Hadronic decays of Higgs boson at NNLO matched with parton shower

We present predictions for hadronic decays of the Higgs boson at next-to-next-to-leading order (NNLO) in QCD matched with parton shower based on the POWHEG framework. Those include decays into bottom quarks with full bottom-quark mass dependence, light quarks, and gluons in the heavy top quark effective theory. Our calculations describe exclusive decays of the Higgs boson with leading logarithmic accuracy in the Sudakov region and next-to-leading order (NLO) accuracy matched with parton shower in the three-jet region, with normalizations fixed to the partial width at NNLO. We estimated remaining perturbative uncertainties taking typical event shape variables as an example and demonstrated the need of future improvements on both parton shower and matrix element calculations. The calculations can be used immediately in evaluations of the physics performances of detector designs for future Higgs factories.Comment: 28 pages, 12 figures; published versio

FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads

The most crucial step in data processing from high-throughput sequencing applications is the accurate and sensitive alignment of the sequencing reads to reference genomes or transcriptomes. The accurate detection of insertions and deletions (indels) and errors introduced by the sequencing platform or by misreading of modified nucleotides is essential for the quantitative processing of the RNA-based sequencing (RNA-Seq) datasets and for the identification of genetic variations and modification patterns. We developed a new, fast and accurate algorithm for nucleic acid sequence analysis, FANSe, with adjustable mismatch allowance settings and ability to handle indels to accurately and quantitatively map millions of reads to small or large reference genomes. It is a seed-based algorithm which uses the whole read information for mapping and high sensitivity and low ambiguity are achieved by using short and non-overlapping reads. Furthermore, FANSe uses hotspot score to prioritize the processing of highly possible matches and implements modified Smith–Watermann refinement with reduced scoring matrix to accelerate the calculation without compromising its sensitivity. The FANSe algorithm stably processes datasets from various sequencing platforms, masked or unmasked and small or large genomes. It shows a remarkable coverage of low-abundance mRNAs which is important for quantitative processing of RNA-Seq datasets

Transfer RNAs Mediate the Rapid Adaptation of Escherichia coli to Oxidative Stress.

Translational systems can respond promptly to sudden environmental changes to provide rapid adaptations to environmental stress. Unlike the well-studied translational responses to oxidative stress in eukaryotic systems, little is known regarding how prokaryotes respond rapidly to oxidative stress in terms of translation. In this study, we measured protein synthesis from the entire Escherichia coli proteome and found that protein synthesis was severely slowed down under oxidative stress. With unchanged translation initiation, this slowdown was caused by decreased translation elongation speed. We further confirmed by tRNA sequencing and qRT-PCR that this deceleration was caused by a global, enzymatic downregulation of almost all tRNA species shortly after exposure to oxidative agents. Elevation in tRNA levels accelerated translation and protected E. coli against oxidative stress caused by hydrogen peroxide and the antibiotic ciprofloxacin. Our results showed that the global regulation of tRNAs mediates the rapid adjustment of the E. coli translation system for prompt adaptation to oxidative stress

De novo diploid genome assembly using long noisy reads

Abstract The high sequencing error rate has impeded the application of long noisy reads for diploid genome assembly. Most existing assemblers failed to generate high-quality phased assemblies using long noisy reads. Here, we present PECAT, a Phased Error Correction and Assembly Tool, for reconstructing diploid genomes from long noisy reads. We design a haplotype-aware error correction method that can retain heterozygote alleles while correcting sequencing errors. We combine a corrected read SNP caller and a raw read SNP caller to further improve the identification of inconsistent overlaps in the string graph. We use a grouping method to assign reads to different haplotype groups. PECAT efficiently assembles diploid genomes using Nanopore R9, PacBio CLR or Nanopore R10 reads only. PECAT generates more contiguous haplotype-specific contigs compared to other assemblers. Especially, PECAT achieves nearly haplotype-resolved assembly on B. taurus (Bison×Simmental) using Nanopore R9 reads and phase block NG50 with 59.4/58.0 Mb for HG002 using Nanopore R10 reads

Lipoprotein FtsB in Streptococcus pyogenes binds ferrichrome in two steps with residues Tyr137 and Trp204 as critical ligands.

Lipoprotein FtsB is a component of the FtsABCD transporter that is responsible for ferrichrome binding and uptake in the Gram-positive pathogen Streptococcus pyogenes. In the present study, FtsB was cloned and purified from the bacteria and its Fch binding characteristics were investigated in detail by using various biophysical and biochemical methods. Based on the crystal structures of homogeneous proteins, FtsB was simulated to have bi-lobal structure forming a deep cleft with four residues in the cleft as potential ligands for Fch binding. With the assistance of site-directed mutagenesis, residue Trp204 was confirmed as a key ligand and Tyr137 was identified to be another essential residue for Fch binding. Kinetics experiments demonstrated that Fch binding in FtsB occurred in two steps, corresponding to the bindings to Tyr137 at N-lobe and Trp204 from C-lobe, respectively, and so that closing the protein conformation. Without either residue Tyr137 or Trp204, Fch binding in the protein as mutants Fch-Y137A and Fch-W204A may have a loose conformation, resembling the apo-proteins in proteolysis resistance and migration behaviors in native gel. This study revealed the inconsistence in the key amino acids among Fch-binding proteins from Gram-positive and -negative bacteria, providing interesting findings for understanding the differences between Gram-positive and -negative bacteria in the mechanism of iron uptake via siderophore (Fch) binding and transport

Protein synthesis measurement under normal condition and oxidative stress using ¹⁵N metabolic labeling and mass spectrometry.

<p>(A) Growth rate constant of <i>E</i>. <i>coli</i> BL21(DE3) cells grown under normal conditions in M9 minimal medium containing ¹⁴NH₄Cl (¹⁴N) or ¹⁵NH₄Cl (¹⁵N). (B) Experimental design for pulse labeling with ¹⁵N under normal and oxidative stress conditions. (C) Bacterial cells were transferred to M9 medium containing ¹⁵N, after which the ¹⁴N/¹⁵N ratio of the <i>E</i>. <i>coli</i> BL21(DE3) proteome was determined by mass spectrometry under normal conditions (upper plot) and oxidative stress induced by exposure to 0.5 mM H₂O₂ (lower plot). The green line indicates the best linear fit of the dataset. The Pearson <i>r</i> correlation coefficient and <i>P</i>-value of the fit are indicated in green text. (D) The same experiment represented in (C) was repeated using the wild-type <i>E</i>. <i>coli</i> BW25113 strain. (E) Examples showing changes in the ¹⁴N/¹⁵N ratio of 4 randomly selected proteins (AtpA, GpmA, Eda, and PurA) in BL21(DE3) cells over time. The fit was determined according to <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005302#pgen.1005302.e008" target="_blank">Eq 6</a> (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005302#sec010" target="_blank">Materials and Methods</a> section). The slope of the linear fit is the synthesis rate constant (<i>k</i>_syn). The black dots indicate the actual data points following protein quantification under normal condition, while the red dots indicate the data points measured under oxidative stress. Linear fits were determined for each dataset, and the Pearson correlation coefficients (<i>r</i>) are indicated in the diagram. (F) The Pearson correlation coefficients (<i>r</i>) values of all proteins were fitted using <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005302#pgen.1005302.e008" target="_blank">Eq 6</a>, under normal condition and oxidative stress. Data generated using the BL21(DE3) and wild-type BW25113 strains are shown. (G) <i>P</i> values (in -log₁₀ scale) of linear fits of all proteins using <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005302#pgen.1005302.e008" target="_blank">Eq 6</a> under normal and oxidative stress conditions. The green line denotes the significance threshold (<i>P</i> = 0.05). The data generated using the BL21(DE3) and wild-type BW25113 strains are shown. (H) Histograms of protein half-lives under normal (blue) and oxidative stress (red) conditions. (I) Comparison of protein half-lives measured under normal and oxidative stress conditions. The grey line is at a 45° angle, which demarks the positions where the protein half-lives were unchanged. Half-lives longer than 500 min are shown as 500 min.</p

Higher tRNA concentrations improve adaptation under oxidative stress.

<p>(A) Cell viability testing results obtained using the PI staining method. <i>E</i>. <i>coli</i> BL21(DE3) cells carrying the empty vector pBAD33 and the pRIL plasmid were tested. A histogram showing cells under 0.5 mM H₂O₂-induced oxidative stress for 15 min was prepared. Cells grown under normal conditions were used as a positive control, and cells killed by incubation at 65°C for 15 min were used as a negative control. (B) Growth rate constants of <i>E</i>. <i>coli</i> BW25113 and BL21(DE3) carrying the pBAD33 and pRIL plasmids, under normal condition. The values shown are the mean ± SD. (C) Growth rate constants of <i>E</i>. <i>coli</i> BW25113 and BL21(DE3) carrying the pBAD33 and pRIL plasmids, under oxidative stress. The actual growth curves of BL21(DE3) carrying these two plasmids are shown respectively. The red line is the moving average observed over 5 min. (D) Cell growth-rate constant under harsh oxidative stress (~1–2 mM H₂O₂). A negative growth rate constant represents the occurrence of cell death. The data shown are the mean ± SD. (E) The growth-rate constant of <i>E</i>. <i>coli</i> BW25113 cells carrying the pBAD33 and pRIL plasmid, cultured in the presence of different concentrations of ciprofloxacin.</p

Under oxidative stress, tRNAs are degraded <i>in vivo</i>, but not in the cell-free <i>in vitro</i> translation system.

<p>(A) Percentages of cleaved tRNA reads. X-axes indicate the number of bases cleaved from the 3′-termini. The Y-axes denote the fraction of such tRNA reads among all tRNA reads relative to each specific tRNA species. Three tRNAs are shown as examples. The observed distributions of the cleavage lengths were compared between normal (blue bars) and oxidative stress conditions (red bars). (B,C) The degradation of full-length tRNA in <i>in vitro</i> translation system. Eleven tRNAs were randomly selected and quantified by qRT-PCR. The difference observed between the oxidative stress and normal conditions are expressed in terms of ΔΔC_T values, normalized using spike-in RNA (B) or 5S rRNA (C). The data are shown as the mean ± SD.</p

Protein biogenesis under oxidative stress.

<p>(A) Polysome profiles under normal and oxidative stress conditions. (B) SufI synthesis in an <i>in vitro</i> translation system, with or without oxidative stress. The SufI gene fused with a C-terminal His₆-tag sequence constructed in a pET-28b plasmid (Novagen) was used as a template in an <i>in vitro</i> translation reaction. The protein product was detected by western blotting with an anti-His₆ antibody. (C) Detergent-insoluble proteins under normal (N) and oxidative stress (OS) conditions. Insoluble proteins extracted from <i>E</i>. <i>coli</i> BL21(DE3) and wild-type BW25113 cells grown at 47°C for 10 min were used as positive controls (Heat). Soluble proteins (Sup) were loaded on the same gel as controls. (D) Western blot analysis of the molecular chaperones GroEL and DnaK in <i>E</i>. <i>coli</i> BL21(DE3) and wild-type BW25113 cells grown under normal (N) conditions, oxidative stress (OS) condition, or heat stress (heat) at 47°C for 30 min.</p