3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing.

There is a need for methods that can image chromosomes with genome-wide coverage, as well as greater genomic and optical resolution. We introduce OligoFISSEQ, a suite of three methods that leverage fluorescence in situ sequencing (FISSEQ) of barcoded Oligopaint probes to enable the rapid visualization of many targeted genomic regions. Applying OligoFISSEQ to human diploid fibroblast cells, we show how four rounds of sequencing are sufficient to produce 3D maps of 36 genomic targets across six chromosomes in hundreds to thousands of cells, implying a potential to image thousands of targets in only five to eight rounds of sequencing.

The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos.

Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts.

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling.

Chromosome organization is crucial for genome function. Here, we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. Using the super-resolution microscopy methods of OligoSTORM and OligoDNA-PAINT, we trace 8 megabases of human chromosome 19, visualizing structures ranging in size from a few kilobases to over a megabase.

Rediscovered parasitism of Andrena savignyi Spinola (Hymenoptera, Andrenidae) by Stylops (Strepsiptera, Stylopidae) and revised taxonomic status of the parasite.

Parasitism of Andrena (Suandrena) savignyi Spinola (Hymenoptera: Andrenidae) by Stylops Kirby (Strepsiptera: Stylopidae) has been recorded only once, and from an individual collected in Egypt almost a century ago, with the parasite described as Stylops savignyi Hofeneder. The recent rediscovery of this Stylops from an individual of Andrena savignyi permits a reinterpretation of the species and its affinities among other Stylops. The bee was collected at flowers of Zilla spinosa (Turra) Prantl.

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes.

Fluorescence in situ hybridization (FISH) is a powerful single-cell technique for studying nuclear structure and organization. Here we report two advances in FISH-based imaging. We first describe the in situ visualization of single-copy regions of the genome using two single-molecule super-resolution methodologies.

A new species of the cleptoparasitic bee genus Thyreus from northern Yemen and southwestern Saudi Arabia (Hymenoptera, Apidae).

A new species of cleptoparasitic bee of the genus Thyreus Panzer (Apinae: Melectini) is described and figured from northern Yemen and southwestern Saudi Arabia. Thyreus shebicus Engel, sp. n.

Cardiovascular changes in atherosclerotic ApoE-deficient mice exposed to Co60 (γ) radiation.

Background: There is evidence for a role of ionizing radiation in cardiovascular diseases. The goal of this work was to identify changes in oxidative and nitrative stress pathways and the status of the endothelinergic system during progression of atherosclerosis in ApoE-deficient mice after single and repeated exposure to ionizing radiation.

Methods And Results: B6.

A new species of Chalicodoma from Saudi Arabia with modified facial setae (Hymenoptera, Megachilidae).

Some bees and pollen wasps have independently evolved simple, stiff, erect, apically-curved, curly or hooked facial setae as adaptations to collect pollen from nototribic flowers. A distinctive new species of Chalicodoma Lepeletier de Saint Fargeau subgenus Pseudomegachile Friese from Saudi Arabia with such morphological adaptations, Chalicodoma riyadhensesp. n.

The large carpenter bees of central Saudi Arabia, with notes on the biology of Xylocopa sulcatipes Maa (Hymenoptera, Apidae, Xylocopinae).

The large carpenter bees (Xylocopinae, Xylocopa Latreille) occurring in central Saudi Arabia are reviewed. Two species are recognized in the fauna, Xylocopa (Koptortosoma) aestuans (Linnaeus) and Xylocopa (Ctenoxylocopa) sulcatipes Maa. Diagnoses for and keys to the species of these prominent components of the central Saudi Arabian bee fauna are provided to aid their identification by pollination researchers active in the region.

A new wild, pollinating bee species of the genus Tetraloniella from the Arabian Peninsula (Hymenoptera, Apidae).

A new species of the eucerine bee genus Tetraloniella Ashmead (Apinae: Eucerini) is described and figured from central Saudi Arabia and Qatar. Tetraloniella (Tetraloniella) persiciformissp. n.

The indigenous honey bees of Saudi Arabia (Hymenoptera, Apidae, Apis mellifera jemenitica Ruttner): Their natural history and role in beekeeping.

Apis mellifera jemenitica Ruttner (= yemenitica auctorum: videEngel 1999) has been used in apiculture throughout the Arabian Peninsula since at least 2000 BC. Existing literature demonstrates that these populations are well adapted for the harsh extremes of the region. Populations of Apis mellifera jemenitica native to Saudi Arabia are far more heat tolerant than the standard races often imported from Europe.

Defective repair of UV-induced DNA damage in cultured primary skin fibroblasts from Saudi thyroid cancer patients.

This study was conducted to examine the sensitivity of primary skin fibroblasts from Saudi thyroid cancer (TC) patients to ultraviolet (UV) irradiation. Cell survival was studied by a colony forming assay and DNA repair defects with a host cell reactivation (HCR) assay using UV-irradiated Herpes Simplex Virus (HSV). In addition, p53 gene expression was examined in the same TC cells exhibiting enhanced radiosensitivity.

Radiation and cardiovascular diseases.

Both epidemiological and experimental evidence emphasize the connection between radiation exposure and cancer. Little effort has been directed toward finding an association between radiation and cardiovascular diseases. Lately, studies on the A-bomb survivors and Chernobyl accident victims have indicated that radiation doses as low as 0.

Deficiency in the repair of UV-induced DNA damage in human skin fibroblasts compromised for the ATM gene.

Ataxia-telangiectasia (A-T), is an autosomal recessive disease characterized by neurological and immunological symptoms, radiosensitivity and cancer predisposition. A-T cells exhibit a greatly decreased survival and a reduction in DNA synthesis inhibition as well as p53 induction in response to ionizing radiation. Occasionally, some strains of A-T cells have been reported to manifest a slightly enhanced sensitivity with no consistent observations of a deficiency in either cell cycle control or the repair of DNA damage after treatment with ultraviolet (UV) light.