The good, the bad, the ugly: validating the mass spectrometric analysis of modified peptides

Mass spectrometric characterization of protein modifications is usually based on single peptides. With the advent of large-scale PTM-focussed MS studies, vast amounts of data are generated continuously, providing biologists extremely valuable and virtually never-ending sources for targeted functional research. However, even more than for proteomics in general, appropriate strategies for quality control of the different steps of the analytical strategy are imperative to prevent functional researchers from doing Sisyphos work on false-positive and unconfident PTM assignments. Here, we describe strategies to address the important issue of quality control for PTM analysis on various levels of the analytical pipeline: sample preparation/processing, analysis/identification and finally data interpretation, for qualitative as well as quantitative studies.     

AmylPepPred: Amyloidogenic Peptide Prediction tool

We present an efficient computational architecture designed using supervised machine learning model to predict amyloid fibril forming protein segments, named AmylPepPred. The proposed prediction model is based on bio-physio-chemical properties of primary sequences and auto-correlation function of their amino acid indices. AmylPepPred provides a user friendly web interface for the researchers to easily observe the fibril forming and non-fibril forming hexmers in a given protein sequence. We expect that this stratagem will be highly encouraging in discovering fibril forming regions in proteins thereby benefit in finding therapeutic agents that specifically aim these sequences for the inhibition and cure of amyloid illnesses.

Availability

AmylPepPred is available freely for academic use at www.zoommicro.in/amylpeppred     

MtnK, methylthioribose kinase, is a starvation-induced protein in Bacillus subtilis

Background  

Methylthioadenosine, the main by-product of spermidine synthesis, is degraded inBacillus subtilisas adenine and methylthioribose. The latter is an excellent sulfur source and the precursor of quorum-sensing signalling molecules. Nothing was known about methylthioribose recycling in this organism.     

Inducible cytochrome P450 activities in renal glomerular mesangial cells: biochemical basis for antagonistic interactions among nephrocarcinogenic polycyclic aromatic hydrocarbons

BACKGROUND: Benzo(a)pyrene (BaP), anthracene (ANTH) and chrysene (CHRY) are polynuclear aromatic hydrocarbons (PAHs) implicated in renal toxicity and carcinogenesis. These PAHs elicit cell type-specific effects that help predict toxicity outcomes in vitro and in vivo. While BaP and ANTH selectively injure glomerular mesangial cells, and CHRY targets cortico-tubular epithelial cells, binary or ternary mixtures of these hydrocarbons markedly reduce the overall cytotoxic potential of individual hydrocarbons. METHODS: To study the biochemical basis of these antagonistic interactions, renal glomerular mesangial cells were challenged with BaP alone (0.03 - 30 microM) or in the presence of ANTH (3 microM) or CHRY (3 microM) for 24 hr. Total RNA and protein will be harvested for Northern analysis and measurements of aryl hydrocarbon hydroxylase (AHH) and ethoxyresorufin-O-deethylase (EROD) activity, respectively, to evaluate cytochrome P450 mRNA and protein inducibility. Cellular hydrocarbon uptake and metabolic profiles of PAHs were analyzed by high performance liquid chromatography (HPLC). RESULTS: Combined hydrocarbon treatments did not influence the cellular uptake of individual hydrocarbons. ANTH or CHRY strongly repressed BaP-inducible cytochrome P450 mRNA and protein expression, and markedly inhibited oxidative BaP metabolism. CONCLUSION: These findings indicate that antagonistic interactions among nephrocarcinogenic PAHs involve altered expression of cytochrome P450s that modulate bioactivation profiles and nephrotoxic/ nephrocarcinogenic potential.     

Intensive cannibalism and feeding on bregmacerotids in <Emphasis Type="Italic">Champsodon snyderi</Emphasis> (Champsodontidae): evidence for pelagic predation

Analysis of the stomach contents of 1002 specimens of Champsodon snyderi (Champsodontidae) (17.3–91.2mm SL) from Tosa Bay, southern Japan, showed that species to primarily feed on crustaceans and fishes (87.9% by frequency, 37.6% by weight for the former; 17.3% and 60.7% for the latter, respectively), although fishes occurred more often in stomachs of individuals larger than 50mm SL. Champsodon snyderi ingested large prey fishes (60.5–101.0% of predator SL), the maximum weight recorded for a single ingested specimen being 50.9% of the predator weight. Mesopelagic Bregmaceros nectabanus were by far the dominant prey fish, followed by C. snyderi (cannibalism), indicating that C. snyderi leaves the bottom to feed in the pelagic environment during the night.     

1H NMR metabolomics reveals increased glutaminolysis upon overexpression of NSD3s or Pdp3 in Saccharomyces cerevisiae

NSD3s, the proline-tryptophan-tryptophan-proline (PWWP) domain-containing, short isoform of the human oncoprotein NSD3, displays high transforming properties. Overexpression of human NSD3s or the yeast protein Pdp3 in Saccharomyces cerevisiae induces similar metabolic changes, including increased growth rate and sensitivity to oxidative stress, accompanied by decreased oxygen consumption. Here, we set out to elucidate the biochemical pathways leading to the observed metabolic phenotype by analyzing the alterations in yeast metabolome in response to NSD3s or Pdp3 overexpression using ¹H nuclear magnetic resonance (NMR) metabolomics. We observed an increase in aspartate and alanine, together with a decrease in arginine levels, on overexpression of NSD3s or Pdp3, suggesting an increase in the rate of glutaminolysis. In addition, certain metabolites, including glutamate, valine, and phosphocholine were either NSD3s or Pdp3 specific, indicating that additional metabolic pathways are adapted in a protein-dependent manner. The observation that certain metabolic pathways are differentially regulated by NSD3s and Pdp3 suggests that, despite the structural similarity between their PWWP domains, the two proteins act by unique mechanisms and may recruit different downstream signaling complexes. This study establishes for the first time a functional link between the human oncoprotein NSD3s and cancer metabolic reprogramming.     

Heterospecific aggression and adaptive divergence in brook stickleback (Culaea inconstans)

Agonistic behavior between heterospecifics, in which individuals of one species attack another, may cause a subordinate species to shift resource or habitat use. Subsequent evolutionary responses to selection may mimic shifts expected under ecological character displacement, but with no role played by exploitative competition. Alternatively, aggressive behavior can evolve when fitness is improved by excluding members of a coexisting species from a defendable resource through interference. We tested whether heterospecific agonistic behavior has evolved in brook stickleback (Culaea inconstans) by comparing replicate allopatric populations to those sympatric with ninespine stickleback (Pungitius pungitius). We also tested for heritable variation in heterospecific aggressive behavior by rearing family groups in a common environment. Allopatric populations of brook stickleback were more aggressive than ninespine stickleback, suggesting that pre-existing aggression in brook stickleback contributed to niche shifts by ninespine stickleback. In addition, sympatric adult brook stickleback were more aggressive toward ninespine stickleback than brook stickleback from allopatric populations. Overt heterospecific aggressive behaviors were heritable, and aggression in juvenile brook stickleback increased with age in sympatric but not in allopatric populations reared in a common environment. Brook stickleback have evolved increased aggression when they coexist with ninespine stickleback. These stickleback communities have been structured by both evolved and pre-existing variation in heterospecific aggressive behavior in brook stickleback.     

Hematological profiles of COVID-19 patients at the Ratlam district,Madhya Pradesh State,India

It is of interest to compare the hematological profile (using Complete blood count) of COVID patients admitted in ICU, private ward, and isolation ward with varying severity. This data will help predict the severity of infection at peripheries and rural areas.  Detailed history and CBC was performed for all the cases. Different ratios and indexes such as systemic inflammatory index (SII), Neutrophil lymphocyte ratio (NLR), platelet lymphocyte ratio (PLR) were assessed. A total of 862 cases with a mean age of 49.9 ±17.4 years were enrolled. Hemoglobin level, lymphocyte (count per liter and percentage) were significantly lower in patients admitted in ICU as compared to patients admitted in the isolation ward and private ward (p <0.05). However, TLC, neutrophils, platelet count were higher in patients admitted to ICU (p <0.05). The Various ratios such as SII, NLR, and PLR showed significantly higher value in cases admitted in ICU (p <0.05). The TLC, neutrophil count, neutrophil percentage, SII, NLR, and PLR were significant predictors of severe disease (admission in ICU) with high diagnostic accuracy. We show that complete blood count method is a simple, readily available, rapid, and inexpensive tool that can be utilized for diagnosis and can predicting the severity of COVID 19 where RTPCR or trained staff is not available. Thus, NLR (%), SII, PLR, and TLC can predict severe illness with high accuracy.     

β—榄香烯吗素抗肿瘤作用的实验研究

β－榄香烯吗素（PIC－BE）是抗癌新药β－榄香烯的水溶性衍生物。本观察了PIC－BE对多药耐药K562／ADM细胞系及其敏感细胞K562的生长抑制和凋亡诱导作用。结果显示,（1）K562／ADM细胞对ADM具有明显的抗性,与K562细胞相比,抗笥倍数约为40倍,而两对PIC－BE的IC50接近,无显差异;（2）PIC－BE（10.0-30.0μg/ml）对K562和K562／ADM细胞不仅具有明显的生长抑制作用,而且显地诱导细胞凋亡,其作用强度在一定的范围内呈相对浓度和时间的依赖性,以上结果提示,PIC－BE是一种有效的抗肿瘤化合物,且已产生MDR的K562／ADM细胞对它不具耐药性。