Current status and trends in forest genomics

Forests are not only the most predominant of the Earth\u27s terrestrial ecosystems, but are also the core supply for essential products for human use. However, global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest degradation. Forest genomics has great potential of increasing forest productivity and adaptation to the changing climate. In the last two decades, the field of forest genomics has advanced quickly owing to the advent of multiple high-throughput sequencing technologies, single cell RNA-seq, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing, and spatial transcriptomes, as well as bioinformatics analysis technologies, which have led to the generation of multidimensional, multilayered, and spatiotemporal gene expression data. These technologies, together with basic technologies routinely used in plant biotechnology, enable us to tackle many important or unique issues in forest biology, and provide a panoramic view and an integrative elucidation of molecular regulatory mechanisms underlying phenotypic changes and variations. In this review, we recapitulated the advancement and current status of 12 research branches of forest genomics, and then provided future research directions and focuses for each area. Evidently, a shift from simple biotechnology-based research to advanced and integrative genomics research, and a setup for investigation and interpretation of many spatiotemporal development and differentiation issues in forest genomics have just begun to emerge

The Protein Partners of GTP Cyclohydrolase I in Rat Organs

GTP cyclohydrolase I (GCH1) is the rate-limiting enzyme for tetrahydrobiopterin biosynthesis and has been shown to be a promising therapeutic target in ischemic heart disease, hypertension, atherosclerosis and diabetes. The endogenous GCH1-interacting partners have not been identified. Here, we determined endogenous GCH1-interacting proteins in rat.A pulldown and proteomics approach were used to identify GCH1 interacting proteins in rat liver, brain, heart and kidney. We demonstrated that GCH1 interacts with at least 17 proteins including GTP cyclohydrolase I feedback regulatory protein (GFRP) in rat liver by affinity purification followed by proteomics and validated six protein partners in liver, brain, heart and kidney by immunoblotting. GCH1 interacts with GFRP and very long-chain specific acyl-CoA dehydrogenase in the liver, tubulin beta-2A chain in the liver and brain, DnaJ homolog subfamily A member 1 and fatty aldehyde dehydrogenase in the liver, heart and kidney and eukaryotic translation initiation factor 3 subunit I (EIF3I) in all organs tested. Furthermore, GCH1 associates with mitochondrial proteins and GCH1 itself locates in mitochondria.GCH1 interacts with proteins in an organ dependant manner and EIF3I might be a general regulator of GCH1. Our finding indicates GCH1 might have broader functions beyond tetrahydrobiopterin biosynthesis

Goodbye Hartmann trial: a prospective, international, multicenter, observational study on the current use of a surgical procedure developed a century ago

Background: Literature suggests colonic resection and primary anastomosis (RPA) instead of Hartmann's procedure (HP) for the treatment of left-sided colonic emergencies. We aim to evaluate the surgical options globally used to treat patients with acute left-sided colonic emergencies and the factors that leading to the choice of treatment, comparing HP and RPA. Methods: This is a prospective, international, multicenter, observational study registered on ClinicalTrials.gov. A total 1215 patients with left-sided colonic emergencies who required surgery were included from 204 centers during the period of March 1, 2020, to May 31, 2020. with a 1-year follow-up. Results: 564 patients (43.1%) were females. The mean age was 65.9 ± 15.6 years. HP was performed in 697 (57.3%) patients and RPA in 384 (31.6%) cases. Complicated acute diverticulitis was the most common cause of left-sided colonic emergencies (40.2%), followed by colorectal malignancy (36.6%). Severe complications (Clavien-Dindo ≥ 3b) were higher in the HP group (P < 0.001). 30-day mortality was higher in HP patients (13.7%), especially in case of bowel perforation and diffused peritonitis. 1-year follow-up showed no differences on ostomy reversal rate between HP and RPA. (P = 0.127). A backward likelihood logistic regression model showed that RPA was preferred in younger patients, having low ASA score (≤ 3), in case of large bowel obstruction, absence of colonic ischemia, longer time from admission to surgery, operating early at the day working hours, by a surgeon who performed more than 50 colorectal resections. Conclusions: After 100 years since the first Hartmann's procedure, HP remains the most common treatment for left-sided colorectal emergencies. Treatment's choice depends on patient characteristics, the time of surgery and the experience of the surgeon. RPA should be considered as the gold standard for surgery, with HP being an exception

Strange hadron production in pp and pPb collisions at √s_(NN) = 5.02 TeV

The transverse momentum (p_T) distributions of Λ, Ξ⁻, and Ω⁻ baryons, their antiparticles, and K⁰_S mesons are measured in proton-proton (pp) and proton-lead (pPb) collisions at a nucleon-nucleon center-of-mass energy of 5.02 TeV over a broad rapidity range. The data, corresponding to integrated luminosities of 40.2 nb⁻¹ and 15.6 μb⁻¹ for pp and pPb collisions, respectively, were collected by the CMS experiment. The nuclear modification factor R_(pPb), which is defined as the ratio of the particle yield in pPb collisions and a scaled pp reference, is measured for each particle. A strong dependence on particle species is observed in the p_T range from 2 to 7 GeV, where R_(pPb) for K⁰_S is consistent with unity, while an enhancement ordered by strangeness content and/or particle mass is observed for the three baryons. In pPb collisions, the strange hadron production is asymmetric about the nucleon-nucleon center-of-mass rapidity. Enhancements, which depend on the particle type, are observed in the direction of the Pb beam. The results are compared with predictions from EPOS LHC, which includes parametrized radial flow. The model is in qualitative agreement with the R_(pPb) data, but fails to describe the dependence on particle species in the yield asymmetries measured away from midrapidity in pPb collisions

Search for Pair-Produced Resonances Each Decaying into at Least Four Quarks in Proton-Proton Collisions at root s=13 TeV

This Letter presents the results of a search for pair-produced particles of masses above 100 GeV that each decay into at least four quarks. Using data collected by the CMS experiment at the LHC in 2015-2016, corresponding to an integrated luminosity of 38.2 fb(-1), reconstructed particles are clustered into two large jets of similar mass, each consistent with four-parton substructure. No statistically significant excess of data over the background prediction is observed in the distribution of average jet mass. Pair-produced squarks with dominant hadronic R-parity-violating decays into four quarks and with masses between 0.10 and 0.72 TeV are excluded at 95% confidence level. Similarly, pair-produced gluinos that decay into five quarks are also excluded with masses between 0.10 and 1.41 TeV at 95% confidence level. These are the first constraints that have been placed on pair-produced particles with masses below 400 GeV that decay into four or five quarks, bridging a significant gap in the coverage of R-parity-violating supersymmetry parameter space.Peer reviewe

Search for the decay of a Higgs boson in the ll gamma channel in proton-proton collisions at root s=13 TeV

A search has been performed for heavy resonances decaying to ZZ or ZW in 2l2q final states, with two charged leptons (l = e, mu) produced by the decay of a Z boson, and two quarks produced by the decay of a W or Z boson. The analysis is sensitive to resonances with masses in the range from 400 to 4500 GeV. Two categories are defined based on the merged or resolved reconstruction of the hadronically decaying vector boson, optimized for high- and low-mass resonances, respectively. The search is based on data collected during 2016 by the CMS experiment at the LHC in proton-proton collisions with a center-of-mass energy of root s = 13 TeV, corresponding to an integrated luminosity of 35.9 fb(-1). No excess is observed in the data above the standard model background expectation. Upper limits on the production cross section of heavy, narrow spin-1 and spin-2 resonances are derived as a function of the resonance mass, and exclusion limits on the production of W' bosons and bulk graviton particles are calculated in the framework of the heavy vector triplet model and warped extra dimensions, respectively.A search has been performed for heavy resonances decaying to ZZ or ZW in 2l2q final states, with two charged leptons (l = e, mu) produced by the decay of a Z boson, and two quarks produced by the decay of a W or Z boson. The analysis is sensitive to resonances with masses in the range from 400 to 4500 GeV. Two categories are defined based on the merged or resolved reconstruction of the hadronically decaying vector boson, optimized for high- and low-mass resonances, respectively. The search is based on data collected during 2016 by the CMS experiment at the LHC in proton-proton collisions with a center-of-mass energy of root s = 13 TeV, corresponding to an integrated luminosity of 35.9 fb(-1). No excess is observed in the data above the standard model background expectation. Upper limits on the production cross section of heavy, narrow spin-1 and spin-2 resonances are derived as a function of the resonance mass, and exclusion limits on the production of W' bosons and bulk graviton particles are calculated in the framework of the heavy vector triplet model and warped extra dimensions, respectively.A search for a Higgs boson decaying into a pair of electrons or muons and a photon is described. Higgs boson decays to a Z boson and a photon (H Z , = e or ), or to two photons, one of which has an internal conversion into a muon pair (H (*) ) were considered. The analysis is performed using a data set recorded by the CMS experiment at the LHC from proton-proton collisions at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 35.9 fb(-1). No significant excess above the background prediction has been found. Limits are set on the cross section for a standard model Higgs boson decaying to opposite-sign electron or muon pairs and a photon. The observed limits on cross section times the corresponding branching fractions vary between 1.4 and 4.0 (6.1 and 11.4) times the standard model cross section for H (*) (H Z ) in the 120-130 GeV mass range of the system. The H (*) and H Z analyses are combined for m(H) =125GeV, obtaining an observed (expected) 95% confidence level upper limit of 3.9 (2.0) times the standard model cross section.Peer reviewe

Measurement of differential cross sections for inclusive isolated-photon and photon+jet production in proton-proton collisions at s=13 TeV\sqrt{s} = 13\,\text {TeV}

Measurements of inclusive isolated-photon and photon+jet production in proton–proton collisions at s √ =13TeV s=13TeV are presented. The analysis uses data collected by the CMS experiment in 2015, corresponding to an integrated luminosity of 2.26fb −1 fb−1 . The cross section for inclusive isolated photon production is measured as a function of the photon transverse energy in a fiducial region. The cross section for photon+jet production is measured as a function of the photon transverse energy in the same fiducial region with identical photon requirements and with the highest transverse momentum jet. All measurements are in agreement with predictions from next-to-leading-order perturbative QCD

Study of the underlying event in top quark pair production in pp collisions at 13 TeV

Measurements of normalized differential cross sections as functions of the multiplicity and kinematic variables of charged-particle tracks from the underlying event in top quark and antiquark pair production are presented. The measurements are performed in proton-proton collisions at a center-of-mass energy of 13<, and are based on data collected by the CMS experiment at the LHC in 2016 corresponding to an integrated luminosity of 35.9fb(-1). Events containing one electron, one muon, and two jets from the hadronization and fragmentation of b quarks are used. These measurements characterize, for the first time, properties of the underlying event in top quark pair production and show no deviation from the universality hypothesis at energy scales typically above twice the top quark mass.Peer reviewe

Azimuthal separation in nearly back-to-back jet topologies in inclusive 2- and 3-jet events in pp{\text {p}} {\text {p}} collisions at s=13 TeV\sqrt{s}=13\,\text {Te}\text {V}

A measurement for inclusive 2- and 3-jet events of the azimuthal correlation between the two jets with the largest transverse momenta, Δϕ 12 Δϕ12 , is presented. The measurement considers events where the two leading jets are nearly collinear (“back-to-back”) in the transverse plane and is performed for several ranges of the leading jet transverse momentum. Proton-proton collision data collected with the CMS experiment at a center-of-mass energy of 13TeV 13TeV and corresponding to an integrated luminosity of 35.9fb −1 35.9fb−1 are used. Predictions based on calculations using matrix elements at leading-order and next-to-leading-order accuracy in perturbative quantum chromodynamics supplemented with leading-log parton showers and hadronization are generally in agreement with the measurements. Discrepancies between the measurement and theoretical predictions are as large as 15%, mainly in the region 177 ∘ <Δϕ 12 <180 ∘. The 2- and 3-jet measurements are not simultaneously described by any of models