Donor substrate recognition in the raffinose-bound E342A mutant of fructosyltransferase <Emphasis Type="Italic">Bacillus subtilis</Emphasis> levansucrase

Background  

Fructans – β-D-fructofuranosyl polymers with a sucrose starter unit – constitute a carbohydrate reservoir synthesised by a considerable number of bacteria and plant species. Biosynthesis of levan (αGlc(1–2)βFru [(2–6)βFru]_n), an abundant form of bacterial fructan, is catalysed by levansucrase (sucrose:2,6-β-D-fructan-6-β-D-fructosyl transferase), utilizing sucrose as the sole substrate. Previously, we described the tertiary structure of Bacillus subtilis levansucrase in the ligand-free and sucrose-bound forms, establishing the mechanistic roles of three invariant carboxylate side chains, Asp86, Asp247 and Glu342, which are central to the double displacement reaction mechanism of fructosyl transfer. Still, the structural determinants of the fructosyl transfer reaction thus far have been only partially defined.     

The communicative potential of bat echolocation pulses

Ecological constraints often shape the echolocation pulses emitted by bat species. Consequently some (but not all) bats emit species-specific echolocation pulses. Because echolocation pulses are often intense and emitted at high rates, they are potential targets for eavesdropping by other bats. Echolocation pulses can also vary within species according to sex, body size, age, social group and geographic location. Whether these features can be recognised by other bats can only be determined reliably by playback experiments, which have shown that echolocation pulses do provide sufficient information for the identification of sex and individual in one species. Playbacks also show that bats can locate conspecifics and heterospecifics at foraging and roost sites by eavesdropping on echolocation pulses. Guilds of echolocating bat species often partition their use of pulse frequencies. Ecology, allometric scaling and phylogeny play roles here, but are not sufficient to explain this partitioning. Evidence is accumulating to support the hypothesis that frequency partitioning evolved to facilitate intraspecific communication. Acoustic character displacement occurs in at least one instance. Future research can relate genetic population structure to regional variation in echolocation pulse features and elucidate those acoustic features that most contribute to discrimination of individuals.     

Analysis of the Pan Genome of <Emphasis Type="Italic">Campylobacter jejuni</Emphasis> Isolates Recovered from Poultry by Pulsed-Field Gel Electrophoresis,Multilocus Sequence Typing (MLST), and Repetitive Sequence Polymerase Chain Reaction (rep-PCR) Reveals Different Discriminatory Capabilities

Campylobacter jejuni is one of the leading bacterial causes of food-borne illness in the USA. Molecular typing methods are often used in food safety for identifying sources of infection and pathways of transmission. Moreover, the identification of genetically related isolates (i.e., clades) may facilitate the development of intervention strategies for control and prevention of food-borne diseases. We analyzed the pan genome (i.e., core and variable genes) of 63 C. jejuni isolates recovered from chickens raised in conventional, organic, and free-range poultry flocks to gain insight into the genetic diversity of C. jejuni isolates recovered from different environments. We assessed the discriminatory power of three genotyping methods [i.e., pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and repetitive extragenic palindromic polymerase chain reaction (rep-PCR)]. The rep-PCR fingerprint was generated by determining the presence of repetitive sequences that are interspersed throughout the genome via repetitive extragenic palindromic PCR, enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR), and BOX element PCR (BOX-PCR) and combining the data to form a composite fingerprint. The genetic fingerprints were subjected to computer-assisted pattern analysis. Comparison of the three genotypic methods revealed that repREB-PCR showed greater discriminatory power than PFGE and MLST. ERIC-PCR and BOX-PCR yielded the highest number of PCR products and greatest reproducibility. Regardless of the genotyping method, C. jejuni isolates recovered from chickens reared in conventional, organic, and free-range environments all exhibit a high level of genotypic diversity.     

Bildung von Ochratoxin A bei der Lagerung von Triticale nach künstlicher Infektion mit<Emphasis Type="Italic">Penicillium verrucosum</Emphasis> in Abhängigkeit unterschiedlicher Feuchtegehalte

Triticale is a frequently cultivated and used in feed rations because of high yields of kernels and straw. Furthermore triticale is cosidered in a culturelandscape program. The storage of triticale and storage conditions become more and more important. In our study Triticale was remoistered to a watercontent of 14, 16, 18, und 19% as well, inoculated withP verrucosum and stored for 28 weeks from november till july in a research granary (tower silo). This experiment should simulate the storage situation in farmscale from cold wintermonths to warm spring times. Every four weeks CO₂ was measured, and samples for moisture, OTA- and CT-analysis were taken. At week 20 and a MC of 19 % 22 μg OTA/kg triticale were found. The maximum of OTA-production in this humidity stage was at week 28 with 635 μg/kg. Also at a MC of 18 % OTA could be found with levels near to the detection limit. In contrast to former investigations with oatsP verrucosum produced in triticale no citrinin even when the OTA concentrations were higher than in our investigations.     

Measuring disease similarity and predicting disease-related ncRNAs by a novel method

Background

Similar diseases are always caused by similar molecular origins, such as diasease-related protein-coding genes (PCGs). And the molecular associations reflect their similarity. Therefore, current methods for calculating disease similarity often utilized functional interactions of PCGs. Besides, the existing methods have neglected a fact that genes could also be associated in the gene functional network (GFN) based on intermediate nodes.

Methods

Here we presented a novel method, InfDisSim, to deduce the similarity of diseases. InfDisSim utilized the whole network based on random walk with damping to model the information flow. A benchmark set of similar disease pairs was employed to evaluate the performance of InfDisSim.

Results

The region beneath the receiver operating characteristic curve (AUC) was calculated to assess the performance. As a result, InfDisSim reaches a high AUC (0.9786) which indicates a very good performance. Furthermore, after calculating the disease similarity by the InfDisSim, we reconfirmed that similar diseases tend to have common therapeutic drugs (Pearson correlation γ²?=?0.1315, p?=?2.2e-16). Finally, the disease similarity computed by infDisSim was employed to construct a miRNA similarity network (MSN) and lncRNA similarity network (LSN), which were further exploited to predict potential associations of lncRNA-disease pairs and miRNA-disease pairs, respectively. High AUC (0.9893, 0.9007) based on leave-one-out cross validation shows that the LSN and MSN is very appropriate for predicting novel disease-related lncRNAs and miRNAs, respectively.

Conclusions

The high AUC based on benchmark data indicates the method performs well. The method is valuable in the prediction of disease-related lncRNAs and miRNAs.

     

Oxidative toxicity in diabetes and Alzheimer’s disease: mechanisms behind ROS/ RNS generation

Reactive oxidative species (ROS) toxicity remains an undisputed cause and link between Alzheimer’s disease (AD) and Type-2 Diabetes Mellitus (T2DM). Patients with both AD and T2DM have damaged, oxidized DNA, RNA, protein and lipid products that can be used as possible disease progression markers. Although the oxidative stress has been anticipated as a main cause in promoting both AD and T2DM, multiple pathways could be involved in ROS production. The focus of this review is to summarize the mechanisms involved in ROS production and their possible association with AD and T2DM pathogenesis and progression. We have also highlighted the role of current treatments that can be linked with reduced oxidative stress and damage in AD and T2DM.     

Evaluation of detection of <Emphasis Type="Italic">Toxoplasma gondii</Emphasis> DNA in animal blood samples by quantitative PCR

Aim of the study: The purpose of this study was to find out the relationship between the phase of infection (acute or persistent) and the ability of quantitative PCR to detect DNA of Toxoplasma gondii in circulating leukocytes in blood. Methodology: Animal serum samples were examined (50 sheep, 47 dogs, 32 dairy cows, 91 wild boars and 36 rabbits) for the occurrence of IgM and IgG antibodies to T. gondii by ELISA. Uncoagulated blood samples from the same animals were examined for the detection of T. gondii DNA in circulating leukocytes by real-time PCR. Results: Only IgM antibodies, characteristic for acute infection, were detected in 45 of the 256 serum samples (17.6%). Only IgG antibodies, corresponding with chronic infection, were detected in 120 of the 256 samples (46.8%). In 91 of the 256 samples (35.5%) neither IgM or IgG were detected by ELISA. For real-time PCR, animals were divided into three groups based on the serological results: (group I — acute infection, group II — chronic infection, and group III — no infection). In group I, the presence of T. gondii DNA was detected in 9 out of 45 samples (20%), whereas in group II only 1 of 120 samples was positive for T. gondii DNA (0.8%). In group III, no DNA of T. gondii (0/91 samples) was detected by real-time PCR. Significance: The proof of DNA by real-time PCR in IgM positive samples was statistically significant in comparison to IgG positive samples (P<0.0001).     

Senescent vs. non-senescent cells in the human annulus in vivo: Cell harvest with laser capture microdissection and gene expression studies with microarray analysis

Background  

Senescent cells are well-recognized in the aging/degenerating human disc. Senescent cells are viable, cannot divide, remain metabolically active and accumulate within the disc over time. Molecular analysis of senescent cells in tissue offers a special challenge since there are no cell surface markers for senescence which would let one use fluorescence-activated cell sorting as a method for separating out senescent cells.     

Relating body size to the role of aquatic subsidies for the riparian spider <Emphasis Type="Italic">Nephila clavata</Emphasis>

We examined the relationship between body size of the riparian spider Nephila clavata and the contribution of allochthonous (aquatic insects) and autochthonous (terrestrial insects) sources to its diet using stable isotope analysis. During the study period from July to September, the body size of the females increased remarkably (about 60-fold) but that of males remained small. The biomass of both aquatic and terrestrial insects trapped on the spider webs increased with spider size, with the biomass of the former ranging between 30 and 70% of that of the terrestrial insects. The average relative contribution of aquatic insects to the diet of the spiders, calculated from δ¹³C values, was 40–50% in spiders in the early juvenile and juvenile stages, 35% in adult males and 4% in adult females. There was a significant negative relationship between the relative contribution of aquatic insects and body size of the female spiders. We conclude that aquatic insects might be an important seasonal dietary subsidy for small spiders and that these allochthonous subsidies may facilitate the growth of riparian spiders, which may in turn enable the spiders to feed on larger prey.