After the initial enthusiasm of the human genome project, it became clear that without additional data pertaining to the epigenome, i.e., how the genome is marked at specific developmental periods, in different tissues, as well as across individuals and species-the promise of the genome sequencing project in understanding biology cannot be fulfilled. This realization prompted several large-scale efforts to map the epigenome, most notably the Encyclopedia of DNA Elements (ENCODE) project. While there is essentially a single genome in an individual, there are hundreds of epigenomes, corresponding to various types of epigenomic marks at different developmental times and in multiple tissue types. Unprecedented advances in next-generation sequencing (NGS) technologies, by virtue of low cost and high speeds that continue to improve at a rate beyond what is anticipated by Moore's law for computer hardware technologies, have revolutionized molecular biology and genetics research, and have in turn prompted innovative ways to reduce the problem of measuring cellular events involving DNA or RNA into a sequencing problem. In this article, we provide a brief overview of the epigenome, the various types of epigenomic data afforded by NGS, and some of the novel discoveries yielded by the epigenomics projects. We also provide ample references for the reader to get in-depth information on these topics.
Biology ; Computers ; DNA ; Epigenomics* ; Genetics ; Genome ; Human Genome Project ; Jurisprudence ; Methylation ; Molecular Biology ; RNA ; Virtues

Many advances have been made in understanding the molecular biology of brain tumors through progress in cell and developmental biology. The molecular characterization of rare genetic disorders and tumors shed light on several common tumorigenic mechanisms: mitogenic signaling, cell cycle control, development, and cell surface-cytoskeleton interactions. Discovery of many new molecular markers and the recent identification of brain tumor stem cells offer new directions in future research for tumor molecular diagnostics and therapies.
Brain Neoplasms* ; Brain* ; Cell Cycle Checkpoints ; Developmental Biology ; Glioma ; Medulloblastoma ; Meningioma ; Molecular Biology* ; Pathology, Molecular ; Stem Cells

This article is a mini-review that provides a general overview for next-generation sequencing (NGS) and introduces one of the most popular NGS applications, whole genome sequencing (WGS), developed from the expansion of human genomics. NGS technology has brought massively high throughput sequencing data to bear on research questions, enabling a new era of genomic research. Development of bioinformatic software for NGS has provided more opportunities for researchers to use various applications in genomic fields. De novo genome assembly and large scale DNA resequencing to understand genomic variations are popular genomic research tools for processing a tremendous amount of data at low cost. Studies on transcriptomes are now available, from previous-hybridization based microarray methods. Epigenetic studies are also available with NGS applications such as whole genome methylation sequencing and chromatin immunoprecipitation followed by sequencing. Human genetics has faced a new paradigm of research and medical genomics by sequencing technologies since the Human Genome Project. The trend of NGS technologies in human genomics has brought a new era of WGS by enabling the building of human genomes databases and providing appropriate human reference genomes, which is a necessary component of personalized medicine and precision medicine.
Chromatin Immunoprecipitation ; Computational Biology ; DNA ; Epigenomics ; Genetics, Medical ; Genome* ; Genome, Human ; Genomics ; High-Throughput Nucleotide Sequencing ; Human Genome Project ; Humans ; Methylation ; Precision Medicine ; Sequence Analysis, RNA ; Transcriptome

For the first time ever, the scientists of J. Craig Venter team have created actual self-replicating synthetic life. The research was just published in the Journal of Science on May 20, 2010. Although this news immediately brings the worry about the possible potential threat to biosecurity and biosafety as well as the ethical disputes, it yet indicates that mankind have made a new step forward in synthetic biology. In the time of post-genome era, we believe the advancement of synthetic biology that might affect or change the future life of human being will be widely used in energy, environment, materials, medication and many other fields.
Biological Science Disciplines ; methods ; Cloning, Organism ; Genome, Human ; genetics ; Human Genome Project ; Humans ; Synthetic Biology ; trends

BACKGROUND: Despite the advent of molecular biology and immunogenetics, the biologic behaviors and disease entities of primary cutaneous B-cell lymphomas(pCBCL) have been undetermined. Moreover, rarity of pCBCL cases and the conflicting datas of current issues have contributed to the dilemmas in understanding of the biology of pCBCL. Until now, a study of the overall features of pCBCL in Korea has been rarely presented. OBJECTIVE: We performed this study in order to identify the histopathologic and immunogenetic characteristics of pCBCL in Korea. METHODS: The histopathologic, immunophenotypic and molecular analysis of preserved specimens of 15 cases with pCBCL were conducted. RESULTS: 1. Of the 15 patients with pCBCL, most common types are follicle center cell lymphomas(73.3%). In REAL classification, diffuse large B-cell lymphoma is most common(66.6%). 2. In bcl-2 immunohistochemical staining, 3 cases(20%) were positive. 3. Only one of 15 cases of pCBCL denoted bcl-2 gene rearrangement by t(14;18) in minor cluster region. 4. Immunohistochemical staining demonstrated overexpression of p53 protein in 3(20%) of 15 cases. 5. 2 cases(13.3%) with point mutations(one for exon 5; the other for exon 8) in p53 DNA sequencing analysis. CONCLUSION: t(14;18) translocation may be rare in pCBCL in Korea. This finding indicates that bcl-2 expression by tumor cells in pCBCL without t(14;18) may occur by different genetic dysregulation. It seems to be that overexpression of p53 protein might not correspond with p53 mutations in pCBCL.
B-Lymphocytes* ; Biology ; Classification ; Exons ; Genes, bcl-2 ; Humans ; Immunogenetics* ; Korea* ; Lymphoma, B-Cell* ; Molecular Biology ; Sequence Analysis, DNA

Variation in human skin and hair color is the most notable aspect of human variability and several studies in evolution, genetics and developmental biology contributed to explain the mechanisms underlying human skin pigmentation, which is responsible for differences in skin color across the world's populations. Despite skin pigmentation is primarily related to melanocytes functionality, the surrounding keratinocytes and extracellular matrix proteins and fibroblasts in the underlying dermal compartment actively contribute to cutaneous homeostasis. Many autocrine/paracrine secreted factors and cell adhesion mechanisms involving both epidermal and dermal constituents determine constitutive skin pigmentation and, whenever deregulated, the occurrence of pigmentary disorders. In particular, an increased expression of such mediators and their specific receptors frequently lead to hyperpigmentary conditions, such as in melasma and in solar lentigo, whereas a defect in their expression/release is related to hypopigmented disorders, as seen in vitiligo. All these interactions underline the relevant role of pigmentation on human evolution and biology.
Biology ; Cell Adhesion ; Developmental Biology ; Extracellular Matrix Proteins ; Fibroblasts ; Genetics ; Hair Color ; Homeostasis ; Humans ; Intercellular Signaling Peptides and Proteins ; Keratinocytes ; Lentigo ; Melanocytes ; Melanosis ; Pigmentation ; Skin Pigmentation* ; Skin* ; Vitiligo

Estimating postmortem interval (PMI) is always the emphasis and difficulty in forensic practice. Forensic entomology plays a significant indispensable role. Recently, the theories and technologies of forensic entomology are increasingly rich. But many problems remain in the research and practice. With proposing the Daubert standard, the reliability and accuracy of estimation PMI by forensic entomology need more demands. This review summarizes the application of the Daubert standard in several aspects of ecology, quantitative genetics, population genetics, molecular biology, and microbiology in the practice of forensic entomology. It builds a bridge for basic research and forensic practice to provide higher accuracy for estimating postmortem interval by forensic entomology.
Animals ; Ecology ; Entomology/methods* ; Forensic Sciences/methods* ; Genetics, Population ; Insecta ; Molecular Biology ; Postmortem Changes ; Reproducibility of Results ; Time Factors

Antibiotics are widely used and prevalently distributed in the environment. The issue of antibiotic resistance genes has posed a huge threat to the global public health. Soil is an important sink of antibiotics in the environment. Antibiotic exposure may introduce adverse effects on soil organisms, and bring indirect but potential risks to human health. Therefore, it is urgent to take actions to remediate antibiotics-contaminated soil. This review summarized effects of antibiotics on phenotype growth of plants, physiological characteristics and community structure of animals, composition and structure of microbial communities, and transmission of antibiotic resistance genes among organisms in soil. Additionally, the potential and prospects of employing antibiotic-resistant soil plants, animals, microorganisms, and their combinations to treat antibiotics-contaminated soil were illustrated. Last but not least, the unaddressed issues in this area were proposed, which may provide insights into relevant research directions in the future.
Animals ; Anti-Bacterial Agents/pharmacology* ; Biodegradation, Environmental ; Drug Resistance, Microbial/genetics* ; Humans ; Soil ; Soil Microbiology ; Soil Pollutants

Metaproteomics is an emerging proteomics technology to analyze large scale protein expression in environmental microbial ecosystem. It is termed as the large-scale characterization of the entire protein complement of environmental microbial community at a given point in time. This review focuses on the research strategies and the recent applications in this field based on the published reports and in combination with our own research experiences.
Bacterial Physiological Phenomena ; Ecology ; methods ; Environmental Microbiology ; Proteomics ; methods

Male homosexuality is a complex phenomenon which is universal and with unknown causes. Researchers believe that both biological and environmental factors have played a role in its pathogenesis. Researches focusing on genetics, neurobiology, development and endocrinology have made certain progress. In this paper, we have reviewed the biological causes of male homosexuality, which may provide clues for further research in this field.
Developmental Biology ; Endocrinology ; Homosexuality, Male ; Humans ; Male ; Neurobiology