FRASS: the web-server for RNA structural comparison

Background  

The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA, SARSA, and LaJolla) are available for the structural comparison of large and intact RNA molecules.     

HOW DO SPERM WHALES CATCH SQUIDS?

Vision may play a central role in sperm whale predation. Two complementary hypotheses regarding the detection and capture of prey items are presented, based on a review of mesopelagic ecology. The first hypothesis postulates that sperm whales locate their prey visually, either silhouetted against the midwater "sky," or by searching for bioluminescence produced by the movements of their prey. The second hypothesis postulates that sperm whales create a zone of stimulated bioluminescence around the mouth, which attracts squids and other visual predators. Studies of midwater fishes and invertebrates document the importance of vision in mesopelagic communities. If sperm whales search for silhouetted prey, they should be oriented upside-down to improve visual coverage and to facilitate the transition from search to prey capture. Prey capture events should be marked by excursions toward the surface. If they lure their prey, they should swim at a steady pace, with little rapid acceleration, and spend most of their time foraging at depths with the greatest potential for stimulated bioluminescence.     

Evidence for the extreme overestimation of choline acetyltransferase in human sperm, human seminal plasma and rat heart: a case of mistaking carnitine acetyltransferase for choline acetyltransferase

Detection of choline acetyltransferase (ChAc) in a number of non-neuronal tissues has been extremely overestimated. There are two major types of errors encountered. Type 1 error occurs when endogenous substrates (e.g. L-carnitine) are acetylated by acetyltransferase enzymes (e.g. carnitine acetyltransferase ( CarAc ) ) yielding an acetylated product mistaken for acetylcholine (AcCh). In the past, human sperm and human seminal plasma putative ChAc activity has been extremely overestimated due to Type 1 error. This study demonstrates (1) an endogenous acetyltransferase and substrate activity in human sperm and human seminal plasma forming an acetylated product that is not AcCh but probably acetylcarnitine ( AcCar ); (2) that the addition of 5 mM choline substrate does not significantly increase acetyltransferase activity; (3) that boiled seminal plasma contains an endogenous acetyltransferase substrate which is not choline, but probably L-carnitine. Type 2 error occurs when endogenous carnitine acetyltransferase synthesizes true AcCh, resulting in mistaken evidence for ChAc. This is demonstrated by the fact that the choline substrate Km-value for the neuronal or true ChAc from mouse brain is 0.73 +/- 0.06 mM while the Km-value of choline substrate for purified CarAc from pigeon breast muscle is 108 +/- 4 mM. Type 2 error has occurred for the estimation of putative ChAc in rat heart. The rat heart ChAc was measured in previous studies utilizing a concentration of 30 mM choline substrate. While saturation of neuronal ChAc is observed at 2-5 mM choline, saturation of the rat heart CarAc enzyme is not reached until over 800 mM. Purified CarAc significantly synthesizes AcCh at 30 mM choline. Thus, putative ChAc has been greatly overestimated in the scientific literature for mammalian sperm, human seminal plasma and rat heart.     

The fine structure of developing locomotor muscles of the pelagic tunicate,Cyclosalpa affinis (Thaliacea:Salpidae)

Salps are free-swimming tunicates whose peculiar life history renders them ideal for developmental studies. The solitary salp reproduces asexually by budding a stolon containing the complete developmental sequence of the aggregate generation. The ultrastructure of developing locomotor muscle of the aggregate generation of Cyclosalpa affinis was studied. The early muscle contains essentially non-striated myofibrils. However, in transverse sections, areas indicating early I-bands and A-bands can be recognized. As development continues, the number of fibrils increases, the Z-lines appear, and the fibrils contain more recognizable striations. The fully developed muscle has the characteristic structure of striated muscle. Longitudinal sections show sarcomeres with irregular and discontinuous (perforated) Z-lines; H-zones are not apparent. No M-lines are seen. Throughout development, the ratio of thin to thick myofilaments is always 2:1, the ratio found in all vertebrate striated muscle. Other findings in C. affinis suggest that: (1) multinucleated muscle cells are formed by the fusion of mononucleated cells, (2) membranes of adjacent mononucleated cells destined to fuse form myelin figures, and (3) these myelin figures become closely associated with mitochondria.     

Ethanol production by genetically modified strains of Saccharomyces

Summary Two polyploid yeast strains and two genetically manipulated yeast strains were subjected to anaerobic fermentations in whole corn mash and defined media. Carbohydrate utilization and ethanol production rates were investigated. Whilst the polyploid strains exhibited superior performance in the whole corn mash, the genetically manipulated strains were so in defined media with glucose as the substrate. The overall fermentation performance of the novel strains however was comparable to the polyploid strains with corn mash as the substrate when most of the solid material had been removed. The flocculating and dextrin utilizing properties of the yeast strains examined play an important role in such fermentations.     

Germ-cell mutagenesis and GSH depression in reproductive tissue of the F-344 rat induced by ethyl methanesulfonate

Sensitivity of male F-344 rats to the dominant lethal (DL) mutagenic effect of ethyl methanesulfonate (EMS) was studied in conjunction with an evaluation of EMS-induced depression of glutathione (GSH) in testis, epididymis and vas deferens. At the maximal effect, during week 3 (days 15-19 post-EMS), a dosage of 50 mg/kg caused 13.3% fetal death (FD) vs. 3.3% in controls, while 100 mg/kg caused 56.6% FD in the same interval. EMS maximally depressed GSH to 33%, 54% and 77% of control in vas, epididymis and testis respectively. The slope of the DL dose-response curve for EMS in rats shows a 3-4-fold greater sensitivity than that reported for mice. The steepness of this curve suggests that small perturbations in endogenous protective mechanisms, such as GSH depression, may exert a greater proportional effect on germ-cell mutagenesis in rats which should be more readily observable than in mice. EMS and other electrophilic toxicants may thus influence their own primary reproductive toxicity and/or that of other agents by depression of GSH in male reproductive tissue.     

The use of Herr four-and-a-half clearing fluid for the rapid microscopic examination of thick sections of normal and neoplastic tissues.

We have demonstrated that Herr's 4 1/2 clearing fluid, developed for use with plant tissues, can be successfully used for the microscopic examination of thick sections of normal and neoplastic mammalian tissues. Rat Novikoff hepatoma, rat liver, and human colon and skin samples were fixed in Bouin's, stained with iron hematoxylin, treated with Herr's 4 1/2 clearing fluid and examined by phase contrast microscopy. Tissue architecture and cytological detail were easily observed by focusing through tissue sections as thick as 70 mu. The method permits rapid microscopic examination of mammalian tissues and enables the investigator to detect readily morphological abnormalities within a tissue.