Short-chain fatty acids reprogram metabolic profiles with the induction of reactive oxygen species production in human colorectal adenocarcinoma cells

Short-chain fatty acids (SCFAs) exhibit anticancer activity in cellular and animal models of colon cancer. Acetate, propionate, and butyrate are the three major SCFAs produced from dietary fiber by gut microbiota fermentation and have beneficial effects on human health. Most previous studies on the antitumor mechanisms of SCFAs have focused on specific metabolites or genes involved in antitumor pathways, such as reactive oxygen species (ROS) biosynthesis. In this study, we performed a systematic and unbiased analysis of the effects of acetate, propionate, and butyrate on ROS levels and metabolic and transcriptomic signatures at physiological concentrations in human colorectal adenocarcinoma cells. We observed significantly elevated levels of ROS in the treated cells. Furthermore, significantly regulated signatures were involved in overlapping pathways at metabolic and transcriptomic levels, including ROS response and metabolism, fatty acid transport and metabolism, glucose response and metabolism, mitochondrial transport and respiratory chain complex, one-carbon metabolism, amino acid transport and metabolism, and glutaminolysis, which are directly or indirectly linked to ROS production. Additionally, metabolic and transcriptomic regulation occurred in a SCFAs types-dependent manner, with an increasing degree from acetate to propionate and then to butyrate. This study provides a comprehensive analysis of how SCFAs induce ROS production and modulate metabolic and transcriptomic levels in colon cancer cells, which is vital for understanding the mechanisms of the effects of SCFAs on antitumor activity in colon cancer.

Computational solutions for spatial transcriptomics

Transcriptome level expression data connected to the spatial organization of the cells and molecules would allow a comprehensive understanding of how gene expression is connected to the structure and function in the biological systems. The spatial transcriptomics platforms may soon provide such information. However, the current platforms still lack spatial resolution, capture only a fraction of the transcriptome heterogeneity, or lack the throughput for large scale studies. The strengths and weaknesses in current ST platforms and computational solutions need to be taken into account when planning spatial transcriptomics studies. The basis of the computational ST analysis is the solutions developed for single-cell RNA-sequencing data, with advancements taking into account the spatial connectedness of the transcriptomes. The scRNA-seq tools are modified for spatial transcriptomics or new solutions like deep learning-based joint analysis of expression, spatial, and image data are developed to extract biological information in the spatially resolved transcriptomes. The computational ST analysis can reveal remarkable biological insights into spatial patterns of gene expression, cell signaling, and cell type variations in connection with cell type-specific signaling and organization in complex tissues. This review covers the topics that help choosing the platform and computational solutions for spatial transcriptomics research. We focus on the currently available ST methods and platforms and their strengths and limitations. Of the computational solutions, we provide an overview of the analysis steps and tools used in the ST data analysis. The compatibility with the data types and the tools provided by the current ST analysis frameworks are summarized.

Metabolic systems analysis identifies a novel mechanism contributing to shock in patients with endotheliopathy of trauma (EoT) involving thromboxane A2 and LTC4

Purpose

Endotheliopathy of trauma (EoT), as defined by circulating levels of syndecan-1 ≥ 40 ng/mL, has been reported to be associated with significantly increased transfusion requirements and a doubled 30-day mortality. Increased shedding of the glycocalyx points toward the endothelial cell membrane composition as important for the clinical outcome being the rationale for this study.

Results

The plasma metabolome of 95 severely injured trauma patients was investigated by mass spectrometry, and patients with EoT vs. non-EoT were compared by partial least square-discriminant analysis, identifying succinic acid as the top metabolite to differentiate EoT and non-EoT patients (VIP score = 3). EoT and non-EoT patients' metabolic flux profile was inferred by integrating the corresponding plasma metabolome data into a genome-scale metabolic network reconstruction analysis and performing a functional study of the metabolic capabilities of each group. Model predictions showed a decrease in cholesterol metabolism secondary to impaired mevalonate synthesis in EoT compared to non-EoT patients. Intracellular task analysis indicated decreased synthesis of thromboxanA2 and leukotrienes, as well as a lower carnitine palmitoyltransferase I activity in EoT compared to non-EoT patients. Sensitivity analysis also showed a significantly high dependence of eicosanoid-associated metabolic tasks on alpha-linolenic acid as unique to EoT patients.

Conclusions

Model-driven analysis of the endothelial cells' metabolism identified potential novel targets as impaired thromboxane A2 and leukotriene synthesis in EoT patients when compared to non-EoT patients. Reduced thromboxane A2 and leukotriene availability in the microvasculature impairs vasoconstriction ability and may thus contribute to shock in EoT patients. These findings are supported by extensive scientific literature; however, further investigations are required on these findings.

Effect of maternal employment on child nutritional status in Bale Robe Town, Ethiopia: a comparative cross-sectional analysis

Adequate nutrition is essential for early childhood to ensure healthy growth, proper organ formation, and function, a strong immune system, neurological and cognitive development. The main aim of the present study was to assess the effect of maternal employment on nutritional status among children aged 6-23 months in the town of Bale Robe, Ethiopia. A community-based comparative cross-sectional study was conducted on about 597 (293 unemployed and 304 employed) having children aged 6-23-month-old children sampled were employed with a multistage sampling technique. A face-to-face interview was conducted using a structured pretested questionnaire. Descriptive statistics, binary and multivariable logistic regression analyses were used for the statistical analysis. The magnitude of stunting (39.9 %), underweight (39⋅9 %) and wasting (22⋅2 %) was greater in 6-23-month-old children born to employed mothers than their counterparts in unemployed ones [stunted (31⋅3 %), underweight (24⋅0 %) and wasted (11⋅8 %)]. Being a girl [AOR 0⋅31; 95 % CI (0⋅17, 0⋅54)] in employed mothers and [AOR 0⋅29; 95 % CI (0⋅16, 0⋅51)] in unemployed people significantly protected stunting. This study demonstrated that the nutritional status of 6-23-month-old children is better among unemployed mothers than among employed mothers. Therefore, concerted efforts may decrease child undernutrition in a study area.

Subjective social status is associated with happiness but not weight status or psychological distress: An analysis of three prospective birth cohorts from low- and middle-income countries

BACKGROUND

Subjective social status (SSS, perception of social position relative to a frame of reference) has been associated with physical, mental and socio-emotional wellbeing. However, these associations may be susceptible to unmeasured confounding by life course objective socio-economic position (SEP; such as wealth, education and employment) and life satisfaction.

PURPOSE

To estimate the association of position on ladders of perceived community respect and perceived economic status with weight, distress and wellbeing, independent of objective SEP in cohorts from three low and middle-income countries.

METHODS

We used data from birth cohorts in Guatemala (n = 1258), Philippines (n = 1323) and South Africa (n = 1393). We estimated the association of perceived community respect and perceived economic status with body mass index (kg/m²), the World Health Organization's Self-Reported Questionnaire-20 (SRQ-20) for psychological distress, and Lyubomirsky's Subjective Happiness Scale. We estimated these associations using robust linear regression models adjusting for indicators of life course objective SEP, early life characteristics, adult covariates, and life satisfaction.

RESULTS

Participants in South Africa (age 27-28y) rated themselves higher on average for both the respect (7 vs 5 in Guatemala and 6 in Philippines) and economic (5 vs 3 in Guatemala and 4 in Philippines) ladder measures. Position on neither community respect nor economic ladders were associated with BMI or psychological distress. Higher position on community respect (Guatemala: 0.03, 95%CI: 0.01, 0.04; Philippines: 0.03, 95% CI: 0.02, 0.05; South Africa: 0.07, 95%CI: 0.04, 0.09) and economic (Guatemala: 0.02, 95%CI: 0, 0.04; Philippines: 0.04, 95%CI: 0.02, 0.07; South Africa: 0.07, 95%CI: 0.04, 0.10) ladders were associated with greater happiness.

CONCLUSIONS

Subjective social status showed small but consistent associations with happiness in birth cohorts independent of life-course SEP.

Changes in asset-based wealth across the life course in birth cohorts from five low- and middle-income countries

Background

Temporally-harmonized asset-based measures of wealth can be used to study the association of life-course wealth exposures in the same scale with health outcomes in low- and middle-income countries (LMICs). The within-individual longitudinal stability of asset-based indices of wealth in LMICs is poorly understood.

Methods

Using data from five birth cohorts from three continents, we developed temporally-harmonized asset indices over the life course through polychoric principal component analysis of a common set of assets collected consistently over time (18 years in Brazil to 50 years in Guatemala). For each cohort, we compared the harmonized index to cross-sectional indices created using more comprehensive asset measures using rank correlations. We evaluated the rank correlation of the harmonized index in early life and adulthood with maternal schooling and own attained schooling, respectively.

Results

Temporally-harmonized asset indices developed from a consistently-collected set of assets (range: 10 in South Africa to 30 in Philippines) suggested that mean wealth improved over time for all birth cohorts. Cross-sectional indices created separately for each study wave were correlated with the harmonized index for all cohorts (Brazil: r = 0.78 to 0.96; Guatemala: r = 0.81 to 0.95; India: 0.75 to 0.93; Philippines: r = 0.92 to 0.99; South Africa: r = 0.84 to 0.96). Maternal schooling (r = 0.15 to 0.56) and attained schooling (r = 0.23 to 0.53) were positively correlated with the harmonized asset index in childhood and adulthood respectively.

Conclusions

Temporally-harmonized asset indices displayed coherence with cross-sectional indices as well as construct validity with schooling.

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Temporally-harmonized asset indices are useful to assess relative importance of wealth at different life stages with health on the same scale.

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Harmonized indices using a subset of assets were correlated with cross-sectional asset indices using all available assets in five LMIC birth cohorts.

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Harmonized indices displayed construct validity, as demonstrated by its correlation with schooling.

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Harmonized indices were robust to alternate specifications such as shorter lists of assets, study years, and factor extraction procedures.

Proteome dynasmics and bioinformatics reveal major alterations in the turnover rate of functionally related cardiac and plasma proteins in a dog model of congestive heart failure

Protein pool turnover is a critically important cellular homeostatic component, yet it has been little explored in the context of heart failure (HF) pathophysiology. We employed in vivo ²H labeling/ proteome dynamics for non-biased discovery of turnover alterations involving functionally linked cardiac and plasma proteins in canine tachypacing-induced HF, an established preclinical model of dilated cardiomyopathy. Compared to control, dogs with congestive HF displayed bidirectional turnover changes of 28 cardiac proteins, i.e. reduced half-life of several key enzymes involved in glycolysis, homocysteine metabolism and glycogenesis, and increased half-life of proteins involved in proteolysis. Changes in plasma proteins were more modest: only 5 proteins, involved in various functions including proteolysis inhibition, hemoglobin, calcium and ferric-iron binding, displayed increased or decreased turnover rates. In other dogs undergoing cardiac tachypacing, we infused for 2 weeks the myokine Follistatin-like protein 1 (FSTL1), known for its ameliorative effects on HF-induced alterations. Proteome dynamics proved very sensitive in detecting the partial or complete prevention, by FSTL1, of cardiac and plasma protein turnover alterations. In conclusion, our study unveiled, for the first time in a large mammal, numerous HF-related alterations that may serve as the basis for future mechanistic research and/or as conceptually new molecular markers.

Relative and absolute wealth mobility since birth in relation to health and human capital in middle adulthood: An analysis of a Guatemalan birth cohort

Background

Wealth mobility, as both relative (positional) and absolute (material) wealth acquisition, may counteract negative consequences of early life adversities on adult health.

Methods

We use longitudinal data (1967–2018) from the INCAP birth cohort, Guatemala (n = 1386). Using wealth as a measure of socio-economic position, we assess the association of life course relative mobility using latent class analysis and absolute material gains using conditional wealth measures. We estimate associations of wealth mobility with indicators of human capital, specifically height, weight status (BMI in kg/m²), psychological distress (WHO SRQ-20 score) and fluid intelligence (Ravens Progressive Matrices score; RPM) in middle adulthood.

Results

We identified four latent classes of relative mobility – Stable Low (n = 498), Stable High (n = 223), Downwardly Mobile (n = 201) and Upwardly Mobile (n = 464). Attained schooling (years) was positively associated with membership in Upwardly Mobile (odds ratio; 1.50, 95%CI: 1.31, 1.71) vs Stable Low, and inversely with membership in Downwardly Mobile (0.65, 95%CI: 0.54, 0.79) vs Stable High. Being Upwardly Mobile (vs Stable Low) was positively associated with height (1.88 cm, 95%CI: 1.04, 2.72), relative weight (1.32 kg/m², 95%CI: 0.57, 2.07), lower psychological distress (−0.82 units, 95%CI: 1.34, −0.29) and fluid intelligence (0.94 units, 95%CI: 0.28, 1.59). Being Downwardly Mobile (vs Stable High) was associated with lower fluid intelligence (−2.69 units, 95%CI: 3.69, −1.68), and higher psychological distress (1.15 units, 95%CI: 0.34, 1.95). Absolute wealth gains (z-scores) from early to middle adulthood were positively associated with relative weight (0.62 kg/m², 95%CI: 0.28, 0.96), lower psychological distress (−0.37 units, 95%CI: 0.60, −0.14) and fluid intelligence (0.50 units, 95%CI: 0.21, 0.79).

Conclusions

Higher attained schooling provided a pathway for upward relative mobility and higher absolute wealth gains as well as protection against downward relative mobility. Upward mobility was associated with lower psychological distress and higher fluid intelligence but also higher weight status.

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Early life wealth and educational attainment are associated with upward wealth mobility, both in relative and absolute terms.

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Upward relative mobility is associated with lower psychological distress, and higher fluid intelligence and BMI.

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Downward relative mobility is associated with lower fluid intelligence, lower height, and higher psychological distress.

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Wealth gains from early to middle adulthood were associated with higher BMI and intelligence and lower psychological distress.

Industrial application of QbD and NIR chemometric models in quality improvement of immediate release tablets

Quality by Design (QbD) and chemometric models are different sides of the same coin. While QbD models utilize experimentally designed settings for optimization of some quality attributes, these settings can also be utilized for chemometric prediction of the same attributes. We aimed to synchronize optimization of comparative dissolution results of carvedilol immediate release tablets with chemometric prediction of dissolution profile and content uniformity of the product. As an industrial application, selection of variables for optimization was done by performing risk assessment utilizing the archived product records at the pharmaceutical site. Experimental tablets were produced with 20 different settings with the variables being contents of sucrose, sodium starch glycolate, lactose monohydrate, and avicel Ph 101. Contents of the excipients were modelled with F1 dissimilarity factor and F2 similarity factor in HCL, acetate, and USP dissolution media to determine the design space. We initiatively utilized Partial Least Square based Structural Equation Modelling (PLS-SEM) to explore how the excipients and their NIR records explained dissolution of the product. Finally, the optimized formula was utilized with varied content of carvedilol for chemometric prediction of the content uniformity.

A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses

The novel corona virus disease or COVID-19 caused by a positive strand RNA virus (PRV) called SARS-CoV-2 is plaguing the entire planet as we conduct this study. In this study a multifaceted analysis was carried out employing dinucleotide signature, codon usage and codon context to compare and unravel the genomic as well as genic characteristics of the SARS-CoV-2 isolates and how they compare to other PRVs which represents some of the most pathogenic human viruses. The main emphasis of this study was to comprehend the codon biology of the SARS-CoV-2 in the backdrop of the other PRVs like Poliovirus, Japanese encephalitis virus, Hepatitis C virus, Norovirus, Rubella virus, Semliki Forest virus, Zika virus, Dengue virus, Human rhinoviruses and the Betacoronaviruses since codon usage pattern along with the nucleotide composition prevalent within the viral genome helps to understand the biology and evolution of viruses. Our results suggest discrete genomic dinucleotide signature within the PRVs. Some of the genes from the different SARS-CoV-2 isolates were also found to demonstrate heterogeneity in terms of their dinucleotide signature. The SARS-CoV-2 isolates also demonstrated a codon context trend characteristically dissimilar to the other PRVs. The findings of this study are expected to contribute to the developing global knowledge base in countering COVID-19.

Nature's therapy for COVID-19: Targeting the vital non-structural proteins (NSP) from SARS-CoV-2 with phytochemicals from Indian medicinal plants

BACKGROUND

Containing COVID-19 is still a global challenge. It has affected the "normal" world by targeting its economy and health sector. The effect is shifting of focus of research from life threatening diseases like cancer. Thus, we need to develop a medical solution at the earliest. The purpose of this present work was to understand the efficacy of 22 rationally screened phytochemicals from Indian medicinal plants obtained from our previous work, following drug-likeness properties, against 6 non-structural-proteins (NSP) from SARS-CoV-2.

METHODS

100 ns molecular dynamics simulations were performed, and relative binding free energies were computed by MM/PBSA. Further, principal component analysis, dynamic cross correlation and hydrogen bond occupancy were analyzed to characterize protein-ligand interactions. Biological pathway enrichment analysis was also carried out to elucidate the therapeutic targets of the phytochemicals in comparison to SARS-CoV-2.

RESULTS

The potential binding modes and favourable molecular interaction profile of 9 phytochemicals, majorly from Withania somnifera with lowest free binding energies, against the SARS-CoV-2 NSP targets were identified. It was understood that phytochemicals and 2 repurposed drugs with steroidal moieties in their chemical structures formed stable interactions with the NSPs. Additionally, human target pathway analysis for SARS-CoV-2 and phytochemicals showed that cytokine mediated pathway and phosphorylation pathways were with the most significant p-value.

CONCLUSIONS

To summarize this work, we suggest a global approach of targeting multiple proteins of SARS-CoV-2 with phytochemicals as a natural alternative therapy for COVID-19. We also suggest that these phytochemicals need to be tested experimentally to confirm their efficacy.

Effect of methyl jasmonate and salicylic acid on the production of metabolites in cell suspensions cultures of Piper cumanense (Piperaceae)

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MeJA and SA induced a differential metabolic production in elicited cell suspensions.

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Production of metabolites was dependent on the type and the concentration of elicitor.

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Elicitation with SA produced the greatest changes in the metabolic profile.

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5-hidroximetilfurfural, (Z)-9-octadecenamide and phenol were induced by elicitation.

Elicitation of cell suspensions culture is a strategy that could increase the production of secondary metabolites under controlled conditions. This research evaluated the effect of methyl jasmonate-MeJA and salicylic acid-SA as elicitors on the production of metabolites in cell suspensions of P. cumanense. The type of elicitor (MeJA or SA), the concentration of elicitor (10 μM and 100 μM), and time of exposition (3, 12, 24 h) on cell suspension were evaluated. Metabolic profiles of intracellular and extracellular extracts were analyzed by UHPLC-DAD and GC–MS. Differential production of metabolites was dependent on the type of elicitor, its concentration, and the time of exposition. Treatments with 100 μM SA were conducted to high production of 5-hydroxymethylfurfural (6.3 %), phenol (6.5 %), and (Z)-9-octadecenamide (8.8 %). This is the first report of elicitation on cell suspensions in the Piper genus and contributes to understanding the effect of MeJA and SA on metabolite production in plant cell culture.

Computational advances of tumor marker selection and sample classification in cancer proteomics

Cancer proteomics has become a powerful technique for characterizing the protein markers driving transformation of malignancy, tracing proteome variation triggered by therapeutics, and discovering the novel targets and drugs for the treatment of oncologic diseases. To facilitate cancer diagnosis/prognosis and accelerate drug target discovery, a variety of methods for tumor marker identification and sample classification have been developed and successfully applied to cancer proteomic studies. This review article describes the most recent advances in those various approaches together with their current applications in cancer-related studies. Firstly, a number of popular feature selection methods are overviewed with objective evaluation on their advantages and disadvantages. Secondly, these methods are grouped into three major classes based on their underlying algorithms. Finally, a variety of sample separation algorithms are discussed. This review provides a comprehensive overview of the advances on tumor maker identification and patients/samples/tissues separations, which could be guidance to the researches in cancer proteomics.

Identification of potential endometriosis biomarkers in peritoneal fluid and blood plasma via shotgun lipidomics

Endometriosis is a recurrent and benign gynecological disorder, defined by the ectopic presence of endometrium. About 10% of reproductive-aged women suffer from endometriosis. There are no non-invasive or minimally invasive tests available in clinical practice to accurately diagnose endometriosis today. Here, we present our efforts to determine the diagnostic accuracy of biomarkers in peritoneal fluid and blood plasma using flow injection analysis with electrospray ionization tandem mass spectrometry (ESI-MS/MS) in 70 women with endometriosis and 20 women from a control group. The presence of endometriosis was confirmed by surgical findings and post-operative pathological examination. A qualitative and quantitative evaluation of the lipids in peritoneal fluids and blood plasma was carried out using electrospray ionization mass spectrometry (ESI-MS). The analysis revealed more than 140 molecular species of lipids, most of which pertained to five classes: phosphatidylcholines, phosphatidylethanolamines, sphingomyelins, di- and triglycerides. The data were analyzed using a statistical multifactorial method (i.e., PLS-DA). It was found that 9 potential biomarkers of endometriosis (LPC 16:0, PE O-20:0, PE O 34:1, PC 36:2, PC 36:4, PC 36:5, PC 38:4, PC 38:6 and SM 34:1) are common in blood plasma and peritoneal fluid, supporting connection with the pathological process. The sensitivity of the method developed for plasma was 93% with a specificity of 95%; for peritoneal fluid, the sensitivity was 90% and the specificity 95%. Accordingly, plasma is the most suitable biological fluid for clinical diagnostics of endometriosis. Further validation of these lipids as serologic biomarkers may enhance non-invasive diagnostic tools for patients with suspected endometriosis and reduce the frequency of diagnostic laparoscopy.

Transcriptomic data on the role of PEST-domain-enriched tyrosine phosphatase in the regulation of antigen-mediated activation and antiallergic action of glucocorticoids in mast cells

Protein tyrosine phosphatases and glucocorticoids are known to regulate allergic and antiallergic action in activated mast cells. Here we provide RNA sequencing and quantitative real-time PCR data from bone marrow derived mast cells, for wild-type and PEST-domain-enriched tyrosine phosphatase (PEP) null mice, activated by immunoglobulin E sensitization and dinitrophenol treatment, and additionally treated with the glucocorticoid dexamethasone. The transcriptomics experiment was performed in duplicate with a total of 16 samples (GSE108972).

Computational study of solution behavior of magainin 2 monomers

Antimicrobial peptides (AMPs) play crucial role as mediators of the primary host defense against microbial invasion. They are considered a promising alternative to antibiotics for multidrug resistant bacterial strains. For complete understanding of the antimicrobial defense mechanism, a detailed knowledge of the dynamics of peptide-membrane interactions, including atomistic studies on AMPs geometry and both peptide and membrane structural changes during the whole process is a prerequisite. We aim at clarifying the conformation dynamics of small linear AMPs in solution as a first step of in silico protocol for establishing a correspondence between certain amino-acid sequence motifs, secondary-structure elements, conformational dynamics in solution and the intensity and mode of interaction with the bacterial membrane. To this end, we use molecular dynamics simulations augmented by well-tempered metadynamics to study the free-energy landscape of two AMPs with close primary structure and different antibacterial activity - the native magainin 2 (MG2) and an analog (MG2m, with substitutions F5Y and F16W) in aqueous solution. We observe that upon solvation, the initial α-helical structures change differently. The native form remains structured, with three shorter α-helical motifs, connected by random coils, while the synthetic analog tends predominantly to a disordered conformation. Our results indicate the importance of the side-chains at positions 5 and 16 for maintaining the solvated peptide conformation. They also provide a modeling background for recent experimental observations, relating the higher α-helical content in solution (peptide pre-folding) in the case of small linear AMPs to a lower antibacterial activity.

Interacting mechanism of ID3 HLH domain towards E2A/E12 transcription factor - An Insight through molecular dynamics and docking approach

Inhibitor of DNA binding protein 3 (ID3) has long been characterized as an oncogene that implicates its functional role through its Helix-Loop-Helix (HLH) domain upon protein-protein interaction. An insight into the dimerization brought by this domain helps in identifying the key residues that favor the mechanism behind it. Molecular dynamics (MD) simulations were performed for the HLH proteins ID3 and Transcription factor E2-alpha (E2A/E12) and their ensemble complex (ID3-E2A/E12) to gather information about the HLH domain region and its role in the interaction process. Further evaluation of the results by Principal Component Analysis (PCA) and Free Energy Landscape (FEL) helped in revealing residues of E2A/E12: Lys570, Ala595, Val598, and Ile599 and ID3: Glu53, Gln63, and Gln66 buried in their HLH motifs imparting key roles in dimerization process. Furthermore the T-pad analysis results helped in identifying the key fluctuations and conformational transitions using the intrinsic properties of the residues present in the domain region of the proteins thus specifying their crucial role towards molecular recognition. The study provides an insight into the interacting mechanism of the ID3-E2A/E12 complex and maps the structural transitions arising in the essential conformational space indicating the key structural changes within the helical regions of the motif. It thereby describes how the internal dynamics of the proteins might regulate their intrinsic structural features and its subsequent functionality.

Risk Factors Associated With Non-Alcoholic Fatty Liver Disease in Indians: A Case-Control Study

BACKGROUND/AIMS

NAFLD has today emerged as the leading cause of liver disorder. There is scanty data on risk factors associated with NAFLD emanating from India. The present study was conducted to identify the risk factors associated with NAFLD.

METHODS

464 consecutive NAFLD patients and 181 control patients were subjected to detailed questionnaire regarding their lifestyle and dietary risk factors. Anthropometric measurements were obtained and biochemical assays were done. Comparison of different variables was made between NAFLD patients and controls using principal component analysis (PCA).

RESULTS

NAFLD patients had higher BMI [26.25 ± 3.80 vs 21.46 ± 3.08 kg/m(2), P = 0.000], waist-hip ratio [0.96 ± 0.12 vs 0.90 ± 0.08, P = 0.000] and waist-height ratio [0.57 ± 0.09 vs 0.50 ± 0.06, P = 0.000] compared to controls. Fasting blood sugar [101.88 ± 31.57 vs 90.87 ± 10.74 mg/dl] and triglyceride levels [196.16 ± 102.66 vs 133.20 ± 58.37 mg/dl] were significantly higher in NAFLD group. HOMA-IR was also higher in NAFLD group [2.53 ± 2.57 vs 1.16 ± 0.58, P = 0.000]. Majority (90.2%) of NAFLD patients were sedentary. Family history of metabolic syndrome (MS) was positively correlated with NAFLD. Dietary risk factors associated with NAFLD were non-vegetarian diet [35% vs 23%, P = 0.002], fried food [35% vs 9%, P = 0.000], spicy foods [51% vs 15%, P = 0.001] and tea [55% vs 39%, P = 0.001]. Diabetes, hypertension, snoring and sleep apnoea syndrome were common factors in NAFLD. On multivariate PCA, waist/height ratio and BMI were significantly higher in the NAFLD patients.

CONCLUSION

The risk factors associated with NAFLD are sedentary lifestyle, obesity family history of MS, consumption of meat/fish, spicy foods, fried foods and tea. Other risk factors associated with NAFLD included snoring and MS.

The C-terminal RNA binding motif of HuR is a multi-functional domain leading to HuR oligomerization and binding to U-rich RNA targets

Human antigen R (HuR) is a 32 kDa protein with 3 RNA Recognition Motifs (RRMs), which bind to Adenylate and uridylate Rich Elements (AREs) of mRNAs. Whereas the N-terminal and central domains (RRM1 and RRM2) are essential for AREs recognition, little is known on the C-terminal RRM3 beyond its implication in HuR oligomerization and apoptotic signaling. We have developed a detergent-based strategy to produce soluble RRM3 for structural studies. We have found that it adopts the typical RRM fold, does not interact with the RRM1 and RRM2 modules, and forms dimers in solution. Our NMR measurements, combined with Molecular Dynamics simulations and Analytical Ultracentrifugation experiments, show that the protein dimerizes through a helical region that contains the conserved W261 residue. We found that HuR RRM3 binds to 5'-mer U-rich RNA stretches through the solvent exposed side of its β-sheet, located opposite to the dimerization site. Upon mimicking phosphorylation by the S318D replacement, RRM3 mutant shows less ability to recognize RNA due to an electrostatic repulsion effect with the phosphate groups. Our study brings new insights of HuR RRM3 as a domain involved in protein oligomerization and RNA interaction, both functions regulated by 2 surfaces on opposite sides of the RRM domain.

Natural (auto)antibodies in calves are affected by age and diet

BACKGROUND

Natural autoantibodies (N(a)ab) were found in every species tested so far, and are likely important in maintaining homeostasis.

OBJECTIVES

(1) To determine N(a)ab in Bos taurus calves, (2) evaluate effects of diet and age on N(a)ab binding repertoires in calves, and (3) delineate bovine liver cell lysate (BLL) antigens related with variation in rumen score and body weight.

ANIMALS AND METHODS

Effects of age and diet on staining of BLL fragments by IgM and IgG antibodies in serum samples collected at 20 or at 26 weeks of age from bull calves either fed a restricted or ad libitum diet were analyzed using quantitative Western blotting. Correlations between fragments stained and grouping of calves were done by Principal Component Analysis (PCA). Redundancy analysis (RDA) was done to relate rumen score and body weight variation at slaughter at 27 weeks of age with stained BLL fragments.

RESULTS

In sera from all calves IgM and IgG antibodies binding BLL antigens were found. Corresponding fragments were stained, but quantitative differences in staining intensities were related to diet and age for both IgM and IgG. PCA revealed that age had a greater influence than diet on BLL fragment staining. RDA suggested that staining by IgM or IgG of specific BLL fragments was related with variation in rumen score and body weight.

CONCLUSIONS AND CLINICAL IMPORTANCE

Analyses of N(a)ab in serum could be a potential tool to estimate the health status of cattle, and be used to evaluate effects of husbandry practices.

MH2c: Characterization of major histocompatibility α-helices - an information criterion approach

Major histocompatibility proteins share a common overall structure or peptide binding groove. Two binding groove domains, on the same chain for major histocompatibility class I or on two different chains for major histocompatibility class II, contribute to that structure that consists of two α-helices ("wall") and a sheet of eight anti-parallel beta strands ("floor"). Apart from the peptide presented in the groove, the major histocompatibility α-helices play a central role for the interaction with the T cell receptor. This study presents a generalized mathematical approach for the characterization of these helices. We employed polynomials of degree 1 to 7 and splines with 1 to 2 nodes based on polynomials of degree 1 to 7 on the α-helices projected on their principal components. We evaluated all models with a corrected Akaike Information Criterion to determine which model represents the α-helices in the best way without overfitting the data. This method is applicable for both the stationary and the dynamic characterization of α-helices. By deriving differential geometric parameters from these models one obtains a reliable method to characterize and compare α-helices for a broad range of applications.

PROGRAM SUMMARY

Program title: MH²c (MH helix curves) Catalogue identifier: AELX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 327 565 No. of bytes in distributed program, including test data, etc.: 17 433 656 Distribution format: tar.gz Programming language: Matlab Computer: Personal computer architectures Operating system: Windows, Linux, Mac (all systems on which Matlab can be installed) RAM: Depends on the trajectory size, min. 1 GB (Matlab) Classification: 2.1, 4.9, 4.14 External routines: Curve Fitting Toolbox and Statistic Toolbox of Matlab Nature of problem: Major histocompatibility (MH) proteins share a similar overall structure. However, identical MH alleles which present different peptides differ by subtle conformational alterations. One hypothesis is that such conformational differences could be another level of T cell regulation. By this software package we present a reliable and systematic way to compare different MH structures to each other. Solution method: We tested several fitting approaches on all available experimental crystal structures of MH to obtain an overall picture of how to describe MH helices. For this purpose we transformed all complexes into the same space and applied splines and polynomials of several degrees to them. To draw a general conclusion which method fits them best we employed the "corrected Akaike Information Criterion". The software is applicable for all kinds of helices of biomolecules. Running time: Depends on the data, for a single stationary structure the runtime should not exceed a few seconds.