Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Coccidioidomycosis Among Hispanic Farm Workers, California, USA, 2018 - Volume 26, Number 7—July 2020 - Emerging Infectious Diseases journal - CDC

To determine occupational risk factors for coccidioidomycosis among adult Hispanic outdoor agricultural workers in California, USA, we conducted a case-control study of workers seen at the Kern County medical facility and referred to the public health laboratory for coccidioidomycosis serologic testing. Participants completed an interviewer-administered health and work questionnaire. Among 203 participants (110 case-patients with positive and 93 controls with negative serologic results), approximately half were women, and more than three quarters were born in Mexico. Associated with coccidioidomycosis were self-reported dust exposure and work with root and bulb vegetable crops. A protective factor was leaf removal, an activity associated with grape cultivation. We conclude that subjective dust exposure and work with root and bulb vegetable crops are associated with increased risk for coccidioidomycosis among Hispanic farm workers. The agricultural industry should evaluate and promote dust-reduction measures, including wetting soil and freshly harvested products

Combining Forces - The Use of Landsat TM Satellite Imagery, Soil Parameter Information, and Multiplex PCR to Detect <i>Coccidioides immitis</i> Growth Sites in Kern County, California

<div><p>Coccidioidomycosis is a fungal disease acquired through the inhalation of spores of <i>Coccidioides</i> spp., which afflicts primarily humans and other mammals. It is endemic to areas in the southwestern United States, including the San Joaquin Valley portion of Kern County, California, our region of interest (ROI). Recently, incidence of coccidioidomycosis, also known as valley fever, has increased significantly, and several factors including climate change have been suggested as possible drivers for this observation. Up to date details about the ecological niche of <i>C. immitis</i> have escaped full characterization. In our project, we chose a three-step approach to investigate this niche: 1) We examined Landsat-5-Thematic-Mapper multispectral images of our ROI by using training pixels at a 750 m×750 m section of Sharktooth Hill, a site confirmed to be a <i>C. immitis</i> growth site, to implement a Maximum Likelihood Classification scheme to map out the locations that could be suitable to support the growth of the pathogen; 2) We used the websoilsurvey database of the US Department of Agriculture to obtain soil parameter data; and 3) We investigated soil samples from 23 sites around Bakersfield, California using a multiplex Polymerase Chain Reaction (PCR) based method to detect the pathogen. Our results indicated that a combination of satellite imagery, soil type information, and multiplex PCR are powerful tools to predict and identify growth sites of <i>C. immitis</i>. This approach can be used as a basis for systematic sampling and investigation of soils to detect <i>Coccidioides</i> spp.</p></div

Location and description of sampling sites used as test data for the remote sensing approach.

<p>Growth sites (GS), accumulation sites (AS) and negative sites (NS) were determined by multiplex PCR results, nd: not determined.</p><p>* Proof of rodent activity was observed in the immediate neighborhood of the sampling site. Soil disturbing activity was also observed by burrowing owls, coyotes, kit foxes, spiders or large ants at some locations. The dominant rodents observed were ground squirrels, kangaroo rats and hares.</p><p>Location and description of sampling sites used as test data for the remote sensing approach.</p

Agreement between multiplex PCR and MLC for the STH vegetation class and the STH-thermal class to predict growth sites of <i>C. immitis</i> (to agree a prediction by either multiplex PCR or MLC must be confirmed at least once for the four years by the other method).

<p>From altogether 25 sites, only 23 were considered, because no multiplex PCR results were obtained for STH sites I and II.</p><p>Agreement between multiplex PCR and MLC for the STH vegetation class and the STH-thermal class to predict growth sites of <i>C. immitis</i> (to agree a prediction by either multiplex PCR or MLC must be confirmed at least once for the four years by the other method).</p

Detailed physical and chemical information obtained from the USDA websoilsurvey database for all sites included in this study.

<p>Indicated in cursive are the parameters which seemed to be most important to distinguish <i>C. immitis</i> growth sites from negative sites.</p><p>Detailed physical and chemical information obtained from the USDA websoilsurvey database for all sites included in this study.</p

high oven

highWithdraw? [check] Seems too obvious to include?Not UsedNot usedWithdrawnChecked by Jordyn Hughes on Tue 21 Apr 201

Example of multiplex PCR results.

<p>White arrows point on a 223 bp fragment that represents <i>C. immitis</i>. Site Bear Mt. Rd. shows the strongest ITS amplicons in all soil layers, whereas sites Cole's Levee Rd. and site Across CALM gave a weaker signal in some soil layers, and site Beech Str. was negative. NC  =  negative control. Bands that indicate the presence of the pathogen in the 2% Agarose gel were confirmed to origin from <i>C. immitis</i> by sequencing.</p

Probability that the sites fall in the STH-vegetation class, as predicted by Landsat data.

<p>(<b>Y</b> = in class [indicated in bold], N = not in class).</p><p>nd* = not determined in this study.</p><p>nd** = not determined in this study, but confirmed as growth site by Swatek (1970).</p><p>growth site* =  sites were <i>C. immitis</i> was detected at least twice in a deeper soil layer during the late winter/spring (February-May).</p><p>accumulation site* =  the pathogen could only be detected on the surface of the sampling site and never in a deeper soil layer over a several year period.</p><p>negative site* = the pathogen could not be detected in any of the soil samples using the multiplex PCR method as described in this study.</p><p>Probability that the sites fall in the STH-vegetation class, as predicted by Landsat data.</p

Extend of soil series in the San Joaquin Valley, CA, which can support the growth of <i>C. immitis</i>.

<p><b>A</b>: Pleito (brown: SE and NE Kern County, dark orange: W Fresno County, light orange: W Merced County, tan: San Joaquin County) <b>B</b>: Chanac (brown: SE, NE and NW Kern County, dark orange: San Louis Obispo County [Paso Robles area], light orange: San Luis Obispo County, [Carrizo Plains]), and <b>C</b>: Garces soil series (brown: NW Kern County, dark orange: Kings County, light orange: W Tulare County, tan: E Fresno Area), Center for Environmental Informatics at Pennsylvania State University (CEI), <a href="http://www.cei.psu.edu/soiltool/semtool.html" target="_blank">http://www.cei.psu.edu/soiltool/semtool.html</a><u>.</u></p