Internal eliminated sequences interrupting the Oxytricha 81 locus: allelic divergence, conservation, conversions, and possible transposon origins

Internal eliminated sequences (IESs) often interrupt ciliate genes in the silent germline nucleus but are exactly excised and eliminated from the developing somatic nucleus from which genes are then expressed. Some long IESs are transposons, supporting the hypothesis that short IESs are ancient transposon relics. In light of that hypothesis and to explore the evolutionary history of a collection of IESs, we have compared various alleles of a particular locus (the 81 locus) of the ciliated protozoa Oxytricha trifallax and O. fallax. Three short IESs that interrupt two genes of the locus are found in alleles from both species, and thus must be relatively ancient, consistent with the hypothesis that short IESs are transposon relics. In contrast, TBE1 transposon interruptions of the locus are allele-specific and probably the results of recent transpositions. These IESs (and the TBE1s) are precisely excised from the DNA of the developing somatic macronucleus. Each IES interrupts a highly conserved sequence. A few nucleotides at the ends of each IES are also conserved, suggesting that they interact critically with IES excision machinery. However, most IES nucleotide positions have evolved at high rates, showing little or no selective constraint for function. Nonetheless, the length of each IES has been maintained (+/- 3 bp). While one IES is approximately 33 bp long, three other IESs have very similar sizes, approximately 70 bp long. Two IESs are surrounded by direct repeats of the sequence TTCTT. No other sequence similarities were found between any of the four IESs. However, the ends of one IES do match the inverted terminal repeat consensus sequence of the "TA" IESs of Paramecium. Three O. trifallax alleles appear to have been recipients in recent conversion events that could have been provoked by double-strand breaks associated with IES ends subsequent to IES transposition. Our findings support the hypothesis that short IESs evolved from ancient transposons that have lost most of their sequences, except those necessary for precise excision during macronuclear development.      

Seasonality of planktonic ciliated protozoa in 20 subtropical Florida lakes of varying trophic state

The planktonic ciliate populations of 20 Florida lakes ranging from oligotrophic to hypereutrophic were examined monthly for one year. Oligotrophic lakes displayed abundance peaks during fall mixis and biomass peaks in late winter and fall. Mesotrophic systems exhibited a spring-fall bimodality in ciliate abundance with a biomass maxima occurring during fall. Eutrophic/hypereutrophic lakes had pronounced abundance and biomass maxima during summer, with the large ciliates Plagiopyla nasuta and Paramecium trichium often contributing heavily to the midsummer biomass peak. Members of the Oligotrichida numerically dominated abundance and biomass peaks in oligotrophic lakes while the Scuticociliatida dominated the communities of higher trophic states. Total ciliate abundance and biomass were strongly correlated with chlorophyll a concentrations as were various ciliate taxonomic groups. The relationship between ciliate seasonal distribution in these subtropical lakes with lake thermal regimes and trophic state is discussed.     

Effects of progesterone or estradiol on uterine tubal transport of ova in the cow

An experiment was designed to determine the effect of progesterone (P) or estradiol benzoate (EB) on uterine tubal transport of ova in the cow. Intramuscular injections of P, EB, or corn oil (C) were administered to heifers 24 hours after the end of estrus. The heifers were euthanatized 60 hours after the end of estrus and the location of the ovum or zygote was determined. Venous serum levels of progesterone and estradiol-17beta were measured by radioimmunoassay. The mean uterine tube (UT) length was 23.9 cm. An ovum or zygote was recovered from 11 of 14 heifers. Serum levels of progesterone and estradiol-17beta were above normal bovine levels following the P and EB treatments, respectively. The mean UT ovum transport rates were 0.42, 0.21 and 0.23 cm/hour in the P, EB and C treatment groups, respectively. The UT ovum transport rate was increased (P<0.05) by the P treatment and EB treatment had no effect (P > 0.05) when compared with the C treatment.     

Thermal regimes of Florida lakes

Water column temperatures were determined monthly for 24 lakes and bimonthly for 5 lakes in peninsular Florida during 1979. Three geographical groups (north, central, south) were delineated from mean monthly water column temperatures for individual lakes. On a monthly basis, northern lakes were least similar to southern lakes, while central Florida lakes displayed greater affinity to the southern than to the northern lake group. Temperature differences between lake groups broke down during late summer. Subtropical lakes have been defined tentatively as those Florida lakes south of 28° latitude which possess warm monomictic circulation and a mean annual temperature of 24.2 ± 4.8 °C with minimum water column temperature rarely less than 14 °C and summer maxima rarely exceeding 31 °C. While all lakes in Florida are clearly warm monomictic annual nutrient cycling and productivity patterns may be influenced by inter-group differences in the timing and duration of water column circulation.     

Interpretation of bryozoan microfossils in lacustrine sediment cores

Bryozoan statoblasts were isolated from the surficial sediments of 30 Florida lakes representing a gradient of trophic conditions. A prerequisite for lake selection was a good data base for water chemistry that was collected within the past 5–10 years. A novel technique of employing 210-Pb as a dilution tracer was used to estimate sedimentation rates for each lake. The net annual accumulation rate for bryozoan statoblasts was calculated for each lake and correlated with twelve physical, chemical, and biological variables. The results suggest that bryozoan distributions are strongly controlled by the extent of the littoral zone and phytoplankton biomass. It appears that bryozoan abundance in excessively weeded lakes may be limited by phytoplankton in spite of the richly developed habitat. Separation of the importance of food requirements from habitat requirements was not possible from this initial survey.     

"Plate cherry picking": a novel semi-sequential screening paradigm for cheaper, faster, information-rich compound selection

This work describes a novel semi-sequential technique for in silico enhancement of high-throughput screening (HTS) experiments now employed at Novartis. It is used in situations in which the size of the screen is limited by the readout (e.g., high-content screens) or the amount of reagents or tools (proteins or cells) available. By performing computational chemical diversity selection on a per plate basis (instead of a per compound basis), 25% of the 1,000,000-compound screening was optimized for general initial HTS. Statistical models are then generated from target-specific primary results (percentage inhibition data) to drive the cherry picking and testing from the entire collection. Using retrospective analysis of 11 HTS campaigns, the authors show that this method would have captured on average two thirds of the active compounds (IC(50) < 10 microM) and three fourths of the active Murcko scaffolds while decreasing screening expenditure by nearly 75%. This result is true for a wide variety of targets, including G-protein-coupled receptors, chemokine receptors, kinases, metalloproteinases, pathway screens, and protein-protein interactions. Unlike time-consuming "classic" sequential approaches that require multiple iterations of cherry picking, testing, and building statistical models, here individual compounds are cherry picked just once, based directly on primary screening data. Strikingly, the authors demonstrate that models built from primary data are as robust as models built from IC(50) data. This is true for all HTS campaigns analyzed, which represent a wide variety of target classes and assay types.     

Cryobanking of viable biomaterials: implementation of new strategies for conservation purposes

Cryobanking, the freezing of biological specimens to maintain their integrity for a variety of anticipated and unanticipated uses, offers unique opportunities to advance the basic knowledge of biological systems and their evolution. Notably, cryobanking provides a crucial opportunity to support conservation efforts for endangered species. Historically, cryobanking has been developed mostly in response to human economic and medical needs — these needs must now be extended to biodiversity conservation. Reproduction technologies utilizing cryobanked gametes, embryos and somatic cells are already vital components of endangered species recovery efforts. Advances in modern biological research (e.g. stem cell research, genomics and proteomics) are already drawing heavily on cryobanked specimens, and future needs are anticipated to be immense. The challenges of developing and applying cryobanking for a broader diversity of species were addressed at an international conference held at Trier University (Germany) in June 2008. However, the magnitude of the potential benefits of cryobanking stood in stark contrast to the lack of substantial resources available for this area of strategic interest for biological science — and society at large. The meeting at Trier established a foundation for a strong global incentive to cryobank threatened species. The establishment of an Amphibian Ark cryobanking programme offers the first opportunity for global cooperation to achieve the cryobanking of the threatened species from an entire vertebrate class.