Holes in the Glycan Shield of the Native HIV Envelope Are a Target of Trimer-Elicited Neutralizing Antibodies

A major advance in the search for an HIV vaccine has been the development of a near-native Envelope trimer (BG505 SOSIP.664) that can induce robust autologous Tier 2 neutralization. Here, potently neutralizing monoclonal antibodies (nAbs) from rabbits immunized with BG505 SOSIP.664 are shown to recognize an immunodominant region of gp120 centered on residue 241. Residue 241 occupies a hole in the glycan defenses of the BG505 isolate, with fewer than 3% of global isolates lacking a glycan site at this position. However, at least one conserved glycan site is missing in 89% of viruses, suggesting the presence of glycan holes in most HIV isolates. Serum evidence is consistent with targeting of holes in natural infection. The immunogenic nature of breaches in the glycan shield has been under-appreciated in previous attempts to understand autologous neutralizing antibody responses and has important potential consequences for HIV vaccine design

Reprogramming the antigen specificity of B cells using genome-editing technologies

We have developed a method to introduce novel paratopes into the human antibody repertoire by modifying the immunoglobulin (Ig) genes of mature B cells directly using genome editing technologies. We used CRISPR-Cas9 in a homology directed repair strategy, to replace the heavy chain (HC) variable region in B cell lines with that from an HIV broadly neutralizing antibody (bnAb), PG9. Our strategy is designed to function in cells that have undergone VDJ recombination using any combination of variable (V), diversity (D) and joining (J) genes. The modified locus expresses PG9 HC which pairs with native light chains (LCs) resulting in the cell surface expression of HIV specific B cell receptors (BCRs). Endogenous activation-induced cytidine deaminase (AID) in engineered cells allowed for Ig class switching and generated BCR variants with improved HIV neutralizing activity. Thus, BCRs engineered in this way retain the genetic flexibility normally required for affinity maturation during adaptive immune responses. Peripheral blood derived primary B cells from three different donors were edited using this strategy. Engineered cells could bind the PG9 epitope and sequenced mRNA showed PG9 HC transcribed as several different isotypes after culture with CD40 ligand and IL-4

Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease

Pan-betacoronavirus neutralizing antibodies may hold the key to developing broadly protective vaccines against novel pandemic coronaviruses and to more effectively respond to SARS-CoV-2 variants. The emergence of Omicron and subvariants of SARS-CoV-2 illustrates the limitations of solely targeting the receptor-binding domain (RBD) of the spike (S) protein. Here, we isolated a large panel of broadly neutralizing antibodies (bnAbs) from SARS-CoV-2 recovered-vaccinated donors, which targets a conserved S2 region in the betacoronavirus spike fusion machinery. Select bnAbs showed broad in vivo protection against all three deadly betacoronaviruses, SARS-CoV-1, SARS-CoV-2, and MERS-CoV, which have spilled over into humans in the past two decades. Structural studies of these bnAbs delineated the molecular basis for their broad reactivity and revealed common antibody features targetable by broad vaccination strategies. These bnAbs provide new insights and opportunities for antibody-based interventions and for developing pan-betacoronavirus vaccines

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

CAPRISA, 2014.Abstract available in pdf

Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies.

CAPRISA, 2014.Antibodies capable of neutralizing HIV-1 often target variable regions 1 and 2 (V1V2) of the HIV-1 envelope, but the mechanism of their elicitation has been unclear. Here we define the developmental pathway by which such antibodies are generated and acquire the requisite molecular characteristics for neutralization. Twelve somatically related neutralizing antibodies (CAP256-VRC26.01-12) were isolated from donor CAP256 (from the Centre for the AIDS Programme of Research in South Africa (CAPRISA)); each antibody contained the protruding tyrosine-sulphated, anionic antigen-binding loop (complementarity-determining region (CDR) H3) characteristic of this category of antibodies. Their unmutated ancestor emerged between weeks 30-38 post-infection with a 35-residue CDR H3, and neutralized the virus that superinfected this individual 15 weeks after initial infection. Improved neutralization breadth and potency occurred by week 59 with modest affinity maturation, and was preceded by extensive diversification of the virus population. HIV-1 V1V2-directed neutralizing antibodies can thus develop relatively rapidly through initial selection of B cells with a long CDR H3, and limited subsequent somatic hypermutation. These data provide important insights relevant to HIV-1 vaccine development

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

CAPRISA, 2014.Abstract available in pdf

Effect of the puroindoline locus and environment on Chinese fresh noodle texture

Grain produced from doubled-haploid (DH)wheat lines, developed from a hard- and a soft-grained wheat cultivar, were bulked according to Pinb (puroindoline b) genotypes for an assessment of Chinese fresh noodle texture by a trained taste panel. Each DH line was designated as 'soft' or 'hard' grained, based on a PCR amplification of the wildtype, soft allele, or the mutant, hard allele. Theoretically, the soft and hard grain bulks represented respective Pinb alleles and an independent assortment of unlinked alleles from the parents, Sunco and Chuanyu 12. Grains from the parents and DH lines were grown at 2 locations in Queensland, Australia, and one in Sichuan, China. The grains were milled and processed for a taste panel evaluation in Chengdu, Sichuan. Results suggest the Pinb alleles had a significant effect on noodle softness and explained 30% of the variation; the 'soft' Pinb allele conferred a softer noodle texture. Location had a significant effect on noodle smoothness; wheat grain grown at Biloela, Queensland, produced a smoother noodle texture than grain grown in Sichuan. The effect of location confirms the importance of environment as a variable for this quality character. This investigation exemplifies the utility of Pinb markers for specifically altering Chinese Fresh Noodle texture

Understanding student perspectives on learning analytics to enable privacy advocacy and policy design

The rise of computing infrastructure and data collection in higher education has opened the door for colleges and universities to begin large-scale data analytics projects, commonly known as learning analytics (LA). These initiatives are defined as the “measurement, collection, analysis, and reporting of [student and other data] for the purposes of understanding and optimizing learning and the environments in which it occurs.” Historically, academic libraries have collected data, such as circulation statistics, without reference to specific users. The extensive data collected by library and higher-education programs and networks now regularly include personal information. More academic libraries are being asked to engage in learning analytics projects or to share data with campus units to demonstrate how library use may correlate with student success measures such as GPA, retention, and time to graduation. Literature in 2018 at the time of the team’s grant application showed a distinct lack of research around student perceptions of LA and library participation. This gap was the driving goal of the research team’s project to understand student perceptions through an IMLS-funded study of undergraduate students at eight institutions. While the researchers hold expertise in the areas of data ethics and privacy, data management, library assessment, qualitative and quantitative research methods, and survey design, they were not involved in the practical application of learning analytics at their various universities. To begin, the team conducted a literature review that brought together the ethical challenges of library participation in LA with respect to librarianship’s professional values, especially privacy. This informed the overall design of the study, which was conducted in three phases: semi-structured interviews, a survey, and finally a series of LA scenario-based focus groups. The initial literature review was used as the basis for the interview protocol of the first phase. The findings from the interviews were then used to develop the survey instrument for the second phase. The results of the survey were subsequently leveraged to develop the focus group scenarios. Due to the COVID-19 pandemic, the project was extended to May 2022 and focus groups were conducted virtually rather than in person

Questions of Trust: A Survey of Student Expectations and Perspectives on Library Learning Analytics

Universities are developing learning analytics initiatives that include academic library participation. Libraries rarely inform their students about learning analytics projects or general library data practices. Without a clear student voice in library learning analytics projects, libraries and librarians are creating potential privacy complications. This study seeks to document students’ thoughts on academic library participation in learning analytics and privacy concerns. A survey was developed and fielded at eight US higher education institutions, and this article covers the findings from the approximately 2,200 responses. Although most students reported high levels of trust in libraries and librarians, a consistent minority indicated little or no trust at all. Findings demonstrate that students considered librarian access to and sharing of personally identifiable information to constitute a privacy violation but also lacked awareness of the data and analytic practices on which libraries rely. Notable demographic differences were also discovered