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Even though learning and memory are universal traits in the Animal Kingdom, closely related species reveal substantial variation in learning rate and memory dynamics. To determine the genetic background of this natural variation, we studied two congeneric parasitic wasp species, Cotesia glomerata and C. rubecula, which lay their eggs in caterpillars of the large and small cabbage white butterfly. A successful egg laying event serves as an unconditioned stimulus (US) in a classical conditioning paradigm, where plant odors become associated with the encounter of a suitable host caterpillar. Depending on the host species, the number of conditioning trials and the parasitic wasp species, three different types of transcription-dependent long-term memory (LTM) and one type of transcription-independent, anesthesia-resistant memory (ARM) can be distinguished. To identify transcripts underlying these differences in memory formation, we isolated mRNA from parasitic wasp heads at three different time points between induction and consolidation of each of the four memory types, and for each sample three biological replicates, where after strand-specific paired-end 100 bp deep sequencing. Transcriptomes were assembled de novo and differential expression was determined for each memory type and time point after conditioning, compared to unconditioned wasps. Most differentially expressed (DE) genes and antisense transcripts were only DE in one of the LTM types. Among the DE genes that were DE in two or more LTM types, were many protein kinases and phosphatases, small GTPases, receptors and ion channels. Some genes were DE in opposing directions between any of the LTM memory types and ARM, suggesting that ARM in Cotesia requires the transcription of genes inhibiting LTM or vice versa. We discuss our findings in the context of neuronal functioning, including RNA splicing and transport, epigenetic regulation, neurotransmitter/peptide synthesis and antisense transcription. In conclusion, these brain transcriptomes provide candidate genes that may be involved in the observed natural variation in LTM in closely related Cotesia parasitic wasp species.

Background: Cellular processes underlying memory formation are evolutionary conserved, but natural variation in memory dynamics between animal species or populations is common. The genetic basis of this fascinating phenomenon is poorly understood. Closely related species of Nasonia parasitic wasps differ in long-term memory (LTM) formation: N. vitripennis will form transcription-dependent LTM after a single conditioning trial, whereas the closely-related species N. giraulti will not. Genes that were differentially expressed (DE) after conditioning in N. vitripennis, but not in N. giraulti, were identified as candidate genes that may regulate LTM formation., Results: RNA was collected from heads of both species before and immediately, 4 or 24 hours after conditioning, with 3 replicates per time point. It was sequenced strand-specifically, which allows distinguishing sense from antisense transcripts and improves the quality of expression analyses. We determined conditioning-induced DE compared to naïve controls for both species. These expression patterns were then analysed with GO enrichment analyses for each species and time point, which demonstrated an enrichment of signalling-related genes immediately after conditioning in N. vitripennis only. Analyses of known LTM genes and genes with an opposing expression pattern between the two species revealed additional candidate genes for the difference in LTM formation. These include genes from various signalling cascades, including several members of the Ras and PI3 kinase signalling pathways, and glutamate receptors. Interestingly, several other known LTM genes were exclusively differentially expressed in N. giraulti, which may indicate an LTM-inhibitory mechanism. Among the DE transcripts were also antisense transcripts. Furthermore, antisense transcripts aligning to a number of known memory genes were detected, which may have a role in regulating these genes., Conclusion: This study is the first to describe and compare expression patterns of both protein-coding and antisense transcripts, at different time points after conditioning, of two closely related animal species that differ in LTM formation. Several candidate genes that may regulate differences in LTM have been identified. This transcriptome analysis is a valuable resource for future in-depth studies to elucidate the role of candidate genes and antisense transcription in natural variation in LTM formation.

Nucleosome positioning dictates eukaryotic DNA compaction and access. To predict nucleosome positions in a statistical mechanics model, we exploited the knowledge that nucleosomes favor DNA sequences with specific periodically occurring dinucleotides. Our model is the first to capture both dyad position within a few base pairs, and free binding energy within 2 k(B)T, for all the known nucleosome positioning sequences. By applying Percus's equation to the derived energy landscape, we isolate sequence effects on genome-wide nucleosome occupancy from other factors that may influence nucleosome positioning. For both in vitro and in vivo systems, three parameters suffice to predict nucleosome occupancy with correlation coefficients of respectively 0.74 and 0.66. As predicted, we find the largest deviations in vivo around transcription start sites. This relatively simple algorithm can be used to guide future studies on the influence of DNA sequence on chromatin organization.

Mutations in the gene COL4A1, encoding collagen IV A1, are associated with familial porencephaly. Previously, COL4A1 mutation-associated antenatal hemorrhages have been suggested by early post-natal imaging. We describe 2 children with fetal intracerebral hemorrhages and a COL4A1 mutation. There was also extensive hemispheric tissue loss in both infants and loss of cerebellar tissue in one infant. This paper show prenatal evidence of fetal hemorrhage in association with a COL4A1 mutation., (© Georg Thieme Verlag KG Stuttgart · New York.)

This study uses molecular and cytogenetic methods to determine the origin of a B chromosome in some males of the wasp Trichogramma kaykai. This so-called paternal sex ratio (PSR) chromosome transmits only through sperm and shortly after fertilization triggers degeneration of the paternal genome, while keeping itself intact. The resulting embryos develop into haploid B-chromosome-carrying males. Another PSR chromosome with a very similar mode of action is found in the distantly related wasp Nasonia vitripennis and its origin was traced by transposon similarity to the genus Trichomalopsis, which is closely related to Nasonia. To determine whether both PSR chromosomes have a similar origin we aimed to reveal the origin of the Trichogramma PSR chromosome. Using fluorescent in situ hybridization, we discovered a major satellite repeat on the PSR chromosome, the 45S ribosomal DNA. Analysis of the internal transcribed spacer 2 (ITS2) of this repeat showed the presence of multiple ITS2 sequences on the PSR chromosome resembling either the ITS2 of T. oleae or of T. kaykai. We therefore conclude that the Trichogramma PSR chromosome originates from T. oleae or a T. oleae-like species. Our results are consistent with different origins for the PSR chromosomes in Trichogramma and Nasonia.

Background: Chromosome structure, DNA metabolic processes and cell type identity can all be affected by changing the positions of nucleosomes along chromosomal DNA, a reaction that is catalysed by SNF2-type ATP-driven chromatin remodelers. Recently it was suggested that in vivo, more than 50% of the nucleosome positions can be predicted simply by DNA sequence, especially within promoter regions. This seemingly contrasts with remodeler induced nucleosome mobility. The ability of remodeling enzymes to mobilise nucleosomes over short DNA distances is well documented. However, the nucleosome translocation processivity along DNA remains elusive. Furthermore, it is unknown what determines the initial direction of movement and how new nucleosome positions are adopted., Methodology/principal Findings: We have used AFM imaging and high resolution PAGE of mononucleosomes on 600 and 2500 bp DNA molecules to analyze ATP-dependent nucleosome repositioning by native and recombinant SNF2-type enzymes. We report that the underlying DNA sequence can control the initial direction of translocation, translocation distance, as well as the new positions adopted by nucleosomes upon enzymatic mobilization. Within a strong nucleosomal positioning sequence both recombinant Drosophila Mi-2 (CHD-type) and native RSC from yeast (SWI/SNF-type) repositioned the nucleosome at 10 bp intervals, which are intrinsic to the positioning sequence. Furthermore, RSC-catalyzed nucleosome translocation was noticeably more efficient when beyond the influence of this sequence. Interestingly, under limiting ATP conditions RSC preferred to position the nucleosome with 20 bp intervals within the positioning sequence, suggesting that native RSC preferentially translocates nucleosomes with 15 to 25 bp DNA steps., Conclusions/significance: Nucleosome repositioning thus appears to be influenced by both remodeler intrinsic and DNA sequence specific properties that interplay to define ATPase-catalyzed repositioning. Here we propose a successive three-step framework consisting of initiation, translocation and release steps to describe SNF2-type enzyme mediated nucleosome translocation along DNA. This conceptual framework helps resolve the apparent paradox between the high abundance of ATP-dependent remodelers per nucleus and the relative success of sequence-based predictions of nucleosome positioning in vivo.

The parasitoid wasp Trichogramma kaykai with a haplo-diploid sex determination has a B chromosome called the paternal sex ratio (PSR) chromosome that confers paternal genome loss during early embryogenesis, resulting in male offspring. So far, it is not well known whether the PSR chromosome has unique DNA sequence characteristics. By comparative AFLP fingerprinting of genomic DNA from wasps with and without the PSR chromosome, we isolated DNA from PSR-specific bands. Fourteen of such DNA fragments were analysed to confirm their PSR specificity. Seven were sequenced and two (PT-AFLP 1 and PT-AFLP1 3) were identified as parts of retrotransposon genes based on BLAST searches. Internal primers designed from a third AFLP fragment allowed PCR amplification of a PSR chromosome specific marker, which can be used to screen for the PSR trait in male wasps. Southern analysis revealed a dispersed repetitive nature of this third sequence in the T. kaykai genome, suggesting that it is part of a transposon. A fourth AFLP fragment (PT-AFLP 5) appears to be a large repetitive sequence on the PSR chromosome. This sequence is also found in the genome of both T. kaykai and the closely related species Trichogramma deion, but its distribution on the PSR chromosome strongly resembles that of T. deion rather than that of T. kaykai. Our results provide further insight into the repetitive nature of sequences comprising B chromosomes and their similarities with their host and closely related species.

ATP-dependent chromatin remodeling is performed by multi-subunit protein complexes. Over the last years, the identity of these factors has been unveiled in yeast and many parallels have been drawn with animal and plant systems, indicating that sophisticated chromatin transactions evolved prior to their divergence. Here we review current knowledge pertaining to the molecular mode of action of ATP-dependent chromatin remodeling, from single molecule studies to genome-wide genetic and proteomic studies. We focus on the budding yeast versions of SWI/SNF, RSC, DDM1, ISWI, CHD1, INO80 and SWR1.

Part of the male population of the wasp Trichogramma kaykai carries a B chromosome that manipulates its host sex ratio in favour of males. The only known repeat on this paternal sex ratio (PSR) chromosome is the 45S rDNA, which includes here five different internal transcribed spacer 2 (ITS2) sequences. In this report, we describe that only part of these ITS2 sequences is transcribed. The absence of transcription of some ITS2 sequences might explain the presence of multiple ITS2 sequences on the PSR chromosome since homogenization of rDNA spacers is thought to occur only in transcribed regions. Analysis of the only other known tandem repeat in Trichogramma, the EcoRI repeat, showed that it is absent from the PSR chromosome, and that the T. kaykai EcoRI repeat has 98 and 77% DNA sequence homology with the T. deion and T. brassicae EcoRI repeats, respectively. The size of the PSR chromosome measures 9 Mbp and is equal to 3.9% of the haploid T. kaykai genome. Finally, fluorescent in situ hybridization with a pool of high and moderate repetitive T. kaykai DNA (C0t-50) revealed only a very few major tandem repeats on the Trichogramma genome and only 45S rDNA on the PSR chromosome.