Biology and genome of a newly discovered sibling species of Caenorhabditis elegans

A ‘sibling’ species of the model organism Caenorhabditis elegans has long been sought for use in comparative analyses that would enable deep evolutionary interpretations of biological phenomena. Here, we describe the first sibling species of C. elegans, C. inopinata n. sp., isolated from fig syconia in Okinawa, Japan. We investigate the morphology, developmental processes and behaviour of C. inopinata, which differ significantly from those of C. elegans. The 123-Mb C. inopinata genome was sequenced and assembled into six nuclear chromosomes, allowing delineation of Caenorhabditis genome evolution and revealing unique characteristics, such as highly expanded transposable elements that might have contributed to the genome evolution of C. inopinata. In addition, C. inopinata exhibits massive gene losses in chemoreceptor gene families, which could be correlated with its limited habitat area. We have developed genetic and molecular techniques for C. inopinata; thus C. inopinata provides an exciting new platform for comparative evolutionary studies

Transforming growth factor-β induced Warburg-like metabolic reprogramming may underpin the development of peritoneal endometriosis

CONTEXT: TGF-β is believed to play a major role in the etiology of peritoneal endometriosis. In tumors, TGF-β induces the metabolic conversion of glucose to lactate via glycolysis, a process referred to as the “Warburg effect.” Lactate increases cell invasion, angiogenesis, and immune suppression, all crucial steps in the development of endometriosis. OBJECTIVE: The aim of this study was to determine whether TGF-β induces a “Warburg-like” effect in peritoneal endometriosis. DESIGN: The study was informed by human tissue analysis and cel culture. SETTING: The study was conducted at the university research institute. PATIENTS OR OTHER PARTICIPANTS: We studied women undergoing surgical investigation for endometriosis. INTERVENTIONS: Concentrations of lactate and TGF-β1 in peritoneal fluid (n = 16) were measured by commercial assay. Expression of genes implicated in glycolysis was measured in endometrial and peritoneal biopsies (n = 31) by quantitative RT-PCR and immunohistochemistry. The effect of TGF-β1 on primary human peritoneal mesothelial cells (n = 6) and immortalized mesothelial (MeT-5A) cells (n = 3) was assessed by quantitative RT-PCR, Western blot, and commercial assays. MAIN OUTCOME MEASURES: Lactate, TGF-β1, and markers of glycolysis were measured. RESULTS: Concentrations of lactate in peritoneal fluid paralleled those of TGF-β1, being significantly higher in women with endometriosis compared to women without (P < .05). Endometriosis lesions expressed higher levels of glycolysis-associated genes HIF1A, PDK1, and LDHA than eutopic endometrium, and adjacent peritoneum had higher levels of HIF1A and SLC2A1 than peritoneum from women without disease (P < .05 to P < .001). Exposure of mesothelial cells to TGF-β1 increased production of lactate (P < .05), increased HIF1A mRNA (P < .05), and protein, and increased concentrations of mRNAs encoded by glycolysis-associated genes (LDHA, PDK1, SLC2A1; P < .05). CONCLUSIONS: A change in the metabolic phenotype of endometriosis lesions and peritoneal mesothelium in women with endometriosis may favor development of endometriosis

GC-Rich Sequence Elements Recruit PRC2 in Mammalian ES Cells

Polycomb proteins are epigenetic regulators that localize to developmental loci in the early embryo where they mediate lineage-specific gene repression. In Drosophila, these repressors are recruited to sequence elements by DNA binding proteins associated with Polycomb repressive complex 2 (PRC2). However, the sequences that recruit PRC2 in mammalian cells have remained obscure. To address this, we integrated a series of engineered bacterial artificial chromosomes into embryonic stem (ES) cells and examined their chromatin. We found that a 44 kb region corresponding to the Zfpm2 locus initiates de novo recruitment of PRC2. We then pinpointed a CpG island within this locus as both necessary and sufficient for PRC2 recruitment. Based on this causal demonstration and prior genomic analyses, we hypothesized that large GC-rich elements depleted of activating transcription factor motifs mediate PRC2 recruitment in mammals. We validated this model in two ways. First, we showed that a constitutively active CpG island is able to recruit PRC2 after excision of a cluster of activating motifs. Second, we showed that two 1 kb sequence intervals from the Escherichia coli genome with GC-contents comparable to a mammalian CpG island are both capable of recruiting PRC2 when integrated into the ES cell genome. Our findings demonstrate a causal role for GC-rich sequences in PRC2 recruitment and implicate a specific subset of CpG islands depleted of activating motifs as instrumental for the initial localization of this key regulator in mammalian genomes.Burroughs Wellcome FundCharles E. Culpeper FoundationMassachusetts General HospitalBroad Institute of MIT and Harvar

The genomic basis of parasitism in the Strongyloides clade of nematodes.

Soil-transmitted nematodes, including the Strongyloides genus, cause one of the most prevalent neglected tropical diseases. Here we compare the genomes of four Strongyloides species, including the human pathogen Strongyloides stercoralis, and their close relatives that are facultatively parasitic (Parastrongyloides trichosuri) and free-living (Rhabditophanes sp. KR3021). A significant paralogous expansion of key gene families--families encoding astacin-like and SCP/TAPS proteins--is associated with the evolution of parasitism in this clade. Exploiting the unique Strongyloides life cycle, we compare the transcriptomes of the parasitic and free-living stages and find that these same gene families are upregulated in the parasitic stages, underscoring their role in nematode parasitism

First behavioural characterisation of a knockout mouse model for the transforming growth factor (TGF)-β superfamily cytokine, MIC-1/GDF15

Macrophage inhibitory cytokine-1 (MIC-1), also known as growth differentiation factor 15 (GDF15), is a stress response cytokine. MIC-1/GDF15 is secreted into the cerebrospinal fluid and increased levels of MIC-1/GDF15 are associated with a variety of diseases including cognitive decline. Furthermore, Mic-1/Gdf15 knockout mice (Mic-1 KO) weigh more, have increased adiposity, associated with increased spontaneous food intake, and exhibit reduced basal energy expenditure and physical activity. The current study was designed to comprehensively determine the role of MIC-1/GDF15 on behavioural domains of male and female knockout mice including locomotion, exploration, anxiety, cognition, social behaviours, and sensorimotor gating. Mic-1 KO mice exhibited a task-dependent increase in locomotion and exploration and reduced anxiety-related behaviours across tests. Spatial working memory and social behaviours were not affected by Mic-1/Gdf15 deficiency. Interestingly, knockout mice formed an increased association with the conditioned stimulus in fear conditioning testing and also displayed significantly improved prepulse inhibition. Overall sex effects were evident for social behaviours, fear conditioning, and sensorimotor gating. This is the first study defining the role of Mic-1/Gdf15 in a number of behavioural domains. Whether the observed impact is based on direct actions of Mic-1/Gdf15 deficiency on the CNS or whether the behavioural effects are mediated by indirect actions on e.g. other neurotransmitter systems must be clarified in future studies

Acoustic startle response (ASR) and sensorimotor gating (i.e. prepulse inhibition: PPI).

<p>(A) ASR to different acoustic startle stimuli, (B) habituation to a 120dB startle stimulus across test trials (i.e. averaged across 3 blocks of 5 trials each), and (C) percentage prepulse inhibition [%PPI] across different prepulse intensities (i.e. 74dB, 82dB, and 86dB)–calculated for the middle 120dB ASR block. Data for control (WT) and <i>Mic-1</i> knockout mice (<i>Mic-1</i> KO) of both males (M) and females (F) are shown as means + SEM. A significant ‘sex’ effect (<i>p</i> < .05) and ‘startle block’ by ‘sex’ by ‘genotype’ interaction effect (<i>p</i> = .03) were found for ASR habituation. Only female mice and control mice (both <i>p</i> = .002) displayed intact ASR habituation. %PPI across prepulse intensities revealed a main effect of ‘genotype’ (<i>p</i> < .001) and a ‘sex’ by ‘prepulse intensity’ interaction (<i>p</i> = .01).</p

Anxiety-related behaviours in the elevated plus maze (EPM) and the open field test (OF).

<p>(A) Percentage time spent on open arms (excluding centre time) [%], (B) percentage of entries into open arms [%], (C) time spent in the central zone of the OF [s], and (D) ratio of total distance travelled in the central zone of the OF. Data for control (WT) and <i>Mic-1</i> knockout mice (<i>Mic-1</i> KO) of both males (M) and females (F) are shown as means + SEM. In the EPM, <i>Mic-1</i> mice spent more time (<i>p</i> = .002) and also showed more locomotion (<i>p</i> = .01) in the open arms. In the OF, knockout mice spent more time (<i>p</i> < .0001) and showed more locomotion (<i>p</i> < .0001) in the centre.</p

Fear-associated memory to context and cue.

<p>(A) Total time spent <i>freezing</i> [s] during the context test, (B) time spent <i>freezing</i> [s] across 1-min blocks in the context test, (C) time spent <i>freezing</i> [s] in the 1-min block prior and post cue presentation, and (D) time spent <i>freezing</i> [s] across 1-min blocks during cue presentation. Data for control (WT) and <i>Mic-1</i> knockout mice (<i>Mic-1</i> KO) of both males (M) and females (F) are shown as means + SEM. Comparing freezing in the last min prior to cue onset with the first min post cue onset revealed effects of ‘sex’ (<i>p</i> < .0001) and ‘genotype’ (<i>p</i> = .005) as well as a significant ‘1 min block’ by ‘genotype’ interaction (<i>p</i> = .01). Three mice (1x male <i>Mic</i>-1 KO, 1x female WT, and 1x male WT) jumped out of the test chamber during conditioning and were therefore not included in the statistical analysis.</p