Understanding Viral Transmission Behavior via Protein Intrinsic Disorder Prediction: Coronaviruses

Besides being a common threat to farm animals and poultry, coronavirus (CoV) was responsible for the human severe acute respiratory syndrome (SARS) epidemic in 2002-4. However, many aspects of CoV behavior, including modes of its transmission, are yet to be fully understood. We show that the amount and the peculiarities of distribution of the protein intrinsic disorder in the viral shell can be used for the efficient analysis of the behavior and transmission modes of CoV. The proposed model allows categorization of the various CoVs by the peculiarities of disorder distribution in their membrane (M) and nucleocapsid (N). This categorization enables quick identification of viruses with similar behaviors in transmission, regardless of genetic proximity. Based on this analysis, an empirical model for predicting the viral transmission behavior is developed. This model is able to explain some behavioral aspects of important coronaviruses that previously were not fully understood. The new predictor can be a useful tool for better epidemiological, clinical, and structural understanding of behavior of both newly emerging viruses and viruses that have been known for a long time. A potentially new vaccine strategy could involve searches for viral strains that are characterized by the evolutionary misfit between the peculiarities of the disorder distribution in their shells and their behavior

Nipah shell disorder, modes of infection, and virulence

The Nipah Virus (NiV) was first isolated during a 1998–9 outbreak in Malaysia. The outbreak initially infected farm pigs and then moved to humans from pigs with a case-fatality rate (CFR) of about 40%. After 2001, regular outbreaks occurred with higher CFRs (~71%, 2001–5, ~93%, 2008–12). The spread arose from drinking virus-laden palm date sap and human-to-human transmission. Intrinsic disorder analysis revealed strong correlation between the percentage of disorder in the N protein and CFR (Regression: r2 = 0.93, p < 0.01, ANOVA: p < 0.01). Distinct disorder and, therefore, genetic differences can be found in all three group of strains. The fact that the transmission modes of the Malaysia strain are different from those of the Bangladesh strains suggests that the correlations may also be linked to the modes of viral transmission. Analysis of the NiV and related viruses suggests links between modes of transmission and disorder of not just the N protein but, also, of M shell protein. The links among shell disorder, transmission modes, and virulence suggest mechanisms by which viruses are attenuated as they passed through different cell hosts from different animal species. These have implications for development of vaccines and epidemiological molecular analytical tools to contain outbreaks

Rigidity of the Outer Shell Predicted by a Protein Intrinsic Disorder Model Sheds Light on the COVID-19 (Wuhan-2019-nCoV) Infectivity

The world is currently witnessing an outbreak of a new coronavirus spreading quickly across China and affecting at least 24 other countries. With almost 65,000 infected, a worldwide death toll of at least 1370 (as of 14 February 2020), and with the potential to affect up to two-thirds of the world population, COVID-19 is considered by the World Health Organization (WHO) to be a global health emergency. The speed of spread and infectivity of COVID-19 (also known as Wuhan-2019-nCoV) are dramatically exceeding those of the Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV). In fact, since September 2012, the WHO has been notified of 2494 laboratory-confirmed cases of infection with MERS-CoV, whereas the 2002–2003 epidemic of SARS affected 26 countries and resulted in more than 8000 cases. Therefore, although SARS, MERS, and COVID-19 are all the result of coronaviral infections, the causes of the coronaviruses differ dramatically in their transmissibility. It is likely that these differences in infectivity of coronaviruses can be attributed to the differences in the rigidity of their shells which can be evaluated using computational tools for predicting intrinsic disorder predisposition of the corresponding viral proteins

Emergence of weight-topology correlations in complex scale-free networks

Different weighted scale-free networks show weights-topology correlations indicated by the non linear scaling of the node strength with node connectivity. In this paper we show that networks with and without weight-topology correlations can emerge from the same simple growth dynamics of the node connectivities and of the link weights. A weighted fitness network is introduced in which both nodes and links are assigned intrinsic fitness. This model can show a local dependence of the weight-topology correlations and can undergo a phase transition to a state in which the network is dominated by few links which acquire a finite fraction of the total weight of the network.Comment: (4 pages,3 figures

Industrial building system : does it good for sustainable building? / S. Roshanfekr, N. M Tawil and N. A. Goh

Housing and building construction is an important principle in sustainable development. The industrialization of building systems has been found to be necessary due to several factors: the fast and continuing progress of today’s world, the industrialization of many aspects of modern living, significant population growth, and the inadequacy and incompetence of conventional construction methods particularly in dense housing situations. This paper investigates the relevance of these factors as the drivers for changing people’s habits and perspectives toward building construction and to justify the introduction of industrialized construction approaches to replace the outdated conventional methods as well as the necessity to provide training in order to achieve product quality

Modified-nano-adsorbents for nitrate efficient removal: a review

Excessive nitrate discharge into the aquatic environment from human activities is the main contributor to groundwater and surface water contamination. Its toxicity in water is a serious concern as it gives huge impacts on aquatic life since it damages the ecosystem and water sources around the globe. Recently, the development of nanomaterials as nano-adsorbent makes adsorption the most attractive solution among them. Nano-adsorbents pose high efficiency to remove pollutants from aqueous media. The exclusive chemical and structural properties of the developed nano-adsorbents are the determinative effects of nitrate adsorption performance. In this mini review, the state-of-the-art development of nano-adsorbents and nano-adsorbents-modified membranes for nitrate from water is discussed, and some challenges faced in this field are also highlighted

Nonlocal evolution of weighted scale-free networks

We introduce the notion of globally updating evolution for a class of weighted networks, in which the weight of a link is characterized by the amount of data packet transport flowing through it. By noting that the packet transport over the network is determined nonlocally, this approach can explain the generic nonlinear scaling between the strength and the degree of a node. We demonstrate by a simple model that the strength-driven evolution scheme recently introduced can be generalized to a nonlinear preferential attachment rule, generating the power-law behaviors in degree and in strength simultaneously.Comment: 4 pages, 4 figures, final version published in PR

A comparative analysis of viral matrix proteins using disorder predictors

Abstract Background A previous study (Goh G.K.-M., Dunker A.K., Uversky V.N. (2008) Protein intrinsic disorder toolbox for comparative analysis of viral proteins. BMC Genomics. 9 (Suppl. 2), S4) revealed that HIV matrix protein p17 possesses especially high levels of predicted intrinsic disorder (PID). In this study, we analyzed the PID patterns in matrix proteins of viruses related and unrelated to HIV-1. Results Both SIVmac and HIV-1 p17 proteins were predicted by PONDR VLXT to be highly disordered with subtle differences containing 50% and 60% disordered residues, respectively. SIVmac is very closely related to HIV-2. A specific region that is predicted to be disordered in HIV-1 is missing in SIVmac. The distributions of PID patterns seem to differ in SIVmac and HIV-1 p17 proteins. A high level of PID for the matrix does not seem to be mandatory for retroviruses, since Equine Infectious Anemia Virus (EIAV), an HIV cousin, has been predicted to have low PID level for the matrix; i.e. its matrix protein p15 contains only 21% PID residues. Surprisingly, the PID percentage and the pattern of predicted disorder distribution for p15 resemble those of the influenza matrix protein M1 (25%). Conclusion Our data might have important implications in the search for HIV vaccines since disorder in the matrix protein might provide a mechanism for immune evasion.</p