Risk of adverse birth outcomes and birth defects among women living with HIV on antiretroviral therapy and HIV-negative women in Uganda, 2015-2021.

Introduction: We assessed the risk of adverse pregnancy and birth outcomes and birth defects among women living with HIV (WLHIV) on antiretroviral therapy (ART) and HIV-negative women.

Methods: We analyzed data on live births, stillbirths, and spontaneous abortions during 2015-2021 from a hospital-based birth defects surveillance system in Kampala, Uganda. ART regimens were recorded from hospital records and maternal self-reports.

Lineage Analysis at Single-Cell Resolution by Twin-Spot MARCM with Lineage-Restricted Drivers.

Cell lineage analysis is primarily undertaken to understand cell fate specification and diversification along a cell lineage tree. Built with dual repressible markers, twin-spot mosaic analysis with repressible cell markers (MARCM) labels the two daughter cells made by a common precursor in distinct colors. The power of twin-spot MARCM to systematically subdivide complex lineages is exemplified in studies of Drosophila neural stem-cell lineages.

Design and Generation of TEMPO Reagents for Sequential Labeling and Manipulation of Vertebrate Cell Lineages.

During development, cells undergo a sequence of specification events to form functional tissues and organs. To investigate complex tissue development, it is crucial to visualize how cell lineages emerge and to be able to manipulate regulatory factors with temporal control. We recently developed TEMPO (Temporal Encoding and Manipulation in a Predefined Order), a genetic tool to label with different colors and genetically manipulate consecutive cell generations in vertebrates.

Single-Cell Profiling of Lineages and Cell Types in the Vertebrate Brain.

CRISPR-Cas tools have recently been adapted for cell lineage tracing during development. Combined with single-cell RNA sequencing, these methods enable scalable lineage tracing with single-cell resolution. Here, I describe, scGESTALTv2, which combines cumulative CRISPR-Cas9 editing of a lineage barcode array with transcriptional profiling via droplet-based single-cell RNA sequencing (scRNA-seq).

CARLIN: A Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression.

The CRISPR-activated repair lineage tracing (CARLIN) mouse line uses DNA barcoding to enable high-resolution tracing of cell lineages in vivo (Bowling et al, Cell 181, 1410-1422.e27, 2020). CARLIN mice contain expressed barcodes that allow simultaneous interrogation of lineage and gene expression information from single cells.

Paired Single-Cell Transcriptome and DNA Barcode Detection in Zebrafish Using ScarTrace.

ScarTrace is a CRISPR/Cas9-based genetic lineage tracing method that allows for uniquely barcoding the DNA of single cells at a target GFP sequence during developing zebrafish embryos. Single cells from barcoded adult zebrafish can be isolated from various tissues (e.g.

Reconstructing Progenitor State Hierarchy and Dynamics Using Lineage Barcoding Data.

Measurements of cell phylogeny based on natural or induced mutations, known as lineage barcodes, in conjunction with molecular phenotype have become increasingly feasible for a large number of single cells. In this chapter, we delve into Quantitative Fate Mapping (QFM) and its computational pipeline, which enables the interrogation of the dynamics of progenitor cells and their fate restriction during development. The methods described here include inferring cell phylogeny with the Phylotime model, and reconstructing progenitor state hierarchy, commitment time, population size, and commitment bias with the ICE-FASE algorithm.

Lineage Tracing by Light-Sheet Microscopy and Computational Reconstruction.

Lineage tracing based on modern live imaging approaches enables to visualize, reconstruct, and analyze the developmental history, fate, and dynamic behaviors of cells in vivo in a direct, comprehensive, and quantitative manner. Light-sheet fluorescence microscopy (LSFM) has greatly boosted lineage tracing efforts, because fluorescently labeled specimens can be imaged in their entirety, over long periods of time, with high spatiotemporal resolution and minimal photodamage. In addition, an increasing arsenal of commercial and open-source software solutions for cell and nuclei segmentation and tracking can be employed to convert data from pixel-based to object-based representations, and to reconstruct the lineages of cells in their native context as they organize in tissues, organs, and whole organisms.

Bayesian Phylogenetic Lineage Reconstruction with Loss of Heterozygosity Mutations Derived from Single-Cell RNA Sequencing.

Mutations are acquired frequently, such t`hat each cell's genome inscribes its history of cell divisions. Loss of heterozygosity (LOH) accumulates throughout the genome, offering large encoding capacity for phylogenetic inference of cell lineage.In this chapter, we demonstrate a method, using single-cell RNA sequencing, for reconstructing cell lineages from inferred LOH events in a Bayesian manner, annotating the lineage with cell phenotypes, and marking developmental time points based on X-chromosome inactivation.

CKD-Associated Pruritus is Associated with Greater Use of Antidepressants and Anti-pruritus Medications.

Introduction: Chronic kidney disease-associated pruritus (CKD-aP) is a common, yet underdiagnosed condition among patients on hemodialysis. Considering the lack of established treatment pathways, we sought to evaluate the use of antidepressant, systemic antihistamines, or gabapentinoid medications among patients with CKD-aP in the year following pruritus assessment.

Methods: We included 6209 patients on hemodialysis in the analysis.

Cerebellar Transcranial AC Stimulation Produces a Frequency-Dependent Bimodal Cerebellar Output Pattern.

Cerebellar transcranial alternating current stimulation (ctACS) has the potential to be an appealing, non-invasive treatment option for psychiatric and neurological disorders. However, realization of this potential has been limited by gaps in our knowledge of how ctACS affects cerebellar output on single cell and population levels. Previously, we showed that AC stimulation applied to the cerebellar surface produced a strong, frequency-dependent modulation of Purkinje cell (PC) and cerebellar nuclear (CN) cell activity.

Resistance training protects the hippocampus and precuneus against atrophy and benefits white matter integrity in older adults with mild cognitive impairment.

Mild cognitive impairment (MCI) refers to cognitive alterations with preservation of functionality. Individuals with this diagnosis have a higher risk of developing dementia. Non-pharmacological interventions, such as physical exercise, are beneficial for the cognition of this population.

Patterning Functional Proteins in Ultrabithorax-Based Materials.

The ability to add bioactivities, such as cell signaling or ligand recognition, to biomaterials has generated the potential to include multiple bioactivities into a single material. In some cases, it is desirable to localize these activities to different areas of the biomaterial, creating functional patterns. While photolithography and 3D printing have been effective techniques for patterning functions in many materials, patterning remains a challenge in materials composed of protein, in part due to how these materials are artificially assembled.

Spatial Genomic Approaches to Investigate HOX Genes in Mouse Brain Tissues.

Spatial transcriptomic tools are an upcoming and powerful way to investigate targeted gene expression patterns within tissues. These tools offer the unique advantage of visualizing and understanding gene expression while preserving tissue integrity, thereby maintaining the spatial context of genes. Curio is a robust spatial transcriptomic tool that facilitates high throughput comprehensive spatial gene expression analysis across the entir e transcriptome with high efficiency.

A Comprehensive Bioinformatics Approach to Analysis of Variants: Variant Calling, Annotation, and Prioritization.

Next-Generation Sequencing (NGS), also known as high-throughput sequencing technologies, has enabled rapid and efficient sequencing of large amounts of DNA and RNA. These technologies have revolutionized the field of genomics, transcriptomics, and proteomics and have been widely used in cancer research, leading to advances in clinical diagnosis and treatment. Improvements in the NGS technologies enabled millions of fragments to be sequenced simultaneously in a time- and cost-effective manner and resulted in large amount of genomic data which require efficient analysis methods.

Guidelines to Analyze ChIP-Seq Data: Journey Through QC and Analysis Considerations.

ChIP-Seq is used to study DNA-protein interactions, unraveling chromatin states and gene regulatory properties of transcription factors. ChIP-Seq involves immunoprecipitation followed by sequencing using Next-Generation sequencing approaches. The ENCODE consortium provides extensive guidelines for ChIP-Seq analysis.

A Simple Method to Analyze Context- and Tissue-Specific Cis-Regulatory Modulations of Homeotic (HOX) Genes Using ChIP.

Homeobox genes (HOX), the master regulators, deploy a unique set of target genes to coordinate and orchestrate the spatiotemporal development of an organism. HOX encoded transcriptional factors regulate the expression of target genes by binding to the specific sequences on the genome. Chromatin Immunoprecipitation (ChIP) and Chromatin Immunoprecipitation with Sequencing (ChIP-Seq) are widely used to map and understand specific gene locus and global regulatory regions on the genome.

Capturing Chromatin Organization by MNase-seq and ATAC-seq.

Hox genes play a pivotal role during development. Their expression is tightly controlled in a spatiotemporal manner, ensuring that specific body structures develop at the correct locations and times during development. Various genomics approaches have been used to capture temporal and dynamic regulation of Hox gene expression at the nucleosome/chromatin level.

Detection of Protein-Nucleic Acid Interaction by Electrophoretic Mobility Shift Assay.

Electrophoretic Mobility Shift Assay (EMSA) is a powerful technique for studying nucleic acid and protein interactions. This technique is based on the principle that nucleic acid-protein complex and nucleic acid migrate at different rates due to differences in size and charge. Nucleic acid and protein interactions are fundamental to various biological processes, such as gene regulation, replication, transcription, and recombination.

Studying the Role of HOX Genes in Thrombocyte Development.

In our laboratory, we study thrombopoiesis and hemostasis using zebrafish as a model organism to unravel the mechanisms of differentiation and development of thrombocytes. We have shown in our earlier work that thrombocytes are functional equivalents of platelets and have transcriptional machinery similar to megakaryocytes. We recently found evidence that hox genes play a role in their development.

Investigating the Functions of Hox Genes Using Planarian Asexual Reproduction.

Hox genes are highly conserved developmental regulators instrumental to the formation of a wide range of diverse body plans across metazoans. While significant progress in the field of Hox gene research has been made, persistent challenges in unraveling their mechanisms of action and full repertoire of functions remain. To date, investigations of Hox gene function have been primarily conducted in research models belonging to ecdysozoa and vertebrata.

Optimized smFISH Pipeline for Studying Nascent Transcription in Mouse Embryonic Tissue Samples.

Understanding the spatial and temporal dynamics of gene expression is crucial for unraveling molecular mechanisms underlying various biological processes. While traditional methods have offered insights into gene expression patterns, they primarily focus on mature mRNA transcripts, lacking real-time visualization of newly synthesized or nascent transcription events. Recent advancements in monitoring nascent transcription in live cells provide valuable insights into transcriptional dynamics.

Re-arranging the Cis-regulatory Modules of Hox Complex in Drosophila via FLP-FRT and CRISPR/Cas9.

FLP-FRT, a well-established technique for genome manipulation, and the revolutionary CRISPR/Cas9, known for its targeted indels, are combined in a novel approach. This unique method is applied to the Hox genes in the Drosophila melanogaster bithorax complex, which are closely located to the cis-regulatory modules that define their spatial-temporal regulation. The number and position of these genes are directly correlated to their expression pattern.

Biology of Hox Genes: Questions and Technological Challenges.

Hox genes are crucial in determining segmentation identity in developing embryos, which ultimately sets an anteroposterior body axis. Over a century of research has discovered the fundamentals of the Hox gene and protein function in animal development and diseases. However, there are still fundamental questions about the specificity of HOX function.

Activity Space Mapping and Pre-Exposure Prophylaxis Uptake Among Gay, Bisexual, and Other Sexual Minority Men in Small Cities and Towns in the United States.

In the US, gay, bisexual, and other sexual minoritized men (GBSMM) remain disproportionately impacted by HIV, and continue to experience unmet needs for pre-exposure prophylaxis (PrEP). A growing body of literature has underscored the need to consider the geographic factors of HIV prevention, particularly beyond administrative boundaries and towards localized spaces that influence the accessibility and utilization of health-promoting resources. Therefore, the purpose of this study is to examine the associations of driving times from activity spaces to PrEP offering facilities and individual PrEP uptake.