The accumulation of heavy metals in Typha latifolia L. grown in a stream carrying secondary effluent

Typha latifolia L. from aquatic plants is widely found throughout Kehli Stream (Elazig, Turkey). This study examined the uptake of some metals by T. latifolia and the transfer from roots to other plant parts. The accumulation of Mn in T. latifolia L. can be suggested as a tolerance strategy due to its transfer factor higher than 1.0. The enrichment coefficients in the leaves of T. latifolia L. were higher than 1.0 for Zn and Mn and often lower than 1.0 for other metals. Similarly, the enrichment coefficients of all metals, except for Cr, in roots of T. latifolia L. were higher than 1.0. This study demonstrated that T. latifolia L. could be considered as either a bio-indicator or a bio-accumulator for sediments and water polluted by metals.     

DEAR1 Is a Dominant Regulator of Acinar Morphogenesis and an Independent Predictor of Local Recurrence-Free Survival in Early-Onset Breast Cancer

Background

Breast cancer in young women tends to have a natural history of aggressive disease for which rates of recurrence are higher than in breast cancers detected later in life. Little is known about the genetic pathways that underlie early-onset breast cancer. Here we report the discovery of DEAR1 (ductal epithelium–associated RING Chromosome 1), a novel gene encoding a member of the TRIM (tripartite motif) subfamily of RING finger proteins, and provide evidence for its role as a dominant regulator of acinar morphogenesis in the mammary gland and as an independent predictor of local recurrence-free survival in early-onset breast cancer.

Methods and Findings

Suppression subtractive hybridization identified DEAR1 as a novel gene mapping to a region of high-frequency loss of heterozygosity (LOH) in a number of histologically diverse human cancers within Chromosome 1p35.1. In the breast epithelium, DEAR1 expression is limited to the ductal and glandular epithelium and is down-regulated in transition to ductal carcinoma in situ (DCIS), an early histologic stage in breast tumorigenesis. DEAR1 missense mutations and homozygous deletion (HD) were discovered in breast cancer cell lines and tumor samples. Introduction of the DEAR1 wild type and not the missense mutant alleles to complement a mutation in a breast cancer cell line, derived from a 36-year-old female with invasive breast cancer, initiated acinar morphogenesis in three-dimensional (3D) basement membrane culture and restored tissue architecture reminiscent of normal acinar structures in the mammary gland in vivo. Stable knockdown of DEAR1 in immortalized human mammary epithelial cells (HMECs) recapitulated the growth in 3D culture of breast cancer cell lines containing mutated DEAR1, in that shDEAR1 clones demonstrated disruption of tissue architecture, loss of apical basal polarity, diffuse apoptosis, and failure of lumen formation. Furthermore, immunohistochemical staining of a tissue microarray from a cohort of 123 young female breast cancer patients with a 20-year follow-up indicated that in early-onset breast cancer, DEAR1 expression serves as an independent predictor of local recurrence-free survival and correlates significantly with strong family history of breast cancer and the triple-negative phenotype (ER⁻, PR⁻, HER-2⁻) of breast cancers with poor prognosis.

Conclusions

Our data provide compelling evidence for the genetic alteration and loss of expression of DEAR1 in breast cancer, for the functional role of DEAR1 in the dominant regulation of acinar morphogenesis in 3D culture, and for the potential utility of an immunohistochemical assay for DEAR1 expression as an independent prognostic marker for stratification of early-onset disease.     

Investigation of various adsorbents for their ability to bind aflatoxin B1

The contamination of animal feed with mycotoxins represents a worldwide problem for the animal industry. The most applied method for protecting animals against aflatoxicosis is the utilization of clay minerals. In the course of a research project adsorption experiments were performed in buffer solutions in order to evaluate the ability to bind Aflatoxin B₁ (AfB₁) at various pH-values. In order to investigate the strength of binding, the chemisorption index was calculated. Isothermal analysis was used to determine the values for the maximum adsorption capacity. Adsorption experiments in simulated gastrointestinal fluid and real gastric juice were carried out. Furthermore binding capability of the materials regarding selected vitamins was examined. Special attention was paid to the formation of AfB_2a during experimental conditions. Based on the obtainedin vitro results, highly promising sorbent materials were ranked for furtherin vivo studies. Some adsorbing bentonites were also analysed mineralogically, but the results did not indicate which smectite property influences the adsorption process for AfB₁ Presented at the 28^th Mykotoxin-Workshop, Bydgoszcz, Poland, May 29–31, 2006 Financial support: Christian Doppler Society     

LFM-Pro: a tool for detecting significant local structural sites in proteins

MOTIVATION: The rapidly growing protein structure repositories have opened up new opportunities for discovery and analysis of functional and evolutionary relationships among proteins. Detecting conserved structural sites that are unique to a protein family is of great value in identification of functionally important atoms and residues. Currently available methods are computationally expensive and fail to detect biologically significant local features. RESULTS: We propose Local Feature Mining in Proteins (LFM-Pro) as a framework for automatically discovering family-specific local sites and the features associated with these sites. Our method uses the distance field to backbone atoms to detect geometrically significant structural centers of the protein. A feature vector is generated from the geometrical and biochemical environment around these centers. These features are then scored using a statistical measure, for their ability to distinguish a family of proteins from a background set of unrelated proteins, and successful features are combined into a representative set for the protein family. The utility and success of LFM-Pro are demonstrated on trypsin-like serine proteases family of proteins and on a challenging classification dataset via comparison with DALI. The results verify that our method is successful both in identifying the distinctive sites of a given family of proteins, and in classifying proteins using the extracted features. AVAILABILITY: The software and the datasets are freely available for academic research use at http://bioinfo.ceng.metu.edu.tr/Pub/LFMPro.     

Immobilization stress in rat tissues: alterations in protein oxidation, lipid peroxidation and antioxidant defense system

We determined the effects of immobilization stress on antioxidant status, protein oxidation and lipid peroxidation in brain, liver, kidney, heart and stomach of rats. Sixteen male Wistar rats (3 months old) were divided into controls (C) and immobilization stress group (IS). IS rats were immobilized for 180 min/day for 15 days. Plasma corticosterone levels were increased in IS group. Copper,zinc-superoxide dismutase activities were increased in brain, liver and kidney, but decreased in the heart and stomach after immobilization. Catalase activities were increased in brain, kidney and heart, and decreased in liver and stomach. Selenium-dependent glutathione peroxidase activities were decreased in brain and kidney, but increased in heart and stomach. Reduced glutathione levels were decreased, while protein carbonyl, conjugated dienes and thiobarbituric acid-reactive substances levels were increased in all tissues. Our results showed that the response of antioxidant defense system to stress differs for each tissue, and protein oxidation and lipid peroxidation is induced by immobilization stress in peripheral tissues.     

Synthesis and evaluation of novel N-H and N-substituted indole-2- and 3-carboxamide derivatives as antioxidants agents

We have previously reported on the synthesis of novel indole derivatives where some compounds showed significant antioxidant activity. Here, we report the synthesis of novel N-H and N-substituted indole-2- and 3-carboxamide derivatives and investigated their antioxidant role in order to identify structural characteristics responsible for activity. Although all compounds showed a strong inhibitory (95-100%) effect on superoxide anion (SOD) only compounds 4, 5 and 6 showed simliar potency for the inhibition of lipid peroxidation (81-94%) which revealed that compounds 4, 5 and 6 possessed highly potent antioxidant properties. Substitution in the 1-position of the indole ring caused the significant differences between the activity results regarding lipid peroxidation inhibition.     

Effect of Thiolated Polymers to Textural and Mucoadhesive Properties of Vaginal Gel Formulations Prepared with Polycarbophil and Chitosan

The aim of this study was to design and evaluate of mucoadhesive gel formulations for the vaginal application of clomiphene citrate (CLM) for local treatment of human papilloma virus (HPV) infections. Chitosan (CHI) and polycarbophil (PC) were covalently modified using the thioglycolic acid and L-cysteine, respectively. The formation of thiol conjugates of chitosan (CHI-TG) and polycarbophil (PC-CYS) were confirmed by FT-IR analysis and PC-CYS and CHI-TG were found to have 148.42 ± 4.16 and 41.17 ± 2.34 μmol of thiol groups per gram of polymer, respectively. One percent CLM gels were prepared by combination of various concentrations of PC and CHI with thiolated conjugates of these polymers. Hardness, compressibility, elasticity, adhesiveness and cohesiveness of the gels were measured by Texture profile analysis and the vaginal mucoadhesion was investigated by mucoadhesion test. The increasing in the amount of the thiol conjugates was found to enhance the elasticity, cohesiveness, adhesiveness and mucoadhesion of the gel formulations but not their hardness and compressibility when compared to gels prepared using their respective parent formulations. Slower release rate of CLM from gels was achieved when the polymer concentrations were increased in the gel formulations. PC and its thiol conjugate were found to prolong the release of CLM longer than 70 h unlike gel formulations prepared using CHI and its thiol conjugate which were able to release CLM up to 12 h. Stability of CLM was preserved during the 3 month stability analysis under controlled room temperature and accelerated conditions.     

Effect of Inoculation with Non-indigenous and Indigenous Rhizobacteria of Erzurum (Turkey) Origin on Growth and Yield of Spring Barley

Two experiments were performed to examine the effects of inoculation of barley cv. Tokak 157/37 with indigenous and non-indigenous bacterial strains. A greenhouse experiment was carried out with 75 strains isolated from Erzurum Plain and Pasinler Plain soils of Turkey, and the 6 non-indigenous strains. The 41 strains had significant positive effects on tiller number per plant, 8 strains on plant height, one strain on dry matter yield, and 24 strains on plant protein concentration. In the second experiment, the response of barley to 20 treatments (9 indigenous strains, 6 non-indigenous strains, 4 levels of N, and a control) was investigated in Erzurum Agricultural Experiment field in 2000 and 2001. Inoculation with certain indigenous and non-indigenous strains clearly benefited growth and increased the yield of field grown barley. On average of years, inoculation with Strain No. 19, Strain No. 39, Strain No. 73, Strain No. 82, BA-7, BA-142 and M-13 increased total biomass by 29.4–15.1%, grain yield by 26.6–17.7%, and total N-yield by 32.7–20.6%, as compared to the control. Indigenous Strain No. 19 was superior to all other treatments in terms of grain yield and N-yields. The higher efficacy of combining Strain No. 19 and Tokak 157/37 indicates the possibility of improved associations using olden and common cultivar and indigenous bacteria. In conclusion, Strain No. 19 seems to be suitable inoculant for barley cultivation in areas such as in Erzurum conditions.     

The Effects of Chronomodulated Therapy with 5-Fluorouracil (5-Fu) and Folinic Acid (Fa) on the Toxicity and Quality of Life in Patients with Advanced Gastric Cancer

This study was designed to assess the tolerability of chronomodulated infusion chemotherapy, individualized by the rhythm of peripheral blood cells. Twenty patients with metastatic gastric cancer were randomized to chronotherapy or day-time arms of 5-fluorouracil (FU) (600 mg/m², 8 h inf.d1-5) and folinic acid (FA) (20 mg/m², iv, d1-5) in the first cycle and crossed-over to the other arm in the following cycles. Ten of 18 evaluable patients were assigned to chronotherapy arm and eight to day-time in the first cycle. Although there was no significant difference between two arms on enrollment, chronotherapy arm yielded an improvement of 45% of QLQ-C30 scores (p = 0.021) and the day-time arm had 11% improvement (p = 0.575). After the crossing-over, chronotherapy arm, again, had a significant improvement in QLQ-C30 scores, compared to the day-time arm (14% vs. -18%, p = 0.001, respectively). Mucositis/diarrhea was significantly higher in the day-time arm compared to chronotherapy arm (p = 0.015). In conclusion, chronomodulated infusion of 5-FU might improve the quality of life.     

Identification and sequence analysis of chicken Toll-like receptors

Toll-like receptors (TLRs) play an important role in the recognition of microbial components. Only chicken TLR2 and -4 have been reported in the literature. The objectives of this study were to identify new chicken TLRs and to evaluate evolutionary significance of these receptors. Searching chicken genomic databases and DNA sequencing revealed five new TLRs, TLR1 (type 1 and 2), -3, -5, and -7. No chicken orthologues of mammalian TLR8, -9, or -10 were found. As in mammals, all chicken TLRs (chTLRs) share identical protein secondary structure that consists of several leucine-rich domains, a transmembrane domain, and Toll/Interleukin-1 receptor domain(s). Phylogenetic analyses indicate that the identified chTLR genes are the orthologues of TLRs in mammals. Analyses of the number of synonymous substitutions per synonymous site and nonsynonymous substitutions per nonsynonymous site indicate that the nucleotide sequences coding for the leucine-rich repeats of chicken TLR1 type 1 and type 2 were significantly under positive Darwinian selection. In contrast, the sequences of other TLRs were under purifying selection. These results support the hypothesis that one of the major evolutionary strategies of the innate immune system is to recognize a few highly conserved microbial components with several conserved TLRs. The results also indicate that the sequence changes in the ligand-binding domains of TLR1 in chickens provide adaptive advantages during evolution.Nucleotide sequence data reported are available in GenBank database under the accession numbers AY633573–AY633577