The function and affinity maturation of HIV-1 gp120-specific monoclonal antibodies derived from colostral B cells.

Despite the risk of transmitting HIV-1, mothers in resource-poor areas are encouraged to breastfeed their infants because of beneficial immunologic and nutritional factors in milk. Interestingly, in the absence of antiretroviral prophylaxis, the overwhelming majority of HIV-1-exposed, breastfeeding infants are naturally protected from infection. To understand the role of HIV-1 envelope (Env)-specific antibodies in breast milk in natural protection against infant virus transmission, we produced 19 HIV-1 Env-specific monoclonal antibodies (mAbs) isolated from colostrum B cells of HIV-1-infected mothers and investigated their specificity, evolution, and anti-HIV-1 functions.

Human Non-neutralizing HIV-1 Envelope Monoclonal Antibodies Limit the Number of Founder Viruses during SHIV Mucosal Infection in Rhesus Macaques.

HIV-1 mucosal transmission begins with virus or virus-infected cells moving through mucus across mucosal epithelium to infect CD4+ T cells. Although broadly neutralizing antibodies (bnAbs) are the type of HIV-1 antibodies that are most likely protective, they are not induced with current vaccine candidates. In contrast, antibodies that do not neutralize primary HIV-1 strains in the TZM-bl infection assay are readily induced by current vaccine candidates and have also been implicated as secondary correlates of decreased HIV-1 risk in the RV144 vaccine efficacy trial.

HIV-1 VACCINES. Diversion of HIV-1 vaccine-induced immunity by gp41-microbiota cross-reactive antibodies.

An HIV-1 DNA prime vaccine, with a recombinant adenovirus type 5 (rAd5) boost, failed to protect from HIV-1 acquisition. We studied the nature of the vaccine-induced antibody (Ab) response to HIV-1 envelope (Env). HIV-1-reactive plasma Ab titers were higher to Env gp41 than to gp120, and repertoire analysis demonstrated that 93% of HIV-1-reactive Abs from memory B cells responded to Env gp41.

Restoring the lattice of Si-based atom probe reconstructions for enhanced information on dopant positioning.

The following manuscript presents a novel approach for creating lattice based models of Sb-doped Si directly from atom probe reconstructions for the purposes of improving information on dopant positioning and directly informing quantum mechanics based materials modeling approaches. Sophisticated crystallographic analysis techniques are used to detect latent crystal structure within the atom probe reconstructions with unprecedented accuracy. A distortion correction algorithm is then developed to precisely calibrate the detected crystal structure to the theoretically known diamond cubic lattice.

Rapid Development of gp120-Focused Neutralizing B Cell Responses during Acute Simian Immunodeficiency Virus Infection of African Green Monkeys.

Unlabelled: The initial phases of acute human immunodeficiency virus type 1 (HIV-1) infection may be critical for development of effective envelope (Env)-specific antibodies capable of impeding the establishment of the latent pool of HIV-1-infected CD4(+) T cells, preventing virus-induced immune hyperactivation to limit disease progression and blocking vertical virus transmission. However, the initial systemic HIV-1 Env-specific antibody response targets gp41 epitopes and fails to control acute-phase viremia. African-origin, natural simian immunodeficiency virus (SIV) hosts do not typically progress to AIDS and rarely postnatally transmit virus to their infants, despite high milk viral loads.

Mining information from atom probe data.

Whilst atom probe tomography (APT) is a powerful technique with the capacity to gather information containing hundreds of millions of atoms from a single specimen, the ability to effectively use this information creates significant challenges. The main technological bottleneck lies in handling the extremely large amounts of data on spatial-chemical correlations, as well as developing new quantitative computational foundations for image reconstruction that target critical and transformative problems in materials science. The power to explore materials at the atomic scale with the extraordinary level of sensitivity of detection offered by atom probe tomography has not been not fully harnessed due to the challenges of dealing with missing, sparse and often noisy data.

Maternal HIV-1 envelope-specific antibody responses and reduced risk of perinatal transmission.

Despite the wide availability of antiretroviral drugs, more than 250,000 infants are vertically infected with HIV-1 annually, emphasizing the need for additional interventions to eliminate pediatric HIV-1 infections. Here, we aimed to define humoral immune correlates of risk of mother-to-child transmission (MTCT) of HIV-1, including responses associated with protection in the RV144 vaccine trial. Eighty-three untreated, HIV-1-transmitting mothers and 165 propensity score-matched nontransmitting mothers were selected from the Women and Infants Transmission Study (WITS) of US nonbreastfeeding, HIV-1-infected mothers.

Transcriptome sequencing of three Ranunculus species (Ranunculaceae) reveals candidate genes in adaptation from terrestrial to aquatic habitats.

Adaptation to aquatic habitats is a formidable challenge for terrestrial angiosperms that has long intrigued scientists. As part of a suite of work to explore the molecular mechanism of adaptation to aquatic habitats, we here sequenced the transcriptome of the submerged aquatic plant Ranunculus bungei, and two terrestrial relatives R. cantoniensis and R.

Using transmission Kikuchi diffraction to study intergranular stress corrosion cracking in type 316 stainless steels.

Transmission Kikuchi diffraction (TKD), also known as transmission-electron backscatter diffraction (t-EBSD) is a novel method for orientation mapping of electron transparent transmission electron microscopy specimen in the scanning electron microscope and has been utilized for stress corrosion cracking characterization of type 316 stainless steels. The main advantage of TKD is a significantly higher spatial resolution compared to the conventional EBSD due to the smaller interaction volume of the incident beam with the specimen. Two 316 stainless steel specimen, tested for stress corrosion cracking in hydrogenated and oxygenated pressurized water reactor chemistry, were characterized via TKD.

Viral receptor-binding site antibodies with diverse germline origins.

Vaccines for rapidly evolving pathogens will confer lasting immunity if they elicit antibodies recognizing conserved epitopes, such as a receptor-binding site (RBS). From characteristics of an influenza-virus RBS-directed antibody, we devised a signature motif to search for similar antibodies. We identified, from three vaccinees, over 100 candidates encoded by 11 different VH genes.

Practical Issues for Atom Probe Tomography Analysis of III-Nitride Semiconductor Materials.

Various practical issues affecting atom probe tomography (APT) analysis of III-nitride semiconductors have been studied as part of an investigation using a c-plane InAlN/GaN heterostructure. Specimen preparation was undertaken using a focused ion beam microscope with a mono-isotopic Ga source. This enabled the unambiguous observation of implantation damage induced by sample preparation.

Nitric Oxide-Enhanced Molecular Imaging of Atheroma using Vascular Cellular Adhesion Molecule 1-Targeted Echogenic Immunoliposomes.

The aim of this study was to determine whether pre-treatment with nitric oxide-loaded echogenic liposomes (NO-ELIP) plus ultrasound can improve highlighting by molecularly targeted (anti-vascular cell adhesion molecule 1 [VCAM-1]) ELIP of atheroma components. Atherosclerotic animals were treated with anti-VCAM-1-ELIP or immunoglobulin (IgG)-ELIP. Each group was selected at random to receive pre-treatment with standard ELIP plus ultrasound, NO-ELIP without ultrasound and NO-ELIP plus ultrasound.

Eliminating antibody polyreactivity through addition of N-linked glycosylation.

Antibody polyreactivity can be an obstacle to translating a candidate antibody into a clinical product. Standard tests such as antibody binding to cardiolipin, HEp-2 cells, or nuclear antigens provide measures of polyreactivity, but its causes and the means to resolve are often unclear. Here we present a method for eliminating antibody polyreactivity through the computational design and genetic addition of N-linked glycosylation near known sites of polyreactivity.

Imaging of radiation damage using complementary field ion microscopy and atom probe tomography.

Radiation damage in tungsten and a tungsten-tantalum alloy, both of relevance to nuclear fusion research, has been characterized using a combination of field ion microscopy (FIM) imaging and atom probe tomography (APT). While APT provides 3D analytical imaging with sub-nanometer resolution, FIM is capable of imaging the arrangements of single atoms on a crystal lattice and has the potential to provide insights into radiation induced crystal damage, all the way down to its smallest manifestation--a single vacancy. This paper demonstrates the strength of combining these characterization techniques.

Quantification of oxide particle composition in model oxide dispersion strengthened steel alloys.

Oxide dispersion strengthened ferritic steels (ODS) are being considered for structural components of future designs of fission and fusion reactors because of their impressive high-temperature mechanical properties and resistance to radiation damage, both of which arise from the nanoscale oxide particles they contain. Because of the critical importance of these nanoscale phases, significant research activity has been dedicated to analysing their precise size, shape and composition (Odette et al., Annu.

Antibodies for prevention of mother-to-child transmission of HIV-1.

Purpose Of Review: Although antiretroviral (ARV) prophylaxis can reduce mother-to-child transmission (MTCT) of HIV-1 to less than 2%, one-quarter of a million infants continue to be infected with HIV-1 annually. ARV prophylaxis alone will fail to eliminate infant HIV-1 infection because of issues of maternal adherence, toxicities, ARV-resistant virus strains, and acute maternal infection. Effective maternal and/or infant immunization will likely be required to achieve the goal of an HIV-free generation.

Antibody light-chain-restricted recognition of the site of immune pressure in the RV144 HIV-1 vaccine trial is phylogenetically conserved.

In HIV-1, the ability to mount antibody responses to conserved, neutralizing epitopes is critical for protection. Here we have studied the light chain usage of human and rhesus macaque antibodies targeted to a dominant region of the HIV-1 envelope second variable (V2) region involving lysine (K) 169, the site of immune pressure in the RV144 vaccine efficacy trial. We found that humans and rhesus macaques used orthologous lambda variable gene segments encoding a glutamic acid-aspartic acid (ED) motif for K169 recognition.

Key mutations stabilize antigen-binding conformation during affinity maturation of a broadly neutralizing influenza antibody lineage.

Affinity maturation, the process in which somatic hypermutation and positive selection generate antibodies with increasing affinity for an antigen, is pivotal in acquired humoral immunity. We have studied the mechanism of affinity gain in a human B-cell lineage in which two main maturation pathways, diverging from a common ancestor, lead to three mature antibodies that neutralize a broad range of H1 influenza viruses. Previous work showed that increased affinity in the mature antibodies derives primarily from stabilization of the CDR H3 loop in the antigen-binding conformation.

Resolving the morphology of niobium carbonitride nano-precipitates in steel using atom probe tomography.

Atom probe is a powerful technique for studying the composition of nano-precipitates, but their morphology within the reconstructed data is distorted due to the so-called local magnification effect. A new technique has been developed to mitigate this limitation by characterizing the distribution of the surrounding matrix atoms, rather than those contained within the nano-precipitates themselves. A comprehensive chemical analysis enables further information on size and chemistry to be obtained.

Atomically resolved tomography to directly inform simulations for structure-property relationships.

Microscopy encompasses a wide variety of forms and scales. So too does the array of simulation techniques developed that correlate to and build upon microstructural information. Nevertheless, a true nexus between microscopy and atomistic simulations is lacking.

Newly developed quantitative transactivation system shows difference in activation by Vitis CBF transcription factors on DRE/CRT elements.

Background: Agroinfiltration-based transactivation systems can determine if a protein functions as a transcription factor, and via which promoter element. However, this activation is not always a yes or no proposition. Normalization for variation in plasmid delivery into plant cells, sample collection and protein extraction is desired to allow for a quantitative comparison between transcription factors or promoter elements.

Immunoglobulin gene insertions and deletions in the affinity maturation of HIV-1 broadly reactive neutralizing antibodies.

Induction of HIV-1 broad neutralizing antibodies (bnAbs) is a goal of HIV-1 vaccine development but has remained challenging partially due to unusual traits of bnAbs, including high somatic hypermutation (SHM) frequencies and in-frame insertions and deletions (indels). Here we examined the propensity and functional requirement for indels within HIV-1 bnAbs. High-throughput sequencing of the immunoglobulin (Ig) VHDJH genes in HIV-1 infected and uninfected individuals revealed that the indel frequency was elevated among HIV-1-infected subjects, with no unique properties attributable to bnAb-producing individuals.

Infant HIV type 1 gp120 vaccination elicits robust and durable anti-V1V2 immunoglobulin G responses and only rare envelope-specific immunoglobulin A responses.

Background: Infant responses to vaccines can be impeded by maternal antibodies and immune system immaturity. It is therefore unclear whether human immunodeficiency virus type 1 (HIV-1) vaccination would elicit similar responses in adults and infants.

Method: HIV-1 Env-specific antibody responses were evaluated in 2 completed pediatric vaccine trials.

HIV-1 envelope gp41 antibodies can originate from terminal ileum B cells that share cross-reactivity with commensal bacteria.

Monoclonal antibodies derived from blood plasma cells of acute HIV-1-infected individuals are predominantly targeted to the HIV Env gp41 and cross-reactive with commensal bacteria. To understand this phenomenon, we examined anti-HIV responses in ileum B cells using recombinant antibody technology and probed their relationship to commensal bacteria. The dominant ileum B cell response was to Env gp41.