The Evolution of Resistance to Simian Immunodeficiency Virus (SIV): A Review

Examining how pathogens cross species boundaries, spread within species, and persist within their hosts is an essential part of understanding the factors that underpin the evolution of virulence and host resistance. Here, we review current knowledge about the genetic diversity, molecular epidemiology, prevalence, and pathogenicity of simian immunodeficiency viruses (SIVs). SIVs have crossed species boundaries from simian hosts to humans on at least 12 separate occasions, one of which led to the global HIV–AIDS crisis. Though SIVs infect a wide range of primates, scientists have only recently begun to describe the natural history of SIV infection in their natural hosts. Several new studies reveal how both viral and host factors are responsible for the transmission to, and adaptation in, new hosts. These studies also suggest that the spread of the virus may be affected by host-specific traits, including social structure, mating system and demographic history. These studies challenge the traditional view that SIV is relatively benign in its natural host, and instead suggest that a highly dynamic relationship exists between SIV and its simian hosts.     

Phylogenetic comparative analysis of RNA structure on Macintosh computers

A Macintosh Hypertalk program (Hypercard ‘stack’)for use in phylogenetic comparative analysis of RNA structureis described. The program identifies covariations and compensatorychanges in RNA sequence alignments, for use in the constructionof secondary structure models or the identification of tertiaryinteractions. The results of an analysis are presented eitheras a list of positions in the alignment which covary, or asa 2-dimensional matrix in which potential helices in the secondarystructure appear as diagonal patterns. Received on January 7, 1991; accepted on March 19, 1991     

Glioma IL13Rα2 Is Associated with Mesenchymal Signature Gene Expression and Poor Patient Prognosis

A major challenge for successful immunotherapy against glioma is the identification and characterization of validated targets. We have taken a bioinformatics approach towards understanding the biological context of IL-13 receptor α2 (IL13Rα2) expression in brain tumors, and its functional significance for patient survival. Querying multiple gene expression databases, we show that IL13Rα2 expression increases with glioma malignancy grade, and expression for high-grade tumors is bimodal, with approximately 58% of WHO grade IV gliomas over-expressing this receptor. By several measures, IL13Rα2 expression in patient samples and low-passage primary glioma lines most consistently correlates with the expression of signature genes defining mesenchymal subclass tumors and negatively correlates with proneural signature genes as defined by two studies. Positive associations were also noted with proliferative signature genes, whereas no consistent associations were found with either classical or neural signature genes. Probing the potential functional consequences of this mesenchymal association through IPA analysis suggests that IL13Rα2 expression is associated with activation of proinflammatory and immune pathways characteristic of mesenchymal subclass tumors. In addition, survival analyses indicate that IL13Rα2 over-expression is associated with poor patient prognosis, a single gene correlation ranking IL13Rα2 in the top ~1% of total gene expression probes with regard to survival association with WHO IV gliomas. This study better defines the functional consequences of IL13Rα2 expression by demonstrating association with mesenchymal signature gene expression and poor patient prognosis. It thus highlights the utility of IL13Rα2 as a therapeutic target, and helps define patient populations most likely to respond to immunotherapy in present and future clinical trials.     

Integrated species delimitation and conservation implications of an endangered weevil Pachyrhynchus sonani (Coleoptera: Curculionidae) in Green and Orchid Islands of Taiwan

Oceanic islands are productive habitats for generating new species and high endemism, which is primarily due to their geographical isolation, smaller population sizes and local adaptation. However, the short divergence times and subtle morphological or ecological divergence of insular organisms may obscure species identity, so the cryptic endemism on islands may be underestimated. The endangered weevil Pachyrhynchus sonani Kôno (Coleoptera: Curculionidae: Entiminae: Pachyrhynchini) is endemic to Green Island and Orchid Island of the Taiwan‐Luzon Archipelago and displays widespread variation in coloration and host range, thus raising questions regarding its species boundaries and degree of cryptic diversity. We tested the species boundaries of P. sonani using an integrated approach that combined morphological (body size and shape, genital shape, coloration and cuticular scale), genetic (four genes and restriction site‐associated DNA sequencing, RAD‐seq) and ecological (host range and distribution) diversity. The results indicated that all the morphological datasets for male P. sonani, except for the colour spectrum, reveal overlapping but statistically significant differences between islands. In contrast, the morphology of the female P. sonani showed minimum divergence between island populations. The populations of P. sonani on the two islands were significantly different in their host ranges, and the genetic clustering and phylogenies of P. sonani established two valid evolutionary species. Integrated species delimitation combining morphological, molecular and ecological characters supported two distinct species of P. sonani from Green Island and Orchid Island. The Green Island population was described as P. jitanasaius sp.n. Chen & Lin, and it is recommended that its threatened conservation status be recognized. Our findings suggest that the inter‐island speciation of endemic organisms inhabiting both islands may be more common than previously thought, and they highlight the possibility that the cryptic diversity of small oceanic islands may still be largely underestimated.