Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map

Gloeostereum incarnatum has edible and medicinal value and was first cultivated and domesticated in China. We sequenced the G. incarnatum monokaryotic strain GiC-126 on an Illumina HiSeq X Ten system and obtained a 34.52-Mb genome assembly sequence that encoded 16,895 predicted genes. We combined the GiC-126 genome with the published genome of G. incarnatum strain CCMJ2665 to construct a genetic linkage map (GiC-126 genome) that had 10 linkage groups (LGs), and the 15 assembly sequences of CCMJ2665 were integrated into 8 LGs. We identified 1912 simple sequence repeat (SSR) loci and detected 700 genes containing 768 SSRs in the genome; 65 and 100 of them were annotated with gene ontology (GO) terms and KEGG pathways, respectively. Carbohydrate-active enzymes (CAZymes) were identified in 20 fungal genomes and annotated; among them, 144 CAZymes were annotated in the GiC-126 genome. The A mating-type locus (MAT-A) of G. incarnatum was located on scaffold885 at 38.9 cM of LG1 and was flanked by two homeodomain (HD1) genes, mip and beta-fg. Fourteen segregation distortion markers were detected in the genetic linkage map, all of which were skewed toward the parent GiC-126. They formed three segregation distortion regions (SDR1–SDR3), and 22 predictive genes were found in scaffold1920 where three segregation distortion markers were located in SDR1. In this study, we corrected and updated the genomic information of G. incarnatum. Our results will provide a theoretical basis for fine gene mapping, functional gene cloning, and genetic breeding the follow-up of G. incarnatum.     

Flavonoids of Tinospora malabarica

A dibenzoylethane and an allyloxyflavone isolated from Tinospora malabarica have been assigned the structures 1-(2′,4′-dimethoxyphenyl)-3-(3″     

Growth condition controls on G-93 parameters of isoprene emission from tropical trees

Despite its major role in global isoprene emission, information on the environmental control of isoprene emission from tropical trees has remained scarce. Thus, in this study, we examined the relationship between parameters of G-93 isoprene emission formula (C_T1, C_T2, and α), growth temperature and light intensity, photosynthesis (?, P_max), isoprene synthase (IspS) level, and 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway metabolites using sunlit and shaded leaves of four tropical trees. The results showed that the temperature dependence of isoprene emission from shaded leaves did not differ significantly from sunlit leaves. In contrast, there was a lower saturation irradiance in shaded leaves than in sunlit leaves, the same as temperate plants. The photosynthesis rate of shaded leaves showed lower saturation irradiance, similar to the light dependence of isoprene emission. In most cases, the concentration of MEP pathway metabolites was of lower tendency in shaded leaves versus in sunlit leaves, whereas no significant difference was noted in IspS level between sunlit and shaded leaves. Correlation analysis between these parameters found that C_T1 of the G-93 parameter was positively correlated with the concentration of DXP and DMADP, whereas C_T2 correlated with the concentration of MEP and the average air temperature for the past 48 h. Similarly, α closely associated with the initial slope (?) of photosynthesis rate, and the basal emission factor is also linked to the photon flux of past days. These results suggest that growth conditions may control the temperature dependence of isoprene emission from tropical trees via the changes in the profiles of MEP pathway metabolites, causing alteration in the parameters of the isoprene emission formula.

     

Determination of inclusion depth in ex vivo animal tissues using surface enhanced deep Raman spectroscopy

This work presents recent developments in spatially offset and transmission Raman spectroscopy for noninvasive detection and depth prediction of a single SERS inclusion located deep inside ex vivo biological tissues. The concept exploits the differential attenuation of Raman bands brought about by their different absorption due to tissue constituents enabling to predict the inclusion depth. Four different calibration models are tested and evaluated to predict the depth of surface enhanced Raman scattering labelled nanoparticles, within an up to 40 mm slab of porcine tissue. An external measurement carried out in transmission mode, with a noninvasively built model on the analysed sample, is shown to be insensitive to variations of the overall thickness of the tissue yielding an average root‐mean‐square error of prediction of 6.7%. The results pave the way for future noninvasive deep Raman spectroscopy in vivo enabling to localise cancer biomarkers for an early diagnosis of multiple diseases.      

The E3 ubiquitin ligase Cul4b promotes CD4+ T cell expansion by aiding the repair of damaged DNA

The capacity for T cells to become activated and clonally expand during pathogen invasion is pivotal for protective immunity. Our understanding of how T cell receptor (TCR) signaling prepares cells for this rapid expansion remains limited. Here we provide evidence that the E3 ubiquitin ligase Cullin-4b (Cul4b) regulates this process. The abundance of total and neddylated Cul4b increased following TCR stimulation. Disruption of Cul4b resulted in impaired proliferation and survival of activated T cells. Additionally, Cul4b-deficient CD4⁺ T cells accumulated DNA damage. In T cells, Cul4b preferentially associated with the substrate receptor DCAF1, and Cul4b and DCAF1 were found to interact with proteins that promote the sensing or repair of damaged DNA. While Cul4b-deficient CD4⁺ T cells showed evidence of DNA damage sensing, downstream phosphorylation of SMC1A did not occur. These findings reveal an essential role for Cul4b in promoting the repair of damaged DNA to allow survival and expansion of activated T cells.

How does T cell receptor signaling prepare T cells for their rapid clonal expansion during pathogen invasion? This study shows that levels of the E3 ubiquitin ligase Cul4b increase following T cell activation; once expressed, Cul4b helps to maintain DNA integrity in CD4+ T lymphocytes by aiding in the repair of replication-induced DNA damage.     

Pharmacodynamic studies on Polypodium vulgare (Linn.)

Aqueous extract of the root of P. vulgare (PV) produced CNS depressant effect. It decreased the spontaneous motor activity, prolonged the pentobarbitone induced hypnosis, reduced body temperature and increased the reaction time to pain stimuli. PV also caused prevention against supramaximal electroshock and pentylenetetrazol induced seizures. PV showed a positive inotropic and chronotropic effect on perfused frog heart and caused hypotension and tachycardia in anaesthetised dogs. The effects were blocked by propranolol. PV produced dose dependent inhibition of contractions of rabbit small intestine and the effect was blocked by propranolol. PV appears to possess CNS depressant and beta-adrenoceptor agonistic activities.     

Food and feeding preferences of Himalayan gray goral (Naemorhedus goral bedfordi) in Pakistan and Azad Jammu and Kashmir

Himalayan gray goral is endemic to Himalayas and Hindukush ranges. Analysis of 15 fecal samples and field observations from different areas of Pakistan and Azad Kashmir suggest that goral consumes foliage of a minimum of 28 plant species. Trees, shrubs and grasses appear in the ratio of 1:36:63 and hence the species is a grazer, though may opt for browsing when forced. The species mainly subsists on six species of grasses (Chrysopogon aucheri=17.97%, Themeda anathera=13.03%, Poa pratensis=11.23%, Digitaria decumbens=9.30%, Apluda mutica=7.51%, Aristida cyanatha=3.15%), though leaves of shrubs (Myrsine africana=11.38%, Daphne oleoides=8.87%, Carissa opaca=5.94%, Dodonaea viscose=4.79%, Rubus ellipticus=2.93%, Gymnosporia royleana=1.29%) are also consumed. Food preference indices (consumed/availability) suggest that grasses are highly preferred (16.86 times of availability), followed by shrubs (3.3 times of availability), whereas trees and herbs are not preferred. Food plants contain water (77.9±0.56%), ash (8.6±0.38%), sugars (6.8±0.16%), proteins (5.6%±0.28%) and fats (1.3±0.08%). Food provides 4,440 kcal of energy and 5.45 L of water/day/adult goral, which is sufficient to meet the requirements of the species. Grasses need to be ensured in the protected area separated for management of goral population. Zoo Biol 27:371–380, 2008. © 2008 Wiley‐Liss, Inc.