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Fulltext Efficient oil palm total RNA extraction with a total RNA extraction kit

Habib SH, Saud HM, Kausar H

Genet. Mol. Res., 2014;13(2):2359-67.
PMID: 24781991 DOI: 10.4238/2014.April.3.8

Oil palm tissues are rich in polyphenols, polysaccharides and secondary metabolites; these can co-precipitate with RNA, causing problems for downstream applications. We compared two different methods (one conventional and a kit-based method - Easy-Blue(TM) Total RNA Extraction Kit) to isolate total RNA from leaves, roots and shoot apical meristems of tissue culture derived truncated leaf syndrome somaclonal oil palm seedlings. The quality and quantity of total RNA were compared through spectrophotometry and formaldehyde gel electrophoresis. The specificity and applicability of the protocols were evaluated for downstream applications, including cDNA synthesis and RT-PCR analysis. We found that the conventional method gave higher yields of RNA but took longer, and it was contaminated with genomic DNA. This method required extra genomic DNA removal steps that further reduced the RNA yield. The kit-based method, on the other hand, produced good yields as well as well as good quality RNA, within a very short period of time from a small amount of starting material. Moreover, the RNA from the kit-based method was more suitable for synthesizing cDNA and RT-PCR amplification than the conventional method. Therefore, we conclude that the Easy-BlueTM Total RNA Extraction Kit method is suitable and superior for isolation of total RNA from oil palm leaf, root and shoot apical meristem.
Fulltext Plant Growth-Promoting Rhizobacteria Enhance Salinity Stress Tolerance in Okra through ROS-Scavenging Enzymes

Habib SH, Kausar H, Saud HM

Biomed Res Int, 2016;2016:6284547.
PMID: 26951880 DOI: 10.1155/2016/6284547

Salinity is a major environmental stress that limits crop production worldwide. In this study, we characterized plant growth-promoting rhizobacteria (PGPR) containing 1-aminocyclopropane-1-carboxylate (ACC) deaminase and examined their effect on salinity stress tolerance in okra through the induction of ROS-scavenging enzyme activity. PGPR inoculated okra plants exhibited higher germination percentage, growth parameters, and chlorophyll content than control plants. Increased antioxidant enzyme activities (SOD, APX, and CAT) and upregulation of ROS pathway genes (CAT, APX, GR, and DHAR) were observed in PGPR inoculated okra plants under salinity stress. With some exceptions, inoculation with Enterobacter sp. UPMR18 had a significant influence on all tested parameters under salt stress, as compared to other treatments. Thus, the ACC deaminase-containing PGPR isolate Enterobacter sp. UPMR18 could be an effective bioresource for enhancing salt tolerance and growth of okra plants under salinity stress.
Hexavalent molybdenum reduction to molybdenum blue by S. marcescens strain Dr. Y6

Shukor MY, Habib SH, Rahman MF, Jirangon H, Abdullah MP, Shamaan NA, et al.

Appl Biochem Biotechnol, 2008 Apr;149(1):33-43.
PMID: 18350385 DOI: 10.1007/s12010-008-8137-z

A molybdate-reducing bacterium has been locally isolated. The bacterium reduces molybdate or Mo(6+) to molybdenum blue (molybdate oxidation states of between 5+ and 6+). Different carbon sources such as acetate, formate, glycerol, citric acid, lactose, fructose, glucose, mannitol, tartarate, maltose, sucrose, and starch were used at an initial concentration of 0.2% (w/v) in low phosphate media to study their effect on the molybdate reduction efficiency of bacterium. All of the carbon sources supported cellular growth, but only sucrose, maltose, glucose, and glycerol (in decreasing order) supported molybdate reduction after 24 h of incubation. Optimum concentration of sucrose for molybdate reduction is 1.0% (w/v) after 24 h of static incubation. Ammonium sulfate, ammonium chloride, valine, OH-proline, glutamic acid, and alanine (in the order of decreasing efficiency) supported molybdate reduction with ammonium sulfate giving the highest amount of molybdenum blue after 24 h of incubation at 0.3% (w/v). The optimum molybdate concentration that supports molybdate reduction is between 15 and 25 mM. Molybdate reduction is optimum at 35 degrees C. Phosphate at concentrations higher than 5 mM strongly inhibits molybdate reduction. The molybdenum blue produced from cellular reduction exhibits a unique absorption spectrum with a maximum peak at 865 nm and a shoulder at 700 nm. The isolate was tentatively identified as Serratia marcescens Strain Dr.Y6 based on carbon utilization profiles using Biolog GN plates and partial 16s rDNA molecular phylogeny.
Fulltext Surface-Functionalized Superparamagnetic Nanoparticles (SPNs) for Enhanced Oil Recovery: Effects of Surface Modifiers and Their Architectures

Khalil M, Aulia G, Budianto E, Mohamed Jan B, Habib SH, Amir Z, et al.

ACS Omega, 2019 Dec 17;4(25):21477-21486.
PMID: 31867543 DOI: 10.1021/acsomega.9b03174

Superparamagnetic nanoparticles (SPNs) have been considered as one of the most studied nanomaterials for subsurface applications, including in enhanced oil recovery (EOR), due to their unique physicochemical properties. However, a comprehensive understanding of the effect of surface functionalization on the ability of the nanoparticles to improve secondary and tertiary oil recoveries remains unclear. Therefore, investigations on the application of bare and surface-functionalized SPNs in EOR using a sand pack were carried out in this study. Here, the as-prepared SPNs were functionalized using oleic acid (OA) and polyacrylamide (PAM) to obtain several types of nanostructure architectures such as OA-SPN, core-shell SPN@PAM, and SPN-PAM. Based on the result, it is found that both the viscosity and mobility of the nanofluids were significantly affected by not only the concentration of the nanoparticles but also the type and architecture of the surface modifier, which dictated particle hydrophilicity. According to the sand pack tests, the nanofluid containing SPN-PAM was able to recover as much as 19.28% of additional oil in a relatively low concentration (0.9% w/v). The high oil recovery enhancement was presumably due to the ability of suspended SPN-PAM to act as a mobility control and wettability alteration agent and facilitate the formation of a Pickering emulsion and disjoining pressure.
Fulltext Minimum inhibitory concentration of nano-silver bactericides for beneficial microbes and its effect on Ralstonia solanacearum and seed germination of Japanese Cucumber (Cucumis sativus)

Sotoodehnia P, Mazlan N, Mohd Saud H, Samsuri WA, Habib SH, Soltangheisi A

PeerJ, 2019;7:e6418.
PMID: 30918747 DOI: 10.7717/peerj.6418

Background: Plant growth-promoting rhizobacteria (PGPR) are highly promising biofertilizers that contribute to eco-friendly sustainable agriculture. There have been many reports on the anti-microbial properties of nanoparticles (NPs). Toxic effects of NPs under laboratory conditions have also reported; however, there is a lack of information about their uptake and mobility in organisms under environmental conditions. There is an urgent need to determine the highest concentration of NPs which is not detrimental for growth and proliferation of PGPR.
Methods: Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) were used to measure the size and shape of NPs. Minimum inhibitory concentrations (MIC) of nano-silver on selected beneficial microbes and Ralstonia solanacearum were measured using the microdilution broth method. The percentage of seed germination was measured under in vitro conditions.
Results: NPs were spherical with a size of 16 ± 6 nm. Nano-silver at 12-40 mg l-1 inhibited the growth of bacteria. Seed application at 40 mg l-1 protected seeds from R. solanacearum and improved the rate of seed germination.
Ginger extract (Zingiber officinale) has anti-cancer and anti-inflammatory effects on ethionine-induced hepatoma rats

Habib SH, Makpol S, Abdul Hamid NA, Das S, Ngah WZ, Yusof YA

Clinics (Sao Paulo), 2008 Dec;63(6):807-13.
PMID: 19061005

OBJECTIVE: To evaluate the effect of ginger extract on the expression of NFkappaB and TNF-alpha in liver cancer-induced rats.
METHODS: Male Wistar rats were randomly divided into 5 groups based on diet: i) control (given normal rat chow), ii) olive oil, iii) ginger extract (100mg/kg body weight), iv) choline-deficient diet + 0.1% ethionine to induce liver cancer and v) choline-deficient diet + ginger extract (100mg/kg body weight). Tissue samples obtained at eight weeks were fixed with formalin and embedded in paraffin wax, followed by immunohistochemistry staining for NFkappaB and TNF-alpha.
RESULTS: The expression of NFkappaB was detected in the choline-deficient diet group, with 88.3 +/- 1.83% of samples showing positive staining, while in the choline-deficient diet supplemented with ginger group, the expression of NFkappaB was significantly reduced, to 32.35 +/- 1.34% (p<0.05). In the choline-deficient diet group, 83.3 +/- 4.52% of samples showed positive staining of TNF-alpha, which was significantly reduced to 7.94 +/- 1.32% (p<0.05) when treated with ginger. There was a significant correlation demonstrated between NFkappaB and TNF-alpha in the choline-deficient diet group but not in the choline-deficient diet treated with ginger extract group.
CONCLUSION: In conclusion, ginger extract significantly reduced the elevated expression of NFkappaB and TNF-alpha in rats with liver cancer. Ginger may act as an anti-cancer and anti-inflammatory agent by inactivating NFkappaB through the suppression of the pro-inflammatory TNF-alpha.
Fulltext Chlorella vulgaris triggers apoptosis in hepatocarcinogenesis-induced rats

Mohd Azamai ES, Sulaiman S, Mohd Habib SH, Looi ML, Das S, Abdul Hamid NA, et al.

J Zhejiang Univ Sci B, 2009 Jan;10(1):14-21.
PMID: 19198018 DOI: 10.1631/jzus.B0820168

Chlorella vulgaris (CV) has been reported to have antioxidant and anticancer properties. We evaluated the effect of CV on apoptotic regulator protein expression in liver cancer-induced rats. Male Wistar rats (200~250 g) were divided into eight groups: control group (normal diet), CDE group (choline deficient diet supplemented with ethionine in drinking water to induce hepatocarcinogenesis), CV groups with three different doses of CV (50, 150, and 300 mg/kg body weight), and CDE groups treated with different doses of CV (50, 150, and 300 mg/kg body weight). Rats were sacrificed at various weeks and liver tissues were embedded in paraffin blocks for immunohistochemistry studies. CV, at increasing doses, decreased the expression of anti-apoptotic protein, Bcl-2, but increased the expression of pro-apoptotic protein, caspase 8, in CDE rats, which was correlated with decreased hepatocytes proliferation and increased apoptosis as determined by bromodeoxy-uridine (BrdU) labeling and terminal deoxynucleotidyl transferase mediated dUTP nick-end labeling (TUNEL) assay, respectively. Our study shows that CV has definite chemopreventive effect by inducing apoptosis via decreasing the expression of Bcl-2 and increasing the expression of caspase 8 in hepatocarcinogenesis-induced rats.