Substrate docking and molecular dynamic simulation for prediction of fungal enzymes from Trichoderma species-assisted extraction of nanocellulose from oil palm leaves

Abstract

Fungi of the Trichoderma species are valued industrial enzymes in support of the ‘zero-waste’ technology to convert agro-industrial biomass into valuable products, i.e. nanocellulose (NC). In this study, an in silico approach using substrate docking and molecular dynamic (MD) simulation was used to predict the order of which the multilayers of cellulosic polymers, i.e. lignin, hemicellulose and cellulose in oil palm leaves (OPL) are degraded by fungal enzymes, endocellulase and exocellulase. The study aimed to establish the catalytic tendencies of the enzymes to optimally degrade the cellulosic components of OPL for high yield production of NC. Energy minimized endocellulase and exocellulase models revealed satisfactory scores of PROCHECK (90.0% and 91.2%), Verify3D (97.23% and 98.85%) and ERRAT (95.24% and 91.00%) assessments. Active site prediction by blind docking, COACH meta-server and multiple sequence alignment indicated the catalytic triads for endocellulase and exocellulase were Ser116–His205–Glu249 and Ser382–Arg124–Asp385, respectively. Binding energy of endocellulase docked with hemicellulose (?6.0 ? kcal mol^?1) was the most favourable followed by lignin (?5.6 ? kcal mol^?1) and cellulose (?4.4 ? kcal mol^?1). Exocellulase, contrarily, bonded favorably with lignin (?8.7 ? kcal mol^?1), closely followed by cellulose (?8.5 ? kcal mol^?1) and hemicellulose (?8.4 ? kcal mol^?1). MDs simulations showed that interactions of complexes, endocellulase–hemicellulose and the exocellulase–cellulose being the most stable. Thus, the findings of the study successfully identified the specific actions of sugar-acting enzymes for NC production.

Communicated by Ramaswamy H. Sarma     

Evaluation of Trichoderma spp. from central and northern regions of Turkey for suppression of Polymyxa betae as a vector of rhizomania disease

In the current study, 18 Trichoderma spp. isolates were obtained from different provinces in central and northern regions of Turkey. The ability of nine selected isolates to suppress the colonisation of roots by P. betae and the multiplication of BNYVV in sugar beet roots under controlled conditions were tested. Roots of seedlings growing in the P. betae-BNYVV-infested soil were analysed by enzyme-linked immunosorbent assay to test for the presence of BNYVV and checked microscopically for the density of cystosori of P. betae. The numbers of P. betae resting spores in cystosori for each treatment were counted using a light microscope. Except for isolates Tr-1 and Tr-5, the effect of selected Trichoderma isolates on suppressing multiplication of BNYVV varied between 4 and 53%. The total number of resting spores in the roots varied between 14.4 and 25.1 for the different Trichoderma spp. treatments. The lowest number of resting spores in clusters was recorded in T. harzianum Tr-8. In addition, the shapes of resting spores were not normal in the Tr-8 treatments. The cystosori from this treatment were also abnormally dark in colour and had deformed walls.     

Functional changes of the SCN in spontaneous hypertension but not after the induction of hypertension

ABSTRACT

The present study investigates the circadian behavior of spontaneously hypertensive rats (SHRs) during the pre-hypertensive and hypertensive stage, with the aim to gain insight into whether observed changes in the functionality of suprachiasmatic nucleus (SCN) in the hypertensive state are cause or consequence of hypertension. Four types of animals were used in this study: (1) SHRs which develop hypertension genetically; (2) their normotensive controls, Wistar Kyoto rats (WKYs); (3) Wistar rats whereby hypertension was surgically induced (2 Kidney 1 Clamp (2K1C) method); and (4) sham-operated control Wistar rats. Period length and activity levels and amplitude changes of locomotor and wheel running activity were determined, in constant conditions, as a measure of the functionality of the SCN. Hereto two conditions were used, constant darkness (0 lux) and constant dim (5 lux) light. SHRs showed a shortened period of their locomotor and running wheel activity rhythms in constant darkness during both pre-hypertensive and hypertensive stages and exhibited period lengthening in constant dim light conditions, only during hypertensive stages. Total amount as well as the amplitude of daily running wheel rhythms showed an inverse correlation with the period length, and this relation was significantly different in SHRs compared to WKYs. None of the aforementioned changes in circadian rhythms were observed after the surgical induction of hypertension. The present findings suggest early functional changes of the SCN in the etiology of spontaneous hypertension.     

First Record of Steinernema kraussei (Rhabditida: Steinernematidae) from Turkey and Its Virulence against Agrotis segetum (Lepidoptera: Noctuidae)

During a survey of entomopathogenic nematodes (EPNs) in the eastern Black Sea region of Turkey in 2009–2012, a steinernematid species was recorded and isolated using the Galleria-baiting method. The isolate was identified as Steinernema kraussei based on its morphological and molecular properties. The analysis of the ITS rDNA sequence placed the Turkish population of S. kraussei in the “feltiae-kraussei” group in the clade that contains different isolates of the species. This is the first record of S. kraussei from Turkey. The efficacy of S. kraussei was tested on Agrotis segetum (Lepidoptera: Noctuidea) larvae at different densities (100, 300, and 500 infective juveniles (IJs) g⁻¹ dry sand ) in laboratory conditions at 25 °C. The highest mortality (98%) was obtained with 500 IJs g⁻¹ dry sand within 7 d after inoculation. Our results indicate that the new isolate is a highly promising biological control agent against A. segetum, one of the most serious soil pests of agricultural area and fruits worldwide.     

Liminality and racial hazing of Muslim migrants: media framing of Albanians in Shepparton,Australia, 1930–1955

This article is a historical empirical study of the Albanian Muslim migrant community of Shepparton. Through analysing newspaper reports, the authors discuss how these migrants were portrayed as liminal between their first arrival and acceptance as Australians a generation later. This is characteristic of a practice which the authors term “migrant hazing”, where a migrant group is demonized as a threat to the society during the liminal phase. Migrant hazing occurs in public discourse, particularly the media, and ceases with the replacement of the group by newer migrants, who are subjected to the same process. Furthermore, migrant hazing remains present in contemporary depictions of Australian Muslims. In this longitudinal study, media reports on Albanian Muslims revolved around three persistent themes: their supposed criminality, the wrongful use of land and the threat of dual-loyalty. These three items constituted the main weapons of the media in hazing the first, liminal generation.     

Comparison of microbially induced calcium carbonate precipitation eligibility using sporosarcina pasteurii and bacillus licheniformis on two different sands

The use of biological means for ground improvement have become popular, which generally works through the process called microbially-induced calcium carbonate precipitation (MICP). Many studies indicate successful application of MICP based improvement with multiple bacteria and on several soils. Given the proven performance of MICP, this study aims to examine the MICP process by comparing the calcium carbonate precipitation ability of widely studied bacteria, i.e., Sporosarcina pasteurii and relatively under-recognized bacteria, i.e., Bacillus licheniformis to outline the formation success. For this purpose, two different sands were tested for observing precipitation behavior using a series of syringe tests. Furthermore, the effect of concentration and inclusion of calcium chloride for nutrition of bacteria, saturation with water, and hybrid use of two bacteria were investigated in some tests for diversification. X-ray diffraction (XRD), scanning electron microscopy (SEM), and energy dispersive x-ray spectroscopy (EDS) were used for the interpretation of results. Results indicated that Sporosarcina pasteurii had performed superior over Bacillus licheniformis when achieving calcium carbonate precipitation in tests for both sands. In addition, many intriguing SEM images contributed to the literature of MICP monitoring, highlighting the effects of the variables investigated.