Cooperative Breeding in the Lake Tanganyika Cichlid Julidochromis ornatus

Cooperative breeding has been described for several cichlids from the genus Julidochromis (Perciformes: Cichlidae) under laboratory conditions, but field evidence is scarce. Here we describe the breeding system of the cichlid Julidochromis ornatus (Boulenger) in Lake Tanganyika (Zambia). Groups defended a breeding shelter under a large flat stone. Smaller group members stayed and fed under or close to the stone, actively guarded by the larger group members. Six out of 28 groups were newly established by breeders, joined by subordinates from a large pool of independent fish (comprising 50–70% of the total population), and four groups were seen to dissolve during a total of 77 observation days. Breeding groups consisted of a large breeding male and female with zero to five smaller subordinates (average 2). Larger breeders and subordinates were found in larger groups. All group members participated in territory defence and -maintenance, but the breeders were only present at the shelter 48% of the time, in contrast to the subordinates which guarded the breeding shelter 94% of the time. Smaller group members showed submissive behaviours to larger group members. We conclude subordinates in J. ornatus are helpers, but we did not find evidence that helpers increased the group’s current reproductive success. Personal observations combined with a literature review revealed at least 19 species of Lake Tanganyika cichlids show evidence of cooperative breeding, entirely confined to the substrate breeding tribe of the Lamprologini (24% of 80 species in total): 2 Chalinochromis spp., 5 Julidochromis spp., 12 Neolamprologus spp. More effort should be put into detecting cooperative breeding in American and Asian substrate breeding cichlid species.     

Genetic and Epigenetic Dynamics of a Retrotransposon After Allopolyploidization of Wheat

Allopolyploidy, or the combination of two or more distinct genomes in one nucleus, is usually accompanied by radical genomic changes involving transposable elements (TEs). The dynamics of TEs after an allopolyploidization event are poorly understood. In this study, we analyzed the methylation state and genetic rearrangements of a high copied, newly amplified terminal-repeat retrotransposon in miniature (TRIM) family in wheat termed Veju. We found that Veju insertion sites underwent massive methylation changes in the first four generations of a newly formed wheat allohexaploid. Hypomethylation or hypermethylation occurred in ∼43% of the tested insertion sites; while hypomethylation was significantly predominant in the first three generations of the newly formed allohexaploid, hypermethylation became predominant in the subsequent generation. In addition, we determined that the methylation state of Veju long terminal repeats (LTRs) might be correlated with the deletion and/or insertion of the TE. While most of the methylation changes and deletions of Veju occurred in the first generation of the newly formed allohexaploid, most Veju insertions were seen in the second generation. Finally, using quantitative PCR, we quantitatively assessed the genome composition of Veju in the newly formed allohexaploid and found that up to 50% of Veju LTRs were deleted in the first generation. Retrotransposition bursts in subsequent generations, however, led to increases in Veju elements. In light of these findings, the underlying mechanisms of TRIM rearrangements are discussed.TRANSPOSABLE elements (TEs) are DNA sequences that range in size from several hundred base pairs to >15 kb and that have the ability to move to different locations within the genome. TE movement occurs through either a copy-and-paste mechanism involving RNA intermediates (class 1) or a cut-and-paste mechanism involving DNA intermediates (class 2). Class 1 elements are also called retrotransposons, or retroelements, and comprise two main types: (1) long terminal repeat (LTR) retrotransposons, flanked by LTRs, and (2) non-LTR elements (such as long interspersed nuclear elements and short interspersed nuclear elements).LTR retrotransposons are the most abundant mobile elements in plant genomes (Feschotte et al. 2002), as the replicative mode of retroelement transposition enables the LTR retrotransposon to accrue in high copy number. Indeed, in some grasses, LTR retrotransposons represent up to 90% of the genome (Bennetzen and Kellogg 1997; Feschotte et al. 2002). As such, retrotransposon sequences function well as substrates for illegitimate and unequal recombinations that can lead to a variety of mutations, such as deletions, insertions, translocations, and others (Parisod et al. 2009).The replicative nature of TEs seems to be stimulated by a variety of specific stress conditions (reviewed by Wessler 1996; Capy et al. 2000; Grandbastien et al. 2005), including challenges to the genome such as interspecific hybridization, an idea first proposed by Barbara McClintock 26 years ago (McClintock 1984). Accordingly, allopolyploidization is usually coupled with rapid and reproducible genomic changes, including the elimination of DNA sequences (Liu et al. 1998a,b; Ozkan et al. 2001; Shaked et al. 2001; Adams and Wendel 2005b; Skalicka et al. 2005), gene silencing (Chen and Pikaard 1997; Comai et al. 2000; Kashkush et al. 2002; Simons et al. 2006), alteration of cytosine methylation (Shaked et al. 2001; Madlung et al. 2002; Salmon et al. 2005; Beaulieu et al. 2009; Xu et al. 2009), activation of genes and retrotransposons (Kashkush et al. 2002, 2003; O''Neill et al. 2002), massively altered gene expression patterns (Kashkush et al. 2002; Wang et al. 2006), and organ-specific subfunctionalization, i.e., differential expression of homeoalleles in different tissues and at different developmental stages (Adams et al. 2003; Adams and Wendel 2004). These and other studies (Levy and Feldman 2002; Osborn et al. 2003; Adams and Wendel 2005a; Rapp and Wendel 2005; Chen and Ni 2006; Chen 2007) demonstrate the dynamic nature of allopolyploid plant genomes.Although allopolyploidization has generally been assumed to induce large bursts of TE activity (Matzke and Matzke 1998), several studies that focused on different allopolyploid systems failed to provide any evidence for a transposition burst and offered only limited evidence for the transposition of specific TEs (Madlung et al. 2005; Ainouche et al. 2009; Beaulieu et al. 2009). In newly formed Arabidopsis allopolyploids, no evidence for transposition bursts was reported (Beaulieu et al. 2009), although limited evidence suggested that transposition events occurred in a specific TE called Sunfish (Madlung et al. 2005). Little evidence of TE transposition was found in a natural population of the 150-year-old allopolyploid, Spartina anglica (Ainouche et al. 2009), and no evidence of transposition of Wis 2-1A retrotransposons in a newly formed wheat allotetraploid was present (Kashkush et al. 2003). The results of these works and others indicate that, in the short term, TE proliferation after allopolyploidization may be restricted to a few specific TEs in particular allopolyploidy systems (Parisod et al. 2009).This study entailed a detailed investigation of the methylation patterns and rearrangements of a one terminal-repeat retrotransposon in miniature (TRIM) family in wheat termed Veju. TRIM elements possess the classical structure of LTR retrotransposons, but they are distinguished by their small overall sizes (0.4 to ∼2.5 kb). A nonautonomous retrotransposon, Veju is 2520 bp long with 374 bp of identical LTRs, yet does not contain the proteins required for retrotransposition (Sanmiguel et al. 2002). However, because Veju elements contain polypurine tracts (PPTs) and primer binding sites (PBSs), they are capable of transposing if the retrotransposition proteins are available from another source. In addition, the identical sequences of the Veju 5′ and 3′ LTRs indicate that some members of the Veju family retain retrotransposition activity.In silico analysis of Veju sequences revealed them to be one of the most active and most recently inserted sequences in the wheat genome (Sanmiguel et al. 2002; Sabot et al. 2005a). As such, we have determined and compared the methylation patterns of >880 Veju insertion sites in the first four generations of a newly formed wheat allohexaploid, as well as in the parental lines. We then tested the correlation between the cytosine methylation and genetic rearrangements (i.e., deletions and insertions) of Veju and addressed the precise developmental timing of these rearrangements. Finally, we successfully tested overall changes in the copy numbers of Veju in the newly formed allohexaploid using real-time quantitative PCR.     

A Dynamic Workflow Approach for the Integration of Bioinformatics Services

Modern biological and chemical studies rely on life science databases as well as sophisticated software tools (e.g., homology search tools, modeling and visualization tools). These tools often have to be combined and integrated in order to support a given study. SIBIOS (System for the Integration of Bioinformatics Services) serves this purpose. The services are both life science database search services and software tools. The task engine is the core component of SIBIOS. It supports the execution of dynamic workflows that incorporate multiple bioinformatics services. The architecture of SIBIOS, the approaches to addressing the heterogeneity as well as interoperability of bioinformatics services, including data integration are presented in this paper.     

The phylogeny of Dendropsophini (Anura: Hylidae: Hylinae)

The relationships of the hyline tribe Dendropsophini remain poorly studied, with most published analyses dealing with few of the species groups of Dendropsophus. In order to test the monophyly of Dendropsophini, its genera, and the species groups currently recognized in Dendropsophus, we performed a total evidence phylogenetic analysis. The molecular dataset included sequences of three mitochondrial and five nuclear genes from 210 terminals, including 12 outgroup species, the two species of Xenohyla, and 93 of the 108 recognized species of Dendropsophus. The phenomic dataset includes 46 terminals, one per species (34 Dendropsophus, one Xenohyla, and 11 outgroup species). Our results corroborate the monophyly of Dendropsophini and the reciprocal monophyly of Dendropsophus and Xenohyla. Some species groups of Dendropsophus are paraphyletic (the D. microcephalus, D. minimus, and D. parviceps groups, and the D. rubicundulus clade). On the basis of our results, we recognize nine species groups; for three of them (D. leucophyllatus, D. microcephalus, and D. parviceps groups) we recognize some nominal clades to highlight specific morphology or relationships and facilitate species taxonomy. We further discuss the evolution of oviposition site selection, where our results show multiple instances of independent evolution of terrestrial egg clutches during the evolutionary history of Dendropsophus.     

Molecular Evidence of Polyandry in the Citrus Mealybug,Planococcus citri (Hemiptera: Pseudococcidae)

The occurrence of polyandry in Planococcus citri , presumed by earlier observations of mating behavior, was confirmed using microsatellite genotyping of pools of over 400 eggs resulting from controlled crosses of one female with two males. The genetic contribution of both mated males was confirmed in 13 out of 43 crosses. In three crosses it was possible to determine that only the first male fertilized the eggs, which may be due to sperm competition or unviable sperm supply. The microsatellite analysis also allowed the confirmation of aspects of the chromosomal inheritance detected previously in cytogenetic studies in Planococcus citri , namely that only one of the alleles is transmitted by the male, indicating that the males are functionally haploid, supporting the observation of Paternal Genome Elimination (PGE) in these insects.     

Oncostatin M inhibits differentiation of rat stem Leydig cells in vivo and in vitro

Oncostatin M (OSM) is a pleiotropic cytokine within the interleukin six family of cytokines, which regulate cell growth and differentiation in a wide variety of biological systems. However, its action and underlying mechanisms on stem Leydig cell development are unclear. The objective of the present study was to investigate whether OSM affects the proliferation and differentiation of rat stem Leydig cells. We used a Leydig cell regeneration model in rat testis and a unique seminiferous tubule culture system after ethane dimethane sulfonate (EDS) treatment to assess the ability of OSM in the regulation of proliferation and differentiation of rat stem Leydig cells. Intratesticular injection of OSM (10 and 100 ng/testis) from post‐EDS day 14 to 28 blocked the regeneration of Leydig cells by reducing serum testosterone levels without affecting serum luteinizing hormone and follicle‐stimulating hormone levels. It also decreased the levels of Leydig cell‐specific mRNAs (Lhcgr, Star, Cyp11a1, Hsd3b1, Cyp17a1 and Hsd11b1) and their proteins by the RNA‐Seq and Western blotting analysis. OSM had no effect on the proliferative capacity of Leydig cells in vivo. In the seminiferous tubule culture system, OSM (0.1, 1, 10 and 100 ng/mL) inhibited the differentiation of stem Leydig cells by reducing medium testosterone levels and downregulating the expression of Leydig cell‐specific genes (Lhcgr, Star, Cyp11a1, Hsd3b1, Cyp17a1 and Hsd11b1) and their proteins. OSM‐mediated action was reversed by S3I‐201 (a STAT3 antagonist) or filgotinib (a JAK1 inhibitor). These data suggest that OSM is an inhibitory factor of rat stem Leydig cell development.     

Identification of Adverse Drug Events from Free Text Electronic Patient Records and Information in a Large Mental Health Case Register

Objectives

Electronic healthcare records (EHRs) are a rich source of information, with huge potential for secondary research use. The aim of this study was to develop an application to identify instances of Adverse Drug Events (ADEs) from free text psychiatric EHRs.

Methods

We used the GATE Natural Language Processing (NLP) software to mine instances of ADEs from free text content within the Clinical Record Interactive Search (CRIS) system, a de-identified psychiatric case register developed at the South London and Maudsley NHS Foundation Trust, UK. The tool was built around a set of four movement disorders (extrapyramidal side effects [EPSEs]) related to antipsychotic therapy and rules were then generalised such that the tool could be applied to additional ADEs. We report the frequencies of recorded EPSEs in patients diagnosed with a Severe Mental Illness (SMI) and then report performance in identifying eight other unrelated ADEs.

Results

The tool identified EPSEs with >0.85 precision and >0.86 recall during testing. Akathisia was found to be the most prevalent EPSE overall and occurred in the Asian ethnic group with a frequency of 8.13%. The tool performed well when applied to most of the non-EPSEs but least well when applied to rare conditions such as myocarditis, a condition that appears frequently in the text as a side effect warning to patients.

Conclusions

The developed tool allows us to accurately identify instances of a potential ADE from psychiatric EHRs. As such, we were able to study the prevalence of ADEs within subgroups of patients stratified by SMI diagnosis, gender, age and ethnicity. In addition we demonstrated the generalisability of the application to other ADE types by producing a high precision rate on a non-EPSE related set of ADE containing documents.

Availability

The application can be found at http://git.brc.iop.kcl.ac.uk/rmallah/dystoniaml.     

Follistatin and follistatin like-3 differentially regulate adiposity and glucose homeostasis

Transforming growth factor-β superfamily ligands, including activin and myostatin, modulate body composition, islet function, and glucose homeostasis. Their bioactivity is controlled by the antagonists follistatin (FST) and FST like-3 (FSTL3). The hypothesis tested was that FST and FSTL3 have distinct roles in regulating body composition, glucose homeostasis, and islet function through regulation of activin and myostatin bioactivity. Three genetic mutant mouse lines were created. FSTL3 knockout (FSTL3 KO), a mouse line producing only the FST288 isoform (FST288-only) and a double mutant (2xM) in which the lines were crossed. FST288-only males were lighter that wild-type (WT) littermates while FSTL3 KO and 2xM males had reduced perigonadal fat pad weights. However, only 2xM mice had increased whole body fat mass and decreased lean mass by quantitative nuclear magnetic resonance (qNMR). Fasting glucose levels in FSTL3 WT and KO mice were lower than FST mice in younger animals but were higher in older mice. Serum insulin and pancreatic insulin content in 2xM mice was significantly elevated over other genotypes. Nevertheless, 2xM mice were relatively insulin resistant and glucose intolerant compared to FST288-only and WT mice. Fractional islet area and proportion of β-cells/islet were increased in FSTL3 KO and 2xM, but not FST288-only mice. Despite their larger size, islets from FSTL3 KO and 2xM mice were not functionally enhanced compared to WT mice. These results demonstrate that body composition and glucose homeostasis are differentially regulated by FST and FSTL3 and that their combined loss is associated with increased fat mass and insulin resistance despite elevated insulin production.     

Lucanthone and its derivative hycanthone inhibit apurinic endonuclease-1 (APE1) by direct protein binding

Lucanthone and hycanthone are thioxanthenone DNA intercalators used in the 1980s as antitumor agents. Lucanthone is in Phase I clinical trial, whereas hycanthone was pulled out of Phase II trials. Their potential mechanism of action includes DNA intercalation, inhibition of nucleic acid biosyntheses, and inhibition of enzymes like topoisomerases and the dual function base excision repair enzyme apurinic endonuclease 1 (APE1). Lucanthone inhibits the endonuclease activity of APE1, without affecting its redox activity. Our goal was to decipher the precise mechanism of APE1 inhibition as a prerequisite towards development of improved therapeutics that can counteract higher APE1 activity often seen in tumors. The IC(50) values for inhibition of APE1 incision of depurinated plasmid DNA by lucanthone and hycanthone were 5 μM and 80 nM, respectively. The K(D) values (affinity constants) for APE1, as determined by BIACORE binding studies, were 89 nM for lucanthone/10 nM for hycanthone. APE1 structures reveal a hydrophobic pocket where hydrophobic small molecules like thioxanthenones can bind, and our modeling studies confirmed such docking. Circular dichroism spectra uncovered change in the helical structure of APE1 in the presence of lucanthone/hycanthone, and notably, this effect was decreased (Phe266Ala or Phe266Cys or Trp280Leu) or abolished (Phe266Ala/Trp280Ala) when hydrophobic site mutants were employed. Reduced inhibition by lucanthone of the diminished endonuclease activity of hydrophobic mutant proteins (as compared to wild type APE1) supports that binding of lucanthone to the hydrophobic pocket dictates APE1 inhibition. The DNA binding capacity of APE1 was marginally inhibited by lucanthone, and not at all by hycanthone, supporting our hypothesis that thioxanthenones inhibit APE1, predominantly, by direct interaction. Finally, lucanthone-induced degradation was drastically reduced in the presence of short and long lived free radical scavengers, e.g., TRIS and DMSO, suggesting that the mechanism of APE1 breakdown may involve free radical-induced peptide bond cleavage.