Development of gene expression markers of acute heat-light stress in reef-building corals of the genus Porites

Coral reefs are declining worldwide due to increased incidence of climate-induced coral bleaching, which will have widespread biodiversity and economic impacts. A simple method to measure the sub-bleaching level of heat-light stress experienced by corals would greatly inform reef management practices by making it possible to assess the distribution of bleaching risks among individual reef sites. Gene expression analysis based on quantitative PCR (qPCR) can be used as a diagnostic tool to determine coral condition in situ. We evaluated the expression of 13 candidate genes during heat-light stress in a common Caribbean coral Porites astreoides, and observed strong and consistent changes in gene expression in two independent experiments. Furthermore, we found that the apparent return to baseline expression levels during a recovery phase was rapid, despite visible signs of colony bleaching. We show that the response to acute heat-light stress in P. astreoides can be monitored by measuring the difference in expression of only two genes: Hsp16 and actin. We demonstrate that this assay discriminates between corals sampled from two field sites experiencing different temperatures. We also show that the assay is applicable to an Indo-Pacific congener, P. lobata, and therefore could potentially be used to diagnose acute heat-light stress on coral reefs worldwide.     

Sodium valproate potentiates staurosporine‐induced apoptosis in neuroblastoma cells via Akt/survivin independently of HDAC inhibition

Sodium valproate (VPA) has been recently identified as a selective class I histone deacetylase (HDAC) inhibitor and explored for its potential as an anti‐cancer agent. The anti‐cancer properties of VPA are generally attributed to its HDAC inhibitory activity indicating a clear overlap of these two actions, but the underlying mechanisms of its anti‐tumor effects are not clearly elucidated. The present study aimed to delineate the molecular mechanism of VPA in potentiating cytotoxic effects of anti‐cancer drugs with focus on inhibition of HDAC activity. Using human neuroblastoma cell lines, SK‐N‐MC, SH‐SY5Y, and SK‐N‐SH, we show that non‐toxic dose (2 mM) of VPA enhanced staurosporine (STS)‐induced cell death as assessed by MTT assay, PARP cleavage, hypodiploidy, and caspase 3 activity. Mechanistically, the effect of VPA was mediated by down regulation of survivin, an anti‐apoptotic protein crucial in resistance to STS‐mediated cytotoxicity, through Akt pathway. Knock down of class I HDAC isoforms remarkably inhibited HDAC activity comparable with that of VPA but had no effect on STS‐induced apoptosis. Moreover, MS‐275, a structurally distinct class I HDAC inhibitor did not affect STS‐mediated apoptosis, nor decrease the levels of survivin and Akt. Valpromide (VPM), an amide analog of VPA that does not inhibit HDAC also potentiated cell death in NB cells associated with decreased survivin and Akt levels suggesting that HDAC inhibition might not be crucial for STS‐induced apoptosis. The study provides new information on the possible molecular mechanism of VPA in apoptosis that can be explored in combination therapy in cancer. J. Cell. Biochem. 114: 854–863, 2013. © 2012 Wiley Periodicals, Inc.     

A population balance model to modulate shear for the control of aggregation in Taxus suspension cultures

Cellular aggregation in plant suspension cultures directly affects the accumulation of high value products, such as paclitaxel from Taxus. Through application of mechanical shear by repeated, manual pipetting through a 10 ml pipet with a 1.6 mm aperture, the mean aggregate size of a Taxus culture can be reduced without affecting culture growth. When a constant level of mechanical shear was applied over eight generations, the sheared population was maintained at a mean aggregate diameter 194 μm lower than the unsheared control, but the mean aggregate size fluctuated by over 600 μm, indicating unpredictable culture variability. A population balance model was developed to interpret and predict disaggregation dynamics under mechanical shear. Adjustable parameters involved in the breakage frequency function of the population balance model were estimated by nonlinear optimization from experimentally measured size distributions. The optimized model predictions were in strong agreement with measured size distributions. The model was then used to determine the shear requirements to successfully reach a target aggregate size distribution. This model will be utilized in the future to maintain a culture with a constant size distribution with the goal of decreasing culture variability and increasing paclitaxel yields.     

Proteomic analysis of homocysteine inhibition of microvascular endothelial cell angiogenesis.

Although homocysteine (Hcy) inhibits angiogenesis in vivo and in vitro, the mechanism(s) underlying this phenomenon are largely unclear. The hypothesis of the present work is that Hcy, while inducing the expression of antiangiogenic factors, inhibits the production of angiogenic factors. Mouse brain microvascular endothelial cells (MVEC) were cultured in the presence and absence of 20 microM Hcy for 24 hr in serum-free medium. Cell homogenates were incubated with Trans-Signal Angiogenesis Antibody Array containing antibodies to angiogenic activators (ANG, HGF, leptin, VEGF, IL-6, IL-8, PIGF, FGF-alpha/beta, TNF-alpha and TGF-alpha) and inhibitors (IFN-gamma, IL-12, IP-10, TIMP-1 and -2). The array membranes were scanned and normalized with positive controls. Angiogenesis and formation of capillaries were measured by culturing the MVEC in Matrigels. The capillary-like structures were identified by transmission microscopy. Hcy decreased the expression of leptin, IL-6, -8, PIGF, FGF-alpha and VEGF, while the levels of anti-angiogenic IL-12, IP-10 (chemokine) and TIMP-1 were increased by Hcy. The vascular tube-like structures by MVEC were decreased by increased Hcy. However, the addition of VEGF to Hcy-treated MVEC ameliorated the decreased Hcy-mediated capillary formation. The results suggest that Hcy inhibits angiogenesis, in part, by decreasing VEGF and increasing TIMP-1.     

Design of a functionally equivalent nonglycosylated analog of the glycopeptide antibiotic formaecin I

Various nonglycosylated analogs were designed in order to explore the role of glycosylation in formaecin I, an antibacterial glycopeptide of insect origin. The functional behavior of a designed nonglycosylated analog (P(7),endo P(8a),DeltaT(11))formaecin I was found to be similar to that of native glycosylated peptide. Both the peptides showed similar antibacterial activities against Escherichia coli and Salmonella strains. The designed nonglycosylated analog (P(7),endo P(8a),DeltaT(11))formaecin I has low binding affinity to LPS identical to that of native glycopeptide, formaecin I. Both the peptides have similar killing kinetics and are nontoxic to erythrocytes. Formaecin I and designed nonglycosylated (P(7),endo P(8a),DeltaT(11))formaecin I have no definite conformational features associated with them. The glycosylated residue of threonine in formaecin I and proline residues in designed peptide [(P(7),endo P(8a),DeltaT(11))formaecin I], possibly help in stabilizing the correct conformation that facilitates presentation of the peptide to its receptor. It is evident that a functionally equivalent nonglycosylated analog of native glycosylated antibacterial peptide can be designed by strategically modifying the sequence.     

DNA barcoding reveals the occurrence of cryptic species in host-associated population of Conogethes punctiferalis (Lepidoptera: Crambidae)

Conogethes punctiferalis (Guénee) is a critical pest that commonly infests castor (Ricinus communis Linnaeus) and cardamom (Elettaria cardamomum Maton) in India. The moths of both castor and cardamom appear to be similar in wing pattern and color. However, the results of behavioral studies elicited a doubt that there may be differences in terms of host specialization. In the present study, we conducted morphological studies and DNA barcode analyses using cytochrome oxidase I gene, which unraveled the mystery of C. punctiferalis breeding on castor and cardamom. The differences in male aedeagus and female bursae were prominent, yet, not sufficient enough to say that they are different species. The results showed high haplotype diversity (0.817 ± 0.073) and nucleotide diversity (0.0285 ± 0.002) in C. punctiferalis. In addition, topologies of neighbor-joining trees indicate that Conogethes sp. breeding on castor belongs to C. punctiferalis while those on cardamom are of a separate clade. Further genetic analysis revealed significant genetic differentiations among the two sampled populations, reflecting limited gene flow. Neutrality tests and mismatch distributions showed population expansion in C. punctiferalis, while the results of an analysis of molecular variance (AMOVA) indicated the existence of significant genetic variation among the examined host races. Conclusively, analysis using mitochondrial DNA showed an amount of genetic divergence between the two host-associated populations compatible with cryptic species rather than host races.     

MTHFR C677T Predisposes to POAG but Not to PACG in a North Indian Population: A Case Control Study

Hyperhomocysteinemia induced by the C677T genetic variant in MTHFR (methylenetetrahydrofolate reductase) has been implicated in neuronal cell death of retinal ganglion cells (RGC), which is a characteristic feature of glaucoma. However, association of MTHFR C677T with glaucoma has been controversial because of inconsistent results across association studies. Association between MTHFR C677T and glaucoma has not been reported in Indian population. Therefore, with a focus on neurodegenerative death of RGC in glaucoma, the current study aimed to investigate association of MTHFR C677T with Primary Open Angle Glaucoma (POAG) and Primary Angle Closure Glaucoma (PACG) in a North Indian population. A total of 404 participants (231 patients and 173 controls) were included in this study. Genotyping was performed by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism. A few random samples were also tested by direct sequencing. Genotypic and allelic distributions of the POAG and PACG cohorts were compared to that of controls by chi-square test and odds ratios were reported with 95% confidence intervals. Genotypic and allelic distributions between POAG cases and controls were significantly different (p = 0.03 and p = 0.01 respectively). Unlike POAG, we did not find significant difference in the genotypic and allelic distributions of C677T between PACG cases and controls (p>0.05). We also observed a higher proportion of TT associated POAG in females than that in males. However, this is a preliminary indication of gender specific risk of C677T that needs to be replicated in a larger cohort of males and females. The present investigation on MTHFR C677T and glaucoma reveals that the TT genotype and T allele of this polymorphism are significant risk factors for POAG but not for PACG in North Indian population. Ours is the first report demonstrating association of MTHFR C677T with POAG but not PACG in individuals from North India.     

Cyanea capillata Bell Kinematics Analysis through Corrected In Situ Imaging and Modeling Using Strategic Discretization Techniques

Obtaining accurate kinematic data of animals is essential for many biological studies and bio-inspired engineering. Many animals, however, are either too large or too delicate to transport to controlled environments where accurate kinematic data can be easily obtained. Often, in situ recordings are the only means available but are often subject to multi-axis motion and relative magnification changes with time leading to large discrepancies in the animal kinematics. Techniques to compensate for these artifacts were applied to a large jellyfish, Cyanea capillata, freely swimming in ocean waters. The bell kinematics were captured by digitizing exumbrella profiles for two full swimming cycles. Magnification was accounted for by tracking a reference point on the ocean floor and by observing the C. capillata exumbrella arclength in order to have a constant scale through the swimming cycles. A linear fit of the top bell section was used to find the body angle with respect to the camera coordinate system. Bell margin trajectories over two swimming cycles confirmed the accuracy of the correction techniques. The corrected profiles were filtered and interpolated to provide a set of time-dependent points along the bell. Discrete models of the exumbrella were used to analyze the bell kinematics. Exumbrella discretization was conducted using three different methods. Fourier series were fitted to the discretized models and subsequently used to analyze the bell kinematics of the C. capillata. The analysis showed that the bell did not deform uniformly over time with different segments lagging behind each other. Looping of the bell trajectory between contraction and relaxation was also present through most of the exumbrella. The bell margin had the largest looping with an outer path during contraction and inner path during relaxation. The subumbrella volume was approximated based on the exumbrella kinematics and was found to increase during contraction.     

Integrated 18F-fluorodeoxyglucose-positron emission tomography/dynamic contrast-enhanced computed tomography to phenotype non-small cell lung carcinoma

AbstractWe applied modern molecular and functional imaging to the pretreatment assessment of lung cancer using combined dynamic contrast-enhanced computed tomography (DCE-CT) and 18F-fluorodeoxyglucose-positron emission tomography (18F-FDG-PET) to phenotype tumors. Seventy-four lung cancer patients were prospectively recruited for 18F-FDG-PET/DCE-CT using PET/64-detector CT. After technical failures, there were 64 patients (35 males, 29 females; mean age [± SD] 67.5 ± 7.9 years). DCE-CT yielded tumor peak enhancement (PE) and standardized perfusion value (SPV). The uptake of 18F-FDG quantified on PET as the standardized uptake value (SUVmax) assessed tumor metabolism. The median values for SUVmax and SPV were used to define four vascular-metabolic phenotypes. There were associations (Spearman rank correlation [rs]) between tumor size and vascular-metabolic parameters: SUVmax versus size (rs = .40, p = .001) and SUV/PE versus size (r = .43, p < .001). Patients with earlier-stage (I-IIA, n = 30) disease had mean (± SD) SUV/PE 0.36 ± 0.28 versus 0.56 ± 0.32 in later-stage (stage IIB-IV, n = 34) disease (p = .007). The low metabolism with high vascularity phenotype was significantly more common among adenocarcinomas (p = .018), whereas the high metabolism with high vascularity phenotype was more common among squamous cell carcinomas (p = .024). Other non-small cell lung carcinoma tumor types demonstrated a high prevalence of the high metabolism with low vascularity phenotype (p = .028). We show that tumor subtypes have different vascular-metabolic associations, which can be helpful clinically in managing lung cancer patients to hone targeted therapy.     

Beyond captions: linking figures with abstract sentences in biomedical articles

Although figures in scientific articles have high information content and concisely communicate many key research findings, they are currently under utilized by literature search and retrieval systems. Many systems ignore figures, and those that do not typically only consider caption text. This study describes and evaluates a fully automated approach for associating figures in the body of a biomedical article with sentences in its abstract. We use supervised methods to learn probabilistic language models, hidden Markov models, and conditional random fields for predicting associations between abstract sentences and figures. Three kinds of evidence are used: text in abstract sentences and figures, relative positions of sentences and figures, and the patterns of sentence/figure associations across an article. Each information source is shown to have predictive value, and models that use all kinds of evidence are more accurate than models that do not. Our most accurate method has an F1-score of 69% on a cross-validation experiment, is competitive with the accuracy of human experts, has significantly better predictive accuracy than state-of-the-art methods and enables users to access figures associated with an abstract sentence with an average of 1.82 fewer mouse clicks. A user evaluation shows that human users find our system beneficial. The system is available at http://FigureItOut.askHERMES.org.