripts can be isolated by co-immunoprecipitating the complexes of mRNAs and epitope-tagged poly(A) binding protein (3× FLAG-PAB-1), expressed in target neurons. However, the conventional protocol requires laborious and time-consuming procedures; chromosomal integration of gene encoding 3× FLAG-PAB-1 and bleaching of obtained integrant animals for the isolation of huge amounts of synchronized animals. In this paper, we have presented a simplified methodology for cell-specific mRNA tagging analysis in C. elegans. We show that mRNA tagging was achieved using transgenic animals expressing 3× FLAG-PAB-1 as an extrachromosomal array under the control of the flp-18 promoter, without the chromosomal integration procedure. Furthermore, we successfully isolated cell-specific mRNAs from adult transgenic animals synchronously grown from eggs laid by gravid adults during a time window of 3h. This simplification facilitates the implementation of cell-specific gene expression analysis of C. elegans, which contributes to the understanding of neural circuitry at a cell-specific resolution., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Objective: The onset of puberty in females has been occurring earlier over the past decades, presumably as a result of improved nutrition in developed countries. However, the underlying molecular mechanisms responsible for the early attainment of puberty as a result of nutrition fortification remain largely unknown. The aim of this study was to evaluate the hormone and gene expression changes in prepubescent gilts fed a high-fat diet to investigate whether these changes could predict the early timing of puberty., Methods: Forty gilts were fed a daily basal diet (LE) or a basal diet with an additional 270 g/d or 340 g/d of fat (HE) during the prepubescent phase. Blood samples were collected during the prepubescent phase to detect hormone secretion changes in insulin-like growth factor-1, kisspeptin, estradiol, progesterone, and leptin. The gene expressions at the hypothalamus-pituitary-gonadal axis were examined on day 73 of the experiment (average age on day 177) during the prepubescent phase., Results: An HE diet resulted in accelerated body weight gain and back-fat thickness at the P2 point compared with LE gilts during the prepubescent phase. Gilts that were fed HE diets attained puberty 12 d earlier than LE gilts, and a larger proportion of HE gilts reached puberty at day 180 or 190 of age. A postmortem analysis revealed a promoted development of the uterus and ovary tissue that was characterized by a 53.7% and 29.5% increase in the uterine and ovary weight, respectively, and an increased length of the uterine horn and oviduct tissue in HE gilts. Real-time quantitative polymerase chain reaction revealed that HE gilts had higher Kiss-1, G protein-coupled receptor 54, gonadotropin-releasing hormone and estrogen receptor α mRNA expression levels in the hypothalamic anteroventral periventricular nucleus; the leptin receptor mRNA expression level was higher in the hypothalamic arcuate nucleus and ovary tissue; the insulin-like growth factor-1 receptor expression was higher in the pituitary and ovary tissues, and the follicle-stimulating hormone and luteinizing hormone mRNA expression levels were higher in the pituitary gland., Conclusion: These data showed that the consumption of additional fat can facilitate early attainment of puberty, which can be predicted by the changes in secreted hormones and gene expression in the hypothalamus-pituitary-gonadal axis., (Copyright © 2014 Elsevier Inc. All rights reserved.)

In order to degrade aflatoxin B₁ (AFB₁), AFB₁-degrading microbes (probiotics) such as Lactobacillus casei, Bacillus subtilis and Pichia anomala, and the AFB₁-degrading enzyme from Aspergillus oryzae were selected and combined to make feed additive. Seventy-five 43-day-old male Arbor Acres broilers were randomly divided into 5 groups, 15 broilers for each group. The broilers were given with 5 kinds of diets such as the basal diet, 400 μg/kg AFB₁ supplement without feed additive, and 200, 400, 800 μg/kg AFB₁ supplement with 0.15% feed additive. The feeding experimental period was 30 d, which was used to determine production performance of broilers. In addition, serum, liver and chest muscle were selected for measuring AFB₁ residues, gene expressions, microscopic and antioxidant analyses. The results showed that adding 0.15% feed additive in broiler diets could significantly relieve the negative effect of AFB₁ on chicken's production performance and nutrient metabolic rates (P<0.05). It could also improve AFB₁ metabolism, hepatic cell structure, antioxidant activity, and many hepatic enzyme gene expressions involved in oxidoreductase, apoptosis, cell growth, immune system and metabolic process (P<0.05). It could be concluded that the feed additive was able to degrade AFB₁ and improve animal production., (Copyright © 2013 Elsevier Ltd. All rights reserved.)