Padrão de pastejo de fêmeas de corte em campo nativo no Sul do Brasil.

JAI

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution

Chromosomal instability (CIN) and somatic copy-number alterations (SCNA) play a key role in the evolutionary process that shapes cancer genomes. SCNAs comprise many classes of clinically relevant events, such as localised amplifications, gains, losses, loss-of-heterozygosity (LOH) events, and recently discovered parallel evolutionary events revealed by multi-sample phasing. These events frequently appear jointly with whole genome doubling (WGD), a transformative event in tumour evolution involving tetraploidization of genomes preceded or followed by individual chromosomal copy-number changes and associated with an overall increase in structural CIN. While SCNAs have been leveraged for phylogeny reconstruction in the past, existing methods do not take WGD events into account and cannot model parallel evolution. They frequently make use of the infinite sites assumption, do not model horizontal dependencies between adjacent genomic loci and can not infer ancestral genomes. Here we present MEDICC2, a new phylogeny inference algorithm for allele-specific SCNA data that addresses these shortcomings. MEDICC2 dispenses with the infinite sites assumption, models parallel evolution and accurately identifies clonal and subclonal WGD events. It times SCNAs relative to each other, quantifies SCNA burden in single-sample studies and infers phylogenetic trees and ancestral genomes in multi-sample or single-cell sequencing scenarios with thousands of cells. We demonstrate MEDICC2's ability on simulated data, real-world data of 2,778 single sample tumours from the Pan-cancer analysis of whole genomes (PCAWG), 10 bulk multi-region prostate cancer patients and two recent single-cell datasets of triple-negative breast cancer comprising several thousands of single cells

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution

Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome doubling (WGD) play key roles in cancer evolution and provide information for the complex task of phylogenetic inference. We present MEDICC2, a method for inferring evolutionary trees and WGD using haplotype-specific somatic copy-number alterations from single-cell or bulk data. MEDICC2 eschews simplifications such as the infinite sites assumption, allowing multiple mutations and parallel evolution, and does not treat adjacent loci as independent, allowing overlapping copy-number events. Using simulations and multiple data types from 2780 tumors, we use MEDICC2 to demonstrate accurate inference of phylogenies, clonal and subclonal WGD, and ancestral copy-number states

Characterisation of a Novel White Laccase from the Deuteromycete Fungus Myrothecium verrucaria NF-05 and Its Decolourisation of Dyes

A novel ‘white’ laccase was purified from the deuteromycete fungus, Myrothecium verrucaria NF-05, which was a high laccase-producing strain (40.2 U·ml−1 on the thirteenth day during fermentation). SDS-PAGE and native-PAGE revealed a single band with laccase activity corresponding to a molecular weight of approximately 66 kDa. The enzyme had three copper and one iron atoms per protein molecule determined by ICP-AES. Furthermore, both UV/visible and EPR spectroscopy remained silence, indicating the enzyme a novel laccase with new metal compositions of active centre and spectral properties. The N-terminal amino acid sequence of the purified protein was APQISPQYPM. Together with MALDI-TOF analysis, the protein revealed a high homology of the protein with that from reported M. verrucaria. The highest activity was detected at pH 4.0 and at 30°C. The enzyme activity was significantly enhanced by Na+, Mn2+, Cu2+ and Zn2+ while inhibited by DTT, NaN3 and halogen anions. The kinetic constant (Km) showed the enzyme was more affinitive to ABTS than other tested aromatic substrates. Twelve structurally different dyes could be effectively decolourised by the laccase within 10 min. The high production of the strain and novel properties of the laccase suggested its potential for biotechnological applications

Determination of Total Polyphenol Content in Food with the Flow-Injection

U ovom radu predložena je modificirana automatizirana metoda ubrizgavanja u protok za određivanje sadržaja ukupnih polifenola u namirnicama bazirana na Folin-Ciocalteauovoj reakciji u 0,5 mol L-1 NaOH. Metoda omogućuje automatiziranu analizu različitih uzoraka brzinom protoka 55 uzoraka na sat uz upotrebu galne kiseline kao standarda. Primjenom predložene metode na konkretne uzorke (bijelo i crno vino, zeleni, indijski te čaj od lipe, metvice i kamilice i bistri voćni sokovi od crnog ribiza i višnje), određen je njihov “indeks ukupnih polifenola” s većom repetibilnošću za razliku od ranije objavljenih metoda, manje ovisno o razrjeđenju uzorka. U odnosu na “batch” metodu, ova je metoda visoko tolerantna prema najčešćim interferentima (SO2, reducirajući šećeri i askorbinska kiselina). Rezultati dobiveni predloženom metodom pokazali su relativno slaganje s onima dobivenim referentnom Folin-Ciocalteauovom metodom.This paper describes an optimised flow-injection method for the determination of total polyphenol in food based on the Folin-Ciocalteau reaction in 0.5 mol L-1 NaOH. The method allows different types of samples to be analysed automatically at a rate of 55 samples per hour by using gallic acid as standard. By applying the proposed method to real samples (white and red wines, green, Indian, lime-tree, mentha and chamomile teas, and blackberry and cherry juices), their total polyphenol indices were determined with a higher reproducibility than obtained by earlier methods, whatever the dilution used. This method is highly tolerant towards the most common interferences (SO2, reducing sugars, and ascorbic acid) associated with the batch method. The results obtained by the proposed method relatively agree with those obtained using the referent Folin-Ciocalteau method