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PubMed2004

The Chlamydomonas genome reveals its secrets: chaperone genes and the potential roles of their gene products in the chloroplast.

The first draft of the Chlamydomonas nuclear genome was searched for genes potentially encoding members of the five major chaperone families, Hsp100/Clp, Hsp90, Hsp70, Hsp60, the small heat shock proteins, and the Hsp70 and Cpn60 co-chaperones GrpE and Cpn10/20, respectively. This search yielded 34 potential (co-)chaperone genes, among them those 8 that have been reported earlier inChlamydomonas. These 34 genes encode all the (co-)chaperones that have been expected for the different compartments and organelles from genome searches in Arabidopsis, where 74 genes have been described to encode basically the same set of (co-)chaperones. Genome data from Arabidopsis and Chlamydomonas on the five major chaperone families are compared and discussed, with particular emphasis on chloroplast chaperones.

Journal Article↗

PubMed2002

Ethical issues in human genome epidemiology: a case study based on the Japanese American Family Study in Seattle, Washington.

Recent completion of the draft sequence of the human genome has been greeted with both excitement and skepticism, and the potential of this accomplishment for advancing public health has been tempered by ethical concerns about the protection of human subjects. This commentary explores ethical issues arising in human genome epidemiology by using a case study approach based on the ongoing Japanese American Family Study at the University of Washington in Seattle (1994-2003). Ethical issues encountered in designing the study, collecting the data, and reporting the study results are considered. When developing studies, investigators must consider whether to restrict the study to specific racial or ethnic groups and whether community involvement is appropriate. Once the study design is in place, further ethical issues emerge, including obtaining informed consent for DNA banking and protecting the privacy and confidentiality of family members. Finally, investigators must carefully consider whether to report genotype results to study participants and whether pedigrees illustrating the results of the study will be published. Overall, the promise of genomics for improving public health must be pursued based on the fundamental ethical principles of respect for persons, beneficence, and justice.

Asian↗

PubMed2003

Germ-line transgenesis of the Tc1/mariner superfamily transposon Minos in Ciona intestinalis.

The tadpole larva of the basal chordate Ciona intestinalis has the most simplified, basic body-plan of chordates. Because it has a compact genome with a complete draft sequence, a large quantity of EST/cDNA information, and a short generation time, Ciona is a suitable model for future genetics. We establish here a transgenic technique in Ciona that uses the Tc1/mariner superfamily transposon Minos. Minos was integrated efficiently into the genome of germ cells and transmitted stably to subsequent generations. In addition, an enhancer-trap line was obtained. This is a demonstration of efficient, Minos-mediated transgenesis in marine invertebrates.

Animals↗

PubMed2003

The genes and brains of mice and men.

The elucidation of the human genome presents a challenge for psychiatry-determining the impact of thousands of genes on brain functions relevant to mental disorders. For both historical and practical reasons, the mouse has become the mammal of choice for applying molecular genetic approaches to gene function. A working draft of the mouse genome has led to estimates that a mouse version may be identified for 99% of human genes. In accord with their genomic homologies, humans and mice share numerous features of brain organization and behavioral responses to many pharmacological agents. Technologies enabling the precise experimental manipulation of the mouse genome provide unprecedented opportunities for exploring genetic contributions to the regulation of complex behavior and to the pathophysiology and treatment of psychiatric disease. The formidable array of mouse molecular genetic tools are applied for two general strategies: 1) exploring the function of particular genes by generating lines of mice with precise genetic alterations and 2) searching broadly for those genes that regulate a particular biological trait of interest. Essential to the effective use of these technologies is the implementation of sound strategies for discerning the impact of genetic manipulations on mouse behaviors relevant to psychiatric conditions. These approaches are having a major impact-examples relevant to psychiatric disorders are discussed. However, advances in implementing and interpreting behavioral assays have not kept pace with molecular genetic technologies. To maximize the extent to which the revolution in mammalian genetics may be effectively applied to psychiatric research, new technologies and strategies for mouse behavioral assessment must be developed.

Animals↗

PubMed2004

Structural and functional analysis of rice genome.

Rice is an excellent system for plant genomics as it represents a modest size genome of 430 Mb. It feeds more than half the population of the world. Draft sequences of the rice genome, derived by whole-genome shotgun approach at relatively low coverage (4-6 X), were published and the International Rice Genome Sequencing Project (IRGSP) declared high quality (>10 X), genetically anchored, phase 2 level sequence in 2002. In addition, phase 3 level finished sequence of chromosomes 1, 4 and 10 (out of 12 chromosomes of rice) has already been reported by scientists from IRGSP consortium. Various estimates of genes in rice place the number at >50,000. Already, over 28,000 full-length cDNAs have been sequenced, most of which map to genetically anchored genome sequence. Such information is very useful in revealing novel features of macro- and micro-level synteny of rice genome with other cereals. Microarray analysis is unraveling the identity of rice genes expressing in temporal and spatial manner and should help target candidate genes useful for improving traits of agronomic importance. Simultaneously, functional analysis of rice genome has been initiated by marker-based characterization of useful genes and employing functional knock-outs created by mutation or gene tagging. Integration of this enormous information is expected to catalyze tremendous activity on basic and applied aspects of rice genomics.

Chromosomes, Plant↗

PubMed2004

Comprehensive search for cysteine cathepsins in the human genome.

Our study was aimed at examinating whether or not the human genome encodes for previously unreported cysteine cathepsins. To this end, we used analyses of the genome sequence and mRNA expression levels. The program TBLASTN was employed to scan the draft sequence of the human genome for the 11 known cysteine cathepsins. The cathepsin-like segments in the genome were inspected, filtered, and annotated. In addition to the known cysteine cathepsins, the scan identified three pseudogenes, closely related to cathepsin L, on chromosome 10, as well as two remote homologs, tubulointerstitial protein antigen and tubulointerstitial protein antigen-related protein. No new members of the family were identified. mRNA expression profiles for 10 known human cysteine cathepsins showed varying expression levels in 46 different human tissues and cell lines. No expression of any of the three cathepsin L-like pseudogenes was found. Based on these results, it is likely that to date all human cysteine cathepsins are known.

Cathepsins↗

PubMed2006

Identification of the lacZ insertion site and beta-galactosidase expression in transgenic chickens.

The quail:chick chimera system is a classical research model in developmental biology. An improvement over the quail:chick chimera system would be a line of transgenic chickens expressing a reporter gene. Transgenic chickens carrying lacZ and expressing bacterial beta-galactosidase have been generated, but complete characterization of the insertion event and characterization of beta-galactosidase expression have not previously been available. The genomic sequences flanking the retroviral insertion site have now been identified by using inverse polymerase chain reaction (PCR), homozygous individuals have been identified by using PCR-based genotyping, and beta-galactosidase expression has been evaluated by using Western analysis and histochemistry. Based upon the current draft of the chicken genome, the viral insertion carrying the lacZ gene has been located on chromosome 11 within the predicted gene for neurotactin/fractalkine (CX3CL1); neurotactin mRNA expression appears to be missing from the brain of homozygous individuals. When Generation 2 (G2) lacZ-positive individuals were inter-mated, they generated 361 G3 progeny; 82 were homozyous for lacZ (22.7%), 97 were wild-type non-transgenic (26.9%), and 182 (50.4%) were hemizygous for lacZ. Western analysis revealed the highest expression in the muscle and liver. With the identification of homozygous birds, the line of chickens is now designated NCSU-Blue1.

Animals↗

PubMedDate not supplied

Genomic medicine in Mexico. Applications of gene therapy for cirrhosis reversion.

Genomic medicine represents a powerful armamentarium to tackle down most of chronic diseases which have not, so far, defeated. Thus, this new and powerful biotechnologic set of weapons enable us to make use of molecular diagnostic to detect silent diseases, otherwise undetectable by conventional analysis. Moreover, elucidation of the complete and final draft of the human genome code will allow, although not in this decade, the design of specific farmaco-genetic treatments for patients on basis of their individual genetic code. Regarding new medical treatments, gene therapy as emerged as a true hope for treatment of many chronic diseases. 636 FDA-.approved clinical protocols are currently undergoing and sooner than later we ll be witness of the results

Genetic Therapy↗

PubMed2006

Genomic and transcriptional analysis of protein heterogeneity of the honeybee venom allergen Api m 6.

Several components of honeybee venom are known to cause allergenic responses in humans and other vertebrates. One such component, the minor allergen Api m 6, has been known to show amino acid variation but the genetic mechanism for this variation is unknown. Here we show that Api m 6 is derived from a single locus, and that substantial protein-level variation has a simple genome-level cause, without the need to invoke multiple loci or alternatively spliced exons. Api m 6 sits near a misassembled section of the honeybee genome sequence, and we propose that a substantial number of indels at and near Api m 6 might be the root cause of this misassembly. We suggest that genes such as Api m 6 with coding-region or untranslated region indels might have had a strong effect on the assembly of this draft of the honeybee genome.

Allergens↗

PubMed2004

Future potential of the Human Epigenome Project.

Deciphering the information encoded in the human genome is key for the further understanding of human biology, physiology and evolution. With the draft sequence of the human genome completed, elucidation of the epigenetic information layer of the human genome becomes accessible. Epigenetic mechanisms are mediated by either chemical modifications of the DNA itself or by modifications of proteins that are closely associated with DNA. Defects of the epigenetic regulation involved in processes such as imprinting, X chromosome inactivation, transcriptional control of genes, as well as mutations affecting DNA methylation enzymes, contribute fundamentally to the etiology of many human diseases. Headed by the Human Epigenome Consortium, the Human Epigenome Project is a joint effort by an international collaboration that aims to identify, catalog and interpret genome-wide DNA methylation patterns of all human genes in all major tissues. Methylation variable positions are thought to reflect gene activity, tissue type and disease state, and are useful epigenetic markers revealing the dynamic state of the genome. Like single nucleotide polymorphisms, methylation variable positions will greatly advance our ability to elucidate and diagnose the molecular basis of human diseases.

CpG Islands↗

PubMed2000

Genomics. Public-private project to deliver mouse genome in 6 months.

Research on the mouse genome lurched into the fast lane last week, as private donors joined the U.S. government to step on the gas. A public-private consortium announced on 6 October that it's kicking $58 million into a new fund that will pay to sequence the DNA of the "black six" (C57BL/6J) strain of laboratory mouse. The consortium aims to produce a draft version of the genome by the end of February.

Animals↗

PubMed2001

Genome comparisons highlight similarity and diversity within the eukaryotic kingdoms.

In 2000, the number of completely sequenced eukaryotic genomes increased to four. The addition of Drosophila and Arabidopsis into this cohort permits additional insights into the processes that have shaped evolution. Analysis and comparisons of both completed genomes and partially sequenced genomes have already shed light on mechanisms such as gene duplication and gene loss that have long been hypothesized to be major forces in speciation. Indeed, duplicate gene pairs in Saccharomyces, Arabidopsis, Caenorhabditis and Drosophila are high: 30%, 60%, 48% and 40%, respectively. Evidence of horizontal gene-transfer, thought to be a major evolutionary force in bacteria, has been found in Arabidopsis. The release of the 'first draft' of the human genome sequence in 2000 heralds a new stage of biological study. Understanding the as-yet-unannotated human genome will be largely based on conclusions, techniques and tools developed during the analysis and comparison of the genome of these four model organisms.

Animals↗

PubMed2002

Towards the molecular dissection of fertilization signaling: Our functional genomic/proteomic strategies.

Recent advances in DNA sequencing techniques and automated informatics has led to clarification of all genome sequence of some model organisms in a very short period. The demonstration of the first draft sequence of the human genome has prompted us to elaborate new approaches in biology, pharmacology and medicine. Such new research will focus on high throughput methods to function on collections of genes, and hopefully, on a genome-wide, quantitative modeling of the cell system as a whole. In this review article, we discuss the present status of "post genome sequencing" approaches in line with our strategies for understanding the molecular mechanism of fertilization and activation of development using the African clawed frog, Xenopus laevis, as a model system.

Animals↗

PubMed2005

The avian genome uncovered.

Our knowledge of avian genomics has increased rapidly over the past few years, culminating in the recent publication of a draft sequence of the chicken genome, a milestone event in avian genetics and evolutionary biology. Comparative analysis reveals a compact avian genome structure containing a similar number of genes as found in mammals but with shorter intergenic DNA sequences and fewer repeats. Recombination is at a higher rate than in mammals, particularly for microchromosomes. These also differ from macrochromosomes in their GC and gene content, and their substitution rate. The avian genome has remained unusually stable during evolution and contrasts sharply with the frequent chromosomal rearrangements seen in the rodent lineage. Detailed analyses of polymorphism levels in chickens, including a genome-wide screening in three chicken breeds yielding a set of 2.8 million SNP markers, reveal unexpectedly high levels of genetic diversity. As a notable exception, the female-specific W chromosome is very low in diversity, a probable consequence of the effect of selection on non-recombining chromosomes. The chicken genome promises to be a useful resource for ecological and evolutionary studies of other bird species.

Journal Article↗

PubMed2001

DNA technology, the clinical laboratory, and the future.

OBJECTIVE: To review the advances in clinically useful molecular biological techniques and their applications in clinical practice as presented at the Ninth Annual William Beaumont Hospital DNA Symposium. DATA SOURCES: The 10 manuscripts submitted were reviewed and their major findings were compared with literature on the same topic. STUDY SELECTION: One manuscript reviewed the development of pharmacogenetics, 3 described analytic approaches to detect aneuploidy or cancer, 1 described transcription factor E2F-1 increase during apoptosis, 2 reported on genetic and pharmacologic factors that influence platelet aggregation, 2 described molecular methods for detecting long QT syndrome or mycobacteria, and 1 reported a modification in collection of buccal DNA. DATA SYNTHESIS: Genomic and proteomic approaches to develop clinically useful assays have been successful. Aneuploidy can be easily detected by comparative genomic hybridization, which does not require cell culture like cytogenetics. Mutations have been characterized for a variety of hereditary cancer syndromes, 2 inherited long QT syndromes, and thromboembolism. PlA1 and PlA2 polymorphisms in platelets are associated with a difference in aggregation inhibition by estrogen, another example of genotypic pharmacogenetics. Protein expression differences may define colorectal cancer stage and explain apoptotic signal transduction. Mycobacterial detection by nucleic acid amplification and simplified buccal DNA collection demonstrate cost-effective strategies. CONCLUSION: The working draft of the Human Genome Project is completed and the number of clinically useful molecular pathologic techniques and assays will expand as additional disease-associated mutations are defined. Expanded use of database software for genomic and proteomic screening should increase the efficiency of clinical useful assay development.

Biotechnology↗

PubMed2000

Genome-wide profiling of gene amplification and deletion in cancer.

Accumulations of genetic changes in somatic cells induce phenotypic transformations leading to cancer. Among these genetic changes, gene amplification and deletion are most frequently observed in several kinds of cancers. Amplification of oncogene and/or deletion of tumor suppressor gene, together with dysfunction of the gene by point mutation, are the main causes of cancer. Genome-wide analysis of amplification and deletion of genes in cancers is basic to resolving the mechanisms of carcinogenesis. Comparative genomic hybridization (CGH) developed in 1992 has been utilized to identify DNA copy number abnormalities in various kind of cancers and several reports have shown its usefulness in screening of the genes involved in carcinogenesis, and also in the identification of prognostic factors in cancer. We have shown that 1q23 gain is associated with neuroblastomas that are resistant to aggressive treatment, and have poor prognosis, and 1q and 13q gains are possibly related to drug resistance in ovarian cancers. Recently, the "rough draft" of the human genome was reported and we are ready to utilize the vast information on genomic sequences in cancer research. Moreover, microarray technology enables us to analyze more than ten thousand genes at a time and revealed genetic abnormalities in cancers at a genome-wide level. By combination of microarray and CGH, a powerful screening method for oncogenes and tumor suppressor genes in cancers, called array-CGH, has been developed by several groups. In this article, we overview these genome-wide analytical methods, CGH and array-CGH, and discuss their potential in molecular characterization of cancers.

Gene Amplification↗

PubMed2002

Genomics-based approaches to gene discovery in innate immunity.

The completion of draft sequences of the human and mouse genomes offers many opportunities for gene discovery in the field of immunology through the application of the methods of computational genomics. One arm of the innate immune system includes the antimicrobial peptides that protect multicellular organisms from a diverse spectrum of microorganisms. The beta-defensins comprise an important family of mammalian antimicrobial peptides. To better define the beta-defensin gene family, we developed an approach to search genomic databases for conserved motifs present in the beta-defensin family using HMMER, a computational search tool based on hidden Markov models (HMMs), in combination with the basic local alignment search tool. The approach was first used to identify candidate second-exon coding regions, and later applied to finding associated first exons. This strategy discovered 28 new human and 43 new mouse beta-defensin genes in five syntenic chromosomal regions. Within each syntenic cluster, the gene sequences and organization were similar, suggesting that each cluster pair arose from a common ancestor and was retained because of conserved functions. These findings demonstrate an important proof-of-principle for a genome-wide search strategy to identify genes with conserved structural motifs. Such an approach may be readily adopted to address other questions of relevance to immunology.

Animals↗

PubMed2004

Strain-specific genomic regions of Ruminococcus flavefaciens FD-1 as revealed by combinatorial random-phase genome sequencing and suppressive subtractive hybridization.

Two closely related strains of the Gram-positive, cellulolytic ruminal bacterium Ruminococcus flavefaciens were compared at the genomic level by suppressive subtractive hybridization. The two strains investigated in this study differ by 1.94% in their respective 16S rDNA genes. Three hundred and eighty-four PCR-amplified products were cloned and then screened for their strain identity by dot blot hybridization. Based on redundancy percentages of the clones sequenced, 9.5% of the genome of the R. flavefaciens FD-1 strain is not present in the JM1 strain. The majority of identities of individual cloned subtracted products (642 bp average length) bore no relation to deposited sequences in GenBank (42% of the subtracted library), whereas of those with putative assigned functions 7% are loosely associated with fibre-degradation, 6% with insertion elements, transposons and phage-like ORFs, 5% with cell membrane associated proteins and 3% with signal transduction. Subtracted sequences were then supplemented with the draft (2 x coverage) genome sequence of R. flavefaciens FD-1 to indicate potential regions of rearrangement within the genome, including a novel insertion sequence.

Base Sequence↗