Impact of calcium on salivary α-amylase activity, starch paste apparent viscosity and thickness perception

Thickness perception of starch-thickened products during eating has been linked to starch viscosity and salivary amylase activity. Calcium is an essential cofactor for α-amylase and there is anecdotal evidence that adding extra calcium affects amylase activity in processes like mashing of beer. The aims of this paper were to (1) investigate the role of salivary calcium on α-amylase activity and (2) to measure the effect of calcium concentration on apparent viscosity and thickness perception when interacting with salivary α-amylase in starch-based samples. α-Amylase activity in saliva samples from 28 people was assessed using a typical starch pasting cycle (up to 95 °C). The activity of the enzyme (as measured by the change in starch apparent viscosity) was maintained by the presence of calcium, probably by protecting the enzyme from heat denaturation. Enhancement of α-amylase activity by calcium at 37 °C was also observed although to a smaller extent. Sensory analysis showed a general trend of decreased thickness perception in the presence of calcium, but the result was only significant for one pair of samples, suggesting a limited impact of calcium enhanced enzyme activity on perceived thickness

The genome and transcriptome of Trichormus sp NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau

The Qinghai-Tibet Plateau (QTP) has the highest biodiversity for an extreme environment worldwide, and provides an ideal natural laboratory to study adaptive evolution. In this study, we generated a draft genome sequence of cyanobacteria Trichormus sp. NMC-1 in the QTP and performed whole transcriptome sequencing under low temperature to investigate the genetic mechanism by which T. sp. NMC-1 adapted to the specific environment. Its genome sequence was 5.9 Mb with a G+C content of 39.2% and encompassed a total of 5362 CDS. A phylogenomic tree indicated that this strain belongs to the Trichormus and Anabaena cluster. Genome comparison between T. sp. NMC-1 and six relatives showed that functionally unknown genes occupied a much higher proportion (28.12%) of the T. sp. NMC-1 genome. In addition, functions of specific, significant positively selected, expanded orthogroups, and differentially expressed genes involved in signal transduction, cell wall/membrane biogenesis, secondary metabolite biosynthesis, and energy production and conversion were analyzed to elucidate specific adaptation traits. Further analyses showed that the CheY-like genes, extracellular polysaccharide and mycosporine-like amino acids might play major roles in adaptation to harsh environments. Our findings indicate that sophisticated genetic mechanisms are involved in cyanobacterial adaptation to the extreme environment of the QTP

Genome-wide signatures of convergent evolution in echolocating mammals

Evolution is typically thought to proceed through divergence of genes, proteins, and ultimately phenotypes(1-3). However, similar traits might also evolve convergently in unrelated taxa due to similar selection pressures(4,5). Adaptive phenotypic convergence is widespread in nature, and recent results from a handful of genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level(6-9). Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution(9,10) although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show for the first time that convergence is not a rare process restricted to a handful of loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four new bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Surprisingly we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognised

An Endogenous Foamy-like Viral Element in the Coelacanth Genome

Little is known about the origin and long-term evolutionary mode of retroviruses. Retroviruses can integrate into their hosts' genomes, providing a molecular fossil record for studying their deep history. Here we report the discovery of an endogenous foamy virus-like element, which we designate ‘coelacanth endogenous foamy-like virus’ (CoeEFV), within the genome of the coelacanth (Latimeria chalumnae). Phylogenetic analyses place CoeEFV basal to all known foamy viruses, strongly suggesting an ancient ocean origin of this major retroviral lineage, which had previously been known to infect only land mammals. The discovery of CoeEFV reveals the presence of foamy-like viruses in species outside the Mammalia. We show that foamy-like viruses have likely codiverged with their vertebrate hosts for more than 407 million years and underwent an evolutionary transition from water to land with their vertebrate hosts. These findings suggest an ancient marine origin of retroviruses and have important implications in understanding foamy virus biology

A surrogate method for comparison analysis of salivary concentrations of Xylitol-containing products

Background: Xylitol chewing gum has been shown to reduce Streptococcus mutans levels and decay. Two studies examined the presence and time course of salivary xylitol concentrations delivered via xylitol-containing pellet gum and compared them to other xylitol-containing products. Methods: A within-subjects design was used for both studies. Study 1, adults (N = 15) received three xylitol-containing products (pellet gum (2.6 g), gummy bears (2.6 g), and commercially available stick gum (Koolerz, 3.0 g)); Study 2, a second group of adults (N = 15) received three xylitol-containing products (pellet gum, gummy bears, and a 33% xylitol syrup (2.67 g). For both studies subjects consumed one xylitol product per visit with a 7-day washout between each product. A standardized protocol was followed for each product visit. Product order was randomly determined at the initial visit. Saliva samples (0.5 mL to 1.0 mL) were collected at baseline and up to 10 time points (~16 min in length) after product consumption initiated. Concentration of xylitol in saliva samples was analyzed using high-performance liquid chromatography. Area under the curve (AUC) for determining the average xylitol concentration in saliva over the total sampling period was calculated for each product. Results: In both studies all three xylitol products (Study 1: pellet gum, gummy bears, and stick gum; Study 2: pellet gum, gummy bears, and syrup) had similar time curves with two xylitol concentration peaks during the sampling period. Study 1 had its highest mean peaks at the 4 min sampling point while Study 2 had its highest mean peaks between 13 to 16 minutes. Salivary xylitol levels returned to baseline at about 18 minutes for all forms tested. Additionally, for both studies the total AUC for the xylitol products were similar compared to the pellet gum (Study 1: pellet gum - 51.3 [micro]g.min/mL, gummy bears - 59.6 [micro]g.min/mL, and stick gum - 46.4 [micro]g.min/mL; Study 2: pellet gum - 63.0 [micro]g.min/mL, gummy bears - 55.9 [micro]g.min/mL, and syrup - 59.0 [micro]g.min/mL). Conclusion: The comparison method demonstrated high reliability and validity. In both studies other xylitol-containing products had time curves and mean xylitol concentration peaks similar to xylitol pellet gum suggesting this test may be a surrogate for longer studies comparing various products.NIDCR-NIH U54 DE14254; Head Start, HRSA 90YD0188/03; and MCHB, HRSA R40MC03622-03

Coastal risk mitigation by green infrastructure in Latin America

This paper aims to highlight the prevailing experiences of Latin America and to clarify what ‘green infrastructure’ entails in addition to describing seven case studies from a range of coastal ecosystems (wetlands, coastal dunes, beaches and coral reefs) at scales varying from local to regional. The case studies are categorised according to their degree of naturalness (nature-based, engineered ecosystems, soft engineering, ecologically enhanced hard infrastructure and de-engineering). Generally, the implementation of green infrastructure projects aims to increase resilience, enhance the provision of ecosystem services, recover biodiversity, reduce the negative effects of hard infrastructure and implement corrective measures. The greatest benefits of these projects relate to the creation of multi-functional spaces, which often combine the above advantages with improved opportunities for recreation and/or economic activities. It is hoped that this paper will disseminate the experience in green infrastructure among academics and practitioners and stimulate wider adoption of green infrastructure projects and good practices

Salivary flow rate, pH, and concentrations of calcium, phosphate, and sIgA in Brazilian pregnant and non-pregnant women

BACKGROUND: Studies on salivary variables and pregnancy in Latin America are scarce. This study aimed to compare salivary flow rate, pH, and concentrations of calcium, phosphate, and sIgA of unstimulated whole saliva in pregnant and non-pregnant Brazilians. METHODS: Cross-sectional study. Sample was composed by 22 pregnant and 22 non-pregnant women attending the Obstetrics and Gynecology Clinics, São Lucas Hospital, in Porto Alegre city, South region of Brazil. Unstimulated whole saliva was collected to determine salivary flow rate, pH, and biochemical composition. Data were analyzed by Student t test and ANCOVA (two-tailed α = 0.05). RESULTS: No difference was found for salivary flow rates and concentrations of total calcium and phosphate between pregnant and non-pregnant women (p > 0.05). Pregnant women had lower pH (6.7) than non-pregnant women (7.5) (p < 0.001), but higher sIgA level (118.9 mg/L) than the latter (90.1 mg/L) (p = 0.026). CONCLUSION: Some of the tested variables of unstimulated whole saliva were different between pregnant and non-pregnant Brazilians in this sample. Overall, the values of the tested salivary parameters were within the range of international references of normality

EzArray: A web-based highly automated Affymetrix expression array data management and analysis system

<p>Abstract</p> <p>Background</p> <p>Though microarray experiments are very popular in life science research, managing and analyzing microarray data are still challenging tasks for many biologists. Most microarray programs require users to have sophisticated knowledge of mathematics, statistics and computer skills for usage. With accumulating microarray data deposited in public databases, easy-to-use programs to re-analyze previously published microarray data are in high demand.</p> <p>Results</p> <p>EzArray is a web-based Affymetrix expression array data management and analysis system for researchers who need to organize microarray data efficiently and get data analyzed instantly. EzArray organizes microarray data into projects that can be analyzed online with predefined or custom procedures. EzArray performs data preprocessing and detection of differentially expressed genes with statistical methods. All analysis procedures are optimized and highly automated so that even novice users with limited pre-knowledge of microarray data analysis can complete initial analysis quickly. Since all input files, analysis parameters, and executed scripts can be downloaded, EzArray provides maximum reproducibility for each analysis. In addition, EzArray integrates with Gene Expression Omnibus (GEO) and allows instantaneous re-analysis of published array data.</p> <p>Conclusion</p> <p>EzArray is a novel Affymetrix expression array data analysis and sharing system. EzArray provides easy-to-use tools for re-analyzing published microarray data and will help both novice and experienced users perform initial analysis of their microarray data from the location of data storage. We believe EzArray will be a useful system for facilities with microarray services and laboratories with multiple members involved in microarray data analysis. EzArray is freely available from <url>http://www.ezarray.com/</url>.</p

Genome-Wide Binding Map of the HIV-1 Tat Protein to the Human Genome

The HIV-1 Trans-Activator of Transcription (Tat) protein binds to multiple host cellular factors and greatly enhances the level of transcription of the HIV genome. While Tat's control of viral transcription is well-studied, much less is known about the interaction of Tat with the human genome. Here, we report the genome-wide binding map of Tat to the human genome in Jurkat T cells using chromatin immunoprecipitation combined with next-generation sequencing. Surprisingly, we found that ∼53% of the Tat target regions are within DNA repeat elements, greater than half of which are Alu sequences. The remaining target regions are located in introns and distal intergenic regions; only ∼7% of Tat-bound regions are near transcription start sites (TSS) at gene promoters. Interestingly, Tat binds to promoters of genes that, in Jurkat cells, are bound by the ETS1 transcription factor, the CBP histone acetyltransferase and/or are enriched for histone H3 lysine 4 tri-methylation (H3K4me3) and H3K27me3. Tat binding is associated with genes enriched with functions in T cell biology and immune response. Our data reveal that Tat's interaction with the host genome is more extensive than previously thought, with potentially important implications for the viral life cycle

Response of Coastal Fishes to the Gulf of Mexico Oil Disaster

The ecosystem-level impacts of the Deepwater Horizon disaster have been largely unpredictable due to the unique setting and magnitude of this spill. We used a five-year (2006–2010) data set within the oil-affected region to explore acute consequences for early-stage survival of fish species inhabiting seagrass nursery habitat. Although many of these species spawned during spring-summer, and produced larvae vulnerable to oil-polluted water, overall and species-by-species catch rates were high in 2010 after the spill (1,989±220 fishes km-towed−1 [μ ± 1SE]) relative to the previous four years (1,080±43 fishes km-towed−1). Also, several exploited species were characterized by notably higher juvenile catch rates during 2010 following large-scale fisheries closures in the northern Gulf, although overall statistical results for the effects of fishery closures on assemblage-wide CPUE data were ambiguous. We conclude that immediate, catastrophic losses of 2010 cohorts were largely avoided, and that no shifts in species composition occurred following the spill. The potential long-term impacts facing fishes as a result of chronic exposure and delayed, indirect effects now require attention