Multi-alignment of orthologous genome regions in five species provides new insights into the evolutionary make-up of mammalian genomes

Evidence has shown that bacterial genomes have undergone random shuffling of genomic elements consisting of one to two genes. In order to delineate such genome-shuffling events in mammals, we constructed a high-resolution map of Sus scrofa chromosome 3 (SSC3) with a total of 116 genes/markers. Alignment of this pig map to orthologous regions in human, dog, mouse and rat led to the identification of 31 provisional conserved ancestral blocks (CABs) in these five species. Among them, only 3 CABs (<10%) had one gene, indicating that one-gene shuffling is not frequent in mammals. The sizes of CABs vary significantly within a species, but each may be relatively consistent in different species with a scale to species-genome evolution. The type and frequency of rearrangement events that takes place, either intra- or interchromosomal, depends on the evolutionary regions and species under comparison. Characterization of 36 tentative breakpoint regions flanking these 31 CABs indicated that they occupied ∼43 Mb in length and featured genome deserts, gene duplications, and birth/death of species-specific genes in humans. Identification of CABs provides an alternative for further determination of the evolutionary make-up of mammalian genomes.     

Analysis of genetic abnormalities provides insights into genetic evolution of hyperdiploid myeloma

Aneuploidy is ubiquitous in human cancer and is seen as whole chromosome gains and losses, unbalanced translocations and inversions, duplications, deletions and loss of heterozygosity. Within this complexity, some subgroups of aneuploid tumors emerge as distinct biological and clinical entities. Hyperdiploid myeloma (H-MM), characterized by hyperdiploid chromosome numbers because of nonrandom trisomies, is one such example. We undertook a comprehensive survey of the karyotypes of a large number of H-MM (n = 469) to describe fully genomic instability in these tumors, to dissect pathways of genetic evolution, and identify distinct subgroups based on their genetic changes. While selective pressure apparently favors the emergence of clones with gains of chromosomes 3, 5, 7, 9, 11, 15, 19, and 21, a background of ongoing genomic instability results in gains of other chromosomes, albeit at a much lower prevalence. A deduced temporal analysis of these karyotypes indicates that selected gains are early events. Other events occurring later in the course of the disease include secondary chromosome translocations and monosomies. The development of these genetic aberrations is thus highly ordered and undoubtedly of biological relevance. Within this framework, we propose a model of genetic evolution in H-MM.     

New insights into mathematical modeling of the immune system

In order to understand the integrated behavior of the immune system, there is no alternative to mathematical modeling. In addition, the advent of experimental tools such as gene arrays and proteomics poses new challenges to immunologists who are now faced with more information than can be readily incorporated into existing paradigms of immunity. We review here our ongoing efforts to develop mathematical models of immune responses to infectious disease, highlight a new modeling approach that is more accessible to immunologists, and describe new ways to analyze microarray data. These are collaborative studies between experimental immunologists, mathematicians, and computer scientists.     

A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment

Acidithiobacillus thiooxidans is a sulfur oxidizing acidophilic bacterium found in many sulfur-rich environments. It is particularly interesting due to its role in bioleaching of sulphide minerals. In this work, we report the genome sequence of At. thiooxidans Licanantay, the first strain from a copper mine to be sequenced and currently used in bioleaching industrial processes. Through comparative genomic analysis with two other At. thiooxidans non-metal mining strains (ATCC 19377 and A01) we determined that these strains share a large core genome of 2109 coding sequences and a high average nucleotide identity over 98%. Nevertheless, the presence of 841 strain-specific genes (absent in other At. thiooxidans strains) suggests a particular adaptation of Licanantay to its specific biomining environment. Among this group, we highlight genes encoding for proteins involved in heavy metal tolerance, mineral cell attachment and cysteine biosynthesis. Several of these genes were located near genetic motility genes (e.g. transposases and integrases) in genomic regions of over 10 kbp absent in the other strains, suggesting the presence of genomic islands in the Licanantay genome probably produced by horizontal gene transfer in mining environments.     

The opossum genome: insights and opportunities from an alternative mammal

The strategic importance of the genome sequence of the gray, short-tailed opossum, Monodelphis domestica, accrues from both the unique phylogenetic position of metatherian (marsupial) mammals and the fundamental biologic characteristics of metatherians that distinguish them from other mammalian species. Metatherian and eutherian (placental) mammals are more closely related to one another than to other vertebrate groups, and owing to this close relationship they share fundamentally similar genetic structures and molecular processes. However, during their long evolutionary separation these alternative mammals have developed distinctive anatomical, physiologic, and genetic features that hold tremendous potential for examining relationships between the molecular structures of mammalian genomes and the functional attributes of their components. Comparative analyses using the opossum genome have already provided a wealth of new evidence regarding the importance of noncoding elements in the evolution of mammalian genomes, the role of transposable elements in driving genomic innovation, and the relationships between recombination rate, nucleotide composition, and the genomic distributions of repetitive elements. The genome sequence is also beginning to enlarge our understanding of the evolution and function of the vertebrate immune system, and it provides an alternative model for investigating mechanisms of genomic imprinting. Equally important, availability of the genome sequence is fostering the development of new research tools for physical and functional genomic analyses of M. domestica that are expanding its versatility as an experimental system for a broad range of research applications in basic biology and biomedically oriented research.     

Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

We present here the complete 2.4-Mb genome of the cellulolytic actinobacterial thermophile Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized and elevating the industrial value of this organism. A sizable fraction of these hydrolytic enzymes break down plant cell walls, and the remaining either degrade components in fungal cell walls or metabolize storage carbohydrates such as glycogen and trehalose, implicating the relative importance of these different carbon sources. Several of the A. cellulolyticus secreted cellulolytic and xylanolytic enzymes are fused to multiple tandemly arranged carbohydrate binding modules (CBM), from families 2 and 3. For the most part, thermophilic patterns in the genome and proteome of A. cellulolyticus were weak, which may be reflective of the recent evolutionary history of A. cellulolyticus since its divergence from its closest phylogenetic neighbor Frankia, a mesophilic plant endosymbiont and soil dweller. However, ribosomal proteins and noncoding RNAs (rRNA and tRNAs) in A. cellulolyticus showed thermophilic traits suggesting the importance of adaptation of cellular translational machinery to environmental temperature. Elevated occurrence of IVYWREL amino acids in A. cellulolyticus orthologs compared to mesophiles and inverse preferences for G and A at the first and third codon positions also point to its ongoing thermoadaptation. Additional interesting features in the genome of this cellulolytic, hot-springs-dwelling prokaryote include a low occurrence of pseudogenes or mobile genetic elements, an unexpected complement of flagellar genes, and the presence of three laterally acquired genomic islands of likely ecophysiological value.Efforts are under way worldwide to develop renewable energy sources as alternatives to fossil fuels. Microorganisms capable of breaking down lignocellulosic plant matter, a bioenergy source, are of enormous interest in the global quest to identify enzymes that can convert biomass into biofuels. Acidothermus cellulolyticus was first isolated in enrichment cultures from acidic hot springs in Yellowstone National Park, in a screen for microorganisms that carry out efficient cellulose degradation at high temperature (Mohagheghi et al. 1986). A. cellulolyticus 11B is acid-tolerant (pH 4–6, with optimal pH 5.5) and thermophilic (growth between 37°C and 70°C; the optimal growth temperature [OGT] is 55°C). It produces many thermostable cellulose-degrading enzymes (Tucker et al. 1989; Baker et al. 1994; Adney et al. 1995; Ding et al. 2003). One of the endoglucanases, E1, which has been crystallized, is highly thermostable to 81°C and has very high specific activity on carboxymethylcellulose (Thomas et al. 1995; Sakon et al. 1996). E1 has been expressed in several plants and shows promise for generating genetically improved feedstock for the production of affordable cellulosic ethanol (Sticklen 2008). Hydrolytic enzymes from A. cellulolyticus have great potential in the biofuels industry because of their thermostability and activity at low pH (Rubin 2008).A. cellulolyticus is a member of the Frankineae, a high G+C, primarily Gram-positive Actinobacterial group (Rainey and Stackebrandt 1993). All of the characterized strains of A. cellulolyticus are thermophilic and do not grow below 37°C (Mohagheghi et al. 1986). This makes the evolutionary context of A. cellulolyticus interesting, because its closest known phylogenetic neighbor is the mesophilic actinobacterium Frankia, based on the analysis of the 16S rRNA, recA, and shc nucleotide sequences (Supplemental Fig. S1; Normand et al. 1996; Marechal et al. 2000; Alloisio et al. 2005). Frankia is a mesophilic (OGT 25°C–28°C), nitrogen-fixing soil organism that forms symbiotic root nodule associations with plants (Benson 1988). The genetic distance between A. cellulolyticus and three Frankia strains—ACN14a, CcI3, and EAN1pec—is very small and comparable to that found between certain strains within the Frankia species. Thus, although Acidothermus and Frankia share a close phylogenetic relationship at the DNA sequence level, they have evolved to live in dramatically diverse environments over the last 200–250 million years (Myr) since their last common ancestor (Normand et al. 2007). Complete genome sequences of three Frankia strains—ACN14a, CcI3, and EAN1pec—as well as those of other close relatives of A. cellulolyticus are now available, including the mesophilic Streptomyces avermitilis, Streptomyces coelicolor, and the terrestrial thermophilic Thermobifida fusca (Omura et al. 2001; Bentley et al. 2002; Ikeda et al. 2003; Lykidis et al. 2007; Normand et al. 2007). Genomic comparison of A. cellulolyticus with the mesophilic as well as thermophilic actinobacteria could provide insight into the nature of adaptation of this aquatic thermophile and add to our understanding of evolution within the actinobacteria.We present analysis of the complete genome of Acidothermus cellulolyticus 11B (ATCC 43068; GenBank accession {"type":"entrez-nucleotide","attrs":{"text":"NC_008578","term_id":"117927211","term_text":"NC_008578"}}NC_008578). Insights into the biomass degradation capabilities of the organism as well as thermophilic features of its genome and proteome are discussed. In addition, we discuss three laterally acquired genomic islands with genes of likely ecophysiological value, as well as the unexpected presence of flagellar genes in the genome.     

Recent insights into mammalian circadian rhythms

This short review highlights recent progress in understanding the mammalian circadian clock. Advances in the understanding of the neuroanatomy of circadian rhythms, the molecular biology of the core clock mechanism, mechanisms of light entrainment of the circadian clock, clock synchronization among multiple tissues, and recent work on the relationship of the mouse circadian clock and cancer are discussed. This review is intended as an overview of recent research activity for the interested sleep disorders clinician or researcher.     

Genome-based insights into the evolution of enterococci

It is now 15 years since the first genome of a free-living organism was sequenced. Subsequent to this milestone, a veritable avalanche of genome sequence data has revolutionized many aspects of microbiology. In this review, we discuss recent progress on the genomics of Enterococcus faecalis and Enterococcus faecium, which are the two enterococcal species that cause the large majority of enterococcal infections. We focus on the genome-based analysis of enterococcal diversity and phylogeny. Studies based on comparative genome hybridization have shown that both species exhibit considerable inter-strain genomic diversity, which is mainly linked to the variable presence of phages, plasmids, pathogenicity islands and conjugative elements. We also discuss how the advent of next-generation sequencing technologies allows for a comprehensive characterization of the gene repertoire of multiple isolates, which can be used for extremely robust analyses of diversity and population structure.     

Discovery of six families of fungal defensin-like peptides provides insights into origin and evolution of the CSalphabeta defensins

The defensins with a conserved cysteine-stabilized alpha-helix and beta-sheet (CSalphabeta) structural motif are a group of unique antimicrobial polypeptides widely distributed in plants and animals. Recently, one defensin-like peptide (DLP) with high degree of sequence and structural similarity to defensins from ancient arthropods and molluscs has been identified in a saprophytic fungus [Mygind, P.H., Fischer, R.L., Schnorr, K.M., Hansen, M.T., S?nksen, C.P., Ludvigsen, S., Raventós, D., Buskov, S., Christensen, B., De Maria, L., Taboureau, O., Yaver, D., Elvig-J?rgensen, S.G., S?rensen, M.V., Christensen, B.E., Kjaerulff, S.K., Frimodt-Moller, N., Lehrer, R.I., Zasloff, M., Kristensen, H.-H., 2005. Plectasin is a peptide antibiotic with therapeutic potential from a saprophytic fungus. Nature 437, 975-980], which poses an important question regarding the evolutionary relationships of this class of effectors of innate immunity in three eukaryotic kingdoms. Here, we report the computational identification of six families of fungal DLPs in which three known defensin types (antibacterial ancient invertebrate-type defensins (AITDs), antibacterial classical insect-type defensins (CITDs), and antifungal plant/insect-type defensins (PITDs)) can be clearly assigned. Sharing of these defensin types between animals and fungi supports their closer evolutionary relationship, consistent with the Opisthokonta Hypothesis. Conservation of the PITDs across three eukaryotic kingdoms suggests their earlier origin than the antibacterial defensins, probably preceded plants and Opisthokonta split. Finally, recognition of an early gene duplication event in the Aspergillus terreus genome allows us to establish a paralogous relationship between AITDs and CITDs, which highlights extensive lineage-specific defensin gene loss during evolution.     

Microbial genome sequencing 2000: new insights into physiology, evolution and expression analysis

The complete genome sequence has been reported for 24 microbial organisms. The genome organization and gene content of these organisms has revealed an incredible diversity. Nearly half of the open reading frames identified by these sequencing projects are for potential genes with no known biological function. Efforts to make evolutionary sense and biological sense of the gene content of these organisms have been initiated. The greatest future challenge of genomics will be to determine function for the unknown genes.     

Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons

The sequencing of the chimpanzee genome and the comparison with its human counterpart have begun to reveal the spectrum of genetic changes that has accompanied human evolution. In addition to gross karyotypic rearrangements such as the fusion that formed human chromosome 2 and the human-specific pericentric inversions of chromosomes 1 and 18, there is considerable submicroscopic structural variation involving deletions, duplications, and inversions. Lineage-specific segmental duplications, detected by array comparative genomic hybridization and direct sequence comparison, have made a very significant contribution to this structural divergence, which is at least three-fold greater than that due to nucleotide substitutions. Since structural genomic changes may have given rise to irreversible functional differences between the diverging species, their detailed analysis could help to identify the biological processes that have accompanied speciation. To this end, interspecies comparisons have revealed numerous human-specific gains and losses of genes as well as changes in gene expression. The very considerable structural diversity (polymorphism) evident within both lineages has, however, hampered the analysis of the structural divergence between the human and chimpanzee genomes. The concomitant evaluation of genetic divergence and diversity at the nucleotide level has nevertheless served to identify many genes that have evolved under positive selection and may thus have been involved in the development of human lineage-specific traits. Genes that display signs of weak negative selection have also been identified and could represent candidate loci for complex genomic disorders. Here, we review recent progress in comparing the human and chimpanzee genomes and discuss how the differences detected have improved our understanding of the evolution of the human genome.     

The 1.4-Mb CMT1A duplication/HNPP deletion genomic region reveals unique genome architectural features and provides insights into the recent evolution of new genes

Duplication and deletion of the 1.4-Mb region in 17p12 that is delimited by two 24-kb low copy number repeats (CMT1A-REPs) represent frequent genomic rearrangements resulting in two common inherited peripheral neuropathies, Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsy (HNPP). CMT1A and HNPP exemplify a paradigm for genomic disorders wherein unique genome architectural features result in susceptibility to DNA rearrangements that cause disease. A gene within the 1.4-Mb region, PMP22, is responsible for these disorders through a gene-dosage effect in the heterozygous duplication or deletion. However, the genomic structure of the 1.4-Mb region, including other genes contained within the rearranged genomic segment, remains essentially uncharacterized. To delineate genomic structural features, investigate higher-order genomic architecture, and identify genes in this region, we constructed PAC and BAC contigs and determined the complete nucleotide sequence. This CMT1A/HNPP genomic segment contains 1,421,129 bp of DNA. A low copy number repeat (LCR) was identified, with one copy inside and two copies outside of the 1.4-Mb region. Comparison between physical and genetic maps revealed a striking difference in recombination rates between the sexes with a lower recombination frequency in males (0.67 cM/Mb) versus females (5.5 cM/Mb). Hypothetically, this low recombination frequency in males may enable a chromosomal misalignment at proximal and distal CMT1A-REPs and promote unequal crossing over, which occurs 10 times more frequently in male meiosis. In addition to three previously described genes, five new genes (TEKT3, HS3ST3B1, NPD008/CGI-148, CDRT1, and CDRT15) and 13 predicted genes were identified. Most of these predicted genes are expressed only in embryonic stages. Analyses of the genomic region adjacent to proximal CMT1A-REP indicated an evolutionary mechanism for the formation of proximal CMT1A-REP and the creation of novel genes by DNA rearrangement during primate speciation.     

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance

Visceral leishmaniasis is a potentially fatal disease endemic to large parts of Asia and Africa, primarily caused by the protozoan parasite Leishmania donovani. Here, we report a high-quality reference genome sequence for a strain of L. donovani from Nepal, and use this sequence to study variation in a set of 16 related clinical lines, isolated from visceral leishmaniasis patients from the same region, which also differ in their response to in vitro drug susceptibility. We show that whole-genome sequence data reveals genetic structure within these lines not shown by multilocus typing, and suggests that drug resistance has emerged multiple times in this closely related set of lines. Sequence comparisons with other Leishmania species and analysis of single-nucleotide diversity within our sample showed evidence of selection acting in a range of surface- and transport-related genes, including genes associated with drug resistance. Against a background of relative genetic homogeneity, we found extensive variation in chromosome copy number between our lines. Other forms of structural variation were significantly associated with drug resistance, notably including gene dosage and the copy number of an experimentally verified circular episome present in all lines and described here for the first time. This study provides a basis for more powerful molecular profiling of visceral leishmaniasis, providing additional power to track the drug resistance and epidemiology of an important human pathogen.     

Structural analysis provides insights into the modular organization of picornavirus IRES

Picornavirus RNA translation is driven by the internal ribosome entry site (IRES) element. The impact of RNA structure on the foot-and-mouth disease virus (FMDV) IRES activity has been analyzed using Selective 2'Hydroxyl Acylation analyzed by Primer Extension (SHAPE) and high throughput analysis of RNA conformation by antisense oligonucleotides printed on microarrays. SHAPE reactivity revealed the self-folding capacity of domain 3 and evidenced a change of RNA structure in a defective GNRA mutant. A modified RNA conformation of this mutant was also evidenced by RNA accessibility to oligonucleotides. Interestingly, comparison of nucleotide reactivity with RNA accessibility revealed that SHAPE reactive nucleotides corresponding to the GNRA motif were not accessible to their respective target oligonucleotides. The differential response was observed both in domain 3 and the entire IRES. Our results demonstrate distant effects of the GNRA motif in the domain 3 RNA conformation, and highlight the modular organization of a picornavirus IRES.     

Connecting and considering: Electrophysiology provides insights into comprehension

The ability to rapidly and systematically access knowledge stored in long-term memory in response to incoming sensory information—that is, to derive meaning from the world—lies at the core of human cognition. Research using methods that can precisely track brain activity over time has begun to reveal the multiple cognitive and neural mechanisms that make this possible. In this article, I delineate how a process of connecting affords an effortless, continuous infusion of meaning into human perception. In a relatively invariant time window, uncovered through studies using the N400 component of the event-related potential, incoming sensory information naturally induces a graded landscape of activation across long-term semantic memory, creating what might be called “proto-concepts”. Connecting can be (but is not always) followed by a process of further considering those activations, wherein a set of more attentionally demanding “active comprehension” mechanisms mediate the selection, augmentation, and transformation of the initial semantic representations. The result is a limited set of more stable bindings that can be arranged in time or space, revised as needed, and brought to awareness. With this research, we are coming closer to understanding how the human brain is able to fluidly link sensation to experience, to appreciate language sequences and event structures, and, sometimes, to even predict what might be coming up next.     

Tissue-specific expression of TIPE2 provides insights into its function

Tumor necrosis factor-alpha-induced protein-8 like-2 (TNFAIP8L2, TIPE2) is a newly discovered negative regulator of innate immunity and cellular immunity. TIPE2 deficiency in mice causes fetal inflammatory diseases and TIPE2 downregulation in humans is associated with systemic autoimmunity. However, TIPE2 deficiency leads to a selective defect in humoral immunity. Due to the lack of a suitable antibody, the nature of cells and tissues that express TIPE2 protein has not been determined. In this study, we generated a highly specific antibody to TIPE2 and examined TIPE2 expression in various murine tissues by immunohistochemistry and RT-PCR. We found that TIPE2 was a cytoplasmic protein expressed preferentially in lymphoid tissues and a small group of non-lymphoid tissues. Within the lymphoid compartment, T cells appear to express high level of TIPE2 protein, while B cells and B cell zones of lymphoid organs were devoid of TIPE2. Within most of the non-lymphoid tissues, TIPE2 was not detected. However, several endocrine tissues and skeletal muscle expressed detectable TIPE2 protein and mRNA. Furthermore, high levels of TIPE2 were detected in monocyte/macrophage derived cell lines and ovarian adenocarcinoma cells, but not detectable or weakly expressed in most human carcinoma cell lines. These results indicate that TIPE2 may perform tissue-specific functions in both lymphoid and non-lymphoid compartments. They may also explain why TIPE2 deficiency enhanced cellular but not humoral immunity.     

New insights into the regulation and functions of Tec family tyrosine kinases in the immune system

The Tec family of protein tyrosine kinases play an important role in signaling through antigen-receptors such as the TCR, BCR and Fcepsilon receptor. Recent studies have generated new insights into the domains in Tec kinases that take part in intramolecular and intermolecular binding. Furthermore, the consequences of these domain interactions for Tec activation and downregulation have been better defined. Genetic studies of kinase-knockout mice have emphasized the importance of Tec kinases in lymphocyte development, differentiation and apoptosis.     

Comparative genomics of the MHC: glimpses into the evolution of the adaptive immune system

MHC gene organization (size, complexity, gene order) differs markedly among different species, and yet all nonmammalian vertebrates examined to date have a true "class I region" with tight linkage of genes encoding the class I presenting and processing molecules. Three paralogous regions of the human genome contain sets of linked genes homologous to various loci in the MHC class I, class II, and/or class III regions, providing insight into the organization of the "proto MHC" before the emergence of the adaptive immune system in the jawed vertebrates.