A computer program to identify potential antimicrobial compounds

A new computer program can help researchers identify new potential antimicrobial peptides with high accuracy and ease, according to a recent study published in the international journal Scientific Reports.

Antimicrobial peptides are small proteins that occur naturally in various animals and plants and confer immunity to bacteria, fungi, and viruses. These have recently gained popularity in clinical practice because they are safe and efficacious. Microbes acquire resistance to available antibiotics in due course of time, which discerns the need to hunt for new antibiotics. Antimicrobial peptides are better alternatives to chemical antibiotics, but searching for them through wet lab experiments is labor intensive and costly.

Researchers at the Indian Agricultural Statistics Research Institute, New Delhi and Janta Vedic College, Baghpat, Uttar Pradesh have developed a computer program that can identify potential antimicrobial peptides with an accuracy of almost 96%. The open access prediction server named iAMPpred is HTML and PHP based and is available freely at http://cabgrid.res.in:8080/amppred.

The server can predict if a protein sequence is antibacterial, antiviral and antifungal after the user enters the protein sequence in a FASTA file format. Within a span of few seconds, the user can know if the protein sequence that he has entered is a potential antibiotic. The prediction server has been tested with more than 1000 peptide sequences from plants, animals, and amphibians. “The accuracies of iAMPpred was found to be much higher than that of other available prediction servers”, claim scientists.

Researchers and clinicians are concerned about the rising antibiotic resistance. New and better software tools can help researchers across the globe to identify new antibiotics in lesser cost, effort, and time.

Published- India Science Wire 

Reference: Scientific Reports 7: 42362.

Microwaving Cereals to Manage Diabetes

Diabetes in on the rise and is estimated to affect nearly 422 million people worldwide (WHO global report on diabetes 2016). The problem is exaggerated because, till date, it cannot be cured but can only be managed. 

An important strategy to manage Diabetes is Diet that should be rich in fibers or foods with low glycemic index. β-D-glucan is a dietary fiber present in cereals such as Barley (Botanical name: Hordeum vulgare, Hindi: Jau) that is known to lower cholesterol, glycemic response, and aid weight management. The properties of β-D-glucan depend on its molecular weight; the lesser the molecular weight, more its antioxidant potential.

Researchers at the University of Kashmir in collaboration with Prince of Songkla University, Thailand have found that a simple home-based treatment of barley can enhance its antioxidant potential making it more beneficial for patients with diabetes. After soaking the cereal in water for 16 hours and germinating it on a muslin cloth for about 24 hours, the seeds are treated in a 950W microwave for 2 minutes. The seeds can then be milled into flour for consumption. This lowers the molecular weight and viscosity of the β-D-glucan making it easy to digest and enhancing its antioxidant properties.

It is a well-known fact that day to day exposure to pollution, food, and occupational hazards increase free radicals in the body that modify fats and proteins, and damage DNA, accelerating the process of aging. The antioxidant property of the treated barley seeds converts free radicals in the body into stable products conferring good health and immunity. A simple process of germinating and microwaving cereals at home can enhance their antioxidant potential and nutritional benefits.

Reference: Carbohydrate Polymers 153: 696-702.

Published: Current Science Fortnight. 

Detecting Dry Root Disease of Chickpea becomes easy

A new method for detecting dry root rot disease of chickpea that causes significant loss of crop yield, has been developed by researchers at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad in their recent study.

Chickpea, also known as Bengal gram accounts for about 45% of total pulses produced in India. India is the largest producer of chickpea with an annual production of 8 million tons, accounting for 70% of total world production.

The dry root rot disease is an emerging disease of chickpea that is often misdiagnosed as wilt, collar rot, or black root rot because all these diseases have symptoms such as loss of green pigment and eventual plant collapse. With rising global temperatures, the disease is becoming more prevalent in agricultural areas. Therefore it is important to timely detect dry root rot disease in the crop to manage the disease efficiently.

The conventional PCR-based method of detecting dry root rot disease is lab intensive, as it requires specialized and expensive machines, and is time-consuming. The new method is cheaper as it does not require an expensive thermal cycling machine. Also, it uses non-mutagenic and eco-friendly reagents, which is safe for the environment.

With this new technique, the disease infection can be judged as positive with the naked eye by seeing a change in color. “ (The new) detection technique can be employed in the diagnosis of disease in field level even also in remote areas where the laboratories are not well equipped”, say scientists. The new test uses 10 femtograms of DNA from the infected plant, which is put in a small tube and kept at 63 degree Celsius for 1 hour.  If the color of the reagents in the tube changes from yellow to orange, the disease in the plant is confirmed.  

They have validated the new test in 94 samples from various sites across India including Andhra Pradesh, Madhya Pradesh, Tamil Nadu, Uttar Pradesh, Delhi, Himachal Pradesh, Uttrakhand, and Jharkhand and published the results in the journal ‘Scientific Reports’.

 “In future, (the new test) kit will be very useful for monitoring the disease complex in fields, further helpful in developing the timely management strategies”, say scientists.

Reference: Scientific Reports 7: 42737.

Published- India Science Wire 

Vigyan Prasar- Indian Science News and Features Service

Modified multi drug therapy may help eliminate leprosy

A new hope for faster and more effective treatment for leprosy is in the offing. A new drug regimen for leprosy has been found to be more effective and safe in clinical trials carried out in India and China. The new drug regime is an improvement over the existing multi-drug therapy (MDT) and has been named uniform-multi drug therapy or U-MDT. 

The study was carried out at six locations in India and two in China (Guizhou and Yunnan), with about 3000 leprosy patients who were followed up for a period of five years. The clinical trial was coordinated by the National Institute of Epidemiology in Chennai, and drugs supplied by the World Health Organisation (WHO). 

U-MDT is a supervised therapy in which patients get a monthly dose of 600 mg rifampicin, 300 mg clofazimine and 100 mg dapsone under the supervision of a doctor or a health worker. This is accompanied by daily doses of 50 mg clofazimine and 100 mg dapsone that patients have to take on their own. The total duration of the new U-MDT regime is 6 months, as against 12 months for conventional MDT. 

The present MDT includes a monthly dose of 600 mg Rifampicin and 300mg Clofazimine and a daily dose of 100 mg Dapsone and 50 mg Clofazimine. And these drugs have to be taken by patients on their own. 

In Geneva, this year, WHO urged all countries including India to intensify efforts to completely eliminate leprosy. After introducing multidrug therapy to cure leprosy in the mid-1980s, the disease burden reduced significantly across the globe. From about 5.2 million people with leprosy in 1985, the numbers have dropped to approximately 0.17million at the end of 2015. Although leprosy was declared as eliminated by most countries in the year 2005, new cases continue to emerge to date. 

The new regime appears promising with more than 94% of the patients completing the new drug regime, which confirmed good acceptability and compliance. About 99% of the patients did not show reappearance of the disease that indicated high efficacy. “Low relapse among the newly detected leprosy patients from India and China demonstrates efficacy and effectiveness of U-MDT regimen,” say researchers. Based on results from the clinical trial, scientists have urged global and national programs to consider adapting the U-MDT for all types of leprosy patients. 

The trial was conducted at six sites including leprosy control program offices in Tiruvannamalai and Villupuram in Tamil Nadu and in Pune. In Kanpur, the trial was conducted by National JALMA Institute for leprosy and other mycobacterial diseases, Agra. In Gaya and Rohtas in Bihar, the Damien foundation India trust in Chennai conducted the trial. Results from the clinical trial have been published in the latest issue of the Indian Journal of Medical Research. 

Reference: Indian J Med Res 144: 525-535. 

For- India Science Wire

Bacteria for Better Soils

In 1971, Professor Ananda Mohan Chakrabarty engineered a new strain of bacteria that could degrade crude oil and aid bioremediation of oil spills, saving millions of dollars and precious marine life. A lobby of scientists argued that it was genetically modified and that hence, its long-term environmental impact is unknown. Scientists across the globe have ever since been searching for naturally occurring microbes and organisms that can degrade pollutants.

Heavy metals and polycyclic aromatic hydrocarbons are increasingly polluting our soils. Released by burning fossil fuels, industrial wastes, coal and tar processing, these pollutants settle down in the soil, polluting it. Are there microorganisms that can tackle this pollution? This is the question that researchers at the Krishnadevaraya University, Anantapur, Andhra Pradesh, asked themselves.

They collaborated with universities from Australia and South Korea to identify 16 phyla of bacteria that were present in polluted soil samples from various sites in Australia. After isolating the bacteria, they identified these organisms by pyrosequencing: a next generation sequencing technique. Using the data of 16S ribosomal RNA the researchers classified them into different phyla or families using bioinformatics tools. They found that approximately 80% of these microorganisms tolerant to metal toxicity and capable of degrading polycyclic aromatic hydrocarbons are Proteobacteria and Actinobacteria. Mass producing these naturally occurring bacteria and using them for soil bioremediation can be an environmental-friendly and sustainable solution, enabling the transformation of polluted areas into cultivable land.

Reference: J. Hazardous Materials 317: 169-179.

Published- Current Science (Science Fortnight) 

Writer For- Vigyan Prasar Indian Science News and Features Service