Azmy Noer - Academia.edu (original) (raw)

Papers by Azmy Noer

Research paper thumbnail of Normal variants of human mitochondrial DNA and translation products: the building of a reference data base

Research paper thumbnail of Flat face expression as a typical Sundanese mother’s social cue

Diversity in Unity: Perspectives from Psychology and Behavioral Sciences

Mothers use social cues to connect and bond while teaching their children. Western-individualisti... more Mothers use social cues to connect and bond while teaching their children. Western-individualistic culture holds that facial expression and gaze are the most significant cues to revealing a mother's intention, but in Eastern-collectivism culture, such as Sundanese culture, it is forbidden to expresses emotion freely. This study explored Sundanese social cues that were utilised by mothers to state their intention while communicating with their children. Data was collected through naturalistic observation in three kabupaten (regencies) in West Java Province. Mother and child interactions in six families were recorded, each for five days. The mothers' instructions were categorised and interpreted based on categories of social cues, from which were identified three vocal intonations, repeating word(s), three facial expressions, two eye gaze(s) and three gesture varieties. The result shows that even though a flat-faced expression does not give any clue about a mother's intention, it is the most frequent cue (82.8%) that Sundanese mothers use, and utilisation of eye contact is restrained. Sun-danese mothers use other modalities to indicate their intention, which are high intonation (62.8%) and pointing gestures (71.2%).

Research paper thumbnail of Raw starch-degrading α-amylase from Bacillus aquimaris MKSC 6.2: isolation and expression of the gene, bioinformatics and biochemical characterization of the recombinant enzyme

Journal of Applied Microbiology, 2013

Aims: The aims were to isolate a raw starch-degrading a-amylase gene baqA from Bacillus aquimaris... more Aims: The aims were to isolate a raw starch-degrading a-amylase gene baqA from Bacillus aquimaris MKSC 6.2, and to characterize the gene product through in silico study and its expression in Escherichia coli. Methods and Results: A 1539 complete open reading frame of a starchdegrading a-amylase gene baqA from B. aquimaris MKSC 6Á2 has been determined by employing PCR and inverse PCR techniques. Bioinformatics analysis revealed that B. aquimaris MKSC 6.2 a-amylase (BaqA) has no starchbinding domain, and together with a few putative a-amylases from bacilli may establish a novel GH13 subfamily most closely related to GH13_1. Two consecutive tryptophans (Trp201 and Trp202, BaqA numbering) were identified as a sequence fingerprint of this novel GH13 subfamily. Escherichia coli cells produced the recombinant BaqA protein as inclusion bodies. The refolded recombinant BaqA protein degraded raw cassava and corn starches, but exhibited no activity with soluble starch. Conclusions: A novel raw starch-degrading B. aquimaris MKSC 6.2 a-amylase BaqA is proposed to be a member of new GH13 subfamily. Significance and Impact of the Study: This study has contributed to the overall knowledge and understanding of amylolytic enzymes that are able to bind and digest raw starch directly.

Research paper thumbnail of mtDNA in congenital myotonic dystrophy

American Journal of Human Genetics, 1993

agaosegel 20 cm in legh an hyrdzto wit radolaele YNH24 probe. Migration distances of the shortest... more agaosegel 20 cm in legh an hyrdzto wit radolaele YNH24 probe. Migration distances of the shortest fragments are 13.55 cm for the father (F) and for the oldest son (C1), 13.40 cm for the second son (C2), and 13.25cm for the mother (M). Fragment length was deduced graphically by comparison with a reference DNA ladder (not shown). A difference of about 50 nucleotides between the small F and C2 alleles was deduced.

Research paper thumbnail of The association of the autoantigens of primary biliary cirrhosis with the mitochondrial H+-ATPase--a reassessment

Biochemistry international, 1989

The claimed association between the M2 autoantigens of primary biliary cirrhosis (PBC) and the mi... more The claimed association between the M2 autoantigens of primary biliary cirrhosis (PBC) and the mitochondrial H+-ATPase has been re-examined in view of the recent reports that PBC autoantibodies react specifically with the lipoate acetyl transferases of 2-oxo acid dehydrogenases. Study of F0F1-ATPase purified from human and yeast mitochondria, and the comparison between immunoprecipitates obtained with antibodies against the H+-ATPase beta subunit and anti-M2 antibodies of PBC, established that the M2 antigens are not associated with the H+-ATPase complex. The M2 antigens did copurify with a crude bovine heart F1-ATPase preparation, but not with F1-ATPase from yeast, human heart or human liver.

Research paper thumbnail of Variants Analysis of Human Mitochondrial Genome Mutation: Study on Indonesian Human Tissues

Comparison of variants of mutations that occur in the Indonesia human mitochondrial genome betwee... more Comparison of variants of mutations that occur in the Indonesia human mitochondrial genome between tissues which origins are from layers of endoderm, mesoderm, and ectoderm have been investigated. In this study, analyzed the diversity of the mtG in various tissues of different origins, namely layer of entoderm, mesoderm, and ectoderm are compared with sequence of revised Cambridge Reference Sequence (rCRS). Determination of mtDNA mutations carried by the isolation procedure followed the protocol of DNA purification from tissues, amplification by using the technique repli-G, determining the nucleotide sequence of the mtG Sanger dideoxy method, and mtDNA in silico sequence analysis. Here we showed that mutation variants between tissues in a normal human individual (not associated with diseases caused by mtDNA mutations) are monomorphic. The results of mutation analysis of mtG variants to rCRS showed that nucleotide mutations in several regions, and found eight variants of the novel mu...

Research paper thumbnail of The e-module development of reaction rate based on guided inquiry as independent teaching materials

Journal of Physics: Conference Series, 2021

E-module reaction rate based guided inquiry has been developed using the Kvisoft flipbook maker. ... more E-module reaction rate based guided inquiry has been developed using the Kvisoft flipbook maker. The e-module is developed using the Plomp development model which consists of three phases namely, the initial investigation phase, the prototype making phase, and the assessment phase. The results of the material validation obtained an average percentage for the content aspects, presentation aspects, language aspects, and graphics aspects are 87.46%, 86.63%, 95.80%, and 81.5% with a very valid category. While the result of media validation obtained an average percentage for the cover design aspect, the content design aspect and the display aspect are 100%, 97.80%, and 85.6% with a very valid category. The result of t h e u s e r response test obtained average percentages are 88.34% and 86.25% with a very good category. Based on the result of the validation and user response test can be concluded that the e-module reaction rate based guided inquiry is feasible to be used in the chemistry...

Research paper thumbnail of The Need for A Joint Effort in the Construction of A Reference Data-Base for Normal Sequence Variants of Human Mtdna - Reply

Research paper thumbnail of Identifikasi Mutasi Heteroplasmi A3243g Dna Mitokondria Dan Studi Pewarisan Maternal Pada Pasien Diabetes Melitus Tipe 2

Mutasi A3243G DNA mitokondria (mtDNA) adalah mutasi subsitusi basa A ke G pada posisi 3243 gen tR... more Mutasi A3243G DNA mitokondria (mtDNA) adalah mutasi subsitusi basa A ke G pada posisi 3243 gen tRNALeu. Salah satu fenotipe klinis yang disebabkan mutasi A3243G mtDNA adalah MIDD (Maternally Inherited Diabetes and Deafness) yang merupakan salah satu bentuk diabetes melitus (DM) tipe 2. Penelitian ini bertujuan untuk mengidentifikasi mutasi heteroplasmi A3243G manusia Indonesia pada pasien DM tipe 2 dan mempelajari pewarisan maternal mutasi A3243G hingga tiga generasi dengan memanfaatkan metode PCRRFLP (Polymerase Chain Reaction–Restriction Fragments Length Polymorphism), PASA (PCR-Amplification of Specific Allelle) dan PCR-SSCP (PCR-Single Strand Conformation Polymorphism). mtDNA diperoleh dari hasil lisis sampel darah. Hasil penelitian menunjukkan bahwa mutasi A3243G teridentifikasi pada 2 dari 101 pasien DM tipe 2. Mutasi heteroplasmi A3243G dapat ditunjukkan dari hasil PCR-RFLP dan PASA. Hasil RFLP menunjukkan adanya tiga fragmen, masing-masing yaitu fragmen utuh 294, 182 dan 112...

Research paper thumbnail of Maternally inherited diabetes pPatients from Manado and Jakarta posses A3243G mutation by PCR-Allele's specific amplification

Mutations in mitochondrial DNA (mtDNA) associate with diabetes that the most common mutation is t... more Mutations in mitochondrial DNA (mtDNA) associate with diabetes that the most common mutation is the A3243G mutation in tRNA Leu(UUR) gene. Previous studies have sugested that this mutation is associated with maternally inherited diabetes, but only when additional features of mitochondrial disease are present. The frequently accompanying feature of maternally inherited diabetes is hearing impairment or deafness (MIDD). This mutation generally occur in heteroplasmic forms, with low levels in leukocytes and high levels in postmitotic tissues (e.g., skeletal muscle and �-cells). However, muscle biopsy cannot be used as a routine examination, especially in diabetic patients. Current methods have limited sensitivity and may lead to potential misclassification of patients with low levels of heteroplasmy. Therefore, the aim of the research was to investigate the role of mtDNA defects in maternally inherited diabetes by first screening for the A3243G mutation by restriction assay, followed b...

Research paper thumbnail of Mitochondrial DNA diversity in indigenous populations of Northern Papua and its implications on native papuan haplogroups

Human mitochondrial DNA (mtDNA) is highly polymorphic due to its high mutation rate, D-loop as re... more Human mitochondrial DNA (mtDNA) is highly polymorphic due to its high mutation rate, D-loop as region of human mitochondrial genome posses highest polymorphism. Another specific characteristic of mtDNA is maternally inherited. At this research reported nucleotide sequence area D-loop uses method direct sequencing for a few tribe individual Biak and Serui in north region Papua Province. Here we show that nucleotide sequence that obtained referred as, then compared to nucleotide sequence regions D-loop: HVSI and HVSII standard namely revised-Cambridge Reference Sequence (rCRS). Result sequencing shows existence of mutation variation from individuals both tribe at Papua population: Biak and Serui with which vary mutation amount. Nevertheless, analysis result homology shows there are some substitution mutation the most often emerging is 16111T, 16232T, and 263G. Appearance of type mutation variability and mutation amount at Papua individual indicating that mutation that happened not hav...

Research paper thumbnail of The development of acid-base e-chemistry magazine as interactive teaching materials

Journal of Physics: Conference Series

E-Chemistry Magazine that has been developed is a teaching materials that utilizes the developmen... more E-Chemistry Magazine that has been developed is a teaching materials that utilizes the development of technology to improve the quality of a learning process. The objective of this research is to develop an interactive e-chemistry magazine for the acid-base course unit. The method used in this research is the Plomp model research and development (R&D) design. This research consists of three phases, (a) preliminary research phase, (b) prototype or development phase, and (c) assessment phase. The result of this research indicates that acid and base e-chemistry magazine is considered to be strongly valid by the content and media experts. The responses from teachers and students regarding the acid and base e-chemistry magazine are very good and very interesting. This suggests that the production of acid and base e-chemistry magazine meets the decent criteria to be used as interactive teaching materials in the learning of chemistry for the acid-base course unit.

Research paper thumbnail of Is that a torpedo near the fovea? Torpedo maculopathy a case report

Acta Ophthalmologica

Purpose: The use of the retina as a window into the brain is a promising avenue of research when ... more Purpose: The use of the retina as a window into the brain is a promising avenue of research when it comes to the identification of imaging biomarkers that can assist in the early diagnosis of neurodegenerative disorders such as Alzheimer's (AD) and Parkinson's (PD) disease. In this work, optical coherence tomography data were used to compute macular images of the six innermost retinal layers and classify eyes into the AD, PD and healthy control groups. Methods: Computed fundus images were analysed by applying local and global texture metrics, to identify criteria that distinguish between healthy controls and patients diagnosed with any of the two neurodegeneration states mentioned above. The possibility of distinguishing between the two disorders themselves, that is, between the AD and PD eyes, was also investigated. The identification of the most significant features and their use in classification models was performed using support vector machines with radial basis function kernel. Results: Median results after 100 consecutive runs of the classification process, with 10-fold cross-validation, are 88.7%, 79.5% and 77.8% for the sensitivity and 84.9%, 92.5% and 97.8% for the specificity in identifying, respectively, healthy control, AD and PD eyes. Notably, when the same subject has their two eyes attributed to the same class, 94.4% (median) of the classifications are correct. Furthermore, when using texture features, only 1.4% (median) of the eyes do not show any difference among the three groups. Conclusions: Achieved results reveal that a significant amount of information concerning AD and PD states is conveyed by optical coherence tomography imaging of the human retina. The diagnosis of the two most common neurodegenerative disorders in the developed world can thus benefit from the information provided by this noninvasive in-vivo imaging technique.

Research paper thumbnail of Retinal biomarkers for Alzheimer's and Parkinson's diseases

Acta Ophthalmologica

Purpose: The use of the retina as a window into the brain is a promising avenue of research when ... more Purpose: The use of the retina as a window into the brain is a promising avenue of research when it comes to the identification of imaging biomarkers that can assist in the early diagnosis of neurodegenerative disorders such as Alzheimer's (AD) and Parkinson's (PD) disease. In this work, optical coherence tomography data were used to compute macular images of the six innermost retinal layers and classify eyes into the AD, PD and healthy control groups. Methods: Computed fundus images were analysed by applying local and global texture metrics, to identify criteria that distinguish between healthy controls and patients diagnosed with any of the two neurodegeneration states mentioned above. The possibility of distinguishing between the two disorders themselves, that is, between the AD and PD eyes, was also investigated. The identification of the most significant features and their use in classification models was performed using support vector machines with radial basis function kernel. Results: Median results after 100 consecutive runs of the classification process, with 10-fold cross-validation, are 88.7%, 79.5% and 77.8% for the sensitivity and 84.9%, 92.5% and 97.8% for the specificity in identifying, respectively, healthy control, AD and PD eyes. Notably, when the same subject has their two eyes attributed to the same class, 94.4% (median) of the classifications are correct. Furthermore, when using texture features, only 1.4% (median) of the eyes do not show any difference among the three groups. Conclusions: Achieved results reveal that a significant amount of information concerning AD and PD states is conveyed by optical coherence tomography imaging of the human retina. The diagnosis of the two most common neurodegenerative disorders in the developed world can thus benefit from the information provided by this noninvasive in-vivo imaging technique.

Research paper thumbnail of Effect of Pseudomonas and Acanthamoeba infection upon inflammation produced by human cornea epithelial cells

Acta Ophthalmologica

Purpose: The use of the retina as a window into the brain is a promising avenue of research when ... more Purpose: The use of the retina as a window into the brain is a promising avenue of research when it comes to the identification of imaging biomarkers that can assist in the early diagnosis of neurodegenerative disorders such as Alzheimer's (AD) and Parkinson's (PD) disease. In this work, optical coherence tomography data were used to compute macular images of the six innermost retinal layers and classify eyes into the AD, PD and healthy control groups. Methods: Computed fundus images were analysed by applying local and global texture metrics, to identify criteria that distinguish between healthy controls and patients diagnosed with any of the two neurodegeneration states mentioned above. The possibility of distinguishing between the two disorders themselves, that is, between the AD and PD eyes, was also investigated. The identification of the most significant features and their use in classification models was performed using support vector machines with radial basis function kernel. Results: Median results after 100 consecutive runs of the classification process, with 10-fold cross-validation, are 88.7%, 79.5% and 77.8% for the sensitivity and 84.9%, 92.5% and 97.8% for the specificity in identifying, respectively, healthy control, AD and PD eyes. Notably, when the same subject has their two eyes attributed to the same class, 94.4% (median) of the classifications are correct. Furthermore, when using texture features, only 1.4% (median) of the eyes do not show any difference among the three groups. Conclusions: Achieved results reveal that a significant amount of information concerning AD and PD states is conveyed by optical coherence tomography imaging of the human retina. The diagnosis of the two most common neurodegenerative disorders in the developed world can thus benefit from the information provided by this noninvasive in-vivo imaging technique.

Research paper thumbnail of UK trainee trabeculectomy outcomes incorporating simulated surgery

Acta Ophthalmologica

Purpose: The use of the retina as a window into the brain is a promising avenue of research when ... more Purpose: The use of the retina as a window into the brain is a promising avenue of research when it comes to the identification of imaging biomarkers that can assist in the early diagnosis of neurodegenerative disorders such as Alzheimer's (AD) and Parkinson's (PD) disease. In this work, optical coherence tomography data were used to compute macular images of the six innermost retinal layers and classify eyes into the AD, PD and healthy control groups. Methods: Computed fundus images were analysed by applying local and global texture metrics, to identify criteria that distinguish between healthy controls and patients diagnosed with any of the two neurodegeneration states mentioned above. The possibility of distinguishing between the two disorders themselves, that is, between the AD and PD eyes, was also investigated. The identification of the most significant features and their use in classification models was performed using support vector machines with radial basis function kernel. Results: Median results after 100 consecutive runs of the classification process, with 10-fold cross-validation, are 88.7%, 79.5% and 77.8% for the sensitivity and 84.9%, 92.5% and 97.8% for the specificity in identifying, respectively, healthy control, AD and PD eyes. Notably, when the same subject has their two eyes attributed to the same class, 94.4% (median) of the classifications are correct. Furthermore, when using texture features, only 1.4% (median) of the eyes do not show any difference among the three groups. Conclusions: Achieved results reveal that a significant amount of information concerning AD and PD states is conveyed by optical coherence tomography imaging of the human retina. The diagnosis of the two most common neurodegenerative disorders in the developed world can thus benefit from the information provided by this noninvasive in-vivo imaging technique.

Research paper thumbnail of Flat face expression as a typical Sundanese mother's social cue

Mothers use social cues to connect and bond while teaching their children. Western-individualisti... more Mothers use social cues to connect and bond while teaching their children. Western-individualistic culture holds that facial expression and gaze are the most significant cues to revealing a mother's intention, but in Eastern-collectivism culture, such as Sundanese culture, it is forbidden to expresses emotion freely. This study explored Sundanese social cues that were utilised by mothers to state their intention while communicating with their children. Data was collected through naturalistic observation in three kabupaten (regencies) in West Java Province. Mother and child interactions in six families were recorded, each for five days. The mothers' instructions were categorised and interpreted based on categories of social cues, from which were identified three vocal intonations, repeating word(s), three facial expressions, two eye gaze(s) and three gesture varieties. The result shows that even though a flat-faced expression does not give any clue about a mother's intent...

Research paper thumbnail of Electrospun polymer nanofibers as substrate/carrier for engineering of human corneal epithelium

Acta Ophthalmologica, 2016

Purpose Electrospun polymer nanofibers present a structure similar to extracellular matrix (ECM) ... more Purpose Electrospun polymer nanofibers present a structure similar to extracellular matrix (ECM) and support the surrounding cells. The type of polymer used, as well as the polymer blending-ratio, affects wettability. This in turn influences cell growth by altering the types of proteins adsorbed from the solution. Human corneal epithelial cells were grown on electrospun biodegradable and non-biodegradable polymer membranes to evaluate the membranes’ potential within ocular surface tissue engineering. Methods The electrospun polymer membranes consisted of cellulose acetate, poly (lactic-co-glycolic acid) (PLGA), polycaprolactone (PCL), and blends of PCL and polyethylene glycol (PEG). Expression of CDH1 (E-cadherin), ITGA6, ITGB4 (Integrin α6β4) and MKI67 (Ki67) genes were measured in all conditions after 14 days of culture using qRT-PCR. Results Cells seeded on all types of membranes expressed MKI67, which is associated with cell cycle activity and correlates with cell growth. MKI67 expression was high in cells grown on 3:2 blends of PCL and PEG (2.88) and PCL (2.75). This amount was 1.75, 1.00 and 1.59 for cells grown on cellulose acetate, 1:1 blend of PCL and PEG and PLGA respectively. The amount of ITGA6, ITGB4 expression was 1.72 in cells grown on PCL membranes, 1.10 for 3:2 blend of PCL and PEG, 1.05 for cellulose acetate, 1.53 for PLGA and 1.01 for 1:1 blend of PCL and PEG. Only cells grown on membranes containing blends of PCL: PEG showed CDH1 expression, which is critical for cell-cell contact. Conclusions All polymer membranes enabled cellular adhesion and proliferation. PCL:PEG and PCL membranes appear to promote the highest proliferative activity and strongest cell-membrane/cell-cell adhesion. Thus, these might be the most promising substrates for epithelial ocular surface tissue engineering.

Research paper thumbnail of Novel molecular design of culture substrates with amino acids

Acta Ophthalmologica, 2016

Research paper thumbnail of The effect of culture medium and carrier on explant culture of human limbal epithelium: A comparison of ultrastructure, keratin profile and gene expression

Experimental Eye Research, 2016

Patients with limbal stem cell deficiency (LSCD) often experience pain and photophobia due to rec... more Patients with limbal stem cell deficiency (LSCD) often experience pain and photophobia due to recurrent epithelial defects and chronic inflammation of the cornea. Successfully restoring a healthy corneal surface in these patients by transplantation of ex vivo expanded human limbal epithelial cells (LECs) may alleviate these symptoms and significantly improve their quality of life. The clinical outcome of transplantation is known to be influenced by the quality of transplanted cells. Presently, several different protocols for cultivation and transplantation of LECs are in use. However, no consensus on an optimal protocol exists. The aim of this study was to examine the effect of culture medium and carrier on the morphology, staining of selected keratins and global gene expression in ex vivo cultured LECs. Limbal biopsies from cadaveric donors were cultured for three weeks on human amniotic membrane (HAM) or on tissue culture coated plastic (PL) in either a complex medium (COM), containing recombinant growth factors, hormones, cholera toxin and fetal bovine serum, or in medium supplemented only with human serum (HS). The expanded LECs were examined by light microscopy (LM), transmission electron microscopy (TEM), immunohistochemistry (IHC) for keratins K3, K7, K8, K12, K13, K14, K15 and K19, as well as microarray and qRT-PCR analysis. The cultured LECs exhibited similar morphology and keratin staining on LM, TEM and IHC examination, regardless of the culture condition. The epithelium was multilayered, with cuboidal basal cells and flattened superficial cells. Cells were attached to each other by desmosomes. Adhesion complexes were observed between basal cells and the underlying carrier in LECs cultured on HAM, but not in LECs cultured on PL. GeneChip Human Gene 2.0 ST microarray (Affymetrix) analysis revealed that 18,653 transcripts were ≥2 fold up or downregulated (p ≤ 0.05). Cells cultured in the same medium (COM or HS) showed more similarities in gene expression than cells cultured on the same carrier (HAM or PL). When each condition was compared to HAM/COM, no statistical difference was found in the transcription level of the selected genes associated with keratin expression, stemness, proliferation, differentiation, apoptosis, corneal wound healing or autophagy. In conclusion, the results indicate that ex vivo cultures of LECs on HAM and PL, using culture media supplemented with COM or HS, yield tissues with similar morphology and keratin staining. The gene expression appears to be more similar in cells cultured in the same medium (COM or HS) compared to cells cultured on the same carrier (HAM or PL).

Research paper thumbnail of Normal variants of human mitochondrial DNA and translation products: the building of a reference data base

Research paper thumbnail of Flat face expression as a typical Sundanese mother’s social cue

Diversity in Unity: Perspectives from Psychology and Behavioral Sciences

Mothers use social cues to connect and bond while teaching their children. Western-individualisti... more Mothers use social cues to connect and bond while teaching their children. Western-individualistic culture holds that facial expression and gaze are the most significant cues to revealing a mother's intention, but in Eastern-collectivism culture, such as Sundanese culture, it is forbidden to expresses emotion freely. This study explored Sundanese social cues that were utilised by mothers to state their intention while communicating with their children. Data was collected through naturalistic observation in three kabupaten (regencies) in West Java Province. Mother and child interactions in six families were recorded, each for five days. The mothers' instructions were categorised and interpreted based on categories of social cues, from which were identified three vocal intonations, repeating word(s), three facial expressions, two eye gaze(s) and three gesture varieties. The result shows that even though a flat-faced expression does not give any clue about a mother's intention, it is the most frequent cue (82.8%) that Sundanese mothers use, and utilisation of eye contact is restrained. Sun-danese mothers use other modalities to indicate their intention, which are high intonation (62.8%) and pointing gestures (71.2%).

Research paper thumbnail of Raw starch-degrading α-amylase from Bacillus aquimaris MKSC 6.2: isolation and expression of the gene, bioinformatics and biochemical characterization of the recombinant enzyme

Journal of Applied Microbiology, 2013

Aims: The aims were to isolate a raw starch-degrading a-amylase gene baqA from Bacillus aquimaris... more Aims: The aims were to isolate a raw starch-degrading a-amylase gene baqA from Bacillus aquimaris MKSC 6.2, and to characterize the gene product through in silico study and its expression in Escherichia coli. Methods and Results: A 1539 complete open reading frame of a starchdegrading a-amylase gene baqA from B. aquimaris MKSC 6Á2 has been determined by employing PCR and inverse PCR techniques. Bioinformatics analysis revealed that B. aquimaris MKSC 6.2 a-amylase (BaqA) has no starchbinding domain, and together with a few putative a-amylases from bacilli may establish a novel GH13 subfamily most closely related to GH13_1. Two consecutive tryptophans (Trp201 and Trp202, BaqA numbering) were identified as a sequence fingerprint of this novel GH13 subfamily. Escherichia coli cells produced the recombinant BaqA protein as inclusion bodies. The refolded recombinant BaqA protein degraded raw cassava and corn starches, but exhibited no activity with soluble starch. Conclusions: A novel raw starch-degrading B. aquimaris MKSC 6.2 a-amylase BaqA is proposed to be a member of new GH13 subfamily. Significance and Impact of the Study: This study has contributed to the overall knowledge and understanding of amylolytic enzymes that are able to bind and digest raw starch directly.

Research paper thumbnail of mtDNA in congenital myotonic dystrophy

American Journal of Human Genetics, 1993

agaosegel 20 cm in legh an hyrdzto wit radolaele YNH24 probe. Migration distances of the shortest... more agaosegel 20 cm in legh an hyrdzto wit radolaele YNH24 probe. Migration distances of the shortest fragments are 13.55 cm for the father (F) and for the oldest son (C1), 13.40 cm for the second son (C2), and 13.25cm for the mother (M). Fragment length was deduced graphically by comparison with a reference DNA ladder (not shown). A difference of about 50 nucleotides between the small F and C2 alleles was deduced.

Research paper thumbnail of The association of the autoantigens of primary biliary cirrhosis with the mitochondrial H+-ATPase--a reassessment

Biochemistry international, 1989

The claimed association between the M2 autoantigens of primary biliary cirrhosis (PBC) and the mi... more The claimed association between the M2 autoantigens of primary biliary cirrhosis (PBC) and the mitochondrial H+-ATPase has been re-examined in view of the recent reports that PBC autoantibodies react specifically with the lipoate acetyl transferases of 2-oxo acid dehydrogenases. Study of F0F1-ATPase purified from human and yeast mitochondria, and the comparison between immunoprecipitates obtained with antibodies against the H+-ATPase beta subunit and anti-M2 antibodies of PBC, established that the M2 antigens are not associated with the H+-ATPase complex. The M2 antigens did copurify with a crude bovine heart F1-ATPase preparation, but not with F1-ATPase from yeast, human heart or human liver.

Research paper thumbnail of Variants Analysis of Human Mitochondrial Genome Mutation: Study on Indonesian Human Tissues

Comparison of variants of mutations that occur in the Indonesia human mitochondrial genome betwee... more Comparison of variants of mutations that occur in the Indonesia human mitochondrial genome between tissues which origins are from layers of endoderm, mesoderm, and ectoderm have been investigated. In this study, analyzed the diversity of the mtG in various tissues of different origins, namely layer of entoderm, mesoderm, and ectoderm are compared with sequence of revised Cambridge Reference Sequence (rCRS). Determination of mtDNA mutations carried by the isolation procedure followed the protocol of DNA purification from tissues, amplification by using the technique repli-G, determining the nucleotide sequence of the mtG Sanger dideoxy method, and mtDNA in silico sequence analysis. Here we showed that mutation variants between tissues in a normal human individual (not associated with diseases caused by mtDNA mutations) are monomorphic. The results of mutation analysis of mtG variants to rCRS showed that nucleotide mutations in several regions, and found eight variants of the novel mu...

Research paper thumbnail of The e-module development of reaction rate based on guided inquiry as independent teaching materials

Journal of Physics: Conference Series, 2021

E-module reaction rate based guided inquiry has been developed using the Kvisoft flipbook maker. ... more E-module reaction rate based guided inquiry has been developed using the Kvisoft flipbook maker. The e-module is developed using the Plomp development model which consists of three phases namely, the initial investigation phase, the prototype making phase, and the assessment phase. The results of the material validation obtained an average percentage for the content aspects, presentation aspects, language aspects, and graphics aspects are 87.46%, 86.63%, 95.80%, and 81.5% with a very valid category. While the result of media validation obtained an average percentage for the cover design aspect, the content design aspect and the display aspect are 100%, 97.80%, and 85.6% with a very valid category. The result of t h e u s e r response test obtained average percentages are 88.34% and 86.25% with a very good category. Based on the result of the validation and user response test can be concluded that the e-module reaction rate based guided inquiry is feasible to be used in the chemistry...

Research paper thumbnail of The Need for A Joint Effort in the Construction of A Reference Data-Base for Normal Sequence Variants of Human Mtdna - Reply

Research paper thumbnail of Identifikasi Mutasi Heteroplasmi A3243g Dna Mitokondria Dan Studi Pewarisan Maternal Pada Pasien Diabetes Melitus Tipe 2

Mutasi A3243G DNA mitokondria (mtDNA) adalah mutasi subsitusi basa A ke G pada posisi 3243 gen tR... more Mutasi A3243G DNA mitokondria (mtDNA) adalah mutasi subsitusi basa A ke G pada posisi 3243 gen tRNALeu. Salah satu fenotipe klinis yang disebabkan mutasi A3243G mtDNA adalah MIDD (Maternally Inherited Diabetes and Deafness) yang merupakan salah satu bentuk diabetes melitus (DM) tipe 2. Penelitian ini bertujuan untuk mengidentifikasi mutasi heteroplasmi A3243G manusia Indonesia pada pasien DM tipe 2 dan mempelajari pewarisan maternal mutasi A3243G hingga tiga generasi dengan memanfaatkan metode PCRRFLP (Polymerase Chain Reaction–Restriction Fragments Length Polymorphism), PASA (PCR-Amplification of Specific Allelle) dan PCR-SSCP (PCR-Single Strand Conformation Polymorphism). mtDNA diperoleh dari hasil lisis sampel darah. Hasil penelitian menunjukkan bahwa mutasi A3243G teridentifikasi pada 2 dari 101 pasien DM tipe 2. Mutasi heteroplasmi A3243G dapat ditunjukkan dari hasil PCR-RFLP dan PASA. Hasil RFLP menunjukkan adanya tiga fragmen, masing-masing yaitu fragmen utuh 294, 182 dan 112...

Research paper thumbnail of Maternally inherited diabetes pPatients from Manado and Jakarta posses A3243G mutation by PCR-Allele's specific amplification

Mutations in mitochondrial DNA (mtDNA) associate with diabetes that the most common mutation is t... more Mutations in mitochondrial DNA (mtDNA) associate with diabetes that the most common mutation is the A3243G mutation in tRNA Leu(UUR) gene. Previous studies have sugested that this mutation is associated with maternally inherited diabetes, but only when additional features of mitochondrial disease are present. The frequently accompanying feature of maternally inherited diabetes is hearing impairment or deafness (MIDD). This mutation generally occur in heteroplasmic forms, with low levels in leukocytes and high levels in postmitotic tissues (e.g., skeletal muscle and �-cells). However, muscle biopsy cannot be used as a routine examination, especially in diabetic patients. Current methods have limited sensitivity and may lead to potential misclassification of patients with low levels of heteroplasmy. Therefore, the aim of the research was to investigate the role of mtDNA defects in maternally inherited diabetes by first screening for the A3243G mutation by restriction assay, followed b...

Research paper thumbnail of Mitochondrial DNA diversity in indigenous populations of Northern Papua and its implications on native papuan haplogroups

Human mitochondrial DNA (mtDNA) is highly polymorphic due to its high mutation rate, D-loop as re... more Human mitochondrial DNA (mtDNA) is highly polymorphic due to its high mutation rate, D-loop as region of human mitochondrial genome posses highest polymorphism. Another specific characteristic of mtDNA is maternally inherited. At this research reported nucleotide sequence area D-loop uses method direct sequencing for a few tribe individual Biak and Serui in north region Papua Province. Here we show that nucleotide sequence that obtained referred as, then compared to nucleotide sequence regions D-loop: HVSI and HVSII standard namely revised-Cambridge Reference Sequence (rCRS). Result sequencing shows existence of mutation variation from individuals both tribe at Papua population: Biak and Serui with which vary mutation amount. Nevertheless, analysis result homology shows there are some substitution mutation the most often emerging is 16111T, 16232T, and 263G. Appearance of type mutation variability and mutation amount at Papua individual indicating that mutation that happened not hav...

Research paper thumbnail of The development of acid-base e-chemistry magazine as interactive teaching materials

Journal of Physics: Conference Series

E-Chemistry Magazine that has been developed is a teaching materials that utilizes the developmen... more E-Chemistry Magazine that has been developed is a teaching materials that utilizes the development of technology to improve the quality of a learning process. The objective of this research is to develop an interactive e-chemistry magazine for the acid-base course unit. The method used in this research is the Plomp model research and development (R&D) design. This research consists of three phases, (a) preliminary research phase, (b) prototype or development phase, and (c) assessment phase. The result of this research indicates that acid and base e-chemistry magazine is considered to be strongly valid by the content and media experts. The responses from teachers and students regarding the acid and base e-chemistry magazine are very good and very interesting. This suggests that the production of acid and base e-chemistry magazine meets the decent criteria to be used as interactive teaching materials in the learning of chemistry for the acid-base course unit.

Research paper thumbnail of Is that a torpedo near the fovea? Torpedo maculopathy a case report

Acta Ophthalmologica

Purpose: The use of the retina as a window into the brain is a promising avenue of research when ... more Purpose: The use of the retina as a window into the brain is a promising avenue of research when it comes to the identification of imaging biomarkers that can assist in the early diagnosis of neurodegenerative disorders such as Alzheimer's (AD) and Parkinson's (PD) disease. In this work, optical coherence tomography data were used to compute macular images of the six innermost retinal layers and classify eyes into the AD, PD and healthy control groups. Methods: Computed fundus images were analysed by applying local and global texture metrics, to identify criteria that distinguish between healthy controls and patients diagnosed with any of the two neurodegeneration states mentioned above. The possibility of distinguishing between the two disorders themselves, that is, between the AD and PD eyes, was also investigated. The identification of the most significant features and their use in classification models was performed using support vector machines with radial basis function kernel. Results: Median results after 100 consecutive runs of the classification process, with 10-fold cross-validation, are 88.7%, 79.5% and 77.8% for the sensitivity and 84.9%, 92.5% and 97.8% for the specificity in identifying, respectively, healthy control, AD and PD eyes. Notably, when the same subject has their two eyes attributed to the same class, 94.4% (median) of the classifications are correct. Furthermore, when using texture features, only 1.4% (median) of the eyes do not show any difference among the three groups. Conclusions: Achieved results reveal that a significant amount of information concerning AD and PD states is conveyed by optical coherence tomography imaging of the human retina. The diagnosis of the two most common neurodegenerative disorders in the developed world can thus benefit from the information provided by this noninvasive in-vivo imaging technique.

Research paper thumbnail of Retinal biomarkers for Alzheimer's and Parkinson's diseases

Acta Ophthalmologica

Purpose: The use of the retina as a window into the brain is a promising avenue of research when ... more Purpose: The use of the retina as a window into the brain is a promising avenue of research when it comes to the identification of imaging biomarkers that can assist in the early diagnosis of neurodegenerative disorders such as Alzheimer's (AD) and Parkinson's (PD) disease. In this work, optical coherence tomography data were used to compute macular images of the six innermost retinal layers and classify eyes into the AD, PD and healthy control groups. Methods: Computed fundus images were analysed by applying local and global texture metrics, to identify criteria that distinguish between healthy controls and patients diagnosed with any of the two neurodegeneration states mentioned above. The possibility of distinguishing between the two disorders themselves, that is, between the AD and PD eyes, was also investigated. The identification of the most significant features and their use in classification models was performed using support vector machines with radial basis function kernel. Results: Median results after 100 consecutive runs of the classification process, with 10-fold cross-validation, are 88.7%, 79.5% and 77.8% for the sensitivity and 84.9%, 92.5% and 97.8% for the specificity in identifying, respectively, healthy control, AD and PD eyes. Notably, when the same subject has their two eyes attributed to the same class, 94.4% (median) of the classifications are correct. Furthermore, when using texture features, only 1.4% (median) of the eyes do not show any difference among the three groups. Conclusions: Achieved results reveal that a significant amount of information concerning AD and PD states is conveyed by optical coherence tomography imaging of the human retina. The diagnosis of the two most common neurodegenerative disorders in the developed world can thus benefit from the information provided by this noninvasive in-vivo imaging technique.

Research paper thumbnail of Effect of Pseudomonas and Acanthamoeba infection upon inflammation produced by human cornea epithelial cells

Acta Ophthalmologica

Purpose: The use of the retina as a window into the brain is a promising avenue of research when ... more Purpose: The use of the retina as a window into the brain is a promising avenue of research when it comes to the identification of imaging biomarkers that can assist in the early diagnosis of neurodegenerative disorders such as Alzheimer's (AD) and Parkinson's (PD) disease. In this work, optical coherence tomography data were used to compute macular images of the six innermost retinal layers and classify eyes into the AD, PD and healthy control groups. Methods: Computed fundus images were analysed by applying local and global texture metrics, to identify criteria that distinguish between healthy controls and patients diagnosed with any of the two neurodegeneration states mentioned above. The possibility of distinguishing between the two disorders themselves, that is, between the AD and PD eyes, was also investigated. The identification of the most significant features and their use in classification models was performed using support vector machines with radial basis function kernel. Results: Median results after 100 consecutive runs of the classification process, with 10-fold cross-validation, are 88.7%, 79.5% and 77.8% for the sensitivity and 84.9%, 92.5% and 97.8% for the specificity in identifying, respectively, healthy control, AD and PD eyes. Notably, when the same subject has their two eyes attributed to the same class, 94.4% (median) of the classifications are correct. Furthermore, when using texture features, only 1.4% (median) of the eyes do not show any difference among the three groups. Conclusions: Achieved results reveal that a significant amount of information concerning AD and PD states is conveyed by optical coherence tomography imaging of the human retina. The diagnosis of the two most common neurodegenerative disorders in the developed world can thus benefit from the information provided by this noninvasive in-vivo imaging technique.

Research paper thumbnail of UK trainee trabeculectomy outcomes incorporating simulated surgery

Acta Ophthalmologica

Purpose: The use of the retina as a window into the brain is a promising avenue of research when ... more Purpose: The use of the retina as a window into the brain is a promising avenue of research when it comes to the identification of imaging biomarkers that can assist in the early diagnosis of neurodegenerative disorders such as Alzheimer's (AD) and Parkinson's (PD) disease. In this work, optical coherence tomography data were used to compute macular images of the six innermost retinal layers and classify eyes into the AD, PD and healthy control groups. Methods: Computed fundus images were analysed by applying local and global texture metrics, to identify criteria that distinguish between healthy controls and patients diagnosed with any of the two neurodegeneration states mentioned above. The possibility of distinguishing between the two disorders themselves, that is, between the AD and PD eyes, was also investigated. The identification of the most significant features and their use in classification models was performed using support vector machines with radial basis function kernel. Results: Median results after 100 consecutive runs of the classification process, with 10-fold cross-validation, are 88.7%, 79.5% and 77.8% for the sensitivity and 84.9%, 92.5% and 97.8% for the specificity in identifying, respectively, healthy control, AD and PD eyes. Notably, when the same subject has their two eyes attributed to the same class, 94.4% (median) of the classifications are correct. Furthermore, when using texture features, only 1.4% (median) of the eyes do not show any difference among the three groups. Conclusions: Achieved results reveal that a significant amount of information concerning AD and PD states is conveyed by optical coherence tomography imaging of the human retina. The diagnosis of the two most common neurodegenerative disorders in the developed world can thus benefit from the information provided by this noninvasive in-vivo imaging technique.

Research paper thumbnail of Flat face expression as a typical Sundanese mother's social cue

Mothers use social cues to connect and bond while teaching their children. Western-individualisti... more Mothers use social cues to connect and bond while teaching their children. Western-individualistic culture holds that facial expression and gaze are the most significant cues to revealing a mother's intention, but in Eastern-collectivism culture, such as Sundanese culture, it is forbidden to expresses emotion freely. This study explored Sundanese social cues that were utilised by mothers to state their intention while communicating with their children. Data was collected through naturalistic observation in three kabupaten (regencies) in West Java Province. Mother and child interactions in six families were recorded, each for five days. The mothers' instructions were categorised and interpreted based on categories of social cues, from which were identified three vocal intonations, repeating word(s), three facial expressions, two eye gaze(s) and three gesture varieties. The result shows that even though a flat-faced expression does not give any clue about a mother's intent...

Research paper thumbnail of Electrospun polymer nanofibers as substrate/carrier for engineering of human corneal epithelium

Acta Ophthalmologica, 2016

Purpose Electrospun polymer nanofibers present a structure similar to extracellular matrix (ECM) ... more Purpose Electrospun polymer nanofibers present a structure similar to extracellular matrix (ECM) and support the surrounding cells. The type of polymer used, as well as the polymer blending-ratio, affects wettability. This in turn influences cell growth by altering the types of proteins adsorbed from the solution. Human corneal epithelial cells were grown on electrospun biodegradable and non-biodegradable polymer membranes to evaluate the membranes’ potential within ocular surface tissue engineering. Methods The electrospun polymer membranes consisted of cellulose acetate, poly (lactic-co-glycolic acid) (PLGA), polycaprolactone (PCL), and blends of PCL and polyethylene glycol (PEG). Expression of CDH1 (E-cadherin), ITGA6, ITGB4 (Integrin α6β4) and MKI67 (Ki67) genes were measured in all conditions after 14 days of culture using qRT-PCR. Results Cells seeded on all types of membranes expressed MKI67, which is associated with cell cycle activity and correlates with cell growth. MKI67 expression was high in cells grown on 3:2 blends of PCL and PEG (2.88) and PCL (2.75). This amount was 1.75, 1.00 and 1.59 for cells grown on cellulose acetate, 1:1 blend of PCL and PEG and PLGA respectively. The amount of ITGA6, ITGB4 expression was 1.72 in cells grown on PCL membranes, 1.10 for 3:2 blend of PCL and PEG, 1.05 for cellulose acetate, 1.53 for PLGA and 1.01 for 1:1 blend of PCL and PEG. Only cells grown on membranes containing blends of PCL: PEG showed CDH1 expression, which is critical for cell-cell contact. Conclusions All polymer membranes enabled cellular adhesion and proliferation. PCL:PEG and PCL membranes appear to promote the highest proliferative activity and strongest cell-membrane/cell-cell adhesion. Thus, these might be the most promising substrates for epithelial ocular surface tissue engineering.

Research paper thumbnail of Novel molecular design of culture substrates with amino acids

Acta Ophthalmologica, 2016

Research paper thumbnail of The effect of culture medium and carrier on explant culture of human limbal epithelium: A comparison of ultrastructure, keratin profile and gene expression

Experimental Eye Research, 2016

Patients with limbal stem cell deficiency (LSCD) often experience pain and photophobia due to rec... more Patients with limbal stem cell deficiency (LSCD) often experience pain and photophobia due to recurrent epithelial defects and chronic inflammation of the cornea. Successfully restoring a healthy corneal surface in these patients by transplantation of ex vivo expanded human limbal epithelial cells (LECs) may alleviate these symptoms and significantly improve their quality of life. The clinical outcome of transplantation is known to be influenced by the quality of transplanted cells. Presently, several different protocols for cultivation and transplantation of LECs are in use. However, no consensus on an optimal protocol exists. The aim of this study was to examine the effect of culture medium and carrier on the morphology, staining of selected keratins and global gene expression in ex vivo cultured LECs. Limbal biopsies from cadaveric donors were cultured for three weeks on human amniotic membrane (HAM) or on tissue culture coated plastic (PL) in either a complex medium (COM), containing recombinant growth factors, hormones, cholera toxin and fetal bovine serum, or in medium supplemented only with human serum (HS). The expanded LECs were examined by light microscopy (LM), transmission electron microscopy (TEM), immunohistochemistry (IHC) for keratins K3, K7, K8, K12, K13, K14, K15 and K19, as well as microarray and qRT-PCR analysis. The cultured LECs exhibited similar morphology and keratin staining on LM, TEM and IHC examination, regardless of the culture condition. The epithelium was multilayered, with cuboidal basal cells and flattened superficial cells. Cells were attached to each other by desmosomes. Adhesion complexes were observed between basal cells and the underlying carrier in LECs cultured on HAM, but not in LECs cultured on PL. GeneChip Human Gene 2.0 ST microarray (Affymetrix) analysis revealed that 18,653 transcripts were ≥2 fold up or downregulated (p ≤ 0.05). Cells cultured in the same medium (COM or HS) showed more similarities in gene expression than cells cultured on the same carrier (HAM or PL). When each condition was compared to HAM/COM, no statistical difference was found in the transcription level of the selected genes associated with keratin expression, stemness, proliferation, differentiation, apoptosis, corneal wound healing or autophagy. In conclusion, the results indicate that ex vivo cultures of LECs on HAM and PL, using culture media supplemented with COM or HS, yield tissues with similar morphology and keratin staining. The gene expression appears to be more similar in cells cultured in the same medium (COM or HS) compared to cells cultured on the same carrier (HAM or PL).