Genetics and Genomics Commons^™

Density, Species, And Size Distribution Of Groupers (Serranidae) In Three Habitats At Elbow Reef, Florida Keys, Robert Sluka, Mark Chiappone, Kathleen Sullivan-Sealey, Thomas Potts, Jose Levy, Emily Schmitt Lavin, Geoff Meester

Emily F Schmitt Lavin

We examined the density, size and species distribution of groupers in three habitats on an inshore-to-offshore transect across Elbow Reef, Florida Keys: high-relief spur-and-groove (4–9 m depth), relict spur-and-groove (10–20 m), and deep fore reef slope (21–30 m). Physical relief was greatest in the high-relief spur-and-groove (up to 3 m), lowest in the relict spur-and-groove habitat (<0.5–1 m), and intermediate in the deep fore reef slope habitat (1–1.5 m). Benthic coverage in the three habitats was dominated by algae (>30%). There were significant differences in the density, size, and species distribution of groupers among the three habitats. Graysby, Epinephelus cruentatus, was numerically dominant, constituting 82–91% of individual observed. Black grouper, Mycteroperca bonaci, and Nassau grouper, E. striatus, were more abundant in high …

Systematic Analysis Of Dynamic Mirna-Target Interactions During C. Elegans Development, Liang Zhang, Molly Hammell, Brian Kudlow, Victor Ambros, Min Han

Victor R. Ambros

Although microRNA (miRNA)-mediated functions have been implicated in many aspects of animal development, the majority of miRNA::mRNA regulatory interactions remain to be characterized experimentally. We used an AIN/GW182 protein immunoprecipitation approach to systematically analyze miRNA::mRNA interactions during C. elegans development. We characterized the composition of miRNAs in functional miRNA-induced silencing complexes (miRISCs) at each developmental stage and identified three sets of miRNAs with distinct stage-specificity of function. We then identified thousands of miRNA targets in each developmental stage, including a significant portion that is subject to differential miRNA regulation during development. By identifying thousands of miRNA family-mRNA pairs with temporally …

Micrornas: Genetically Sensitized Worms Reveal New Secrets, Victor Ambros

Victor R. Ambros

Why do many microRNA gene mutants display no evident phenotype? Multiply mutant worms that are selectively impaired in genetic regulatory network activities have been used to uncover previously unknown functions for numerous Caenorhabditis elegans microRNAs.

Three-Dimensional Confocal Microscopy Indentation Method For Hydrogel Elasticity Measurement, Donghee Lee, Md Mahmudur Rahman, You Zhou, Sangjin Ryu

Md Mahmudur Rahman

No abstract provided.

Dorsoventral Boundary For Organizing Growth And Planar Polarity In The Drosophila Eye, Amit Singh, Janghoo Lim, Kwang-Wook Choi

Amit Singh

A fundamental feature of developing tissues and organs is generation of planar polarity of cells in an epithelium with respect to the body axis.

The Drosophila compound eye shows two-tier dorsoventral (DV) planar polarity. At the individual ommatidium level, the eight photoreceptors in each unit eye form a dorsoventrally asymmetric cluster. At the level of eye field, hundreds of ommatidia in the upper and lower halves of an eye are uniformly polarized dorsally or ventrally, respectively. This results in DV mirror symmetries about the equator. The uniform orientations of photoreceptor clusters over long distance in the eye field provide an …

The Genetics Of Hepatitis C Virus Underlie Its Ability To Escape Humoral Immunity, Jay Kolls, Gyongyi Szabo

Gyongyi Szabo

Hepatitis C virus (HCV) is a leading cause of chronic liver disease, and efforts to develop therapeutic vaccine strategies have been limited by immune escape due to HCV variants that are resistant to current vaccines or HCV variants that rapidly acquire new resistance-conferring mutations. Recently, the crystal structure of the viral envelope protein E2 region was resolved as well as how E2 docks to the host CD81 protein; therefore, antibodies that block this interaction should prevent viral entry into host cells. In this issue of the JCI, Bailey and colleagues show that immune escape of HCV can occur by naturally …

Hnrnp A1 And Secondary Structure Coordinate Alternative Splicing Of Mag, Nancy Zearfoss, Emily Johnson, Sean Ryder

Sean P. Ryder

Myelin-associated glycoprotein (MAG) is a major component of myelin in the vertebrate central nervous system. MAG is present in the periaxonal region of the myelin structure, where it interacts with neuronal proteins to inhibit axon outgrowth and protect neurons from degeneration. Two alternatively spliced isoforms of Mag mRNA have been identified. The mRNA encoding the shorter isoform, known as S-MAG, contains a termination codon in exon 12, while the mRNA encoding the longer isoform, known as L-MAG, skips exon 12 and produces a protein with a longer C-terminal region. L-MAG is required in the central nervous system. How inclusion of …

Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective, Matthieu Foll, Yu Poh, Nicholas Renzette, Anna Admetlla, Claudia Bank, Hyunjin Shim, Anna Malaspinas, Gregory Ewing, Ping Liu, Daniel Wegmann, Daniel Caffrey, Konstantin Zeldovich, Daniel Bolon, Jennifer Wang, Timothy Kowalik, Celia Schiffer, Robert Finberg, Jeffrey Jensen

Celia A. Schiffer

The challenge of distinguishing genetic drift from selection remains a central focus of population genetics. Time-sampled data may provide a powerful tool for distinguishing these processes, and we here propose approximate Bayesian, maximum likelihood, and analytical methods for the inference of demography and selection from time course data. Utilizing these novel statistical and computational tools, we evaluate whole-genome datasets of an influenza A H1N1 strain in the presence and absence of oseltamivir (an inhibitor of neuraminidase) collected at thirteen time points. Results reveal a striking consistency amongst the three estimation procedures developed, showing strongly increased selection pressure in the presence …

Xk Aprosencephaly And Anencephaly In Sibs, Phillip Townes, Karen Reuter, E. Rosquete, B. Magee

B. Dale Magee

Recent studies have suggested a causal and pathogenetic relationship between holoprosencephaly and anencephaly. In support of the proposed relationship we report a sibship that includes anencephalic male twins and a female infant with a severe form of alobar holoprosencephaly, radial aplasia, and oligodactyly. The upper limb and brain malformations are considered to represent aprosencephaly syndrome. The coexistence of anencephaly and aprosencephaly within a sibship suggests that XK aprosencephaly syndrome may be an autosomal recessive disorder.

Transgenesis In Animal Agriculture And Zoonotic Disease Resistance, Michael Greger

Michael Greger, M.D.

In 2009, the US Food and Drug Administration (FDA) released guidelines for the commercialization of genetically engineered (GE) farm animals. Numerous applications for approval of transgenic species are currently pending. Anthropocentric concerns raised to date have tended to neglect the impact of the physiological trade-off between production efficiency and immune function. Given animal agriculture's track record of prioritizing productivity - even at the expense of animal health - the incorporation of biotechnological tools to further stress production towards biological limits may continue to undermine immunocompetence. Regulatory schemata to avert adverse public health outcomes are discussed. Given the rising incidence of …

Human Treg Responses Allow Sustained Recombinant Adeno-Associated Virus-Mediated Transgene Expression, Christian Mueller, Jeffrey Chulay, Bruce Trapnell, Margaret Humphries, Brenna Carey, Robert Sandhaus, Noel Mcelvaney, Louis Messina, Qiushi Tang, Farshid Rouhani, Martha Campbell-Thompson, Ann Fu, Anthony Yachnis, David Knop, Guo-Jie Ye, Mark Brantly, Roberto Calcedo, Suryanarayan Somanathan, Lee Richman, Robert Vonderheide, Maigan Hulme, Todd Brusko, James Wilson, Terence Flotte

Christian Mueller

Recombinant adeno-associated virus (rAAV) vectors have shown promise for the treatment of several diseases; however, immune-mediated elimination of transduced cells has been suggested to limit and account for a loss of efficacy. To determine whether rAAV vector expression can persist long term, we administered rAAV vectors expressing normal, M-type alpha-1 antitrypsin (M-AAT) to AAT-deficient subjects at various doses by multiple i.m. injections. M-specific AAT expression was observed in all subjects in a dose-dependent manner and was sustained for more than 1 year in the absence of immune suppression. Muscle biopsies at 1 year had sustained AAT expression and a reduction …

Identification Of Muscidifurax Spp. By Polymerase Chain Reaction-Restriction Fragment Length Polymorphism, David Taylor, Allen Szalanski

David B. Taylor

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the nuclear ribosomal ITS1 region was used to differentiate Muscidifurax (Hymenoptera: Pteromalidae) species which are parasitoids of filth fly pupae. Three restriction enzymes, Dpn 11, Mse I, and Taq I, produced restriction patterns which were diagnostic for the four species analyzed, M. raptor, M. raptorellus, M. uniraptor, and M. zaraptor. Seven other restriction enzymes were able to differentiate one or more of the species and can be used alone, or in combination with other enzymes, to verify identifications. No intraspecific variation was observed among the populations examined. The utility of the …

Genetic Similarity Among Pheromone And Voltinism Races Of Ostrinia Nubilalis (Hubner) (Lepidoptera: Crambidae), P. C. R. G. Marcon, David B. Taylor, C. E. Mason, R. L. Hellmich, Blair Siegfried

David B. Taylor

The genetic variability of seven European corn borer populations, Ostrinia nubilalis, from North America and Europe was assessed by polymerase chain reaction- restriction fragment length polymorphism (PCRRFLP) analysis and DNA sequencing. The nuclear ribosomal internal transcribed spacer 1 (ITS-1) region (≈ 500 base pair [bp]) and four mitochondrial (mtDNA) regions (1550 bp total) were examined. The smartweed borer, Ostrinia obumbratalis, and south-Western corn borer, Diatraea grandiosella, were used for comparisons. Of 106 restriction sites identified (80 in mtDNA and 26 in ITS-1), none differentiated geographical populations, pheromone races, or voltine ecotypes of the European corn borer. The lack of variation …

Population Genetics And Gene Variation In Secondary Screwworm (Diptera: Calliphoridae), David Taylor, Richard Peterson Ii

David B. Taylor

Allozyme variation in 4 populations of secondary screwworm, Cochliomyia macellaria (F.), representing North, Central, and South America was examined . Variability was observed in 12 of 13 enzyme loci, and the frequency of the most common allele was <0.95 for 6 loci . Observed and expected heterozygosities were 0.149 and 0.154, respectively. Nei's genetic distances were ≤ 0.001. Goodness-of-fit statistics for Hardy-Weinberg equilibrium and Wright's FIS statistics indicated random mating within populations . Wright's FST statistics and chi-square contingency analyses indicated homogeneous gene frequencies among the populations. These data suggest that C. macellaria is a panmictic species with high levels …

Sugar Feeding In Adult Stable Flies, David Taylor, Dennis R. Berkebile

David B. Taylor

Adult stable flies (Stomoxys calcitrans L.) are known to feed readily on sugars in the laboratory. However, little is known concerning the extent of stable fly sugar feeding in wild populations. We examined the frequency of sugar feeding in stable flies collected on Alsynite sticky traps in rural and urban environments. In addition, stable flies were visually examined to determine whether blood was present in the gut. In laboratory studies, sugars were detectable with the anthrone technique in stable flies for ~3 d after being imbibed, and blood could be visually detected in the gut for 24-48 h after feeding. …

When Should Judges Admit Or Compel Genetic Tests?, Diane Hoffmann, Karen Rothenberg

Diane Hoffmann

No abstract provided.

Clustering With Exclusion Zones: Genomic Applications, Mark Segal, Yuanyuan Xiao, Fred Huffer

Mark R Segal

Methods for formally evaluating the clustering of events in space or time, notably the scan statistic, have been richly developed and widely applied. In order to utilize the scan statistic and related approaches, it is necessary to know the extent of the spatial or temporal domains wherein the events arise. Implicit in their usage is that these domains have no “holes”—hereafter “exclusion zones”—regions in which events a priori cannot occur. However, in many contexts, this requirement is not met. When the exclusion zones are known, it is straightforward to correct the scan statistic for their occurrence by simply adjusting the …

Identification Of Yeast Transcriptional Regulation Networks Using Multivariate Random Forests, Yuanyuan Xiao, Mark Segal

Mark R Segal

The recent availability of whole-genome scale data sets that investigate complementary and diverse aspects of transcriptional regulation has spawned an increased need for new and effective computational approaches to analyze and integrate these large scale assays. Here, we propose a novel algorithm, based on random forest methodology, to relate gene expression (as derived from expression microarrays) to sequence features residing in gene promoters (as derived from DNA motif data) and transcription factor binding to gene promoters (as derived from tiling microarrays). We extend the random forest approach to model a multivariate response as represented, for example, by time-course gene expression …

Chess, Chance And Conspiracy, Mark Segal

Mark R Segal

Chess and chance are seemingly strange bedfellows. Luck and/or randomness have no apparent role in move selection when the game is played at the highest levels. However, when competition is at the ultimate level, that of the World Chess Championship (WCC), chess and conspiracy are not strange bedfellows, there being a long and colorful history of accusations levied between participants. One such accusation, frequently repeated, was that all the games in the 1985 WCC (Karpov vs Kasparov) were fixed and prearranged move by move. That this claim was advanced by a former World Champion, Bobby Fischer, argues that it ought …