APOBEC Mutagenesis and Copy-Number Alterations Are Drivers of Proteogenomic Tumor Evolution and Heterogeneity in Metastatic Thoracic Tumors

1. Download high-res image (249KB)
2. Download full-size image

     

Brevundimonas vesicularis MF276770, a new strain for gelatinase production by utilizing chicken feet gelatin

The utilization of waste has gained momentum in the field of waste management and industrial bioprocess. In this study, waste chicken feet were used as the source for extraction of a natural inducer, i.e. gelatin for the synthesis of proteolytic enzyme gelatinase. Microorganisms with gelatinolytic activity were screened from mixed culture isolates obtained from a local poultry waste dumping site. The strain which had shown maximum activity was identified as Brevundimonas vesicularis MF276770 using 16S rRNA gene sequencing. The composition of chicken feet gelatin was analysed and further characterized by Fourier transform infrared analysis and SDS-PAGE. The maximum gelatinase activity of 18.8?U/mL was achieved for the isolated Brevundimonas vesicularis MF276770 at 12?h under optimized conditions of pH 7, substrate concentration (2%), inoculums age (12?h), inoculum volume (2%, v/v), temperature (50?°C) and RPM (140). The enzyme kinetics parameters V_max and K_m were observed as 7.4?U/mL and 0.422 µmol, respectively. The molecular weight of the produced gelatinase was determined as 67?kDa. The produced gelatinase was employed to strip the gelatin silver layer from X-ray polyester film with 1.93?U/mL of gelatinase activity.     

Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor‐made rice with enhanced genetic gains

Though several genes governing various major traits have been reported in rice, their superior haplotype combinations for developing ideal variety remains elusive. In this study, haplotype analysis of 120 previously functionally characterized genes, influencing grain yield (87 genes) and grain quality (33 genes) revealed significant variations in the 3K rice genome (RG) panel. For selected genes, meta‐expression analysis using already available datasets along with co‐expression network provided insights at systems level. Also, we conducted candidate gene based association study for the 120 genes and identified 21 strongly associated genes governing 10‐grain yield and quality traits. We report superior haplotypes upon phenotyping the subset of 3K RG panel, SD1‐H8 with haplotype frequency (HF) of 30.13% in 3K RG panel, MOC1‐H9 (HF: 23.08%), IPA1‐H14 (HF: 6.64%), DEP3‐H2 (HF: 5.59%), DEP1‐H2 (HF: 37.53%), SP1‐H3 (HF: 5.05%), LAX1‐H5 (HF: 1.56%), LP‐H13 (3.64%), OSH1‐H4 (5.52%), PHD1‐H14 (HF: 15.21%), AGO7‐H15 (HF: 3.33%), ROC5‐H2 (31.42%), RSR1‐H8 (HF: 4.20%) and OsNAS3‐H2 (HF: 1.00%). For heading date, Ghd7‐H8 (HF: 3.08%), TOB1‐H10 (HF: 4.60%) flowered early, Ghd7‐H14 (HF: 42.60%), TRX1‐H9 (HF: 27.97%), OsVIL3‐H14 (HF: 1.72%) for medium duration flowering, while Ghd7‐H6 (HF: 1.65%), SNB‐H9 (HF: 9.35%) were late flowering. GS5‐H4 (HF: 65.84%) attributed slender, GS5‐H5 (HF: 29.00%), GW2‐H2 (HF: 4.13%) were medium slender and GS5‐H9 (HF: 2.15%) for bold grains. Furthermore, haplotype analysis explained possible genetic basis for superiority of selected mega‐varieties. Overall, this study suggests the possibility for developing next‐generation tailor‐made rice with superior haplotype combinations of target genes suiting future food and nutritional demands via haplotype‐based breeding.     

Microbial Variants from Iron Ore Slimes: Mineral Specificity and pH Tolerance

This paper describes the isolation of the native bacterial strains from the iron ore mines slime pond and its extremophilic characteristics. The two microbial isolates designated as CNIOS-1 and CNIOS-2 were grown in selective silicate broth at pH 7.0 and the organisms were tested for their selective adhesion on silicate and alumina minerals. The silicate bacteria with their exopolymers are very potent to grow over aluminosilicates. It was established that CNIOS-1 grew preferentially in the presence of silicate mineral compared to CNIOS-2 which grew in the presence of alumina. The organisms were tested for growth at various pH and trials were carried to define their efficacy for eventual applications to remove gangue minerals of silica and alumina from the raw material.

Electronic supplementary material

The online version of this article (doi:10.1007/s12088-015-0544-6) contains supplementary material, which is available to authorized users.     

A New Species of Microhyla (Anura: Microhylidae) from Nilphamari,Bangladesh

A new species of Microhyla frog from the Nilphamari district of Bangladesh is described and compared with its morphologically similar and geographically proximate congeners. Molecular phylogeny derived from mitochondrial DNA sequences revealed that although the new species – designated here as Microhyla nilphamariensis sp. nov. – forms a clade with M. ornate, it is highly divergent from M. ornata and all of its congeners, with 5.7 – 13.2% sequence divergence at the 16S rRNA gene. The new species can be identified phenotypically on the basis of a set of diagnostic (both qualitative and quantitative) characters as follows: head length is 77% of head width, distance from front of eyes to the nostril is roughly six times greater than nostril–snout length, internarial distance is roughly five times greater than nostril–snout length, interorbital distance is two times greater than internarial distance, and distance from back of mandible to back of the eye is 15% of head length. Furthermore, inner metacarpal tubercle is small and ovoid-shaped, whereas outer metacarpal tubercle is very small and rounded. Toes have rudimentary webbing, digital discs are absent, inner metatarsal tubercle is small and round, outer metatarsal tubercle is ovoid-shaped, minute, and indistinct.     

Early- and late-emerging Drosophila melanogaster fruit flies differ in their sensitivity to light during morning and evening

The authors derived early and late populations of fruit flies showing increased incidence of emergence during morning or evening hours by imposing selection for timing of emergence under 12:12 h light/dark (LD) cycles. From previous studies, it was clear that the increased incidence of adult emergence during morning and evening hours in early and late populations was a result of evolution of divergent and characteristic emergence waveforms in these populations. Such characteristic waveforms are henceforth referred to as "evolved emergence waveforms" (EEWs). The early and late populations also evolved different circadian clocks, which is evident from the divergence in their clock period (τ) and photic phase response curve (PRC). Although correlation between emergence waveforms and clock properties suggests functional significance of circadian clocks, τ and PRCs do not satisfactorily explain the early and late emergence phenotypes. In order to understand the functional significance of the PRC for early and late emergence phenotypes, the authors investigated whether circadian clocks of these flies exhibit any difference in photosensitivity under entrained conditions. Such differences would suggest that the light requirement for circadian entrainment of the emergence rhythm in early and late populations is different. To test this, they examined if early and late flies differ in their light utilization behavior, first by assaying their emergence rhythm under complete photoperiod and then in three different skeleton photoperiods. The results showed that early and late populations require different durations of light during the morning and evening to achieve their EEWs, suggesting that for the circadian entrainment of the emergence rhythm, early and late flies utilize light from different parts of the day.     

Stimulus change detection in phasic auditory units in the frog midbrain: frequency and ear specific adaptation

Neural adaptation, a reduction in the response to a maintained stimulus, is an important mechanism for detecting stimulus change. Contributing to change detection is the fact that adaptation is often stimulus specific: adaptation to a particular stimulus reduces excitability to a specific subset of stimuli, while the ability to respond to other stimuli is unaffected. Phasic cells (e.g., cells responding to stimulus onset) are good candidates for detecting the most rapid changes in natural auditory scenes, as they exhibit fast and complete adaptation to an initial stimulus presentation. We made recordings of single phasic auditory units in the frog midbrain to determine if adaptation was specific to stimulus frequency and ear of input. In response to an instantaneous frequency step in a tone, 28 % of phasic cells exhibited frequency specific adaptation based on a relative frequency change (delta-f = ±16 %). Frequency specific adaptation was not limited to frequency steps, however, as adaptation was also overcome during continuous frequency modulated stimuli and in response to spectral transients interrupting tones. The results suggest that adaptation is separated for peripheral (e.g., frequency) channels. This was tested directly using dichotic stimuli. In 45 % of binaural phasic units, adaptation was ear specific: adaptation to stimulation of one ear did not affect responses to stimulation of the other ear. Thus, adaptation exhibited specificity for stimulus frequency and lateralization at the level of the midbrain. This mechanism could be employed to detect rapid stimulus change within and between sound sources in complex acoustic environments.     

Chem‐bioinformatics: QSTR studies on TIBO derivatives

In the present study, effort has been made to develop a mathematical model for the set of 19 (tetrahydromidazo [4,5,1‐jk][1,4] benzodizepin‐2(1H)‐one) (TIBO) derivatives. The biological activity modeled in the present investigation is cytotoxic concentration (log 1/C). To investigate the cytotoxic behavior of TIBO derivatives, classical and nonconventional physicochemical properties are tested separately. Out of the two categories, the classical physicochemical properties play a dominating role in the modeling of cytotoxicity. On the basis of the results obtained and with the help of molecular modeling parameters, we discovered that the molecular property is most responsible for the cytotoxicity of TIBO derivatives. © 2009 Wiley Periodicals, Inc. J Biochem Mol Toxicol 23:166–171, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20270