A genomic perspective on the shortcomings of mitochondrial DNA for "barcoding" identification

Approximately 600-bp sequences of mitochondrial DNA (mtDNA) have been designated as "DNA barcodes" and have become one of the most contentious and animated issues in the application of genetic information to global biodiversity assessment and species identification. Advocates of DNA barcodes have received extensive attention and promotion in many popular and refereed scientific publications. However, we suggest that the utility of barcodes is suspect and vulnerable to technical challenges that are particularly pertinent to mtDNA. We review the natural history of mtDNA and discuss problems for barcoding which are particularly associated with mtDNA and inheritance, including reduced effective population size, maternal inheritance, recombination, inconsistent mutation rate, heteroplasmy, and compounding evolutionary processes. The aforementioned could significantly limit the application and utility of mtDNA barcoding efforts. Furthermore, global use of barcodes will require application and acceptance of a barcode-based species concept that has not been evaluated in the context of the extensive literature concerning species designation. Implementation of mtDNA barcodes in spite of technical and practical shortcomings we discuss may degrade the longstanding synthesis of genetic and organism-based research and will not advance studies ranging from genomic evolution to biodiversity assessment.     

Attenuation of IL-7 receptor signaling is not required for allelic exclusion

Allelic exclusion prevents pre-B cells from generating more than one functional H chain, thereby ensuring the formation of a unique pre-BCR. The signaling processes underlying allelic exclusion are not clearly understood. IL-7R-dependent signals have been clearly shown to regulate the accessibility of the Ig H chain locus. More recent work has suggested that pre-BCR-dependent attenuation of IL-7R signaling returns the H chain loci to an inaccessible state; this process has been proposed to underlie allelic exclusion. Importantly, this model predicts that preventing pre-BCR-dependent down-regulation of IL-7R signaling should interfere with allelic exclusion. To test this hypothesis, we made use of transgenic mice that express a constitutively active form of STAT5b (STAT5b-CA). STAT5b-CA expression restores V(D)J recombination in IL-7R(-/-) B cells, demonstrating that IL-7 regulates H chain locus accessibility and V(D)J recombination via STAT5 activation. To examine the effects of constitutively active STAT5b on allelic exclusion, we crossed STAT5b-CA mice (which express the IgM(b) allotype) to IgM(a) allotype congenic mice. We found no difference in the percentage of IgM(a)/IgM(b)-coexpressing B cells in STAT5b-CA vs littermate control mice; identical results were observed when crossing STAT5b-CA mice with hen egg lysozyme (HEL) H chain transgenic mice. The HEL transgene enforces allelic exclusion, preventing rearrangement of endogenous H chain genes; importantly, rearrangement of endogenous H chain genes was suppressed to a similar degree in STAT5b-CA vs HEL mice. Thus, attenuation of IL-7R/STAT5 signaling is not required for allelic exclusion.     

Differential interactions between transforming growth factor-beta3/TbetaR1, TAB1, and CD2AP disrupt blood-testis barrier and Sertoli-germ cell adhesion

The biochemical basis that regulates the timely and selective opening of the blood-testis barrier (BTB) to migrating preleptotene/leptotene spermatocytes at stage VIII of the epithelial cycle in adult rat testes is virtually unknown. Recent studies have shown that cytokines (e.g. transforming growth factor (TGF)-beta3) may play a crucial role in this event. However, much of this information relies on the use of toxicants (e.g. CdCl(2)), making it difficult to relay these findings to normal testicular physiology. Here we report that overexpression of TGF-beta3 in primary Sertoli cells cultured in vitro indeed perturbed the tight junction (TJ) barrier with a concomitant decline in the production of BTB constituent proteins as follows: occludin, N-cadherin, and ZO-1. Additionally, local administration of TGF-beta3 to testes in vivo was shown to reversibly perturb the BTB integrity and Sertoli-germ cell adhesion via the p38 MAPK and ERK signaling pathways. Most importantly, the simultaneous activation of p38 and ERK signaling pathways is dependent on the association of the TGF-beta3-TbetaR1 complex with adaptors TAB1 and CD2AP because if TbetaR1 was associated preferentially with CD2AP, only Sertoli-germ cell adhesion was perturbed without compromising the BTB. Collectively, these data illustrate that local production of TGF-beta3, and perhaps other TGF-betas and cytokines, by Sertoli and germ cells into the microenvironment at the BTB during spermatogenesis transiently perturbs the BTB and Sertoli-germ cell adhesion to facilitate germ cell migration when the activated TbetaRI interacts with adaptors TAB1 and CD2AP. However, TGF-beta3 selectively disrupts Sertoli-germ cell adhesion in the seminiferous epithelium to facilitate germ cell migration without compromising BTB when TbetaRI interacts only with adaptor CD2AP.     

Genome Sequence of Francisella tularensis subspecies holarctica Strain FSC200, Isolated from a Child with Tularemia

Here we report the complete, accurate 1.89-Mb genome sequence of Francisella tularensis subsp. holarctica strain FSC200, isolated in 1998 in the Swedish municipality Ljusdal, which is in an area where tularemia is highly endemic. This genome is important because strain FSC200 has been extensively used for functional and genetic studies of Francisella and is well-characterized.     

The SNF2-Family Member Fun30 Promotes Gene Silencing in Heterochromatic Loci

Chromatin regulates many key processes in the nucleus by controlling access to the underlying DNA. SNF2-like factors are ATP-driven enzymes that play key roles in the dynamics of chromatin by remodelling nucleosomes and other nucleoprotein complexes. Even simple eukaryotes such as yeast contain members of several subfamilies of SNF2-like factors. The FUN30/ETL1 subfamily of SNF2 remodellers is conserved from yeasts to humans, but is poorly characterized. We show that the deletion of FUN30 leads to sensitivity to the topoisomerase I poison camptothecin and to severe cell cycle progression defects when the Orc5 subunit is mutated. We demonstrate a role of FUN30 in promoting silencing in the heterochromatin-like mating type locus HMR, telomeres and the rDNA repeats. Chromatin immunoprecipitation experiments demonstrate that Fun30 binds at the boundary element of the silent HMR and within the silent HMR. Mapping of nucleosomes in vivo using micrococcal nuclease demonstrates that deletion of FUN30 leads to changes of the chromatin structure at the boundary element. A point mutation in the ATP-binding site abrogates the silencing function of Fun30 as well as its toxicity upon overexpression, indicating that the ATPase activity is essential for these roles of Fun30. We identify by amino acid sequence analysis a putative CUE motif as a feature of FUN30/ETL1 factors and show that this motif assists Fun30 activity. Our work suggests that Fun30 is directly involved in silencing by regulating the chromatin structure within or around silent loci.     

Conservation of the protein composition and electron microscopy structure of Drosophila melanogaster and human spliceosomal complexes

Comprehensive proteomics analyses of spliceosomal complexes are currently limited to those in humans, and thus, it is unclear to what extent the spliceosome's highly complex composition and compositional dynamics are conserved among metazoans. Here we affinity purified Drosophila melanogaster spliceosomal B and C complexes formed in Kc cell nuclear extract. Mass spectrometry revealed that their composition is highly similar to that of human B and C complexes. Nonetheless, a number of Drosophila-specific proteins were identified, suggesting that there may be novel factors contributing specifically to splicing in flies. Protein recruitment and release events during the B-to-C transition were also very similar in both organisms. Electron microscopy of Drosophila B complexes revealed a high degree of structural similarity with human B complexes, indicating that higher-order interactions are also largely conserved. A comparison of Drosophila spliceosomes formed on a short versus long intron revealed only small differences in protein composition but, nonetheless, clear structural differences under the electron microscope. Finally, the characterization of affinity-purified Drosophila mRNPs indicated that exon junction complex proteins are recruited in a splicing-dependent manner during C complex formation. These studies provide insights into the evolutionarily conserved composition and structure of the metazoan spliceosome, as well as its compositional dynamics during catalytic activation.     

Expanded Breadth of the T-Cell Response to Mosaic Human Immunodeficiency Virus Type 1 Envelope DNA Vaccination

An effective AIDS vaccine must control highly diverse circulating strains of human immunodeficiency virus type 1 (HIV-1). Among HIV-1 gene products, the envelope (Env) protein contains variable as well as conserved regions. In this report, an informatic approach to the design of T-cell vaccines directed to HIV-1 Env M group global sequences was tested. Synthetic Env antigens were designed to express mosaics that maximize the inclusion of common potential T-cell epitope (PTE) 9-mers and minimize the inclusion of rare epitopes likely to elicit strain-specific responses. DNA vaccines were evaluated using intracellular cytokine staining in inbred mice with a standardized panel of highly conserved 15-mer PTE peptides. One-, two-, and three-mosaic sets that increased theoretical epitope coverage were developed. The breadth and magnitude of T-cell immunity stimulated by these vaccines were compared to those for natural strain Envs; additional comparisons were performed on mutant Envs, including gp160 or gp145 with or without V regions and gp41 deletions. Among them, the two- or three-mosaic Env sets elicited the optimal CD4 and CD8 responses. These responses were most evident in CD8 T cells; the three-mosaic set elicited responses to an average of eight peptide pools, compared to two pools for a set of three natural Envs. Synthetic mosaic HIV-1 antigens can therefore induce T-cell responses with expanded breadth and may facilitate the development of effective T-cell-based HIV-1 vaccines.The development of AIDS vaccines has been advanced recently by demonstrations of increased survival and decreased viral load following vaccination with T-cell vaccines in nonhuman primate models (12, 19, 23, 26, 31, 37). Although such vaccine studies have implied that T cells may contribute to the control of viremia in the highly lethal simian immunodeficiency virus SIVmac251 challenge model, the applicability of these results in human studies remains uncertain. The major concern regarding the efficacy of human immunodeficiency virus (HIV) vaccines in humans is the extraordinary genetic diversity of the virus. The sequence similarity of HIV type 1 (HIV-1) envelope from diverse isolates within a clade can diverge by as much as 15%, and divergence between alternative clades may approach 30% (10). In addition, the diversity of the viral Gag gene product can approach similar levels, particularly in p17 and p15, which are much more diverse than p24 (6), although Gag does not have the extreme localized diversity seen in the highly variable regions of Env (6, 10). While the approach to viral diversity has been addressed in existing vaccines through the use of envelopes derived from representative viruses in the major clades, increasing knowledge about the genetic diversity of naturally occurring isolates has enabled alternative approaches that enhance population coverage of vaccine-elicited T-cell responses.Approaches under consideration include the use of central gene sequences based on ancestral, consensus, or center-of-the-tree genetic analyses (5, 10, 18, 31, 36). Such prototypes are derived by selection of the most common amino acids at each residue (10, 16, 17, 21, 25, 36), identifying the most recent common ancestor of diverging viruses in a vaccine target population (5, 10, 18, 36), or modeling the sequence at the center of the phylogenetic tree (29), respectively. Peptides based on any of these three centralized protein strategies enhanced the detection of T-cell responses in natural infection relative to the use of peptides based on natural strains; however, all three strategies behaved equivalently (7).The use of a single M group consensus/ancestral Env sequence has been shown to elicit T-cell responses with greater breadth of cross-reactivity than single natural strains in animal models (31, 36). Such central sequences do not exist in nature, and even phylogenetic ancestral reconstructions are just an approximate model of an ancestral state of the virus (8). Thus, central sequence strategies have provided evidence that various informatically derived gene products can elicit immune responses to T-cell epitopes found in diverse circulating strains, leading to the possibility of using computational strategies to design polyvalent vaccines which optimize T-cell coverage (6, 24). In this study, we have evaluated for the first time the ability of nonnatural mosaic Env immunogens (6) to elicit T-cell responses of increased cross-reactivity against epitopes represented in naturally circulating viruses in animals.Mosaic HIV-1 envelope genes were derived using an informatic approach, whereby in silico-generated recombinants of natural variants from the Los Alamos database M group Env alignment were created, scored, and selected in combination to optimize the coverage of 9-mers in the global database for a given vaccine cocktail size. While mosaic proteins are artificial constructs that do not occur in nature, they align well to natural proteins, and any short span found in mosaics will tend to be found repeatedly among natural strains (although some of the hypervariable loop regions of Env are so extremely variable that they are not repeated among circulating strains, and this necessitates bridging these regions with segments found in a single strain). In silico recombination breakpoints are constrained to create fusion points found in natural sequences. It is possible to provide increased breadth of coverage with a single mosaic, providing the maximum possible single-antigen diversity coverage for stretches of nine amino acids. Alternatively, multiple mosaics can increase the breadth of representation but have the drawback of requiring the synthesis of additional vectors for clinical use. Mosaics also preserve a natural Env-like sequence to retain normal antigen processing. Here, we have compared single-, double-, or triple-mosaic envelope antigen sets to naturally circulating strains or other derivatives for their ability to elicit immune responses of increased breadth. The data suggest that mosaic HIV-1 envelope sequences provide an approach that may be useful in the development of HIV vaccines that respond to T-cell epitopes represented in naturally circulating strains.     

The Quantum Co-Evolution Unit: An Example of ‘Awa (Kava—<Emphasis Type="Italic">Piper methysticum</Emphasis> G. Foster) in Hawaiian Culture

The Quantum Co-Evolution Unit: An Example of ‘Awa (Kava— Piper methysticum G. Foster) in Hawaiian Culture. The process of co-evolution occurs in many kinds of relationships and on various scales. One example of a co-evolutionary relationship is that of a plant and a culture with which it interacts. Such relationships are dynamic and ever changing. Researchers have discussed this concept and its implications for decades, yet no quantifiable unit or standardized scale has been accepted with which to measure this change. The theoretical “quantum co-evolution unit” (QCU) is proposed as the smallest measurable scale of interactions between plants and people. A collection of QCUs for a linked plant and human population would be its “ethnobotanical population.” This could be measured at various points in time to quantify the changing relationships between plants and people. These models set up a structure to discuss methodologies for quantifying co-evolutionary relationships such as are seen in the evolution of ethnobotanical populations. The co-evolving relationship between ‘awa (kava—Piper methysticum) and Hawaiian culture is used as an example to illustrate this idea.     

Rickettsial agents in Egyptian ticks collected from domestic animals

To assess the presence of rickettsial pathogens in ticks from Egypt, we collected ticks from domestic and peridomestic animals between June 2002 and July 2003. DNA extracts from 1019 ticks were tested, using PCR and sequencing, for Anaplasma spp., Bartonella spp., Coxiella burnetii, Ehrlichia spp., and Rickettsia spp. Ticks included: 29 Argas persicus, 10 Hyalomma anatolicum anatolicum, 55 Hyalomma anatolicum excavatum, 174 Hyalomma dromedarii, 2 Hyalomma impeltatum, 3 Hyalomma marginatum rufipes, 55 unidentified nymphal Hyalomma, 625 Rhipicephalus (Boophilus) annulatus, 49 Rhipicephalus sanguineus, and 17 Rhipicephalus turanicus. Ticks were collected predominantly (>80%) from buffalo, cattle, and camels, with smaller numbers from chicken and rabbit sheds, sheep, foxes, a domestic dog, a hedgehog, and a black rat. We detected Anaplasma marginale, Coxiella burnetii, Rickettsia aeschlimannii, and four novel genotypes similar to: “Anaplasma platys,” Ehrlichia canis, Ehrlichia spp. reported from Asian ticks, and a Rickettsiales endosymbiont of Ixodes ricinus.