A Genetic System for Clostridium ljungdahlii: a Chassis for Autotrophic Production of Biocommodities and a Model Homoacetogen

Methods for genetic manipulation of Clostridium ljungdahlii are of interest because of the potential for production of fuels and other biocommodities from carbon dioxide via microbial electrosynthesis or more traditional modes of autotrophy with hydrogen or carbon monoxide as the electron donor. Furthermore, acetogenesis plays an important role in the global carbon cycle. Gene deletion strategies required for physiological studies of C. ljungdahlii have not previously been demonstrated. An electroporation procedure for introducing plasmids was optimized, and four different replicative origins for plasmid propagation in C. ljungdahlii were identified. Chromosomal gene deletion via double-crossover homologous recombination with a suicide vector was demonstrated initially with deletion of the gene for FliA, a putative sigma factor involved in flagellar biogenesis and motility in C. ljungdahlii. Deletion of fliA yielded a strain that lacked flagella and was not motile. To evaluate the potential utility of gene deletions for functional genomic studies and to redirect carbon and electron flow, the genes for the putative bifunctional aldehyde/alcohol dehydrogenases, adhE1 and adhE2, were deleted individually or together. Deletion of adhE1, but not adhE2, diminished ethanol production with a corresponding carbon recovery in acetate. The double deletion mutant had a phenotype similar to that of the adhE1-deficient strain. Expression of adhE1 in trans partially restored the capacity for ethanol production. These results demonstrate the feasibility of genetic investigations of acetogen physiology and the potential for genetic manipulation of C. ljungdahlii to optimize autotrophic biocommodity production.     

The effects of vitamin C supplementation on oxidative stress and antioxidant content in the brains of chronically exercised rats

The purpose of this study was to ascertain whether vitamin C supplementation during chronic exercise training alters rat brain antioxidant content. Female Wistar albino rats were exercised on a treadmill for 30 min/day for 6.5 weeks and were administered daily intraperitoneal injections of vitamin C (20 mg/kg). After the training period, chronically exercised rats showed no significant changes in total brain thiobarbituric acid reactive substances (TBARS) levels. In contrast, rats supplemented with vitamin C during the training period showed significantly elevated brain TBARS levels. If such results were extrapolated to man, where vitamin supplementation is a common practice, this would indicate that vitamin C supplementation may not protect brain tissue against exercise-induced oxidative damage, in such circumstances, this water-soluble antioxidant behaves as a pro-oxidant. (Mol Cell Biochem xxx: 135–138, 2005)     

Effect of nitrogen limitation on enrichment of activated sludge for PHA production

Polyhydroxyalkanoates (PHA) are good candidates to plastics because of their material properties similar to conventional plastics and complete biodegradability. The use of activated sludge can be a cheaper alternative to pure cultures for PHA production. In this study, effect of nitrogen limitation during acclimatization period of biomass on production of polyhydroxyalkanoate was investigated. Activated sludge was selected in two sequencing batch reactors operated with and without nitrogen limitation. Batch tests were performed to examine polymer productions of activated sludges acclimatized to different nitrogen regimes. Responses of biomass to different organic loading rates, organic acids, and carbon to nitrogen (C/N) ratios were studied by determining specific polymer storage rate, polymer storage yield, and sludge polymer content of biomasses. Results obtained from batch experiments showed that concentrations of polymer accumulated by two different sludges increased directly with initial substrate concentration. Observed highest polymer yields for the biomasses enriched with and without nitrogen deficiency were 0.69 g COD PHA g(-1) COD S and 0.51 g COD PHA g(-1) COD S, and corresponding polymer contents of biomasses were 43.3% (g COD PHA g(-1) COD X) and 38.3% (g COD PHA g(-1) COD X), respectively. Polymer yields for both biomasses decreased with substrate shift however, biomass enriched with nitrogen deficiency adapted well to acetate-propionate mixture. The results presented in this study showed that polymer storage ability of biomass was improved more under dynamic conditions with nitrogen deficiency when compared to that without nitrogen deficiency. Limiting ammonia availability during batch experiments also caused higher polymer production by suppressing growth, as well as during enrichment of biomass.     

Forward genetic analysis of visual behavior in zebrafish

The visual system converts the distribution and wavelengths of photons entering the eye into patterns of neuronal activity, which then drive motor and endocrine behavioral responses. The gene products important for visual processing by a living and behaving vertebrate animal have not been identified in an unbiased fashion. Likewise, the genes that affect development of the nervous system to shape visual function later in life are largely unknown. Here we have set out to close this gap in our understanding by using a forward genetic approach in zebrafish. Moving stimuli evoke two innate reflexes in zebrafish larvae, the optomotor and the optokinetic response, providing two rapid and quantitative tests to assess visual function in wild-type (WT) and mutant animals. These behavioral assays were used in a high-throughput screen, encompassing over half a million fish. In almost 2,000 F2 families mutagenized with ethylnitrosourea, we discovered 53 recessive mutations in 41 genes. These new mutations have generated a broad spectrum of phenotypes, which vary in specificity and severity, but can be placed into only a handful of classes. Developmental phenotypes include complete absence or abnormal morphogenesis of photoreceptors, and deficits in ganglion cell differentiation or axon targeting. Other mutations evidently leave neuronal circuits intact, but disrupt phototransduction, light adaptation, or behavior-specific responses. Almost all of the mutants are morphologically indistinguishable from WT, and many survive to adulthood. Genetic linkage mapping and initial molecular analyses show that our approach was effective in identifying genes with functions specific to the visual system. This collection of zebrafish behavioral mutants provides a novel resource for the study of normal vision and its genetic disorders.     

Investigation of ash deposition in a pilot-scale fluidized bed combustor co-firing biomass with lignite

This study presents the results from investigation of ash deposition characteristics of a high ash and sulfur content lignite co-fired with three types of biomass (olive residue, 49 wt%; hazelnut shell, 42 wt%; and cotton residue, 41 wt%) in 0.3 MW(t) Middle East Technical University (METU) Atmospheric Bubbling Fluidized Bed Combustion (ABFBC) Test Rig. Deposit samples were collected on an air-cooled probe at a temperature of 500 degrees C. Samples were analyzed by SEM/EDX and XRD methods. The results reveal that co-firing lignite with olive residue, hazelnut shell and cotton residue show low deposition rates. High concentrations of silicon, calcium, sulfur, iron, and aluminum were found in deposit samples. No chlorine was detected in deposits. Calcium sulfate and potassium sulfate were detected as major and minor components of the deposits, respectively. High sulfur and alumina-silicate content of lignite resulted in formation of alkali sulfates instead of alkali chlorides. Therefore, fuel blends under consideration can be denoted to have low-fouling propensity.     

POLLINATION BIOLOGY,SEED PRODUCTION,AND POPULATION STRUCTURE IN QUEEN-OF-THE-PRAIRIE,FILIPENDULA RUBRA (ROSACEAE) AT BOTKIN FEN,MISSOURI

Queen-of-the-prairie, Filipendula rubra (Rosaceae), is a perennial, rhizomatous herb restricted to calcareous fens, spring seeps, and wet prairies, and is distributed in the northcentral United States from Iowa to New York. Because of the scarcity of adequate habitat, F. rubra is a rare and endangered species in several states. At Botkin Fen and other fens in Missouri, F. rubra possesses limited sexual reproduction. A study was conducted to determine causal mechanisms of its limited seed production that may be barriers to establishing this rare and endangered species in other fens in Missouri. A genetic-ecological hypothesis was supported. F. rubra was found to be self-incompatible. At Botkin Fen, most inflorescences produced very few seeds because most (85.4%) belonged to a single clone. Pollinators (Lassioglossum sp.) had a high probability of transporting pollen with the same self-incompatibility alleles. A few genetically different clones did produce significant quantities of seed. However, this seed, with its significant pool of genetic variability, was not recruited into the population. Apparently, competition from the dense sedges and grasses prevented the establishment of new seedlings.     

Applications of DNA genetic markers to the study of plant growth and development

DNA genetic markers, such as restriction fragment length polymorphisms (RFLPs) and random amplified polymorphic DNA markers (RAPDs), are powerful tools for studying the genetics of plant growth and development. DNA markers are defined sequences of DNA that can be used in traditional linkage mapping. Using DNA marker technology, scientists can uncover relationships between cloned cDNA sequences and classically characterized genes. DNA markers make it possible to dissect the contributions of multiple genetic loci underlying complex developmental processes. Moreover, changes in genome organization that occur during development or in response to environmental signals can be monitored using RFLP technology. In the future, it may be possible to clone any gene based solely on its map position. This will involve the use of tightly linked DNA markers as entry points for chromosome walking, in which a series of overlapping genomic clones reaching from the tightly linked DNA marker to the gene of interest are identified.     

A single mutation in the NAD-specific formate dehydrogenase from Candida methylica allows the enzyme to use NADP

An homology model of Candida methylica formate dehydrogenase (cmFDH) was constructed based on the Pseudomonas sp. 101 formate dehydrogenase (psFDH) structure. An aspartic acid residue in the model was predicted to interact with the adenine ribose of the NAD cofactor, in common with many NAD-dependent oxoreductases. Replacement of this aspartic acid residue by serine in cmFDH removed the absolute requirement for NAD over NADP shown by the wild type enzyme. Taken with similar results shown by d- and l-lactate dehydrogenases, this suggests that an aspartic acid in this position is a major determinant of coenzyme specificity in NAD/NADP-dependent dehydrogenases.     

Tumor necrosis factor alpha and beta and interferon gamma gene polymorphisms in Turkish breast cancer patients

Cytokine genes are important for researching cancer predisposition to cancers that elicit anti-tumor immune response. In this study, we investigated the association between breast cancer and tumor necrosis factor alpha (TNF-α) -308 (G>A), TNF-β +252 (A>G), and interferon gamma (IFN-γ) +874 (T>A) gene polymorphisms in a Turkish population. This study involved 204 female breast cancer patients and 204 healthy female controls. Genomic DNA was extracted from EDTA-preserved peripheral venous blood of patients and controls by a salting-out method and analyzed by polymerase chain reaction, allele-specific oligonucleotide polymerase chain reaction, and restriction fragment length polymorphism. TNF-α -308 genotype was found to have no effect on breast cancer susceptibility. However, there were statistically significant differences between the genotype frequencies of patients and controls for TNF-β polymorphism (p?=?0.016) and the allele and genotype frequencies for the IFN-γ polymorphism (p?=?0.0312 and p?=?0.001, respectively). In the composite genotype analysis, the TNF-α/β GAAG composite genotype (p?=?0.0424), the TNF-α/IFN-γ GGTT and GATT composite genotypes (p?=?0.0296 and p?=?0.0129, respectively), the TNF-β/IFN-γ AGTT composite genotype (p?=?0.0003), and the TNF-α/β/IFN-γ GGAGTT and GAAGTT composite genotypes (p?=?0.0437 and p?=?0.0038, respectively) were estimated to have a protective effect against breast cancer. However, the TNF-α/IFN-γ GGTA composite genotype is a risk factor for breast cancer (p?=?0.0156). In conclusion, TNF-β +252GG genotype was found more frequent in Turkish breast cancer patients than controls and IFN-γ TA+AA genotypes were estimated to increase breast cancer risk significantly in Turkish population.