LBT/PTD dual tagged vector for purification, cellular protein delivery and visualization in living cells

Cellular protein delivery is an emerging technique, by which exogenous recombinant proteins are delivered into mammalian cells across the membrane. We have developed an E. coli expression vector suited for protein cellular delivery experiments. The plasmid is designed to generate a C-terminal fusion with the 12 amino acid HIV-Tat peptide as a protein transduction domain (PTD), whereas the protein N-terminus is fused to an 17-residue peptide lanthanide-binding tag (LBT). LBT is used for both purification by affinity chromatography and fluorescent detection with Tb(3+) as a coordinating metal. We have employed the TA-cloning site between the two tags, LBT and PTD, according to the PRESAT-vector methodology [N. Goda, T. Tenno, H. Takasu, H. Hiroaki, M. Shirakawa, The PRESAT-vector: asymmetric T-vector for high-throughput screening of soluble protein domains for structural proteomics, Protein Sci. 13 (2004) 652-658], which facilitates unidirectional cloning of any PCR-amplified DNA fragments corresponding to the protein of interest. A simple three-step protocol consisting of affinity purification of LBT/PTD dual-tagged proteins has also been developed, in which the proteins are purified by heparin-, then immobilized Ni(2+)-, and then heparin-affinity chromatography, in this order. The purified protein is ready for protein delivery experiment, and the delivered protein is visible by fluorescent microscopy. Our LBT/PTD dual-tagged PRESAT-vector provides a powerful research tool for exploring cellular functions of proteins in the post-genomic era.     

High penetrance of sequencing errors and interpretative shortcomings in mtDNA sequence analysis of LHON patients

For identifying mutation(s) that are potentially pathogenic it is essential to determine the entire mitochondrial DNA (mtDNA) sequences from patients suffering from a particular mitochondrial disease, such as Leber hereditary optic neuropathy (LHON). However, such sequencing efforts can, in the worst case, be riddled with errors by imposing phantom mutations or misreporting variant nucleotides, and moreover, by inadvertently regarding some mutations as novel and pathogenic, which are actually known to define minor haplogroups. Under such circumstances it remains unclear whether the disease-associated mutations would have been determined adequately. Here, we re-analyse four problematic LHON studies and propose guidelines by which some of the pitfalls could be avoided.     

A study on growth characteristics and nutrient consumption of Lactobacillus plantarum in A-stat culture

Lactobacillus plantarum was grown in complex media containing glucose and yeast extract. The maximum growth yield based on yeast extract consumption was 0.5 g dwt g^-1. Growth yield Y_ATP 15–17 g dwt mol ATP^-1 was almost constant in the glucose limited A-stat experiment whereas in the yeast extract limited culture it increased with dilution rate. The maximum specific growth rate observed, 0.5 h^-1, was similar for both A-stat and batch cultures. Specific oxygen consumption, Q_O2, reached the value of 1.8 mmol O₂ h^-1 g dwt^-1. It was shown that Val, Ile, Leu, Tyr and Phe, were consumed mainly as free amino acids, while Asp, Pro, Lys and Arg were derived from peptides. Significantly more Asp, Ser, Glu, Val, Ile, Leu and Phe were consumed than needed to build up cell protein whereas some Pro, Gly, Ala and Lys was synthesized. A network of metabolic reactions in L. plantarum was proposed on the basis of the experimental data.     

Sulfate-reducing anaerobic ammonium oxidation as a potential treatment method for high nitrogen-content wastewater

After sulfate-reducing ammonium oxidation (SRAO) was first assumed in 2001, several works have been published describing this process in laboratory-scale bioreactors or occurring in the nature. In this paper, the SRAO process was performed using reject water as a substrate for microorganisms and a source of NH(4) (+), with SO(4) (2-) being added as an electron acceptor. At a moderate temperature of 20°C in a moving bed biofilm reactor (MBBR) sulfate reduction along with ammonium oxidation were established. In an upflow anaerobic sludge blanket reactor (UASBR) the SRAO process took place at 36°C. Average volumetric TN removal rates of 0.03?kg-N/m3/day in the MBBR and 0.04?kg-N/m3/day in the UASBR were achieved, with long-term moderate average removal efficiencies, respectively. Uncultured bacteria clone P4 and uncultured planctomycete clone Amx-PAn30 were detected from the biofilm of the MBBR, from sludge of the UASBR uncultured Verrucomicrobiales bacterium clone De2102 and Uncultured bacterium clone ATB-KS-1929 were found also. The stoichiometrical ratio of NH(4) (+) removal was significantly higher than could be expected from the extent of SO(4) (2-) reduction. This phenomenon can primarily be attributed to complex interactions between nitrogen and sulfur compounds and organic matter present in the wastewater. The high NH(4) (+) removal ratio can be attributed to sulfur-utilizing denitrification/denitritation providing the evidence that SRAO is occurring independently and is not a result of sulfate reduction and anammox. HCO(3) (-) concentrations exceeding 1,000?mg/l were found to have an inhibiting effect on the SRAO process. Small amounts of hydrazine were naturally present in the reaction medium, indicating occurrence of the anammox process. Injections of anammox intermediates, hydrazine and hydroxylamine, had a positive effect on SRAO process performance, particularly in the case of the UASBR.     

From Bacteria to Piscivorous Fish: Estimates of Whole-Lake and Component-Specific Metabolism with an Ecosystem Approach

The influence of functional group specific production and respiration patterns on a lake''s metabolic balance remains poorly investigated to date compared to whole-system estimates of metabolism. We employed a summed component ecosystem approach for assessing lake-wide and functional group-specific metabolism (gross primary production (GPP) and respiration (R)) in shallow and eutrophic Lake Võrtsjärv in central Estonia during three years. Eleven functional groups were considered: piscivorous and benthivorous fish; phyto-, bacterio-, proto- and metazooplankton; benthic macroinvertebrates, bacteria and ciliates; macrophytes and their associated epiphytes. Metabolism of these groups was assessed by allometric equations coupled with daily records of temperature and hydrology of the lake and measurements of food web functional groups biomass. Results revealed that heterotrophy dominated most of the year, with a short autotrophic period observed in late spring. Most of the metabolism of the lake could be attributed to planktonic functional groups, with phytoplankton contributing the highest share (90% of GPP and 43% of R). A surge of protozooplankton and bacterioplankton populations forming the microbial loop caused the shift from auto- to heterotrophy in midsummer. Conversely, the benthic functional groups had overall a very small contribution to lake metabolism. We validated our ecosystem approach by comparing the GPP and R with those calculated from O₂ measurements in the lake. Our findings are also in line with earlier productivity studies made with ¹⁴C or chlorophyll a (chl-a) based equations. Ideally, the ecosystem approach should be combined with diel O₂ approach for investigating critical periods of metabolism shifts caused by dynamics in food-web processes.     

Sex-specific outcomes of diabetic patients with acute myocardial infarction who have undergone percutaneous coronary intervention: a register linkage study

ABSTRACT: BACKGROUND: The presence of diabetes mellitus poses a challenge in the treatment of patients with acute myocardial infarction (AMI). We aimed to evaluate the sex-specific outcomes of diabetic and non-diabetic patients with AMI who have undergone percutaneous coronary intervention (PCI). METHODS: Data of the Estonian Myocardial Infarction Registry for years 2006[EN DASH]2009 were linked with the Health Insurance Fund database and the Population Registry. Hazard ratios (HRs) with the 95 % confidence intervals (CIs) for the primary composite outcome (non-fatal AMI, revascularization, or death whichever occurred first) and for the secondary outcome (all cause mortality) were calculated comparing diabetic with non-diabetic patients by sex. RESULTS: In the final study population (n = 1652), 14.6 % of the men and 24.0 % of the women had diabetes. Overall, the diabetics had higher rates of cardiovascular risk factors, co-morbidities, and 3[EN DASH]4 vessel disease among both men and women (p < 0.01). Among women, the diabetic patients were younger, they presented later and less often with typical symptoms of chest pain than the non-diabetics (p < 0.01). Women with diabetes received aspirin and reperfusion for ST-segment elevation AMI less often than those without diabetes (p < 0.01). During a follow-up of over two years, in multivariate analysis, diabetes was associated with worse outcomes only in women: the adjusted HR for the primary outcome 1.44 (95 % CI 1.05 [MINUS SIGN] 1.96) and for the secondary outcome 1.83 (95 % CI 1.17 [MINUS SIGN] 2.89). These results were largely driven by a high (12.0 %) mortality during hospitalization of diabetic women. CONCLUSIONS: Diabetic women with AMI who have undergone PCI are a high-risk group warranting special attention in treatment strategies, especially during hospitalization. There is a need to improve the expertise to detect AMI earlier, decrease disparities in management, and find targeted PCI strategies with adjunctive antithrombotic regimes in women with diabetes.     

Sexual size dimorphism within species increases with body size in insects

Studies examining interspecific differences in sexual size dimorphism (SSD) typically assume that the degree of sexual differences in body size is invariable within species. This work was conducted to assess validity of this assumption. As a result of a systematic literature survey, datasets for 158 insect species were retrieved. Each dataset contained adult or pupal weights of males and females for two or more different subsets, typically originating from different conditions during immature development. For each species, an analysis was conducted to examine dependence of SSD on body size, the latter variable being used as a proxy of environmental quality. A considerable variation in SSD was revealed at the intraspecific level in insects. The results suggest that environmental conditions may strongly affect the degree, though not the direction of SSD within species. In most species, female size appeared to be more sensitive to environmental conditions than male size: with conditions improving, there was a larger relative increase in female than male size. As a consequence, sexual differences in size were shown to increase with increasing body size in species with female-biased SSD (females were the larger sex in more than 80% of the species examined). The results were consistent across different insect orders and ecological subdivisions. Mechanisms leading to intraspecific variation in SSD are discussed. This study underlines the need to consider intraspecific variation in SSD in comparative studies.     

Exploitative competition and coexistence in a parasitoid assemblage

Most insect populations are exploited by a complex of different parasitoid species, providing ample opportunities for competitive interactions among the latter. Despite this, resource-mediated competition (i.e., exploitative competition) among insect parasitoids remains poorly documented in natural systems. Here we propose a novel way to infer the presence of competitive interactions from covariance patterns in parasitism levels, and illustrate the use of this approach on a relatively well-defined and simple host–parasitoid system. The parasitism levels caused by three parasitoid species on a shared host showed a highly consistent negative covariance among samples. With the levels of parasitism by one species increasing, the levels of parasitism attributable to the two others decreased. Importantly, negative covariance between parasitism levels by different species appeared at high abundance, but not at low abundance of the phenologically earlier parasitoid species. This as well as several other lines of evidence indicates the importance of competitive interactions in this system. Feeding biology and phenology of the parasitoids suggest that competition in this parasitoid assemblage is primarily resource-mediated rather than occurring through direct interference. The species attacking earlier stages of the host are competitively superior to those attacking their host later in the season. Better dispersal ability and use of alternative host species by the inferior species could contribute to the coexistence of these competing parasitoids.