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21.
The profile hidden Markov model (PHMM) is widely used to assign the protein sequences to their respective families. A major limitation of a PHMM is the assumption that given states the observations (amino acids) are independent. To overcome this limitation, the dependency between amino acids in a multiple sequence alignment (MSA) which is the representative of a PHMM can be appended to the PHMM. Due to the fact that with a MSA, the sequences of amino acids are biologically related, the one-by-one dependency between two amino acids can be considered. In other words, based on the MSA, the dependency between an amino acid and its corresponding amino acid located above can be combined with the PHMM. For this purpose, the new emission probability matrix which considers the one-by-one dependencies between amino acids is constructed. The parameters of a PHMM are of two types; transition and emission probabilities which are usually estimated using an EM algorithm called the Baum-Welch algorithm. We have generalized the Baum-Welch algorithm using similarity emission matrix constructed by integrating the new emission probability matrix with the common emission probability matrix. Then, the performance of similarity emission is discussed by applying it to the top twenty protein families in the Pfam database. We show that using the similarity emission in the Baum-Welch algorithm significantly outperforms the common Baum-Welch algorithm in the task of assigning protein sequences to protein families. 相似文献
22.
Aghajani Marjan Mokhtarzadeh Ahad Aghebati-Maleki Leili Mansoori Behzad Mohammadi Ali Safaei Sahar Asadzadeh Zahra Hajiasgharzadeh Khalil Khaze Shahgoli Vahid Baradaran Behzad 《Molecular biology reports》2020,47(5):3691-3703
Molecular Biology Reports - One of the major barriers in cancer therapy is the resistance to conventional therapies and cancer stem cells (CSCs) are among the main causes of this problem. CD133 as... 相似文献
23.
Abdi Sheyda Montazeri Vahid Garjani Alireza Shayanfar Ali Pirouzpanah Saeed 《Molecular biology reports》2020,47(4):2459-2473
Molecular Biology Reports - Low levels of coenzyme Q10 (CoQ10) have been reported in the circulation of patients with breast cancer, particularly in metastatic features. Our objective was to study... 相似文献
24.
Hojjatollah Nazari Asieh Heirani-Tabasi Maryam Hajiabbas Milad Salimi Bani Mahnaz Nazari Vahid Pirhajati Mahabadi Iman Rad Mousa Kehtari Seyed Hossein Ahmadi Tafti Masoud Soleimani 《Journal of cellular biochemistry》2020,121(4):2981-2993
Mimicking the structure of extracellular matrix (ECM) of myocardium is necessary for fabrication of functional cardiac tissue. The superparamagnetic iron oxide nanoparticles (SPIONs, Fe3O4), as new generation of magnetic nanoparticles (NPs), are highly intended in biomedical studies. Here, SPION NPs (1 wt%) were synthesized and incorporated into silk-fibroin (SF) electrospun nanofibers to enhance mechanical properties and topography of the scaffolds. Then, the mouse embryonic cardiac cells (ECCs) were seeded on the scaffolds for in vitro studies. The SPION NPs were studied by scanning electron microscope (SEM), X-ray diffraction (XRD), and transmission electron microscope (TEM). SF nanofibers were characterized after incorporation of SPIONs by SEM, TEM, water contact angle measurement, and tensile test. Furthermore, cytocompatibility of scaffolds was confirmed by 3-(4, 5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay. SEM images showed that ECCs attached to the scaffolds with elongated morphologies. Also, the real-time PCR and immunostaining studies approved upregulation of cardiac functional genes in ECCs seeded on the SF/SPION-casein scaffolds including GATA-4, cardiac troponin T, Nkx 2.5, and alpha-myosin heavy chain, compared with the ones in SF. In conclusion, incorporation of core-shells in SF supports cardiac differentiation, while has no negative impact on ECCs' proliferation and self-renewal capacity. 相似文献
25.
Zahra Moallemzadegan Vahid Hosseininaveh 《Archives Of Phytopathology And Plant Protection》2013,46(16):1560-1571
Activity of α-amylase was revealed in the midgut and salivary glands of the wheat and barley pentatomid pest, A. acuminata. The activity was determined in salivary gland more than those in midgut. Optimal activity of the enzyme occurred at 40°C. Optimal pH activity in salivary gland (pH = 6) was more than those in the midgut (pH = 4.5). pH stability analysis of the enzyme showed that the enzyme is more stable at slightly acidic pHs than those at acidic and alkaline pHs. However, α-amylase is more stable at acidic pH in long period of time. Temperature stability analysis determined the enzyme was remarkably active over a broad range of temperature (5–40°C). α-Amylase activity was decreased after addition of MgCl2, Tris, Triton X-100, CuSO4, SDS, urea and CaCl2. The salts NaCl and KCl increased the enzyme activity from midgut and salivary glands. Zymogram analysis of midgut and salivary gland extract showed at least two bands of amylase activity in the midgut and salivary glands. 相似文献
26.
Vahid Mahdavi Moosa Saber Hooshang Rafiee-Dastjerdi Ali Mehrvar Mehdi Hassanpour 《Archives Of Phytopathology And Plant Protection》2013,46(7):841-848
Exposing to sub-lethal and low lethal doses of pesticides may cause changes in natural enemy behavioural, such as functional, response. In this study, the effects of chlorpyrifos, carbaryl, abamectin and spinosad were evaluated on the functional response of the Habrobracon hebetor to different densities of last instar larvae of Anagasta kuehniella Zeller. Young adult females of the parasitoid were exposed to LC30 of chlorpyrifos, carbaryl, abamectin and spinosad that were 0.32, 4.03, 3.05 and 17.51?mg a.i./l for 24?h, respectively. Host densities of 2, 4, 8, 16, 32 and 64 were offered to treated young females for 2?h in 10-cm Petri dishes and then the parasitism data were recorded. Experiments were conducted in eight replications. Functional response type was determined using logistic regression and the parameters were appraised by non-linear regression using statistical analysis software. Functional response was type Ш in control and insecticide treatments. Searching efficiency in control, chlorpyrifos-, carbaryl-, abamectin- and spinosad-treated wasps were 0.008?±?0.002, 0.002?±?0.0009, 0.0034?±?0.0013, 0.0076?±?0.002 and 0.0073?±?0.002?h?1and handling times were 1.38?±?0.1, 7.64?±?1.01, 3.3?±?0.315, 1.55?±?0.1 and 1.46?±?0.11?h, respectively. Chlorpyrifos and carbaryl had the highest effect on searching efficiency of H. hebetor. Spinosad and abamectin showed less adverse effect on the functional response parameters. Finally, after conducting the advanced field studies, spinosad and abamectin may be used as a compatible chemical material with biological control agent in integrated pest management programmes. 相似文献
27.
Hasan Hosseinzadeh Saeid Nasrollanejad Zahra Dordiani Vahid Jamshidnezhad 《Archives Of Phytopathology And Plant Protection》2013,46(16):1879-1883
Sharka disease is one of the most damaging diseases of fruit trees in the world, which is caused by Plum pox virus (PPV) that belongs to the genus Potyvirus in the family Potyviridae. Each year, this virus decreases the yield and causes substantial economic damages to its host plants worldwide. This virus is quarantined in Iran but in recent years, suspicious symptoms of the disease were observed in different grown areas, such as Golestan province. During 2010, 420 samples with mosaic, chlorosis, necrosis, ring pattern, blotches, etc. symptoms were collected from the gardens in Golestan province that included 100 samples from plum, 100 from peach and 240 from nectarine. These samples were evaluated using a double-antibody sandwich-ELISA (DAS-ELISA) method and a polyclonal antibody. The results of this survey indicated that among the total of 420 samples, none of them showed positive reaction in DAS-ELISA test. 相似文献
28.
Hamid Mahmoudzadeh-Niknam Ghader Khalili Firoozeh Abrishami Ali Najafy Vahid Khaze 《The Korean journal of parasitology》2013,51(1):69-74
Leishmania tropica is one of the causative agents of leishmaniasis in humans. Routes of infection have been reported to be an important variable for some species of Leishmania parasites. The role of this variable is not clear for L. tropica infection. The aim of this study was to explore the effects of route of L. tropica infection on the disease outcome and immunologic parameters in BALB/c mice. Two routes were used; subcutaneous in the footpad and intradermal in the ear. Mice were challenged by Leishmani major, after establishment of the L. tropica infection, to evaluate the level of protective immunity. Immune responses were assayed at week 1 and week 4 after challenge. The subcutaneous route in the footpad in comparison to the intradermal route in the ear induced significantly more protective immunity against L. major challenge, including higher delayed-type hypersensitivity responses, more rapid lesion resolution, lower parasite loads, and lower levels of IL-10. Our data showed that the route of infection in BALB/c model of L. tropica infection is an important variable and should be considered in developing an appropriate experimental model for L. tropica infections. 相似文献
29.
Ultrasonic technology was applied for polysaccharide extraction from the leaves of Dodonaea viscosa and response surface methodology (RSM) was used to optimize the effects of processing parameters on polysaccharide extraction yield. Three independent variables were extraction time (X1), extraction temperature (X2) and ultrasonic power (X3), respectively. The statistical analysis indicated the independent variables (X1, X2, X3), the quadratic terms (X11 and X33) and the interaction terms (X1X2, X1X3, X2X3) had significant effects on the yield of polysaccharides (P < 0.05). The optimal extraction conditions of D. viscosa leaf were determined as follows: extraction time 50.54 min, extraction temperature 85 °C and ultrasonic power 400 W. Under these conditions, the experimental yield of polysaccharides was 9.455 ± 0.24%, which was agreed closely with the predicted value (9.398%). The evaluation of anti-oxidant activity suggested that the polysaccharide exhibited significant protection against DPPH and hydroxyl radicals and could be explored as a nutraceutical agent. 相似文献
30.
Hooshang Hamidian Roya Tagizadeh Samieh Fozooni Vahid Abbasalipour Ali Taheri Mohadeseh Namjou 《Bioorganic & medicinal chemistry》2013,21(7):2088-2092
Six new azo dyes containing of 5(4H)-oxazolone ring were prepared by diazotization of 4-aminohippuric acid and coupling with N,N-dimethylaniline, 1-naphthol and 2-naphthol and condensation with 4-fluoro benzaldehyde or 4-trifluoromethoxy benzaldehyde. The new compounds were fully characterized by spectroscopic techniques. All synthesized compounds exhibited high tyrosinase inhibitory behavior. The results of mushroom tyrosinase inhibition assays indicate that the 4-trifluoromethoxy derivatives have high degrees of inhibition and N,N-dimethylaniline derivatives are better for tyrosinase inhibition than 1-naphthol and 2-naphthol derivatives. All synthesized azo compounds (4a–4f) showed the most potent mushroom tyrosinase inhibition, comparable to that of Kojic acid and l-mimosine, as reference standard inhibitors. 相似文献