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Targeted Next-Generation Sequencing Reveals a Novel Frameshift Mutation in the MERTK Gene in a Chinese Family with Retinitis Pigmentosa
No full textBackground: Retinitis pigmentosa (RP) is a group of inherited retinal diseases that result in severe progressive visual impairment. Aims: The purpose of this article was to apply targeted next-generation sequencing (NGS) to identify the causative mutation in a Chinese RP family. Methods: Blood samples were collected from a Chinese proband diagnosed with RP and her family members. A total of 163 genes that have been previously found to be involved in inherited retinal diseases were selected for NGS. Rigorous NGS data analysis; Sanger sequencing validation; and segregation analysis were applied to evaluate a novel frameshift mutation. Results: Sequence analysis revealed that the proband and her affected sister both carried a novel homozygous frameshift mutation in MERTK (p.I103Nfs*4). Other family members carrying a heterozygous mutation were unaffected. This mutation was found to cosegregate with the disease phenotype in this family. This mutation was not found in 1,000 control individuals. Conclusions: The targeted NGS strategy employed provides an efficient tool for RP pathogenic gene detection. This study identified a new autosomal recessive mutation in the RP-related gene MERTK, which expands the spectrum of RP disease-causing mutations
Characterization of Imprinted Genes in Rice Reveals Conservation of Regulation and Imprinting with Other Plant Species
No full textGenomic imprinting is an epigenetic phenomenon by which certain genes display differential expression in a parent-of-origin-dependent manner. Hundreds of imprinted genes have been identified from several plant species. Here, we identified, with a high level of confidence, 208 imprinted gene candidates from rice (Oryza sativa). Imprinted genes of rice showed limited association with the transposable elements, which contrasts with findings from Arabidopsis (Arabidopsis thaliana). Generally, imprinting in rice is conserved within a species, but intraspecific variation also was detected. The imprinted rice genes do not show signatures of selection, which suggests that domestication has had a limited evolutionary consequence on genomic imprinting. Although conservation of imprinting in plants is limited, we show that some loci are imprinted in several different species. Moreover, our results suggest that different types of epigenetic regulation can be established either before or after fertilization. Imprinted 24-nucleotide small RNAs and their neighboring genes tend to express alleles from different parents. This association was not observed between 21-nucleotide small RNAs and their neighboring genes. Together, our findings suggest that the regulation of imprinting can be diverse, and genomic imprinting has evolutionary and biological significance
Lanostane-type C-31 triterpenoid derivatives from the fruiting bodies of cultivated Fomitopsis palustris
No full textFifteen undescribed and five known lanostane-type C-31 triterpenoid derivatives were isolated from the aqueous EtOH extract of the fruiting bodies of cultivated Fomitopsis palustris. Their structures were identified from the spectroscopic data and chemical degradation studies. The structures of palustrisoic acids A and H were confirmed by X-ray crystallography. Polyporenic acid B showed strong cytotoxicity against the HCT116, A549, and HepG2 cell lines with IC50 values of 8.4, 12.1, and 12.2 mu M, respectively. Palustrisolides A, C, and G displayed weak cytotoxicity. (C) 2018 Elsevier Ltd. All rights reserved
Low ecological representation in the protected area network of China
No full textProtected areas are considered as an essential strategy to halt the decline of biodiversity. Ecological representation in protected areas is crucial for assessment on the progress toward conservation targets. Although China has established a large number of protected areas since the 1950s, ecological representation of protected areas is poorly understood. Here, we performed the complementarity analysis to evaluate ecological representation of protected areas in China. We used a database of the geographical distribution for 10,396 woody plant species, 2,305 fern species, 406 amphibian species, 460 reptile species, 1,364 bird species, and 590 mammal species from 2,376 counties across China. We identified complementary sets of counties for all species or threatened species of plant and vertebrate species using a complementarity algorithm. We evaluated ecological representation of 3,627 protected areas and discerned conservation gaps by comparing the distribution of protected areas with complementary sets. The results show that the spatially representative and complementary sites for biodiversity are poorly covered, and a fairly large proportion of protected areas is not designed to efficiently represent biodiversity at the national scale. Our methodology can serve as a generic framework for assessment on ecological representation of protected areas at the national scale
The effects of photoperiod and nutrition on duckweed (Landoltia punctata) growth and starch accumulation
No full textDuckweed has been considered as a renewable feedstock for bioethanol production due to its fast generation of biomass and high starch accumulation capability. In order to obtain high starch content in duckweed, Landoltia punctata was cultivated under 16:8 h or 24:0 h light/dark photoperiod cycles, each combined with a nutrient starvation or Hoagland's solution. The results showed that the starch percentage and starch yield under 24:0 h/nutrient starvation was higher than other conditions, with the maximum percentage of 60.03% and 76.45 g m(-2) (dry weight) in 21 days. Moreover, the results showed that long photoperiod cycles and nutrient starvation had more positive effects on starch accumulation, but nutritional concentration has no significant effect on the biomass production in short-term culturing (7 days). Notably, the biomass yield was: 24:0 h/Hoagland's > 24:0 h/nutrient starvation > 16:8 h/Hoagland's > 16:8 h/nutrient starvation in 21 days. This study provides optimized photoperiods and nutritional conditions for future industrial large-scale duckweed cultivation
Traditional plant based medicines used to treat musculoskeletal disorders in Northern Pakistan
No full textIntroduction: This paper provides significant information about traditional knowledge of medicinal plants to treat musculoskeletal disorders in Northern Pakistan. The study aimed to document data regarding traditional uses of plants in health-care practices among the rural communities of areas which may lead to natural drug discovery development. Methods: In total, 215 informants were interviewed using semi structured questionnaire. Documented ethno-medicinal data is analyzed using quantitative index of frequency citation (FC), relative frequency of citation (RFC), disease-consensus index (DCI), used value (UV), fidelity level (FL), jaccard index (JI), family important value (FIV), Relative popularity levely (RPL) and Rank priority order (ROP) and ethno-medicinal findings were compared with 25 previous published studies to report novel uses of plants against musculoskeletal disorder. Results: A total of 142 plants belonging to 69 families were reported with their medicinal usage to treat musculoskeletal disorders. The most dominant were herbs (57%), decoction was preferred method of utilization (35.2%) and leaves were the most used plant part (44.3%). The highest used category was recorded for rheumatism (44%) and the most used species were Celastrus paniculatus and Cyperus rotundus. RFC ranged from 0.098 to 0.586, Triticum aestivium with highest DCI (0.68) and Salvadoraceae was dominant family in terms of FIV (58.60). Conclusion: This study provides significant information about medicinal plants usage for musculoskeletal disorders among indigenous communities of Northern Pakistan. The baseline findings of this study might be useful in compiling data for future phytochemical and pharmacological screening of plants leading to natural drug discovery and development
Thinning-induced canopy opening exerted a specific effect on soil nematode community
No full textChanges in microclimate, soil physicochemical properties, understory vegetation cover, diversity, and composition as well as soil microbial community resulting from silvicultural practices are expected to alter soil food webs. Here, we investigated whether and how contrasting-sized canopy openings affect soil nematode community within a 30year-aged spruce plantation. The results indicated that the responses of soil nematodes to canopy opening size were dependant on their feeding habit. The abundance of total nematodes and that of free-living nematodes was negatively correlated with soil bulk density, whereas the abundance of omnivore-predators was negatively correlated with soil bulk density and shrubs cover, respectively. The ratio of the sum abundance of predators and omnivores to the plant parasites' abundance, Simpson's dominance index, Pielou's evenness index, and sigma maturity index, maturity index (MI), MI2-5, basal index, enrichment index, and structure index was sensitive to alteration in canopy opening size. Multivariate analysis indicated that thinning-induced gap size resulted in contrasting nematode assemblages. In conclusion, soil nematodes should be integrated as an indicator to monitor soil multifunctionality change due to thinning
Transcription of mcrA Gene Decreases Upon Prolonged Non-flooding Period in a Methanogenic Archaeal Community of a Paddy-Upland Rotational Field Soil
No full textMethanogenic archaea survive under aerated soil conditions in paddy fields, and their community is stable under these conditions. Changes in the abundance and composition of an active community of methanogenic archaea were assessed by analyzing mcrA gene (encoding alpha subunit of methyl-coenzyme M reductase) and transcripts during a prolonged drained period in a paddy-upland rotational field. Paddy rice (Oryza sativa L.) was planted in the flooded field and rotated with soybean (Glycine max [L.] Merr.) under upland soil conditions. Soil samples were collected from the rotational plot in the first year, with paddy rice, and in the two successive years, with soybean, at six time points, before seeding, during cultivation, and after harvest as well as from a consecutive paddy (control) plot. By the time that soybean was grown in the second year, the methanogenic archaeal community in the rotational plot maintained high mcrA transcript levels, comparable with those of the control plot community, but the levels drastically decreased by over three orders of magnitude after 2 years of upland conversion. The composition of active methanogenic archaeal communities that survived upland conversion in the rotational plot was similar to that of the active community in the control plot. These results revealed that mcrA gene transcription of methanogenic archaeal community in the rotational field was affected by a prolonged non-flooding period, longer than 1 year, indicating that unknown mechanisms maintain the stability of methanogenic archaeal community in paddy fields last up to 1 year after the onset of drainage
RECENT (2000-2015) DEVELOPMENTS IN THE ANALYSIS OF MINOR UNKNOWN NATURAL PRODUCTS BASED ON CHARACTERISTIC FRAGMENT INFORMATION USING LC-MS
No full textLiquid chromatography-Mass Spectrometry (LC-MS) has been widely used in natural product analysis. Global detection and identification of nontargeted components are desirable in natural product research, for example, in quality control of Chinese herbal medicine. Nontargeted components analysis continues to expand to exciting life science application domains such as metabonomics. With this background, the present review summarizes recent developments in the analysis of minor unknown natural products using LC-MS and mainly focuses on the determination of the molecular formulae, selection of precursor ions, and characteristic fragmentation patterns of the known compounds. This review consists of three parts. Firstly, the methods used to determine unique molecular formula of unknown compounds such as accurate mass measurements, MSn spectra, or relative isotopic abundance information, are introduced. Secondly, the methods improving signal-to-noise ratio of MS/MS spectra by manual-MS/MS or workflow targeting-only signals were elucidated; pure precursor ions can be selected by changing the precursor ion isolated window. Lastly, characteristic fragmentation patterns such as Retro-Diels-Alder (RDA), McLafferty rearrangements, "internal residue loss," and so on, occurring in the molecular ions of natural products are summarized. Classical application of characteristic fragmentation patterns in identifying unknown compounds in extracts and relevant fragmentation mechanisms are presented (RDA reactions occurring readily in the molecular ions of flavanones or isoflavanones, McLafferty-type fragmentation reactions of some natural products such as epipolythiodioxopiperazines; fragmentation by "internal residue loss" possibly involving ion-neutral complex intermediates). (c) 2016 Wiley Periodicals, Inc
Predatory Cues Influence the Behavioral Responses and Metamorphic Traits of Polypedates maculatus (Anura: Rhacophoridae)
Get PDFMechanisms of predator detection and the influence of the presence of nonlethal predators on antipredator defense behavior and metamorphic traits were studied in the Indian tree frog, Polypedates maculatus. Exposure of P. maculatus tadpoles to chemical cues of caged predator (crabs, Barytelphusa spp.) fed with either conspecific or heterogeneric tadpoles, or were starved elicited defense behavior (by avoiding predator zone) in them. Such a behavior was not evident when exposed to predators housed in a glass beaker (visual cues). Both early (Gosner stage 27–28) and later (Gosner stage 35–36) stage tadpoles when exposed to caged predators (fed with conspecific tadpoles), prey tadpoles spent less time swimming and remained motionless for longer periods. Yet, the time spent by prey in feeding was unaffected. Further, the predator avoidance behavior exhibited by them was of the same intensity regardless of whether the caged predators were fed or starved implying the influence of predator’s kairomones. Tadpoles reared with caged predator reached the metamorphic climax stage (MC stage; Gosner stage 42) earlier than those reared without a predator. Size at emergence (Gosner stage 46) was comparable in both the groups. The findings suggest that P. maculatus tadpoles assess predation risk chiefly by sensing kairomones of the predator in eliciting antipredator defense behaviors. Accelerated development and early metamorphosis without any compromise of the size at emergence may be due to their unaltered feeding activity