Performance of biological methods on self-healing and mechanical properties of concrete using S. pasteurii.

Biological methods (adding bacteria to the concrete mixtures) among the most recently investigated procedures increase the durability of concrete and repair concrete cracks. In the present study, different biological methods were used to heal the cracks of concrete and the most suitable method was subsequently introduced as the main aim of the research. For this purpose, the culture medium, various sources of calcium salts as bacterial nutrients, and the effect of air-entrained agent on the healing process were studied. The results showed that the use of bacterial nutrient inside the concrete mixes has an affirmative impact on the mechanical properties and self-healing characteristics of concretes. Simultaneous use of Sporosarcina pasteurii bacteria and calcium nitrate-urea or calcium chloride-urea as a bacterial nutrient in the concrete mixture increased the 28 days compressive strength of concretes by 23.4% and 7.5%, respectively. The utilization of bacterial cells, nutrients, and culture in the concrete mixture provided the ability to heal wide cracks where the healing time was significantly reduced (about 8 days). On the other hand, separation of the bacterial culture medium slightly reduced the self-healing performance of the concretes.

Data-Driven and Knowledge-Based Algorithms for Gene Network Reconstruction on High-Dimensional Data.

Previous efforts in gene network reconstruction have mainly focused on data-driven modeling, with little attention paid to knowledge-based approaches. Leveraging prior knowledge, however, is a promising paradigm that has been gaining momentum in network reconstruction and computational biology research communities. This paper proposes two new algorithms for reconstructing a gene network from expression profiles with and without prior knowledge in small sample and high-dimensional settings. First, using tools from the statistical estimation theory, particularly the empirical Bayesian approach, the current research estimates a covariance matrix via the shrinkage method. Second, estimated covariance matrix is employed in the penalized normal likelihood method to select the Gaussian graphical model. This formulation allows the application of prior knowledge in the covariance estimation, as well as in the Gaussian graphical model selection. Experimental results on simulated and real datasets show that, compared to state-of-the-art methods, the proposed algorithms achieve better results in terms of both PR and ROC curves. Finally, the present work applies its method on the RNA-seq data of human gastric atrophy patients, which was obtained from the EMBL-EBI database. The source codes and relevant data can be downloaded from: https://github.com/AbbaszadehO/DKGN.

TLR2 and TLR4 Signaling Pathways and Gastric Cancer: Insights from Transcriptomics and Sample Validation

Background: Pattern recognition receptors, especially toll-like receptors (TLRs), as the first line of defense for pathogen detection, were found to be associated with H.¬ pylori infection and gastric cancer (GC). However, the expression levels of TLRs, i.e. TLR2 and TLR4, as the main receptors sensed by H.¬ pylori, still remain largely ambiguous. We aimed to investigate the patterns of key transcripts of TLR2 and TLR4 in 100 GC transcriptome data. Additionally, we evaluated TLR2 and TLR4 gene expressions in gastric biopsies of Iranian GC patients, in order to validate RNA-seq outputs. Methods: For this study, 100 runs of GC samples and controls were processed and analyzed using map read to reference. Differential gene expression method was used to distinguish between GC and normal samples in the expression of TLRs and other innate immune molecules. Also, using qRT-PCR assay, transcripts of TLRs molecules for 15 GC and 15 control samples were analyzed based on the analysis of variance and least significant differences. Results: The results clearly showed that all signaling pathways molecules of TLR4, especially TLR4 (p = 0.019), NF-κB (p ¬= 0.047), IL-1ß (p = 0.0096), and TNF-α (p = 0.048), were upregulated in a cancerous condition in different parts and at various stages of GC. Conclusion: Our findings suggested that molecules involved in inflammation, including TLR4 and its related pro-inflammatory cytokines, may be responsible for the development and progression of GC. Accordingly, the control of H. pylori infection reduces inflammation in the gastric system and can play an important role in preventing gastrointestinal disorders.

Kefiran ameliorates malfunctions in primary and functional immune cells caused by lipopolysaccharides.

Kefiran is a water-soluble polysaccharide well recognized as a bioactive ingredient to enhance nutritional and health-promoting features. Also, some therapeutic properties have made this macromolecule an active ingredient in ointments and oral anti-inflammatory drugs. However, the details of the molecular and cellular aspects of these effects have not been addressed. In this study, lipopolysaccharides (LPS)-induced monocytes, lymphocytes, and monocyte-derived dendritic cells (MDDCs) as representative cells for both innate and adaptive immunity were treated with kefiran for 2 h. Kefiran had an anti-inflammatory effect on monocytes to reduce pro-inflammatory cytokines, interleukin 1 ß (IL-1ß) & tumor necrosis factor α (TNF-α), as well as nuclear factor kappa b (NF-kb). However, it did not affect lymphocytes. Overexpression of Toll-like receptor 4 (TLR4) in LPS-induced cells was not reduced after kefiran treatment. Kefiran balanced MDDCs secretion of pro/anti-inflammatory cytokines by reducing and enhancing the expression of IL-1ß and interleukin 10 (IL-10), respectively. Also, kefiran decreased the number of apoptotic immature MDDCs and promoted dose-dependent phagocytosis capacity of MDDCs. According to the results of the current study, it may be concluded that the immunomodulatory effects of kefiran are due to antagonist against innate immune receptors especially TLR4. The results of this study can be used as a guide to developing kefiran-based non-aggressive anti-inflammatory drugs. Furthermore, understanding the immunobiological effects of kefiran on monocytes and lymphocytes was another outcome of this study.

Differential expression of genes in olive leaves and buds of ON- versus OFF-crop trees.

Alternate bearing (AB) refers to the tendency of trees to have an irregular crop load from 1 year (ON) to the next year (OFF). Despite its economic importance, it is not fully understood how gene networks and their related metabolic pathways may influence the irregular bearing in olive trees. To unravel molecular mechanisms of this phenomenon in olive (cv. Conservalia), the whole transcriptome of leaves and buds from ON and OFF-trees was sequenced using Illumina next generation sequencing approach. The results indicated that expressed transcripts were involved in metabolism of carbohydrates, polyamins, phytohormones and polyphenol oxidase (POD) related to antioxidant system. Expression of POD was increased in leaf samples of ON- versus OFF-trees. The expression pattern of the greater number of genes was changed more in buds than in leaves. Up-regulation of gene homologues to the majority of enzymes that were involved in photorespiration metabolism pathway in buds of ON-trees was remarkable that may support the hypotheses of an increase in photorespiratory metabolism in these samples. The results indicated changes in expression pattern of homologous to those taking part of abscisic acid and cytokinin synthesis which are connected to photorespiration. Our data did not confirm expression of homologue (s) to those of chlorogenic acid metabolism, which has been addressed earlier that have a probable role in biennial bearing in olive. Current findings provide new candidate genes for further functional analysis, gene cloning and exploring of molecular basses of AB in olive.

In vitro immunobiological assays of methotrexate-stearic acid conjugate in human PBMCs.

In the present research, a lipophilic methotrexate (MTX) prodrug was developed by covalent conjugating of MTX to stearic acid (SA) as a lipid moiety via amid bond. The structure of synthesized conjugate, MTX-SA, was confirmed by IR and NMR spectra. To evaluate inflammatory response of MTX-SA conjugate and MTX, human PBMCs were isolated and exposed to 50, 500 and 5000 nM of MTX-SA conjugate and free MTX. The expression of four key genes involved in inflammation and apoptosis including IL-8, IL-1ß, IL-10 and Bcl2 depicted that the MTX-SA had controversial behavior in different doses on the inflammatory transcription. Also, MTX-SA statically decreased the number of immune live cells in comparison to MTX. However, MTX-SA did not capture PBMCs cell cycle in G0/G1 phase. Totally, these results showed MTX-SA with long lipid chain has different effect on immune responses and it is irrefutable that detailed studies of its immunotoxicity and immunogenicity ought to be taken into account.

Fumaric acids as a novel antagonist of TLR-4 pathway mitigates arsenic-exposed inflammation in human monocyte-derived dendritic cells.

Exposure to environmentally relevant doses of arsenic has several harmful effects on the human immune system. In traditional Eastern medicines, nettle has been used as an anti-inflammatory agent to treat rheumatism and osteoarthritis. Fumaric acid (FA) as a major effective compound in nettle was chosen based on very accurate virtual screening to find antagonist for TLR4/MD structure. In this study, the in vitro therapeutic effects of FA on arsenic-exposed monocytes-derived dendritic cells (MDDCs) were evaluated. All the canonical functions of dendritic cells in bridging innate and adaptive immune system including phagocytosis and antigen-presenting capacity, and also cytokines secretion, were evaluated after exposure to arsenic/FA. FA profoundly over-expressed antigen-presenting capacity of MDDCs after exposure to arsenic through the upregulation of MHCιι. However, phagocytosis capacity of arsenic-exposed MDDCs is not compensated for, by treatment with FA. Arsenic up-regulates pro-inflammatory cytokines independents of TLR4 pathway. FA surprisingly mitigates the up-regulation of IL-1ß and TNF-α but not TLR4 and NF-kB. Moreover, FA increases the viability of MDDCs even at a high dose of arsenic. Totally, FA reduced inflammatory factors induced by arsenic. This finding confirmed that nettle and other medicinal plants containing similar structures with FA could be further analyzed as valuable candidates for the reduction of drastic effects of arsenic in human immune systems.

Data on environmentally relevant level of aflatoxin B1-induced human dendritic cells' functional alteration.

We assessed the effects of naturally occurring levels of AFB1 on the expression of key immune molecules and function of human monocyte-derived dendritic cells (MDDCs) by cell culture, RT-qPCR, and flow cytometry. Data here revealed that an environmentally relevant level of AFB1 led to remarkably weakened key functional capacity of DCs, up-regulation of key transcripts and DCs apoptosis, down-regulation of key phagocytic element, CD64, and creation of pseudolicensing direction of DCs. Flow cytometry data confirmed a damage towards DCs, i.e., increased apoptosis. The detailed data and their mechanistic effects and the outcome are available in this research article (Mehrzad et al., 2018) [1]. The impaired phagocytosis capacity with triggered pseudolicensing direction of MDDCs caused by AFB1 and dysregulation of the key functional genes could provide a mechanistic explanation for the observed in vivo immunotoxicity associated with this mycotoxin.

Immunobiologically relevant level of aflatoxin B1 alters transcription of key functional immune genes, phagocytosis and survival of human dendritic cells.

The effects of naturally occurring levels of aflatoxin (AF) B1 on the expression of key molecules and function of dendritic cells (DCs) were investigated on human monocyte-derived DCs (MDDCs) by cell culture, RT-qPCR, and flow cytometry. An environmentally relevant level of AFB1 remarkably impaired the phagocytic capacity of MDDCs. Furthermore, AFB1 significantly affected the transcript levels of some key functional genes in MDDCs. It caused an up-regulation of key transcripts in cytochrome P450 (CYP) family, MyD88, NF-KB, TNF-α, TLR2, TLR4, COX-2, HLA-DR, CCR7, CD209, LFA3 and CD16. AFB1 down-regulated the expression of AhR, TGF-ß, CD11c and CD64 within 2-12 h post-exposure. In contrast, the transcription of some other key genes, including IL-10, IL-1ß, AKR7A2, GSTM1, IL-6. IL-8 and C5aR in post-AFB1 treated MDDCs was only slightly changed. The results indicate that an environmentally relevant level of AFB1 impairs the phagocytosis capacity of MDDCs and dysregulates the key functions in these pivotal immune cells. This could provide a mechanistic explanation for the observed in vivo immunotoxicity associated with this mycotoxin, and further emphasize the essential need for reduction of AFB1 levels in agricultural commodities.

Environmentally relevant dose of arsenic interferes in functions of human monocytes derived dendritic cells.

Arsenic is a major environmental pollutant and highly hazardous toxin to human health, which well established as carcinogen and immune deregulatory properties. Dendritic cells (DCs) have a pivotal role in cell-mediated immunity for T-cell activation and antigen presentation. In this study, T cell activation, some key functional genes expression, cell stability and phagocytosis capacity of human monocytes derived DCs (MDDCs) were analyzed after in vitro exposure to very low dose of arsenic for 12 and 24h. Arsenic decreased continually phagocytosis capacity of MDDCs. Furthermore, down-regulation of the cell-surface expression of the co-stimulatory molecule CD40 after 24h post treatment with arsenic, confirmed arsenic interferers in the phagocytosis process. Pro inflammatory cytokines, IL1ß and TNFα were more expressed in arsenic-treated MDDCs while IL6 transiently was down regulated. In general, our novel findings here strongly suggest that low level of arsenic dysregulates four fundamental immune processes of DCs. Mechanistically; this could explain the observed immunodeficiency activity of Arsenic, and give direction for comprehension the pathogenesis of Arsenic-induced diseases.

Functional and Key Gene Expression Analyses of Chicken Monocyte-derived Dendritic Cells with Recombinant Interleukin 4.

The central role of dendritic cells (DCs) as bridging innate and adaptive immunity leads to the expanding use of these cells in the poultry vaccine studies. The most effective way to produce enough DCs is monocyte transformation by combined induction of interleukin-4 (IL-4) and granulocyte-macrophage colony-stimulating factor (GM-CSF). In this study full length of chicken IL-4 (cIL-4) cDNA was cloned, characterized and expressed in Escherichia coli. Subsequently, the expressed IL-4 was used to induce monocytes- derived DCs (MDDC). Typical features of DCs such as long membrane protrusions, apparently was dominant only four days after cytokine induction. Analyses of selected key genes' expression also confirmed that most of the monocytes shifted to DCs. The findings of the present study strongly suggest that the cloning and expression of cIL-4 in the bacterial host without any codon optimization or other modifications could produce mature MDDC in six to seven days.

GST-M1 is transcribed moreso than AKR7A2 in AFB1-exposed human monocytes and lymphocytes.

Glutathione-S-transferases (GST) and aldo-keto reductases (AKR) are key aflatoxin (AF)-detoxifying enzymes. In this study, the expression of GST-M1, GST-T1, AKR-7A2, and AKR-7A3 genes in human monocytes and lymphocytes was analyzed after in vitro exposure to 10 or 100 ng AFB1/ml for 2 h. Unlike in pilot studies that showed that all four examined genes were present in HepG2 cells, in lymphocytes and monocytes, only GST-M1 and AKR-7A2 were detected. In fact, the induced expression of both GST-M1 and AKR-7A2 genes in human monocytes was moreso than that seen in AFB1-exposed lymphocytes. In addition, analyses of the effects of the exposures on cell cycle status were performed as, in cells lacking adequate detoxification capacities, it would be expected the cells would arrest at checkpoints in the cell cycle or progress to apoptotic/necrotic states. The results here indicated that only the high dose of AFB1 led to a change in cell cycle profiles and only in the monocytes (i.e. cells in S phase were significantly reduced). In general, the results here strongly suggest that human immune cell lineages appear to be able to increase their expression of AFB1-detoxifying enzymes (albeit to differing degrees) and, as a result, are able to counter potential toxicities from AFB1 and (likely) its metabolites.

Cytochrome P450 isoforms are differently up-regulated in aflatoxin B1-exposed human lymphocytes and monocytes.

CONTEXT: Aflatoxins (AFs) are highly hazardous mycotoxins with potent carcinogenic, mutagenic and immune disregulatory properties. Cytochrome P450 (CYP) isoforms are central for enhanced AFB1 toxicity in situ. It remains to be seen whether and how these AFB1 activators work in human leukocytes. OBJECTIVE: To investigate the involvement of CYP isoforms in AFB1 toxicity of circulating mononuclear cells, we examined the impact of environmentally relevant levels of AFB1 on lymphocytes and monocytes. MATERIALS AND METHODS: Very low and moderate doses of AFB1 with/without CYP inducers on transcription of key CYP isoforms and toll-like receptor 4 (TLR4) were examined in human lymphocytes, monocytes and HepG2 cells; cell cycle distribution and viability were also analyzed in AFB1-exposed lymphocytes and monocytes. RESULTS: Only CYP1A1, CYP1B1, CYP3A4, CYP3A5 and CYP3A7 expressed in lymphocytes and monocytes. TLR4 much more expressed in monocytes than in lymphocytes, but HepG2 showed little TLR4 transcription. While CYP1A1, CYP1B1 and CYP3A4 were highly induced by AFB1 in monocytes, in lymphocytes only CYP1A1 was induced. Among CYP1A1, CYP1B1 and CYP3A4 only CYP1A1 responded to low and moderate levels of AFB1. Enhanced transcripts of CYPs by AFB1 yielded little synergies on TLR4 transcription in lymphocytes and monocytes. Cell cycle arrest and necrosis were also detected in AFB1-exposed lymphocytes and monocytes. CONCLUSIONS: Our novel findings indicate that AFB1 more intensively stimulates CYP genes expression in monocytes than in lymphocytes. Mechanistically, this could explain a more pronounced immunotoxicity of AFB1 in myeloid than in lymphoid lineage cells in vitro/situ/vivo.

Outcome following decompressive craniectomy in children with severe traumatic brain injury: a 10-year single-center experience with long-term follow up.

OBJECT: The authors examine the indications for and outcomes following decompressive craniectomy in a single-center pediatric patient population with traumatic brain injury (TBI). METHODS: A retrospective review of data was performed using a prospectively acquired database of patients who underwent decompressive craniectomy at the authors' institution between January 1995 and April 2006. The patients' neuroimages were examined to evaluate the extent of intracranial injury, and the patients' records were reviewed to determine the admission Glasgow Coma Scale (GCS) score, the extent of systemic injuries, the time to craniectomy, and the indications for craniectomy. Long-term functional outcome and independence levels were evaluated using the Glasgow Outcome Scale (GOS) and a Likert patient quality-of-life rating scale. Twenty-three craniectomies were performed in children during the study period. The mean patient age at craniectomy was 11.9 years (range 2-19 years). In all patients, the computed tomography scans obtained at presentation revealed pathological findings, with diffuse axonal injury and traumatic contusions being the most common abnormalities. The median presenting GCS score was 4.6 (range 3-9). Nineteen patients (83%) suffered from other systemic injuries. One patient (4%) died intraoperatively and six patients (26%) died postoperatively. Postoperative intracranial pressure (ICP) control was obtained in 19 patients (83%); an ICP greater than 20 mm Hg was found to have the strongest correlation with subsequent brain death (p = 0.001). The mean follow-up duration was 63 months (range 11-126 months, median 49 months). The mean GOS score at the 2-year follow-up examination was 4.2 (median 5). At the most recent follow-up examination, 13 (81%) of 16 survivors had returned to school and only three survivors (18%) were dependent on caregivers. CONCLUSIONS: Although the mortality rate for children with severe TBI remains high, decompressive craniectomy is effective in reducing ICP and is associated with good outcomes in surviving patients.