Search

An introduction to research by the Telomere-to-Telomere (T2T) Consortium, reporting on the endeavor to complete a comprehensive human reference genome is presented.

The article presents the discussion on progress in human genomics producing insights applicable for treating cancer, identifying drug targets, and diagnosing disease understanding human evolution, cancer, polygenic traits, and functional genomics.

The fourth and last part of an essay on human genome sequencing reports the views of invited authors on having had access to human genome information. The writings of several individuals are presented including those of Broad Institute of Harvard and MIT President Eric S. Lander, also a U.S. Presidential science advisor, Director Peter Donnelly of the Wellcome Trust Centre for Human Genetics, and Director David Botstein of the Lewis-Sigler Institute for Integrative Genomics.

The article discusses how scientists aiming to better understand the effects of genetic diversity in healthy individuals launched the Genotype-Tissue Expression (GTEx) Consortium. It further highlights the third and final phase of the project, presenting the results from the analysis of the version 8 (v8) GTEx release.

The article focuses on the molecular genetic studies that have identified numerous genes that affect A-, B-, and C-functions by regulating specific genes of flowers. The genes act at both the transcriptional and posttranscriptional levels and encode a variety of regulatory proteins. Discoveries and analysis of the genes provide a further understanding of the molecular mechanisms underlying floral development.

The MADS-box gene AGAMOUS ( AG) plays a key role in determining floral meristem and organ identities. We identified three AG homologs, EScaAG1, EScaAG2, and EScaAGL11 from the basal eudicot Eschscholzia californica (California poppy). Phylogenetic analyses indicate that EScaAG1 and EScaAG2 are recent paralogs within the AG clade, independent of the duplication in ancestral core eudicots that gave rise to the euAG and PLENA ( PLE) orthologs. EScaAGL11 is basal to core eudicot AGL11 orthologs in a clade representing an older duplication event after the divergence of the angiosperm and gymnosperm lineages. Detailed in situ hybridization experiments show that expression of EScaAG1 and EScaAG2 is similar to AG; however, both genes appear to be expressed earlier in floral development than described in the core eudicots. A thorough examination of available expression and functional data in a phylogenetic context for members of the AG and AGL11 clades reveals that gene expression has been quite variable throughout the evolutionary history of the AG subfamily and that ovule-specific expression might have evolved more than twice. Although sub- and neofunctionalization are inferred to have occurred following gene duplication, functional divergence among orthologs is evident, as is convergence, among paralogs sampled from different species. We propose that retention of multiple AG homologs in several paralogous lineages can be explained by the conservation of ancestral protein activity combined with evolutionarily labile regulation of expression in the AG and AGL11 clades such that the collective functions of the AG subfamily in stamen and carpel development are maintained following gene duplication. [ABSTRACT FROM AUTHOR]

Members of the SEPALLATA (SEP) MADS-box subfamily are required for specifying the ‘floral state’ by contributing to floral organ and meristem identity. SEP genes have not been detected in gymnosperms and seem to have originated since the lineage leading to extant angiosperms diverged from extant gymnosperms. Therefore, both functional and evolutionary studies suggest that SEP genes may have been critical for the origin of the flower. To gain insights into the evolution of SEP genes, we isolated nine genes from plants that occupy phylogenetically important positions. Phylogenetic analyses of SEP sequences show that several gene duplications occurred during the evolution of this subfamily, providing potential opportunities for functional divergence. The first duplication occurred prior to the origin of the extant angiosperms, resulting in the AGL2/3/4 and AGL9 clades. Subsequent duplications occurred within these clades in the eudicots and monocots. The timing of the first SEP duplication approximately coincides with duplications in the DEFICIENS/GLOBOSA and AGAMOUS MADS-box subfamilies, which may have resulted from either a proposed genome-wide duplication in the ancestor of extant angiosperms or multiple independent duplication events. Regardless of the mechanism of gene duplication, these pairs of duplicate transcription factors provided new possibilities of genetic interactions that may have been important in the origin of the flower. [ABSTRACT FROM AUTHOR]

An introdusction is presented in which the editors discusses articles in the issue on the theme of manifestation of genome including observable human phenotype consists of multiple traits from genetic variants of single genome; and factors that influence the development of the human phenotype.

An introduction is presented to a section with studies on ruminants in relation genomic analysis of their evolutionary relationships and adaptations.

The third part of an essay is presented on human genome sequencing that reports the views of invited authors on having had access to human genome information. The writings of several individuals are presented including those of science and technology studies professor Sheila Jasanoff, medicine and genome sciences professor Maynard V. Olson, and stem cell research institute director Shinya Yamanaka.

News briefs associated with genomics research and the human genome sequence are provided. Archbishop Emeritus of Cape Town, South Africa Desmond Tutu examines ways in which the publication of the human genome sequence may benefit the South African people. University of Geneva Medical School professor Emmanouil T. Dermitzakis discusses the societal impacts of genomics. Beijing Genome Institute Executive Director Jun Wang discusses the implications of deoxyribonucleic acid (DNA) profiling.

An essay is presented on human genome sequencing that reports the views of invited authors on having had access to human genome information. The writings of several individuals are presented including those of U.S. National Institutes of Health (NIH) Director Francis S. Collins, J. Craig Venter Institute President J. Craig Venter, and Professor Molly Przeworski.

The article offers information on the study of genomics. It mentions the biological processes, such as the complement of molecules and their locations within the cell, as well as technological advances in the field of neuroscience and discoveries about immune system and brain. It also mentions cellular and disease identification and treatment.

The article discusses the Synthetic Yeast Genome Project (Sc2.0) that reports on the development of the new synthetic yeast chromosomes constructed with the motive of making synthetic eukaryotic genome with its full formation using synthetic biology.

An introduction is presented in which the editor discusses various reports within the issue on topics including the adaptation of humans to new climes, the influence of environment to cellular level, and the genetic and epigenetic changes caused by changes in diets, lifestyles, and exposures.

The article presents an introduction to a special section on using DNA sequencing technology to investigate genetic mutations, which can cause diseases across a population group or on an individual basis.

The article presents an introduction to a special section about cancer genomics research which includes a review by B. Vogelstein and team on cancer genome sequencing, an article about cancer diagnostics by O. Kilpivaara and L. A. Aaltonen, and a report on cancer epigenetics by M. L. Suvà and team.

An introduction is presented to various reports in a special section in the issue about plant metabolism, including an article about medical botany by De Luca and team, an article about secondary metabolite diversity by Weng and colleagues, and an article about nitrogen metabolism by Gutiérrez and team.

The article reviews the film “A Road Not Taken,” directed by Christina Hemauer and Roman Keller.

The article discusses various reports published within the issue including one on how plant genomes help investigations from biochemistry to ecosystems and another one on why polyploidy is so common in plants and its evolutionary and ecological consequences.

The article reviews the film "Gimme Green," directed by Isaac Brown and Eric Flagg.

The article introduces a series of articles on Rhesus Macaque Monkey published within the issue. The topics discussed include Human-Specific Changes of Genom Structure Detected by Genomic Trianautation and Mobile DNA in Old World monkeys, and Demographic Histories and Patterns of Linkage Disequilibrium in Chinese and Indian Rhesus Macaques.

The origin and rapid diversification of the angiosperms (Darwin's "Abominable Mystery") has engaged generations of researchers. Here, we examine the floral genetic programs of phylogenetically pivotal angiosperms (water lily, avocado, California poppy, and Arabidopsis) and a nonflowering seed plant (a cycad) to obtain insight into the origin and subsequent evolution of the flower. Transcriptional cascades with broadly overlapping spatial domains, resembling the hypothesized ancestral gymnosperm program, are deployed across morphologically intergrading organs in water lily and avocado flowers. In contrast, spatially discrete transcriptional programs in distinct floral organs characterize the more recently derived angiosperm lineages represented by California poppy and Arabidopsis. Deep evolutionary conservation in the genetic programs of putatively homologous floral organs traces to those operating in gymnosperm reproductive cones. Female gymnosperm cones and angiosperm carpels share conserved genetic features, which may be associated with the ovule developmental program common to both organs. However, male gymnosperm cones share genetic features with both perianth (sterile attractive and protective) organs and stamens, supporting the evolutionary origin of the floral perianth from the male genetic program of seed plants. [ABSTRACT FROM AUTHOR]

An introduction is presented in which the editor discusses articles in the issue on topics including chromatin plasticity, the impact of modifications in RNA in modulating gene expression during development, and dynamic DNA methylation.

An introduction is presented in which the editor discusses various reports within a special section of the issue on topics related to computational biology including computer models that simulate biological processes, heat stress adaptation in animals, and phenotypic variation.

The article introduces short reviews of books chosen as finalists in the 2011 Science Books and Films Prizes for Excellence in Science Books that honor works that stimulate interest in and understanding of science among young readers.