Influence of pH adjustment on physicochemical properties of microfiltration retentates of skim milk and rehydration properties of resulting powders

Effects of pH adjustment on physicochemical properties of microfiltration retentates of skim milk and rehydration of resulting micellar casein concentrate (MCC) powders were investigated. Aliquots of retentate (pH 6.9) were adjusted to pH 7.3, 7.6 or 7.6 followed by readjustment to pH 6.9 (6.9R) prior to powder preparation. The retentates with pH 6.9, 7.3, and 7.6 had casein micelle size of 179, 189 and 197 nm, respectively, while sample 6.9R had size of 183 nm, similar to retentate at pH 6.9. Higher retentate pH resulted in lower ionic calcium and higher conductivity, with sample 6.9R having higher values for both parameters than the pH 6.9 sample. The MCC powders displayed poorer wettability and enhanced dispersibility with increasing retentate pH. Interestingly, the 6.9R powder had the best wettability and dispersibility. This study demonstrated that pH-mediated modifications of the physicochemical properties of retentates improve the rehydration properties of resultant MCC powders

Evolution of allostery in the cyclic nucleotide binding module

Analysis of cyclic nucleotide binding (CNB) domains shows that they have evolved to sense a wide variety of second messenger signals; a mechanism for allosteric regulation by CNB domains is proposed

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

BACKGROUND: Most of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of species. METHODOLOGY/PRINCIPAL FINDINGS: We designed and implemented new methods for analyzing metagenomic data and used them to search the Global Ocean Sampling (GOS) expedition data set for novel lineages in three gene families commonly used in phylogenetic studies of known and unknown organisms: small subunit rRNA and the recA and rpoB superfamilies. Though the methods available could not accurately identify very deeply branched ss-rRNAs (largely due to difficulties in making robust sequence alignments for novel rRNA fragments), our analysis revealed the existence of multiple novel branches in the recA and rpoB gene families. Analysis of available sequence data likely from the same genomes as these novel recA and rpoB homologs was then used to further characterize the possible organismal source of the novel sequences. CONCLUSIONS/SIGNIFICANCE: Of the novel recA and rpoB homologs identified in the metagenomic data, some likely come from uncharacterized viruses while others may represent ancient paralogs not yet seen in any cultured organism. A third possibility is that some come from novel cellular lineages that are only distantly related to any organisms for which sequence data is currently available. If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them

Combined thickness of uterus and placenta, foetal heart rate oscillations and progesterone concentration in last week of canine gestation

This study aimed to evaluate the combined thickness of uterus and placenta, foetal heart rate and serum progesterone concentration in prepartum bitches. Eighteen pregnant female dogs in the last week of gestation were subjected to ultrasonographic examination and progesterone assay to evaluate changes prior to impending whelping. No significant difference was found in the combined thickness of uterus and placenta measurements in the last week of gestation. However, foetal heart rate showed oscillations and progesterone declined 12h prior to whelping

Armed to Farm: Developing Training Programs For Military Veterans in Agriculture

Farming offers a viable avenue for returning veterans to transition into society and capitalizes on skills that made them successful in the military. However, these opportunities may be missed due to a lack of targeted training programs, guidance, and information for the veteran community. Programs directed toward educating beginning farmers, along with increased awareness and demand for local food production, have provided an opportunity for individuals interested in farming. However, few programs have focused on the needs of veterans interested in agriculture. Since 2007, our team has directly supported approximately 300 veterans interested in farming through workshops, internships, research, and training opportunities and an additional 650 veterans nationally through the Farmer Veteran Coalition. As more programs develop for veterans in agricultural disciplines, we believe lessons learned from our partnership with veterans may be beneficial to those working with this population of farmers

Library preparation methodology can influence genomic and functional predictions in human microbiome research.

Observations from human microbiome studies are often conflicting or inconclusive. Many factors likely contribute to these issues including small cohort sizes, sample collection, and handling and processing differences. The field of microbiome research is moving from 16S rDNA gene sequencing to a more comprehensive genomic and functional representation through whole-genome sequencing (WGS) of complete communities. Here we performed quantitative and qualitative analyses comparing WGS metagenomic data from human stool specimens using the Illumina Nextera XT and Illumina TruSeq DNA PCR-free kits, and the KAPA Biosystems Hyper Prep PCR and PCR-free systems. Significant differences in taxonomy are observed among the four different next-generation sequencing library preparations using a DNA mock community and a cell control of known concentration. We also revealed biases in error profiles, duplication rates, and loss of reads representing organisms that have a high %G+C content that can significantly impact results. As with all methods, the use of benchmarking controls has revealed critical differences among methods that impact sequencing results and later would impact study interpretation. We recommend that the community adopt PCR-free-based approaches to reduce PCR bias that affects calculations of abundance and to improve assemblies for accurate taxonomic assignment. Furthermore, the inclusion of a known-input cell spike-in control provides accurate quantitation of organisms in clinical samples

A comparative study of mutation screening of sarcomeric genes (MYBPC3, MYH7, TNNT2) using single gene approach versus targeted gene panel next generation sequencing in a cohort of HCM patients in Egypt

Background: NGS enables simultaneous sequencing of large numbers of associated genes in genetic heterogeneous disorders, in a more rapid and cost-effective manner than traditional technologies. However there have been limited direct comparisons between NGS and more established technologies to assess the sensitivity and false negative rates of this new approach. The scope of the present manuscript is to compare variants detected in MYBPC3, MYH7 and TNNT2 genes using the stepwise dHPLC/ Sanger versus targeted NGS.Methods: In this study, we have analysed a group of 150 samples of patients from the Bibliotheca Alexandrina-Aswan Heart Centre National HCM program. The genetic testing was simultaneously undertaken by high throughput denaturing high-performance liquid chromatography (dHPLC) followed by Sanger based sequencing and targeted next generation deep sequencing using panel of inherited cardiac genes (ICC). The panel included over 100 genes including the 3 sarcomeric genes. Analysis of the sequencing data of the 3 genes was undertaken in a double blinded strategy.Results: NGS analysis detected all pathogenic and likely pathogenic variants identified by dHPLC (50 in total, some samples had double hits). There was a 0% false negative rate for NGS based analysis. Nineteen variants were missed by dHPLC and detected by NGS, thus increasing the diagnostic yield in this co- analysed cohort from 22.0% (33/150) to 31.3% (47/150). Of interest to note that the mutation spectrum in this Egyptian HCM population revealed a high rate of homozygosity in MYBPC3 and MYH7 genes in comparison to other population studies (6/150, 4%). None of the homozygous samples were detected by dHPLC analysis.Conclusion: NGS provides a useful and rapid tool to allow panoramic screening of several genes simultaneously with a high sensitivity rate amongst genes of known etiologic role allowing high throughput analysis of HCM patients and relevant control series in a less characterised population

The landscape model: a model for exploring trade-offs between agricultural production and the environment

We describe a model framework that simulates spatial and temporal interactions in agricultural landscapes and that can be used to explore trade-offs between production and environment so helping to determine solutions to the problems of sustainable food production. Here we focus on models of agricultural production, water movement and nutrient flow in a landscape. We validate these models against data from two long-term experiments, (the first a continuous wheat experiment and the other a permanent grass-land experiment) and an experiment where water and nutrient flow are measured from isolated catchments. The model simulated wheat yield (RMSE 20.3–28.6%), grain N (RMSE 21.3–42.5%) and P (RMSE 20.2–29% excluding the nil N plots), and total soil organic carbon particularly well (RMSE 3.1 − 13.8 %), the simulations of water flow were also reasonable (RMSE 180.36 and 226.02%). We illustrate the use of our model framework to explore trade-offs between production and nutrient losses