HLA topography enforces shared and convergent immunodominant B cell and antibody alloresponses in transplant recipients.

Donor-specific antibody (DSA) responses against human leukocyte antigen (HLA) proteins mismatched between kidney transplant donors and recipients cause allograft loss. The rules governing the immunogenicity of non-self donor HLA are poorly understood. Using single-cell, molecular, structural, and proteomic techniques, we profiled the HLA-specific B cell response in the kidney and blood of a transplant recipient with antibody-mediated rejection (AMR).

Accuracy and Reliability of Single-Camera Measurements of Ankle Clonus and Quadriceps Hyperreflexia.

Objective: To evaluate the accuracy and reliability of a simple, single-camera smartphone-based method, named the Reflex Tracker (RT) system, for measuring reflex threshold angles related to ankle clonus and quadriceps hyperreflexia.

Design: A prospective comparison study using a high-fidelity reference standard was constructed employing a 2 × 2 × 2 factorial design, with factors of rater (tester) type (student and experienced physical therapist), joint (ankle and knee), and repetition (2 per condition).

Setting: This multicenter study was conducted at 4 outpatient rehabilitation clinics.

New ^{13}C(α,n)^{16}O Cross Section with Implications for Neutrino Mixing and Geoneutrino Measurements.

Precise antineutrino measurements are very sensitive to proper background characterization. We present an improved measurement of the ^{13}C(α,n)^{16}O reaction cross section which constitutes significant background for large ν[over ¯] detectors. We greatly improve the precision and accuracy by utilizing a setup that is sensitive to the neutron energies while making measurements of the excited state transitions via secondary γ-ray detection.

New Measurement of ^{12}C+^{12}C Fusion Reaction at Astrophysical Energies.

Carbon and oxygen burning reactions, in particular, ^{12}C+^{12}C fusion, are important for the understanding and interpretation of the late phases of stellar evolution as well as the ignition and nucleosynthesis in cataclysmic binary systems such as type Ia supernovae and x-ray superbursts. A new measurement of this reaction has been performed at the University of Notre Dame using particle-γ coincidence techniques with SAND (a silicon detector array) at the high-intensity 5U Pelletron accelerator. New results for ^{12}C+^{12}C fusion at low energies relevant to nuclear astrophysics are reported.

Irradiation-induced reactions at the CeO/SiO/Si interface.

The influence of high-energy (1.6 MeV) Ar irradiation on the interfacial interaction between cerium oxide thin films (∼15 nm) with a SiO/Si substrate is investigated using transmission electron microscopy, ultrahigh vacuum x-ray photoelectron spectroscopy (XPS), and a carbon monoxide (CO) oxidation catalytic reaction using ambient pressure XPS. The combination of these methods allows probing the dynamics of vacancy generation and its relation to chemical interactions at the CeO/SiO/Si interface.

Experimental Investigation of the ^{19}Ne(p,γ)^{20}Na Reaction Rate and Implications for Breakout from the Hot CNO Cycle.

The ^{19}Ne(p,γ)^{20}Na reaction is the second step of a reaction chain which breaks out from the hot CNO cycle, following the ^{15}O(α,γ)^{19}Ne reaction at the onset of x-ray burst events. We investigate the spectrum of the lowest proton-unbound states in ^{20}Na in an effort to resolve contradictions in spin-parity assignments and extract reliable information about the thermal reaction rate. The proton-transfer reaction ^{19}Ne(d,n)^{20}Na is measured with a beam of the radioactive isotope ^{19}Ne at an energy around the Coulomb barrier and in inverse kinematics.

The Cystic Fibrosis Transmembrane Conductance Regulator Potentiator Ivacaftor Augments Mucociliary Clearance Abrogating Cystic Fibrosis Transmembrane Conductance Regulator Inhibition by Cigarette Smoke.

Acquired cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction may contribute to chronic obstructive pulmonary disease pathogenesis and is a potential therapeutic target. We sought to determine the acute effects of cigarette smoke on ion transport and the mucociliary transport apparatus, their mechanistic basis, and whether deleterious effects could be reversed with the CFTR potentiator ivacaftor (VX-770). Primary human bronchial epithelial (HBE) cells and human bronchi were exposed to cigarette smoke extract (CSE) and/or ivacaftor.

Rapid algal culture diagnostics for open ponds using multispectral image analysis.

This article presents a multispectral image analysis approach for probing the spectral backscattered irradiance from algal cultures. It was demonstrated how this spectral information can be used to measure algal biomass concentration, detect invasive species, and monitor culture health in real time. To accomplish this, a conventional RGB camera was used as a three band photodetector for imaging cultures of the green alga Chlorella sp.

Secreted proteases control autolysin-mediated biofilm growth of Staphylococcus aureus.

Staphylococcus epidermidis, a commensal of humans, secretes Esp protease to prevent Staphylococcus aureus biofilm formation and colonization. Blocking S. aureus colonization may reduce the incidence of invasive infectious diseases; however, the mechanism whereby Esp disrupts biofilms is unknown.

Structure of Streptococcus agalactiae tip pilin GBS104: a model for GBS pili assembly and host interactions.

The crystal structure of a 75 kDa central fragment of GBS104, a tip pilin from the 2063V/R strain of Streptococcus agalactiae (group B streptococcus; GBS), is reported. In addition, a homology model of the remaining two domains of GBS104 was built and a model of full-length GBS104 was generated by combining the homology model (the N1 and N4 domains) and the crystal structure of the 75 kDa fragment (the N2 and N3 domains). This rod-shaped GBS104 model is constructed of three IgG-like domains (the N1, N2 and N4 domains) and one vWFA-like domain (the N3 domain).

Multispectral image analysis for algal biomass quantification.

This article reports a novel multispectral image processing technique for rapid, noninvasive quantification of biomass concentration in attached and suspended algae cultures. Monitoring the biomass concentration is critical for efficient production of biofuel feedstocks, food supplements, and bioactive chemicals. Particularly, noninvasive and rapid detection techniques can significantly aid in providing delay-free process control feedback in large-scale cultivation platforms.

Purification, crystallization and preliminary X-ray diffraction analysis of the Staphylococcus epidermidis extracellular serine protease Esp.

Esp, an extracellular serine protease from Staphylococcus epidermidis, has been shown to inhibit S. aureus biofilm formation and nasal colonization. The full-length 27 kDa pro-Esp was purified and digested with thermolysin to obtain mature Esp.

Community structure in time-dependent, multiscale, and multiplex networks.

Network science is an interdisciplinary endeavor, with methods and applications drawn from across the natural, social, and information sciences. A prominent problem in network science is the algorithmic detection of tightly connected groups of nodes known as communities. We developed a generalized framework of network quality functions that allowed us to study the community structure of arbitrary multislice networks, which are combinations of individual networks coupled through links that connect each node in one network slice to itself in other slices.

The crystal structure of cobra venom factor, a cofactor for C3- and C5-convertase CVFBb.

Cobra venom factor (CVF) is a functional analog of human complement component C3b, the active fragment of C3. Similar to C3b, in human and mammalian serum, CVF binds factor B, which is then cleaved by factor D, giving rise to the CVFBb complex that targets the same scissile bond in C3 as the authentic complement convertases C4bC2a and C3bBb. Unlike the latter, CVFBb is a stable complex and an efficient C5 convertase.

The structure of C2b, a fragment of complement component C2 produced during C3 convertase formation.

The second component of complement (C2) is a multi-domain serine protease that provides catalytic activity for the C3 and C5 convertases of the classical and lectin pathways of human complement. The formation of these convertases requires the Mg(2+)-dependent binding of C2 to C4b and the subsequent cleavage of C2 by C1s or MASP2, respectively. The crystal structure of full-length C2 is not yet available, although the structure of its C-terminal catalytic segment C2a has been determined.

The crystal structure of C2a, the catalytic fragment of classical pathway C3 and C5 convertase of human complement.

The multi-domain serine protease C2 provides the catalytic activity for the C3 and C5- convertases of the classical and lectin pathways of complement activation. Formation of these convertases requires the Mg(2+)-dependent binding of C2 to C4b, and the subsequent cleavage of C2 by C1s or MASP2, respectively. The C-terminal fragment C2a consisting of a serine protease (SP) and a von Willebrand factor type A (vWFA) domain, remains attached to C4b, forming the C3 convertase, C4b2a.

Structural analysis of engineered Bb fragment of complement factor B: insights into the activation mechanism of the alternative pathway C3-convertase.

The C-terminal fragment, Bb, of factor B combines with C3b to form the pivotal C3-convertase, C3bBb, of alternative complement pathway. Bb consists of a von Willebrand factor type A (vWFA) domain that is structurally similar to the I domains of integrins and a serine protease (SP) domain that is in inactive conformation. The structure of the C3bBb complex would be important in deciphering the activation mechanism of the SP domain.

New structural motifs on the chymotrypsin fold and their potential roles in complement factor B.

Factor B and C2 are two central enzymes for complement activation. They are multidomain serine proteases and require cofactor binding for full expression of proteolytic activities. We present a 2.

Structural basis of profactor D activation: from a highly flexible zymogen to a novel self-inhibited serine protease, complement factor D.

The crystal structure of profactor D, determined at 2.1 A resolution with an Rfree and an R-factor of 25.1 and 20.

Recombinant and native zymogen forms of human complement factor D.

We have expressed a full-length cDNA clone encoding human factor D by using a baculovirus expression system. The purified recombinant protein reacted with Ab against native factor D, but was hemolytically inactive and slightly larger than factor D. These results suggested that the recombinant protein was the elusive zymogen of factor D.

Preliminary crystallographic studies on human complement pro-factor D.

The recombinant zymogen of the human complement protein factor D has been crystallized. Crystals were grown by vapor diffusion using polyethylene glycol 6000 as precipitant. Two crystal forms obtained at pH 5.

cDNA cloning and characterization of the protein encoded by RD, a gene located in the class III region of the human major histocompatibility complex.

The RD gene, initially defined in the mouse, has been mapped between the Bf and C4A genes in the human major histocompatibility complex class III region. Using the mouse cDNA as a probe, we isolated and sequenced human RD cDNA clones. The composite nucleotide sequence consisted of 1301 nucleotides, excluding a poly(A) tail at the 3' end.

Structure of the human C2 gene.

A human genomic cosmid clone, S22A, was used to characterize the structure of the human C2 gene. Eighteen exons spanning 18 kb of DNA were mapped by nucleotide sequencing of exon-containing subclones and by Southern blotting. Introns vary in length between 83 bp and 4.

Probing the phosphocholine-binding site of human C-reactive protein by site-directed mutagenesis.

Human C-reactive protein (CRP) can activate the classical pathway of complement and function as an opsonin only when it is complexed to an appropriate ligand. Most known CRP ligands bind to the phosphocholine (PCh)-binding site of the protein. In the present study, we used oligonucleotide-directed site-specific mutagenesis to investigate structural determinants of the PCh-binding site of CRP.

Major histocompatibility complex class III genes and susceptibility to immunoglobulin A deficiency and common variable immunodeficiency.

We have proposed that significant subsets of individuals with IgA deficiency (IgA-D) and common variable immunodeficiency (CVID) may represent polar ends of a clinical spectrum reflecting a single underlying genetic defect. This proposal was supported by our finding that individuals with these immunodeficiencies have in common a high incidence of C4A gene deletions and C2 rare gene alleles. Here we present our analysis of the MHC haplotypes of 12 IgA-D and 19 CVID individuals from 21 families and of 79 of their immediate relatives.