The dual role of N6-methyladenosine on mouse maternal RNAs and 2-cell specific RNAs revealed by ULI-MeRIP sequencing

N6-methyladenosine (m6A) and its regulatory components play critical roles in various developmental processes in mammals(1-5). However, the landscape and function of m6A in the maternal-to-zygotic transition (MZT) remain unclear due to limited materials. Here, by developing an ultralow-input MeRIP-seq method, we revealed the dynamics of the m6A RNA methylome during the MZT process in mice. We found that more than 1/3 maternal decay and 2/3 zygotic mRNAs were modified by m6A. Moreover, m6As are highly enriched in the RNA of transposable elements MTA and MERVL, which are highly expressed in oocytes and 2-cell embryos, respectively. Notably, maternal depletion of Kiaa1429, a component of the m6A methyltransferase complex, leads to a reduced abundance of m6A-marked maternal RNAs, including both genes and MTA, in GV oocytes, indicating m6A-dependent regulation of RNA stability in oocytes. Interestingly, when the writers were depleted, some m6A-marked 2-cell specific RNAs, including Zscan4 and MERVL, appeared normal at the 2-cell stage but failed to be decayed at later stages, suggesting that m6A regulates the clearance of these transcripts. Together, our study uncovered that m6As function in context-specific manners during MZT, which ensures the transcriptome stability of oocytes and regulates the stage specificity of zygotic transcripts after fertilization.

Stage Specificity, the Dynamic Regulators and the Unique Orchid Arundina graminifolia

Orchids take years to reach flowering, but the unique bamboo orchid (Arundina graminifolia) achieves reproductive maturity in six months and then keeps on year round flowering. Therefore, studying different aspects of its growth, development and flowering is key to boost breeding programs for orchids. This study uses transcriptome tools to discuss genetic regulation in five stages of flower development and four tissue types. Stage specificity was focused to distinguish genes specifically expressed in different stages of flower development and tissue types. The top 10 highly expressed genes suggested unique regulatory patterns for each stage or tissue. The A. graminifolia sequences were blasted in Arabidopsis genome to validate stage specific genes and to predict important hormonal and cell regulators. Moreover, weighted gene co-expression network analysis (WGCNA) modules were ascertained to suggest highly influential hubs for early and late stages of flower development, leaf and root. Hormonal regulators were abundant in all data sets, such as auxin (LAX2, GH3.1 and SAUR41), cytokinin (LOG1), gibberellin (GASA3 and YAB4), abscisic acid (DPBF3) and sucrose (SWEET4 and SWEET13). Findings of this study, thus, give a fine sketch of genetic variability in Orchidaceae and broaden our understanding of orchid flower development and the involvement of multiple pathways.

Antiplasmodial Compounds from Deep-Water Marine Invertebrates

Novel drug leads for malaria therapy are urgently needed because of the widespread emergence of resistance to all available drugs. Screening of the Harbor Branch enriched fraction library against the Plasmodium falciparum chloroquine-resistant strain (Dd2) followed by bioassay-guided fractionation led to the identification of two potent antiplasmodials; a novel diterpene designated as bebrycin A (1) and the known C21 degraded terpene nitenin (2). A SYBR Green I assay was used to establish a Dd2 EC50 of 1.08 ± 0.21 and 0.29 ± 0.02 µM for bebrycin A and nitenin, respectively. Further analysis was then performed to assess the stage specificity of the inhibitors antiplasmodial effects on the Dd2 intraerythrocytic life cycle. Exposure to bebrycin A was found to block parasite maturation at the schizont stage if added any time prior to late schizogony at 42 hours post invasion, (HPI). In contrast, early life cycle exposure to nitenin (prior to 18 HPI) was identified as crucial to parasite inhibition, suggesting nitenin may target the maturation of the parasite during the transition from ring to early trophozoite (6–18 HPI), a novel property among known antimalarials.

Efficacy, metabolism and pharmacokinetics of Ro 15-5458, a forgotten schistosomicidal 9-acridanone hydrazone

Background Treatment of schistosomiasis, a neglected disease, relies on just one partially effective drug, praziquantel. We revisited the 9-acridanone hydrazone, Ro 15-5458, a largely forgotten antischistosomal lead compound. Methods Ro 15-5458 was evaluated in juvenile and adult Schistosoma mansoni-infected mice. We studied dose–response, hepatic shift and stage specificity. The metabolic stability of Ro 15-5458 was measured in the presence of human and mouse liver microsomes, and human hepatocytes; the latter also served to identify metabolites. Pharmacokinetic parameters were measured in naive mice. The efficacy of Ro 15-5458 was also assessed in S. haematobium-infected hamsters and S. japonicum-infected mice. Results Ro 15-5458 had single-dose ED50 values of 15 and 5.3 mg/kg in mice harbouring juvenile and adult S. mansoni infections, respectively. An ED50 value of 17 mg/kg was measured in S. haematobium-infected hamsters; however, the compound was inactive at up to 100 mg/kg in S. japonicum-infected mice. The drug-induced hepatic shift occurred between 48 and 66 h post treatment. A single oral dose of 50 mg/kg of Ro 15-5458 had high activity against all tested S. mansoni stages (1-, 7-, 14-, 21- and 49-day-old). In vitro, human hepatocytes produced N-desethyl and glucuronide metabolites; otherwise Ro 15-5458 was metabolically stable in the presence of microsomes or whole hepatocytes. The maximum plasma concentration was approximately 8.13 μg/mL 3 h after a 50 mg/kg oral dose and the half-life was approximately 4.9 h. Conclusions Ro 15-5458 has high activity against S. mansoni and S. haematobium, yet lacks activity against S. japonicum, which is striking. This will require further investigation, as a broad-spectrum antischistosomal drug is desirable.

Effects of Certain cis-Regulatory Elements on Stage-Specific vitellogenin Expression in the Bombyx mori (Lepidoptera: Bombycidae)

Bombyx mori vitellogenin (BmVg) is highly upregulated during pupation, and the 20-hydroxyecdysone and amino acids may regulate stage-specific BmVg expression. However, previous studies showed that other factors may also affect stage-specific BmVg expression. Here, we characterized effective BmVg transcription factors by identifying the corresponding cis-regulatory elements (CREs). We prepared transgenic B. mori, in which DsRed was driven by various lengths of BmVg promoter. qRT-PCR analysis showed that DsRed expression driven by a 1.0-kb BmVg promoter (VgP1.0K) was consistent with endogenous BmVg. VgP1.0K specificity was closer to the endogenous BmVg promoter than that of VgP0.8K. These results suggest that CREs affecting stage-specific BmVg expression were localized to the 1.0-kb BmVg promoter. We investigated the effects of certain CREs that could influence the stage specificity of BmVg promoter on BmVg expression in transgenic B. mori. The relative DsRed expression was significantly reduced in transgenic female B. mori and the peak in DsRed expression was delayed after E-box CRE mutation. These results demonstrate that the E-box element enhanced BmVg expression and also affected stage-specific BmVg expression. Moreover, the relative DsRed expression was significantly increased in transgenic female of B. mori after 3×BD CRE mutation in BmVg promoter. However, the stage specificity of the mutated promoter was consistent with that of the endogenous BmVg promoter. The 3×BD element downregulated BmVg but had no effect on stage-specific BmVg expression. The present study promoted the process of elucidating the regulatory network for stage-specific BmVg expression and furnished a theoretical basis for the application of BmVg promoter.

Alles F&E? Performance-Effekte phasenspezifischer externer Kooperation in KMU

Zusammenfassung Kleine und mittlere Unternehmen (KMU) sind stark auf externes Wissen angewiesen. Gleichzeitig weisen KMU einen geringen Strukturierungsgrad in der unternehmensinternen Forschung und Entwicklung (F&E) auf, wodurch der Zugriff auf externes Wissen auch über kooperative F&E hinaus erfolgen muss. Basierend auf Argumenten aus der ressourcenbasierten Sicht auf das Unternehmen (RBV) und aus der Forschung zu organisationaler Absorptionsfähigkeit wird argumentiert, dass KMU in verschiedenen Phasen des Innovationsprozesses von der Kooperation mit unternehmensexternen Partnern profitieren. Die aufgestellten Hypothesen werden anhand von Daten aus dem Mannheimer Innovation Panel (MIP) getestet. Der Datensatz umfasst 1.475 KMU. Der Einfluss von phasenspezifischer Kooperation auf den innovativen Umsatz geht weit über F&E hinaus und ist vom gewählten Partner abhängig. Abstract Small and medium sized enterprises (SMEs) strongly depend on external knowledge. At the same time, SMEs face several resource constraints. Especially the marginally structured internal research and development (R&D) function leads to knowledge sourcing beyond cooperative R&D. Using arguments from the Resource-Based View of the firm (RBV) and Absorptive Capacity (AC), this study hypothesizes on external collaboration and innovative sales taking partner- and stage-specificity into account. Data originates from the Mannheim Innovation Panel (MIP) comprising 1.475 SMEs Results suggest a broad impact of stage-specific collaboration on innovative sales, which depends on the type of partner.

Neuroimaging in Parkinson’s disease dementia: connecting the dots

Dementia is a common and devastating symptom of Parkinson’s disease but the anatomical substrate remains unclear. Some evidence points towards hippocampal involvement but neuroimaging abnormalities have been reported throughout the brain and are largely inconsistent across studies. Here, we test whether these disparate neuroimaging findings for Parkinson’s disease dementia localize to a common brain network. We used a literature search to identify studies reporting neuroimaging correlates of Parkinson’s dementia (11 studies, 385 patients). We restricted our search to studies of brain atrophy and hypometabolism that compared Parkinson’s patients with dementia to those without cognitive involvement. We used a standard coordinate-based activation likelihood estimation meta-analysis to assess for consistency in the neuroimaging findings. We then used a new approach, coordinate-based network mapping, to test whether neuroimaging findings localized to a common brain network. This approach uses resting-state functional connectivity from a large cohort of normative subjects (n = 1000) to identify the network of regions connected to a reported neuroimaging coordinate. Activation likelihood estimation meta-analysis failed to identify any brain regions consistently associated with Parkinson’s dementia, showing major heterogeneity across studies. In contrast, coordinate-based network mapping found that these heterogeneous neuroimaging findings localized to a specific brain network centred on the hippocampus. Next, we tested whether this network showed symptom specificity and stage specificity by performing two further analyses. We tested symptom specificity by examining studies of Parkinson’s hallucinations (9 studies, 402 patients) that are frequently co-morbid with Parkinson’s dementia. We tested for stage specificity by using studies of mild cognitive impairment in Parkinson’s disease (15 studies, 844 patients). Coordinate-based network mapping revealed that correlates of visual hallucinations fell within a network centred on bilateral lateral geniculate nucleus and correlates of mild cognitive impairment in Parkinson’s disease fell within a network centred on posterior default mode network. In both cases, the identified networks were distinct from the hippocampal network of Parkinson’s dementia. Our results link heterogeneous neuroimaging findings in Parkinson’s dementia to a common network centred on the hippocampus. This finding was symptom and stage-specific, with implications for understanding Parkinson’s dementia and heterogeneity of neuroimaging findings in general.

Increasing the Efficacy of GA3 Sprays in Cluster Elongation and Berry Thinning in Tas-A-Ganesh Grape (Vitis vinifera L.) in Tropical Viticulture

In view of the stage specificity for the efficacy of blanket sprays of GA3 for berry thinning, a field trial was laid out to achieve uniform flowering in Tas-A-Ganesh grapevines subjected to chemical defoliation prior to and hydrogen cyanamide application at fruit pruning in the double pruning and single cropping system during 2013-14 and 2014-15 fruiting seasons in growers’ vineyards around Nashik, Maharashtra by removing the un-uniformly thick canes. GA3 at different doses was sprayed two or three times to address the variation in uniform flowering, if any in cluster elongation and reducing the berry number/cluster. Cane regulation and GA3 sprays were used to achieve uniformity in bud break and flowering. Cluster compactness was derived by multiplying the number of berries/ cm length of rachis with berry diameter. Regression analysis of the variation has revealed that the cane diameter, through uniformity in bud break, influenced the uniformity in flowering which in turn influenced the cluster compactness through increased efficacy of blanket GA3 sprays in reducing the berry number/ cluster. Based on the optimum values of the contributory factors to cluster compactness, cane removal coupled with two blanket sprays of GA3 @ 30 g a.i./ha or retention of all canes coupled with three blanket sprays of GA3 @ 20 g a.i./ha was found to be ideal to obtain loose to well filled clusters. Taking together into account the effect of treatments on cluster compactness, yield and quality, retention of all canes coupled with three sprays of GA3 @ 20 g a.i./ha was considered appropriate for table grape production in Tas-A-Ganesh cv. of grapes.