Analysis of MALDI-TOF mass spectrometry data for discovery of peptide and glycan biomarkers of hepatocellular carcinoma

This paper presents computational methods to analyze MALDI-TOF mass spectrometry data for quantitative comparison of peptides and glycans in serum. The methods are applied to identify candidate biomarkers in serum samples of 203 participants from Egypt; 73 hepatocellular carcinoma (HCC) cases, 52 patients with chronic liver disease (CLD) consisting of cirrhosis and fibrosis cases, and 78 population controls. Two complementary sample preparation methods were applied prior to generating mass spectra: (1) low molecular weight (LMW) enrichment of each serum sample was carried out for MALDI-TOF quantification of peptides, and (2) glycans were enzymatically released from proteins in each serum sample and permethylated for MALDI-TOF quantification of glycans. A peak selection algorithm was applied to identify the most useful peptide and glycan peaks for accurate detection of HCC cases from high-risk population of patients with CLD. In addition to global peaks selected by the whole population based approach, where identically labeled patients are treated as a single group, subgroup-specific peaks were identified by searching for peaks that are differentially abundant in a subgroup of patients only. The peak selection process was preceded by peak screening, where we eliminated peaks that have significant association with covariates such as age, gender, and viral infection based on the peptide and glycan spectra from population controls. The performance of the selected peptide and glycan peaks was evaluated in terms of their ability in detecting HCC cases from patients with CLD in a blinded validation set and through the cross-validation method. Finally, we investigated the possibility of using both peptides and glycans in a panel to enhance the diagnostic capability of these candidate markers. Further evaluation is needed to examine the potential clinical utility of the candidate peptide and glycan markers identified in this study.     

Biomphalaria tenagophila: genetic variability within intermediate snail hosts susceptible and resistant to Schistosoma mansoni infection

DNA analysis by molecular techniques has significantly expanded the perspectives of the study and understanding of genetic variability in molluscs that are vectors of schistosomiasis. In the present study, the genetic variability of susceptible and resistant B. lenagophila strains to S. mansoni infection was investigated using amplification of their genomic DNA by RAPD-PCR. The products were analyzed by PAGE and stained with silver. The results showed polymorphism between tested strains with four different primers. We found two bands of 1,900 and 3,420 bp that were characteristic of the susceptible strains with primer 2. The primers 9 and 10 identified a single polymorphic band that was also characteristic of (3,136 and 5,041 bp, respectively) susceptible snails. Two polymorphic bands were detected by primer 15: one with 1,800 bp was characteristic of the resistant strain and the other with approximately equal to 1,700 bp in the susceptible one. These results provide additional evidence showing that the RAPD-PCR technique is adequate for the study of polymorphisms in intermediate hosts snails of S. mansoni. The obtained results are expected to expand the knowledge about the genetic variability of the snails and to permit the future identification of genomic sequences specifically related to the resistance/susceptibility of Biomphalaria to the larval forms of S. mansoni.     

Role of some fermentation parameters on cyclosporin A production by a new isolate of Aspergillus terreus

A local isolate of Aspergillus terreus was selected among different microorganisms as a new cyclosporin A (Cy A) producing culture. The formation of Cy A was investigated under different fermentation conditions (including selection of the cultivation medium, fermentation time course, inoculum nature, medium volume, agitation rate, pH value). Relatively high Cy A productivities were maintained when the fermentation process was carried out using a medium composed of (g/L): glucose, 50; bactopeptone, 10; KH(2)PO(4), 5; KCl, 2.5; pH 5.3, inoculated with 2% standard inoculum of 48 h age, shaken at 200 rpm for 10 days.     

Identification and mapping of brain natriuretic peptide in the normal ventricular myocardium of a desert-dwelling mammalian model,the camel (Camelus dromedarius): Immunohistochemical and ultrastructural study

Brain natriuretic peptide (BNP) is mainly produced in the ventricular myocardium, where it is released into the circulation, producing rapid volume decrease by diuresis, natriuresis, and water shift into the extracellular space, and vasodilation. The dromedary camel, a mammalian model of the desert nomads, lives under unfavorable physiological stresses during thirst, starvation, desiccation, and hot climate, thus has a special demand for water homeostasis. The present studies characterized BNP in the ventricular myocardium of healthy camels, immunohistochemically with a specific antibody, and ultrastructurally identified the endocrine property of the cardiomyocytes and Purkinje fibers. The paranuclear, granular, immunoreactive material was not restricted to the cardiomyocytes, as it was also visible in the Purkinje fibers and their associated nerve varicosities. The intensity of immunoreactive BNP showed a transmural gradient from the subepicardium to the myocardium. Intense immunoreactivity was also noted among the perivascular cardiomyocytes. At the electron microscopic level, specific granules were demonstrated in the paranuclear cytosol of cardiomyocytes and Purkinje fibers. The current study provides the first immunohistochemical localization pattern of BNP in the camel myocardium and suggests a relationship between the intense subepicardial BNP-immunoexpression and a possible translocation of the active hormone to the pericardial fluid for further paracrine actions on the heart and its coronaries.     

The Involvement of Immune Semaphorins in the Pathogenesis of Inflammatory Bowel Diseases (IBDs)

ResultsThe percentage (%) of T regulatory cells (Tregs) expressing sema3A in patients with active CD (64.5% ±14.49%) and active UC (49.8% ±16.45%) was significantly lower when compared to that of healthy controls (88.7% ±3.6%, p< 0.001 and p< 0.0001, respectively). This expression was seen to be in negative correlation with CD activity. Serum levels of Sema4A were significantly lower in patients with CD and UC when compared to that of controls (5.69±1.48ng\ml for CD, 5.26±1.23 ng/ml for UC patients vs 9.74±2.73ng/ml for normal controls, P<0.001). Sema4A was highly expressed in lymphocytes of the lamina propria of CD and UC patients but absent in patients with diverticulitis or in normal individuals.ConclusionsAltered % of Tregs expressing sema3A in patients with inflammatory bowel diseases (IBD) is partially responsible for their failure in preventing CD4+ effector T cell induced inflammation in IBD in peripheral blood. The increased expression of sema4A in bowel biopsies from CD and UC patients is suggestive of its central role in regulating local tissue inflammation in the bowel.     

Effect of Enclosure Quality on Reactivity and Welfare of Captive Soemmerring's Gazelle (Gazella soemmerringii)

The welfare of nonhuman animals in zoos is a great challenge to the zookeeper. Changes in the behavioral response of captive animals to their immediate environment can be used as a method for evaluating their welfare status. This study evaluates reactive responses of 3 groups of captive Soemmerring's gazelle (Gazella soemmerringii) kept in enclosures of different quality at Giza Zoo, Egypt. The study ascribes variations in observed behaviors to the differences in the living standards of the 3 groups. The group most concealed from visitors' disturbance (Group 3) was the least reactive. With the morning onset of human-nonhuman animal interaction, reactivity reached significantly higher levels. The study noted no difference in reactivity between male and female animals. The main sign of the animals' alertness was their attention to sources of disturbances; vocalization was minimal. Animals in Groups 1 and 2, those most accessible to visitors, had higher agonistic reactions than animals in Group 3.     

Regulation of metabolomics in Atriplex halimus growth under salt and drought stress

Forty-day-old Atriplex halimus seedlings were treated with either NaCl (50, 300 and 550?mM) for the subsequent 30?days or PEG for the following 3, 6 and 10?days. Shoot fresh and dry weights were significantly increased by 50?mM NaCl; nevertheless, the other concentrations had no effect. However, the growth was reduced by drought only after 10?days. Meanwhile, Na⁺ was accumulated in treated plants; the magnitude of accumulation was highest with high NaCl concentration or PEG for 10?days. The metabolite profiles showed discrimination particularly up-regulation of the amino acids proline, valine, isoleucine, and methionine. Moreover, the macro analysis revealed that NaCl- and PEG-treated plants shared 10?% of the metabolites in the positive mode, however, 87?% were unique to NaCl and 46?% were unique to PEG whereas in the negative mode, 8?% were in share while 90 or 53?% were restricted to NaCl or PEG, respectively. Additionally, sucrose in particular was significantly increased up to threefold and fivefold by 300 and 550?mM NaCl, respectively and up to 2.5-fold by drought for 10?days, nevertheless, the other sugar fractions remained largely unchanged. Also, proline was significantly increased by only the high NaCl concentrations and the long-term drought, nonetheless, the other treatments led, if any, to decreases. These results conclude that NaCl affects the metabolite profiles more than PEG and these metabolites might contribute to osmotic adjustments to act as osmoprotectants rather than osmolytes. These changes of metabolomics might function in many resistance and stress responses.     

The effects of acute tryptophan depletion on reactive aggression in adults with attention-deficit/hyperactivity disorder (ADHD) and healthy controls

Background

The neurotransmitter serotonin (5-HT) has been linked to the underlying neurobiology of aggressive behavior, particularly with evidence from studies in animals and humans. However, the underlying neurobiology of aggression remains unclear in the context of attention-deficit/hyperactivity disorder (ADHD), a disorder known to be associated with aggression and impulsivity. We investigated the effects of acute tryptophan depletion (ATD), and the resulting diminished central nervous serotonergic neurotransmission, on reactive aggression in healthy controls and adults with ADHD.

Methodology/Principal Findings

Twenty male patients with ADHD and twenty healthy male controls were subjected to ATD with an amino acid (AA) beverage that lacked tryptophan (TRP, the physiological precursor of 5-HT) and a TRP-balanced AA beverage (BAL) in a double-blind, within-subject crossover-study over two study days. We assessed reactive aggression 3.25 hours after ATD/BAL intake using a point-subtraction aggression game (PSAG) in which participants played for points against a fictitious opponent. Point subtraction was taken as a measure for reactive aggression. Lowered rates of reactive aggression were found in the ADHD group under ATD after low provocation (LP), with controls showing the opposite effect. In patients with ADHD, trait-impulsivity was negatively correlated with the ATD effect on reactive aggression after LP. Statistical power was limited due to large standard deviations observed in the data on point subtraction, which may limit the use of this particular paradigm in adults with ADHD.

Conclusions/Significance

Together with previous findings, the data provide preliminary evidence of an inverse association between trait-impulsivity and the ATD effect on reactive aggression after LP (as assessed by the PSAG) in patients with ADHD and that this relationship can be found in both adolescents and adults. Because of limited statistical power larger sample sizes are needed to find main effects of ATD/BAL administration on reactive aggression in adults with ADHD.     

A Novel Method to Identify Routes of Hepatitis C Virus Transmission

Background

We propose a new approach based on genetic distances among viral strains to infer about risk exposures and location of transmission at population level.

Methods

We re-analysed 133 viral sequences obtained during a cross-sectional survey of 4020 subjects living in a hepatitis C virus (HCV) endemic area in 2002. A permutation test was used to analyze the correlation between matrices of genetic distances in the NS5b region of all pairwise combinations of the 133 viral strains and exposure status (jointly exposed or not) to several potential HCV risk factors.

Results

Compared to subjects who did not share the same characteristics or iatrogenic exposures, the median Kimura genetic distances of viral strains were significantly smaller between brothers and sisters (0.031 versus 0.102, P<0.001), mother and child (0.044 versus 0.102, P<0.001), father and child (0.045 versus 0.102, P<0.001), or subjects exposed to periodontal treatment (0.084 versus 0.102, P = 0.02). Conversely, viral strains were more divergent between subjects exposed to blood transfusions (0.216 versus 0.102, P = 0.04) or tooth filling or extraction (0.108, versus 0.097, P = 0.05), suggesting acquisition of the virus outside of the village.

Conclusion

This method provided insights on where infection took place (household, village) for several socio-demographic characteristics or iatrogenic procedures, information of great relevance for targeting prevention interventions. This method may have interesting applications for virologists and epidemiologists studying transmission networks in health-care facilities or among intravenous drug users.     

The effect of Red Seaweed (Chondrus crispus) on the fertility of male albino rats

At different parts of the world, Red Seaweeds are one component of human diets especially at Southeast Asia. Red Seaweeds structurally contain bioactive molecules so; we studied the effect of Chondrus crispus on increasing the male albino rat fertility. Twelve male albino rats are used in this study as two group pre-treated group and post- treated one each with 6 animals. The pretreated group was dissected before the post-treated group injection. Each post treated rat injected intramuscular with 1 mg of Chondrus crispus with dose 0.1 ml/ twice per week for 48 day (Mukhtar et al., 2013).The results showed that increasing on the total testosterone levels insignificantly, sperm motility significantly, and decreasing in both FSH and DPPH levels insignificantly and significantly for the MDA levels in the post-treated group. The morphological appearance and histological examination for the sperm, testis and liver were normal as the pretreated group. The molecular studies showed absence of any DNA fragmentation for the testis of both group.The Red Seaweed has an enhanced effect in the testicular function of the animal which might increase their fertility and sexual activities.