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"Hernandez, Tim Z"
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Mañana means heaven
Set against an ominous backdrop of California in the 1940's, deep in the agricultural heartland of the Great Central Valley, \"Manana Means Heaven\" reveals the desperate circumstances that lead a married woman to an illicit affair with an young, aspiring writer.
BOOK
A Genomics Approach to Deciphering Lignin Biosynthesis in Switchgrass
It is necessary to overcome recalcitrance of the biomass to saccharification (sugar release) to make switchgrass (Panicum virgatum) economically viable as a feedstock for liquid biofuels. Lignin content correlates negatively with sugar release efficiency in switchgrass, but selecting the right gene candidates for engineering lignin biosynthesis in this tetraploid outcrossing species is not straightforward. To assist this endeavor, we have used an inducible switchgrass cell suspension system for studying lignin biosynthesis in response to exogenous brassinolide. By applying a combination of protein sequence phylogeny with whole-genome microarray analyses of induced cell cultures and developing stem internode sections, we have generated a list of candidate monolignol biosynthetic genes for switchgrass. Several genes that were strongly supported through our bioinformatics analysis as involved in lignin biosynthesis were confirmed by gene silencing studies, in which lignin levels were reduced as a result of targeting a single gene. However, candidate genes encoding enzymes involved in the early steps of the currently accepted monolignol biosynthesis pathway in dicots may have functionally redundant paralogues in switchgrass and therefore require further evaluation. This work provides a blueprint and resources for the systematic genome-wide study of the monolignol pathway in switchgrass, as well as other C4 monocot species.
Journal Article
IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry
The identification of bacteria is central to the microbiological sciences. While gene sequencing methods have been the standard to identify bacteria, use of MALDI-TOF mass spectrometry (MS) in clinical microbiology provides high-throughput identification to the subspecies level. However, biotyping has yet to be adopted outside of clinical settings due to the lack of a centralized public database of MS protein signatures that would facilitate strain identification via spectral comparison. Herein we present the IDBac web platform, a crowd-sourced central knowledgebase of protein MS signatures of >1400 strains spanning 6 bacterial phyla. Accompanying the knowledgebase is analysis infrastructure to identify unknown isolates, probe relationships within culture collections, and visualize specialized metabolite differences within groups of closely related bacteria. We highlight this utility by demonstrating the dereplication of bacterial isolates using the seed knowledgebase, identifying trends in culture collections using metadata integration, and reporting the discovery of a new metabolite from a
isolate.
Journal Article
The Anatomy of a Personal Health Agent
Health is a fundamental pillar of human wellness, and the rapid advancements in large language models (LLMs) have driven the development of a new generation of health agents. However, the application of health agents to fulfill the diverse needs of individuals in daily non-clinical settings is underexplored. In this work, we aim to build a comprehensive personal health agent that is able to reason about multimodal data from everyday consumer wellness devices and common personal health records, and provide personalized health recommendations. To understand end-users' needs when interacting with such an assistant, we conducted an in-depth analysis of web search and health forum queries, alongside qualitative insights from users and health experts gathered through a user-centered design process. Based on these findings, we identified three major categories of consumer health needs, each of which is supported by a specialist sub-agent: (1) a data science agent that analyzes personal time-series wearable and health record data, (2) a health domain expert agent that integrates users' health and contextual data to generate accurate, personalized insights, and (3) a health coach agent that synthesizes data insights, guiding users using a specified psychological strategy and tracking users' progress. Furthermore, we propose and develop the Personal Health Agent (PHA), a multi-agent framework that enables dynamic, personalized interactions to address individual health needs. To evaluate each sub-agent and the multi-agent system, we conducted automated and human evaluations across 10 benchmark tasks, involving more than 7,000 annotations and 1,100 hours of effort from health experts and end-users. Our work represents the most comprehensive evaluation of a health agent to date and establishes a strong foundation towards the futuristic vision of a personal health agent accessible to everyone.
Paper
ISOGENIC AUTOSOMES TO BE APPLIED IN OPTIMAL SCREENING FOR NOVEL MUTANTS WITH VIABLE PHENOTYPES IN DROSOPHILA MELANOGASTER
Most insertional mutagenesis screens of Drosophila performed to date have not used target chromosomes that have been checked for their suitability for phenotypic screens for viable phenotypes. To address this, we have generated a selection of stocks carrying either isogenized second chromosomes or isogenized third chromosomes, in a genetic background derived from a Canton-S wild-type strain. We have tested these stocks for a range of behavioral and other viable phenotypes. As expected, most lines are statistically indistinguishable from Canton-S in most phenotypes tested. The lines generated are now being used as target chromosomes in mutagenesis screens, and the characterization reported here will facilitate their use in screens of these lines for behavioral and other viable phenotypes.
Journal Article
CLASSY IV: Exploring UV diagnostics of the interstellar medium in local high-\\(z\\) analogs at the dawn of the JWST era
The COS Legacy Archive Spectroscopic SurveY (CLASSY) HST/COS treasury program provides the first high-resolution spectral catalogue of 45 local high-z analogues in the UV (1200-2000\\AA) to investigate their stellar and gas properties. We present a toolkit of UV interstellar medium (ISM) diagnostics, analyzing the main emission lines of CLASSY spectra (i.e., NIV]\\(\\lambda\\lambda\\)1483,87, CIV\\(\\lambda\\lambda\\)1548,51, HeII\\(\\lambda\\)1640, OIII]\\(\\lambda\\lambda\\)1661,6, SiIII]\\(\\lambda\\lambda\\)1883,92, CIII]\\(\\lambda\\lambda\\)1907,9). Specifically, we focus our investigation on providing accurate diagnostics for reddening, electron density and temperature, gas-phase metallicity and ionization parameter, taking into account the different ionization zones of the ISM. We calibrate our UV toolkit using well-known optical diagnostics, analyzing archival optical spectra for all the CLASSY targets. We find that UV density diagnostics estimate ne values that are ~1-2 dex higher (e.g., ne(CIII]\\(\\lambda\\lambda\\)}1907,9)~10\\(^4\\)cm\\(^{-3}\\)) than those inferred from their optical counterparts (e.g., ne([SII]\\(\\lambda\\lambda\\)6717,31)~10\\(^2\\)cm\\(^{-3}\\)). Te derived from the hybrid ratio OIII]\\(\\lambda\\)1666/[OIII]\\(\\lambda\\)}5007 proves to be a reliable Te diagnostic, with differences in 12+log(O/H) within ~\\(\\pm\\)0.3dex. We also investigate the relation between the stellar and gas E(B-V), finding consistent values at high specific star formation rates, while at low sSFR we confirm an excess of dust attenuation in the gas. Finally, we investigate UV line ratios and equivalent widths to provide correlations with 12+log(O/H) and log(U), but note there are degeneracies between the two. With this suite of UV-based diagnostics, we illustrate the pivotal role CLASSY plays in understanding the chemical and physical properties of high-z systems that JWST can observe in the rest-frame UV.
Paper