Sequence- and interactome-based prediction of viral protein hotspots targeting host proteins: a case study for HIV Nef

Virus proteins alter protein pathways of the host toward the synthesis of viral particles by breaking and making edges via binding to host proteins. In this study, we developed a computational approach to predict viral sequence hotspots for binding to host proteins based on sequences of viral and host proteins and literature-curated virus-host protein interactome data. We use a motif discovery algorithm repeatedly on collections of sequences of viral proteins and immediate binding partners of their host targets and choose only those motifs that are conserved on viral sequences and highly statistically enriched among binding partners of virus protein targeted host proteins. Our results match experimental data on binding sites of Nef to host proteins such as MAPK1, VAV1, LCK, HCK, HLA-A, CD4, FYN, and GNB2L1 with high statistical significance but is a poor predictor of Nef binding sites on highly flexible, hoop-like regions. Predicted hotspots recapture CD8 cell epitopes of HIV Nef highlighting their importance in modulating virus-host interactions. Host proteins potentially targeted or outcompeted by Nef appear crowding the T cell receptor, natural killer cell mediated cytotoxicity, and neurotrophin signaling pathways. Scanning of HIV Nef motifs on multiple alignments of hepatitis C protein NS5A produces results consistent with literature, indicating the potential value of the hotspot discovery in advancing our understanding of virus-host crosstalk.     

Comparative study of ammonium transporters in different organisms by study of a large number of structural protein features via data mining algorithms

Ammonium is an excellent nitrogen source, and ammonium transfer is a fundamental process in most organisms. Membrane transport of ammonium is the key component of nitrogen metabolism mediated by Ammonium Transporter/Methylamine Permease/Rhesus (AMT/MEP/Rh) protein family. Ammonium transporters play different physiological roles in various organisms. Here, we looked at the protein characteristics of ammonium transporters in different organisms to create a link between protein characteristics and the organism. In order to increase the accuracy and precision of the employed models, for the first time, an attempt was made to cover all structural aspects of ammonium transporters in animals, bacteria, fungi, plants, and human by extracting and calculating 874 protein attributes of primary, secondary, and tertiary structures for each ammonium transporter. Then, various weighting and modeling algorithms were applied to determine how structural protein features change between organisms. Considering a large number of protein attributes made it possible to detect key protein characteristics in the structure of ammonium transporters. The results, for the first time, indicated that His-based features including count/frequency of His and frequency/count of Ile-His were the most significant features generating different types of ammonium transporters within organisms. Within different tested models, the C5.0 model was the most efficient and precise model for discrimination of organism type, based on ammonium transporter sequence, with the precision of 94.85%. The determination of protein characteristics of ammonium transporters in different organisms provides a new vista for understanding the evolution of transporters based on the modulation of protein characteristics and facilitates engineering of new transporters. In our point of view, dissecting a large number of structural protein characteristics through data mining algorithms provides a novel functional strategy for studying evolution and phylogeny. This research will serve as a basis for future studies on engineering novel ammonium transporters.     

Vaccination with Plasmodium knowlesi AMA1 formulated in the novel adjuvant co-vaccine HT™ protects against blood-stage challenge in rhesus macaques

Plasmodium falciparum apical membrane antigen 1 (PfAMA1) is a leading blood stage vaccine candidate. Plasmodium knowlesi AMA1 (PkAMA1) was produced and purified using similar methodology as for clinical grade PfAMA1 yielding a pure, conformational intact protein. Combined with the adjuvant CoVaccine HT™, PkAMA1 was found to be highly immunogenic in rabbits and the efficacy of the PkAMA1 was subsequently tested in a rhesus macaque blood-stage challenge model. Six rhesus monkeys were vaccinated with PkAMA1 and a control group of 6 were vaccinated with PfAMA1. A total of 50 µg AMA1 was administered intramuscularly three times at 4 week intervals. One of six rhesus monkeys vaccinated with PkAMA1 was able to control parasitaemia, upon blood stage challenge with P. knowlesi H-strain. Four out of the remaining five showed a delay in parasite onset that correlated with functional antibody titres. In the PfAMA1 vaccinated control group, five out of six animals had to be treated with antimalarials 8 days after challenge; one animal did not become patent during the challenge period. Following a rest period, animals were boosted and challenged again. Four of the six rhesus monkeys vaccinated with PkAMA1 were able to control the parasitaemia, one had a delayed onset of parasitaemia and one animal was not protected, while all control animals required treatment. To confirm that the control of parasitaemia was AMA1-related, animals were allowed to recover, boosted and re-challenged with P. knowlesi Nuri strain. All control animals had to be treated with antimalarials by day 8, while five out of six PkAMA1 vaccinated animals were able to control parasitaemia. This study shows that: i) Yeast-expressed PkAMA1 can protect against blood stage challenge; ii) Functional antibody levels as measured by GIA correlated inversely with the day of onset and iii) GIA IC₅₀ values correlated with estimated in vivo growth rates.     

Monte Carlo dose calculation of GZP6 60Co stepping source based on a matrix shift technique

Background

As a routine method for stepping source simulation, a Monte Carlo program is run according to the number of steps and then the summation of dose from each run is taken to obtain total dose distribution. This method is time consuming.

Aim

As an alternative method, a matrix shift based technique was applied to simulate a stepping source for brachytherapy.

Materials and methods

The stepping source of GZP6 brachytherapy unit was simulated. In a matrix shift method, it is assumed that a radiation source is stationary and instead the data matrix is shifted based on the number of steps. In this study, by running MCNPX program for one point and calculation of the dose matrix using the matrix shift method, the isodose curves for the esophageal cancer tumor lengths of 4 and 6 cm were obtained and compared with the isodose curves obtained by running MCNPX programs in each step position separately (15 and 23 steps for esophageal cancer tumor lengths of 4 and 6 cm, respectively).

Results

The difference between the two dose matrixes for the stepping and matrix shift methods based on the average dose differences are 3.85 × 10⁻⁴ Gy and 5.19 × 10⁻⁴ Gy for treatment length of 4 cm and 6 cm, respectively. Dose differences are insignificant and these two methods are equally valid.

Conclusions

The matrix shift method presented in this study can be used for calculation of dose distribution for a brachytherapy stepping source as a quicker tool compared to other routine Monte Carlo based methods.     

Effects of Dominant/Subordinate Social Status on Formalin-Induced Pain and Changes in Serum Proinflammatory Cytokine Concentrations in Mice

Current investigations regarding social stress primarily focus on the health consequences of being in stressful social hierarchies. The repetitive nature of social conflicts seems to favor an induction of hyperalgesia or hypoalgesia, both in rodents and humans. Additionally, social conflicts may affect the immune system. In order to better establish the pain and immune responses to stress, the present study implemented a sensory contact model on 32 male BALB/c mice. Subsequent to establishing a dominance/submissive social relationship, each mouse was injected with formalin (20 μl, 2%) and their pain behavior was scored and serum concentrations of proinflammatory cytokines IL-1 and IL-6, and corticosterone were also measured. Test results revealed that subordinate mice were hypoalgesic during chronic phase of formalin test compared to control and dominant mice (P<0.05). On the other hand, subordinate mice were hyperalgesic compared to dominant mice during the whole acute phase of formalin test (P<0.05). Corticosterone, IL-1 and IL-6 concentrations were much higher in serum of dominant and subordinate mice than in the control group (p<0.05). The results indicated that, although both dominant and subordinate animals displayed an increase in serum corticosterone and proinflammatory cytokines during social interactions, their response to pain perception differently was affected with the social status.     

Impacts of Agricultural Practices on Insecticide Resistance in the Malaria Vector Anopheles arabiensis in Khartoum State,Sudan

Background

Agricultural pesticides may play a profound role in selection of resistance in field populations of mosquito vectors. The objective of this study is to investigate possible links between agricultural pesticide use and development of resistance to insecticides by the major malaria vector Anopheles arabiensis in northern Sudan.

Methodology/Principal Findings

Entomological surveys were conducted during two agricultural seasons in six urban and peri-urban sites in Khartoum state. Agro-sociological data were collected from 240 farmers subjected to semi-structured questionnaires based on knowledge attitude and practice (KAP) surveys. Susceptibility status of An. arabiensis (n=6000) was assessed in all sites and during each season using WHO bioassay tests to DDT, deltamethrin, permethrin, Malathion and bendiocarb. KAP analysis revealed that pesticide application was common practice among both urban and peri-urban farmers, with organophosphates and carbamates most commonly used. Selection for resistance is likely to be greater in peri-urban sites where farmers apply pesticide more frequently and are less likely to dispose of surpluses correctly. Though variable among insecticides and seasons, broad-spectrum mortality was slightly, but significantly higher in urban than peri-urban sites and most marked for bendiocarb, to which susceptibility was lowest. Anopheles arabiensis from all sites showed evidence of resistance or suspected resistance, especially pyrethroids. However, low-moderate frequencies of the L1014F kdr allele in all sites, which was very strongly associated with DDT, permethrin and deltamethrin survivorship (OR=6.14-14.67) suggests that resistance could increase rapidly.

Conclusions

Ubiquitous multiple-resistance coupled with presence of a clear mechanism for DDT and pyrethroids (kdr L1014F) in populations of An. arabiensis from Khartoum-Sudan suggests careful insecticide management is essential to prolong efficacy. Our findings are consistent with agricultural insecticide use as a source of selection for resistance and argue for coordination between the integrated vector control program and the Ministry of Agriculture to permit successful implementation of rational resistance management strategies.     

Counteracting effects of heavy metals and antioxidants on male fertility

Infertility is regarded as a global health problem affecting 8–12% of couples. Male factors are regarded as the main cause of infertility in 40% of infertile couples and contribute to this condition in combination with female factors in another 20% of cases. Abnormal sperm parameters such as oligospermia, asthenospermia, and teratozoospermia result in male factor infertility. Several studies have shown the deteriorative impact of heavy metals on sperm parameters and fertility in human subjects or animal models. Other studies have pointed to the role of antioxidants in counteracting the detrimental effects of heavy metals. In the currents study, we summarize the main outcomes of studies that assessed the counteracting impacts of heavy metal and antioxidants on male fertility. Based on the provided data from animal studies, it seems rational to administrate appropriate antioxidants in persons who suffer from abnormal sperm parameters and infertility due to exposure to toxic elements. Yet, further human studies are needed to approve the beneficial effects of these antioxidants.

     

Crosstalk between MMP-13, CD44, and TWIST1 and its role in regulation of EMT in patients with esophageal squamous cell carcinoma

Molecular and Cellular Biochemistry - Matrix metalloproteinases (MMPs) play key roles in epithelial-mesenchymal transition (EMT) for the development of cancer cell invasion and metastasis. MMP-13...