Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains

Background

Chromosome four of Drosophila melanogaster, known as the dot chromosome, is largely heterochromatic, as shown by immunofluorescent staining with antibodies to heterochromatin protein 1 (HP1) and histone H3K9me. In contrast, the absence of HP1 and H3K9me from the dot chromosome in D. virilis suggests that this region is euchromatic. D. virilis diverged from D. melanogaster 40 to 60 million years ago.

Results

Here we describe finished sequencing and analysis of 11 fosmids hybridizing to the dot chromosome of D. virilis (372,650 base-pairs) and seven fosmids from major euchromatic chromosome arms (273,110 base-pairs). Most genes from the dot chromosome of D. melanogaster remain on the dot chromosome in D. virilis, but many inversions have occurred. The dot chromosomes of both species are similar to the major chromosome arms in gene density and coding density, but the dot chromosome genes of both species have larger introns. The D. virilis dot chromosome fosmids have a high repeat density (22.8%), similar to homologous regions of D. melanogaster (26.5%). There are, however, major differences in the representation of repetitive elements. Remnants of DNA transposons make up only 6.3% of the D. virilis dot chromosome fosmids, but 18.4% of the homologous regions from D. melanogaster; DINE-1 and 1360 elements are particularly enriched in D. melanogaster. Euchromatic domains on the major chromosomes in both species have very few DNA transposons (less than 0.4 %).

Conclusion

Combining these results with recent findings about RNAi, we suggest that specific repetitive elements, as well as density, play a role in determining higher-order chromatin packaging.     

Biologically relevant effects of mRNA amplification on gene expression profiles

Background  

Gene expression microarray technology permits the analysis of global gene expression profiles. The amount of sample needed limits the use of small excision biopsies and/or needle biopsies from human or animal tissues. Linear amplification techniques have been developed to increase the amount of sample derived cDNA. These amplified samples can be hybridised on microarrays. However, little information is available whether microarrays based on amplified and unamplified material yield comparable results.     

Small molecule inhibitors of IgE synthesis

A novel series of small molecule inhibitors of IgE synthesis are described. Compounds were optimized for potency, metabolic stability and absence of genetic toxicology.     

Ecological effects of longline fishing and climate change on the pelagic ecosystem off eastern Australia

Pelagic longline fisheries target (or catch incidently) large apex predators in the open ocean (e.g. tunas, billfish and sharks) and have the potential to disrupt the ecosystem functionality if these predators exert strong top–down control. In contrast, warming of oceans from climate change may increase bottom–up effects from increases in primary productivity. An ecosystem model of a large pelagic ecosystem off eastern Australia was constructed to explore the potential ecological effects of climate change and longlining by Australia’s Eastern Tuna and Billfish Fishery. The model reproduced historic biomass and fishery catch trends from 1952 to 2006 for seven functional groups. Simulated changes in fishing effort and fishing mortality rate on individual target species from 2008 to 2018 resulted in only modest (<20%) changes in the biomass of target species and their direct predators or competitors. A simulated increase in phytoplankton biomass due to climate change resulted in only small increases (<11%) in the biomass of all groups. However, climate-related changes to the biomass of micronekton fish (−20%) and cephalopods (+50%) resulted in trophic cascades. Our results suggest there may be ecological redundancy among high trophic level predators since they share a diverse suite of prey and collectively only represent <1% of the total system biomass. In contrast, micronekton fishes and cephalopods have high biomasses and high production and consumption rates and are important as both prey and predators. They appear to exert ‘wasp–waist’ control of the ecosystem rather than top–down or bottom–up processes reported to drive other pelagic systems.     

不同放牧强度下短花针茅荒漠草原植被的空间异质性

分析不同放牧强度下植物群落中物种的空间分布特征, 有助于阐明群落在放牧胁迫下的演替规律。该研究基于幂函数法则, 探讨了不同放牧强度下短花针茅(Stipa breviflora)荒漠草原群落植物的频率和空间异质性。结果表明: 不同放牧强度下物种空间分布与幂函数法则能很好地吻合; 不同物种空间异质性具有特异性, 随着放牧强度的增加, 提高群落空间异质性的物种分别由无芒隐子草(Cleistogenes songorica)、冷蒿(Artemisia frigida)、短花针茅、银灰旋花(Convolvulus ammannii)等多个物种逐渐转变为以无芒隐子草、短花针茅为主的少数物种, 同时, 物种空间异质性大于群落空间异质性的物种数逐渐减少。     

A nicotinic acetylcholine receptor transmembrane point mutation (G275E) associated with resistance to spinosad in Frankliniella occidentalis

High levels of resistance to spinosad, a macrocyclic lactone insecticide, have been reported previously in western flower thrips, Frankliniella occidentalis, an economically important insect pest of vegetables, fruit and ornamental crops. We have cloned the nicotinic acetylcholine receptor (nAChR) α6 subunit from F. occidentalis (Foα6) and compared the nucleotide sequence of Foα6 from susceptible and spinosad‐resistant insect populations (MLFOM and R1S respectively). A single nucleotide change has been identified in Foα6, resulting in the replacement of a glycine (G) residue in susceptible insects with a glutamic acid (E) in resistant insects. The resistance‐associated mutation (G275E) is predicted to lie at the top of the third α‐helical transmembrane domain of Foα6. Although there is no direct evidence identifying the location of the spinosad binding site, the analogous amino acid in the C. elegans glutamate‐gated chloride channel lies in close proximity (4.4 Å) to the known binding site of ivermectin, another macrocyclic lactone pesticide. The functional consequences of the resistance‐associated mutation have been examined in the human nAChR α7 subunit. Introduction of an analogous (A272E) mutation in α7 abolishes the modulatory effects of spinosad whilst having no significant effect upon activation by acetylcholine, consistent with spinosad having an allosteric mechanism of action.     

Amblyomma sculptum: genetic diversity and rickettsias in the Brazilian Cerrado biome

Amblyomma sculptum (Ixodida: Ixodidae) Berlese, 1888 is the most important tick vector in Brazil, transmitting the bioagent of the most severe form of spotted fever (SF) in part of the Cerrado (in the states of Minas Gerais and São Paulo). In another part of the Cerrado (Central‐West region of Brazil), a milder form of SF has been recorded. However, neither the rickettsia nor the vector involved have been characterized. The aim of the current study was to analyse genetic variation and the presence of rickettsia in A. sculptum in Cerrado, from silent areas and with the milder form of SF. Samples were subjected to DNA extraction, amplification and sequencing of 12S rDNA, cytochrome oxidase subunit II and D‐loop mitochondrial genes (for tick population analyses), and gltA, htrA, ompA and gene D (sca4) genes for rickettsia researches. Exclusive haplotypes with low frequencies, high haplotype diversity and low nucleotide diversity, star‐shaped networks and significant results in neutrality tests indicate A. sculptum population expansions in some areas. Rickettsia amblyommatis, Candidatus Rickettsia andeanae and Rickettsia felis were detected. The A. sculptum diversity is not geographically, or biome delimited, pointing to a different potential in vector capacity, possibly associated with differing tick genetic profiles.     

Characterization of sodium transport in gustatory epithelia from the hamster and rat

The transduction of sodium salts occurs through a variety of mechanisms, including sodium influx through amiloride-sensitive sodium channels, anion-dependent sodium movement through intercellular junctions and unidentified amiloride-insensitive mechanisms. Characterizations of sodium transport in lingual epithelium mounted in Ussing chambers have focused almost exclusively on epithelia containing only fungiform taste buds. In the present study we have investigated sodium transport by measuring NaCl-induced short-circuit current from lingual epithelia containing fungiform, foliate, vallate and palatine taste buds in the hamster and the rat. All areas show measurable sodium transport, yet significant differences were noted between the epithelia from the rat and the hamster and among the different epithelia within a single species in terms of current density, transepithelial resistance and mucosal amiloride sensitivity. In general, epithelia from the anterior tongue were of a lower resistance and transported sodium more effectively than from the posterior tongue. Moreover, fungiform- and vallate-containing epithelia in the rat had a greater current density than did the corresponding tissues in the hamster. Amiloride sensitivity also differed between the rat and the hamster. In the hamster all gustatory areas showed some amiloride sensitivity, while in the rat the vallate-containing epithelia were devoid of amiloride- sensitive sodium transport. The results are consistent with the interpretation that all chemosensitive areas may participate in the detection of salts but the degree of salt transport and the mechanism of transport is variable among different lingual epithelia and different species.