Detecting drug targets with minimum side effects in metabolic networks

High-throughput techniques produce massive data on a genome-wide scale which facilitate pharmaceutical research. Drug target discovery is a crucial step in the drug discovery process and also plays a vital role in therapeutics. In this study, the problem of detecting drug targets was addressed, which finds a set of enzymes whose inhibition stops the production of a given set of target compounds and meanwhile minimally eliminates non-target compounds in the context of metabolic networks. The model aims to make the side effects of drugs as small as possible and thus has practical significance of potential pharmaceutical applications. Specifically, by exploiting special features of metabolic systems, a novel approach was proposed to exactly formulate this drug target detection problem as an integer linear programming model, which ensures that optimal solutions can be found efficiently without any heuristic manipulations. To verify the effectiveness of our approach, computational experiments on both Escherichia coli and Homo sapiens metabolic pathways were conducted. The results show that our approach can identify the optimal drug targets in an exact and efficient manner. In particular, it can be applied to large-scale networks including the whole metabolic networks from most organisms.

Characterization of specific egg yolk immunoglobulin (IgY) against mastitis-causing Staphylococcus aureus

AIMS

To evaluate the in vitro activity of egg yolk immunoglobulin (IgY) against mastitis-causing Staphylococcus aureus.

METHODS AND RESULTS

Specific IgY was produced by immunizing hens with formaldehyde-killed Staph. aureus, using a bacterial strain known to cause mastitis. The IgY, of 94% purity, was obtained from yolks by water dilution, salt precipitations, ultrafiltration and gel filtration. ELISA indicated that the IgY produced was specific to the antigen and five Staph. aureus isolates obtained from mastitic cows. The growth of Staph. aureus was inhibited by specific IgY at concentrations from 1 to 10 mg ml(-1) in a dose-dependent manner. The phagocytosis of Staph. aureus by milk macrophages was enhanced in the presence of specific IgY with the highest phagocytic percentage being 30% higher than that without IgY (P < 0.05).

CONCLUSIONS

The specific IgY against mastitis-causing Staph. aureus inhibited the growth of Staph. aureus and enhanced the phagocytosis of Staph. aureus by milk macrophages.

SIGNIFICANCE AND IMPACT OF THE STUDY

Specific IgY would be a potential treatment for bovine mastitis.

Gestational age and dose influence on placental transfer of 63Ni in rats

The effects of gestational age and dose of nickel exposure on regulating and influencing placental transfer were investigated. Pregnant rats on gestational day (GD) 12, 15 or 20 were injected intraperitoneally with saline, 64,320 or 640 kBq/kg body weight of (63)Ni. Twenty-four hours after administration, samples were harvested from each for measurement of radioactivity by liquid scintillation counting and for autoradiography. In placenta, amniotic fluid and fetal membrane, (63)Ni concentrations increased with increasing doses and gestational age. In fetus, (63)Ni concentrations reached a maximum on GD 15 and then declined on GD 20 although they maintained a dose-dependency for each GD group. In fetal blood on GD 20, (63)Ni concentration increased dose-dependently and was higher than in maternal blood. The autoradiographs demonstrated that (63)Ni radioactivity was located within placental basal lamina, fetal bones and most organs. These findings suggest that the nickel uptake, retention and transport in placenta increase dose- and gestation age-dependently, and nickel transfer through placental barrier is primarily from mother into the fetus, but hardly from fetus to mother.

Glycoprotein clearance is rapid and suppressed by mannan in chicken embryos

Carbohydrates are thought to function as tags that mark circulatory glycoproteins for rapid clearance. Scavenger endothelial cells (SECs) play the primary role in clearing glycoproteins via receptor-mediated endocytosis in adult animals. We found that horseradish peroxidase (HRP), a glycoprotein, was removed quickly, mostly by receptor mediation from the chicken embryo circulation, but bovine serum albumin was not. The half-life of HRP in the circulation varied with the embryo stage and fell rapidly from 0.73 h at embryonic day 4 (E4) to 0.23 h at E5, with no great difference among stages after E5. HRP clearance was far slower at E3.5 than at E5, but was obviously suppressed by mannan. These results imply that the function of clearing glycoprotein or waste macromolecules from the circulation via receptor-mediated endocytosis appears early in the embryo.

Pharmacological characterization of cis-nitromethylene neonicotinoids in relation to imidacloprid binding sites in the brown planthopper, Nilaparvata lugens

Neonicotinoid insecticides, such as imidacloprid, are selective agonists of the insect nicotinic acetylcholine receptors (nAChRs) and extensively used in areas of crop protection and animal health to control a variety of insect pest species. Here we describe that two cis-nitromethylene neonicotinoids (IPPA152002 and IPPA152004), recently synthesized in our laboratory, discriminated between the high and low affinity imidacloprid binding sites in the brown planthopper, Nilaparvata lugens, a major insect pest of rice crops in many parts of Asia. [(3)H]imidacloprid has two binding sites with different affinities (Kd value of 0.0035 +/- 0.0006 nM for the high-affinity site and 1.47 +/- 0.22 nM for the low-affinity site). Although the cis-nitromethylene neonicotinoids showed low displacement ability (Ki values of 0.15 +/- 0.03 microM and 0.42 +/- 0.07 microM for IPPA152002 and IPPA152004, respectively) against [(3)H]imidacloprid binding, low concentrations (0.01 microM) of IPPA152002 completely inhibited [(3)H]imidacloprid binding at its high-affinity site. In Xenopus oocytes co-injected with cRNA encoding Nlalpha1 and rat beta2 subunits, obvious inward currents were detected in response to applications of IPPA152002 and IPPA152004, although the agonist potency is reduced to that of imidacloprid. The previously identified Y151S mutation in Nlalpha1 showed significant effects on the agonist potency of IPPA152002 and IPPA152004, such as a 75.8% and 70.6% reduction in Imax, and a 2.4- and 2.1-fold increase in EC(50). This data clearly shows that the two newly described cis-nitromethylene neonicotinoids act on insect nAChRs and like imidacloprid, discriminated between high and low affinity binding sites in N. lugens native nAChRs. These compounds may be useful tools to further elucidate the pharmacology and nature of neonicotinoid binding sites.

A novel HLA-B*54 allele, B*5417, identified in a Northern Chinese Han individual

The full-length sequence of HLA-B*5417 differs from HLA-B*5401 only by single-nucleotide change at nt 709 where A-->C resulting in a amino acid substitution from Ile (ATC) to Val (GTC) at codon 213 in exon 4.

A novel allele, HLA-A*110203, was identified in a Chinese individual

This allele is characterized by a nucleotide substitution (C>T) in exon 4 at position nt 672, codon 200 (ACC>ACT), no coding change.

A frame shift due to a two-nucleotide deletion results in an HLA-B null allele, B*9549N

This report describes the identification of a new human leukocyte antigen (HLA) class I null allele, B*9549N, resulting from a premature stop codon in exon 3.

Hypoxia inducible factors in cancer stem cells

Oxygen is an essential regulator of cellular metabolism, survival, and proliferation. Cellular responses to oxygen levels are monitored, in part, by the transcriptional activity of the hypoxia inducible factors (HIFs). Under hypoxia, HIFs regulate a variety of pro-angiogenic and pro-glycolysis pathways. In solid cancers, regions of hypoxia are commonly present throughout the tissue because of the chaotic vascular architecture and regions of necrosis. In these regions, the hypoxic state fluctuates in a spatial and temporal manner. Transient hypoxic cycling causes an increase in the activity of the HIF proteins above what is typical for non-pathologic tissue. The extent of hypoxia strongly correlates to poor patient survival, therapeutic resistance and an aggressive tumour phenotype, but the full contribution of hypoxia and the HIFs to tumour biology is an area of active investigation. Recent reports link resistance to conventional therapies and the metastatic potential to a stem-like tumour population, termed cancer stem cells (CSCs). We and others have shown that within brain tumours CSCs reside in two niches, a perivascular location and the surrounding necrotic tissue. Restricted oxygen conditions increase the CSC fraction and promote acquisition of a stem-like state. Cancer stem cells are critically dependant on the HIFs for survival, self-renewal, and tumour growth. These observations and those from normal stem cell biology provide a new mechanistic explanation for the contribution of hypoxia to malignancy. Further, the presence of hypoxia in tumours may present challenges for therapy because of the promotion of CSC phenotypes even upon successful killing of CSCs. The current experimental evidence suggests that CSCs are plastic cell states governed by microenvironmental conditions, such as hypoxia, that may be critical for the development of new therapies targeted to disrupt the microenvironment.

Hydrodynamic conditions in designed spiral photobioreactors

In this work, a series of spiral tube PBRs were introduced. Flow dynamics of microalgae fluid, light intensity histories of tracked cells and swirl numbers within the spiral PBRs were numerically simulated. Results show that strong swirl motions are formed in the cross-sections along axial coordinate of spiral PBRs, but no such vortice is observed for tubular PBR. The light intensity histories identify that the microalgae cells experience the so-called light/dark cycle, which is necessary to their growth. With high swirl numbers ranging from 0.15 to 0.35, the mixing performances of the spiral tube PBRs are much better than that of tubular PBR, indicating such innovative geometries of spiral tube PBRs may be applicable for large scale commercial cultivation of microalgae in the future.

Flocculation properties of a bioflocculant produced by Bacillus licheniformis

Studies of the flocculation properties of bioflocculant combined with its structure characterization are helpful to develop more effective bioflocculant. This paper reports findings of our research on the flocculation properties of the bioflocculant ZS-7 in the kaolin suspension based on its structure characterization. With the addition of 2 mg/L ZS-7 and 9 mM CaCl(2), the optimum temperature for flocculation performance of ZS-7 in the kaolin suspension is about 30°C, giving the highest flocculating activity 99.2%. Studies of the flocculation properties revealed that it was stable at 60-100°C and pH 4-10. Moreover, it could flocculate a kaolin suspension over a wide range of pH (2-12) and temperatures (4-95°C) in the presence of CaCl(2).

Pseudomonas aeruginosa serological analysis in young children with cystic fibrosis diagnosed through newborn screening

BACKGROUND

With newborn screening (NBS) for cystic fibrosis (CF), eradication of Pseudomonas aeruginosa (PA) is possible if PA detection occurs early. A serological response to infection likely precedes culture positivity in CF patients, so PA serological testing is very appealing in this population. However, controversies continue to exist about serology testing, titer cutoffs for enzyme-linked immunosorbent assay (ELISA) antibody tests, and their value in children with CF.

METHODS

This longitudinal, prospective study collected respiratory secretions as oropharyngeal swabs or expectorated sputum for culture and also sera over 6 years in 69 patients diagnosed by NBS. Serology assessed PA antibody titers against cell lysate, exotoxin A, and elastase. A novel statistical approach with weighted receiver operating characteristic (ROC) curves was used to determine best antibody titer cutoff values to predict subsequent PA positive cultures.

RESULTS

Using these weighted ROC curves, the order of sensitivity was found to be cell lysate, exotoxin A, and then elastase while age-specific cutoffs were better than fixed cutoffs previously used. Age-specific serological cutoffs both predict and detect PA respiratory infections with a higher sensitivity and specificity. Serological responses to the PA antigens determined that a response to cell lysate occurs significantly earlier than culture positivity.

CONCLUSIONS

Age-specific serological cutoffs rather than fixed values against common PA antigens improve early PA identification in infants and young children diagnosed with NBS. Regular serological assessment with age-specific cutoffs in these children appears to be a worthy diagnostic tool.

A novel HLA-B*37 allele, B*370105, was identified in a Chinese Han individual

We report here the sequence of a novel human leukocyte antigen B*37 allele, B*370105, which is identical to B*370101 except for a single nucleotide substitution in exon 3 at nucleotide 558 where C>A, codon 162 GGC>GGA, no coding change.

A novel HLA-DRB1 allele, DRB1*112802, was identified in a Chinese individual

We report here a novel human leukocyte antigen-DRB1 allele, DRB1*112802, which was identified from a Chinese individual during sequence-based typing. The new allele is identical to DRB1*112801 except for one nucleotide change at nucleotide 189 (A --> G ), codon 34 Q (CAA) --> Q (CAG), no coding change.