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Nucleotide Sequence, Structural Investigation and Homology Modeling Studies of a Ca2+-independent α-amylase with Acidic pH-profile

  • Sajedi, Reza Hassan;Taghdir, Majid;Naderi-Manesh, Hossein;Khajeh, Khosro;Ranjbar, Bijan
    • BMB Reports
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    • v.40 no.3
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    • pp.315-324
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    • 2007
  • The novel $\alpha$-amylase purified from locally isolated strain, Bacillus sp. KR-8104, (KRA) (Enzyme Microb Technol; 2005; 36: 666-671) is active in a wide range of pH. The enzyme maximum activity is at pH 4.0 and it retains 90% of activity at pH 3.5. The irreversible thermoinactivation patterns of KRA and the enzyme activity are not changed in the presence and absence of $Ca^{2+}$ and EDTA. Therefore, KRA acts as a $Ca^{2+}$-independent enzyme. Based on circular dichroism (CD) data from thermal unfolding of the enzyme recorded at 222 nm, addition of $Ca^{2+}$ and EDTA similar to its irreversible thermoinactivation, does not influence the thermal denaturation of the enzyme and its Tm. The amino acid sequence of KRA was obtained from the nucleotide sequencing of PCR products of encoding gene. The deduced amino acid sequence of the enzyme revealed a very high sequence homology to Bacillus amyloliquefaciens (BAA) (85% identity, 90% similarity) and Bacillus licheniformis $\alpha$-amylases (BLA) (81% identity, 88% similarity). To elucidate and understand these characteristics of the $\alpha$-amylase, a model of 3D structure of KRA was constructed using the crystal structure of the mutant of BLA as the platform and refined with a molecular dynamics (MD) simulation program. Interestingly enough, there is only one amino acid substitution for KRA in comparison with BLA and BAA in the region involved in the calcium-binding sites. On the other hand, there are many amino acid differences between BLA and KRA at the interface of A and B domains and around the metal triad and active site area. These alterations could have a role in stabilizing the native structure of the loop in the active site cleft and maintenance and stabilization of the putative metal triad-binding site. The amino acid differences at the active site cleft and around the catalytic residues might affect their pKa values and consequently shift its pH profile. In addition, the intrinsic fluorescence intensity of the enzyme at 350 nm does not show considerable change at pH 3.5-7.0.

Determination of Flood Reduction Alternatives for responding to climate change in Gyeongan Watershed (기후변화 대응을 위한 경안천 유역의 홍수저감 대안 선정)

  • Han, Daegun;Choi, Changhyun;Kim, Duckhwan;Jung, Jaewon;Kim, Jungwook;Kim, Soo Jun
    • Journal of Wetlands Research
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    • v.18 no.2
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    • pp.154-165
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    • 2016
  • Recently, the frequency of extreme rainfall event has increased due to climate change and impermeable area also has increased due to rapid urbanization. Therefore, we ought to prepare countermeasures for flood reduction to reduce the damage. To consider climate change, the frequency based rainfall was calculated according to the aimed period(reference : 1971~2010, Target period I : 2011~2040, Target period II : 2041~2070, Target period III : 2071~2100) and the flood discharge was also calculated by climate change using HEC-HMS model. Also, the flood elevation was calculated by each alternative through HEC-RAS model, setting 5 sizes of drainage pumps and reservoirs respectively. The flood map was constructed using topographical data and flood elevation, and the economic analysis was conducted for reduction of flood damage using Multi dimension - Flood Damage Analysis, MD-FDA. As a result of the analysis on the flood control effect, a head of drainage pump was reduced by 0.06m up to 0.44m while it was reduced by 0.01m up to 1.86m in the case of a detention pond. The flooded area shrunk by up to 32.64% from 0.3% and inundation depth also dropped. As a result of a comparison of the Benefit/Cost index estimated by the economic analysis, detention pond E in period I and pump D in period II and III were deemed appropriate as an alternative for climate change. The results are expected to be used as good practices when implementing the flood control works considering climate change.

Circulating Cell-free miRNA Expression and its Association with Clinicopathologic Features in Inflammatory and Non-Inflammatory Breast Cancer

  • Hamdi, K;Blancato, J;Goerlitz, D;Islam, MD;Neili, B;Abidi, A;Gat, A;Ayed, F Ben;Chivi, S;Loffredo, CA;Jillson, I;Elgaaied, A Benammar;Marrakchi, R
    • Asian Pacific Journal of Cancer Prevention
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    • v.17 no.4
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    • pp.1801-1810
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    • 2016
  • Recent discovery showing the presence of microRNAs (miRNAs) in the circulation sparked interest in their use as potential biomarkers. Our previous studies showed the diagnostic potential of miR-451 as a serological marker for inflammatory breast cancer (IBC), miR-337-5p and miR-30b for non-inflammatory breast cancer (non-IBC). The aim of this study is to investigate the prognostic values of circulating miRNAs by comparing the amounts of 12 circulating miRNAs in the serum of IBC and non-IBC from Tunisian breast cancer patients, and by determinating whether correlated pairs of miRNAs could provide useful information in the diagnosis of IBC and non-IBC patients. TaqMan qPCR was performed to detect circulating expression of miRNAs in serum of 20 IBC, 20 non-IBC and 20 healthy controls. Nonparametric rank Spearman rho correlation coefficient was used to examine the prognostic value of miRNAs and to assess the correlation profile between miRNAs expression. Further, a large number of miRNAs were highly correlated (rho>0.5) in both patients groups and controls. Also, the correlations profiles were different between IBC, non-IBC and healthy controls indicating important changes in molecular pathways in cancer cells. Our results showed that miR-335 was significantly overexpressed in premenopausal non-IBC patients; miR-24 was significantly overexpressed in non-IBC postmenopausal patients. Patients with previous parity had higher serum of miR-342-5p levels than those without. Furthermore, patients with HER2+ IBC present lower serum levels of miR-15a than patients with HER2-disease. Together, these results underline the potential of miRNAs to function as diagnostic and prognostic markers for IBC and non-IBC, with links to the menopausal state, Her2 status and parity.

THE USE OF NEAR INFRARED REFLECTANCE SPECTROSCOPY(NIRS) TO PREDICT CHEMICAL COMPOSITION ON MAIZE SILAGE

  • D.Cozzolino;Fassio, A.;Mieres, J.;Y.Acosta
    • Proceedings of the Korean Society of Near Infrared Spectroscopy Conference
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    • 2001.06a
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    • pp.1610-1610
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    • 2001
  • Microbiological examination of silage is of little value in gauging the outcome of silage, and so chemical analysis is more reliable and meaningful indicator of quality. On the other hand chemical assessments of the principal fermentation products provide an unequivocal basis on which to judge quality. Livestock require energy, protein, minerals and vitamins from their food. While fresh forages provide these essential items, conserved forages on the other hand may be deficient in one or more of them. The aim of the conservation process is to preserve as many of the original nutrients as possible, particularly energy and protein components (Woolford, 1984). Silage fermentation is important to preservation of forage with respect of feeding value and animal performance. Chemical and bacteriological changes in the silo during the fermentation process can affect adversely nutrient yield and quality (Moe and Carr, 1984). Many of the important chemical components of silage must be assayed in fresh or by extraction of the fresh material, since drying either by heat or lyophilisation, volatilises components such as acids or nitrogenous components, or effects conversion to other compounds (Abrams et al., 1987). Maize silage dorms the basis of winter rations for the vast majority of dairy and beef cattle production in Uruguay. Since nutrient intake, particularly energy, from forages is influenced by both voluntary dry matter intake and digestibility; there is a need for a rapid technique for predicting these parameters in farm advisory systems. Near Infrared Reflectance Spectroscopy (NIRS) is increasingly used as a rapid, accurate method of evaluating chemical constituents in cereals and dried forages. For many years NIRS was applied to assess chemical composition in dry materials (Norris et al., 1976, Flinn et al., 1992; Murray, 1993, De Boever et al., 1996, De la Roza et al., 1998). The objectives of this study were (1) to determine the potential of NIRS to assess the chemical composition of dried maize samples and (2) to attempt calibrations on undried samples either for farm advisory systems or for animal nutrition research purposes in Uruguay. NIRS were used to assess the chemical composition of whole - plant maize silage samples (Zea mays, L). A representative population of samples (n = 350) covering a wide distribution in chemical characteristics were used. Samples were scanned at 2 nm intervals over the wavelength range 400-2500 nm in a NIRS 6500 (NIRSystems, Silver Spring, MD, USA) in reflectance mode. Cross validation was used to avoid overfitting of the equations. The optimum calibrations were selected on the basis of minimizing the standard error of cross validation (SECV). The calibration statistics were R$^2$ 0. 86 (SECV: 11.4), 0.90 (SECV: 5.7), 0.90 (SECV: 16.9) for dry matter (DM), crude protein (CP), acid detergent fiber (ADF) in g kg$\^$-1/ on dry matter, respectively for maize silage samples. This work demonstrates the potential of NIRS to analyse whole - maize silage in a wide range of chemical characteristics for both advisory farm and nutritive evaluation.

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Bone marrow stem cells incubated with ellipticine regenerate articular cartilage by attenuating inflammation and cartilage degradation in rabbit model

  • Mohammad Amjad Hossain;Soyeon Lim;Kiran D. Bhilare;Md Jahangir Alam;Baicheng Chen;Ajay Vijayakumar;Hakyoung Yoon;Chang Won Kang;Jong-Hoon Kim
    • Journal of Veterinary Science
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    • v.24 no.6
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    • pp.83.1-83.12
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    • 2023
  • Background: Ellipticine (Ellip.) was recently reported to have beneficial effects on the differentiation of adipose-derived stem cells into mature chondrocyte-like cells. On the other hand, no practical results have been derived from the transplantation of bone marrow stem cells (BMSCs) in a rabbit osteoarthritis (OA) model. Objectives: This study examined whether autologous BMSCs incubated with ellipticine (Ellip.+BMSCs) could regenerate articular cartilage in rabbit OA, a model similar to degenerative arthritis in human beings. Methods: A portion of rabbit articular cartilage was surgically removed, and Ellip.+BMSCs were transplanted into the lesion area. After two and four weeks of treatment, the serum levels of proinflammatory cytokines, i.e., tumor necrosis factor α (TNF-α) and prostaglandin E2 (PGE2), were analyzed, while macroscopic and micro-computed tomography (CT) evaluations were conducted to determine the intensity of cartilage degeneration. Furthermore, immuno-blotting was performed to evaluate the mitogen-activated protein kinases, PI3K/Akt, and nuclear factor-κB (NF-κB) signaling in rabbit OA models. Histological staining was used to confirm the change in the pattern of collagen and proteoglycan in the articular cartilage matrix. Results: The transplantation of Ellip.+BMSCs elicited a chondroprotective effect by reducing the inflammatory factors (TNF-α, PGE2) in a time-dependent manner. Macroscopic observations, micro-CT, and histological staining revealed articular cartilage regeneration with the downregulation of matrix-metallo proteinases (MMPs), preventing articular cartilage degradation. Furthermore, histological observations confirmed a significant boost in the production of chondrocytes, collagen, and proteoglycan compared to the control group. Western blotting data revealed the downregulation of the p38, PI3K-Akt, and NF-κB inflammatory pathways to attenuate inflammation. Conclusions: The transplantation of Ellip.+BMSCs normalized the OA condition by boosting the recovery of degenerated articular cartilage and inhibiting the catabolic signaling pathway.

Clinical Study on Hemolytic Uremic Syndrome in Children: Review of 23 Cases (소아 용혈성 요독 증후군 23예에 대한 임상적 고찰)

  • Oh Seungjin;Yook Jinwon;Kim Ji Hong;Kim Pyung-Kil
    • Childhood Kidney Diseases
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    • v.4 no.2
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    • pp.136-143
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    • 2000
  • Purpose : The hemolytic uremic syndrome (HUS) is characterized by microangiopathic hemolytic anemia thrombocytopenia, and acute renal failure. It is ole of tile most common cause of acute renal failure in children but few reports are available in Korea. Thus we investigated the 23 patients diagnosed as HUS during last 14 years. Method : We retrospectively investigated the etiologic factor, clinical manifestations laboratory findings, treatment modalities, and final outcomes of the patients. Then patients were divided into two groups according to outcome, md comparison was performed. Group A(8) comprised patients who progressed to end-stage renal disease or expired. Group B(15) comprised patients who completely recovered after dialysis treatment. Result The number of patients aged less than 4 years were 17; between 5 and 10 were 4 and more than 10 were 2. The gende ratio was M:F=2 : 1. The etiologic factors were as follows: acute gastroenteritis in 14 patients including 4 bloody diarrhea, upper respiratory tract infection in 7 patients, and 1 patient with herbal mediation. The overall mortality rate was 22$\%$: 2 patients died of US complications, 2 patients died of sepsis, and 1 patient died of pulmonary hemorrhage. Group A (Hb 4.8${\pm}$1.2 g/dL) showed lower value in hemoglobin than group B (Hb 6.3${\pm}$1.7 g/dL) during hospital stay (P< 0.05), And the time interval between tile disease onset and dialysis treatment was significantly longer in group A ($11.9{\pm}9.1\;days\;vs\;2.8{\pm}2.1\;days$) (P< 0.05). Conclusion : Overall mortality rate was 22$\%$. Low hemoglobin value and the prolonged time interval between the disease onset and dialysis treatment were related with poor prognosis. So early diagnosis and appropriate intensive care including dialysis treatment is essential to achieve better outcome in children.

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The Effects on Dose Distribution Characteristics by Changing Beam Tuning Parameters of Digital Linear Accelerator in Medicine (의료용 디지털 선형가속기의 빔조정 인자변화가 선량분포특성에 미치는 영향)

  • 박현주;이동훈;이동한;권수일;류성렬;지영훈
    • Progress in Medical Physics
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    • v.10 no.1
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    • pp.17-22
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    • 1999
  • INJ-I, INJ-E, PFN, BMI, and PRF were selected among the various factors which constitute a digital linear accelerator to find effects on the dose distribution by changing current and voltage within the permitted scale which Mevatron automatically maintained. We measured the absorbed dose using an ion chamber, analyzed the waveform of beam output using an oscilloscope, and measured symmetry and flatness using a dosimetry system. An RFA plus (Scanditronix, Sweden) device was used as a dosimetry system. Then an 0.6cc ion chamber (PR06C, USA), an electrometer (Capintec192, USA), and an oscilloscope (Tektronix, USA) were employed to measure the changes on the dose distribution characteristics by changing the beam-tuning parameters. When the currents and the voltages of INJ-I, INJ-E, PFN, BMI, and PRF were modified, we were able to see the notable change on the dose rate by examining the change of the output pulse using the oscilloscope and by measuring them using the ion chamber. However, the results of energy and flatness graph from RF A plus were almost identical. The factors had fine differences: INJ-I, INJ-E, PFN, BMI, and PRF had 0.01∼0.02% differences in D10/D20, 0.1∼0.2 % differences in symmetry, and 0.1∼0.4% differences in flatness. Since Mevatron controlled itself automatically to keep the reference value of the factor, it was not able to see large differences in the dose distribution. There were fine differences on the dose rate distribution when the voltage and the currents of the digitized factors were modified Nonetheless, a basic operational management information was achieved.

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Antimicrobial Drug Resistance and R-plasmid of Salmonella species (Salmonella 균속의 항균제 내성 및 R-plasmid)

  • Lee Myung-Won;Chung Tae-Wha;Lee Yun-Tai;Kang Jeung-bok
    • Journal of environmental and Sanitary engineering
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    • v.3 no.2 s.5
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    • pp.23-41
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    • 1988
  • Two hundred and eighty-six strains of Salmonella species were isolated from the twelve provincial institutes of health and 19 general hospitals of urban and rural areas in Korea from January to December in 1986. The antimicrobial susceptibility test of these cultures was done by the method of agar diluton. The resistance frequency of Salmonella cultures was $29.7\%$. Among these resistant cultures, the most provalent resistance pattern of Salmonella was ampicillin, carbenicillin, chloramphenicol, tetracycline, streptomycin, and its resistance frequency was $15\%$. In plasmid profile of resistance strains, average number of plasmid harboring in Salmonella was 1-4 and molecular weight of plasmid ranged 1.6 to 70 megadalton (Md.). Plasmid pattern of strains isolated from Seoul and Kang-won showed the same or similar profiles. Plasmid pattern was identical in the same resistance pattern.

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Effect of Essential and Nonessential Amino Acids in North Carolina State University (NCSU)-23 Medium on Development of Porcine In vitro Fertilized Embryos

  • Hashem, Md. Abul;Bhandari, Dilip P.;Hossein, Mohammad Shamim;Jeong, Yeon Woo;Kim, Sue;Kim, Ji-Hye;Koo, Ok-Jae;Park, Seon Mi;Lee, Eu Gine;Park, Sun Woo;Kang, Sung Keun;Lee, Byeong Chun
    • Asian-Australasian Journal of Animal Sciences
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    • v.20 no.5
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    • pp.693-700
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    • 2007
  • The present study was conducted to examine the effect of different levels of essential and nonessential amino acid in NCSU-23 medium on the in vitro-produced porcine embryo as it develops from the zygote to the blastocyst stage. Four experiments were performed, each with a completely randomized design involving 5 to 8 replications of treatments. In order to know the effect of nonessential amino acids in NCSU-23 medium, 0, 5, 10 and $20{\mu}/ml$ MEM were supplemented there to, (Exp. 1) and the medium was supplemented with same level of essential amino acids (Exp. 2). The combined effect of nonessential (0, 5, 10 and $20{\mu}/ml$ MEM) and essential amino acids (0, 5, 10 and $10{\mu}/ml$ MEM) in NCSU-23 medium (Exp. 3), first 72 h with non-essential amino acids (at 0, 5, 10 and $20{\mu}/ml$ MEM), and last 4 d with essential amino acids with the same level as NEAA (Exp. 4) were examined. The embryo development was monitored and the quality of blastocysts was evaluated by counting the number of total cells and determining the ratio of inner cell mass (ICM) to trophoectoderm (TE) cells. When Eagle's nonessential amino acids (MEM) added to NCSU-23 medium, it significantly increased the likelihood of development to the 2- to 4-cell stage and subsequent blastocyst development. Supplementation of different levels of essential amino acids in the NCSU-23 medium decreased cleavage rate, rate of morula and blastocyst development and the number of ICMs. In the case of the combined effect of essential and nonessential amino acids, better and significant results were found for blastocysts, hatching blastocysts and for ICM numbers which were also dose dependent. With respect to the biphasic effect of nonessential and essential amino acids, nonessential amino acids increased cleavage whereas essential amino acids increased the total cell number. Neither the nonessential nor the essential group of amino acids, on their own, affected blastocyst cell number or the differentiation of cells in the blastocyst. In conclusion, this study determined the role of nonessential and essential amino acids in the culture of the porcine embryo and showed that the embryo requires different levels of amino acids as it develops from the zygote to the blastocyst stage.

Peel strength of denture liner to PMMA and polyamide: laser versus air-abrasion

  • Korkmaz, Fatih Mehmet;Bagis, Bora;Ozcan, Mutlu;Durkan, Rukiye;Turgut, Sedanur;Ates, Sabit Melih
    • The Journal of Advanced Prosthodontics
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    • v.5 no.3
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    • pp.287-295
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    • 2013
  • PURPOSE. This study investigated the effect of laser parameters and air-abrasion on the peel strength of silicon-based soft denture liner to different denture resins. MATERIALS AND METHODS. Specimens (N=180) were prepared out of three different denture base resins (Rodex, cross-linked denture base acrylic resin; Paladent, heat-cured acrylic resin; Deflex, Polyamide resin) ($75mm{\times}25mm{\times}3mm$). A silicon-based soft denture liner (Molloplast B) was applied to the denture resins after the following conditioning methods: a) Air-abrasion ($50{\mu}m$), b) Er,Cr:YSGG laser (Waterlase MD Turbo, Biolase Technology) at 2 W-20 Hz, c) Er,Cr:YSGG laser at 2 W-30 Hz, d) Er,Cr:YSGG laser at 3 W-20 Hz, e) Er,Cr:YSGG laser at 3 W-30 Hz. Non-conditioned group acted as the control group. Peel test was performed in a universal testing machine. Failure modes were evaluated visually. Data were analyzed using two-way ANOVA and Tukey's test (${\alpha}$=.05). RESULTS. Denture liner tested showed increased peel strength after laser treatment with different parameters ($3.9{\pm}0.4-5.58{\pm}0.6$ MPa) compared to the control ($3.64{\pm}0.5-4.58{\pm}0.5$ MPa) and air-abraded groups ($3.1{\pm}0.6-4.46{\pm}0.3$ MPa), but the results were not statistically significant except for Paladent, with the pretreatment of Er,Cr:YSGG laser at 3 W-20 Hz. Polyamide resin after air-abrasion showed significantly lower peel strength than those of other groups ($3.1{\pm}0.6$ MPa). CONCLUSION. Heat-cured acrylic resin, PMMA, may benefit from Er,Cr:YSGG laser treatment at 3 W-20 Hz irradiation. Air-abrasion of polyamide resins should be avoided not to impair their peel bond strengths to silicon-based soft denture liners.