An assessment of soil bacterial community structure and physicochemistry in two microtopographic locations of a palustrine forested wetland

We studied redoximorphic features, field indicators and bacterial communities of soils in hummocks and hollows of a palustrine forested wetland in Virginia. We hypothesized that presence of hydric soils, soil physicochemistry and soil bacterial community structure would differ between hummocks and hollows. We fingerprinted soils collected from different microtopographic locations using Length Heterogeneity Polymerase Chain Reaction (LH-PCR) to study their bacterial community structures. Two hummocks had silty/sandy loam soils with mean chroma values of > 4, showing no indication of ‘hydric soils’ (i.e., wetland soils). Two hollows, however, had clay loam soils with mean chroma values of 2 with gleying and redox concentrations observed, indicative of seasonally inundated wetlands. The soils of hollows also had higher organic matter content and soil moisture compared to the soils of hummocks (P < 0.05). Multidimensional scaling (MDS) and Analysis of similarity (ANOSIM) of the fingerprints revealed differences in soil microbial community structures between hummocks and hollows (Global R = 0.30, P < 0.01). The diversity measures of the fingerprints (Shannon’s H′) were also different by microtopography with higher diversity in hollows relative to hummocks (P < 0.05). LH-PCR proves to be a useful tool in examining bacterial community composition of wetland soils in this study. However, cloning and sequencing of specific community LH-PCR profiles of interest is necessary to fully characterize the community down to genus/species level. With species identities we should be able to not only better explain differences observed in the community profiles, but study their relations to hydrologic and/or physicochemical conditions of wetlands.     

The Approach to Sample Acquisition and Its Impact on the Derived Human Fecal Microbiome and VOC Metabolome

Recent studies have illustrated the importance of the microbiota in maintaining a healthy state, as well as promoting disease states. The intestinal microbiota exerts its effects primarily through its metabolites, and metabolomics investigations have begun to evaluate the diagnostic and health implications of volatile organic compounds (VOCs) isolated from human feces, enabled by specialized sampling methods such as headspace solid-phase microextraction (hSPME). The approach to stool sample collection is an important consideration that could potentially introduce bias and affect the outcome of a fecal metagenomic and metabolomic investigation. To address this concern, a comparison of endoscopically collected (in vivo) and home collected (ex vivo) fecal samples was performed, revealing slight variability in the derived microbiomes. In contrast, the VOC metabolomes differ widely between the home collected and endoscopy collected samples. Additionally, as the VOC extraction profile is hyperbolic, with short extraction durations more vulnerable to variation than extractions continued to equilibrium, a second goal of our investigation was to ascertain if hSPME-based fecal metabolomics studies might be biased by the extraction duration employed. As anticipated, prolonged extraction (18 hours) results in the identification of considerably more metabolites than short (20 minute) extractions. A comparison of the metabolomes reveals several analytes deemed unique to a cohort with the 20 minute extraction, but found common to both cohorts when the VOC extraction was performed for 18 hours. Moreover, numerous analytes perceived to have significant fold change with a 20 minute extraction were found insignificant in fold change with the prolonged extraction, underscoring the potential for bias associated with a 20 minute hSPME.     

Bacterial Community Composition and Diversity in Methane Charged Sediments Revealed by Multitag Pyrosequencing

Bacterial diversity in sediments obtained along the Chilean margin from areas containing methane seeps, and a hydrate mound were explored by cloning and sequencing and multitag pyrosequencing (MTPS). These libraries were statistically compared to determine the robustness of taxonomic assignment derived from multiplexed pyrosequencing strategies targeting variable regions V1 and V2 of the small subunit rRNA gene for environmental studies. There was no statistical difference in the composition of the libraries, thus, MTPS was utilized to describe diversity in three geochemical zones in these environments. Unidentified Cyanobacteria isolates were abundant in the sulfate reduction zone (SRZ), Deltaproteobacteria were concentrated at the sulfate methane transition zone (SMTZ) and Chloroflexi/GNS dominated methanogenesis zone (MGZ). Although there was variation among specific groups, communities in the SRZ and MGZ did not differ significantly. However, the community dominated by Deltaproteobacteria differentiates the SMTZ from the other zones. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental file.     

A comparison of DNA damage induced by aflatoxin B1 in hepatocyte-like cells, their progenitor mesenchymal stem cells and CD34(+) cells isolated from umbilical cord blood

This study compared the sensitivity of differentiated hepatocyte-like cells, their progenitor mesenchymal stem cells (MSCs) and CD34(+) stem cells to DNA damage and toxicity induced by aflatoxin B1 (AFB1). The hepatocyte-like cells and their progenitor cells (isolated from umbilical cord blood (UCB)) were each treated with AFB1 on day 15 of differentiation. Cell toxicity and genotoxicity effects were assessed using MTT and alkaline comet assays. AFB1 treatment resulted in a dose- and time-dependent inhibition of cell growth. The IC(50) values of AFB1 for hepatocytes differentiated from CD34(+) and MSCs were within the same range (44.7-46.8μM). The IC(50) calculated for non-differentiated MSCs and CD34(+) cells was slightly lower (42.0-43.4μM) than that calculated for their differentiated counterparts. However, the extent of DNA damage was different in differentiated and non-differentiated cells. The percentages of DNA (% DNA) in comet tails measured in hepatocytes differentiated from MSCs exposed to AFB1 (0, 2.5, 10 and 20μM) for 24h were ～15, 55, 65 and 70%, respectively. In comparison, hepatocytes from CD34(+) cells were more resistant to AFB1-induced DNA damage. Hepatocyte-MSCs were most sensitive to DNA damage, followed by UCB-CD34(+) cells, then UCB-MSCs and finally hepatocyte-CD34(+) cells. These results clearly showed that stem cells from different sources have different sensitivities to DNA damaging agents. These differences can be assigned to the expression levels of cytochrome P450 (CYP) particularly CYP3A4 in non-differentiated and differentiated cells. These data are useful in better understanding the susceptibility/resistance of stem cells in the process of differentiation to environmental toxicants.     

l-Arginine is a feasible supplement to heal chronic anal fissure via reducing internal anal sphincter pressure: a randomized clinical trial study

Amino Acids - The hypertonicity of internal anal sphincter resting pressure is one of the main causes of chronic anal fissure. Therefore, the aim of this study was to assess the effect of oral...     

Higher plasma levels of F2-isoprostanes are associated with slower psychomotor speed in healthy older adults

Oxidative stress has been identified as a process which is detrimental to brain health, and associated with age-related cognitive declines. Few studies to-date have examined the relationship between in vivo oxidative stress biomarkers and cognitive performance within healthy elderly populations. The current study investigated the relationship between reaction time and oxidative stress, as measured by blood plasma concentrations of F₂-isoprostanes using a sample of 251 healthy, non-demented, elderly volunteers (Male; 111: Female 140) aged 60–75 years from the Australian Research Council Longevity Intervention (ARCLI) study cohort. A Jensen Box was used in conjunction with the Hick paradigm in order to differentiate simple from choice reaction time (two, four and eight-choice conditions) as well as movement (MT) and decision times (DT). MT, but not DT, was found to be significantly slower for participants in the high F₂-isoprostane group compared to the low F₂-isoprostane group, across all stimulus choices. F₂-isoprostanes, age and Wechsler Abbreviated Scale of Intelligence (WASI) full scale intelligence quotient (IQ) were found to be significant predictors of average MT in the sample as a whole. These findings provide preliminary evidence to suggest that higher levels of oxidative stress may be associated with impaired psychomotor speed in the healthy elderly population.     

Association of cyclin-dependent kinase inhibitor 2A/B with increased risk of developing breast cancer

There is a growing body of data reporting the association of genetic alterations in chromosome 9P21 with the risk of developing cancer. In the current study, we studied the association of a genetic variant in CDKN2A/B, rs1333049, with the risk of developing breast cancer. A total of 339 participants with and without breast cancer entered to the study. Genotyping was done by the TaqMan real-time polymerase chain reaction (RT-PCR) method and gene expression analysis was ran by RT-PCR. Our data showed that the minor allele homozygote in the total population was 10%, whereas for heterozygote was 38%. The dominant genetic model demonstrated that individuals with breast cancer had advanced TNM classification. Moreover, the logistic regression revealed that individuals who had CC/CG genotypes might have an enhanced risk of developing breast cancer when compared to the holders of GG genotype (e.g., OR = 2.8; 95% CI,1.4–5.4; p = .001), after regulated for confounders; age and body mass index. Furthermore, our analysis showed that the CDKN2A/B gene was downregulated in patients (p < .001). We showed a meaningful relationship of CDKN2A/B with the risk of breast cancer, cancer, showing the importance of studies in great sample size and several centers for studying the value of the marker as a risk classification in the management of patients with breast cancer.     

Production of human single-chain fragment antibody (ScFv) against human epidermal growth factor receptor-2 (HER-2) by phage display technology

Breast cancer with more than 1.7 million diagnoses per year has been known as one of the most prevalent cancers among women worldwide. Despite the availability of advanced treatment options, cancer progression and metastasis is observed in 20% of patients. Human epidermal growth factor receptor-2 (HER-2) is considered as an important prognostic and diagnostic tumor marker for breast cancer. While HER-2 is expressed on the surface of normal cells, its overexpression occurs in 20–25% on breast cancer tumor cells. This type of tumor which is referred to as HER-2+ is the most aggressive type of breast cancer and shows more resistance to radiotherapy. Single-chain fragment antibodies (ScFvs) offer several advantages in comparison to conventional whole antibodies due to their small size. Particularly, ScFv fragments show improved diffusion and solid tumor penetration. In this study, a human ScFv antibody library was used to isolate anti-HER-2 ScFv antibodies through cell panning and mix antigen-cell panning strategies. Analysis of the binding activity and specificity of isolated ScFv antibodies against HER-2-expressing cell lines and recombinant HER-2 antigen indicated the higher efficiency of the cell panning strategy in isolation of ScFv antibody fragments.     

A novel flexible model for lot sizing and scheduling with non-triangular,period overlapping and carryover setups in different machine configurations

This paper develops and tests an efficient mixed integer programming model for capacitated lot sizing and scheduling with non-triangular and sequence-dependent setup times and costs incorporating all necessary features of setup carryover and overlapping on different machine configurations. The model’s formulation is based on the asymmetric travelling salesman problem and allows multiple lots of a product within a period. The model conserves the setup state when no product is being processed over successive periods, allows starting a setup in a period and ending it in the next period, permits ending a setup in a period and starting production in the next period(s), and enforces a minimum lot size over multiple periods. This new comprehensive model thus relaxes all limitations of physical separation between the periods. The model is first developed for a single machine and then extended to other machine configurations, including parallel machines and flexible flow lines. Computational tests demonstrate the flexibility and comprehensiveness of the proposed models.