Improving the reliability of the jpHMM recombination prediction in HIV

Accurate classification of HIV and the identification of recombinants, including precise breakpoint definitions, is of crucial importance for epidemiological monitoring and the design of potential drugs. Recently we developed jpHMM, a new method to detect recombinations in HIV-l genomes. jpHMM predicts phylogenetic recombination breakpoints in a query sequence and assigns to each segment of the sequence one of the major HIV-l subtypes. For the user the reliability of the predicted breakpoint positions and parental subtypes is most important. For this reason we extended the output of jpHMM to include the information on regions where the model is 'uncertain' about the parental subtype and an interval estimate of the breakpoint. This information is determined using the posterior probabilities of the subtypes at each query sequence position

Ruler elements in chromatin remodelers set nucleosome array spacing and phasing

Arrays of regularly spaced nucleosomes dominate chromatin and are often phased by alignment to reference sites like active promoters. How the distances between nucleosomes (spacing), and between phasing sites and nucleosomes are determined remains unclear, and specifically, how ATP-dependent chromatin remodelers impact these features. Here, we used genome-wide reconstitution to probe how Saccharomyces cerevisiae ATP-dependent remodelers generate phased arrays of regularly spaced nucleosomes. We find that remodelers bear a functional element named the ‘ruler’ that determines spacing and phasing in a remodeler-specific way. We use structure-based mutagenesis to identify and tune the ruler element residing in the Nhp10 and Arp8 modules of the INO80 remodeler complex. Generally, we propose that a remodeler ruler regulates nucleosome sliding direction bias in response to (epi)genetic information. This finally conceptualizes how remodeler-mediated nucleosome dynamics determine stable steady-state nucleosome positioning relative to other nucleosomes, DNA bound factors, DNA ends and DNA sequence elements

jpHMM: Improving the reliability of recombination prediction in HIV-1

Previously, we developed jumping profile hidden Markov model (jpHMM), a new method to detect recombinations in HIV-1 genomes. The jpHMM predicts recombination breakpoints in a query sequence and assigns to each position of the sequence one of the major HIV-1 subtypes. Since incorrect subtype assignment or recombination prediction may lead to wrong conclusions in epidemiological or vaccine research, information about the reliability of the predicted parental subtypes and breakpoint positions is valuable. For this reason, we extended the output of jpHMM to include such information in terms of ‘uncertainty’ regions in the recombination prediction and an interval estimate of the breakpoint. Both types of information are computed based on the posterior probabilities of the subtypes at each query sequence position. Our results show that this extension strongly improves the reliability of the jpHMM recombination prediction. The jpHMM is available online at http://jphmm.gobics.de/

Effect of Lactobacillus plantarum Fermentation on the Surface and Functional Properties of Pea Protein-Enriched Flour

Istražen je utjecaj fermentacije s pomoću Lactobacillus plantarum na funkcionalna i fizikalno-kemijska svojstva brašna graška obogaćenog proteinima. Tijekom fermentacije povećavao se stupanj hidrolize do maksimuma od 13,5 % nakon 11 h. Prije mjerenja površinske hidrofobnosti i naboja te ispitivanja funkcionalnih svojstava podešena je pH-vrijednost fermentiranog brašna na pH=4 ili 7. Pri pH=4 površinski naboj, mjeren pomoću zeta potencijala, povećao se s +14 na +27 mV nakon 1 h fermentacije, a zatim smanjio na +10 mV nakon 11 h, dok se pri pH=7 naboj postepeno povećavao s -37 na -27 mV tijekom fermentacije. Površinska hidrofobnost znatno se smanjila tijekom fermentacije pri pH=4, dok se pri pH=7 neznatno smanjila. Kapacitet pijenjenja bio je najveći u emulziji brašna fermentiranog tijekom 5 h pri pH=4, dok je stabilnost pjene bila niska pri obje pH-vrijednosti u svim uzorcima. Emulgirajuća svojstva naglo su se smanjila nakon 5 h fermentacije pri pH=4, a stabilnost emulzija poboljšala se nakon 5 h fermentacije pri pH=7, u usporedbi s kontrolom. Sposobnost vezivanja ulja povećala se s 1,8 g/g pri 0 h na 3,5 g/g nakon 11 h fermentacije, a vode smanjila nakon 5 h, te zatim povećala nakon 9 h fermentacije. Rezultati pokazuju da se fermentacijom brašna graška obogaćenog proteinima mogu mijenjati njegova svojstva te na taj način proizvesti novi funkcionalni sastojci.The effect of Lactobacillus plantarum fermentation on the functional and physicochemical properties of pea protein-enriched flour (PPF) was investigated. Over the course of the fermentation the extent of hydrolysis increased continuously until reaching a maximum degree of hydrolysis of 13.5 % after 11 h. The resulting fermented flour was then adjusted to either pH=4 or 7 prior to measuring the surface and functional attributes as a function of fermentation time. At pH=4 surface charge, as measured by zeta potential, initially increased from +14 to +27 mV after 1 h of fermentation, and then decreased to +10 mV after 11 h; whereas at pH=7 the charge gradually increased from –37 to –27 mV over the entire fermentation time. Surface hydrophobicity significantly increased at pH=4 as a function of fermentation time, whereas at pH=7 fermentation induced only a slight decrease in PPF surface hydrophobicity. Foam capacity was highest at pH=4 using PPF fermented for 5 h whereas foam stability was low at both pH values for all samples. Emulsifying activity sharply decreased after 5 h of fermentation at pH=4. Emulsion stability improved at pH=7 after 5 h of fermentation as compared to the control. Oil-holding capacity improved from 1.8 g/g at time 0 to 3.5 g/g by the end of 11 h of fermentation, whereas water hydration capacity decreased after 5 h, then increased after 9 h of fermentation. These results indicate that the fermentation of PPF can modify its properties, which can lead towards its utilization as a functional food ingredient

HIV Types, Groups, Subtypes and Recombinant Forms: Errors in Replication, Selection Pressure and Quasispecies

HIV-1 is a chimpanzee virus which was transmitted to humans by several zoonotic events resulting in infection with HIV-1 groups M P, and in parallel transmission events from sooty mangabey monkey viruses leading to infections with HIV-2 groups A H. Both viruses have circulated in the human population for about 80 years. In the infected patient, HIV mutates, and by elimination of some of the viruses by the action of the immune system individual quasispecies are formed. Along with the selection of the fittest viruses, mutation and recombination after superinfection with HIV from different groups or subtypes have resulted in the diversity of their patterns of geographic distribution. Despite the high variability observed, some essential parts of the HIV genome are highly conserved. Viral diversity is further facilitated in some parts of the HIV genome by drug selection pressure and may also be enhanced by different genetic factors, including HLA in patients from different regions of the world. Viral and human genetic factors influence pathogenesis. Viral genetic factors are proteins such as Tat, Vif and Rev. Human genetic factors associated with a better clinical outcome are proteins such as APOBEC, langerin, tetherin and chemokine receptor 5 (CCR5) and HLA B27, B57, DRB1{*}1303, KIR and PARD3B. Copyright (C) 2012 S. Karger AG, Base

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

<p>Abstract</p> <p>Background</p> <p>With next-generation sequencing technologies, experiments that were considered prohibitive only a few years ago are now possible. However, while these technologies have the ability to produce enormous volumes of data, the sequence reads are prone to error. This poses fundamental hurdles when genetic diversity is investigated.</p> <p>Results</p> <p>We developed ShoRAH, a computational method for quantifying genetic diversity in a mixed sample and for identifying the individual clones in the population, while accounting for sequencing errors. The software was run on simulated data and on real data obtained in wet lab experiments to assess its reliability.</p> <p>Conclusions</p> <p>ShoRAH is implemented in C++, Python, and Perl and has been tested under Linux and Mac OS X. Source code is available under the GNU General Public License at <url>http://www.cbg.ethz.ch/software/shorah</url>.</p

Effect of Fermentation on the Protein Digestibility and Levels of Non-Nutritive Compounds of Pea Protein Concentrate

Radi utvrđivanja utjecaja fermentacije na kakvoću proteina u koncentratu proteina graška ispitani su sljedeći parametri: udjel ukupnih fenola i tanina, aktivnost inhibitora proteaze, sastav aminokiselina i probavljivost proteina in vitro nakon 11 sati fermentacije s pomoću bakterije Lactobacillus plantarum. Maseni se udjel fenola u koncentratu proteina graška, izražen kao ekvivalent katehina, povećao na bazi suhe tvari s 2,5 pri 0 h na 4,9 mg/g nakon 11 sati fermentacije. Udjel tanina se povećao s 0,14 pri 0 h na maksimalnih 0,96 mg/g koncentrata nakon 5 h fermentacije, a zatim se smanjio na 0,79 mg/g nakon 11 h fermentacije. Nakon 9 h fermentacije smanjila se aktivnost inhibitora tripsina, međutim, pri svim ostalim vremenima fermentacije dobivene su vrijednosti slične onima pri 0 h. Aktivnost se inhibitora kimotripsina smanjila s 3,7 na 1,1 jedinicu inhibicije kimotripsina po mg nakon 11 sati fermentacije. Probavljivost je proteina dosegla maksimalnu vrijednost od 87,4 % nakon 5 sati fermentacije, međutim vrijednost aminokiselina koje sadržavaju sumpor smanjila se s 0,84 pri 0 h na 0,66 nakon 11 h fermentacije. Smanjenjem udjela sumpora promijenila se vrijednost aminokiselina korigirana probavljivošću proteina in vitro s 67,0 pri 0 h na 54,6 % nakon 11 h fermentacije. Dobiveni podaci potvrđuju da je, iako je fermentacija valjana metoda za smanjenje udjela nekih nenutritivnih sastojaka u koncentratu proteina graška, potrebno odabrati odgovarajuće bakterije koje nemaju izraženu sposobnost razgradnje aminokiselina što sadržavaju sumpor.In order to determine the impact of fermentation on protein quality, pea protein concentrate (PPC) was fermented with Lactobacillus plantarum for 11 h and total phenol and tannin contents, protease inhibitor activity, amino acid composition and in vitro protein digestibility were analyzed. Phenol levels, expressed as catechin equivalents (CE), increased on dry mass basis from 2.5 at 0 h to 4.9 mg CE per 1 g of PPC at 11 h. Tannin content rose from 0.14 at 0 h to a maximum of 0.96 mg CE per 1 g of PPC after 5 h, and thereafter declined to 0.79 mg/g after 11 h. After 9 h of fermentation trypsin inhibitor activity decreased, however, at all other fermentation times similar levels to the PPC at time 0 h were produced. Chymotrypsin inhibitor activity decreased from 3.7 to 1.1 chymotrypsin inhibitory units (CIU) per mg following 11 h of fermentation. Protein digestibility reached a maximum (87.4 %) after 5 h of fermentation, however, the sulfur amino acid score was reduced from 0.84 at 0 h to 0.66 at 11 h. This reduction in sulfur content altered the in vitro protein digestibility-corrected amino acid score from 67.0 % at 0 h to 54.6 % at 11 h. These data suggest that while fermentation is a viable method of reducing certain non-nutritive compounds in pea protein concentrate, selection of an alternative bacterium which metabolises sulfur amino acids to a lesser extent than L. plantarum should be considered