Kaposi’s sarcoma: a computational approach through protein–protein interaction and gene regulatory networks analysis

Interactomic data for Kaposi’s Sarcoma Associated Herpes virus (KSHV)—the causative agent of vascular origin tumor called Kaposi’s sarcoma—is relatively modest to date. The objective of this study was to assign functions to the previously uncharacterized ORFs in the virus using computational approaches and subsequently fit them to the host interactome landscape on protein, gene, and cellular level. On the basis of expression data, predicted RNA interference data, reported experimental data, and sequence based functional annotation we also tried to hypothesize the ORFs role in lytic and latent cycle during viral infection. We studied 17 previously uncharacterized ORFs in KSHV and the host-virus interplay seems to work in three major functional pathways—cell division, transport, metabolic and enzymatic in general. Studying the host-virus crosstalk for lytic phase predicts ORF 10 and ORF 11 as a predicted virus hub whereas PCNA is predicted as a host hub. On the other hand, ORF31 has been predicted as a latent phase inducible protein. KSHV invests a lion’s share of its coding potential to suppress host immune response; various inflammatory mediators such as IFN-γ, TNF, IL-6, and IL-8 are negatively regulated by the ORFs while Il-10 secretion is stimulated in contrast. Although, like any other computational prediction, the study requires further validation, keeping into account the reproducibility and vast sample size of the systems biology approach the study allows us to propose an integrated network for host-virus interaction with good confidence. We hope that the study, in the long run, would help us identify effective dug against potential molecular targets.     

Acyldepsipeptide activated ClpP1P2 macromolecule of Leptospira,an ideal Achilles’ heel to hamper the cell survival and deregulate ClpP proteolytic activity

Antibiotic acyldepsipeptide (ADEP) targets the bacterial ClpP serine protease and can inhibit the growth of numerous bacterial species by activating/dysregulating the protease activity within the cell. The spirochete Leptospira interrogans harbors two ClpP isoforms (LepClpP1 and LepClpP2). Supplementation of ADEP in the Leptospira growth medium resulted in the inhibition of bacterial growth. The ADEP mediated activation of the LepClpP mixture was dependent on the time allowed for the self-assembly of LepClpP1 and LepClpP2. The dynamic light scattering of the LepClpP mixture in the presence of the ADEP indicated a conformational transformation of the LepClpP machinery. Serine 98, a catalytic triad residue of the LepClpP1 in the LepClpP1P2 heterocomplex, was critical for the ADEP mediated activation. The computational prototype of the LepClpP1P2 structure suggested that the hydrophobic pockets wherein the ADEPs or the physiological chaperone ClpX predominantly dock are exclusively present in the LepClpP2 heptamer. Using the ADEP as a tool, this investigation provides an insight into the molecular function of the LepClpP1P2 in a coalition with its ATPase chaperone LepClpX. The shreds of the evidence illustrated in this investigation verify that ADEP1 possesses the ability to control the LepClpP system in an unconventional approach than the other organisms.     

Use of the composite asthma severity index in a pediatric subspecialty clinic

BackgroundThe Composite Asthma Severity Index (CASI) is a comprehensive tool to assess asthma severity, which has been applied in the research setting.ObjectiveTo evaluate, in an outpatient setting, whether a CASI score accurately predicts asthma severity or control as determined by means of subspecialist assessment. Asthma Control Test (ACT) and childhood ACT (C-ACT) scores were generated to provide additional context for CASI scores in relationship to assessments using another clinical tool.MethodsChildren aged 5 to 18 years with a physician diagnosis of persistent asthma were recruited from a tertiary care center. A pediatric pulmonologist made determinations on each participant’s asthma severity and control during a clinic visit. A CASI and ACT/C-ACT score was generated for each patient. Logistic regression and Spearman correlations were used to determine how well CASI scores predicted physician assessments. Agreement between ACT/C-ACT scores and physician assessment of asthma control was determined in supplemental analyses.ResultsCASI scores strongly predicted physician assessment of severity (Spearman correlation = 0.61, P < .001); unadjusted odds ratio (OR) equal to 36.67 (95% confidence interval [CI]: 8.83-152.34); and adjusted OR equal to 32.76 (95% CI: 85.70-188.44). In supplemental analyses, ACT/C-ACT scores strongly predicted physician assessment of control (Spearman correlation = 0.72, P < .001) with an unadjusted OR equal to 42.12 (95% CI: 13.34-133.00) and adjusted OR equal to 55.34 (95% CI: 13.62-224.89).ConclusionUse of the CASI was feasible and accurately predicted physician assessments of asthma severity and control in this sample, which are not distinct entities. The CASI is a robust tool that may be used successfully in ambulatory pediatric asthma care.     

Integration of light scattering with machine learning for label free cell detection

Light scattering has been used for label-free cell detection. The angular light scattering patterns from the cells are unique to them based on the cell size, nucleus size, number of mitochondria, and cell surface roughness. The patterns collected from the cells can then be classified based on different image characteristics. We have also developed a machine learning (ML) method to classify these cell light scattering patterns. As a case study we have used this light scattering technique integrated with the machine learning to analyze staurosporine-treated SH-SY5Y neuroblastoma cells and compare them to non-treated control cells. Experimental results show that the ML technique can provide a classification accuracy (treated versus non-treated) of over 90%. The predicted percentage of the treated cells in a mixed solution is within 5% of the reference (ground-truth) value and the technique has the potential to be a viable method for real-time detection and diagnosis.     

STEAP: a prostate-specific cell-surface antigen highly expressed in human prostate tumors

In search of novel genes expressed in metastatic prostate cancer, we subtracted cDNA isolated from benign prostatic hypertrophic tissue from cDNA isolated from a prostate cancer xenograft model that mimics advanced disease. One novel gene that is highly expressed in advanced prostate cancer encodes a 339-amino acid protein with six potential membrane-spanning regions flanked by hydrophilic amino- and carboxyl-terminal domains. This structure suggests a potential function as a channel or transporter protein. This gene, named STEAP for six-transmembrane epithelial antigen of the prostate, is expressed predominantly in human prostate tissue and is up-regulated in multiple cancer cell lines, including prostate, bladder, colon, ovarian, and Ewing sarcoma. Immunohistochemical analysis of clinical specimens demonstrates significant STEAP expression at the cell-cell junctions of the secretory epithelium of prostate and prostate cancer cells. Little to no staining was detected at the plasma membranes of normal, nonprostate human tissues, except for bladder tissue, which expressed low levels of STEAP at the cell membrane. Protein analysis located STEAP at the cell surface of prostate-cancer cell lines. Our results support STEAP as a cell-surface tumor-antigen target for prostate cancer therapy and diagnostic imaging.     

Effect of postural angle on back muscle activities in aging female workers performing computer tasks

[Purpose] This study investigated the effects of postural angle on back muscle activity during a computer task in aging women. [Subjects] Seventeen women ≥50 years old participated. [Methods] The participants were instructed to perform computer-related tasks for 20 minutes on a workstation that simulated typical office working conditions. Back posture was measured from the measured trunk and pelvic angles. Electromyography activities were recorded simultaneously from the cervical erector spinae, longissimus, and multifidus muscles. [Results] The lowest mean percentages of maximum voluntary contraction for the cervical erector spinae and longissimus muscles were obtained when the upper trunk and pelvic angles were between 0° to −5° from the sagittal plane. The back muscle activities increased as the upper trunk and pelvic angles exceeded 0°. Statistical analysis showed significant correlations between upper trunk angle and cervical erector spinae and longissimus muscle activities. Similarly, pelvic angle was significantly correlated with cervical erector spinae and multifidus muscle activities. [Conclusion] A neutral back posture minimizes muscle activities in aging women performing computer tasks.Key words: Postural angle, Muscle activity, Aging     

Epithelioid hemangioendothelioma in pleural effusion

Epithelioid hemangioendothelioma (EHE) is a rare mesenchymal tumor of vascular origin with variable morphological features and unpredictable biological behavior. EHE occasionally involves the pleural fluid. However, the cytomorphology of EHE found in pleural fluid has not been well characterized in the literature. Herein we describe a case of EHE, initially presenting as multiple liver lesions plus several small nodular densities at the bases of the lungs followed by bilateral pleural effusions. Diagn. Cytopathol. 2015;43:751–755. © 2015 Wiley Periodicals, Inc.