HIV drug resistance in children and adolescents on NNRTI-based antiretroviral therapy and subsequent virologic response to dolutegravir-based regimens in Ghana.

HIV drug resistance (HIVDR) was retrospectively characterized among 20 children and adolescents with HIV with virologic failure on non-nucleoside reverse transcriptase inhibitor (NNRTI)-based therapy, and virologic response in those switched to dolutegravir (DTG)-based therapy described. All participants had at least one NNRTI resistance mutation, most commonly K103N (N = 12) and 15 (75%) had nucleoside reverse transcriptase inhibitor (NRTI) resistance mutations, most commonly M184I/V (N = 15). Five (45%) of 11 participants who were switched to DTG-based regimens for a median of 50 months had HIV suppression.

Initial and Subsequent Engagement of Recently Diagnosed Persons Living with HIV in Contact Tracing Interviews Conducted by Public Health Practitioners.

Contact tracing is effective in disrupting HIV transmission, but may be limited by the reluctance or inability of recently HIV-diagnosed persons (RDPs) to engage collaboratively with public health. Leveraging an ongoing study endeavoring to increase the yield of standard-of-care contact tracing by re-interviewing a subset of RDPs, we assessed RDP engagement during first and second interviews and compared the two. We used Likert scale scores to develop and employ a 35-point index tool, to assess engagement during first interviews (standard of care) and second interviews (executed in a parent study to inform RDPs of clustering in an attempt to identify additional contacts).

Newly Diagnosed Individuals in Molecular HIV-1 Clusters in Rhode Island over Three Decades.

Background: Characterizing clustering rates of people with HIV in high-risk populations can offer insights on the HIV epidemic, enhancing efforts to control its spread.

Methods: We investigated longitudinal dynamics of clustering rates among individuals newly diagnosed with HIV-1. Data were extracted from medical records of all people with HIV in Rhode Island with available viral sequences.

Prospective Evaluation of Routine Statewide Integration of Molecular Epidemiology and Contact Tracing to Disrupt Human Immunodeficiency Virus Transmission.

Background: Human immunodeficiency virus (HIV) remains a global challenge and novel measures for transmission disruption are needed. Contact tracing is limited by reluctance or inability of newly diagnosed individuals to name at-risk contacts. Molecular cluster analysis is mostly used for outbreak investigations, and its role in routine public health activities remains uncertain.

Limited Short-Term Evolution of SARS-CoV-2 RNA-Dependent RNA Polymerase under Remdesivir Exposure in Upper Respiratory Compartments.

Background: The extent of the SARS-CoV-2 short-term evolution under Remdesivir (RDV) exposure and whether it varies across different upper respiratory compartments are not fully understood.

Methods: Patients hospitalized for COVID-19, with or without RDV therapy, were enrolled and completed up to three visits, in which they provided specimens from four respiratory compartments. Near full-length genome SARS-CoV-2 sequences were obtained from viral RNA, standard lineage and variant assignments were performed, and viral mutations in the RNA-dependent RNA polymerase (RdRp) region-the RDV target gene-were detected and compared between participants with and without RDV, across the four compartments, within participants across visits, and versus a larger sequence dataset.

Integrating HIV Cluster Analysis in Everyday Public Health Practice: Lessons Learned From a Public Health--Academic Partnership.

Background: The use of molecular HIV cluster analysis to supplement public health contact tracing has shown promise in addressing HIV outbreaks. However, the potential of HIV cluster analysis as an adjunct to daily, person-by-person HIV prevention efforts remains unknown. We documented lessons learned within a unique public health-academic partnership while guiding workaday HIV prevention efforts with near-real-time molecular cluster analysis.

An Automated Bioinformatics Pipeline Informing Near-Real-Time Public Health Responses to New HIV Diagnoses in a Statewide HIV Epidemic.

Molecular HIV cluster data can guide public health responses towards ending the HIV epidemic. Currently, real-time data integration, analysis, and interpretation are challenging, leading to a delayed public health response. We present a comprehensive methodology for addressing these challenges through data integration, analysis, and reporting.

Engineering sorghum for higher 4-hydroxybenzoic acid content.

Engineering bioenergy crops to accumulate coproducts can increase the value of lignocellulosic biomass and enable a sustainable bioeconomy. In this study, we engineered sorghum with a bacterial gene encoding a chorismate pyruvate-lyase () to reroute the plastidial pool of chorismate from the shikimate pathway into the valuable compound 4-hydroxybenzoic acid (4-HBA). A gene encoding a feedback-resistant version of 3-deoxy-d-arabino-heptulonate-7-phosphate synthase () was also introduced in an attempt to increase the carbon flux through the shikimate pathway.

Edit at will: Genotype independent plant transformation in the era of advanced genomics and genome editing.

The combination of advanced genomics, genome editing and plant transformation biology presents a powerful platform for basic plant research and crop improvement. Together these advances provide the tools to identify genes as targets for direct editing as single base pair changes, deletions, insertions and site specific homologous recombination. Recent breakthrough technologies using morphogenic regulators in plant transformation creates the ability to introduce reagents specific toward their identified targets and recover stably transformed and/or edited plants which are genotype independent.

Transformation of Recalcitrant Sorghum Varieties Facilitated by Baby Boom and Wuschel2.

Most reliable transformation protocols for cereal crops, including sorghum (Sorghum bicolor L. Moench), rely on the use of immature embryo explants to generate embryogenic callus cells that are then transformed using Agrobacterium- or particle-bombardment-mediated DNA delivery. Subsequent to DNA transfer, most protocols rely on selectable markers for the recovery of stably transformed callus that is then regenerated to produce T plants.

Morphogenic Regulator-Mediated Transformation of Maize Inbred B73.

Maize B73 is a reference genome and has long been a major resource for genetics and molecular biology research. We have developed an efficient B73 transformation protocol by enabling somatic embryogenesis through differential co-expression of maize morphogenic regulators BBM and WUS2. We describe a successful protocol that utilizes Agrobacterium tumefaciens strain AGL1 harboring binary vector PHP78891 that comprises a BBM and WUS2 expression cassette as well as a green fluorescent protein (GFP) reporter cassette.

Selectable marker independent transformation of recalcitrant maize inbred B73 and sorghum P898012 mediated by morphogenic regulators BABY BOOM and WUSCHEL2.

Discriminatory co-expression of maize BBM and WUS transcriptional factor genes promoted somatic embryogenesis and efficient Agrobacterium -mediated transformation of recalcitrant maize inbred B73 and sorghum P898012 genotypes without use of a selectable marker gene. The use of morphogenic regulators to overcome barriers in plant transformation is a revolutionary breakthrough for basic plant science and crop applications. Current standard plant transformation systems are bottlenecks for genetic, genomic, and crop improvement studies.

Control of sexuality by the -encoded UDP-glycosyltransferase of maize.

Sex determination in maize involves the production of staminate and pistillate florets from an initially bisexual floral meristem. Pistil elimination in staminate florets requires jasmonic acid signaling, and functional pistils are protected by the action of the () gene. The gene was identified and found to encode a previously uncharacterized family 1 uridine diphosphate glycosyltransferase that localized to the plant peroxisomes.

In situ embryo rescue for generation of wide intra- and interspecific hybrids of Panicum virgatum L.

Wide crosses have been used for decades as a method for transferring novel genetic material and traits in plant breeding. Historically, many products of wide crosses require tedious and inefficient surgical embryo rescue prior to embryo abortion to recover single plantlets. We have utilized transgenic switchgrass (Panicum virgatum L.

Genomic Characterization of Interspecific Hybrids and an Admixture Population Derived from Panicum amarum × P. virgatum.

Switchgrass (Panicum virgatum L.) and its relatives are regarded as top bioenergy crop candidates; however, one critical barrier is the introduction of useful genetic diversity and the development of new cultivars and hybrids. Combining genomes from related cultivars and species provides an opportunity to introduce new traits.

Turf Grasses.

A reliable and efficient genetic transformation protocol for various turfgrass species and elite cultivars has been achieved using Agrobacterium tumefaciens. We describe a general protocol for the establishment of embryogenic cell cultures, Agrobacterium tumefaciens-mediated transformation, selection, and regeneration of transgenic turfgrass plants. Embryogenic callus is initiated from mature seeds, maintained by visual selection, and infected with an Agrobacterium tumefaciens strain (LBA4404) that contains either an herbicide-resistant bar gene or an antibiotic-resistant hyg gene driven either by a rice ubiquitin or CaMV35S promoter.