Characterization of secondary metabolite compounds correlated with the seasons in Artemisia princeps var. orientalis (Pamp.) H. Hara leaves using direct sample injection and gas chromatography-mass spectrometry: contribution to phytotoxicity

Mamun, M.I.R.,Abd El-Aty, A.M.,Musfiqur Rahman, Md.,Choi, Jeong-Heui,Yun, Kyeong Won,Shin, Ho-Chul,Shim, Jae-Han The Korean Society for Applied Biological Chemistr 2015 Applied Biological Chemistry (Appl Biol Chem) Vol.58 No.2

Leaves from a natural population of Artemisia princeps var. orientalis (Pamp.) H. Hara were collected monthly from April through October and characterized for composition of secondary metabolite compounds and their phytotoxic effects on seed germination and seedling growth of Achyranthes japonica and Lactuca sativa. The compounds were identified using gas chromatography/mass spectrometry (GC/MS) coupled with a solvent-free solid injector (SFSI). GC/MS analyses of all samples revealed qualitative variability in the composition of secondary metabolites. The greatest number of compounds was identified in July (56) followed by September (30) and April (24), and the lowest number was found in June (2) and August (2). Among 92 compounds, the major compounds were various terpenes (23) (mono-, sesqui, di-, and tri-terpenes) followed by heterocyclic compounds (18) and hydrocarbons (14). The higher the concentration of the secondary metabolites, the lower the seed germination and seedling growth of A. japonica and L. sativa. Plant samples collected in July and August were most detrimental. Taken together, variability in the secondary metabolites compounds of A. princeps var. orientalis was verified during different seasons, and the compounds were successfully identified by a combination of SFSI and GC/MS. Notably, the antimicrobial and antioxidative effects were inconsistent throughout the various seasons.

Characterization of secondary metabolite compounds correlated with the seasons in Artemisia princeps var. orientalis (Pamp.) H. Hara leaves using direct sample injection and gas chromatography–mass spectrometry: contribution to phytotoxicity

M. I. R. Mamun,A. M. Abd El-Aty,Md. Musfiqur Rahman,최정희,윤경원,신호철,심재한 한국응용생명화학회 2015 Applied Biological Chemistry (Appl Biol Chem) Vol.58 No.2

Leaves from a natural population of Artemisia princeps var. orientalis (Pamp.) H. Hara were collected monthly from April through October and characterized for composition of secondary metabolite compounds and their phytotoxic effects on seed germination and seedling growth of Achyranthes japonica and Lactuca sativa. The compounds were identified using gas chromatography/ mass spectrometry (GC/MS) coupled with a solvent-free solid injector (SFSI). GC/MS analyses of all samples revealed qualitative variability in the composition of secondary metabolites. The greatest number of compounds was identified in July (56) followed by September (30) and April (24), and the lowest number was found in June (2) and August (2). Among 92 compounds, the major compounds were various terpenes (23) (mono-, sesqui, di-, and tri-terpenes) followed by heterocyclic compounds (18) and hydrocarbons (14). The higher the concentration of the secondary metabolites, the lower the seed germination and seedling growth of A. japonica and L. sativa. Plant samples collected in July and August were most detrimental. Taken together, variability in the secondary metabolites compounds of A. princeps var. orientalis was verified during different seasons, and the compounds were successfully identified by a combination of SFSI and GC/MS. Notably, the antimicrobial and antioxidative effects were inconsistent throughout the various seasons.

Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight

Al-Mamun, Hawlader A.,Kwan, Paul,Clark, Samuel A.,Ferdosi, Mohammad H.,Tellam, Ross,Gondro, Cedric BioMed Central 2015 Genetics, selection, evolution Vol.47 No.1

<P><B>Background</B></P><P>Body weight (BW) is an important trait for meat production in sheep. Although over the past few years, numerous quantitative trait loci (QTL) have been detected for production traits in cattle, few QTL studies have been reported for sheep, with even fewer on meat production traits. Our objective was to perform a genome-wide association study (GWAS) with the medium-density Illumina Ovine SNP50 BeadChip to identify genomic regions and corresponding haplotypes associated with BW in Australian Merino sheep.</P><P><B>Methods</B></P><P>A total of 1781 Australian Merino sheep were genotyped using the medium-density Illumina Ovine SNP50 BeadChip. Among the 53 862 single nucleotide polymorphisms (SNPs) on this array, 48 640 were used to perform a GWAS using a linear mixed model approach. Genotypes were phased with <I>hsphase</I>; to estimate SNP haplotype effects, linkage disequilibrium blocks were identified in the detected QTL region.</P><P><B>Results</B></P><P>Thirty-nine SNPs were associated with BW at a Bonferroni-corrected genome-wide significance threshold of 1 %. One region on sheep (<I>Ovis aries</I>) chromosome 6 (OAR6) between 36.15 and 38.56 Mb, included 13 significant SNPs that were associated with BW; the most significant SNP was OAR6_41936490.1 (<I>P</I> = 2.37 × 10<SUP>−16</SUP>) at 37.69 Mb with an allele substitution effect of 2.12 kg, which corresponds to 0.248 phenotypic standard deviations for BW. The region that surrounds this association signal on OAR6 contains three genes: <I>leucine aminopeptidase 3</I> (<I>LAP3</I>), which is involved in the processing of the oxytocin precursor; <I>NCAPG non-SMC condensin I complex, subunit G</I> (<I>NCAPG)</I>, which is associated with foetal growth and carcass size in cattle; and <I>ligand dependent nuclear receptor corepressor-like</I> (<I>LCORL</I>), which is associated with height in humans and cattle.</P><P><B>Conclusions</B></P><P>The GWAS analysis detected 39 SNPs associated with BW in sheep and a major QTL region was identified on OAR6. In several other mammalian species, regions that are syntenic with this region have been found to be associated with body size traits, which may reflect that the underlying biological mechanisms share a common ancestry. These findings should facilitate the discovery of causative variants for BW and contribute to marker-assisted selection.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12711-015-0142-4) contains supplementary material, which is available to authorized users.</P>

Fracture toughness of amorphus SiC thin films using nanoindentation and simulation

Mamun, M.A.,Elmustafa, A.A. Techno-Press 2020 Advances in materials research Vol.9 No.1

Fracture toughness of SiC on Si thin films of thicknesses of 150, 750, and 1500 nm were measured using Agilent XP nanoindenter equipped with a Dynamic Control Module (DCM) in Load Control (LC) and Continuous Stiffness Method (CSM) protocols. The fracture toughness of the Si substrate is also measured. Nanovision images implied that indentations into the films and well deep into the Si caused cracks to initiate at the Si substrate and propagate upward to the films. The composite fracture toughness of the SiC/Si was measured and the fracture toughness of the SiC films was determined based on models that estimate film properties from substrate properties. The composite hardness and modulus of the SiC films were measured as well. For the DCM, the hardness decreases from an average of 35 GPa to an average of 13 GPa as the film thick increases from 150 nm to 1500 nm. The hardness and moduli of the films depict the hardness and modulus of Si at deep indents of 12 and 200 GPa respectively, which correlate well with literature hardness and modulus values of Si. The fracture toughness values of the films were reported as 3.2 MPa√m.

Genetic tests for estimating dairy breed proportion and parentage assignment in East African crossbred cattle

Strucken, Eva M.,Al-Mamun, Hawlader A.,Esquivelzeta-Rabell, Cecilia,Gondro, Cedric,Mwai, Okeyo A.,Gibson, John P. BioMed Central 2017 Genetics, selection, evolution Vol.49 No.1

<P><B>Background</B></P><P>Smallholder dairy farming in much of the developing world is based on the use of crossbred cows that combine local adaptation traits of indigenous breeds with high milk yield potential of exotic dairy breeds. Pedigree recording is rare in such systems which means that it is impossible to make informed breeding decisions. High-density single nucleotide polymorphism (SNP) assays allow accurate estimation of breed composition and parentage assignment but are too expensive for routine application. Our aim was to determine the level of accuracy achieved with low-density SNP assays.</P><P><B>Methods</B></P><P>We constructed subsets of 100 to 1500 SNPs from the 735k-SNP Illumina panel by selecting: (a) on high minor allele frequencies (MAF) in a crossbred population; (b) on large differences in allele frequency between ancestral breeds; (c) at random; or (d) with a differential evolution algorithm. These panels were tested on a dataset of 1933 crossbred dairy cattle from Kenya/Uganda and on crossbred populations from Ethiopia (N = 545) and Tanzania (N = 462). Dairy breed proportions were estimated by using the ADMIXTURE program, a regression approach, and SNP-best linear unbiased prediction, and tested against estimates obtained by ADMIXTURE based on the 735k-SNP panel. Performance for parentage assignment was based on opposing homozygotes which were used to calculate the separation value (<I>sv</I>) between true and false assignments.</P><P><B>Results</B></P><P>Panels of SNPs based on the largest differences in allele frequency between European dairy breeds and a combined Nelore/N’Dama population gave the best predictions of dairy breed proportion (r<SUP>2</SUP> = 0.962 to 0.994 for 100 to 1500 SNPs) with an average absolute bias of 0.026. Panels of SNPs based on the highest MAF in the crossbred population (Kenya/Uganda) gave the most accurate parentage assignments (<I>sv</I> = −1 to 15 for 100 to 1500 SNPs).</P><P><B>Conclusions</B></P><P>Due to the different required properties of SNPs, panels that did well for breed composition did poorly for parentage assignment and vice versa. A combined panel of 400 SNPs was not able to assign parentages correctly, thus we recommend the use of 200 SNPs either for breed proportion prediction or parentage assignment, independently.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12711-017-0342-1) contains supplementary material, which is available to authorized users.</P>

Determination of Methoxyfenozide Residues in Water and Soil by Liquid Chromatography: Evaluation of its Environmental Fate Under Laboratory Conditions

Choi, Jeong-Heui,Mamun, M.I.R.,Shin, Eun-Ho,Kim, Hee-Kwon,El-Aty, A.M. Abd,Shim, Jae-Han Korean Society of ToxicologyKorea Environmental Mu 2008 Toxicological Research Vol.25 No.4

Pesticide residues play several key roles as environmental and food pollutants and it is crucial to develop a method for the rapid determination of pesticide residues in environments. In this study, a simple, effective, and sensitive method has been developed for the quantitative analysis of methoxyfenozide in water and soil when kept under laboratory conditions. The content of methoxyfenozide in water and soil was analyzed by first purifying the compound through liquid-liquid extraction and partitioning followed by florisil gel filtration. Upon the completion of the purification step the residual levels were monitored through high performance liquid chromatography(HPLC) using a UV absorbance detector. The average recoveries of methoxyfenozide from three replicates spiked at two different concentrations and were ranged from 83.5% to 110.3% and from 98.1% to 102.8% in water and soil, respectively. The limits of detection(LODs) and limits of quantitation(LOQs) were 0.004 vs. 0.012 ppm and 0.008 vs. 0.024 ppm, respectively. The method was successfully applied to evaluate the behavioral fate of a 21% wettable powder(WP) methoxyfenozide throughout the course of 14 days. A first-order model was found to accurately fit the dissipation of methoxyfenozide in water with and a $DT_{50}$ value of 3.03 days was calculated from the fit. This result indicates that methoxyfenozide dissipates rapidly and does not accumulate in water.

T-RFLP reveals high &bgr;-Proteobacteria diversity in microbial fuel cells enriched with domestic wastewater

Lefebvre, O.,Ha Nguyen, T.T.,Al-Mamun, A.,Chang, I.S.,Ng, H.Y. Blackwell Publishing Ltd 2010 Journal of applied microbiology Vol.109 No.3

<P>Abstract</P><P>Aims: </P><P>To assess the biodiversity of a large number of microbial fuel cell (MFC) anodes from a variety of MFC designs, all enriched with domestic wastewater, using a molecular fingerprinting method.</P><P>Methods and Results: </P><P>We optimized a protocol allowing the rapid characterization of MFC communities using terminal restriction fragment length polymorphism (T-RFLP) with two different sets of primers and a varying number of restriction enzymes. This protocol was further validated by direct comparison with bacterial clone libraries. Twenty-one MFC anodes were analysed by T-RFLP. We also provided a statistical comparison with other bacterial communities from environments sharing common features.</P><P>Conclusions: </P><P>Bacterial communities were dominated by &bgr;-Proteobacteria, mostly belonging to the Burkholderiales order, that are known to play an active role in the cycle of metals such as iron and manganese. This property may allow them to properly pass electrons to the anode of an MFC.</P><P>Significance and Impact of the Study: </P><P>Unlike other groups, &bgr;-Proteobacteria have seldom been acknowledged as potentially efficient electrochemically active bacteria (EAB) in MFCs. Yet, they are plentiful in natural environments like biocorrosion biofilms and acid mine drainages that consequently show some potential for MFC enrichment.</P>

Analytical procedure to simultaneously measure trace amounts of trenbolone acetate and β-trenbolone residues in porcine muscle using HPLC-UVD and MS

Liu, Xue,Abd El-Aty, A. M.,Choi, Jeong-Heui,Khay, Sathya,Mamun, M. I. R.,Jeon, Hyang-Rang,Lee, Soon-Ho,Chang, Byung-Joon,Lee, Chi-Ho,Shin, Ho-Chul,Shim, Jae-Han WILEY-VCH Verlag 2008 Journal of Separation Science Vol.31 No.22

<P>The current study was undertaken to validate the performance for the determination of both TBA and β-trenbolone (β-TB) residues in porcine muscle at concentrations required to monitor compliance with the maximum residue limit (MRL). The method involves a one phase liquid–liquid extraction, cleanup with low-temperature fat precipitation, separation of the respective compounds by HPLC on a Capcell pak C<SUB>18</SUB> column, use of a methanol–water isocratic system as an eluent, and measurement by UV absorbance detection at 340 nm. Both compounds were confirmed using LC-MS/MS with electrospray interface (ESI) and a triple quadrupole (QqQ) analyzer. The method was found to be precise and accurate, with a linearity range of 1–10 μg/kg (r<SUP>2</SUP> >0.973). The intra- and interday precision showed good reproducibility with RSDs ⪇13.25%. The LODs were 0.12 and 0.22 μg/kg, and the LOQs were 0.37 and 0.66 μg/kg, for TBA and β-TB, respectively. The applicability of the method was demonstrated by analyzing real samples collected from major cities in the Republic of Korea. No residues of the selected compounds were detected in any of the samples. The advantages of our method are that it is: selective, sensitive, requires a short time for analysis (13 min), and performs simple sample extraction and clean-up procedure with low-temperature fat precipitation as compared to the previously published methods.</P>

Determination of Methoxyfenozide Residues in Water and Soil by Liquid Chromatography

Jeong-Heui Choi,M. I. R. Mamun,Eun-Ho Shin,Hee Kwon Kim,A. M. Abd El-Aty,Jae-Han Shim 한국독성학회 2008 Toxicological Research Vol.24 No.3

Pesticide residues play several key roles as environmental and food pollutants and it is crucial to develop a method for the rapid determination of pesticide residues in environments. In this study, a simple, effective, and sensitive method has been developed for the quantitative analysis of methoxyfenozide in water and soil when kept under laboratory conditions. The content of methoxyfenozide in water and soil was analyzed by first purifying the compound through liquid-liquid extraction and partitioning followed by florisil gel filtration. Upon the completion of the purification step the residual levels were monitored through high performance liquid chromatography (HPLC) using a UV absorbance detector. The average recoveries of methoxyfenozide from three replicates spiked at two different concentrations and were ranged from 83.5% to 110.3% and from 98.1% to 102.8% in water and soil, respectively. The limits of detection (LODs) and limits of quantitation (LOQs) were 0.004 vs. 0.012 ppm and 0.008 vs. 0.024 ppm, respectively. The method was successfully applied to evaluate the behavioral fate of a 21% wettable powder (WP) methoxyfenozide throughout the course of 14 days. A first-order model was found to accurately fit the dissipation of methoxyfenozide in water with and a DT50 value of 3.03 days was calculated from the fit. This result indicates that methoxyfenozide dissipates rapidly and does not accumulate in water.

Roles of Negatively-charged Heavy Ions and Nonextensivity in Cylindrical and Spherical Dust-ion-acoustic Shock Waves

S. A. Ema,M. Ferdousi,S. Sultana,A. A. Mamun 한국물리학회 2015 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.66 No.11

A rigorous theoretical investigation has been carried out on the propagation of nonplanar (cylindrical and spherical) dust-ion-acoustic (DIA) waves in an unmagnetized dusty multi-ion plasma system containing nonextensive electrons, inertial negatively-charged heavy ions, positively-charged Maxwellian light ions, and negatively-charged stationary dust. The well-known reductive perturbation technique has been used to derive the modified Burgers-type equation (which describes the shock wave’s properties), and its numerical solution is obtained. The basic features (viz. polarity, amplitude, width, etc.) of the cylindrical and the spherical DIA shock waves are investigated. The basic features of the cylindrical and the spherical DIA shock waves are found to have been significantly modified in a way that depends on the intrinsic parameters (viz. electron nonextensivity, heavy-ion’s kinematic viscosity, heavy-to-light-ion number density ratio, electron-to-light-ion temperature ratio, etc.) of the considered plasma system. The characteristics of the cylindrical and the spherical DIA shock waves are observed to be qualitatively different from those of planar ones.