Objective: To describe the systematic analysis of constitutional de novo apparently balanced translocations in patients presenting with abnormal phenotypes, characterise the structural chromosome ...rearrangements, map the translocation breakpoints, and report detectable genomic imbalances. Methods: DNA microarrays were used with a resolution of 1 Mb for the detailed genome-wide analysis of the patients. Array CGH was used to screen for genomic imbalance and array painting to map chromosome breakpoints rapidly. These two methods facilitate rapid analysis of translocation breakpoints and screening for cryptic chromosome imbalance. Breakpoints of rearrangements were further refined (to the level of spanning clones) using fluorescence in situ hybridisation where appropriate. Results: Unexpected additional complexity or genome imbalance was found in six of 10 patients studied. The patients could be grouped according to the general nature of the karyotype rearrangement as follows: (A) three cases with complex multiple rearrangements including deletions, inversions, and insertions at or near one or both breakpoints; (B) three cases in which, while the translocations appeared to be balanced, microarray analysis identified previously unrecognised imbalance on chromosomes unrelated to the translocation; (C) four cases in which the translocation breakpoints appeared simple and balanced at the resolution used. Conclusions: This high level of unexpected rearrangement complexity, if generally confirmed in the study of further patients, will have an impact on current diagnostic investigations of this type and provides an argument for the more widespread adoption of microarray analysis or other high resolution genome-wide screens for chromosome imbalance and rearrangement.
Microbial and phytoplankton processes, and their effect on water quality were examined over a 3-week period in five high-intensity (120 animals m
−2) shrimp (
Litopenaeus vannamei) ponds of varying ...crop ages at Belize Aquaculture Ltd., (BAL) in Central America. These ponds were characterized by zero water exchange throughout the crop, plastic lining and high aeration rates. Nitrogen (N) and organic carbon (C) inputs, in the form of fishmeal-based feed, grain-based feed and molasses, resulted in high concentrations of dissolved organic and inorganic N (2.29–5.56 and 0.17–10.66 mg l
−1, respectively) and dissolved organic C (14.20–48.10 mg l
−1). Phosphate levels were also high, ranging from 0.07 to 1.17 mg l
−1. The high nutrient concentrations promoted the growth of bacteria, phytoplankton (mostly autotrophic flagellates) and protozoa. Up to 40% of the bacteria were associated with flocculated matter. However, bacterial numbers and oxygen (O
2) consumption in the water column did not appear to increase with crop age. This may be due to a reduction in the C/N ratio below the optimum for bacterial growth. Up to 22% of the O
2 consumption was due to nitrification and there was some indication of lowering of total ammoniacal N (TAN) concentrations and an increase in nitrite and nitrate levels in older crops. Both phytoplankton and bacteria were responsible for high rates of ammonium uptake. In ponds with high nitrate concentrations, nitrate uptake rates were also high. Phytoplankton productivity remained high irrespective of crop age and ponds fluctuated between net O
2 production (autotrophy) and net O
2 consumption (heterotrophy) irrespective of crop age. This reflected the highly dynamic nature of the bacterial and phytoplankton populations with frequent blooms and crashes of individual phytoplankton species. The high mixing rates resulted in phytoplankton and other detritus remaining suspended in the water column. However, a small area of sludge (<2% of pond area) did accumulate containing a high N and C content, and high pore water TAN. This study showed that despite what is generally considered as poor water quality in the ponds, i.e. high nutrient concentrations, high and unstable phytoplankton numbers, and high bacterial numbers, shrimp production was high relative to conventional ponds. There appeared to be scope for increasing bacterial production in these systems by increasing the C/N ratio, and hence C availability for bacterial growth. However, it remains to be established which microbial processes are likely to be promoted, and if the benefits of this outweigh the costs.
High-intensity, zero-exchange shrimp ponds contain a high density of flocculated particles, rich in bacteria and phytoplankton, compared with flow-through systems. The flocculated particles provide a ...potential food source for shrimp. Short-term tank experiments were conducted to determine the retention of nitrogen (N) from natural biota, dominated by flocculated particles, in white shrimp (
Litopenaeus vannamei) at a high-intensity, zero-exchange shrimp farm in Central America (Belize Aquaculture (BAL)). There were two treatments: ‘floc’ and ‘floc+20%’ (3×1000-l replicate tanks each) based on two densities of flocculated particles. The floc density in the ‘floc’ treatment was typical of shrimp growout ponds at BAL, whereas the ‘floc+20%’ treatment had a 20% higher density of flocculated particles. Three consecutive experiments were conducted with 1, 5 and 9 g shrimp, respectively. At the start of the experiment,
15N-ammonium was added to the tanks and assimilated by the natural biota. Shrimp were maintained in these tanks for 48 h after the
15N-nitrogen enrichment. After this time, shrimp were found to be enriched with
15N-nitrogen. It was calculated that between 1% and 3% of the particulate nitrogen in the tanks, principally from the flocculated particles, was retained by the shrimp. The proportion of estimated daily nitrogen retention of the shrimp contributed by the natural biota was calculated to be 18% to 29% for 1 to 9 g animals in the floc treatment. There was a tendency for greater retention in the floc+20% treatments, but this trend was not consistent. This study suggests that natural biota, which in this system was largely flocculated particles, can contribute substantially to the nutrition of
L. vannamei. There are, therefore, benefits for shrimp in the promotion of flocculated particles in
L. vannamei ponds. Whether this translates into improvements in shrimp growth and production efficiency remains to be established.
Chromosome 6 is a metacentric chromosome that constitutes about 6% of the human genome. The finished sequence comprises 166,880,988 base pairs, representing the largest chromosome sequenced so far. ...The entire sequence has been subjected to high-quality manual annotation, resulting in the evidence-supported identification of 1,557 genes and 633 pseudogenes. Here we report that at least 96% of the protein-coding genes have been identified, as assessed by multi-species comparative sequence analysis, and provide evidence for the presence of further, otherwise unsupported exons/genes. Among these are genes directly implicated in cancer, schizophrenia, autoimmunity and many other diseases. Chromosome 6 harbours the largest transfer RNA gene cluster in the genome; we show that this cluster co-localizes with a region of high transcriptional activity. Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome.
The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of ...human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.
Objective: The authors describe a method, termed array painting, which allows the rapid, high resolution analysis of the content and breakpoints of aberrant chromosomes. Methods: Array painting is ...similar in concept to reverse chromosome painting and involves the hybridisation of probes generated by PCR of small numbers of flow sorted chromosomes on large insert genomic clone DNA microarrays. Results and Conclusions: By analysing patients with cytogenetically balanced chromosome rearrangements, the authors show the effectiveness of array painting as a method to map breakpoints prior to cloning and sequencing chromosome rearrangements.
Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in ...B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.
The finished sequence of human chromosome 10 comprises a total of 131,666,441 base pairs. It represents 99.4% of the euchromatic DNA and includes one megabase of heterochromatic sequence within the ...pericentromeric region of the short and long arm of the chromosome. Sequence annotation revealed 1,357 genes, of which 816 are protein coding, and 430 are pseudogenes. We observed widespread occurrence of overlapping coding genes (either strand) and identified 67 antisense transcripts. Our analysis suggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count on chromosome 10. Multispecies comparative analysis indicated that we can readily annotate the protein-coding genes with current resources. We estimate that over 95% of all coding exons were identified in this study. Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence.
Objective: To describe a considerably advanced method of array painting, which allows the rapid, ultra-high resolution mapping of translocation breakpoints such that rearrangement junction fragments ...can be amplified directly and sequenced. Method: Ultra-high resolution array painting involves the hybridisation of probes generated by the amplification of small numbers of flow-sorted derivative chromosomes to oligonucleotide arrays designed to tile breakpoint regions at extremely high resolution. Results and discussion: How ultra-high resolution array painting of four balanced translocation cases rapidly and efficiently maps breakpoints to a point where junction fragments can be amplified easily and sequenced is demonstrated. With this new development, breakpoints can be mapped using just two array experiments: the first using whole-genome array painting to tiling resolution large insert clone arrays, the second using ultra-high-resolution oligonucleotide arrays targeted to the breakpoint regions. In this way, breakpoints can be mapped and then sequenced in a few weeks.
PDF
