A network of conserved co-occurring motifs for the regulation of alternative splicing

Cis-acting short sequence motifs play important roles in alternative splicing. It is now possible to identify such sequence motifs as conserved sequence patterns in genome sequence alignments. Here, we report the systematic search for motifs in the neighboring introns of alternatively spliced exons by using comparative analysis of mammalian genome alignments. We identified 11 conserved sequence motifs that might be involved in the regulation of alternative splicing. These motifs are not only significantly overrepresented near alternatively spliced exons, but they also co-occur with each other, thus, forming a network of cis-elements, likely to be the basis for context-dependent regulation. Based on this finding, we applied the motif co-occurrence to predict alternatively skipped exons. We verified exon skipping in 29 cases out of 118 predictions (25%) by EST and mRNA sequences in the databases. For the predictions not verified by the database sequences, we confirmed exon skipping in 10 additional cases by using both RT–PCR experiments and the publicly available RNA-Seq data. These results indicate that even more alternative splicing events will be found with the progress of large-scale and high-throughput analyses for various tissue samples and developmental stages.     

Oral cancer,cigarette smoke and mitochondrial 18 kDa translocator protein (TSPO) — In vitro,in vivo,salivary analysis

Oral cancer features high rates of mortality and morbidity, and is in dire need for new approaches. In the present study we analyzed 18 kDa translocator protein (TSPO) expression in oral (tongue) cancer tumors by immunohistochemistry. We also assayed TSPO binding in human tongue cancer cell lines and in the cellular fraction of saliva from tongue cancer patients, heavy cigarette smokers, and non-smoking healthy people as controls. Concurrently, TSPO protein levels, cell viability, mitochondrial membrane potential (Δψ_m), and general protein levels were analyzed. TSPO expression could be significantly enhanced in oral cancer tumors, compared to unaffected adjacent tissue. We also found that five-year survival probability dropped from 65% in patients with TSPO negative tumors to 7% in patients with highly expressed TSPO (p < 0.001). TSPO binding capacity was also pronounced in the human oral cancer cell lines SCC-25 and SCC-15 (3133 ± 643 fmol/mg protein and 6956 ± 549 fmol/mg protein, respectively). Binding decreased by 56% and 72%, in the SCC-25 and SCC-15 cell lines, respectively (p < 0.05) following CS exposure in cell culture. In the cellular fraction of saliva of heavy smokers TSPO binding was lower than in non-smokers (by 53%, p < 0.05). Also the cellular fraction of saliva exposed to CS in vitro showed decreased TSPO binding compared to unexposed saliva (by 30%, p < 0.001). Interestingly, oral cancer patients also displayed significantly lower TSPO binding in the cellular fraction of saliva compared to healthy controls (by 40%, p < 0.01). Our results suggest that low TSPO binding found in the cellular fraction of saliva may depend on genetic background as well as result from exposure to CS. We suggest that this may be related to a predisposition for occurrence of oral cancer.     

Discovery of 2-substituted benzoxazole carboxamides as 5-HT3 receptor antagonists

A new class of 2-substituted benzoxazole carboxamides are presented as potent functional 5-HT(3) receptor antagonists. The chemical series possesses nanomolar in vitro activity against human 5-HT(3)A receptors. A chemistry optimization program was conducted and identified 2-aminobenzoxazoles as orally active 5-HT(3) receptor antagonists with good metabolic stability. These novel analogues possess drug-like characteristics and have potential utility for the treatment of diseases attributable to improper 5-HT(3) receptor function, especially diarrhea predominant irritable bowel syndrome (IBS-D).     

A survey of entodiniomorphid ciliates in chimpanzees and bonobos

Intestinal entodiniomorphid ciliates are commonly diagnosed in the feces of wild apes of the genera Pan and Gorilla. Although some authors previously considered entodiniomorphid ciliates as possible pathogens, a symbiotic function within the intestinal ecosystem and their participation in fiber fermentation has been proposed. Previous studies have suggested that these ciliates gradually disappear under captive conditions. We studied entodiniomorphid ciliates in 23 captive groups of chimpanzees, three groups of captive bonobos and six populations of wild chimpanzees. Fecal samples were examined using Sheather's flotation and Merthiolate‐Iodine‐Formaldehyde Concentration (MIFC) methods. We quantified the number of ciliates per gram of feces. The MIFC method was more sensitive for ciliate detection than the flotation method. Ciliates of genus Troglodytella were detected in 13 groups of captive chimpanzees, two groups of bonobos and in all wild chimpanzee populations studied. The absence of entodiniomorphids in some captive groups might be because of the extensive administration of chemotherapeutics in the past or a side‐effect of the causative or prophylactic administration of antiparasitic or antibiotic drugs. The infection intensities of ciliates in captive chimpanzees were higher than in wild ones. We suppose that the over‐supply of starch, typical in captive primate diets, might induce an increase in the number of ciliates. In vitro studies on metabolism and biochemical activities of entodiniomorphids are needed to clarify their role in ape digestion. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.     

Copper handling machinery of the brain

Copper plays an indispensable role in the physiology of the human central nervous system (CNS). As a cofactor of dopamine-β-hydroxylase, peptidyl-α-monooxygenase, superoxide dismutases, and many other enzymes, copper is a critical contributor to catecholamine biosynthesis, activation of neuropeptides and hormones, protection against reactive oxygen species, respiration and other processes essential for normal CNS function. Copper content in the CNS is tightly regulated, and changes in copper levels in the brain are associated with a wide spectrum of pathologies. However, the mechanistic understanding of copper transport in the CNS is still in its infancy. Little is known about copper distribution among various cell types or cell-specific regulation of copper homeostasis, despite the fact that the molecules mediating copper transport and distribution in the brain (CTR1, Atox1, CCS, ScoI/II, ATP7A and ATP7B) have been identified and their importance in CNS function increasingly understood. In this review, we summarize current knowledge about copper levels and uses in the CNS and describe the molecules involved in maintaining copper homeostasis in the brain.     

The invention of the pilidium larva in an otherwise perfectly good spiralian phylum Nemertea

One of the most remarkable larval types among spiralians, and invertebrates in general, is the planktotrophic pilidium. The pilidium is found in a single clade of nemerteans, called the Pilidiophora, and appears to be an innovation of this group. All other nemerteans have either planktotrophic or lecithotrophic juvenile-like planuliform larvae or have direct development. The invention of the pilidium larva is associated with the formation of an extensive blastocoel that supports the delicate larval frame and elaborate ciliary band. Perhaps the most striking characteristic of the pilidium is the way the juvenile worm develops inside the larva from a series of isolated rudiments, called the imaginal discs. The paired cephalic discs, cerebral organ discs, and trunk discs originate as invaginations of larval epidermis and subsequently grow and fuse around the larval gut to form the juvenile. The fully formed juvenile ruptures the larval body and, more often than not, devours the larva during catastrophic metamorphosis. This review is an attempt to examine the pilidium in the context of recent data on development of non-pilidiophoran nemerteans, and speculate about the evolution of pilidial larval development. The author emphasizes the difference between the planuliform larvae of Palaeonemerteans and Hoplonemerteans, and suggest a new name for the hoplonemertean larvae--the decidula.