cDNA Cloning, Sequence Analysis and Molecular Modeling of a New Peptide from the Scorpion Buthotus saulcyi Venom

Nikkhah, Maryam,Naderi-Manesh, Hossein,Taghdir, Majid,Talebzadeh, Mehdi,Sadeghi-Zadeh, Majid,Schaller, Janatan,Sarbolouki, Mohamad N. Korean Society for Biochemistry and Molecular Biol 2006 Journal of biochemistry and molecular biology Vol.39 No.3

In this study, the cDNA of a new peptide from the venom of the scorpion, Buthotus saulcyi, was cloned and sequenced. It codes for a 64 residues peptide (Bsaul1) which shares high sequence similarity with depressant insect toxins of scorpions. The differences between them mainly appear in the loop1 which connects the $\beta$-strand1 to the $\alpha$-helix and seems to be functionally important in long chain scorpion neurotoxins. This loop is three amino acids longer in Bsaul1 compared to other depressant toxins. A comparative amino acid sequence analysis done on Bsaul1 and some of $\alpha$-, $\beta$-, excitatory and depressant toxins of scorpions showed that Bsaul1 contains all the residues which are highly conserved among long chain scorpion neurotoxins. Structural model of Bsaul1 was generated using Ts1 (a $\beta$-toxin that competes with the depressant insect toxins for binding to $Na^+$ channels) as template. According to the molecular model of Bsaul1, the folding of the polypeptide chain is being composed of an anti-parallel three-stranded $\beta$-sheet and a stretch of $\alpha$-helix, tightly bound by a set of four disulfide bridges. A striking similarity in the spatial arrangement of some critical residues was shown by superposition of the backbone conformation of Bsaul1 and Ts1.

Cyber Kill Chain-Based Taxonomy of Advanced Persistent Threat Actors: Analogy of Tactics, Techniques, and Procedures

Pooneh Nikkhah Bahrami,Ali Dehghantanha,Tooska Dargahi,Reza M. Parizi,Kim-Kwang Raymond Choo,Hamid H. S. Javadi 한국정보처리학회 2019 Journal of information processing systems Vol.15 No.4

The need for cyber resilience is increasingly important in our technology-dependent society where computingdevices and data have been, and will continue to be, the target of cyber-attackers, particularly advancedpersistent threat (APT) and nation-state/sponsored actors. APT and nation-state/sponsored actors tend to bemore sophisticated, having access to significantly more resources and time to facilitate their attacks, which inmost cases are not financially driven (unlike typical cyber-criminals). For example, such threat actors oftenutilize a broad range of attack vectors, cyber and/or physical, and constantly evolve their attack tactics. Thus,having up-to-date and detailed information of APT’s tactics, techniques, and procedures (TTPs) facilitates thedesign of effective defense strategies as the focus of this paper. Specifically, we posit the importance oftaxonomies in categorizing cyber-attacks. Note, however, that existing information about APT attackcampaigns is fragmented across practitioner, government (including intelligence/classified), and academicpublications, and existing taxonomies generally have a narrow scope (e.g., to a limited number of APTcampaigns). Therefore, in this paper, we leverage the Cyber Kill Chain (CKC) model to “decompose” anycomplex attack and identify the relevant characteristics of such attacks. We then comprehensively analyze morethan 40 APT campaigns disclosed before 2018 to build our taxonomy. Such taxonomy can facilitate incidentresponse and cyber threat hunting by aiding in understanding of the potential attacks to organizations as wellas which attacks may surface. In addition, the taxonomy can allow national security and intelligence agenciesand businesses to share their analysis of ongoing, sensitive APT campaigns without the need to disclose detailedinformation about the campaigns. It can also notify future security policies and mitigation strategy formulation.

cDNA Cloning, Sequence Analysis and Molecular Modeling of a New Peptide from the Scorpion Buthotus saulcyi Venom

( Maryam Nikkhah ),( Hossein Naderi Manesh ),( Majid Taghdir ),( Mehdi Talebzadeh ),( Majid Sadeghi Zadeh ),( Janatan Schaller ),( Mohamad N. Sarbolouki ) 생화학분자생물학회 2006 BMB Reports Vol.39 No.3

Application of SSR Markers for Characterization of Genetic Diversity within Iranian Grapevine Cultivars (‘Askari’ and ‘Keshmeshi’)

Rahim Nikkhah,Ali Ebadi,Mohammad Reza Naghavi,Mauro Cresti,Monica Scali,Mehdi Hadadynejad 한국원예학회 2010 Horticulture, Environment, and Biotechnology Vol.51 No.1

The present study was designed to identify intra-varietal diversity via SSR markers within ‘Askari’ and ‘Keshmeshi’ (Vitis vinifera L.). These two semi-seedless grape cultivars are used as table grape and raisin. Some accessions of these cultivars are morphologically different. For instance, some accessions had big berries with big bunches and empty seeds, whereas others had small berries in small bunches with soft seed traces. In order to evaluate these differences at the genetic level, we selected 14 SSR loci to evaluate intra-cultivar diversity. In total, 42 accessions of ‘Askari’, 10 accessions of ‘Keshmeshi’ and one accession of Sultanina as a control were analysed, using a capillary electrophoresis fragment sizing system. Genetic analysis discriminated six accessions of ‘Askari’ (No. A3, A21, A31, A44, A46, and A114) which were different from other accessions. These accessions were also different in some morphological traits. Accessions no. A3 and no. A21 had soft seed traces with berries and bunches that were smaller than others. Other accessions had empty seeds. Accessions no. A44, A46 and A114 had big bunches, big berries and empty seeds. In accession no. A31 berry shape was approximately round vs. oval shape in other accessions. The remaining accessions (36 accessions) were identical in 14 SSR loci. In ‘Keshmeshi’ four different accessions (No. K6, K8, K15, and K27) were discriminated in genetic analysis. In accessions no. K6 and no. K8, the number of bunch and yield per vine was higher than other accessions. In accessions no. K15 and no. K27, berries and bunches were bigger than others and the number of seed traces were higher than other accessions. Other six accessions were identical in14 SSR loci. Cluster analysis of all three cultivars divided accessions to three groups (each cultivar in one group) at 0.67 similarity coefficient. Our study showed SSR markers can be useful for identifying of intra-cultivar diversity.

Salicylic Acid Retards Petal Senescence in Cut Lisianthus (Eustoma grandiflorum ‘Miarichi Grand White’) Flowers

Sara Nikkhah Bahrami,Hedayat Zakizadeh,Yousef Hamidoghli,Mahmood Ghasemnezhad 한국원예학회 2013 Horticulture, Environment, and Biotechnology Vol.54 No.6

The effect of exogenous salicylic acid (SA) on the vase life of cut lisianthus flowers was investigated. ‘Miarichi Grand White’ flowers were obtained from a commercial grower and were pulse-treated with a 0, 50, 100, 150or 200 mg·L-1 SA solution containing 200 mg·L-1 8-hydroxyquinoline sulphate (HQS) and 5% (w/v) sucrose for 18 hours. As compared to distilled water (DW) as the control, the greatest delay in petals senescence was obtained in cut flowers pulsed with 100 mg·L-1 SA. Vase life of flowers increased by 4.5 days in the above mentioned treatment. The characteristics such as water uptake (WUP), relative fresh weight (RFW), protein concentration, proline accumulation,and activities of lipoxygenase (LOX) and superoxide dismutase (SOD) were measured in the 0 and 100 mg·L-1 SA treatments over the period of vase life. The WUP and RFW were obviously greater in the SA-treated flowers than in the control. Degradation of protein and accumulation of proline during vase life was shown to be suppressed by 100 mg·L-1 SA. The activity of LOX was gradually increased with progressing flower senescence, while the activity of SOD was declined. The flowers which had been pulsed with 100 mg·L-1 SA exhibited lower LOX and a higher SOD activities. Overall, the results suggest that SA can increase the vase life of lisianthus cut flowers by improving the antioxidant system and reducing damages caused by oxidative stress during senescence.

Modeling and nonlinear analysis of a micro-switch under electrostatic and piezoelectric excitations with curvature and piezoelectric nonlinearities

Mansour Nikkhah Bahrami,Aghil Yousefi-Koma,Hamed Raeisifard 대한기계학회 2014 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.28 No.1

In this paper, a comprehensive model of a micro-switch with both electrostatic and piezoelectric excitations, which accounts for thenonlinearities due to inertia, curvature, electrostatic forces and piezoelectric actuator is presented to demonstrate the mechanical characteristicsof such a micro-system. Dynamic equations of this model are derived by the Lagrange method. Static analysis of this model is performedwith five modes through the Galerkin method. The micro-switch beam is assumed as an elastic Euler-Bernoulli beam withclamped-free end conditions. The electrostatic actuation results are compared with other existing experimental and numerical results. Whereas the major drawback of electrostatically actuated micro-switches is the high driving voltage, using the piezoelectric actuator inthese systems can provide less driving voltage and control the pull-in voltage. The study demonstrates that when the ratio of electrostaticactuation distance to length of micro-switch is small, the nonlinear piezoelectric term has a significant effect on the pull-in phenomenon. There are three ways to influence the design and control of the mechanical characteristics of this micro-switch: the softening effect due toelectrostatic actuation, the hardening effect due to piezoelectric actuation, and varying the length and thickness of the piezoelectric actuator.

Cyber Kill Chain-Based Taxonomy of Advanced Persistent Threat Actors: Analogy of Tactics, Techniques, and Procedures

Bahrami, Pooneh Nikkhah,Dehghantanha, Ali,Dargahi, Tooska,Parizi, Reza M.,Choo, Kim-Kwang Raymond,Javadi, Hamid H.S. Korea Information Processing Society 2019 Journal of information processing systems Vol.15 No.4

The need for cyber resilience is increasingly important in our technology-dependent society where computing devices and data have been, and will continue to be, the target of cyber-attackers, particularly advanced persistent threat (APT) and nation-state/sponsored actors. APT and nation-state/sponsored actors tend to be more sophisticated, having access to significantly more resources and time to facilitate their attacks, which in most cases are not financially driven (unlike typical cyber-criminals). For example, such threat actors often utilize a broad range of attack vectors, cyber and/or physical, and constantly evolve their attack tactics. Thus, having up-to-date and detailed information of APT's tactics, techniques, and procedures (TTPs) facilitates the design of effective defense strategies as the focus of this paper. Specifically, we posit the importance of taxonomies in categorizing cyber-attacks. Note, however, that existing information about APT attack campaigns is fragmented across practitioner, government (including intelligence/classified), and academic publications, and existing taxonomies generally have a narrow scope (e.g., to a limited number of APT campaigns). Therefore, in this paper, we leverage the Cyber Kill Chain (CKC) model to "decompose" any complex attack and identify the relevant characteristics of such attacks. We then comprehensively analyze more than 40 APT campaigns disclosed before 2018 to build our taxonomy. Such taxonomy can facilitate incident response and cyber threat hunting by aiding in understanding of the potential attacks to organizations as well as which attacks may surface. In addition, the taxonomy can allow national security and intelligence agencies and businesses to share their analysis of ongoing, sensitive APT campaigns without the need to disclose detailed information about the campaigns. It can also notify future security policies and mitigation strategy formulation.

Investigation of the interface between polyethylene and functionalized graphene: A computer simulation study

S. Javan Nikkhah,M.R. Moghbeli,S.M. Hashemianzadeh 한국물리학회 2015 Current Applied Physics Vol.15 No.10

The effect of surface chemical functionalization of a single graphene layer on its thermodynamic work of adhesion (WA) with polyethylene (PE) chains has been investigated using molecular dynamics (MD) simulation. For this purpose, amine (NH2), carboxyl (COOH), hydroxyl (OH), and methyl (CH3) functional groups were distributed randomly throughout the graphene surface using a Monte Carlo (MC) algorithm to achieve graphene functionalized structures with minimized potential energies. The MD simulation results showed that the thermodynamic WA between the PE and the functionalized graphene was larger than that between the PE and the pristine graphene. In fact, the electronegativity of functional groups and Van der Waals forces play influential roles in the thermodynamic WA between the PE and the functionalized graphene. In addition, the amount of thermodynamic WA was increased with increasing the functional group surface density, except for the graphene functionalized with the methyl groups. The segmental density of the PE chains near the single sheet surface was determined based on the density profile calculation. The polymer segments exhibited strong ordering and sharp density variations near the PE/graphene interface. The dynamic of chains was quantitatively characterized by calculating mean square displacement (MSD). Furthermore, the influence of functionality on the glass transition temperature (Tg) of the PE at the PE/graphene interface region was investigated. The results showed that the Tg at the PE/graphene interface was much higher than that of the bulk polymer. In fact, the functionalization of the graphene surface seems to considerably enhance the Tg of the polymer due to lowering the chains mobility.

Effects of Gamma Irradiation on Chemical Composition, Antinutritional Factors, Ruminal Degradation and In vitro Protein Digestibility of Full-fat Soybean

Taghinejad, M.,Nikkhah, A.,Sadeghi, A.A.,Raisali, G.,Chamani, M. Asian Australasian Association of Animal Productio 2009 Animal Bioscience Vol.22 No.4

The aim of this study was to evaluate the effects of gamma irradiation (${\gamma}$-irradiation) at doses of 15, 30 and 45 kGy on chemical composition, anti-nutritional factors, ruminal dry matter (DM) and crude protein (CP) degradibility, in vitro CP digestibility and to monitor the fate of true proteins of full-fat soybean (SB) in the rumen. Nylon bags of untreated or ${\gamma}$-irradiated SB were suspended in the rumens of three ruminally-fistulated bulls for up to 48 h and resulting data were fitted to a nonlinear degradation model to calculate degradation parameters of DM and CP. Proteins of untreated and treated SB bag residues were fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Digestibility of rumen undegraded CP was estimated using the three-step in vitro procedure. The chemical composition of raw and irradiated soybeans was similar. Results showed that phytic acid in ${\gamma}$-irradiated SB at dose of 30 kGy was eliminated completely. The trypsin inhibitor activity of 15, 30 and 45 kGy ${\gamma}$-irradiated SB was decreased (p<0.01) by 18.4, 55.5 and 63.5%, respectively. From in sacco results, ${\gamma}$-irradiation decreased (p<0.05) the washout fractions of DM and CP at doses of 30 and 45 kGy, but increased (p<0.05) the potentially degradable fractions. Gamma irradiation at doses of 15, 30 and 45 kGy decreased (p<0.05) effective degradability of CP at a rumen outflow rate of 0.05 $h^{-1}$ by 4.4, 14.4 and 26.5%, respectively. On the contrary, digestibility of ruminally undegraded CP of irradiated SB at doses of 30 and 45 kGy was improved (p<0.05) by 12 and 28%, respectively. Electrophoretic analysis of untreated soybean proteins incubated in the rumen revealed that ${\beta}$-conglycinin subunits had disappeared at 2 h of incubation time, whereas the subunits of glycinin were more resistant to degradation until 16 h of incubation. From the SDS-PAGE patterns, acidic subunits of 15, 30 and 45 kGy ${\gamma}$-irradiated SB disappeared after 8, 8 and 16 h of incubation, respectively, while the basic subunits of glycinin were not degraded completely until 24, 48 and 48 h of incubation, respectively. It was concluded that ${\gamma}$-irradiated soybean proteins at doses higher than 15 kGy could be effectively protected from ruminal degradation.

Effect of Dietary Fish oil and Soybean Oil on Milk Production and Composition of Holstein Cows in Early Lactation

Fatahnia, Farshid,Nikkhah, Ali,Zamiri, Mohammad Javad,Kahrizi, Danial Asian Australasian Association of Animal Productio 2008 Animal Bioscience Vol.21 No.3

Milk was collected from 20 primiparous Holstein cows that were distributed into four groups and arranged in a completely randomized design with a 35-day period to determine the effect of feeding fish oil, soybean oil, or their combination on milk production and composition. Experimental diets consisted of: 1) control diet; 2) a diet with 3% (DM basis) added fat from menhaden fish oil; 3) a diet with 3% added fat from soybean oil; and 4) a diet with 1.5% added fat from fish oil and 1.5% fat from soybean oil. The dry matter intake (18.5, 18.9, 18.3, and 18.6 kg/d, for control, fish oil, soybean oil and combination diets, respectively) and milk production (30.31, 32.15, 31.19, and 31.59 kg/d, respectively) were higher for cows that consumed the 3% fish oil-containing diet. Milk from cows fed control, fish oil, soybean oil and fish oil with soybean oil diets contained 3.45, 2.72, 2.96, and 2.87% fat, respectively. Concentration of total omega-3 fatty acids (0.87, 1.28, 0.96, and 1.18 g/100 g of fatty acids, respectively) in milk fat were higher for cows that consumed either fish oil-containing diet, especially the 3% fish oil diet. The n-6:n-3 ratio (4.57, 2.62, 6.17, and 4.08, respectively) in milk fat was lower for the fish oil diet. These results showed that fish oil modified fatty acid profile of milk fat and increased the proportion of beneficial fatty acids for human health.