Deletion of BCY1 from the Saccharomyces cerevisiae genome is semidominant and induces autolytic phenotypes suitable for improvement of sparkling wines

Autolysis of Saccharomyces cerevisiae is the main source of molecules that contribute to the quality of sparkling wines made by the traditional method. In this work the possibility of accelerating this slow process in order to improve the quality of sparkling wines by using genetically engineered wine yeast strains was explored. The effect of partial or total deletion of BCY1 (which encodes a regulatory subunit of cAMP-dependent protein kinase A) in haploid and diploid (heterozygous and homozygous) yeast strains was studied. We proved that heterozygous strains having partial or complete BCY1 deletions have a semidominant phenotype for several of the properties studied, including autolysis under simulated second-fermentation conditions, in contrast to previously published reports describing mutations in BCY1 as recessive. Considering the degree of autolysis, ethanol tolerance, and technical feasibility, we propose that deletion of the 3' end of the open reading frame of a single copy of BCY1 is a way to improve the quality of sparkling wines.     

A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples

The Cariaco Basin off the Venezuelan coast in the Caribbean Sea is the world's largest truly marine body of anoxic water. The first rRNA survey of microbial eukaryotes in this environment revealed a number of novel lineages, but sampled only a fraction of the entire diversity. The goal of this study was to significantly improve recovery of protistan rRNA from the Basin. This was achieved by a systematic application of multiple PCR primer sets and substantially larger sequencing efforts. We focused on the most diverse habitat in the basin, anoxic waters approximately 100m below the oxic-anoxic interface, and detected novel lineages that escaped the single PCR primer approach. All clones obtained proved unique. A 99% sequence similarity cut-off value combined these clones into operational taxonomic units (OTUs), over 75% of which proved novel. Some of these OTUs form deep branches within established protistan groups. Others signify discovery of novel protistan lineages that appear unrelated to any known microeukaryote. Surprisingly, even this large-scale multi-primer rRNA approach still missed a substantial part of the samples' rRNA diversity. The overlap between the species lists obtained with different primers is low, with only 4% of OTUs shared by all three libraries, and the number of species detected only once is large (55%). This strongly indicates that, at least in anoxic environments, protistan diversity may be much larger than is commonly thought. A single sample appears to contain thousands of largely novel protistan species. Multiple PCR primer combinations may be needed to capture these species.     

Influence of head models on neuromagnetic fields and inverse source localizations

Background  

The magnetoencephalograms (MEGs) are mainly due to the source currents. However, there is a significant contribution to MEGs from the volume currents. The structure of the anatomical surfaces, e.g., gray and white matter, could severely influence the flow of volume currents in a head model. This, in turn, will also influence the MEGs and the inverse source localizations. This was examined in detail with three different human head models.     

Time-related improvement of survival in resectable gastric cancer: the role of Japanese-style gastrectomy with D2 lymphadenectomy and adjuvant chemotherapy

Background

Late presentation of patients at advanced stages when little or no benefit can be derived from any form of therapy is the hallmark of breast cancer in Nigerian women. Recent global cancer statistics indicate rising global incidence of breast cancer and the increase is occurring at a faster rate in populations of the developing countries that hitherto enjoyed low incidence of the disease. Worried by this prevailing situation and with recent data suggesting that health behavior may be influenced by level of awareness about breast cancer, a cross-sectional study was designed to assess the knowledge, attitude and practices of community-dwelling women in Nigeria towards breast cancer.

Methods

One thousand community-dwelling women from a semi-urban neighborhood in Nigeria were recruited for the study in January and February 2000 using interviewer-administered questionnaires designed to elicit sociodemographic information and knowledge, attitude and practices of these women towards breast cancer. Data analysis was carried out using Statistical Analysis Software (SAS) version 8.2.

Results

Study participants had poor knowledge of breast cancer. Mean knowledge score was 42.3% and only 214 participants (21.4%) knew that breast cancer presents commonly as a painless breast lump. Practice of breast self examination (BSE) was low; only 432 participants (43.2%) admitted to carrying out the procedure in the past year. Only 91 study participants (9.1%) had clinical breast examination (CBE) in the past year. Women with higher level of education (X² = 80.66, p < 0.0001) and those employed in professional jobs (X² = 47.11, p < 0.0001) were significantly more knowledgeable about breast cancer. Participants with higher level of education were 3.6 times more likely to practice BSE (Odds ratio [OR] = 3.56, 95% Confidence interval [CI] 2.58–4.92).

Conclusion

The results of this study suggest that community-dwelling women in Nigeria have poor knowledge of breast cancer and minority practice BSE and CBE. In addition, education appears to be the major determinant of level of knowledge and health behavior among the study participants. We recommend the establishment and sustenance of institutional framework and policy guidelines that will enhance adequate and urgent dissemination of information about breast cancer to all women in Nigeria.     

Effect of the presence of the plant growth promoting rhizobacterium (PGPR) Chryseobacterium balustinum Aur9 and salt stress in the pattern of flavonoids exuded by soybean roots

In this work we studied how biotic and abiotic stresses can alter the pattern of flavonoids exuded by Osumi soybean roots. A routine method was developed for the detection and characterization of the flavonoids present in soybean root exudates using HPLC-MS/MS. Then, a systematic screening of the flavonoids exuded under biotic stress, the presence of a plant growth promoting rhizobacterium, and salt stress was carried out. Results obtained indicate that the presence of Chryseobacterium balustinum Aur9 or 50 mM NaCl changes qualitatively the pattern of flavonoids exuded when compared to control conditions. Thus, in the presence of C. balustinum Aur9, soybean roots did not exude quercetin and naringenin and, under salt stress, flavonoids daidzein and naringenin could not be detected. Soybean root exudates obtained under saline conditions showed a diminished capacity to induce the expression of the nodA gene in comparison to the exudates obtained in the absence of salt. Moreover, lipochitooligosaccharides (LCOs) were not detected or weakly detected when Sinorhizobium fredii SMH12 was grown in the exudates obtained under salt stress conditions or under salt stress in the presence of C. balustinum Au9, respectively.     

Engineered Respiro-Fermentative Metabolism for the Production of Biofuels and Biochemicals from Fatty Acid-Rich Feedstocks

Although lignocellulosic sugars have been proposed as the primary feedstock for the biological production of renewable fuels and chemicals, the availability of fatty acid (FA)-rich feedstocks and recent progress in the development of oil-accumulating organisms make FAs an attractive alternative. In addition to their abundance, the metabolism of FAs is very efficient and could support product yields significantly higher than those obtained from lignocellulosic sugars. However, FAs are metabolized only under respiratory conditions, a metabolic mode that does not support the synthesis of fermentation products. In the work reported here we engineered several native and heterologous fermentative pathways to function in Escherichia coli under aerobic conditions, thus creating a respiro-fermentative metabolic mode that enables the efficient synthesis of fuels and chemicals from FAs. Representative biofuels (ethanol and butanol) and biochemicals (acetate, acetone, isopropanol, succinate, and propionate) were chosen as target products to illustrate the feasibility of the proposed platform. The yields of ethanol, acetate, and acetone in the engineered strains exceeded those reported in the literature for their production from sugars, and in the cases of ethanol and acetate they also surpassed the maximum theoretical values that can be achieved from lignocellulosic sugars. Butanol was produced at yields and titers that were between 2- and 3-fold higher than those reported for its production from sugars in previously engineered microorganisms. Moreover, our work demonstrates production of propionate, a compound previously thought to be synthesized only by propionibacteria, in E. coli. Finally, the synthesis of isopropanol and succinate was also demonstrated. The work reported here represents the first effort toward engineering microorganisms for the conversion of FAs to the aforementioned products.Concerns about climate change and the depletion and cost of petroleum resources have ignited interest in the establishment of a bio-based industry (5, 49, 61), and the conceptual model of a biorefinery has emerged (27, 28, 45). Given its abundance in nature, the carbohydrate portion of edible crops such as sugarcane, sugar beet, maize (corn), and sorghum is currently used as the primary feedstock in the biological production of fuels and chemicals (12, 49, 52). Although the use of nonedible lignocellulosic sugars has been proposed as an efficient and sustainable avenue to the aforementioned processes, the availability of fatty acid (FA)-rich feedstocks and recent progress in the development of oil-accumulating organisms make FAs an attractive alternative. Edible oil-rich crops such as rapeseed, sunflower, soybean, and palm are currently available and widely used as feedstocks for chemical conversion to biodiesel (6), while oleaginous algae and nonedible FA-rich crops along with industrial by-products are receiving greater attention as longer-term alternatives. These nonedible FA-rich feedstocks are presently generated in large amounts and can be exploited for the biological production of fuels and chemicals (14, 22, 51, 56, 57). Unfortunately, microbial platforms to enable this are at present almost absent.FAs not only are abundant but also offer several advantages when used for fuel and chemical production. For example, their metabolism to the key intermediate metabolite acetyl coenzyme A (acetyl-CoA) is very efficient, as it results in 100% carbon recovery (Fig. ​(Fig.1).1). Since many fuels and chemicals can be derived from acetyl-CoA, high yields can be realized if FAs are used as the carbon source. In contrast, sugar metabolism generates one molecule of carbon dioxide (or formate) per molecule of acetyl-CoA, limiting the yield of products derived from acetyl-CoA (Fig. ​(Fig.1).1). The product yield advantage of FAs over sugars is also supported by the more highly reduced nature of their carbon atoms. Table ​Table11 provides a comparison of maximum theoretical yields, on both weight and carbon bases, for the production of biofuels and biochemicals from FAs and lignocellulosic sugars. Maximum theoretical yields have been calculated from stoichiometry based on the pathways shown in Fig. ​Fig.11 for the utilization of FAs and glucose, the synthesis of products, the tricarboxylic acid (TCA) cycle, and oxidative phosphorylation. The stoichiometric coefficients were obtained by conducting elemental balances on carbon, hydrogen, and oxygen, and an ATP balance was also included in the analysis. As an example, when production of biofuels (e.g., ethanol and butanol) is considered, utilization of FAs (e.g., palmitic acid [C_16:0]) as a substrate returns product yields 2.7-fold (wt/wt) or 1.4-fold (C/C) higher than those for sugars (calculations are provided for glucose but are equally valid for other lignocellulosic sugars). Although the current prices of feedstocks on a weight basis are comparable (lower than 20¢/pound), the data reported in Fig. S1a in the supplemental material show that the price per carbon for glucose derived from corn is remarkably higher. Regardless of the basis used for calculations (i.e., weight or carbon basis), when maximum theoretical yields and costs of FA and sugar feedstocks are accounted for, the advantages of using FAs are remarkable (see Fig. S1b in the supplemental material).Open in a separate windowFIG. 1.Pathways engineered in E. coli for the conversion of fatty acids to fuels (red) and chemicals (green). Also shown is the catabolism of fatty acids via the β-oxidation pathway (orange) and of glucose through the Embden-Meyerhof-Parnas pathway (blue). Relevant reactions are represented by the names of the genes coding for the enzymes (E. coli genes unless otherwise specified in parentheses as follows: C. acetobutylicum, ca; C. beijerinckii, cb): aceA, isocitrate lyase; aceB, malate synthase A; adc, acetoacetate decarboxylase (ca); ackA, acetate kinase; adh, secondary alcohol dehydrogenase (cb); adhE, acetaldehyde/alcohol dehydrogenase; adhE2, secondary alcohol dehydrogenase (ca); atoA and atoD, acetyl-CoA:acetoacetyl-CoA transferase; atoB, acetyl-CoA acetyltransferase; bcd, butyryl-CoA dehydrogenase (ca); crt, crotonase (ca); etfAB, electron transfer flavoprotein (ca); fadA, 3-ketoacyl-CoA thiolase; fadB, enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase; fadD, acyl-CoA synthetase; fadE, acyl-CoA dehydrogenase; hbd, β-hydroxybutyryl-CoA dehydrogenase (ca); icd, isocitrate dehydrogenase; pta, phosphate acetyltransferase; sdhABCD, succinate dehydrogenase; scpA, methylmalonyl-CoA mutase; scpB, methylmalonyl-CoA decarboxylase; scpC, propionyl-CoA:succinate CoA transferase; sucA, 2-oxoglutarate dehydrogenase; sucB, dihydrolipoyltranssuccinylase; and sucCD, succinyl-CoA synthetase. Abbreviations: 2[H] = NADH = FADH₂ = QH₂ = H₂; P/O, amount of ATP produced per oxygen consumed in the oxidative phosphorylation.

TABLE 1.

Comparison of maximum theoretical yields for the production of biofuels and biochemicals from fatty acids (palmitic acid) and lignocellulosic sugars (glucose)