Cruise report: summer 2009 Sapelo Island National Estuarine Research Reserve ecological characterization (June 7 - June 13, 2009)

This cruise report is a summary of a field survey conducted within the Sapelo Island National Estuarine Research Reserve (SINERR), located on the Georgia coastline, June 7 – June 13, 2009. Multiple indicators of ecological condition and human dimensions were sampled synoptically at each of 30 stations throughout SINERR using a random probabilistic sampling design. Samples were collected for the analysis of benthic community structure and composition; concentrations of chemical contaminants (metals, pesticides, PAHs, PCBs, PBDEs) in sediments and target demersal biota; nutrient and chlorophyll levels in the water column; bacterial contaminants in the water column; and other basic habitat characteristics such as depth, salinity, temperature, dissolved oxygen, turbidity, total suspended solids, pH, sediment grain size, and organic carbon content. In addition to the fish samples that were collected for analysis of chemical contaminants relative to human-health consumption limits, other human-dimension indicators were sampled as well including presence or absence of fishing gear, vessels, surface trash, and noxious sediment odors. The overall purpose of the survey was to collect data to assess the status of ecosystem condition and potential stressor impacts throughout SINERR, based on these various indicators and corresponding management thresholds, and to provide this information as a baseline for determining how such conditions may be changing with time. While sample analysis is still ongoing a few preliminary results and observations are reported here. A final report will be completed once all data have been processed. The results will provide a comprehensive weight-of-evidence basis for evaluating current condition (aka a “state-of-the-SINEER environmental report”) and serve as a quantitative benchmark for tracking any future changes due to either natural or human disturbances. Another goal of the study is to demonstrate its utility as a possible model for assessing the status of condition at other NEERS sites using similar and consistent methods to promote system-wide regional and national comparisons.

Manipulation of chromosomes in fish: review of various techniques and their implications in aquaculture

Human ingenuity has made it possible to advent the chromosome manipulation techniques to produce individuals with differing genomic status in a number of fish using various causal agents such as physical shocks (temperature or hydrostatic pressure), chemical (endomitotics) and anesthetic treatments either to suppress the second meiotic division shortly after fertilization of eggs or to prevent the first mitotic division shortly prior to mitotic cleavage formation. This results in the induction of polyploidy (triploidy and tetraploidy), gynogenesis (both meiotic and mitotic leading to clonal lines) and androgenesis in fish population. The rationale for the induction of such ploidy in fish has been its potential for generating sterile individuals, rapidly inbred lines and masculinized fish, which could be of benefit to fish farming and aquaculture. In this paper, these are critically reviewed and the implication of recently developed chromosome manipulation techniques to various fin fishes is discussed.

Reciprocal chromosome painting illuminates the history of genome evolution of the domestic cat, dog and human

Domestic cats and dogs are important companion animals and model animals in biomedical research. The cat has a highly conserved karyotype, closely resembling the ancestral karyotype of mammals, while the dog has one of the most extensively rearranged mammalian karyotypes investigated so far. We have constructed the first detailed comparative chromosome map of the domestic dog and cat by reciprocal chromosome painting. Dog paints specific for the 38 autosomes and the X chromosomes delineated 68 conserved chromosomal segments in the cat, while reverse painting of cat probes onto red fox and dog chromosomes revealed 65 conserved segments. Most conserved segments on cat chromosomes also show a high degree of conservation in G-banding patterns compared with their canine counterparts. At least 47 chromosomal fissions (breaks), 25 fusions and one inversion are needed to convert the cat karyotype to that of the dog, confirming that extensive chromosome rearrangements differentiate the karyotypes of the cat and dog. Comparative analysis of the distribution patterns of conserved segments defined by dog paints on cat and human chromosomes has refined the human/cat comparative genome map and, most importantly, has revealed 15 cryptic inversions in seven large chromosomal regions of conserved synteny between humans and cats.

Conserved chromosome segments in Hylobates hoolock revealed by human and H-leucogenys paint probes

A complete comparative chromosome map of the white-browed gibbon (Hylobates hoolock, 2n = 38), white-cheeked gibbon (Hylobates leucogenys, 2n = 52), and human has been established by hybridising H. leucogenys chromosome-specific paints and human 24-colour paints onto H. hoolock metaphase chromosomes. In the 18 H. hoolock autosomes, we identified 62 conserved segments that showed DNA homology to regions of the 25 H. leucogenys autosomes, Numerous interchromosomal rearrangements differentiate the karyotypes of H. leucogenys and H. hoolock. Only H. hoolock chromosome 10 showed homology to one entire autosome of H. leucogenys. The hybridisation of human 24-colour paints not only confirmed most of the chromosome correspondences between human and H. hoolock established previously but also helped to correct five erroneous assignments and revealed three new segments. Our results demonstrate that the karyotypes of the extant gibbons have arisen mainly through extensive translocation events and that the karyotype of H. hoolock more closely resembles the ancestral karyotype of Hylobates, rather than the karyotype of H. leucogenys. Copyright (C) 2001 S. Karger AG, Basel.

Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype

The Afrotheria, a supraordinal grouping of mammals whose radiation is rooted in Africa, is strongly supported by DNA sequence data but not by their disparate anatomical features. We have used flow-sorted human, aardvark, and African elephant chromosome painting probes and applied reciprocal painting schemes to representatives of two of the Afrotherian orders, the Tubulidentata (aardvark) and Proboscidea (elephants), in an attempt to shed additional light on the evolutionary affinities of this enigmatic group of mammals. Although we have not yet found any unique cytogenetic signatures that support the monophyly of the Afrotheria, embedded within the aardvark genome we find the strongest evidence yet of a mammalian ancestral karyotype comprising 2n = 44. This karyotype includes nine chromosomes that show complete conserved synteny to those of man, six that show conservation as single chromosome arms or blocks in the human karyotype but that occur on two different chromosomes in the ancestor, and seven neighbor-joining combinations (i.e., the synteny is maintained in the majority of species of the orders studied so far, but which corresponds to two chromosomes in humans). The comparative chromosome maps presented between human and these Afrotherian species provide further insight into mammalian genome organization and comparative genomic data for the Afrotheria, one of the four major evolutionary clades postulated for the Eutheria.

Refined genome-wide comparative map of the domestic horse, donkey and human based on cross-species chromosome painting: insight into the occasional fertility of mules

We have made a complete set of painting probes for the domestic horse by degenerate oligonucleotide-primed PCR amplification of flow-sorted horse chromosomes. The horse probes, together with a full set of those available for human, were hybridized onto metaphase chromosomes of human, horse and mule. Based on the hybridization results, we have generated genome-wide comparative chromosome maps involving the domestic horse, donkey and human. These maps define the overall distribution and boundaries of evolutionarily conserved chromosomal segments in the three genomes. Our results shed further light on the karyotypic relationships among these species and, in particular, the chromosomal rearrangements that underlie hybrid sterility and the occasional fertility of mules.

Chromosome painting between human and lorisiform prosimians: Evidence for the HSA 7/16 Synteny in the primate ancestral karyotype

Multidirectional chromosome painting with probes derived from flow-sorted chromosomes of humans (Homo sapiens, HSA, 2n = 46) and galagos (Galago moholi, GMO, 2n = 38) allowed us to map evolutionarily conserved chromosomal segments among humans, galagos, a

African origin of modern humans in East Asia: A tale of 12,000 Y chromosomes

To test the hypotheses of modern human origin in East Asia, we sampled 12,127 male individuals from 163 populations and typed for three Y chromosome biallelic markers (YAP, M89, and M130). All the individuals carried a mutation at one of the three sites.

Molecular evolution of microcephalin, a gene determining human brain size

Microcephalin gene is one of the major players in regulating human brain development. It was reported that truncated mutations in this gene can cause primary microcephaly in humans with a brain size comparable with that of early hominids. We studied the m

STUDIES ON THE CHROMOSOMES OF GENUS NYCTICEBUS

The karyotypes of three species (N. coucang, N. intermedius, and N. pygmaeus) of genus Nycticebus, collected from the southern Yunnan of China, have been studied. All individuals from three species possess 2n=50 chromosomes, and all chromosomes in their complement are biarm chromosomes. The karyotype of slow loris (N. coucang) is characterized by having a secondary constriction and Ag-NORs in the short arms of pair No. 1. The G-banding patterns of three species are very similar. Three species are found to have multiple Ag-NORs. In N. coucang, NORs were observed on five pairs (Nos. 1, 6, 9, 15, and 23) and in N. intermedius and N. pygmaeus, NORs were found on four pairs (Nos. 6, 9, 15, and 20). This finding indicates that slow lorises, as primitive primates, also have multiple NOR-bearing chromosomes. Finally, the classification of genus Nycticebus by karyotype analysis is discussed, and our results suggest that there are at least two valid species, namely: N. coucang and N. pygmaeus.

Localization of Sry gene on Y chromosome of Muntjac munticus vaginalis

The chromosomes 1, Y-1, Y-2 of Muntjac munticus vaginalis were isolated by fluorescence activated chromosome sorting and amplified by degenerate oligonucleotide primed-polymerase chain reaction ( DOP-PCR). A primer pair within human Sry HMG box was design

SECRETORY MONOCLONAL IGA ANTIBODY TO HUMAN SPERM PRODUCED BY GASTROINTESTINAL IMMUNIZATION INHIBITS HUMAN SPERM ACTIVITY AND MOUSE INVITRO FERTILIZATION

BALB/c mice were immunized intragastrically with human sperm. Cells from the Peyer's patches and spleens of the immunized mice were for the preparation of hybridomas secreting antisperm monoclonal IgA (mcIgA). The specific ratio of IgA-secreting cells in Peyer's patches was much higher than that in spleen. The binding site on human sperm of 9 of 19 mcIgA was in the post-acrosomal region using an immunofluorescent assay. Two of eight selected mcIgA caused strong human sperm agglutination and three of them produced significant inhibition of mouse in vitro fertilization. No mcIgA tested caused obvious human sperm immobilization or inhibited mouse in vivo fertilization. In vitro assembly of selected mcIgA in ascites with mouse secretory component (SC) caused no significant changes in effects on sperm function and in vitro fertilization. By use of Western blotting, dimer or higher polymers were demonstrated in all selected mcIgAs and corresponding protein antigens in 6 of 8 selected mcIgAs. These results suggest that human sperm function may be inhibited and fertilization rate reduced by specific secretory IgA to human sperm and that secretory immunity to protein antigens of human sperm could be induced by intragastrointestinal immunization.

Molecular modeling on some human interleukins sharing gamma c of interleukin-2 receptor, and structure-function relationships

Five models for human interleukin-7 (HIL-7), HIL-9, HIL-13, HIL-15 and HIL-17 have been generated by SYBYL software package. The primary models were optimized using molecular dynamics and molecular mechanics methods. The final models were optimized using a steepest descent algorithm and a subsequent conjugate gradient method. The complexes with these interleukins and the common gamma chain of interleukin-2 receptor (IL-2R) were constructed and subjected to energy minimization. We found residues, such as Gln127 and Tyr103, of the common gamma chain of IL-2R are very important. Other residues, e.g. Lys70, Asn128 and Glu162, are also significant. Four hydrophobic grooves and two hydrophilic sites converge at the active site triad of the gamma chain. The binding sites of these interleukins interaction with the common gamma chain exist in the first helical and/or the fourth helical domains. Therefore, we conclude that these interleukins binds to the common gamma chain of IL-2R by the first and the fourth helix domain. Especially at the binding sites of some residues (lysine, arginine, asparagine, glutamic acid and aspartic acid), with a discontinuous region of the common gamma chain of IL-2R, termed the interleukins binding sites (103-210). The study of these sites can be important for the development of new drugs. (C) 2000 Elsevier Science B.V. All rights reserved.