Tip and Trik menulis artikel ilmiah

Apr

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Manajemen Laboratorium berbasis GLP dan Penyusunan Dokumen

By Prof. Fatchiyah, Ph.D.

Oct

Kemenristekdikti sangat mendukung publikasi ilmiah di berbagai jurnal bereputasi nasional dan internasional. Untuk mendukung program tersebut lembaga riset di universitas maupun non universitas sebaiknya memiliki laboratorium-2 yang berstandar GLP atau good laboratory practice dan manajemen laboratorium yang memenuhi persyaratan sesuai dengan fungsi laboratorium yang ditetapkan masing-2 institusi. Manajemen laboratorium yang benar wajib menyusun dokumen-2 mutu dan pendukungnya.

Lampiran-lampiran yang bisa dipelajari

1. Modul Bimtek bioengineering Manajemen laboratorium

2. SNI-ISO-IEC-17025-2008-Standard

3. Pedoman gap_analysis_17025_2017_rev (1)_KAN

4. GLP Mangement and Document Fatchiyah

5. Pedoman Baru ISO 17025 2017 Fatchiyah_New

6. Peran PLP dalam Manajemen Laboratorium Pendidikan (Fatchiyah).compressed

SEMOGA BERMANFAAT

TABLE of GENETIC DISORDERS

By Prof. Fatchiyah, Ph.D.

Sep

Disease	Category	Pathogenesis / Heredity	Pathology, Cardinal Symptoms
Cystic Fibrosis		Autosomal Recessive. CFTR gene defect on Chrom 7 ——> No Cl^– transport and failure to hydrate mucous secretions (no NaCl transport) ——> excessively viscous mucoid exocrine secretions	Meconium ileus (caused by thick, mucoid meconium), respiratory bronchiectasis,Pseudomonas pneumonia, pancreatic insufficiency, hypertonic (high Cl^–concentration) sweat.
Fanconi Anemia		Autosomal Recessive congenital pancytopenia.	Normocytic anemia with neutropenia.Short stature, microcephaly, hypogenitalism, strabismus, anomalies of the thumbs, radii, and kidneys, mental retardation, and microphthalmia.
Hartnup’s Disease		Autosomal Recessive. Defect in GI uptake of neutral amino acids ——> malabsorption oftryptophan (niacin precursor) ——> niacin deficiency among other things.	Pellagra-like syndrome (diarrhea, dementia, dermatitis), light-sensitive skin rash, temporary cerebellar ataxia.
Kartagener’s Syndrome		Autosomal Recessive. Defect in dynein arms ——> lost motility of cilia	Recurrent sinopulmonary infections (due to impaired ciliary tract). *Situs inversus*, due to impaired ciliary motion during embryogenesis: lateral transposition of lungs, abdominal and thoracic viscera are on opposite sides of the body as normal. Possible dextrocardia, male sterility.
Pyruvate Dehydrogenase Deficiency		Autosomal Recessive. Pyruvate Dehydrogenase deficiency ——> buildup of lactate and pyruvate ——> lactic acidosis.	Neurologic defects.Treatment: Increase intake of ketogenic nutrients (leucine, lysine) ——> increase formation of Acetyl-CoA from other sources.
Xeroderma Pigmentosum		Autosomal Recessive. Defect in DNA repair, inability to repair thymine dimers resulting fromUV-light exposure ——> excessive skin damage and skin cancer.	Dry skin, melanomas, pre-malignant lesions, other cancers. Ophthalmic and neurologic abnormalities.
Familial Hypercholesterolemia	Autosomal Dominant Disorders	Autosomal Dominant. LDL-Receptor defect.	Heterozygous: accelerated atherosclerosis. Homozygous: accelerated atherosclerosis, MI by age 35, xanthomas.
Hereditary Hemorrhagic Telangiectasia (Osler-Weber-Rendu Syndrome)	Autosomal Dominant Disorders	Autosomal Dominant.	Telangiectasias of skin and mucous membranes.
Hereditary Spherocytosis	Autosomal Dominant Disorders	Autosomal Dominant. Band-3 deficiency in RBC membrane ——> spherical shape to cells. Other RBC structural enzyme deficiencies can cause it, too.	Sequestration of spherocytes in spleen ——> hemolytic anemia.
Huntington’s Disease	Autosomal Dominant Disorders	Autosomal Dominant, 100% penetrance.Genetic defect on Chrom 4 ——> atrophy of caudate nuclei, putamen, frontal cortex.	Progressive dementia with onset in adulthood, choreiform movements, athetosis.
Marfan’s Syndrome	Autosomal Dominant Disorders	Autosomal Dominant. Fibrillin deficiency ——> faulty scaffolding in connective tissue (elastin has no anchor).	Arachnodactyly, dissecting aortic aneurysms, ectopia lentis (subluxation of lens), mitral valve prolapse.
Neurofibromatosis (Von Recklinghausen Disease)	Autosomal Dominant Disorders	Autosomal Dominant. NF1 gene defect (no GTPase protein) ——> dysregulation of Ras tumor-suppressor protein.	Multiple neurofibromas (Café au Lait spots) which may become malignant,Lisch nodules (pigmented hamartomas of the iris).Increased risk for tumors: pheochromocytoma, Wilms tumor, Rhabdomyosarcoma, leukemias.
Tuberous Sclerosis	Autosomal Dominant Disorders	Autosomal Dominant.	Tubers (glial nodules), seizures, mental retardation. Associated with adenoma sebaceum (facial lesion), myocardial rhabdomyomas, renal angiomyolipomas.
Von Hippel-Lindau Syndrome	Autosomal Dominant Disorders	Autosomal Dominant, short arm of chromosome 3. Same genetic region is associated with incidence of renal cell carcinoma.	(1) Hemangioblastomas of cerebellum, medulla, or retina, (2) adenomas, (3) cysts in visceral organs. High risk for renal cell carcinoma.
Congenital Fructose Intolerance	Carbohydrate Metabolism Defect	Autosomal Recessive. Aldolase B deficiency ——> buildup of Fructose-1-Phosphate in tissues ——> inhibit glycogenolysis and gluconeogenesis.	Severe hypoglycemia. Treatment: Remove fructose from diet.
Galactosemia	Carbohydrate Metabolism Defect	Autosomal Recessive. Inability to convert galactose to glucose ——> accumulation of galactose in many tissues.(1) Classic form: Galactose-1-phosphate Uridyltransferase deficiency.(2) Rarer form: Galactokinase deficiency.	Failure to thrive, infantile cataracts, mental retardation. Progressive hepatic failure, cirrhosis, death.Galactokinase-deficiency: infantile cataracts are prominent.Treatment: in either case,remove galactose from diet.
Angelman Syndrome	Chromosomal	Deletion of part of short arm of chromosome 15, maternal copy. An example of genomic imprinting.	Mental retardation, ataxic gait, seizures.Inappropriate laughter.
Cri du Chat Syndrome	Chromosomal	5p-, deletion of the long arm of chromosome 5.	“Cry of the cat.” Severe mental retardation, microcephaly, cat-like cry. Low birth-weight, round-face, hypertelorism (wide-set eyes), low-set ears, epicanthal folds.
Down Syndrome(Trisomy 21)	Chromosomal	Trisomy 21, with risk increasing with maternal age. Familial form (no age-associated risk) is translocation t(21,x) in a minority of cases.	Most common cause of mental retardation. Will see epicanthal folds, simian crease, brushfield spots in eyes. Associated syndromes: congenital heart disease, leukemia,premature Alzheimer’s disease (same morphological changes).
Edward’s Syndrome(Trisomy 18)	Chromosomal	Trisomy 18	Mental retardation, micrognathia, rocker-bottom feet, congenital heart disease, flexion deformities of fingers. Death by 1 year old.
Patau’s Syndrome(Trisomy 13)	Chromosomal	Trisomy 13	Mental retardation, microphthalmia, cleft lip and palate, polydactyly, rocker-bottom feet, congenital heart disease. Similar to and more severe than Edward’s Syndrome. Death by 1 year old.
Prader-Willi Syndrome	Chromosomal	Deletion of part of short arm of chromosome 15, paternal copy. An example of genomic imprinting.	Mental retardation, short stature, hypotonia, obesity and huge appetite after infancy. Small hands and feet, hypogonadism.
Fragile-X Syndrome	ChromosomalSex chromosome	Progressively longer tandem repeats on the long arm of the X-chromosome. The longer the number of repeats, the worse the syndrome. Tandem repeats tend to accumulate through generations.	Second most common cause of mental retardation next to Down Syndrome. Macro-orchidism (enlarged testes) in males.
Klinefelter’s Syndrome (XXY)	ChromosomalSex chromosome	Non-disjunction of the sex chromosome during Anaphase I of meiosis ——> Trisomy (47,XXY)	Hypogonadism, tall stature, gynecomastia. Mild mental retardation. Usually not diagnosed until after puberty. One Barr body seen on buccal smear.
Turner’s Syndrome (XO)	ChromosomalSex chromosome	Non-disjunction of the sex chromosome during Anaphase I of meiosis ——> Monosomy (45,X)	Streak gonads, primary amenorrhea, webbed neck, short stature, coarctation of Aorta, infantile genitalia. No mental retardation. No Barr bodies visible on buccal smear.
XXX Syndrome	ChromosomalSex chromosome	Trisomy (47,XXX) and other multiple X-chromosome abnormalities.	Usually phenotypically normal. May see menstrual abnormalities or mild mental retardation in some cases.
Ehlers-Danlos Syndrome	Connective Tissue disease	Various defects in collagen synthesis. Type-I: Autosomal dominant, mildest form. Type-IV: autosomal dominant. Defect in reticular collagen (type-III) Type-VI: autosomal-recessive. Type-VII: Defect in collagen type I Type-IX: X-linked recessive	Laxity of joints, hyperextensibility of skin, poor wound healing, aneurysms. Type-I: Diaphragmatic hernia. Common, normal life-expectancy. Type-IV: Ecchymoses, arterial rupture. Dangerousdue to rupture aneurysms. Type-VI: Retinal detachment, corneal rupture
Osteogenesis Imperfecta	Connective tissue disease	Defects in Collagen Type I formation.	Multiple fractures after birth, blue sclerae, thin skin, progressive deafness in some types (due to abnormal middle ear ossicles).Type-I is most common;Type-II is most severe;Type-IV is mildest form.
Cori’s Disease(Glycogen Storage Disease Type III)	Glycogen Storage Disease	Autosomal Recessive. Debranching enzyme deficiency (can only break down linear chains of glycogen, not at branch points) ——> accumulate glycogen in liver, heart, skeletal muscle.	Stunted growth, hepatomegaly, hypoglycemia.
McArdle’s Disease(Glycogen Storage Disease Type V)	Glycogen Storage Disease	Autosomal Recessive. muscle phosphorylase deficiency (cannot utilize glycogen in skeletal muscle) ——> accumulation of glycogen in skeletal muscle.	Muscle cramps, muscle weakness, easy fatigability. Myoglobinuria with strenuous exercise.
Pompe’s Disease(Glycogen Storage Disease Type II)	Glycogen Storage Disease	Autosomal Recessive. alpha-1,4-Glucosidase deficiency (cannot break down glycogen) ——> accumulate glycogen in liver, heart, skeletal muscle.	Cardiomegaly, hepatomegaly, and systemic findings, leading to early death.
Von Gierke’s Disease(Glycogen Storage Disease Type I)	Glycogen Storage Disease	Autosomal Recessive. Glucose-6-Phosphatase deficiency (cannot break down glycogen) ——> accumulate glycogen in liver and kidney.	Severe fastinghypoglycemia, hepatomegaly from lots of glycogen in liver.
Hemophilia A (Factor VIII Deficiency)	Hemophilia	X-Linked Recessive. Factor VIII deficiency	Hemorrhage, hematuria, hemarthroses. Prolonged PTT.
Hemophilia B (Factor IX Deficiency)	Hemophilia	X-Linked Recessive. Factor IX deficiency.	Milder than Hemophilia A. Hemorrhage, hematuria, hemarthroses. Prolonged PTT.
Von Willebrand Disease	Hemophilia	Autosomal dominant and recessive varieties. Von Willebrand Factor deficiency ——> defect in initial formation of platelet plugs, and shorter half-life of Factor VIII in blood.	Hemorrhage, similar to hemophilia.Type-I: Most mild. Type-II: Intermediate. Type-III: most severe, with recessive inheritance (complete absence).
Ataxia-Telangiectasia	Immune deficiencyCombined Deficiency	Autosomal Recessive. Unknown. Numerous chromosomal breaks and elevated AFP is found. Symptomatic by age 2 years.	Cerebellar ataxia, telangiectasia (enlarged capillaries of face and skin), B and T-Cell deficiencies, IgA deficiency.
Chédiak-Higashi Syndrome	Immune deficiencyPhagocyte Deficiency	Defect in polymerization of microtubules in neutrophils ——> failure in neutrophil migration and phagocytosis. Also results in failure in lysosomal function in neutrophils.	Recurrent pyogenic infections, Staphylococcus, Streptococcus.
Chronic Granulomatous Disease	Immune deficiencyPhagocyte Deficiency	X-Linked (usually) NADPH Oxidase deficiency ——> no formation of peroxides and superoxides ——> no oxidative burst in phagocytes.	Failure of phagocytes leads to susceptibility to infections, especially Staph Aureus and Aspergillus spp. B and T cells usually remain normal.
Chronic Mucocutaneous Candidiasis	Immune deficiencyT-Cell Deficiency	T-Cell deficiency specific to Candida.	Selective recurrentCandida infections. Treat with anti-fungal drugs.
Job’s Syndrome	Immune deficiencyPhagocyte Deficiency	A failure to produce gamma-Interferon by T-Helper cells, leading to an increase in T_H2 cells (no negative feedback) ——> excessively high levels of IgE.	High histamine levels, eosinophilia. Recurrentcold (non-inflammatory) Staphylococcal abscesses(resulting from high histamine), eczema.
Selective IgA Deficiency	Immune deficiencyB-Cell Deficiency	IgA deficiency may be due to a failure of heavy-chain gene switching.	The most common congenital immune deficiency. There also exists selective IgM and IgG deficiencies, but they are less common.
Severe Combined Immunodeficiency (SCID)	Immune deficiencyCombined Deficiency	Autosomal Recessive. Adenosine Deaminase deficiency ——> accumulation of dATP ——> inhibit ribonucleotide reductase ——> decrease in DNA precursors	Severe deficiency in both humoral and cellular immunity, due to impaired DNA synthesis. Bone marrow transplant may be helpful in treatment.
Thymic Aplasia (DiGeorge Syndrome)	Immune deficiencyT-Cell Deficiency	Failure of development of the 3^rd and 4^th Pharyngeal Pouches ——> agenesis of the thymus and parathyroid glands.	T-Cell deficiency from no thymus. Hypocalcemic tetany from primary parathyroid deficiency.
Wiskott-Aldrich Syndrome	Immune deficiencyCombined Deficiency	Inability to mount initial IgM response to the capsular polysaccharides of pyogenic bacteria.	In infancy, recurrent pyogenic infections, eczema, thrombocytopenia, excessive bleeding. IgG levels remain normal.
X-Linked Agammaglobulinemia (Bruton’s Disease)	Immune deficiencyB-Cell Deficiency	X-Linked. Mutation in gene coding for tyrosine kinase causes failure of Pre-B cells to differentiate into B-Cells.	Recurrent pyogenic infections after 6 months (when maternal antibodies wear off). Can treat with polyspecific gamma globulin preparations.
Fabry’s Disease	Lysosomal Storage Disease	X-Linked Recessive. alpha-Galactosidase A deficiency ——> buildup of ceramide trihexosidein body tissues.	Angiokeratomas (skin lesions) over lower trunk, fever, severe burning pain in extremities, cardiovascular and cerebrovascular involvement.
Gaucher’s Disease	Lysosomal Storage Disease	Autosomal Recessive. Glucocerebrosidase deficiency ——> accumulation of glucocerebrosides (gangliosides, sphingolipids) in lysosomes throughout the body.	Type-I: Adult form. 80% of cases, retain partial activity. Hepatosplenomegaly, erosion of femoral head, mild anemia. Normal lifespan with treatment. Type-II: Infantile form. Severe CNS involvement. Death before age 1. Type-III: Juvenile form. Onset in early childhood, involving both CNS and viscera, but less severe than Type II.
Niemann-Pick Lipidosis	Lysosomal Storage Disease	Autosomal Recessive. Sphingomyelinase deficiency ——> accumulation of sphingomyelin in phagocytes.	Sphingomyelin-containingfoamy histiocytes in reticuloendo-thelial system and spleen. Hepatosplenomegaly, anemia, fever, sometimes CNS deterioration. Death by age 3.
Hunter’s Syndrome	Lysosomal Storage Disease	X-Linked Recessive. L-iduronosulfate sulfatase deficiency ——> buildup ofmucopolysaccharides (heparan sulfate and dermatan sulfate)	Similar to but less severe than Hurler Syndrome. Hepatosplenomegaly, micrognathia, retinal degeneration, joint stiffness, mild retardation, cardiac lesions.
Hurler’s Syndrome	Lysosomal Storage Disease	Autosomal Recessive. alpha-L-iduronidase deficiency ——> accumulation ofmucopolysaccharides (heparan sulfate, dermatan sulfate) in heart, brain, liver, other organs.	Gargoyle-like facies, progressive mental deterioration, stubby fingers, death by age 10. Similar to Hunter’s Syndrome.
Tay-Sachs Disease	Lysosomal Storage Disease	Autosomal Recessive. Hexosaminidase A deficiency ——> accumulation of G_M2 ganglioside in neurons.	CNS degeneration, retardation, cherry red-spot of macula, blindness (amaurosis). Death before age 4.
Albinism	Nitrogen Metabolism Defect	Autosomal Recessive. Tyrosinase deficiency ——> inability to synthesize melanin from tyrosine. Can result from a lack of migration of neural crest cells.	Depigmentation, pink eyes, increased risk of skin cancer.
Alkaptonuria	Nitrogen Metabolism Defect	Autosomal Recessive. Homogentisic Oxidase deficiency (inability to metabolize Phe and Tyr) ——> buildup and urinary excretion of homogentisic acid.	Urine turns dark and black on standing, ochronosis(dark pigmentation of fibrous and cartilage tissues), ochronotic arthritis, cardiac valve involvement. Disease is generally benign.
Homocystinuria	Nitrogen Metabolism Defect	Autosomal Recessive. Cystathionine synthase defect (either deficiency, or lost affinity for pyridoxine, Vit. B₆) ——> buildup of homocystine and deficiency of cysteine.	Mental retardation, ectopia lentis, sparse blond hair, genu valgum, failure to thrive, thromboembolic episodes, fatty changes of liver.Treatment: Cysteine supplementation, give excess pyridoxine to compensate for lost pyridoxine affinity.
Lesch-Nyhan Syndrome	Nitrogen Metabolism Defect	X-Linked Recessive. Hypoxanthine-Guanine Phosphoribosyltransferase (HGPRT) deficiency ——> no salvage pathway for purine re-synthesis ——> buildup of purine metabolites	Hyperuricemia (gout), mental retardation, self-mutilation (autistic behavior), choreoathetosis, spasticity.
Maple Syrup Urine Disease	Nitrogen Metabolism Defect	Autosomal Recessive. Deficiency of branched chain keto-acid decarboxylase ——> no degradation of branched-chain amino acids ——> buildup of isoleucine, valine, leucine.	Severe CNS defects, mental retardation, death. Person smells like maple syrup or burnt sugar. Treatment: remove the amino acids from diet.
Phenylketonuria (PKU)	Nitrogen Metabolism Defect	Autosomal Recessive. Phenylalanine hydroxylase deficiency (cannot break down Phe nor make Tyr) ——> buildup of phenylalanine, phenyl ketones (phenylacetate, phenyl lactate, phenylpyruvate) in body tissues and CNS.	Symptoms result from accumulation of phenylalanine itself. Mental deterioration, hypopigmentation (blond hair and blue eyes), mousy body odor (from phenylacetic acid in urine and sweat).Treatment: remove phenylalanine from diet.
Glucose-6-Phosphate Dehydrogenase (G6PD) Deficiency	RBC Disease	X-Linked Recessive. Glucose-6-Phosphate Dehydrogenase (G6PD) deficiency ——> no hexose monophosphate shunt ——> deficiency in NADPH ——> inability to maintain glutathione in reduced form, in RBC’s	Susceptibility to oxidative damage to RBC’s, leading to hemolytic anemia. Can be elicited by drugs (primaquine, sulfonamides, aspirin), fava beans (favism). More prevalent in blacks.
Glycolytic enzyme deficiencies	RBC Disease	Autosomal Recessive. Defect in hexokinase, glucose-phosphate isomerase, aldolase, triose-phosphate isomerase, phosphate-glycerate kinase, or enolase. Any enzyme in glycolysis pathway.	Hemolytic anemia results from any defect in the glycolysis pathway, as RBC’s depend on glycolysis for energy.
Autosomal Recessive Polycystic Kidney Disease (ARPKD)	Renal	Autosomal Recessive.	Numerous, diffuse bilateral cysts formed in the collecting ducts. Associated with hepatic fibrosis.
Bartter’s Syndrome	Renal	Juxtaglomerular Cell Hyperplasia, leading to primary hyper-reninemia.	Elevated renin and aldosterone, hypokalemic alkalosis. No hypertension.
Fanconi’s Syndrome Type I(Child-onset cystinosis)	Renal	Autosomal Recessive. Deficient resorption in proximal tubules.	(1) Cystine deposition throughout body, cystinuria. (2) Defective tubular resorption leads to amino-aciduria, polyuria, glycosuria, chronic acidosis;Hypophosphatemia andVitamin-D-resistant Rickets.
Fanconi’s Syndrome II(Adult-onset)	Renal	Autosomal Recessive. Defective resorption in proximal tubules.	Similar to Fanconi Syndrome Type I, but without the cystinosis. Adult onset osteomalacia, amino-aciduria, polyuria, glycosuria.
Autosomal Dominant Polycystic Kidney Disease (ADPKD)	RenalAutosomal Dominant Disorders	Autosomal Dominant.	Numerous, disparate, heterogenous renal cysts occurring bilaterally. Onset in adult life. Associated with liver cysts.

TABLE of GENETIC DISORDERS PDF

Ref.

http://www.kumc.edu/AMA-MSS/Study/table_of_genetic_disorders.htm

https://www.genome.gov/10001204/specific-genetic-disorders/

Jadual Kuliah Biologi Molekuler (MAB 4162: 2sks) JB-UB, Semester Ganjil 2016-2017 Kelas: B

By Prof. Fatchiyah, Ph.D.

Sep

Hari: Rabu 9:20-11:00 Ruang: MP 2.4

Tanggal	Topik	Dosen	Ket
1	Pendahuluan, konsep dasar dan prespektif biologi molekuler	F	Ceramah, Diskusi, Laptop, LCD
2	Struktur Molekuler dari gen dan Kromosom Replikasi DNA	F	Presentasi, Makalah, Diskusi Laptop. LCD, Video
3	Proses Transkripsi Gen pada sintesis protein	F	Presentasi, Makalah, Diskusi Laptop. LCD, Video
4	Proses Translasi Gen pada sintesis protein	F	Presentasi, Makalah, Diskusi Laptop. LCD, Video
5	Mekanisme regulasi secara umum level seluler & molekuler	ELA	Ceramah, Diskusi, Laptop, LCD,
6	Mekanisme regulasi gen prokariota	ELA	Presentasi, Diskusi Laptop. LCD, Video, Kuis
7	Mekanisme regulasi gen eukariota, Tanaman	ELA	Presentasi, Diskusi Laptop. LCD, Video
	UTS

10	Mekanisme regulasi gen eukariota: Human and animal	ELA	Presentasi, Diskusi Laptop. LCD, Video, Kuis
11	Struktur dasar Protein: determinasi & klasifikasi	SW	Ceramah, Diskusi, Laptop, LCD
12	Protein modification	SW	Ceramah, Diskusi, Laptop, LCD, Kuis
13	Functional Protein	SW	Presentasi, Makalah,Diskusi Laptop. LCD, Video
14	Interaksi antara DNA-Protein & Protein-Protein	SW	Presentasi, Makalah, Diskusi Laptop. LCD, Video, Kuis
15	Proteomics, Metabolomics, and Systems Biology Gene Regulation in Development and Evolution	Dosen Tamu	Ceramah, Diskusi, Laptop, LCD, Kuis

Keterangan:

Dosen Utama: F (Fatchiyah, Ph.D); ELA (Dr.Ir. Estri Laras A., MSc.St), SW (Dr. Sri Widyarti, MS)

Dosen tamu: akan ditetapkan kemudian

Jadual Kuliah Biologi Molekuler (MAB 4162: 2sks) JB-UB, Semester Ganjil 2016-2017 Kelas: A

By Prof. Fatchiyah, Ph.D.

Sep

Hari: Rabu 07:30-09:15 Ruang: MP 2.4

Minggu ke	Topik	Dosen	Ket
1, 7.8.16	Pendahuluan, konsep dasar dan prespektif biologi molekuler	F	Ceramah, Diskusi, Laptop, LCD
2	Struktur Molekuler dari gen dan Kromosom Replikasi DNA	F	Presentasi, Diskusi Laptop. LCD, Video
3	Proses Transkripsi Gen pada sintesis protein	F	Presentasi, Diskusi Laptop. LCD, Video
4	Proses Translasi Gen pada sintesis protein	F	Presentasi, Diskusi Laptop. LCD, Video
5	Mekanisme regulasi secara umum level seluler & molekuler	ELA	Ceramah, Diskusi, Laptop, LCD,
6	Mekanisme regulasi gen prokariota	ELA	Presentasi, Diskusi Laptop. LCD, Video, Kuis
7	Mekanisme regulasi gen eukariota, Tanaman	ELA	Presentasi, Diskusi Laptop. LCD, Video
24-10	UTS

10	Mekanisme regulasi gen eukariota: Human and animal	ELA	Presentasi, Diskusi Laptop. LCD, Video, Kuis
11	Struktur dasar Protein: determinasi & klasifikasi	SW	Ceramah, Diskusi, Laptop, LCD
12	Protein modification	SW	Ceramah, Diskusi, Laptop, LCD, Kuis
13	Functional Protein	SW	Presentasi, Diskusi Laptop. LCD, Video
14	Interaksi antara DNA-Protein & Protein-Protein	SW	Presentasi, Diskusi Laptop. LCD, Video, Kuis
15	Proteomics, Metabolomics, and Systems Biology Gene Regulation in Development and Evolution	Dosen Tamu	Ceramah, Diskusi, Laptop, LCD, Kuis

Keterangan:

Dosen Utama: F (Fatchiyah, Ph.D); ELA (Dr.Ir. Estri Laras A., MSc.St), SW (Dr. Sri Widyarti, MS)

Dosen tamu: akan ditetapkan kemudian

Schedule Lecture of Human Genetics (S1: MAB4161/ 2 sks) and Medical Genetics (S2) Biology Dept. UB, Odd Semester, Year 2016-2017

By Prof. Fatchiyah, Ph.D.

Sep

Day: Tuesday 14:45 – 16:30 Room: RB

week	Lerning Outcome	Focus study			Topics		Subtopics		Learning methods		Lecturer
1 start on 7.9.2015	Understand basic concepts of human genetics	Basic concepts of human genetics			Role of lectureBasic concepts of human genetics		–		Lecture and discussion		F
2	Understand Mendelian inheritance patterns of the different types of inheritance patterns of human disease.	Identify and Compare a Mendelian inheritance pattern of different types of inheritance patterns of human disease			Mendelian inheritance pattern of human disease Types of inheritance patterns of human disease		Mendel law, single gene and polygenetics factors Sex-linked, multifactorial and maternal inheritance		Presentation, Lecture and discussion, student homework		F
3-4	Understand Gene-environment interaction in behavior related Genomics to the study of complex diseases	Identifify Gene-environment interaction in behavior related Genomics to the study of complex diseases			Mapping and characterizing “complex” genetic diseases		Genomics for the study of complex diseases, genetic study of type 2 diabetes and obesity, Gene-environment interaction in behavior, pharmacogenetics		Presentation, Lecture and discussion		F
5-6	Understanding gene inheritance: Genes to proteins to traits	Identify Gene to protein synthesis			Transcription, post-transcription (mRNA maturation) and translation , post-translation (functional protein modification)		how a gene provides the instructions for making a protein and how genes can cause albinism or sickle cell anemia or other disease		Presentation, Lecture and discussion student homework		WN
6-8	Understand multigenic inheritance patterns.	Identify a multigenic inheritance pattern.			Mapping and characterizing “simple” genetic disease		Mapping disease genes, disease-associated mutations, diseases associated with a gene loss-function effect, nuclear and mitochondrial genome mutations, Evolution of a gene cluster and divergence of function		Presentation, Lecture and discussion student homework		WN
MIDDLE SEMESTER EXAMINATION
9-10	Understand the current research into epigenetic and transgenerational inheritance.		Explain the basics of epigenetic and transgenerational inheritance.	Sex, prions, and epigenetics		Epigenetic inheritance of chromatin states / Role of DNA methylation in human disease,dysregulation of the histone modification machinery, transgenerational epigenetic inheritance, sex determination, prion diseases		Presentation, Lecture and discussion student homework		WN
11-12	Understand how to interpret data from a genome-wide association (GWA) study and Genetic Testing		Analyze data from genome-wide association studies.	Genome-wide association (GWA) study and Genetic Testing		Genome-wide association (GWA) studyType, across the life span (prenatal, pediatric and adult), technology, molecular, clinical and ethical perspectives		Presentation, Lecture and discussion student homework		WN
13	Understand Chromosomal and genomic disorders		Identify Chromosomal and genomic disorders	Chromosomal and genomic disorders		Mechanisms and maternal age influence the origin of aneuploidy in humans, mechanisms causing these aberrations, fragile X syndrome		Presentation, Lecture and discussion student homework		F
14	Understand the potential implications of personalized and genomic medicine		Explain the potential benefits and risks/challenges of genomic medicine.	Natural genetics resources: the potential benefits and risks/challenges		Pharcogenenomic and/orNutrigenomic: Bioactive compound, phytopharmaca, functional food for healthy controlling		Presentation, Lecture and discussion student homework		F
15	Understand some of the ethical issues facing genomic researchers.		Explain some of the ethical challenges raised by the prevalence of genomic data	Medical genetics and the associated ethical, legal, and social implications		Ethical clearanceInform consent ELSI for medical research based on samples of human or animal model		Presentation, Lecture and discussion		F

Lecturer: F (Prof. Fatchiyah, PhD) and WN (Prof. Wolfgang Nellen)

Daftar Pustaka

Rick Lewis. 2011. Basic Human Genetics. Routledge Taylor & Francis group, NY · ISBN-10: 0415579864 · ISBN-13: 978-0415579865,

Ricki Lewis. 2011. Human Genetics concepts and application. McGraw-Hill Education; 10 edition ISBN-13: 978-0073525303, ISBN-10: 0073525308 or ISBN: 007246268x

Tom Strachan & Andrew Read.2003. Human Molecular genetics. Garland Science; 3 edition. · ISBN-10: 0815341822 · ISBN-13: 978-0815341826

Julian Knight.2009. Human Genetic Diversity. Oxford Univrsity Press. London.

Robert Nussbaum, Roderick R. McInnes, and Huntington F Willard. 2007. Genetics in Medicine, 7th Edition. Sounders. · ISBN: 9781416030805

John Quackenbush. 2011. The Human Genome: Book of Essential Knowledge. ISBN-13: 978-1936140152

Bruce R. Korf and Mira B. Irons. 2013. Human Genetics and Genomics. 4th Edition. Wiley-Blackwell. ISBN-10: 0470654473; ISBN-13: 978-0470654477

Jadual Kuliah Sidik Jari Molekuler (MAB4266: 2sks) JB-UB, Semester Ganjil 2016-2017

By Prof. Fatchiyah, Ph.D.

Sep

Hari: Selasa 13:00-14:45 Ruang: RB

Week	Topic	Learning Methods	lecture
Pertama 6.9.2016	Overview DNA Fingerprinting & DNA typing on Forensic Biology	Lecture	F
2	Sample tracking: Sample collection. extraction, purification, & storage Molecular sample preparation: isolasi dan analysis sampel molecular dan sekuensing	Lecture, Practice, mini project Lecture, Practice, mini project	F
3	Genetic basis of DNA typing (genomic or mtDNA)	Lecture, discussion of article DNA typing	F
4	Comparation of Fingerprinting DNA & Forensic DNA (CODIS, Y-chromosome, SNP, STR, SSP, DDGE)	discussion of articles on forensic DNA testing	F
5	Biomarker for microbe DNA Barcoding analysis	Lecture, Practice, mini project	F
6	DNA Barcoding analysis on molecular biodiversity and taxonomy of microbe	discussion of articles on microbe DNA typing & Barcoding	F
	Middle test	Two weeks	F
7	Bioinformatic Analysis: DNA Seq analysis, alignment, phylogenetic tree	Lecture Practice, online	NK
8	Molecular data Interpretation (UPGM, stat analysis, Clad)	Lecture, Practice, mini project	NK
9	Biomarker for animal DNA Barcoding analysis	Lecture, Practice, mini project	NK
10	DNA Barcoding analysis on animal molecular biodiversity and taxonomy	discussion of articles on insect DNA Barcoding	NK
11	DNA Barcoding analysis on animal molecular biodiversity and taxonomy	discussion of articles on insect DNA Barcoding	NK
12	Biomarker for plant DNA Finge typing and Barcoding analysis	Lecture, Practice, mini project	ELA
13	DNA Fingerprinting analayis on molecular biodiversity and taxonomy of plant	discussion of articles on Plant DNA Fingerprinting	ELA
14	DNA Fingerprinting analayis on molecular biodiversity and taxonomy of plant	discussion of articles on Plant DNA Fingerprinting	ELA

Tim Dosen: Prof. Fatchiyah, M.Kes., PhD. (F, Koordinator), Prof. Dr.Ir.Estri Laras Arumingtyas, MScSt (ELA), dan Nia Kurniawan, MP, Ph.D. (NK).

Practice dan Mini Project akan dilakukan saat praktikum–>Praktikum Mandiri

Acuan Bacaan

Bashinski, J. “Laboratory Standards: Accreditation, Training, and Certification of Staff in the Forensic Context.” p. 159-173. Ballantyne J, Sensabaugh G. DNA Technology and Forensic Science, Cold Spring Harbor, NY: Cold Spring Harbor Press, 1989.

Balke, M. and Schmidt S. 2012. Training of Trainers and Students Module II: DNA Barcoding Course material. Implementation of Indonesian-German Network for Teaching, Training and Research Collaborations (IGN-TTRC) UB Councils. Zoologische Staatssammlung, Munchen. German

Hughey, J. Bio 13- Introduction To Forensic DNA Analysis Lecture Manual: Section 5052, Fall 2011.

Kobilinsky, L., Liotti, T. F. & Oeser-Sweat, J. DNA: Forensic and Legal Applications. Wiley-Interscience, New Jersey, 2004. ISBN: 0471414786.

Kirby, L.T. 1990. DNA Fingerprinting: An Introduction. W. H. Freeman.

Krawczak, M. & J. Schmidtke. 1994. DNA Fingerprinting. Books International, Inc.

Moriniere, Jerome. 2012. Apractical lab manual for molecularphylogenetics, barcoding and friends. Bavarian state collection of zoology. Zoologische Staatssammlung, Munchen. German

OSHA Bloodborne Pathogen Standard. 1992. Fisher Scientific.

Saferstein, R. 2001. Forensic Science Handbook. Prentice Hall

Weedn VW, Roby RK. Forensic DNA Testing. Arch Pathol Lab Med 1993;117:486-491

Weblink:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0014448

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028832

http://fatchiyah.lecture.ub.ac.id

Inviting Speaker on Int Conf Obesity & Chronic Disease, LV, Nevada, USA July 25-27, 2016

By Prof. Fatchiyah, Ph.D.

Jul

Black Tea Leaves and Rambutan Peel from Indonesia Natural Plant has Biological Function as Anti-obesity Agents: Nutritional Genomic Study

Fatchiyah Fatchiyah

Head of Research Center of Smart Molecule from Natural Genetics Resources, Department of Biology, Faculty of Mathematic and Natural Sciences, Brawijaya University, Jl. Veteran, Malang 5145, INDONESIA. Email: fatchiya@ub.ac.id; +62 341575841

Abstract

Obesity is one global problem not only in developed countries, but also developing country. The number of obese people in Indonesia is increasing in line with the change of lifestyle. Nowadays, Indonesia entered into the top ten countries with developing overweight and obesity, around 40% of the adult population. This is alarming to become a major public health concern. Obesity is a complex disease causing lack energy balance in the body, genetics & environmental factors, lifestyle and malnutrition. Indeed, Indonesia has a rich of natural plants such as tea leaves, rambutan peels, legumes, brown rice, fruits and vegetables. The ingredients of natural plants are able to control the developing obesity through the cell signaling pathway which is organized at the level of proteins and biological active compounds and has ability to interact and modulate molecular mechanisms underlying an organism’s physiological function. Our previous studies by animal model and in silico analysis shown the catechin of black tea leaves could lose the rat body weight gain and inhibit the Igf-1 protein and Igf-1 receptor interaction in the adipocyte. The ability of EC, EGC and EGCG of black tea was only prevented the L1-domain of IGF-1R binds of IGF-1 protein and reduced the adipocyte proliferation. The rambutan peel extract (RPE) was also protected the receptor of Igf-1 interact with its ligand protein in obese rats, both expressions were lower than control rat group. RPE has an ability to down regulate directly the adipogenesis regulation of PPARγ gene expression and mRNA level of FABP4 genes and also prevent the body weight gain by the declining size of the adipocyte in an obese rat model, respectively. Conclusion: catechin of black tea leaves and bioactive compound of rambutan peel extract has potential as an anti-obesity agents through regulation of the molecular signaling pathway of the adipogenesis gene cascade.

Keywords: adipogenesis, black tea, catechin, obese animal model, rambutan peel extract

USG_ICOCD-2016_Program

New Publication 2016

By Prof. Fatchiyah, Ph.D.

Jul

Takeshi Ohta, Yasufumi Toriniwa, Naruhiko Ryumon, Nobuhiro Inaba, Tadaaki Hirao, Saori Yamanaka, Takayuki Maeno, Wakako Sakakibara, Morio Sumikawa, Kaoru Chiba, Akiko Nakamura, Katsuhiro Miyajima, Fatchiyah Fatchiyah, And Takahisa Yamada. Maternal high-fat diet promotes onset of diabetes in rat offspring. Animal Science Journal (2016) ••, ••–••, doi:10.1111/asj.12606

Siti Nur Aisyah, Hafid Harnas, Sulastri Sulastri, Retmi Retmi, Helmi Fuaddi, Fatchiyah Fatchiyah, Amri Bakhtiar, Jamsari Jamsari. Enhancement of a Novel Isolate of Serratia plymuthica as Potential Candidate for an Antianthracnose. Pakistan Journal of Biological Sciences. 2016: 1-9 ISSN 1028-8880, DOI: 10.3923/pjbs.2016

Elly Syafriani , Femi Riwany, Rahmi Kamelia, Istino Ferita, Fatchiyah Fatchiyah, Jamsari Jamsari. A Promising Novel Rhizobacteria Isolate UBCR_12 as Antifungal for Colletotrichum gloeosporioides. Research Journal of Pharmaceutical, Biological and Chemical Sciences. May 2016; 7 (3): 2201-2209

Hasil-hasil Riset peneliti RG Smonagenes UB disitasi dalam Sigma-Aldrich

By Prof. Fatchiyah, Ph.D.

Feb

Hasil-hasil Riset peneliti RG Smonagenes UB disitasi dalam Sigma-Aldrich bisa dicek di

Pogestemon herba

http://www.sigmaaldrich.com/catalog/papers/25484897

http://www.sigmaaldrich.com/catalog/papers/23559751#

Pachouil alcohol

http://www.sigmaaldrich.com/catalog/papers/61adea67-e075-46a4-8c40-00af77f419ab#

http://www.sigmaaldrich.com/catalog/papers/26483598

http://www.sigmaaldrich.com/catalog/papers/26005274#

http://www.sigmaaldrich.com/catalog/papers/8e007c84-23a7-4a3a-a358-407eaa2f7552#

http://www.sigmaaldrich.com/catalog/papers/aabdb08b-4ab0-41ec-ade7-1b91555c4e93

http://www.sigmaaldrich.com/catalog/papers/3997fd80-a96d-487f-a74d-db48b9ac8c3f

http://www.sigmaaldrich.com/catalog/papers/90d936e5-aeb0-4343-8a1f-2d70b712692a

Obese Rambutan peel

PPAR gamma rambutan peel

CSN1S2 RA disease RAGE

CSN1S2 Pre-Osteoblast

CSN1S2 Diabetes

CSN1S2 RA disease

CSN1S2 Jak-Stat3

Lecture Bio-Ethics Research: Guideline of Ethical Research using non-Human animal

By Prof. Fatchiyah, Ph.D.

Feb

Bioethics research:

Morality is a unique feature of the life of human beings. It is deeply influenced by several cultural factors, such as history, traditions, education, religious beliefs, etc.
The intellectual analysis of this human dimension in all of its complexity is the goal of the discipline called Ethics. Ethics does not create morality or moral behavior.
The goal of ethics is much more modest: to explore the nature of moral experience, its universality and its diversity.
Ethics and morality are generally taken as synonyms, because they originally had the same meaning: the study of the disposition, character, or attitude of a specific person, group of people or culture, and ways of promoting or perfecting it.

As a field of study, psychology examines a broad range of research and applied areas. Important parts of such work are teaching and research on the behavior of nonhuman animals, which contribute to the understanding of basic principles underlying behavior and to advancing the welfare of both human and nonhuman animals. While psychologists must conduct their teaching and research in a manner consonant with relevant laws and regulations, ethical concerns further mandate that psychologists consider the costs and benefits of procedures involving animals before proceeding with these activities.

The 3Rs Principle of Replacement, Reduction and Refinement is central to the Guidelines. Since the concept of the 3Rs was first introduced by William Russell and Rex Burch in The Principles of Humane Experimental Technique in 1959, the 3Rs have been internationally accepted as the basis of the care and use of animals for scientific purposes. These are: to Replace the need for animal use by alternative means, to Reduce
the numbers of animals used to an unavoidable minimum, and to Refine any procedures necessarily used, so as to minimize the impact on animals, consistent with the achievement of a justifiable scientific purpose, and which is necessary because there is no other way of achieving that purpose. The incorporation of the 3Rs at the planning stages ensures that full consideration of the principle is exercised at every juncture of the process.

1. care-animal-non human research guidelines (PDF)

2. NACLAR-guide Lines using animal model (PDF)

bioethic syllabi WHO

Lect 2 Laik Ethik riset dengan Hewan Coba FAT

Lec 1 – Bioethics-Research

JADWAL MK Bioetika penelitian hayati

JADWAL KULIAH BIOINFORMATIKA SEMESTER GENAP JURUSAN BIOLOGI FMIPA UNIVERSITAS BRAWIJAYA

By Prof. Fatchiyah, Ph.D.

Feb

Hari : Rabu

Pukul : 09.20 – 11.05 WIB

Tempat : MC3.1

NO.	TANGGAL	TOPIK	DOSEN
1.	18-2-2015	Pendahuluan	F
2.	25-2-2015	Dasar-dasar browsing and Searching GeneBank: Nucleotide Database	F
3.	4-3-2015	Nucleotide sequence analysis	F
4.	11-3-2015	dbSNP sequence Variation (Kuis)	F
5.	18-3-2015	Student Presentation: Nucleotide database to genome mapping and analysis (SCL)	F
6.	25-3-2015	Polymorfisme and variation genome	F
7.	1-4-2015	Comparative genome, Taxonomy and evolution (Kuis)	F
8.	8-4-2015	Student Presentation: Polymorphisme to taxonomy mapping (SCL)	F
9.	15-4-2015	UJIAN TENGAH SEMESTER	F

10.	29-4-2015	Dasar-dasar browsing and Searching GeneBank: protein and PDB Database	W
11.	6-5-2015	Protein sequence analysis	W
12.	13-5-2015	3D protein analysis (kuis)	W
13.	20-5-2015	Protein folding	W
14.	27-5-2015	Protein network pathway (TT)	W
15.	3-6-2015	Student Presentation: 3D protein to protein folding & network pathway (SCL)	W
		UJIAN AKHIR SEMESTER	W

Keterangan: F : Prof. Fatchiyah, M.Kes., Ph.D. W : Widodo, S.Si., M.Si., Ph.D.Med.Sc.

SCL: berupa mini projek.

ASSESMENT

Nilai Kuliah (NK):

Ujian Tengah Semester : 35%
Ujian akhir : 35%
Kuis :10%
Diskusi/keaktifan di kelas :10%
Tugas : 10%

Nilai Praktikum (NP):

Placements test : 20 %
Laporan : 40 %
Ujian Akhir Praktikum : 40 %

Nilai Akhir (NA) : (2 NK + 1 NP)/3

Skor Nilai Akhir (Nilai Huruf = NH):

≥80 : A

76-<80 : B+

70- <76 : B

60- <70 : C+

56- <60 : C

50- <56 : D+

46- <50 : D

>46 : E

Daftar Pustaka:

Fatchiyah. 2015. Prinsip Dasar Bioinformatika. UB Press. Malang
Marketa Zvelebil and Jeremy O. Baum, 2008, Understanding bioinformatic, Garland Science, Taylor and Francis group publisher
Jean-Michel Claverie, Ph. D., Cedric Notredame, Ph.D. 2006, Bioinformatics For Dummies, 2nd Edition, For Dummies Publisher
Cynthia Gibas and Per Jambeck, 2001, Developing Bioinformatics Computer Skills, O’Reilly Media publisher.
Huaiyu Mi and Paul Thomas. Methods in Molecular Biology, 2009, Volume 563, Part 2, 123-140

GeneBank: NCBI GeneBank: www.ncbi.nlm.nih.gov/,
DDBJ: http://www.ddbj.nig.ac.jp/
Embl: http://www.ebi.ac.uk/
Protein analysis: http://www.expasy.ch/sprot/sprot-top.html
protein characterization http://www.mips.biochem.mpg.de dan http://www.protomap.cs.huji.ac.il
Database alligment sequence: Hovergen http://pbil.univ-lyon1.fr/databases/hovergen.html (vertebrate alignments)
Pfam http://www.sanger.ac.uk/Software/Pfam/ (protein domain alignments and profile HMMs)
BLOCKS http://blocks.fhcrc.org/

14. Ribosomal Database Project http://rdp.cme.msu.edu/html/ alignments and trees derived from rRNA sequences

JADWAL KULIAH TEKNIK ANALISIS BIOLOGI (GENETIK) MOLEKULER SEMESTER GENAP JURUSAN BIOLOGI FMIPA UNIVERSITAS BRAWIJAYA

By Prof. Fatchiyah, Ph.D.

Feb

Hari : Kamis

Pukul :09.20 – 11.05 WIB

Tempat :R. Biologi

NO.	TANGGAL	TOPIK	DOSEN
1.	26-2-2015	Pendahuluan	ELA
2.	5-3-2015	Teknik dasar analisis bahan genetic (DNA, RNA) dan cara pengukuran biomolekul secara kualitatif & kuantitatif	ELA
3.	12-3-2015	Dasar teknik amplifikasi DNA-RNA dan aplikasinya (SCL)	ELA
4.	19-3-2015	Pembuatan Probe	F
5.	26-3-2015	Analisis polimorfisme & Manipulasi genetik	F
6.	2-4-2015	Hibridisasi: Sistem deteksi gen & level mRNA (kuiz)	F
7.	9-4-2015	DNA sequencing (SCL)	F
8.	16-4-2015	UJIAN TENGAH SEMESTER	TIM
9.	23-4-2015
10.	30-4-2015	Dasar teknik-teknik kloning Molekuler (kuiz)	F
11.	7-5-2015	Teknik dasar isolasi dan presipitasi protein	SW
12.	21-5-2015	Pembuatan kurva protein standard dan mengukur kadar Protein (SCL)	SW
13.	28-5-2015	Electrophoresis protein	SW
14.	4-6-2015	Analisis Protein (immunoblotting)	SW
15.	11-6-2015	Immunohistochemistry (SCL)	SW
16.		UJIAN AKHIR SEMESTER	TIM

Keterangan: F : Prof. Fatchiyah, M.Kes., Ph.D., ELA: Prof. Dr. Ir. Estri Laras Arumningtyas, M.Sc.St., SW: Dr. Sri Widyarti, M.Si.

SCL: diisi dengan mini projek dari kelompok mahasiswa yang telah ditetapkan.

ASSESMENT

Nilai Kuliah (NK):

Ujian Tengah Semester : 35%
Ujian akhir : 35%
Kuis :10%
Diskusi/keaktifan di kelas :10%
Tugas : 10%

Nilai Praktikum (NP):

Placements test : 20 %
Laporan : 40 %
Ujian Akhir Praktikum : 40 %

Nilai Akhir (NA) : (NK + NP)/2

Skor Nilai Akhir (Nilai Huruf = NH):

≥80 : A

76-<80 : B+

70- <76 : B

60- <70 : C+

56- <60 : C

50- <56 : D+

46- <50 : D

>46 : E

D. DAFTAR PUSTAKA

Fatchiyah, Sri Widyarti, Estri Laras Arumingtyas, Sri Rahayu, 2008, Teknik Dasar Analisis Biologi Molekuler, Universitas Brawijaya, Malang.
Fatchiyah, Sri Widyarti, Estri Laras Arumingtyas, Sri Rahayu, 2011. Biologi Molekuler: Prinsip Dasar Analisis. Penerbit Erlangga, Jakarta.
Andrews AT. 1980. Electrophoresis: Theory, Techniques & Biochemical and Clinical Apllication. 2^nd Ed. Clarendon Press, Oxford.
Ausubel FM., Brent R., Kingston RE., Moore D., Seidman JG. Smith JA. Struhl K. 2002. Short Protocols in Molecular Biology. 5^rd Ed. John Wiley & Sons.
GeneBank: NCBI GeneBank: www.ncbi.nlm.nih.gov/,5

DDBJ: http://www.ddbj.nig.ac.jp/

Embl: http://www.ebi.ac.uk/

Innis MA. Gelfand DH., Sninsky JJ. 1999. PCR Application Protocol for Functional Genomics. Academics Press
Sambrook J. & Russel DW. 2001. Molecular Cloning: A laboratory manual. Cold Spring Harbor. www.cshl.org/sambrook
Bollag DM., & Edelstein SJ. 1991. Protein Methods. A John Wiley & Sons.
Harlow E. & Lane D. 1988. Antibodies: A laboratory manual. ColdSpring
Harbor Konfermann R. & Dubel S. 2001. Antibody Engeneering. Springer Lab. Manual. www.duebel.uni-hd.de
Robyt JF & White BJ. 1990. Biochemical Techniques: Theory & Practice. Brooks/Cole Pub.
Wilson K & Walker J. 2004. Principles & Techniques of Practical Biochemistry. 4^th Ed. Cambridge University Press. www.cup.cam.ac.uk/wilson Atau www.cup.org/wilson

New publication on RG Smonagenes UB

By Prof. Fatchiyah, Ph.D.

Feb

My group publication has been published on Research-gate

https://www.researchgate.net/profile/Fatchiyah_Fatchiyah/publications/

2015

Fatchiyah F, Setiawan B,Suharjono S, Noor Z. The anti-osteoporosis effects of CSN1S2 protein of goat milk and yoghurt on a complete Freund’s adjuvant-induced rheumatoid arthritis model in rats. Biomarkers and Genomic Medicine (2015b) xx, 1-8. http://dx.doi.org/10.1016/j.bgm.2015.10.001

Vita Agustina, Bambang Setiawan , Fatchiyah Fatchiyah. 2015. Acute toxicity of caprine alpha S2-casein protein on the microstructures and mineral profiles of rat ileum. Asian Pacific Journal of Tropical Disease, 08/2015; 5(9):721-725. DOI:10.1016/S2222-1808(15)60920-3

B Tong, G Q Gao, Y Muramatsu, T Ohta, H Kose, G P Li, F Fatchiyah, T Yamada. Association of the expression levels in the longissimus muscle and a SNP in the CDC10 gene with marbling in Japanese Black beef cattle. Meat Science 108:28-31 May 2015

Rista Nikmatu Rohmah, Ferlany Hardiyanti, Fatchiyah Fatchiyah. Inhibition on JAK-STAT3 Signaling Transduction Cascade Is Taken by Bioactive Peptide Alpha-S2 Casein Protein from Goat Ethawah Breed Milk. Acta Informatica Medica 07/2015; 23(4):233-238. DOI:10.5455/aim.2015.23.233-238

Lecture teknik analisis sidik jari molekuler

By Prof. Fatchiyah, Ph.D.

Sep

lecture-Teknik Analisis sidikjari molekuler OK

material lecture of Molecular Fingerprint

By Prof. Fatchiyah, Ph.D.

Sep

material lecture:

1. DNA fingerprinting and barcoding (fat-UB 2015)

2. Lecture Intro Forensic Science DNA Testing

3. 5.dbSnp of nucleotide Seq Variation

4. Lecture DNA Barcode (taxmol or molEvo)

5. dbSNP variation

Jadual Kuliah Biologi Molekuler (MAB 4162) Kelas A dan B JB UB

By Prof. Fatchiyah, Ph.D.

Sep

Jadual Kuliah Biologi Molekuler (MAB 4162: 2sks)

JB-UB, Semester Ganjil 2015-2016

Kelas: A

Hari: Rabu 07:30-09:15 Ruang: MP 2.4

No	Tanggal	Topik	Dosen	Ket
1	09-9-15	Pendahuluan, konsep dasar dan prespektif biologi molekuler	F	Ceramah, Diskusi, Laptop, LCD
2	16-9-15	Struktur Molekuler dari gen dan Kromosom Replikasi DNA	F	Presentasi, Diskusi Laptop. LCD, Video
3	23-9-15	Proses Transkripsi Gen pada sintesis protein	F	Presentasi, Diskusi Laptop. LCD, Video
4	30-9-15	Proses Translasi Gen pada sintesis protein	F	Presentasi, Diskusi Laptop. LCD, Video
5	7-10-15	Mekanisme regulasi secara umum level seluler & molekuler	ELA	Ceramah, Diskusi, Laptop, LCD,
6	14-10-15	Mekanisme regulasi gen prokariota	ELA	Presentasi, Diskusi Laptop. LCD, Video, Kuis
7	21-10-15	Mekanisme regulasi gen eukariota, Tanaman	ELA	Presentasi, Diskusi Laptop. LCD, Video
8	28-10-15	UTS
	04-11-15
9	11-11-15	Mekanisme regulasi gen eukariota: Human and animal	ELA	Presentasi, Diskusi Laptop. LCD, Video, Kuis
10	18-11-15	Struktur dasar Protein: determinasi & klasifikasi	SW	Ceramah, Diskusi, Laptop, LCD
11	25-11-15	Protein modification	SW	Ceramah, Diskusi, Laptop, LCD, Kuis
12	02-12-15	Functional Protein	SW	Presentasi, Diskusi Laptop. LCD, Video
13	09-12-15	Interaksi antara DNA-Protein & Protein-Protein	SW	Presentasi, Diskusi Laptop. LCD, Video, Kuis
14	16-12-15	Proteomics, Metabolomics, and Systems Biology	WDD	Ceramah, Diskusi, Laptop, LCD, Kuis
15	23-12-15	Gene Regulation in Development and Evolution	SBS	Ceramah, Diskusi, Laptop, LCD, Kuis
16		UAS

Keterangan:

Dosen Utama: F (Fatchiyah, Ph.D); ELA (Dr.Ir. Estri Laras A., MSc.St), SW (Dr. Sri Widyarti, MS)

Dosen tamu: WDD (Widodo, PhD.) and SBS (Prof. Sutiman B. Sumitro, SU, D.Sc.).

Jadual Kuliah Biologi Molekuler (MAB 4162: 2sks)

JB-UB, Semester Ganjil 2015-2016

Kelas: B

Hari: Rabu 9:20-11:00 Ruang: MP 2.4

No	Tanggal	Topik	Dosen	Ket
1	090-9-15	Pendahuluan, konsep dasar dan prespektif biologi molekuler	F	Ceramah, Diskusi, Laptop, LCD
2	16-9-15	Struktur Molekuler dari gen dan Kromosom Replikasi DNA	F	Presentasi, Makalah, Diskusi Laptop. LCD, Video
3	23-9-15	Proses Transkripsi Gen pada sintesis protein	F	Presentasi, Makalah, Diskusi Laptop. LCD, Video
4	30-9-15	Proses Translasi Gen pada sintesis protein	F	Presentasi, Makalah, Diskusi Laptop. LCD, Video
5	7-10-15	Mekanisme regulasi secara umum level seluler & molekuler	ELA	Ceramah, Diskusi, Laptop, LCD,
6	14-10-15	Mekanisme regulasi gen prokariota	ELA	Presentasi, Diskusi Laptop. LCD, Video, Kuis
7	21-10-15	Mekanisme regulasi gen eukariota, Tanaman	ELA	Presentasi, Diskusi Laptop. LCD, Video
8	28-10-15	UTS
	04-11-15
9	11-11-15	Mekanisme regulasi gen eukariota: Human and animal	ELA	Presentasi, Diskusi Laptop. LCD, Video, Kuis
10	18-11-15	Struktur dasar Protein: determinasi & klasifikasi	SW	Ceramah, Diskusi, Laptop, LCD
11	25-11-15	Protein modification	SW	Ceramah, Diskusi, Laptop, LCD, Kuis
12	02-12-15	Functional Protein	SW	Presentasi, Makalah,Diskusi Laptop. LCD, Video
13	09-12-15	Interaksi antara DNA-Protein & Protein-Protein	SW	Presentasi, Makalah, Diskusi Laptop. LCD, Video, Kuis
14	16-12-15	Proteomics, Metabolomics, and Systems Biology	WDD	Ceramah, Diskusi, Laptop, LCD, Kuis
15	23-12-15	Gene Regulation in Development and Evolution	SBS	Ceramah, Diskusi, Laptop, LCD, Kuis
16		UAS

Keterangan:

Dosen Utama: F (Fatchiyah, Ph.D); ELA (Dr.Ir. Estri Laras A., MSc.St), SW (Dr. Sri Widyarti, MS)

Dosen tamu: WDD (Widodo, PhD.) and SBS (Prof. Sutiman B. Sumitro, SU, D.Sc.).

Malang,

Koordinator

Prof. Fatchiyah, Ph.D

assigment 1 of human genetics lecture

By Prof. Fatchiyah, Ph.D.

Sep

Home works of Human Genetics Lecture: Pedigree Analysis

The answers of home work send to email: molbiol.bio.ub@gmail.com

Before September 17, 2015

HOME WORKS Pedegree analysis (pre exam 1)

Materi Workshop Pengelolaan Laboratorium oleh RG Smonagenes UB

By Prof. Fatchiyah, Ph.D.

Sep

Workshop Pengelolaan Laboratorium diselenggarakan oleh RG Smonagenes UB dalam rangka PHK C

workshop ini diberikan ke peserta non PLP di UB, dan PLP di PTN dan PTS serta SMU se Kodya Malang,

Di ruang pertemuan MIPA center, Universitas Brawijaya, Malang. Durasi workshop selama 40 jam kerja, dimulai hari Senin 7 September 2015.

pemateri : Prof Fatchiyah, Dr.Ir. Gatot Ciptadi, Dr. Arie Srihardyastutie, M.Biomed., Instruktur: Dr.dr. Nurdiana, M.Kes., Dr. Titin Andri Wihastuti, Luluk, Setyowati, Rista NR, Faraline, dan Antonius Christianto.

materi pemateri 1:

1. Peran PLP dalam Manajemen Laboratorium Pendidikan (Fatchiyah)

2. Seluk beluk Pranata Laboratorium Pendidikan Perguruan Tinggi

RPS MK Sidik Jari Molekuler

By Prof. Fatchiyah, Ph.D.

Sep

Matriks Rencana Pembelajaran Semester Mata Kuliah Sidik Jari Molekuler.

Minggu ke	Kemampuan Akhir yang Diharapkan (CLO)	Bahan kajian	Pokok Bahasan (topics)	Sub Pokok Bahasan (subtopics)	Bentuk Pembelajaran (Learning methods)	Indikator/Kriteria Penilaian (Value Criteria)	Bobot Nilai (%)	Fasilitas Pembelajaran (learning Facility)
1	Menjelaskan Dasar-dasar sidik jari DNA dan DNA typing dalam forensik	Dasar-dasar sidik jari DNA dan DNA typing dalam forensik	Overview Dasar-dasar sidik jari DNA dan DNA typing dalam forensik	DNA Fingerprinting & DNA typing on Forensic Biology	Lecture and discussion	Kebenaran dan ketepatan analisis	6	Laptop, LCD, module
2	Melakukan pengambilan sampel, purifikasi, penyimpanan	Pengambilan sampel, purifikasi, penyimpanan	Sample tracking	Sample collection, extraction, purification & storage	Presentation, Lecture and discussion	Kebenaran dan ketepatan analisis	6	Laptop, LCD, module, paper exam
3	Menetapkan metode isolasi dan analysis sampel molecular dan sekuensing	Molecular sample preparation	isolasi dan analysis sampel molecular dan sekuensing	DNA isolation, PCR, DDGE and Sequencing	Presentation, Lecture and discussion	Kebenaran dan ketepatan analisis	10	Laptop, LCD, module, paper exam
4	Memahami perbedaan genome dan mitokodria typing	Genetic basis of DNA typing	Basic Analysis of DNA typing	Genomic or mitokondria DN A	Presentation, Mini Project Lecture and discussion	Kebenaran dan ketepatan analisis	6	Laptop, LCD, module, paper exam
5	Membedakan Fingerprinting DNA & Forensic DNA system	Comparation of Fingerprinting DNA & Forensic DNA system	Fingerprinting DNA & Forensic DNA system	CODIS, Y-chromosome, SNP, STR, SSP, HLA typing	Presentation, Mini Project Lecture and discussion	Kebenaran dan ketepatan analisis	6	Laptop, LCD, module, paper exam
6	Menganlisis data molekuler secara in silico	Analisis data molekuler secara in silico	Bioinformatic Analysis	DNA Seq analysis, alignment, phylogenetic tree	Presentation, mini project, Lecture and discussion	Kebenaran dan ketepatan analisis	10	Laptop, LCD, module, paper exam
7	Menjelasakan Dasar teori DNA Barcoding	Dasar teori DNA Barcoding	DNA Barcoding analysis	What is DNA Barcoding? Biomarker for DNA animal barcode	Presentation, Lecture and discussion	Kebenaran dan ketepatan analisis	6	Laptop, LCD, module, paper exam
8			Middle test
9	Membandingkan analisis DNA Barcoding pada biodiversitas dan kekerabatan hewan	Analisis DNA Barcoding pada biodiversitas dan kekerabatan hewan	DNA Barcoding analysis on animal molecular biodiversity and taxonomy	Barcode of Life Data Systems (BOLD) database GeneBank Database for DNA & Protein	Presentation, Mini Project Lecture and discussion	Kebenaran dan ketepatan analisis	16	Laptop, LCD, module, paper exam
10	Membandingkan dasar analisis kekerabatan spesies	Dasar-dasar analisis kekerabatan spesies	Molecular data Interpretation	UPGM, statistics analysis, Clad	Presentation, Lecture and discussion	Kebenaran dan ketepatan analisis	6	Laptop, LCD, module, paper exam
11	Membandingkan analisis DNA Barcoding pada biodiversitas dan kekerabatan pada mikrobia	Analisis DNA Barcoding pada biodiversitas dan kekerabatan pada mikrobia	Biomarker for microbe DNA Barcoding analysis	16SRNA, SNP, SST	Presentation, Mini Project Lecture and discussion	Kebenaran dan ketepatan analisis	6	Laptop, LCD, module, paper exam
12	Membandingkan dasar analisis DNA Barcoding utuk kekerabatan spesies	Dasar analisis DNA Barcoding utuk kekerabatan spesies	DNA Barcoding analysis on molecular biodiversity and taxonomy of microbe	Bacteri, Virus, Jamur	Presentation, Lecture and discussion	Kebenaran dan ketepatan analisis	6	Laptop, LCD, module, paper exam
13-14	Menenetapkan biomarker untuk analisis sisdik jari pada tanaman	Type biomarker untuk analisis sisdik jari pada tanaman	Biomarker for plant DNA Fingertyping and Barcoding analysis	Minisatelite, microsatelite	Presentation, Lecture and discussion	Kebenaran dan ketepatan analisis	6	Laptop, LCD, module, paper exam
15	Membandingkan analisis DNA Barcoding pada biodiversitas dan kekerabatan pada tanaman	Analisis DNA Barcoding pada biodiversitas dan kekerabatan pada tanaman	DNA Fingerprinting analayis on molecular biodiversity and taxonomy of plant	RFLP, Simple sequence length polymorphisms (SSLP), RAPD	Presentation, Mini Project, Lecture and discussion	Kebenaran dan ketepatan analisis	6	Laptop, LCD, module, paper exam

Daftar Pustaka

John M Butler. 2009. Fundamentals of Forensic DNA Typing 1st Edition. Academic Press. ISBN-13: 978-0123749994. ISBN-10: 0123749999

Richads Li. 2015. Forensic Biology. 2nd Edition. CRS. · ISBN-10: 1439889708 · ISBN-13: 978-1439889701

Jörg Epplen and Thomas Lubjuhnn. 1999. DNA Profiling and DNA Fingerprinting. Birkhäuser. ISBN-10: 3764360186. ISBN-13: 978-3764360184

Ricki Lewis. 2011. Human Genetics concepts and application. McGraw-Hill Education; 10 edition ISBN-13: 978-0073525303, ISBN-10: 0073525308 or ISBN: 007246268x

Tom Strachan & Andrew Read.2003. Human Molecular genetics. Garland Science; 3 edition. · ISBN-10: 0815341822 · ISBN-13: 978-0815341826

Julian Knight.2009. Human Genetic Diversity. Oxford Univrsity Press. London.

Robert Nussbaum, Roderick R. McInnes, and Huntington F Willard. 2007. Genetics in Medicine, 7th Edition. Sounders. · ISBN: 9781416030805

Ida Lopez and David L. Erickson. 2012. DNA Barcodes: Methods and Protocols (Methods in Molecular Biology). Human Press. ISBN-13: 978-1617795909. ISBN-10: 1617795909

Nikolaus J. Sucher and James R. Hennell. 2012. Plant DNA Fingerprinting and Barcoding: Methods and Protocols (Methods in Molecular Biology). Human Press. ISBN-13: 978-1617796081. ISBN-10: 1617796085

Erich Grotewold and Joseph Chappel. 2015. Plant Genes, Genomes and Genetics. Willey Blackwell. ISBN-13: 978-1119998877. ISBN-10: 1119998875

Cecie Starr, Ralph Taggart, Christine Evers, & Lisa Starr. Biology: The Unity and Diversity of Life 14th Edition. Brooks Cole. ISBN-13: 978-1305073951. ISBN-10: 1305073959

Gene Helfman and Bruce B. Collette. 2009. The Diversity of Fishes: Biology, Evolution, and Ecology. Wiley-Blackwell; 2 edition. ISBN-10: 1405124946. ISBN-13: 978-1405124942

Jacques Izard and Maria Rivera. 2014. Metagenomics for Microbiology. !rst Ed. Academic Press. ISBN-13: 978-0124104723. ISBN-10: 012410472X

Sandra Tscherwizek. 2008. 16S Ribosomal RNA Gene Sequencing: Establishment of a Method for the Identification of Microorganisms in Biopharmaceutical Production Areas. VDM Verlag Dr Muller. ISBN-13: 978-3639109030. ISBN-10: 3639109031

RPS MK Human genetics (Medical genetics)

By Prof. Fatchiyah, Ph.D.

Sep

Matriks Rencana Pembelajaran Semester MK Genetika Manusia atau Genetika Medik.

Week	Lerning Outcome	Focus study	Pokok Bahasan (topics)	Sub Pokok Bahasan (subtopics)	Bentuk Pembelajaran (Learning methods)	Indikator/Kriteria Penilaian (Value Criteria)	Bobot Nilai (%)	Fasilitas Pembelajaran (learning Facility)
1	Understand basic concepts of human genetics	Basic concepts of human genetics			Lecture and discussion		6	Laptop, LCD, module
2	Understand Mendelian inheritance patterns of the different types of inheritance patterns of human disease.	Identify and Compare a Mendelian inheritance pattern of different types of inheritance patterns of human disease	Mendelian inheritance pattern of human disease Types of inheritance patterns of human disease	Mendel law, single gene and polygenetics factors Sex-linked, multifactorial and maternal inheritance	Presentation, Lecture and discussion	Kebenaran dan ketepatan analisis	6	Laptop, LCD, module, paper exam
3-4	Understand multigenic inheritance patterns.	Identify a multigenic inheritance pattern.	Mapping and characterizing “simple” genetic disease	Mapping disease genes, disease-associated mutations, diseases associated with a gene loss-function effect, nuclear and mitochondrial genome mutations, Evolution of a gene cluster and divergence of function	Presentation, Lecture and discussion	Kebenaran dan ketepatan analisis	18	Laptop, LCD, module, paper exam
5-6	Understand Gene-environment interaction in behavior related Genomics to the study of complex diseases	Identifify Gene-environment interaction in behavior related Genomics to the study of complex diseases	Mapping and characterizing “complex” genetic diseases	Genomics for the study of complex diseases, genetic study of type 2 diabetes and obesity, Gene-environment interaction in behavior, pharmacogenetics	Presentation, Lecture and discussion	Kebenaran dan ketepatan analisis	16	Laptop, LCD, module, paper exam
6-8	Understand the current research into epigenetic and transgenerational inheritance.	Explain the basics of epigenetic and transgenerational inheritance.	Sex, prions, and epigenetics	Epigenetic inheritance of chromatin states / Role of DNA methylation in human disease,dysregulation of the histone modification machinery, transgenerational epigenetic inheritance, sex determination, prion diseases	Presentation, Lecture and discussion	Kebenaran dan ketepatan analisis	12	Laptop, LCD, module, paper exam
9-10	Understand Chromosomal and genomic disorders	Identify Chromosomal and genomic disorders	Chromosomal and genomic disorders	Mechanisms and maternal age influence the origin of aneuploidy in humans, mechanisms causing these aberrations, fragile X syndrome	Presentation, Lecture and discussion	Kebenaran dan ketepatan analisis	12	Laptop, LCD, module, paper exam
11-12	Understand the potential implications of personalized and genomic medicine	Explain the potential benefits and risks/challenges of genomic medicine.	Natural genetics resources: the potential benefits and risks/challenges	Pharcogenenomic and/orNutrigenomic: Bioactive compound, phytopharmaca, functional food for healthy controlling	Presentation, Lecture and discussion	Kebenaran dan ketepatan analisis	6	Laptop, LCD, module, paper exam
13	Understand some of the ethical issues facing genomic researchers.	Explain some of the ethical challenges raised by the prevalence of genomic data	Medical genetics and the associated ethical, legal, and social implications	Ethical clearanceInform consent ELSI for medical research based on samples of human or animal model	Presentation, Lecture and discussion	Kebenaran dan ketepatan analisis	6	Laptop, LCD, module, paper exam
14-15	Understand how to interpret data from a genome-wide association (GWA) study and Genetic Testing	Analyze data from genome-wide association studies.	Genome-wide association (GWA) study and Genetic Testing	Genome-wide association (GWA) studyType, across the life span (prenatal, pediatric and adult), technology, molecular, clinical and ethical perspectives	Presentation, Lecture and discussion	Kebenaran dan ketepatan analisis	16	Laptop, LCD, module, paper exam

Daftar Pustaka

Rick Lewis. 2011. Basic Human Genetics. Routledge Taylor & Francis group, NY · ISBN-10: 0415579864 · ISBN-13: 978-0415579865,

Ricki Lewis. 2011. Human Genetics concepts and application. McGraw-Hill Education; 10 edition ISBN-13: 978-0073525303, ISBN-10: 0073525308 or ISBN: 007246268x

Tom Strachan & Andrew Read.2003. Human Molecular genetics. Garland Science; 3 edition. · ISBN-10: 0815341822 · ISBN-13: 978-0815341826

Julian Knight.2009. Human Genetic Diversity. Oxford Univrsity Press. London.

Robert Nussbaum, Roderick R. McInnes, and Huntington F Willard. 2007. Genetics in Medicine, 7th Edition. Sounders. · ISBN: 9781416030805

Atau pustaka yang terbaru sesuai dengan materi kuliah

How to get published in an academic journal: TOP TIPS from Some EDITORS

By Prof. Fatchiyah, Ph.D.

Jul

Writing for academic journals is highly competitive. Even if you overcome the first hurdle and generate a valuable idea or piece of research – how do you then sum it up in a way that will capture the interest of reviewers?

There’s no simple formula for getting published – editors’ expectations can vary both between and within subject areas. But there are some challenges that will confront all academic writers regardless of their discipline. How should you respond to reviewer feedback? Is there a correct way to structure a paper? And should you always bother revising and resubmitting? We asked journal editors from a range of backgrounds for their tips on getting published.

The writing stage

1) Focus on a story that progresses logically, rather than chronologically

Take some time before even writing your paper to think about the logic of the presentation. When writing, focus on a story that progresses logically, rather than the chronological order of the experiments that you did.
Deborah Sweet, editor of Cell Stem Cell and publishing director at Cell Press

2) Don’t try to write and edit at the same time

Open a file on the PC and put in all your headings and sub-headings and then fill in under any of the headings where you have the ideas to do so. If you reach your daily target (mine is 500 words) put any other ideas down as bullet points and stop writing; then use those bullet points to make a start the next day.

If you are writing and can’t think of the right word (eg for elephant) don’t worry – write (big animal long nose) and move on – come back later and get the correct term. Write don’t edit; otherwise you lose flow.
Roger Watson, editor-in-chief, Journal of Advanced Nursing

3) Don’t bury your argument like a needle in a haystack

If someone asked you on the bus to quickly explain your paper, could you do so in clear, everyday language? This clear argument should appear in your abstract and in the very first paragraph (even the first line) of your paper. Don’t make us hunt for your argument as for a needle in a haystack. If it is hidden on page seven that will just make us annoyed. Oh, and make sure your argument runs all the way through the different sections of the paper and ties together the theory and empirical material.
Fiona Macaulay, editorial board, Journal of Latin American Studies

4) Ask a colleague to check your work

One of the problems that journal editors face is badly written papers. It might be that the writer’s first language isn’t English and they haven’t gone the extra mile to get it proofread. It can be very hard to work out what is going on in an article if the language and syntax are poor.
Brian Lucey, editor, International Review of Financial Analysis

5) Get published by writing a review or a response

Writing reviews is a good way to get published – especially for people who are in the early stages of their career. It’s a chance to practice at writing a piece for publication, and get a free copy of a book that you want. We publish more reviews than papers so we’re constantly looking for reviewers.

Some journals, including ours, publish replies to papers that have been published in the same journal. Editors quite like to publish replies to previous papers because it stimulates discussion.
Yujin Nagasawa, co-editor and review editor of the European Journal for Philosophy of Religion, philosophy of religion editor of Philosophy Compass

6) Don’t forget about international readers

We get people who write from America who assume everyone knows the American system – and the same happens with UK writers. Because we’re an international journal, we need writers to include that international context.
Hugh McLaughlin, editor in chief, Social Work Education – the International Journal

7) Don’t try to cram your PhD into a 6,000 word paper

Sometimes people want to throw everything in at once and hit too many objectives. We get people who try to tell us their whole PhD in 6,000 words and it just doesn’t work. More experienced writers will write two or three papers from one project, using a specific aspect of their research as a hook.
Hugh McLaughlin, editor in chief, Social Work Education – the International Journal

Submitting your work

8) Pick the right journal: it’s a bad sign if you don’t recognise any of the editorial board

Check that your article is within the scope of the journal that you are submitting to. This seems so obvious but it’s surprising how many articles are submitted to journals that are completely inappropriate. It is a bad sign if you do not recognise the names of any members of the editorial board. Ideally look through a number of recent issues to ensure that it is publishing articles on the same topic and that are of similar quality and impact.
Ian Russell, editorial director for science at Oxford University Press

9) Always follow the correct submissions procedures

Often authors don’t spend the 10 minutes it takes to read the instructions to authors which wastes enormous quantities of time for both the author and the editor and stretches the process when it does not need to
Tangali Sudarshan, editor, Surface Engineering

10) Don’t repeat your abstract in the cover letter
We look to the cover letter for an indication from you about what you think is most interesting and significant about the paper, and why you think it is a good fit for the journal. There is no need to repeat the abstract or go through the content of the paper in detail – we will read the paper itself to find out what it says. The cover letter is a place for a bigger picture outline, plus any other information that you would like us to have.
Deborah Sweet, editor of Cell Stem Cell and publishing director at Cell Press

11) A common reason for rejections is lack of context

Make sure that it is clear where your research sits within the wider scholarly landscape, and which gaps in knowledge it’s addressing. A common reason for articles being rejected after peer review is this lack of context or lack of clarity about why the research is important.
Jane Winters, executive editor of the Institute of Historical Research’s journal, Historical Research and associate editor of Frontiers in Digital Humanities: Digital History

12) Don’t over-state your methodology

Ethnography seems to be the trendy method of the moment, so lots of articles submitted claim to be based on it. However, closer inspection reveals quite limited and standard interview data. A couple of interviews in a café do not constitute ethnography. Be clear – early on – about the nature and scope of your data collection. The same goes for the use of theory. If a theoretical insight is useful to your analysis, use it consistently throughout your argument and text.
Fiona Macaulay, editorial board, Journal of Latin American Studies

Dealing with feedback

13) Respond directly (and calmly) to reviewer comments

When resubmitting a paper following revisions, include a detailed document summarising all the changes suggested by the reviewers, and how you have changed your manuscript in light of them. Stick to the facts, and don’t rant. Don’t respond to reviewer feedback as soon as you get it. Read it, think about it for several days, discuss it with others, and then draft a response.
Helen Ball, editorial board, Journal of Human Lactation

14) Revise and resubmit: don’t give up after getting through all the major hurdles

You’d be surprised how many authors who receive the standard “revise and resubmit” letter never actually do so. But it is worth doing – some authors who get asked to do major revisions persevere and end up getting their work published, yet others, who had far less to do, never resubmit. It seems silly to get through the major hurdles of writing the article, getting it past the editors and back from peer review only to then give up.
Fiona Macaulay, editorial board, Journal of Latin American Studies

15) It is acceptable to challenge reviewers, with good justification

It is acceptable to decline a reviewer’s suggestion to change a component of your article if you have a good justification, or can (politely) argue why the reviewer is wrong. A rational explanation will be accepted by editors, especially if it is clear you have considered all the feedback received and accepted some of it.
Helen Ball, editorial board of Journal of Human Lactation

16) Think about how quickly you want to see your paper published

Some journals rank more highly than others and so your risk of rejection is going to be greater. People need to think about whether or not they need to see their work published quickly – because certain journals will take longer. Some journals, like ours, also do advance access so once the article is accepted it appears on the journal website. This is important if you’re preparing for a job interview and need to show that you are publishable.
Hugh McLaughlin, editor in chief, Social Work Education – the International Journal

17) Remember: when you read published papers you only see the finished article

Publishing in top journals is a challenge for everyone, but it may seem easier for other people. When you read published papers you see the finished article, not the first draft, nor the first revise and resubmit, nor any of the intermediate versions – and you never see the failures.
Philip Powell, managing editor of the Information Systems Journal

http://www.theguardian.com/education/2015/jan/03/how-to-get-published-in-an-academic-journal-top-tips-from-editors

10 tips Writing your scientific article for an academic journal

By Prof. Fatchiyah, Ph.D.

Jul

1) Have a strategy, make a plan

Why do you want to write for journals? What is your purpose? Are you writing for research assessment? Or to make a difference? Are you writing to have an impact factor or to have an impact? Do you want to develop a profile in a specific area? Will this determine which journals you write for? Have you taken their impact factors into account?

Have you researched other researchers in your field – where have they published recently? Which group or conversation can you see yourself joining? Some people write the paper first and then look for a ‘home’ for it, but since everything in your article – content, focus, structure, style – will be shaped for a specific journal, save yourself time by deciding on your target journal and work out how to write in a way that suits that journal.

Having a writing strategy means making sure you have both external drivers – such as scoring points in research assessment or climbing the promotion ladder – and internal drivers – which means working out why writing for academic journals matters to you. This will help you maintain the motivation you’ll need to write and publish over the long term. Since the time between submission and publication can be up to two years (though in some fields it’s much less) you need to be clear about your motivation.

2) Analyse writing in journals in your field

Take a couple of journals in your field that you will target now or soon. Scan all the abstracts over the past few issues. Analyse them: look closely at all first and last sentences. The first sentence (usually) gives the rationale for the research, and the last asserts a ‘contribution to knowledge’. But the word ‘contribution’ may not be there – it’s associated with the doctorate. So which words are used? What constitutes new knowledge in this journal at this time? How can you construct a similar form of contribution from the work you did? What two sentences will you write to start and end your abstract for that journal?

Scan other sections of the articles: how are they structured? What are the components of the argument? Highlight all the topic sentences – the first sentences of every paragraph – to show the stages in the argument. Can you see an emerging taxonomy of writing genres in this journal? Can you define the different types of paper, different structures and decide which one will work best in your paper? Select two types of paper: one that’s the type of paper you can use as a model for yours, and one that you can cite in your paper, thereby joining the research conversation that is ongoing in that journal.

3) Do an outline and just write

Which type of writer are you: do you always do an outline before you write, or do you just dive in and start writing? Or do you do a bit of both? Both outlining and just writing are useful, and it is therefore a good idea to use both. However, make your outline very detailed: outline the main sections and calibrate these with your target journal.

What types of headings are normally used there? How long are the sections usually? Set word limits for your sections, sub-sections and, if need be, for sub-sub-sections. This involves deciding about content that you want to include, so it may take time, and feedback would help at this stage.

When you sit down to write, what exactly are you doing:using writing to develop your ideas or writing to document your work? Are you using your outline as an agenda for writing sections of your article? Define your writing task by thinking about verbs – they define purpose: to summarise, overview, critique, define, introduce, conclude etc.

4) Get feedback from start to finish

Even at the earliest stages, discuss your idea for a paper with four or five people, get feedback on your draft abstract. It will only take them a couple of minutes to read it and respond. Do multiple revisions before you submit your article to the journal.

5) Set specific writing goals and sub-goals

Making your writing goals specific means defining the content, verb and word length for the section. This means not having a writing goal like, ‘I plan to have this article written by the end of the year’ but ‘My next writing goal is to summarise and critique twelve articles for the literature review section in 800 words on Tuesday between 9am and 10.30’. Some people see this as too mechanical for academic writing, but it is a way of forcing yourself to make decisions about content, sequence and proportion for your article.

6) Write with others

While most people see writing as a solitary activity, communal writing – writing with others who are writing – can help to develop confidence, fluency and focus. It can help you develop the discipline of regular writing. Doing your academic writing in groups or at writing retreats are ways of working on your own writing, but – if you unplug from email, internet and all other devices – also developing the concentration needed for regular, high-level academic writing.

At some point – ideally at regular intervals – you can get a lot more done if you just focus on writing. If this seems like common sense, it isn’t common practice. Most people do several things at once, but this won’t always work for regular journal article writing. At some point, it pays to privilege writing over all other tasks, for a defined period, such as 90 minutes, which is long enough to get something done on your paper, but not so long that it’s impossible to find the time.

7) Do a warm up before you write

While you are deciding what you want to write about, an initial warm up that works is to write for five minutes, in sentences, in answer to the question: ‘What writing for publication have you done [or the closest thing to it], and what do you want to do in the long, medium and short term?’

Once you have started writing your article, use a variation on this question as a warm up – what writing for this project have you done, and what do you want to do in the long, medium and short term? Top tip: end each session of writing with a ‘writing instruction’ for yourself to use in your next session, for example, ‘on Monday from 9 to 10am, I will draft the conclusion section in 500 words’.

As discussed, if there are no numbers, there are no goals. Goals that work need to be specific, and you need to monitor the extent to which you achieve them. This is how you learn to set realistic targets.

8) Analyse reviewers’ feedback on your submission

What exactly are they asking you to do? Work out whether they want you to add or cut something. How much? Where? Write out a list of revision actions. When you resubmit your article include this in your report to the journal, specifying how you have responded to the reviewers’ feedback. If your article was rejected, it is still useful to analyse feedback, work out why and revise it for somewhere else.

Most feedback will help you improve your paper and, perhaps, your journal article writing, but sometimes it may seem overheated, personalised or even vindictive. Some of it may even seem unprofessional. Discuss reviewers’ feedback – see what others think of it. You may find that other people – even eminent researchers – still get rejections and negative reviews; any non-rejection is a cause for celebration. Revise and resubmit as soon as you can.

9) Be persistent, thick-skinned and resilient

These are qualities that you may develop over time – or you may already have them. It may be easier to develop them in discussion with others who are writing for journals.

10) Take care of yourself

Writing for academic journals is highly competitive. It can be extremely stressful. Even making time to write can be stressful. And there are health risks in sitting for long periods, so try not to sit writing for more than an hour at a time. Finally, be sure to celebrate thoroughly when your article is accepted. Remind yourself that writing for academic journals is what you want to do – that your writing will make a difference in some way.

These points are taken from the 3rd edition of Writing for Academic Journals.

http://www.theguardian.com/higher-education-network/blog/2013/sep/06/academic-journal-writing-top-tips

2015 smonagenes group publication

By Prof. Fatchiyah, Ph.D.

Jul

Rike Oktarianti, Kartika Senjarini, Toshiya Hayano , Fatchiyah Fatchiyah , Aulanni’am. Proteomic analysis of immunogenic proteins from salivary glands of Aedes aegypti. Journal of Infection and Public Health (2015) xxx, xxx—xxx (InPress) doi:10.1016/j.jiph.2015.04.022

Rista Nikmatu Rohmah, Edi Widjajanto, Fatchiyah Fatchiyah. Protective effect of CSN1S2 protein of goat milk on ileum microstructure and inflammation in rat-CFA-induced rheumatoid arthritis. Asian Pac J Trop Dis 2015; 5(7): 564-568. http://dx.doi.org/10.1016/S2222-1808(15)60837-4

Rivqi Rifa Bia, Regina Putri Virgirinia, Bambang Setiawan, Aris Soewondo,Fatchiyah Fatchiyah. Goat milk CSN1S2 is able to decrease the severity scoring, tumor necrosis factor-alpha, and advanced glycation end products receptor expression in complete Freund’s adjuvant-induced rheumatoid arthritis model of rats. Biomarker and Genomic Medicine. 2015, xx: 1-8 DOI: http://dx.doi.org/10.1016/j.bgm.2015.02.001

Fatchiyah Fatchiyah, Ferlany Hardiyanti, Nashi Widodo Selective Inhibition on RAGE-binding AGEs Required by Bioactive Peptide Alpha-S2 Case in Protein from Goat Ethawah Breed Milk: Study of Biological Modeling. Acta Informatica Medica01/2015; 23(2): 90-96. DOI:10.5455/aim.2015.23.90-96

Sri hardyastutie, A, D.W.Soeatmadji, Fatchiyah Fatah, and Aulanni’am. Relation of Elevated Serum Lipase to Indonesian Type 2 Diabetes Mellitus Progression.Biomedical Research 2015; 26 (2): 293-298

Fatchiyah Fatchiyah, SJ Raharjo, FRP Dewi. Virtual Selectivity Peptides of Csn1s2 Protein of Local Goat Ethawah Breeds Milk Modulate Biological Mechanism Of Calmodulin. Int J Pharm Bio Sci 2015 April;; 6(2): (B) 707 – 718

Choirunil Chotimah, Gatot Ciptadi, Bambang Setiawan, Fatchiyah Fatchiyah. CSN1S2 protein of goat milk inhibits the decrease of viability and increases the proliferation of MC3T3E1 pre-osteoblast cell in methyl glyoxal exposure. Elsevier – Asian Pacific J Tropical Disease 2015; 5(3): 219-223

Research and knowledge Management

By Prof. Fatchiyah, Ph.D.

Apr

by Fatchiyah (Dept Biology, FMIPA UB)

•Research Management (RM) focuses mainly on abilities to prepare, execute, disseminate, evaluate and sustain research activities within a certain frame with different settings and strategies in higher education systems or in private sector.

•

•Knowledge management (KM)focuses on how an organization (either higher education system or private sector) identifies, creates, captures , acquires, shares and leverages knowledge.

•

•Both consist of

RM KM

•To Get To build

•To Use To Assess

•To Learn To Sustain

•To Contribute To divest

Indicators Components of Research Performance

• Organizational knowledge

• Innovation

• Organizational learning

• R & D personnel

• Technology transfer

• Contract services

• Research project time

• R & D facilitations

• Technology implicit transfer

• Customers‘ satisfaction

• Job satisfaction

• Information

Trust & Scientific Work

Criterion required for an egalitarian cooperation: Understanding research as part of the job-description or business
Quality of Research: Articles published in international refereed journals; scientific books by internationally well-known publishers; citations
Research Activity: Minimum quality standard; reports in national journals; working papers; conference proceedings; conference presentation
Impact of Research: citation by other researchers; invited and plenary presentations; number of foreign co-authors
Activity in Educating young scientists: doctoral degree produced; number of doctoral students supervised
Activity in scientific community: membership in editorial boards; edited books and special issues of journals; services as an expert; scientific conferences organized, memberships in program committees

more detail; Research and Knowledge management

Pembuatan Roadmap Penelitian

Fatchiyah – Molecular Genetics

Brawijaya University

Tip and Trik menulis artikel ilmiah

Manajemen Laboratorium berbasis GLP dan Penyusunan Dokumen

TABLE of GENETIC DISORDERS

Jadual Kuliah Biologi Molekuler (MAB 4162: 2sks) JB-UB, Semester Ganjil 2016-2017 Kelas: B

Jadual Kuliah Biologi Molekuler (MAB 4162: 2sks) JB-UB, Semester Ganjil 2016-2017 Kelas: A

Schedule Lecture of Human Genetics (S1: MAB4161/ 2 sks) and Medical Genetics (S2) Biology Dept. UB, Odd Semester, Year 2016-2017

Jadual Kuliah Sidik Jari Molekuler (MAB4266: 2sks) JB-UB, Semester Ganjil 2016-2017

Inviting Speaker on Int Conf Obesity & Chronic Disease, LV, Nevada, USA July 25-27, 2016

New Publication 2016

Hasil-hasil Riset peneliti RG Smonagenes UB disitasi dalam Sigma-Aldrich

Lecture Bio-Ethics Research: Guideline of Ethical Research using non-Human animal

JADWAL KULIAH BIOINFORMATIKA SEMESTER GENAP JURUSAN BIOLOGI FMIPA UNIVERSITAS BRAWIJAYA

JADWAL KULIAH TEKNIK ANALISIS BIOLOGI (GENETIK) MOLEKULER SEMESTER GENAP JURUSAN BIOLOGI FMIPA UNIVERSITAS BRAWIJAYA

New publication on RG Smonagenes UB

2015

Lecture teknik analisis sidik jari molekuler

material lecture of Molecular Fingerprint

Jadual Kuliah Biologi Molekuler (MAB 4162) Kelas A dan B JB UB

assigment 1 of human genetics lecture

Materi Workshop Pengelolaan Laboratorium oleh RG Smonagenes UB

RPS MK Sidik Jari Molekuler

RPS MK Human genetics (Medical genetics)

How to get published in an academic journal: TOP TIPS from Some EDITORS

10 tips Writing your scientific article for an academic journal

2015 smonagenes group publication

Research and knowledge Management

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