Cell-Type-Specific Cytokinin Distribution within the Arabidopsis Primary Root Apex

Cytokinins (CKs) play a crucial role in many physiological and developmental processes at the levels of individual plant components (cells, tissues, and organs) and by coordinating activities across these parts. High-resolution measurements of intracellular CKs in different plant tissues can therefore provide insights into their metabolism and mode of action. Here, we applied fluorescence-activated cell sorting of green fluorescent protein (GFP)-marked cell types, combined with solid-phase microextraction and an ultra-high-sensitivity mass spectrometry (MS) method for analysis of CK biosynthesis and homeostasis at cellular resolution. This method was validated by series of control experiments, establishing that protoplast isolation and cell sorting procedures did not greatly alter endogenous CK levels. The MS-based method facilitated the quantification of all the well known CK isoprenoid metabolites in four different transgenic Arabidopsis thaliana lines expressing GFP in specific cell populations within the primary root apex. Our results revealed the presence of a CK gradient within the Arabidopsis root tip, with a concentration maximum in the lateral root cap, columella, columella initials, and quiescent center cells. This distribution, when compared with previously published auxin gradients, implies that the well known antagonistic interactions between the two hormone groups are cell type specific

Structure of S. aureus HPPK and discovery of a new inhibitor

The first structural and biophysical data on the folate pathway enzyme and drug target, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK), from the pathogenic bacterium Staphylococcus aureus is presented. HPPK is the second essential enzyme in the folate biosynthesis pathway, responsible for catalysing pyrophosphoryl transfer from cofactor (ATP) to the substrate (6-hydroxymethyl- 7,8-dihydropterin, HMDP). In-silico screening led to the discovery of a substrate competitive inhibitor, San1, which was subsequently co-crystallised with HPPK. A 1.65 Å resolution x-ray structure showed this to bind at the pterin site sharing many of the key intermolecular interactions of the substrate. ITC and SPR measurements yielded an equilibrium binding constant, Kd, of ~13 μM for San1. An IC50 of ~12 μM was determined by means of a new convenient tri-enzyme-coupled spectrophotometric assay. ITC and SPR further showed that the San1 inhibitor has no requirement for magnesium or ATP cofactor for competitive binding to the substrate site. According to 15N heteronuclear NMR measurements, the fast motion of the pterin loop (L2) is partially dampened in the ternary complex between SaHPPK, HMDP and , -methylene adenosine 5-triphosphate (AMPCPP), but the ATP loop (L3) remains mobile on the μs timescale. In contrast, for the SaHPPK/San1/AMPCPP ternary complex, loop L2 becomes rigid on the fast timescale and loop L3 becomes more ordered which are supported by a large entropic penalty associated with San1 binding as revealed by ITC. Backbone assignments and chemical shift perturbations implicate the sulphur in San1 as a likely important loop L2/L3 stabilizing mediato

Uncertainty-Informed Deep Learning Models Enable High-Confidence Predictions for Digital Histopathology

A model's ability to express its own predictive uncertainty is an essential attribute for maintaining clinical user confidence as computational biomarkers are deployed into real-world medical settings. In the domain of cancer digital histopathology, we describe a novel, clinically-oriented approach to uncertainty quantification (UQ) for whole-slide images, estimating uncertainty using dropout and calculating thresholds on training data to establish cutoffs for low- and high-confidence predictions. We train models to identify lung adenocarcinoma vs. squamous cell carcinoma and show that high-confidence predictions outperform predictions without UQ, in both cross-validation and testing on two large external datasets spanning multiple institutions. Our testing strategy closely approximates real-world application, with predictions generated on unsupervised, unannotated slides using predetermined thresholds. Furthermore, we show that UQ thresholding remains reliable in the setting of domain shift, with accurate high-confidence predictions of adenocarcinoma vs. squamous cell carcinoma for out-of-distribution, non-lung cancer cohorts

Evidence for a new resonance and search for the Y(4140) in γγ→ϕJ/ψ\gamma \gamma \to \phi J/\psi

The process \gamma \gamma \to \phi \jpsi is measured for \phi \jpsi masses between threshold and 5 GeV/${\it c}^2$, using a data sample of 825 fb$^{-1}$ collected with the Belle detector. A narrow peak of $8.8^{+4.2}_{-3.2}$ events, with a significance of 3.2 standard deviations including systematic uncertainty, is observed. The mass and natural width of the structure (named X(4350)) are measured to be $(4350.6^{+4.6}_{-5.1}(\rm{stat})\pm 0.7(\rm{syst})) \hbox{MeV}/{\it c}^2$ and $(13^{+18}_{-9}(\rm{stat})\pm 4(\rm{syst})) \hbox{MeV}$, respectively. The product of its two-photon decay width and branching fraction to \phi\jpsi is $(6.7^{+3.2}_{-2.4}(\rm{stat}) \pm 1.1(\rm{syst})) \hbox{eV}$ for $J^P=0^+$, or $(1.5^{+0.7}_{-0.6}(\rm{stat}) \pm 0.3(\rm{syst})) \hbox{eV}$ for $J^P=2^+$. No signal for the Y(4140)\to \phi \jpsi structure reported by the CDF Collaboration in B\to K^+ \phi \jpsi decays is observed, and limits of \Gamma_{\gamma \gamma}(Y(4140)) \BR(Y(4140)\to\phi \jpsi)<41 \hbox{eV} for $J^P=0^+$ or $<6.0 \hbox{eV}$ for $J^P=2^+$ are determined at the 90% C.L. This disfavors the scenario in which the Y(4140) is a $D_{s}^{\ast+} {D}_{s}^{\ast-}$ molecule.Comment: 9 pages, 3 figures, publication in Phys. Rev. Lett. 104, 112004, 201

Bounds on the width, mass difference and other properties of X(3872) --> pi+pi-J/psi decays

We present results from a study of X(3872) --> pi+pi- J/psi decays produced via exclusive B--> K X(3872) decays. We determine the mass to be M_X(3872)= (3871.84\pm 0.27 (stat)\pm 0.19 (syst)) MeV, a 90% CL upper limit on the natural width of Gamma_X(3872) K+X(3872))xBf(X(3872)-->pi+pi-J/psi)=(8.61 \pm 0.82(stat) \pm 0.52 (syst)) x10^{-6}, and a ratio of branching fractions Bf(B0--> K0 X(3872))/BF(B+--> K+ X(3872))=0.50\pm 0.14(stat)\pm0.04(syst). The difference in mass between the X(3872)-->pi+pi-J/psi signals in B+ and B0 decays is Delta M_{X(3872)= (-0.69 \pm 0.97 (stat)} \pm 0.19 (syst)) MeV. A search for a charged partner of the X(3872) in the decays Bbar0-->K- X+ or B+-->K0X+, X+-->pi+pi0 J/psi resulted in upper limits on the product branching fractions for these processes that are well below expectations for the case that the X(3872) is the neutral member of an isospin triplet. In addition, we examine possible J^{PC} quantum number assignments for the X(3872) based on comparisons of angular correlations between final state particles in X(3872)-->pi+pi-J/psi decays with simulated data for J^{PC} values of 1^{++} and 2^{-+}. We examine the influence of rho-omega interference in the M(pi+pi-) spectrum. The analysis is based on a 711fb^{-1} data sample that contains 772 million BBbar meson pairs collected at the Upsilon(4S) resonance in the Belle detector at the KEKB e+e- collider.Comment: 15 pages, 10 figures and 6 tables. Submitted to Physical Review

Search for CP violation in tau -> K^0_S pi nu_tau decays at Belle

We report on a search for CP violation in tau -> K^0_S pi nu_tau decays using a data sample of 699 fb^{-1} collected in the Belle experiment at the KEKB electron-positron asymmetric-energy collider. The CP asymmetry is measured in four bins of the invariant mass of the K^0_S pi system and found to be compatible with zero with a precision of O(10^{-3}) in each mass bin. Limits for the CP violation parameter Im(eta_S) are given at a 90 % confidence level. These limits are |Im(eta_S)|<0.026 or better, depending on the parameterization used to describe the hadronic form factors and improve upon previous limits by one order of magnitude

Observation of X(3872)→J/ψγX(3872)\to J/\psi \gamma and search for X(3872)→ψ′γX(3872)\to\psi'\gamma in B decays

We report a study of $B\to (J/\psi \gamma) K$ and $B\to (\psi' \gamma)K$ decay modes using $772\times 10^{6}$ $B\bar{B}$ events collected at the \Upsilon(4S)$resonance with the Belle detector at the KEKB energy-asymmetric$e^+ e^-$collider. We observe$X(3872) \to J/\psi \gamma$and report the first evidence for$\chi_{c2} \to J/\psi \gamma$in$B\to (X_{c\bar{c}}\gamma) K$decays, while in a search for$X(3872) \to \psi' \gamma$no significant signal is found. We measure the branching fractions,$\mathcal{B}(B^{\pm} \to X(3872) K^{\pm}) \mathcal{B}(X(3872) \to J/\psi\gamma)$$=$$(1.78^{+0.48}_{-0.44}\pm 0.12)\times 10^{-6}$,$\mathcal{B} (B^{\pm} \to\chi_{c2} K^{\pm})$$=$$(1.11^{+0.36}_{-0.34} \pm 0.09) \times 10^{-5}$,$\mathcal{B}(B^{\pm} \to X(3872) K^{\pm}) \mathcal{B}(X(3872) \to \psi'\gamma)$$<$$3.45\times 10^{-6}$ (upper limit at 90% C.L.) and also provide upper limits for other searches.Comment: 6 pages, 3 figure

Search for charmonium and charmonium-like states in \Upsilon(2S) radiative decays

Using a sample of 158 million \Upsilon(2S) events collected with the Belle detector, charmonium and charmonium-like states with even charge parity are searched for in \Upsilon(2S) radiative decays. No significant \chi_{cJ} or \eta_c signal is observed and the following upper limits at 90% confidence level (C.L.) are obtained: BR(\Upsilon(2S)\to \gamma \chi_{c0})< 1.0 \times 10^{-4}, BR(\Upsilon(2S) \to \gamma \chi_{c1})<3.6 \times 10^{-6}, BR(\Upsilon(2S) \to \gamma \chi_{c2})<1.5 \times 10^{-5}, and BR(\Upsilon(2S) \to \gamma \eta_c)< 2.7 \times 10^{-5}. No significant signal of any charmonium-like state is observed, and we obtain the limits \BR(\Upsilon(2S)\to \gamma X(3872))\times\BR(X(3872)\to\pi^+\pi^-J/\psi)< 0.8 \times 10^{-6}, BR(\Upsilon(2S) \to \gamma X(3872))\times BR(X(3872)\to\pi^+\pi^-\pi^0 J/\psi)< 2.4\times 10^{-6}, BR(\Upsilon(2S) \to \gamma X(3915))\times BR(X(3915)\to\omega J/\psi)< 2.8\times 10^{-6}, BR(\Upsilon(2S) \to \gamma Y(4140))\times BR(Y(4140)\to\phi J/\psi)) < 1.2\times 10^{-6}, and BR(\Upsilon(2S) \to \gamma X(4350))\times BR(X(4350)\to\phi J/\psi))< 1.3\times 10^{-6} at 90% C.L.Comment: 7 pages, 6 figures, 1 tabl