High-Resolution Genomic Profiling of Chromosomal Abnormalities in Human Stem Cells Using the 135 K StemArray

Culturing stem cells for an extended period of time can lead to acquired chromosomal aberrations. Determining the copy number variant (CNV) profile of stem cell lines is critical since CNVs can have dramatic effects on gene expression and tumorigenic potential. Here, we describe an improved version of our StemArray, a stem-cell-focused comparative genomic hybridization (aCGH) microarray, which contains 135,000 probes and covers over 270 stem cell and cancer related genes at the exon level. We have dramatically increased the median probe spacing throughout the genome in order to obtain a higher resolution genetic profile of the cell lines. To illustrate the importance of using the StemArray, we describe a karyotypically normal iPSC line in which we detected acquired chromosomal variations that could affect the cellular phenotype of the cells. Identifying adaptive chromosomal aberrations in stem cell lines is essential if they are to be used in regenerative medicine

Characterization of Pallid Sturgeon (\u3ci\u3eScaphirhynchus albus\u3c/i\u3e) Spawning Habitat in the Lower Missouri River

Acipenseriformes (sturgeons and paddlefish) globally have declined throughout their range due to river fragmentation, habitat loss, overfishing, and degradation of water quality. In North America, pallid sturgeon (Scaphirhynchus albus) populations have experienced poor to no recruitment, or substantial levels of hybridization with the closely related shovelnose sturgeon (S. platorynchus). The Lower Missouri River is the only portion of the species’ range where successful reproduction and recruitment of genetically pure pallid sturgeon have been documented. This paper documents spawning habitat and behavior on the Lower Missouri River, which comprises over 1,300 km of unfragmented river habitat. The objective of this study was to determine spawning locations and describe habitat characteristics and environmental conditions (depth, water velocity, substrate, discharge, temperature, and turbidity) on the Lower Missouri River. We measured habitat characteristics for spawning events of ten telemetry-tagged female pallid sturgeon from 2008–2013 that occurred in discrete reaches distributed over hundreds of kilometers. These results show pallid sturgeon select deep and fast areas in or near the navigation channel along outside revetted banks for spawning. These habitats are deeper and faster than nearby river habitats within the surrounding river reach. Spawning patches have a mean depth of 6.6 m and a mean depth-averaged water-column velocity of 1.4 m per second. Substrates in spawning patches consist of coarse bank revetment, gravel, sand, and bedrock. Results indicate habitat used by pallid sturgeon for spawning is more common and widespread in the present-day channelized Lower Missouri River relative to the sparse and disperse coarse substrates available prior to channelization. Understanding the spawning habitats currently utilized on the Lower Missouri River and if they are functioning properly is important for improving habitat remediation measures aimed at increasing reproductive success. Recovery efforts for pallid sturgeon on the Missouri River, if successful, can provide guidance to sturgeon recovery on other river systems; particularly large, regulated, and channelized rivers

Sanger Confirmation Is Required to Achieve Optimal Sensitivity and Specificity in Next-Generation Sequencing Panel Testing

Next-generation sequencing (NGS) has rapidly replaced Sanger sequencing as the method of choice for diagnostic gene-panel testing. For hereditary-cancer testing, the technical sensitivity and specificity of the assay are paramount as clinicians use results to make important clinical management and treatment decisions. There is significant debate within the diagnostics community regarding the necessity of confirming NGS variant calls by Sanger sequencing, considering that numerous laboratories report having 100% specificity from the NGS data alone. Here we report our results from 20,000 hereditary-cancer NGS panels spanning 47 genes, in which all 7845 nonpolymorphic variants were Sanger- sequenced. Of these, 98.7% were concordant between NGS and Sanger sequencing and 1.3% were identified as NGS false-positives, located mainly in complex genomic regions (A/T-rich regions, G/C-rich regions, homopolymer stretches, and pseudogene regions). Simulating a false-positive rate of zero by adjusting the variant-calling quality-score thresholds decreased the sensitivity of the assay from 100% to 97.8%, resulting in the missed detection of 176 Sanger-confirmed variants, the majority in complex genomic regions (n = 114) and mosaic mutations (n = 7). The data illustrate the importance of setting quality thresholds for panel testing only after thousands of samples have been processed and the necessity of Sanger confirmation of NGS variants to maintain the highest possible sensitivity

Contract Report for FY 2019 & FY 2020 National Geological & Geophysical Data Preservation Project

The Bureau of Economic Geology has a rich history of mineral exploration and mining that predates its role as the Geological Survey of Texas, established in 1858. Many publications from the United States Geological Survey, United States Bureau of Mines, and Bureau of Economic Geology addressing mineral resources were published before the digital age and the development of the internet. Most of this valuable information is preserved and archived as annual mineral reports, reports of investigations, mineral circulars, and other products published between 1858 and 1990. As part of the National Geological and Geophysical Data Preservation Project funded through the United States Geological Survey, two project goals were developed to assist in the identification of critical minerals in Texas. Project Goal 1 for 2019 and 2020 aimed to acquire and review all publications, materials, and data that reference and describe mineral information, mineral deposits, and occurrences hosting critical minerals. This data was transcribed into provided spreadsheets and information templates, including details such as name, location, geology, resource information on contained commodities, production information, resource or reserve estimations, ore grade, deposit type, mining history, reference citations, and other relevant information. Project Goal 2 aimed to develop a statewide depth to Precambrian basement map in common geospatial digital data format using the national Geologic Map Schema (GeMS) and available seismic and drill core data. Although Precambrian basement has been mapped and interpolated in oil and gas basins, and identified as surface (and near-surface) exposure in central and western Texas, there had not been an effort to compile all of these data into a complete and distributable geospatial dataset and published basement map. The state of Texas boasts abundant well log data, and the Bureau of Economic Geology, functioning as the state geological survey, possesses numerous seismic and geophysical surveys, as well as thousands of cross-sections and drill core data. This project aimed to leverage these resources to create a comprehensive and accessible dataset and map of Precambrian basement depths across the state.Bureau of Economic Geolog

Repetitive Sampling and Control Threshold Improve 16S rRNA Gene Sequencing Results From Produced Waters Associated With Hydraulically Fractured Shale

Sequencing microbial DNA from deep subsurface environments is complicated by a number of issues ranging from contamination to non-reproducible results. Many samples obtained from these environments – which are of great interest due to the potential to stimulate microbial methane generation – contain low biomass. Therefore, samples from these environments are difficult to study as sequencing results can be easily impacted by contamination. In this case, the low amount of sample biomass may be effectively swamped by the contaminating DNA and generate misleading results. Additionally, performing field work in these environments can be difficult, as researchers generally have limited access to and time on site. Therefore, optimizing a sampling plan to produce the best results while collecting the greatest number of samples over a short period of time is ideal. This study aimed to recommend an adequate sampling plan for field researchers obtaining microbial biomass for 16S rRNA gene sequencing, applicable specifically to low biomass oil and gas-producing environments. Forty-nine different samples were collected by filtering specific volumes of produced water from a hydraulically fractured well producing from the Niobrara Shale. Water was collected in two different sampling events 24 h apart. Four to five samples were collected from 11 specific volumes. These samples along with eight different blanks were submitted for analysis. DNA was extracted from each sample, and quantitative polymerase chain reaction (qPCR) and 16S rRNA Illumina MiSeq gene sequencing were performed to determine relative concentrations of biomass and microbial community composition, respectively. The qPCR results varied across sampled volumes, while no discernible trend correlated contamination to volume of water filtered. This suggests that collecting a larger volume of sample may not result in larger biomass concentrations or better representation of a sampled environment. Researchers could prioritize collecting many low volume samples over few high-volume samples. Our results suggest that there also may be variability in the concentration of microbial communities present in produced waters over short (i.e., hours) time scales, which warrants further investigation. Submission of multiple blanks is also vital to determining how contamination or low biomass effects may influence a sample set collected from an unknown environment

Savanna responses to feral buffalo in Kakadu National Park, Australia

Savannas are the major biome of tropical regions, spanning 30% of the Earth\u27s land surface. Tree: grass ratios of savannas are inherently unstable and can be shifted easily by changes in fire, grazing, or climate. We synthesize the history and ecological impacts of the rapid expansion and eradication of an exotic large herbivore, the Asian water buffalo (Bubalus bubalus), on the mesic savannas of Kakadu National Park (KNP), a World Heritage Park located within the Alligator Rivers Region (ARR) of monsoonal north Australia. The study inverts the experience of the Serengeti savannas where grazing herds rapidly declined due to a rinderpest epidemic and then recovered upon disease control. Buffalo entered the ARR by the 1880s, but densities were low until the late 1950s when populations rapidly grew to carrying capacity within a decade. In the 1980s, numbers declined precipitously due to an eradication program. We show evidence that the rapid population expansion and Sudden removal of this exotic herbivore created two ecological cascades by altering around cover abundance and composition, which in turn affected competitive regimes and fuel loads with possible further, long-term effects due to changes in fire regimes. Overall, ecological impacts varied across a north-south gradient in KNP that corresponded to the interacting factors of precipitation, landform, and vegetation type but was also contingent upon the history of buffalo harvest. Floodplains showed the greatest degree of impact during the period of rapid buffalo expansion, but after buffalo removal, they largely reverted to their prior state. Conversely, the woodlands experienced less visible impact during the first cascade. However, in areas of low buffalo harvest and severe impact, there was little recruitment of juvenile trees into the canopy due to the indirect effects of grazing and high frequency of prescribed fires once buffalo were removed. Rain forests were clearly heavily impacted during the first cascade, but the long term consequences of buffalo increase and removal remain unclear. Due to hysteresis effects, the simple removal of an exotic herbivore was not sufficient to return savanna systems to their previous state

Ortho-semantic learning of novel words: An event-related potential study of grade 3 children

Introduction: As children become independent readers, they regularly encounter new words whose meanings they must infer from context, and whose spellings must be learned for future recognition. The self-teaching hypothesis proposes orthographic learning skills are critical in the transition to fluent reading, while the lexical quality hypothesis further emphasizes the importance of semantics. Event-related potential (ERP) studies of reading development have focused on effects related to the N170 component—print tuning (letters vs. symbols) and lexical tuning (real words vs. consonant strings)—as well as the N400 reflecting semantic processing, but have not investigated the relationship of these components to word learning during independent reading. Methods: In this study, children in grade 3 independently read short stories that introduced novel words, then completed a lexical decision task from which ERPs were derived. Results: Like real words, newly-learned novel words evoked a lexical tuning effect, indicating rapid establishment of orthographic representations. Both real and novel words elicited significantly smaller N400s than pseudowords, suggesting that semantic representations of the novel words were established. Further, N170 print tuning predicted accuracy on identifying the spellings of the novel words, while the N400 effect for novel words was associated with reading comprehension. Discussion: Exposure to novel words during self-directed reading rapidly establishes neural markers of orthographic and semantic processing. Furthermore, the ability to rapidly filter letter strings from symbols is predictive of orthographic learning, while rapid establishment of semantic representations of novel words is associated with stronger reading comprehension

An Approach to Measuring Step Excrescence Effects in the Presence of a Pressure Gradient

An experimental study was undertaken to determine the effects of step excrescences on boundary layer transition using a unique ground test facility in which the test model was propelled though still air. The models used were designed to have a nominally constant pressure gradient so that the results would be relevant to laminar flow aircraft whose wings often have long runs of mildly favorable pressure gradient. The models had an integrated continuously adjustable two-dimensional step, which could be adjusted to be forward-facing or aft-facing. The large model was used to increase the Reynolds numbers examined so that the results are applicable to laminar flow flight vehicles. Multiple measurement methods, including Preston tubes, hot wires, accelerometers, a boundary layer traverse, and static pressure taps were used to provide comparison data, and to add to the physical understanding of the results. The propelled-model test approach required that the instrumentation be self-contained and ride along with the model as the carrier vehicle moved down the test track. Due to the relatively short times available for data-taking (approximately 15-30 seconds per run), the initialization and data analysis techniques had to be tailored for this application

High Quality, Low Cost Egg Incubator for BIC Church in Choma, Zambia

The Egg Incubator team is partnering with the Brethren in Christ Church located in Choma, Zambia to design a high-quality, low-cost chicken egg incubator to supply the pastors and church members with a means of food and income. The design will need to take into account the accessibility and cost of the tools and materials. The current prototype features separate heating and humidity systems, a control system to maintain a set temperature and humidity, and tilting egg racks. The heating system consists of two stovetop coils to produce heat and a fan to transfer it to the air. The humidifier utilizes an atomizer in a pan of water to create a mist that mixes with the hot air to create humidity. The control system uses a proportional integral derivative controller (PID) to keep the temperature at 37 ± 1 °C and the humidity at 60–70%. The egg racks are tilted by a motor that runs every 6 hours to prevent the embryos from sticking to the shell. With a fully functioning prototype, the team has begun to incubate 60 real fertilized eggs. During the 21-day incubation process, a final prototype iteration is being designed and will be built on-site in Zambia in May 2022. Funding for this work provided by The Collaboratory for Strategic Partnerships and Applied Research.https://mosaic.messiah.edu/engr2022/1004/thumbnail.jp

Evidence of two deeply divergent co-existing mitochondrial genomes in the Tuatara reveals an extremely complex genomic organization

Animal mitochondrial genomic polymorphism occurs as low-level mitochondrial heteroplasmy and deeply divergent co-existing molecules. The latter is rare, known only in bivalvian mollusks. Here we show two deeply divergent co-existing mt-genomes in a vertebrate through genomic sequencing of the Tuatara (Sphenodon punctatus), the sole-representative of an ancient reptilian Order. The two molecules, revealed using a combination of short-read and long-read sequencing technologies, differ by 10.4% nucleotide divergence. A single long-read covers an entire mt-molecule for both strands. Phylogenetic analyses suggest a 7–8 million-year divergence between genomes. Contrary to earlier reports, all 37 genes typical of animal mitochondria, with drastic gene rearrangements, are confirmed for both mt-genomes. Also unique to vertebrates, concerted evolution drives three near-identical putative Control Region non-coding blocks. Evidence of positive selection at sites linked to metabolically important transmembrane regions of encoded proteins suggests these two mt-genomes may confer an adaptive advantage for an unusually cold-tolerant reptile