Clean Lighting Leads to Improved Health in Rural Africa: Field Study and Design of a Dirt-Powered Generator

Two billion people world-wide use kerosene-burning lamps for household lighting. These lamps produce large quantities of soot. In Chapter 2, I describe our field study examining 230 people in rural Uganda. I show that kerosene lamps are a major source of smoke exposure in the developing world, and that replacing such lamps with solar-powered lights reduces indoor soot levels 17-fold, leading to significant improvements in health within months. This finding is particularly notable because respiratory disease is the #1 cause of death in children under 5 worldwide. Because solar cells are a challenge to manufacture in the developing world, I next examined the potential of harvesting electrons from soil-based microbes as a source of clean energy. Such devices are known as microbial fuel cells (MFCs); because soil is available everywhere, MFCs can, in principle, be locally constructed all over the world. In Chapter 3, I describe our exploration of the biology of MFCs, using high-throughput DNA sequencing to demonstrate a role for genus Pseudomonas in energy production. I also examine numerous agricultural products available throughout the developing world to determine whether any could serve as a suitable ‘feed’ for MFC soil. I find that dried animal blood increases MFC energy production 10-fold. In Chapter 4, I describe our design of a modular, stackable MFC, demonstrate that it can be easily constructed in rural Africa, and use it to power lights and to charge a cell phone battery

Quantitative Analysis of Culture Using Millions of Digitized Books

We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of ‘culturomics,’ focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. Culturomics extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities.MathematicsPsycholog

Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function.

EndoC-βH1 is emerging as a critical human β cell model to study the genetic and environmental etiologies of β cell (dys)function and diabetes. Comprehensive knowledge of its molecular landscape is lacking, yet required, for effective use of this model. Here, we report chromosomal (spectral karyotyping), genetic (genotyping), epigenomic (ChIP-seq and ATAC-seq), chromatin interaction (Hi-C and Pol2 ChIA-PET), and transcriptomic (RNA-seq and miRNA-seq) maps of EndoC-βH1. Analyses of these maps define known (e.g., PDX1 and ISL1) and putative (e.g., PCSK1 and mir-375) β cell-specific transcriptional cis-regulatory networks and identify allelic effects on cis-regulatory element use. Importantly, comparison with maps generated in primary human islets and/or β cells indicates preservation of chromatin looping but also highlights chromosomal aberrations and fetal genomic signatures in EndoC-βH1. Together, these maps, and a web application we created for their exploration, provide important tools for the design of experiments to probe and manipulate the genetic programs governing β cell identity and (dys)function in diabetes

Wilms Tumor Chromatin Profiles Highlight Stem Cell Properties and a Renal Developmental Network

Wilms tumor is the most common pediatric kidney cancer. To identify transcriptional and epigenetic mechanisms that drive this disease, we compared genome-wide chromatin profiles of Wilms tumors, embryonic stem cells (ESCs), and normal kidney. Wilms tumors prominently exhibit large active chromatin domains previously observed in ESCs. In the cancer, these domains frequently correspond to genes that are critical for kidney development and expressed in the renal stem cell compartment. Wilms cells also express “embryonic” chromatin regulators and maintain stem cell-like p16 silencing. Finally, Wilms and ESCs both exhibit “bivalent” chromatin modifications at silent promoters that may be poised for activation. In Wilms tumor, bivalent promoters correlate to genes expressed in specific kidney compartments and point to a kidney-specific differentiation program arrested at an early-progenitor stage. We suggest that Wilms cells share a transcriptional and epigenetic landscape with a normal renal stem cell, which is inherently susceptible to transformation and may represent a cell of origin for this disease

Improved reference genome of Aedes aegypti informs arbovirus vector control

Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector

Mechanistic dissection of chromatin topology disruption in the 5q14.3 MEF2C locus as an indirect driver of neurodevelopmental disorders

Structural variants have the potential to create long-range positional effects, uncouple genes from regulatory elements, and facilitate aberrant 3D chromatin folding. In an independent study, we revealed a significant enrichment of intergenic balanced chromosomal abnormality (BCA) breakpoints from congenital anomaly cases at chromosome 5q14.3. All 11 5q14.3 BCA carriers had breakpoints disrupting the topologically associated domain (TAD) housing MEF2C, a known driver of neurodevelopmental disorders. In a second study, we showed, using 4C-seq, that MEF2C forms proximal and distal interaction loops within this TAD, contacting multiple neuronal enhancers. To understand the functional impact of these BCAs, we performed a mechanistic dissection of the 3D regulatory network at the 5q14.3 locus and its constituent functional elements using Cas9-based genome editing. We generated >200 cell lines, representing deletions of MEF2C alongside five MEF2C TAD boundary and interaction loop targets in iPS-derived neural stem cells (NSCs) and cortical induced neurons (iNs). We profiled changes in expression and 3D chromatin interactions within these models using RNA-seq and 4C-seq. MEF2C was variably differentially expressed upon deletion of proximal and distal MEF2C loop regions, with effects depending on cell type and variant class. Underlying chromatin interaction patterns revealed evidence of loop maintenance in these models, possibly via CTCF buffering, highlighting compensatory mechanisms against 3D chromatin disruption. In contrast, deletion of the proximal TAD boundary facilitated increased contacts with predicted enhancers in the adjacent TAD. Our results suggest novel regulatory mechanisms driving phenotypic outcomes for the 5q14.3 region, with significant implications for interpretation of pathogenic structural variation

A rapid, low-cost, and highly sensitive SARS-CoV-2 diagnostic based on whole-genome sequencing

Early detection of SARS-CoV-2 infection is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying SARS-CoV-2 infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this method amplifies the entirety of the SARS-CoV-2 genome. This contrasts with typical RT-PCR-based diagnostic tests, which amplify only a few loci. To achieve this goal, we combine a SARS-CoV-2 enrichment method developed by the ARTIC Network (https://artic.network/) with short-read DNA sequencing and&nbsp;de novo&nbsp;genome assembly. Using this method, we can reliably (&gt;95% accuracy) detect SARS-CoV-2 at a concentration of 84 genome equivalents per milliliter (GE/mL). The vast majority of diagnostic methods meeting our analytical criteria that are currently authorized for use by the United States Food and Drug Administration with the Coronavirus Disease 2019 (COVID-19) Emergency Use Authorization require higher concentrations of the virus to achieve this degree of sensitivity and specificity. In addition, we can reliably assemble the SARS-CoV-2 genome in the sample, often with no gaps and perfect accuracy given sufficient viral load. The genotypic data in these genome assemblies enable the more effective analysis of disease spread than is possible with an ordinary binary diagnostic. These data can also help identify vaccine and drug targets. Finally, we show that the diagnoses obtained using POLAR of positive and negative clinical nasal mid-turbinate swab samples 100% match those obtained in a clinical diagnostic lab using the Center for Disease Control&rsquo;s 2019-Novel Coronavirus test. Using POLAR, a single person can manually process 192 samples over an 8-hour experiment at the cost of ~$36 per patient (as of December 7th, 2022), enabling a 24-hour turnaround with sequencing and data analysis time. We anticipate that further testing and refinement will allow greater sensitivity using this approach.</p

Chromatin alternates between A and B compartments at kilobase scale for subgenic organization

Abstract Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF’s RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted