• Advances in environmental research
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• v.6 no.2
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• pp.127-137
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• 2017

Cotton is the major fiber crop in Pakistan that accounts for 2% of total national gross domestic product (GDP). After picking of cotton, the dry stalks are major organic waste that has no fate except burning to cook food in villages. Present research focuses use of cotton stalks as feedstock for biochar production, its characterization and effects on soil characteristics. Dry cotton stalks collected from agricultural field of Bahauddin Zakariya University, Multan, Pakistan were combusted under anaerobic conditions at $450^{\circ}C$. The physicochemical analysis of biochar and cotton stalks show higher values of % total carbon, phosphorus and potassium concentrations in biochar as compared to cotton stalks. The concentration of nitrogen was decreased in biochar. Similarly biochar had greater values of fixed carbon that suggest its role for carbon sequestration and as a soil amendment. The fourier transformation infrared spectroscopic spectra (FTIR) of cotton stalks and biochar exposed more acidic groups in biochar as compared to cotton stalks. The newly developed functional groups in biochar have vital role in increasing surface properties, cation exchange capacity, and water holding capacity, and are responsible for heavy metal remediation in contaminated soil. In a further test, results show increase in the water holding capacity and nutrient retention by a sandy soil amended with biochar. It is concluded that cotton stalks can be effectively used to prepare biochar.

• Journal of Microbiology and Biotechnology
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• v.23 no.6
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• pp.759-765
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• 2013

The gene encoding squalene synthase (SQS) of the lipid-producing heterotrophic microalga Aurantiochytrium sp. KRS101 was cloned and characterized. The krsSQS gene is 1,551 bp in length and has two exons and one intron. The open reading frame of the gene is 1,164 bp in length, yielding a polypeptide of 387 predicted amino acid residues with a molecular mass of 42.7 kDa. The deduced krsSQS sequence shares at least four conserved regions known to be required for SQS enzymatic activity in other species. The protein, tagged with $His_6$, was expressed into soluble form in Escherichia coli. The purified protein catalyzed the conversion of farnesyl diphosphate to squalene in the presence of NADPH and $Mg^{2+}$. This is the first report on the characterization of an SQS from a Thraustochytrid microalga.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.6
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• pp.880-884
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• 2001

Rumen microbiology research has undergone several evolutionary steps: the isolation and nutritional characterization of readily cultivated microbes; followed by the cloning and sequence analysis of individual genes relevant to key digestive processes; through to the use of small subunit ribosomal RNA (SSU rRNA) sequences for a cultivation-independent examination of microbial diversity. Our knowledge of rumen microbiology has expanded as a result, but the translation of this information into productive alterations of ruminal function has been rather limited. For instance, the cloning and characterization of cellulase genes in Escherichia coli has yielded some valuable information about this complex enzyme system in ruminal bacteria. SSU rRNA analyses have also confirmed that a considerable amount of the microbial diversity in the rumen is not represented in existing culture collections. However, we still have little idea of whether the key, and potentially rate-limiting, gene products and (or) microbial interactions have been identified. Technologies allowing high throughput nucleotide and protein sequence analysis have led to the emergence of two new fields of investigation, genomics and proteomics. Both disciplines can be further subdivided into functional and comparative lines of investigation. The massive accumulation of microbial DNA and protein sequence data, including complete genome sequences, is revolutionizing the way we examine microbial physiology and diversity. We describe here some examples of our use of genomics- and proteomics-based methods, to analyze the cellulase system of Ruminococcus flavefaciens FD-1 and explore the genome of Ruminococcus albus 8. At Illinois, we are using bacterial artificial chromosome (BAC) vectors to create libraries containing large (>75 kbases), contiguous segments of DNA from R. flavefaciens FD-1. Considering that every bacterium is not a candidate for whole genome sequencing, BAC libraries offer an attractive, alternative method to perform physical and functional analyses of a bacterium's genome. Our first plan is to use these BAC clones to determine whether or not cellulases and accessory genes in R. flavefaciens exist in clusters of orthologous genes (COGs). Proteomics is also being used to complement the BAC library/DNA sequencing approach. Proteins differentially expressed in response to carbon source are being identified by 2-D SDS-PAGE, followed by in-gel-digests and peptide mass mapping by MALDI-TOF Mass Spectrometry, as well as peptide sequencing by Edman degradation. At Ohio State, we have used a combination of functional proteomics, mutational analysis and differential display RT-PCR to obtain evidence suggesting that in addition to a cellulosome-like mechanism, R. albus 8 possesses other mechanisms for adhesion to plant surfaces. Genome walking on either side of these differentially expressed transcripts has also resulted in two interesting observations: i) a relatively large number of genes with no matches in the current databases and; ii) the identification of genes with a high level of sequence identity to those identified, until now, in the archaebacteria. Genomics and proteomics will also accelerate our understanding of microbial interactions, and allow a greater degree of in situ analyses in the future. The challenge is to utilize genomics and proteomics to improve our fundamental understanding of microbial physiology, diversity and ecology, and overcome constraints to ruminal function.

• Proceedings of the Materials Research Society of Korea Conference
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• 2012.05a
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• pp.68.1-68.1
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• 2012

The best part of graphene is - charge-carriers in it are mass less particles which move in near relativistic speeds. Comparing to other materials, electrons in graphene travel much faster - at speeds of $10^8cm/s$. A graphene sheet is pure enough to ensure that electrons can travel a fair distance before colliding. Electronic devices few nanometers long that would be able to transmit charge at breath taking speeds for a fraction of power compared to present day CMOS transistors. Many researches try to check a possibility to make it a perfect replacement for silicon based devices. Graphene has shown high potential to be used as interconnects in the field of high frequency electrical devices. With all those advantages of graphene, we demonstrate characteristics of electrical and optical properties of graphene such as the effect of graphene geometry on the microwave properties using the measurements of S-parameter in range of 500 MHz - 40 GHz at room temperature condition. We confirm that impedance and resistance decrease with increasing the number of graphene layer and w/L ratio. This result shows proper geometry of graphene to be used as high frequency interconnects. This study also presents the optical properties of graphene oxide (GO), which were deposited in different substrate, or influenced by oxygen plasma, were confirmed using different characterization techniques. 4-6 layers of the polycrystalline GO layers, which were confirmed by High resolution transmission electron microscopy (HRTEM) and electron diffraction analysis, were shown short range order of crystallization by the substrate as well as interlayer effect with an increase in interplanar spacing, which can be attributed to the presence of oxygen functional groups on its layers. X-ray photoelectron Spectroscopy (XPS) and Raman spectroscopy confirms the presence of the $sp^2$ and $sp^3$ hybridization due to the disordered crystal structures of the carbon atoms results from oxidation, and Fourier Transform Infrared spectroscopy (FTIR) and XPS analysis shows the changes in oxygen functional groups with nature of substrate. Moreover, the photoluminescent (PL) peak emission wavelength varies with substrate and the broad energy level distribution produces excitation dependent PL emission in a broad wavelength ranging from 400 to 650 nm. The structural and optical properties of oxygen plasma treated GO films for possible optoelectronic applications were also investigated using various characterization techniques. HRTEM and electron diffraction analysis confirmed that the oxygen plasma treatment results short range order crystallization in GO films with an increase in interplanar spacing, which can be attributed to the presence of oxygen functional groups. In addition, Electron energy loss spectroscopy (EELS) and Raman spectroscopy confirms the presence of the $sp^2$ and $sp^3$ hybridization due to the disordered crystal structures of the carbon atoms results from oxidation and XPS analysis shows that epoxy pairs convert to more stable C=O and O-C=O groups with oxygen plasma treatment. The broad energy level distribution resulting from the broad size distribution of the $sp^2$ clusters produces excitation dependent PL emission in a broad wavelength range from 400 to 650 nm. Our results suggest that substrate influenced, or oxygen treatment GO has higher potential for future optoelectronic devices by its various optical properties and visible PL emission.

• Journal of Microbiology
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• v.45 no.2
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• pp.153-157
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• 2007

5-enolpyruvylshikimate-3-phosphate synthase (EPSP synthase, EC 2.5.1.19) is the sixth enzyme in the shikimate pathway which is essential for the synthesis of aromatic amino acids and many secondary metabolites. The enzyme is widely involved in glyphosate tolerant transgenic plants because it is the primary target of the nonselective herbicide glyphosate. In this study, the Dunaliella salina EPSP synthase gene was cloned by RT-PCR approach. It contains an open reading frame encoding a protein of 514 amino acids with a calculated molecular weight of 54.6 KDa. The derived amino acid sequence showed high homology with other EPSP synthases. The Dunaliella salina EPSP synthase gene was expressed in Escherichia coli and the recombinant EPSP synthase were identified by functional complementation assay.

• Molecules and Cells
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• v.39 no.5
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• pp.367-374
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• 2016

Since the RNA world hypothesis was proposed, a large number of regulatory noncoding RNAs (ncRNAs) have been identified in many species, ranging from microorganisms to mammals. During the characterization of these newly discovered RNAs, RNAs having both coding and noncoding functions were discovered, and these were considered bifunctional RNAs. The recent use of computational and high-throughput experimental approaches has revealed increasing evidence of various sources of bifunctional RNAs, such as protein-coding mRNAs with a noncoding isoform and long ncRNAs bearing a small open reading frame. Therefore, the genomic diversity of Janusfaced RNA molecules that have dual characteristics of coding and noncoding indicates that the functional roles of RNAs have to be revisited in cells on a genome-wide scale. Such studies would allow us to further understand the complex gene-regulatory network in cells. In this review, we discuss three major genomic sources of bifunctional RNAs and present a handful of examples of bifunctional RNA along with their functional roles.

• Bulletin of the Korean Chemical Society
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• v.32 no.spc8
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• pp.3045-3050
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• 2011

The synthesis of copolymers containing thiophene and benzimidazole unit by Stille polymerization is reported. The polymers with many unsubstituted thiophene units in the backbone have been reported to show low solubility, which has been a problem for spin-coating for the device fabrication. In dihexyl-2H-benzimidazole, the sulfur at 2-position of BT unit was replaced with dialkyl substituted carbon, while keeping the 1,2-quinoid form, to improve the solubility of the polymers. The PL emission spectra of the PHBIT1, PHBIT2 and PHBIT3 in chloroform solutions show maximum peaks at 500~561 nm. In thin films, maximum peaks of the PHBITs appeared at 529, 562 and 569 nm, respectively. The EL emission maxima of the PHBIT1 and PHBIT2 appear at around 588 and 576 nm, respectively. The current density and maximum luminescence of the LED with the configuration of ITO/PEDOT/ PHBIT2/Ca/Al are 552 mA/$cm^2$ and 46 cd/$m^2$, respectively.

• Proceedings of the Korean Vacuum Society Conference
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• 2015.08a
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• pp.109.1-109.1
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• 2015

Understanding the reaction mechanisms and structures underlying the adsorption of biomolecules on semiconductors is important for functionalizing semiconductor surfaces for various bioapplications. Herein, we describe the characteristic behavior of a primary nucleobase adsorbed on the semiconductor Ge(100). The adsorption configuration of guanine, a primary nucleobase found in DNA and RNA, on the semiconductor Ge(100) at an atomic level was investigated using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. When adsorbed on Ge(100) at room temperature, guanine appears dark in STM images, indicating that the adsorption of guanine on Ge(100) occurs through N-H dissociation. In addition, DFT calculations revealed that "N(1)-H dissociation through an O dative bonded structure" is the most favorable adsorption configuration of all the possible ones. We anticipate that the characterization of guanine adsorbed on Ge(100) will contribute to the development of semiconductor-based biodevices.

• BMB Reports
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• v.34 no.2
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• pp.102-108
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• 2001

A time-dependent folding process was used to determine whether or not protein disulfide isomerase (PDI) plays an important role in the maturation of nascent lactoferrin polypeptides. Interaction between lactoferrin and PDI was analyzed according to the co-immunoprecipitation of the two proteins. The results indicate that lactoferrin folding requires a significant interaction with PDI and its binding is relatively brief compared to other nascent polypeptides. The amount of lactoferrin interacting with PDI increases up to half a minute and sharply decreases beyond this time point. During the refolding process that follows reduction by DTT, lactoferrin polypeptides heavily interact with PDI and the interaction period was extended compared to the normal folding process. In terms of the temperature effect on PDI-lactoferrin interaction, PDI binds to lactoferrin polypeptides longer at a lower temperature (here, $25^{\circ}C$) than $37^{\circ}C$. The lactoferrin-PDI interaction was also studied in vitro. According to the in vitro experiment data, PDI was still functional in cell lysates assisting lactoferrin folding into the mature form. PDI interacts with lactoferrin polypeptides for an extended period during the folding in vitro. During the refolding process in vitro, intermolecular aggregates and refolding oligomers matured into a functional form after PDI binds to the lactoferrin. These results suggest that PDI provides a prolonged chaperoning activity in the refolding processes and that there appears to be a greater requirement for PDI chaperone activity in the refolding of lactoferrin polypeptides.

• Journal of Microbiology and Biotechnology
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• v.15 no.4
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• pp.694-700
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• 2005

Defects in the mitotic spindle or in the attachment of chromosomes to the spindle are believed to release an activated form of spindle checkpoint complex that inhibits APC-dependent ubiquitination and subsequently arrests the cell cycle at metaphase. When the spindle assembly is disrupted, the fission yeast mitotic arrest deficient (mad) mutants fail to arrest and rapidly lose viability. To enhance our understanding of the molecular mechanisms for the pathway of checkpoint function, the functional characterizations of Mad 1 p from Schizosaccharomyces pombe involved in this process have been carried out. Yeast two-hybrid and various deletion analyses of S. pombe Mad1 p reveal that the C terminus of Mad1p is critical for the binding of Mad2p and maintenance of Mad 1 p-Mad2p interaction. In addition, it was found. that the Mad1p region (residues 206-356) is essential for Mad1p-other checkpoint components. Mad1p truncating this region is sufficient to bind Mad2p but abolishes the checkpoint function, indicating that the checkpoint function is necessary for interaction of Mad 1 p-other checkpoint components. The possible functions of S. pombe Mad1p at the cell cycle checkpoint are discussed.