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Research & Reviews: A Journal of Bioinformatics ISSN: 2393-8722(online)

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Sequence database and Sequence Alignment

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Biological networks , protein –protein interaction networks

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DNA Assembly, Clustering , Mapping

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Research & Reviews: A Journal of Bioinformatics

Contents

1. Correlation Between eAG Values Calculated from Hba1c Values Obtained from Three Different Techniques and Fasting Plasma Glucose Levels for Diagnosis and Prognosis of Diabetes Omkar Kadhane, Usha Mukundan, Shirish Malvankar, Nikhil Ranade

2. The HbA1C Values Used in Diagnosis of Diabetes in Indiaâ&#x20AC;&#x201D;A Review Omkar Kadhane, Usha Mukundan

3. A Review: Quantitative Structure Activity Relationship Ravikash Srivastava

4. Hereditary Disease and Ethical Awareness in Students of Greater Noida, India Babita Sharma, Jyoti Singh, Raghav Singh

5. Isolation and Characterization of Lantibiotic Producing Lactic Acid Bacteria from Ambali, Aged Mango Pickle Probiotics Revansiddappa, Chandrashekhar Naik

Research & Reviews: A Journal of Bioinformatics

ISSN: 2393-8722(online) Volume 3, Issue 3 www.stmjournals.com

Correlation Between eAG Values Calculated from Hba1c Values Obtained from Three Different Techniques and Fasting Plasma Glucose Levels for Diagnosis and Prognosis of Diabetes 1

Omkar Kadhane1,*, Usha Mukundan1, Shirish Malvankar2, Nikhil Ranade2

Department of Biotechnology, Ramniranjan Jhunjhunwala College, Ghatkopar (West), Mumbai, Maharashtra, India 2 Department of Hematology and Biochemistry, Pyramid Grouplab, New Panvel, Maharashtra, India

Abstract

The objective of the present study was to correlate estimated average glucose (eAG) values calculated from HbA1c values obtained from Tosoh TLC-723 G8 based on cation exchange based HPLC, TBA 12 FR enzymatic fructosyl peptide oxidase (FPOX) method and D10 HbA1c analyser Bio Rad Laboratories (USA) with fasting plasma glucose (FPG) levels by hexakinase method for diagnosis and prognosis of diabetes. A total of 300 randomly selected patient samples were analysed for FPG by hexakinase method and HbA1c values were estimated by using Tosoh TLC-723 G8 analyser based on cation exchange HPLC, enzymatic FPOX (Manufacture by Seikisui Medical Co. Ltd., Japan) programmed on TBA 12 FR biochemistry analyser and D10 HbA1c analyser Bio Rad Laboratories (USA). The eAG values were calculated using Nanthanâ&#x20AC;&#x2122;s regression equation for both HbA1c values. The correlation between FPG, HbA1c and eAG values has been done by Pearson correlation (r) and regression analysis was done by SPSS software. The correlation was good in entire data and poor in differentiated groups. Male data has shown good correlation between FPG and eAG as compared to female data with higher mean levels of FPG, eAG and HbA1c values. Both HPLC methods have shown closer correlation between eAG values calculated from it and FPG values from which Tosoh HLC-723 G8 has shown closer correlation. The overall correlation between eAG and FPG was good in entire data but mean value difference was found to be slightly high. So for diabetes diagnosis, HbA1c values along with calculated eAG value along with FPG values are recommended as per the American Diabetes Association (ADA) guidelines. As both the HPLC methods have shown good correlation between eAG and FPG values, we recommend that HbA1c values and eAG values calculated from it has to be used for diagnosis and prognosis of diabetes along with FPG values and other relevant clinical findings of patients. Tosoh HLC-723 G8 HPLC HbA1c analyser could be preferred technique for HbA1c estimation due to closer correlation with FPG values and true separation of labile and stable fraction of HbA1c. The use of HbA1c values alone for diagnosis and prognosis of diabetes still need multicentre studies with large sample size in different population. Keywords: estimated average glucose (eAG), HbA1c, fasting plasma glucose (FPG), diabetes

INTRODUCTION

Diabetes mellitus is a chronic metabolic disorder marked by hyperglycemia with alteration in normal status of carbohydrate, protein and fat metabolism resulting from defects in insulin secretion, insulin action or both. Diabetes mellitus is associated with retinopathy, nephropathy, peripheral

neuropathy, cardiovascular disorder and other lethal complications of organ system [1]. According to the International Diabetes Federation (IDF) 2013, prevalence of type 2 diabetes mellitus is increasing in epidemic proportions worldwide and developing countries like India has alarming situation for this disease. The number of people living with

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Research & Reviews: A Journal of Bioinformatics

ISSN: 2393-8722(online) Volume 3, Issue 3 www.stmjournals.com

The HbA1C Values Used in Diagnosis of Diabetes in India: A Review Omkar Kadhane1,*, Usha Mukundan2

Abstract

Diabetes mellitus (DM) is a chronic metabolic disorder associated with retinopathy, nephropathy, cardiovascular disorder and other lethal complication of organ system. It has huge burden globally and expected to grow more in upcoming years; with alarming presence in epidemic proportions in countries like India and China. India currently faces challenges to handle the potential burden of DM which demands accurate and precise diagnosis by various clinical parameters. Since 2009, HbA1c was recommended as diagnosis of DM and management of related complications. Still in India, fasting plasma glucose (FPG), post-meal glucose and oral glucose tolerance test (OGTT) are commonly used, due to unregulated diagnostic sector and lack of awareness. However, combination of FPG, OGTT and HbA1c are reported by laboratories having adequate facilities. In depth studies on impact of laboratory quality and education of physicians, healthcare providers, pathologist may improve harmonisation and quality of patient care in DM in India. Keywords: Diabetes mellitus (DM), HbA1c, hyperglycemia, fasting plasma glucose (FPG), oral glucose tolerance test (OGTT)

INTRODUCTION

Since ancient ages, Diabetes mellitus (DM) has shown its presence worldwide by various and diverse terminologies. In India, DM is known as “Madhumeha” (sweet urine) as early as 2500 BC. DM is a chronic metabolic disorder marked by hyperglycemia with alteration in normal status of carbohydrate, protein and fat metabolism resulting from defects in insulin secretion, insulin action or both. DM is associated with retinopathy, nephropathy, peripheral neuropathy, cardiovascular disorder and other lethal complications of organ system [1]. According to International Diabetes Federation (IDF) 2013, prevalence of type 2 DM is increasing in epidemic proportions worldwide and countries like India, and China has alarming situation for this disease. The number of people living with diabetes is expected to rise from 382 million in 2013 to 592 million by 2035. As per the International Diabetes Federation (IDF) report, India alone has more than 65 million people living with diabetes and this number is expected to reach 109 million by 2030. In 2004, Diabetes India released a random multistage cross-sectional

population survey report, which clearly indicated DM as a major health problem in India with the standardized prevalence rate for DM in the total Indian, urban and rural populations was 4.3%, 5.9%, and 2.7%, respectively. In 2005, Ramchandran released complied report of research done in India for last three decades. According to his study, availability of improved modes of transport, decreased physical activity, improved economic conditions have produced changes in diet habits in rural area, which were the major reasons for increase in DM patients in rural area [2]. The conditions are more favourable for expression of diabetes and related complication in the population, which already has a racial and genetic susceptibility of the disease. Early diagnosis of high risk groups and appropriate intervention by lifestyle modification may provide a solution for the disease burden.

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ISSN: 2393-8722(online) Volume 3, Issue 3 www.stmjournals.com

A Review: Quantitative Structure Activity Relationship Ravikash Srivastava* Department of Biochemistry, Chhatrapati Shahu Ji Maharaj University, Kanpur, Uttar Pradesh, India Abstract

Drug discovery is a risky, costly and time-consuming process depending on multidisciplinary methods to create safe and effective medicines. Although considerable progress has been made by high-throughput screening methods in drug design, the cost of developing contemporary approved drugs did not match that in the past decade. The major reason is the late-stage clinical failures in Phases II and III because of the complicated interactions between drug-specific, human body and environmental aspects affecting the safety and efficacy of a drug. There is a growing hope that systems-level consideration may provide a new perspective to overcome such current difficulties of drug discovery and development. Therefore, the present review is an attempt to introduce how holistic systems pharmacology that integrated in silico ADME/T (i.e., absorption, distribution, metabolism, excretion and toxicity), target fishing and network pharmacology facilitates the discovery of small molecular drugs at the system level. Keywords: Drug discovery, pharmacology, QSAR, ADME/T

INTRODUCTION

The quantitative structure activity relationship (QSAR) paradigm is based on the assumption that there is an underlying relationship between the molecular structure and biological activity. On this assumption, QSAR attempts to establish a correlation between various molecular properties of a set of molecules with their experimentally known biological activity. There are two main objectives for the development of QSAR: 1. Development of predictive and robust QSAR, with a specified chemical domain, for prediction of activity of untested molecules. 2. It acts as an informative tool by extracting significant patterns in descriptors related to the measured biological activity leading to understanding of mechanisms of given biological activity. This could help in suggesting design of novel molecules with improved activity profile. QSAR's most general mathematical form is: Activity =f (physiochemical and/or structural properties) Data Requirement and Handling: Biological Activity For QSAR analysis, a dataset of a series of synthesized molecules tested for its desired

biological activity is required. For a QSAR to be valid and reliable, the activity of all of the chemicals covered must be elicited by a common mechanism. The quality of the model is totally dependent on the quality of the experimental data used for building the model. Biological activity can be of two types: 1. Continuous Response: MEC, IC50, ED50, % inhibition, and 2. Categorical Response: Active/Inactive. In order to have confidence in QSAR analysis, biological data of at least 20 molecules is recommended: 1. Preferably tested in the same lab and by the same biological assay method. 2. With wide range and uniform distribution of the activity data. 3. Activity should well-defined in terms of either real number (continuous response, and cannot be, e.g. >1000 or <1000) or in a particular class (categorical response). In Silico ADME/T (Absorption, Distribution, Metabolism, Excretion and Toxicity) Assessment for Drug Discovery The development of combinatorial chemistry and high throughput medicinal chemistry programs give us more opportunities to synthesize a large amount of compounds at

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ISSN: 2393-8722(online) Volume 3, Issue 3 www.stmjournals.com

Hereditary Disease and Ethical Awareness in Students of Greater Noida, India Babita Sharma, Jyoti Singh, Raghav Singh* Department of Biotechnology, College of Engineering and Technologies, Institute for Integrated Learning in Management, Academy of Higher Learning, Greater Noida, Gautam Budh Nagar, Uttar Pradesh, India Abstract

Hereditary diseases are diseases that are transmitted from parents to offsprings. These diseases cause many deaths and sufferings in the world. Often majority of people in developing countries suffer because of illiteracy and ignorance, and are not able to take right decision when the problem persists in the family. Therefore, a survey has been designed and conducted on students of engineering and management branches between age group 18 and 25 years to check general awareness regarding hereditary diseases. In the survey, fifteen questions were asked. The result shows general awareness to be present among most of the students about ethics and inherited diseases. Most of the students think that parents should go for pre-genetic counseling before giving birth to their forthcoming child if the disease is hereditary one. Majority believes that parents should maintain confidentiality from children and society about hereditary disease because of mass discrimination for one or other reasons. However, the suspected individual with a family history of hereditary disease should opt for DNA testing so that diseases can be prevented, treated or cured in advance. In case of incurable inheritable disease, students feel that the knowledge may mislead and cause stress, pain, depression and anxiety. The present article highlights the different views and perspectives of students on different aspects of inherited diseases and ethical awareness related to it. Keywords: Hereditary, genetic counseling, DNA testing

INTRODUCTION

Hereditary diseases are diseases that are transmitted from parents to their children. Heritable (genetic) diseases or disorders result from alterations (mutations) in genes or chromosomes in germ line cells or gametes. The germ line cells are the cells that produce male or female gametes in male and female individuals respectively. The gametes unite during fertilization to produce zygote. Healthy male and female gametes produce healthy embryos while gametes carrying mutations in DNA present on either autosomes or sex chromosome of gametes can indicate susceptibility to (carriers) or certainty of disease. â&#x20AC;&#x2DC;Some of the autosomal dominant inheritable diseases are polycystic kidney disease, Marfans disease and Huntingtonâ&#x20AC;&#x2122;s chorea. Some of the inheritable autosomal recessive diseases are sickle cell anaemia, cystic fibrosis, Tay-sachs disease and phenylketonuria. The well-known X-linked

diseases are Duchenne muscular dystrophy and haemophilia [1]. Environmental factors play a crucial role on events in the person's development that further have a major role in deciding when and to what extent a person with the genetic defect or abnormality will actually suffer from the disease. In fact, some highly heritable traits can be modified by simple changes in the environment. Phenylketonuria (PKU), for example, is a genetic disease with high heritability that can be checked by restricting intake of the amino acid phenylalanine. Even if Alzheimer's disease has a relatively high heritability, environmental factors and changes may alter disease progression and severity. Ethical Issues Ethical issues related to genetic diseases are many. The issues for genetic testing include

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ISSN: 2393-8722(online) Volume 3, Issue 3 www.stmjournals.com

Isolation and Characterization of Lantibiotic Producing Lactic Acid Bacteria from Ambali, Aged Mango Pickle Probiotics Revansiddappa*, Chandrashekhar Naik

Department of Biotechnology, Sir M. Visvesvaraya Institute of Technology, Hunasamaranahalli, International Airport Road, Bangaluru, Karnataka, India

Abstract

Each year in the US at least 2 million people are sickened with antibiotic resistant infection. The development of antibiotics was one of the most important advances of medicine. Many bacterial infections (e.g. tuberculosis and infected wounds) that previously had no effective treatment and often killed people became treatable with antibiotics, saving millions of lives. Now, because of the overuse and misuse of antibiotics, bacterial infections that were once easily cured with antibiotics are becoming harder to treat. This is due to antibiotic resistance. The World Health Organization has called this as one of the biggest threats to human health today (World Health Organization 2014). Antibiotics have transformed human health and saved millions of lives. Now, as a result of overuse, they are no longer working. The golden age of medicine has come to an end (Joe Shute). But 99% of microbes will not grow in laboratory conditions leaving researchers frustrated that they could not get to the life-saving natural drugs. The dramatic rise in the incidence of antibiotic resistance demands that new therapeutic options will have to be developed. One potentially interesting class of antimicrobials is the modified bacteriocins termed lantibiotics, which are bacterially produced, post-translationally modified, lanthionine/methyllanthionine containing peptides. The present study was aimed at isolating bacteriocinogenic LAB from a traditional fermented food, “Ambali”. Twenty five colonies of LAB were isolated and screened for bacteriocin production potential. Ten isolates showed good antimicrobial activity against Gram-positive viz., Bacillus cereus, Staphylococcus aureus, Listeria monocytogenes as well as Gramnegative viz., Pseudomonas aeruginosa, Vibrio parahaemolyticus and Aeromonas hydrophila microorganisms. During characterization of these strains, two of them were found to resemble two other strains. One of the bacilli has been reported earlier. Therefore, in this study characterization of seven isolates through morphological, physiological, biochemical and carbohydrate fermentation tests as well as cell wall protein profiles have been reported. Five of them were cocci, identified as Pediococcus pentosaceous (four strains) and the other as Tetragenococcus halophilus, while the remaining two being rods and were found to be Lactobacillus plantarum. Keywords: Antibiotics, bacteriocinogenic, tuberculosis

INTRODUCTION

Isolation and screening of microorganisms from naturally occurring processes have always been the most powerful means for obtaining useful cultures for scientific and commercial purposes [1]. This certainly holds true for lactic acid bacteria (LAB), which are used throughout the world for manufacture of a wide variety of traditional fermented foods. Since they are involved in numerous food fermentations, known to man for millennia, it is assumed that most representatives of this group do not pose any health risk to man, and are designated as GRAS (Generally Recognized as Safe) organisms. The LABs,

generally considered as “food grade” organisms, show special promise for selection and implementation as protective cultures. There are many potential applications of protective cultures in various food systems [2]. These organisms have been isolated from grains, dairy and meat products, fermenting vegetables, and the mucosal surfaces of animals [3].

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