Dinoflagellate bloom development and collapse in Lake Kinneret: a sediment trap study

Warm monomictic Lake Kinneret, Israel, is characterized by awinter–spring water bloom of the large (~50 µm diameter)dinoflagellate Peridinium gatunense Nygaard. Usually the P.gatunense bloom declines in May–June and a less prominentbloom of smaller dinoflagellates (mostly Peridiniopsis spp.of ~20–30 µm diameter) develops. Water column abundancesand sedimentation losses to those dinoflagellates were followedthroughout 1994 and 1995. The objective was to quantify thevariables that describe population dynamics, that in turn willshed more light on the seasonal patterns of bloom dynamics.Sedimentation losses were measured by means of sediment trapswith and without a preservative (formaldehyde) that were exposedfor 24 h once every 2–3 weeks. Annual sedimentation lossesof Peridinium (hypolimnetic trap catches) were 209 g wet wtm^-2 year^-1 in 1994 and 187 g wet wt m^-2 year^-1 in 1995, whichconstituted 16 and 23% of Peridinium production in those years,respectively. This study revealed that increased death ratespreceded a mass sedimentation flux of Peridinium and causedthe decline of the bloom in Lake Kinneret. Annual sedimentationlosses of Peridiniopsis were 55 g wet wt m^-2 year^-1 in 1994and 34 g wet wt m^-2 year^-1 in 1995. In contrast to live Peridiniumcells, Peridiniopsis cells continued to swim to the lower trapafter the onset of thermal stratification, possibly taking advantageof the higher nutrient concentrations below the thermocline,at a time when the lake is already stratified and the epilimnionis nutrient depleted. This could be an important factor allowingPeridiniopsis spp. to peak after the decline of Peridinium.     

Uptake and fate of IAA in apple callus tissue using IAA-1-14C

Incubation of young growing and older non-growing apple callustissues in a medium containing IAA-1-¹⁴C resulted in rapid disappearanceof the IAA. In old calluses (3 months), the major portion ofIAA was lost by decarboxylation (90% after 4 hr) and very little(1.4%) was maintained by the tissue. In young calluses, after4 hr in light, decarboxylation reached 20% and absorption 35%of the labelled IAA. Some decomposition of IAA was caused byphotolysis and autoclaving (19% and 3%, respectively) but thefinal distribution of radioactivity was not affected. Factorssuch as sucrose concentration in the incubation medium, distilledwater as incubation medium, and cutting of the callus did notaffect tissue behavior. Special precautions were taken to eliminatenon-biological decomposition of IAA. Therefore, we believe thatthe rapid CO₂ evolution is of enzymatic nature. This theoryis supported by the drop in decarboxylation after killing ofthe callus, and the increase of decarboxylation with age. Noenzyme was secreted by the callus into the medium after 24 hrof incubation, and IAA decomposition in old tissues is doneprobably on the surface. Absorption of IAA increased with increasingcallus size and decarboxylation decreased. ¹ Contribution from the Agricultural Research Organization,The Volcani Center, Bet Dagan, Israel. 1973 Series, No. 274-E. (Received May 30, 1974; )     

Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper

Across the life sciences, processing next generation sequencing data commonly relies upon a computationally expensive process where reads are mapped onto a reference sequence. Prior to such processing, however, there is a vast amount of information that can be ascertained from the reads, potentially obviating the need for processing, or allowing optimized mapping approaches to be deployed. Here, we present a method termed FlexTyper which facilitates a “reverse mapping” approach in which high throughput sequence queries, in the form of k-mer searches, are run against indexed short-read datasets in order to extract useful information. This reverse mapping approach enables the rapid counting of target sequences of interest. We demonstrate FlexTyper’s utility for recovering depth of coverage, and accurate genotyping of SNP sites across the human genome. We show that genotyping unmapped reads can correctly inform a sample’s population, sex, and relatedness in a family setting. Detection of pathogen sequences within RNA-seq data was sensitive and accurate, performing comparably to existing methods, but with increased flexibility. We present two examples of ways in which this flexibility allows the analysis of genome features not well-represented in a linear reference. First, we analyze contigs from African genome sequencing studies, showing how they distribute across families from three distinct populations. Second, we show how gene-marking k-mers for the killer immune receptor locus allow allele detection in a region that is challenging for standard read mapping pipelines. The future adoption of the reverse mapping approach represented by FlexTyper will be enabled by more efficient methods for FM-index generation and biology-informed collections of reference queries. In the long-term, selection of population-specific references or weighting of edges in pan-population reference genome graphs will be possible using the FlexTyper approach. FlexTyper is available at https://github.com/wassermanlab/OpenFlexTyper.     

The levels of cyclic GMP and glucose 1,6-diphosphate,and the activity of phosphofructokinase,in muscle from normal and dystrophic mice

A striking reduction in the levels of glucose 1,6-diphosphate and an increase in cyclic GMP were found in muscle from dystrophic mice. Concomitant to these changes, the allosteric activity of phosphofructokinase was found to be markedly reduced. These findings could offer an explanation for the observed reduction in glycolysis in the dystrophic muscle.     

Animal models for Gaucher disease research

Gaucher disease (GD), the most common lysosomal storage disorder (LSD), is caused by the defective activity of the lysosomal hydrolase glucocerebrosidase, which is encoded by the GBA gene. Generation of animal models that faithfully recapitulate the three clinical subtypes of GD has proved to be more of a challenge than first anticipated. The first mouse to be produced died within hours after birth owing to skin permeability problems, and mice with point mutations in Gba did not display symptoms correlating with human disease and also died soon after birth. Recently, conditional knockout mice that mimic some features of the human disease have become available. Here, we review the contribution of all currently available animal models to examining pathological pathways underlying GD and to testing the efficacy of new treatment modalities, and propose a number of criteria for the generation of more appropriate animal models of GD.     

The giant cells produced by Telenomus remus (Hymenoptera: Scelionidae)

The parasitic larva of Telenomus remus is surrounded by giant cells throughout its first instar. These cells arise in the embryonic serosa of the parasite and grow in size, starting with a radius of 5nm and ending with 27nm. Young cells are round and mononuclear, whereas older ones are often polynuclear and have varied, irregular contours. Most cells are profusely vacuolated, the vacuoles being especially large in some of the older cells. Only a few of the giant cells are devoured by the first instar parasite larva, but all disappear at the end of this stage. No giant cells seem to be produced by supernumerary larvae. Once the parasite egg hatches, the host tissue disintegrates almost instantaneously.