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Feb 15, 2020
Category: General
Posted by: admin

The puzzle for Feb 2020 was created by Aparajita (MSc Student). The competition was held on 14-Feb-2020 and the winners are- First: Meenu, and Second: Nupur. More details here. The pictures of winners of Puzzle 10 and Puzzle 11 have also been updated.

Feb 15, 2020
Category: General
Posted by: admin

Two new microblogs has been published authored by Shubhi Khare and Tanishqua Pawar respectively, both MSc students. They can be read here.

Feb 11, 2020
Category: General
Posted by: admin

The Department organized 'Sports Day' on 07th Feb 2020. All students, staff, and faculty members participated in various games and activities. The winners received prizes and everyone enjoyed. Report and pictures are here.

CMS - 2.2.7 - Skookumchuck
 

MicroBlogs

15-Feb-2020

Supra-Kingdom of Life

By: Shubhi Khare (MSc student)

A scientist is never off duty and this was shown by graduate student at Dalhousie University Yana Eglit. She was on a hike with her friends in Canadian woods from where she picked up the dirt and soaked in water. After few days she checked to see if the water had revived any dormant microbes. She found two different types of hemimastigote in the soil, one of which was an entirely new species, and team named it Hemimastix kukwesjijk.

The hemimastigote were first identified in 19th century, but remain mystery due to the inability of scientist to figure out the kingdom of these creatures. Hemimastigote are about two hundredth of mm in length. They run quickly using dozen of flagella on their surface. Unlike other microorganisms they move their flagella in random directions rather in a coordinated manner. They belong to domain of eukaryotes. They represent 'known unknown’ protist lineages- moderately well described groups, but their position on tree of life is unknown because they are difficult to culture in labs and sequence. An advance genetic analysis done by a team at Dalhousie University shows that they more different from other organism and they represent a new “Major Branch” of evolutionary tree sequence and they represent their own distinct lineage apart from other super groups.Their DNA is present in the form of chromosomes within a distinct nucleus. The organisms have no common ancestors with any other living thing in the last billion years and they are described as “Voracious Little Ogres”.

The discoveries like these will more profoundly tell us about the steadily growing number of taxonomic addition. We will keep uncovering not new species or classes but entirely new kingdom of life and these kind of data will reshape the tree of life because many more branches will be discovered.


Further reading:
1. Quanta Magazine
2. CBC News

 

14-Feb-2020

Newly found Bacteriophage is a little too big

By: Tanishqua Pawar (MSc student)

Earth’s ecosystem is no less than a box full of surprises. UC Berkeley researchers unraveled a new mystery about earth’s microbiomes by recently discovering 351 different phages which have genome size of around 200 kbp which is way too larger than the genome sizes of some of the already known bacteria, which ranges from 130 kbp to 14 Mbp. These huge phages are 15 times larger than the usual phage genome size i.e. 50 kbp.
Among these newly discovered phages, one of them have a genome size of around 735,000 base-pairs, which is nearly 15 times larger than the usual phage genome, making it the largest phage genome in the world as of now.

Because of the huge size of the genome, the 351 megaphages were thus divided into 10 groups, which were named to pay homage to the authors that contributed in the publishing of the paper by naming them after the languages spoken in their native countries. Mahaphage (Sanskrit), Kabirphage, Dakhmphage and Jabbarphage (Arabic); Kyodaiphage (Japanese); Biggiephage (Australian), Whopperphage (American); Judaphage (Chinese), Enormephage (French); and Kaempephage (Danish), these were the names given as per the words for “Big” in their respective languages.

The researchers and collaborators did commendable work by searching the grounds of 30 different environments, ranging from the guts of premature infants and pregnant women to a Tibetan hot spring, a South African bioreactor, hospital rooms, oceans, lakes and deep underground. The huge phage’s DNA can make a protein which is an analogous of a Cas9 protein named as Cas∅(phi) which is a part of gene-editing tool. CRISPR –Cas9 is a revolutionary tool developed by Jennifer Doudna of UC Berkeley and her European colleague, Emmanuelle Charpentier.

The huge phages DNA also has a gene for translation process, usually these ribosomal machinery are found in bacteria and archaea but not in viruses.
This discovery might be able to explain how phage genes are involved in antibiotic resistance and pathogenesis in human. It could also explain how the phages are co-existing in the human gut along with archaea and bacteria. Jill Banfield, who is a CZ Biohub investigator and also director of microbial research at the Innovative Genomics Institute (IGI) said, "Some diseases are caused indirectly by phages, because phages move around genes involved in pathogenesis and antibiotic resistance. And the larger the genome, the larger the capacity you have to move around those sorts of genes, and the higher the probability that you will be able to deliver undesirable genes to bacteria in human microbiomes.”

The metagenomic sequencing reveals large sizes of phage genome and its similarity with each other. These phages carry a lot of potential that might help us to find new tools which could be found useful in genetic engineering. It could also become a source of unknown proteins that might find applications in various industries ranging from medical to agricultural.

Further reading:

1. Berkeley News
2. Science Daily

 

23-Jan-2020

The Wuhan “Seafood market” Coronavirus

By: Vishal Dashora (PhD Scholar)VISHAL

 Once upon a time in China, there was monster called Nian which would appear in the middle of the night and eat the villagers, especially children. One day all the villagers decided to hide from the beast but one old man, Yanhuang decided to take revenge. With red clothes on his back and firecrackers in his hand, he managed to scare the monster away and since then every year during spring time the Chinese people celebrate the New Calendar year by decorating the country in red and bursting fire crackers to keep Nian away. But this year it seems that the mythical beast has managed to creep its way through.

There were six reported strains of Coronavirus in humans, until the 31st December of 2019, when a novel strain of Coronavirus was identified in the city of Wuhan, China. Out of 27 suspected cases of the “pneumonia of unknown cause”, majority were stallholders in the Wuhan South China Seafood Market. Being the seventh-largest city of China, Wuhan is a hub for import-export of goods as well as people and hence, neighboring countries like Thailand and Singapore began the basic monitoring of the inbound passengers. On 5th January 2020, the health officials ruled out SARS, MERS and bird flu in the confirmed 59 cases and were already starting the quarantine procedures for the patients as well as the initial contacts.

WHO has confirmed that a novel coronavirus has been isolated from one of the patients, and named it as 2019-nCoV. The first death occurred on 9th January 2020 and the victim was a 61 year old man who regularly shopped at the seafood market. By 11th January the genome of this newly isolated menace was submitted in GenBank and travel guidance was issued all over the country. The first case outside of China was that of a 60 year old Wuhan-resident Chinese woman who had flown to Bangkok. The alarm bells finally rang loud on 14th January, when the officials noticed a couple among the listed cases in Wuhan, only one of which had gone to the market recently. This clearly suggested a human-to-human transmission of the virus.

By 20th January several individual cases has been reported in Japan, Thailand, South Korea and even Washington State where a male patient in his 30s is still being kept in isolation after he was diagnosed with the “mystery virus” when returned from Wuhan. With the Chinese New Year approaching on 25th January 2020, the WHO has conducted an emergency meeting on 22nd January to assess the “potential pandemic risk of the outbreak” as the “Year of the Rat” will attract thousands of tourists the Mainland China. Although the genetic sequence of 2019-nCoV is distinct from SARS and MERS, the previously known antivirals are being repurposed due to the lack of newer vaccines and drugs.

As of 23rd January 2020, 17 people have lost their lives to this havoc and where most of the world has already rejoiced in the wake of a new calendar year, the people of China will be celebrating the “Zhōngguó xīnnián” in considerable apprehension.

Further reading:

1.New York times report
2.CDC Media release
3.WHO statement
4.Wikipedia

 

 

22-Jan-2020

The Serendipitous Immune T-cell Discovery

By: Juhi Jain (PhD Scholar)Juhi

A new Human T Lymphocyte (T cell) has been accidently discovered by the Prof. Andrew Sewell at Cardiff University in the UK which can target and kill most kind of cancer cells and ignore healthy cells. The new TCR is found to have a broad cancer specificity which raised the prospect of “universal” cancer therapy if it pass all the clinical trials. This T cell is equipped with a novel T cell receptor (TCR) named MR1 which they found by performing Genome-wide CRISPR-Cas9 screening. These MR1 having T cell sense the cancer cells and kill it like HLA. In the in vitro study, this new T cell has been shown to kill lung, skin, blood, colon, breast, bone, prostate, ovarian, kidney and cervical cancer cells, while ignoring healthy cells. To test the therapeutic potential of these cells in vivo, the T-cells having MR1 has been injected into mice with human cancer and a human immune system, that resulted in clearance of cancer cells .These T-cells would be the perfect candidate for T-cell therapy as they could provide a “one-size-fits-all” cancer treatment. The Cardiff group further take out the T-cells of melanoma patients and genetically modified them to express this new TCR and then injected back into the patients. These modified T-cells could not only kill the patient’s own cancer cells, but also other patient’s cancer cells in the laboratory, regardless of the patient’s HLA type which is a promising result in the pave of cancer therapy.

 Further reading:

1. BBC New report
2. Original research article in Nature Immunology 

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