Viral suppression of the interferon system

Type I interferons (IFN-alpha/beta) were originally discovered by their strong and direct antiviral activity [A. Isaacs, J. Lindenmann, Virus interference. I. The interferon, Proc. R. Soc. Lond. B Biol. Sci. 147 (1957) 258-267]. (see review by J. Lindenmann on p. 719, in this issue). Nevertheless, only very recently it was entirely realized that viruses would not succeed without efficient tools to undermine this potent host defense system. Current investigations are revealing an astonishing variety of viral IFN antagonistic strategies targeting virtually all parts of the IFN system, often in a highly specific manner. Viruses were found to interfere with induction of IFN synthesis, IFN-induced signaling events, the antiviral effector proteins, or simply shut off the host cell macromolecule synthesis machinery to avoid booting of the antiviral host defense. Here, we will describe a few well-characterized examples to illustrate the sophisticated and often multi-layered anti-IFN mechanisms employed by viruses.     

Distribution of human papillomavirus types in different histological subtypes of cervical adenocarcinoma

Little information is available regarding distribution of HPV types in different histological subtypes of adenocarcinoma (AC). Thus, in this study we examined the frequency of high-risk (hr) HPV types in AC, adenocarcinoma in situ (AIS) and adenosquamous carcinoma (ADSQ). A total of 102 cases of primary cervical adenocarcinoma (26 AIS and 76 invasive AC) obtained from pathology files from 1995-2006 were histologically subtyped. Our results demonstrated that endocervical type occupied the major subtype of AC (22/66) followed by ADSQ (17/66) where as in the group of AIS endocervical type (12/23) was followed by intestinal type of AIS (7/23). Successful DNA extraction was obtained in 89 samples; 81 out of 89 (91.0%) tested positive for HPV DNA. The prevalence of HPV DNA in AIS, AC and ADSQ was 91.3% (21/23), 90.9% (60/66) and 94.1% (16/17), respectively. We found HPV 18 type to be the most predominant type in AIS (11/21) and AC (17/60) followed by HPVof undeternmined type in AIS (3/21) and HPV 16 in AC (9/60) as the sole viral type. HPV 18 was most frequently detected type in all histological subtypes of AIS and AC. We have detected HPV DNA in all 5 samples of clear cell carcinoma (CCC), although other studies have reported a highly variable prevalence of HPVDNA in CCC. The most prevalent HPV type in ADSQ was HPV-16 followed by HPV 33 as single type. The observed overall predominance of HPV 18 in AIS (chi(2) = 6.109, p< or = 0.025) and AC (chi(2) = 8.927, p< or =0.01) as well as of HPV 16 in ADSQ (chi(2) = 10.164, p < or = 0.01) was statistically significant. Our data revealed statistically significant predominance of single hrHPV infections in AIS (16/21; chi(2) = 11.523, p < 0.001) and AC (37/60; X2 = 6.533, p < 0.025) whereas multiple hrHPV infections were more abundant in AC comparing to AIS (23/81and 5/81, respectively; chi(2) = 13.989, p< or =0.001).     

Novel pyrrolidine melanin-concentrating hormone receptor 1 antagonists with reduced hERG inhibition

We discovered novel pyrrolidine MCHR1 antagonist 1 possessing moderate potency. Profiling of pyrrolidine 1 demonstrated that it was an inhibitor of the hERG channel. Investigation of the structure-activity relationship of this class of pyrrolidines allowed us to optimize the MCHR1 potency and decrease the hERG inhibition. Increasing the acidity of the amide proton by converting the benzamide in lead 1 to an anilide provided single digit nanomolar MCHR1 antagonists while replacing the dimethoxyphenyl ring of 1 with alkyl groups possessing increased polarity dramatically reduced the hERG inhibition.     

Metabolic capabilities and systems fluctuations in Haloarcula marismortui revealed by integrative genomics and proteomics analyses

The 1310 Haloarcula marismortui proteins identified from mid-log and late-log phase soluble and membrane proteomes were analyzed in metabolic and cellular process networks to predict the available systems and systems fluctuations upon environmental stresses. When the connected metabolic reactions with identified proteins were examined, the availability of a number of metabolic pathways and a highly connected amino acid metabolic network were revealed. Quantitative spectral count analyses suggested 300 or more proteins might have expression changes in late-log phase. Among these, integrative network analyses indicated approximately 106 were metabolic proteins that might have growth-phase dependent changes. Interestingly, a large proportion of proteins in affected biomodules had the same trend of changes in spectral counts. Disregard the magnitude of changes, we had successfully predicted and validated the expression changes of nine genes including the rimK, gltCP, rrnAC0132, and argC in lysine biosynthesis pathway which were downregulated in late-log phase. This study had not only revealed the expressed proteins but also the availability of biological systems in two growth phases, systems level changes in response to the stresses in late-log phase, cellular locations of identified proteins, and the likely regulated genes to facilitate further analyses in the postgenomic era.     

Metabolic phenotyping of the Crohn's disease-like IBD etiopathology in the TNF(ΔARE/WT) mouse model

The underlying biochemical consequences of inflammatory bowel disease (IBD) on the systemic and gastrointestinal metabolism have not yet been fully elucidated but could help to better understand the disease pathogenesis and to identify tissue-specific markers associated with the different disease stages. Here, we applied a metabonomic approach to monitor metabolic events associated with the gradual development of Crohn's disease (CD)-like ileitis in the TNF(ΔARE/WT) mouse model. Metabolic profiles of different intestinal compartments from the age of 4 up to 24 weeks were generated by combining proton nuclear magnetic resonance ((1)H NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS). From 8 weeks onward, mice developed CD similar to the immune and tissue-related phenotype of human CD with ileal involvement, including ileal histological abnormalities, reduced fat mass and body weight, as well as hallmarks of malabsorption with higher energy wasting. The metabonomic approach highlighted shifts in the intestinal lipid metabolism concomitant to the histological onset of inflammation. Moreover, the advanced disease status was characterized by a significantly altered metabolism of cholesterol, triglycerides, phospholipids, plasmalogens, and sphingomyelins in the inflamed tissue (ileum) and the adjacent intestinal parts (proximal colon). These results describe different biological processes associated with the disease onset, including modifications of the general cell membrane composition, alteration of energy homeostasis, and finally the generation of inflammatory lipid mediators. Taken together, this provides novel insights into IBD-related alterations of specific lipid-dependant processes during inflammatory states.     

Compensatory responses in lepidopteran larvae: a test of growth rate maximisation

It is often claimed that some organisms maximise individual growth rates (within limits set by physiological and environmental constraints) whereas others do not. Adequate experimental protocol to test for these hypotheses has not been available. We proceeded from the idea that a maximiser should be unable to further improve its growth performance, i.e. there should be no adaptive plasticity in relative growth rates. In the case of an insect larva always maximising its weight gain, we should thus expect no increase in growth rate following a short-term environmental perturbation. Another prediction is that initial and final weights of a larval instar should be highly correlated. We applied this approach to test for the growth rate maximiser status of the geometrid moth Epirrita autumnata . Based on various lines of ecological evidence it had previously been suggested that this spring-feeding species is strongly selected for high growth rates, and may be growing at its maximum physiological potential. Contrary to expectations, the larvae responded to starvation treatments by a subsequent compensatory increase in their relative growth rates. Such a plasticity may indicate that the rates of gaining weight are not maximised even in a 'classical' example a time-constrained organism. This observation supports the idea that endogenous regulation of growth rates is widespread, and it remains to be shown if true maximisation ever exists in nature. In contrast, possibilities to compensate for adverse conditions experienced early in larval development appeared to be limited. This was indicated by the strong correlation between initial weight in the last instar, and pupal weight. Though consistent with our expectations, such an inability to compensate can hardly be ascribed to growth rate maximisation, as indicated by quantitatively similar patterns found in an unrelated species with different ecology, the butterfly Polygonia c-album .     

Different population histories of the Mundari- and Mon-Khmer-speaking Austro-Asiatic tribes inferred from the mtDNA 9-bp deletion/insertion polymorphism in Indian populations

Length variation in the human mtDNA intergenic region between the cytochrome oxidase II (COII) and tRNA lysine (tRNA^lys) genes has been widely studied in world populations. Specifically, Austronesian populations of the Pacific and Austro-Asiatic populations of southeast Asia most frequently carry the 9-bp deletion in that region implying their shared common ancestry in haplogroup B. Furthermore, multiple independent origins of the 9-bp deletion at the background of other mtDNA haplogroups has been shown in populations of Africa, Europe, Australia, and India. We have analyzed 3293 Indian individuals belonging to 58 populations, representing different caste, tribal, and religious groups, for the length variation in the 9-bp motif. The 9-bp deletion (one copy) and insertion (three copies) alleles were observed in 2.51% (2.15% deletion and 0.36% insertion) of the individuals. The maximum frequency of the deletion (45.8%) was observed in the Nicobarese in association with the haplogroup B5a D-loop motif that is common throughout southeast Asia. The low polymorphism in the D-loop sequence of the Nicobarese B5a samples suggests their recent origin and a founder effect, probably involving migration from southeast Asia. Interestingly, none of the 302 (except one Munda sample, which has 9-bp insertion) from Mundari-speaking Austro-Asiatic populations from the Indian mainland showed the length polymorphism of the 9-bp motif, pointing either to their independent origin from the Mon-Khmeric-speaking Nicobarese or to an extensive admixture with neighboring Indo-European-speaking populations. Consistent with previous reports, the Indo-European and Dravidic populations of India showed low frequency of the 9-bp deletion/insertion. More than 18 independent origins of the deletion or insertion mutation could be inferred in the phylogenetic analysis of the D-loop sequences.     

Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction

To better understand the molecular basis of the defense response against the rice blast fungus (Magnaporthe grisea), a large-scale expressed sequence tag (EST) sequencing approach was used to identify genes involved in the early infection stages in rice (Oryza sativa). Six cDNA libraries were constructed using infected leaf tissues harvested from 6 conditions: resistant, partially resistant, and susceptible reactions at both 6 and 24 h after inoculation. Two additional libraries were constructed using uninoculated leaves and leaves from the lesion mimic mutant spl11. A total of 68,920 ESTs were generated from 8 libraries. Clustering and assembly analyses resulted in 13,570 unique sequences from 10,934 contigs and 2,636 singletons. Gene function classification showed that 42% of the ESTs were predicted to have putative gene function. Comparison of the pathogen-challenged libraries with the uninoculated control library revealed an increase in the percentage of genes in the functional categories of defense and signal transduction mechanisms and cell cycle control, cell division, and chromosome partitioning. In addition, hierarchical clustering analysis grouped the eight libraries based on their disease reactions. A total of 7,748 new and unique ESTs were identified from our collection compared with the KOME full-length cDNA collection. Interestingly, we found that rice ESTs are more closely related to sorghum (Sorghum bicolor) ESTs than to barley (Hordeum vulgare), wheat (Triticum aestivum), and maize (Zea mays) ESTs. The large cataloged collection of rice ESTs in this study provides a solid foundation for further characterization of the rice defense response and is a useful public genomic resource for rice functional genomics studies.