A Genotyping Array for the Globally Invasive Vector Mosquito, Aedes albopictus

BACKGROUND: Although whole-genome sequencing (WGS) is the preferred genotyping method for most genomic analyses, limitations are often experienced when studying genomes characterized by a high percentage of repetitive elements, high linkage, and recombination deserts. The Asian tiger mosquito (Aedes albopictus), for example, has a genome comprising up to 72% repetitive elements, and therefore we set out to develop a single-nucleotide polymorphism (SNP) chip to be more cost-effective. Aedes albopictus is an invasive species originating from Southeast Asia that has recently spread around the world and is a vector for many human diseases. Developing an accessible genotyping platform is essential in advancing biological control methods and understanding the population dynamics of this pest species, with significant implications for public health. METHODS: We designed a SNP chip for Ae. albopictus (Aealbo chip) based on approximately 2.7 million SNPs identified using WGS data from 819 worldwide samples. We validated the chip using laboratory single-pair crosses, comparing technical replicates, and comparing genotypes of samples genotyped by WGS and the SNP chip. We then used the chip for a population genomic analysis of 237 samples from 28 sites in the native range to evaluate its usefulness in describing patterns of genomic variation and tracing the origins of invasions. RESULTS: Probes on the Aealbo chip targeted 175,396 SNPs in coding and non-coding regions across all three chromosomes, with a density of 102 SNPs per 1 Mb window, and at least one SNP in each of the 17,461 protein-coding genes. Overall, 70% of the probes captured the genetic variation. Segregation analysis found that 98% of the SNPs followed expectations of single-copy Mendelian genes. Comparisons with WGS indicated that sites with genotype disagreements were mostly heterozygotes at loci with WGS read depth \u3c 20, while there was near complete agreement with WGS read depths \u3e 20, indicating that the chip more accurately detects heterozygotes than low-coverage WGS. Sample sizes did not affect the accuracy of the SNP chip genotype calls. Ancestry analyses identified four to five genetic clusters in the native range with various levels of admixture. CONCLUSIONS: The Aealbo chip is highly accurate, is concordant with genotypes from WGS with high sequence coverage, and may be more accurate than low-coverage WGS

Microfluidics: reframing biological enquiry

The underlying physical properties of microfluidic tools have led to new biological insights through the development of microsystems that can manipulate, mimic and measure biology at a resolution that has not been possible with macroscale tools. Microsystems readily handle sub-microlitre volumes, precisely route predictable laminar fluid flows and match both perturbations and measurements to the length scales and timescales of biological systems. The advent of fabrication techniques that do not require highly specialized engineering facilities is fuelling the broad dissemination of microfluidic systems and their adaptation to specific biological questions. We describe how our understanding of molecular and cell biology is being and will continue to be advanced by precision microfluidic approaches and posit that microfluidic tools - in conjunction with advanced imaging, bioinformatics and molecular biology approaches - will transform biology into a precision science

Receipt for payment from John Cocke, Greensboro, Alabama, for Thomas Cocke to Justin E. Beebe, March 28, 1837

This document is part of the John Cocke papers that contains the personal, business, and legal papers of this 19th century Marengo County, Alabama, plantation owner, who not only managed his own plantation but also served as an agent for various family members. Financial papers consist of receipts from grocers and suppliers detailing purchases (including slave purchases); account books for his blacksmith shop; and labor accounts with payroll. There are cotton records that contain correspondence as well as accounts

Recovery of Thumb and Finger Extension and Its Relation to Grasp Performance After Stroke

This study investigated how the ability to extend the fingers and thumb recovers early after stroke and how the ability to extend all of the digits affects grasping performance. We studied 24 hemiparetic patients at 3 and 13 wk post stroke. At each visit, we tested the subjects' ability to actively extend all five digits of their contralesional, affected hand against gravity and to perform a grasp movement with the same hand. Three-dimensional motion analysis captured: 1) maximal voluntary extension excursion of each digit and 2) grasp performance variables of movement time, peak aperture, peak aperture rate, and aperture path ratio. We found that finger and thumb extension improved from 3 to 13 wk, with average improvements ranging from 12 to 19° across the five digits. Grasp performance improved on two of the four variables measured. Peak apertures and peak aperture rates improved from 3 to 13 wk, but self-selected movement time and aperture path ratio did not. Stepwise multiple regression models showed that the majority of variance in grasp performance at 13 wk could be predicted by the ability to extend the index or middle finger at 3 wk, plus the change in the ability to extend the index finger from 3 to 13 wk. R2 values ranged from 0.55 to 0.89. Our data indicate that the amount of recovery in finger and thumb extension and grasping is small from 3 to 13 wk post stroke. In people with relatively pure motor hemiparesis, one important factor underlying deficits in hand shaping during grasping is the inability to extend the fingers and thumb. Without sufficient volitional control of finger and thumb extension, successful grasping of objects will not occur

Morphologies and cytoskeletal structure for HT-1080 fibrosarcoma cells (HT-1080s) and primary human dermal fibroblasts (hDFs) in synthetic extracellular matrix (ECM).

<div><p>(<b>A</b>) Schematic representation of synthetic extracellular matrix (synthetic ECM) formed through “thiol-ene” photopolymerization chemistry to couple norbornene C=C bonds on 4-arm poly(ethylene glycol) (PEG) molecules with thiol (-SH) bonds of cysteine-containing peptides. Crosslinks were formed using matrix metalloproteinase (MMP)-degradable peptides with cysteine groups on each end while adhesion was promoted using pendant RGD-containing peptides (C<b>RGDS</b>) with a single cysteine (2.5 or 3 wt% by mass PEG-NB + MMP-degradable crosslinking peptide, shear moduli = 140 Pa or 220 Pa respectively). Constant total pendant peptide was maintained using non-bioactive C<i><b>RDGS</b></i> (1500 μM active C<b>RGDS</b> + non-active C<i><b>RDGS</b></i>). </p> <p>(<b>B</b>-<b>I</b>) Projected z-stack immunofluorescence (IF) images illustrating hDFs and HT-1080s seeded in synthetic ECM (220 Pa, 1000 μM CRGDS). All overlay images are counterstained with TRITC-conjugated phalloidin (F-actin, red) and DAPI (nuclei, blue). (<b>B</b>,<b>C</b>) Overview to illustrate morphological differences (F-actin, red; Nuclei, blue) for (<b>B</b>) hDFs and (<b>C</b>) HT-1080s. (<b>D</b>-<b>F</b>) IF images illustrating myosin IIb expression for hDFs: (<b>D</b>) Overlay image (Myosin IIb, green; F-actin, red; Nuclei, blue); Single channel images (grayscale) illustrate (<b>E</b>) F-actin and (<b>F</b>) Myosin IIb. White arrows point to actomyosin filaments. (<b>G</b>-<b>I</b>) IF images illustrating myosin IIb expression for <b><i>HT-1080s</i></b>: (<b>G</b>) Overlay (Myosin IIb, green; F-actin, red; Nuclei, blue); Single channel images (grayscale) illustrate (<b>H</b>) F-actin and (<b>I</b>) Myosin IIb. </p> <p>(<b>J</b>-<b>L</b>) Comparison of quantified mean (<b>J</b>) circularity and (<b>K</b>) elongation for hDFs and HT-1080s calculated using Nikon NIS Elements software (n > 150 cells, ≥ 6 hydrogels, at least two separate experiments; *** = p<0.001). (<b>L</b>) Fraction of elongated (Elongation ≥ 3.0), middle (2.0 ≤ Elongation < 3.0), and rounded (Elongation < 2.0) cells. Differences in fraction of elongated and rounded hDFs compared to HT-1080s were each statistically significant (N ≥ 6 total gels, at least two separate experiments; *** = p<0.001). </p></div

Matrix influences on migration and morphologies for HT-1080s in synthetic ECM.

<p>(<b>A</b>) Cell speed and (<b>B</b>) directionality (DTO/TD) for HT-1080s as a function of matrix conditions (≥ 6 gels, ≥ 40 cells, at least two separate experiments; * = p<0.05; ** = p<0.01). X-axis: Modulus in Pa / RGD concentration in μM. <i>Box</i> and <i>whisker </i><i>plot </i><i>for </i><i>cell </i><i>speed</i>: White diamond = mean, white line = median, boxes = middle upper (top) and middle lower (bottom) quartile of the cell population, whiskers = highest (above) and lowest (below) migration speeds. Error bars for DTO/TD represent standard error of the mean for individual cells. There is also a statistical difference in cell speed for the 140 Pa (1500 μM RGD) and 220 Pa (250 μM RGD) conditions (p<0.05, not shown on graph for clarity). (<b>C</b>) A comparison of the fraction of rounded HT-1080s (Elongation Index < 2.0) as a function of synthetic ECM conditions (x-axis: Modulus in Pa / RGD concentration in μM; white bar = 140 Pa; black bars = 220 Pa). Error bars represent standard deviation for fraction of rounded cells per gel (≥ 6 gels, at least two separate experiments; * = p<0.05; ** = p<0.01; *** = p<0.001). </p

Contractile movement for HT-1080s in 3D culture.

<div><p>(<b>A</b>) Propagation of a constriction ring (arrow) for an HT-1080 migrating in synthetic ECM (220 Pa, 1000 μM CRGDS; 10 min / frame, see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081689#pone.0081689.s014" target="_blank">Movie S3</a>). (<b>B</b>) Propagation of a constriction ring (arrow) for an HT-1080 migrating in collagen (1.7 mg/mL; 15 min./frame, see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081689#pone.0081689.s020" target="_blank">Movie S9</a>). Scale bars = 25 μm.</p> <p>(<b>C</b>-<b>G</b>) Z-projected immunofluorescence images illustrating myosin IIb expression for an HT-1080 in synthetic ECM (220 Pa, 1000 μM CRGDS): (<b>C</b>) Overlay image illustrating myosin IIb (green), counterstained with TRITC-conjugated phalloidin (F-actin, red) and DAPI (nucleus, blue). Single channel images (grayscale) illustrate (<b>D</b>) F-actin and (<b>E</b>) Myosin IIb. Profile plots generated using ImageJ “Interactive 3D Surface Plot” function (“Spectrum” intensity scale, projection for middle 3 planes) illustrate (<b>F</b>) F-actin and (<b>G</b>) Myosin IIb. Two consecutive single plane images (grayscale) illustrate (<b>H</b>) F-actin and (<b>I</b>) Myosin IIb.</p></div