Friday, October 31, 2014

Seeing beyond the Scene: Metagenomics Demystified

Our world is diversely inhabited by micro-organisms, they practically thrive everywhere. From the high-altitude mountains, to the subterranean layers, deep oceans, and even extreme environments that were once thought to be free of living organisms – acidic and highly saline waters, and even harsh temperatures of hot springs and subzero regions of the Antarctic. With this massive and highly distributed population, they hold the secrets in transforming the world around them. They are the boss, and if we want to gain more knowledge about biological processes, it is logical to get to know more about them in molecular level.

Since the advent of microbiological cultivation techniques, which started in mid-1800s, we have studied microbes as individual organisms isolated in pure cultures without or with very little inclusion of ecological factors such as presence of other microorganisms, tremendously high temperatures and other biotic and abiotic factors because of laboratory limitations, making our knowledge of them narrow and inadequate.

Metagenomics, one of the emerging neo-sciences, can be a tool for discovering novel genes and enzymes from environmental samples, especially in extreme environments. Extreme environments are interesting source of enzymes or biocatalysts that are active during extreme conditions and that can have biotechnologically valuable properties. An example is the hot and thermal environments like hot springs and mudsprings. One benefit of metagenomic analysis from hot environments is that it can better understand the microbial diversity and composition in hot springs and their relationship with geo-chemical conditions. The features of the microbial community gathered from hot  environments can be documented and analyzed for fu-ture studies. Also, the study of this can lead to the discovery of novel genes and enzymes, species and other features. Examples of novel enzymes harnessed in hot environments through metagenomics are lipases/esterase, Fe-superoxide dismutase and Taq DNA polymerase.

Far from the concept of genomics, metagenomics, traverses the lab-cultured dependent methods of sequencing and analyzing ge-nomes. Only 0.1 to 1.0% of the living bacteria that can be collected in soils can be grown in the laboratory in standard conditions, while most resist being cultured. According to a book published by the National Research Council (US) Committee on Metagenomics, entitled “The Science of Metagenomics: Revealing the Secrets of Our Microbial Planet”, most microorganisms interact with one another as communities, and separating the specimen from the group will alter its normal response to factors that will be induced. If ordinary methods of microbiology apply, organisms that require extreme conditions or community interaction will be difficult or cannot be cultivated, thus sequencing of isolates is not possible, hence no genome analysis and studies about that certain microorganism can be conducted.

On the other hand, metagenomics smites the problem of “unculturability” - the ball and chains of microbiological studies. General methods in metagenomics involves nucleic acid (e.g. DNA) extraction from the microbial community directly obtained from the environment, cloning into a surrogate host, and then analysis by sequencing or screening for expression of activities of interest, bypassing the need for artificial cultivation, therefore more efficient analysis of data. In example, metabolic processes, microbial diversity and relationship with geo-chemical conditions of microorganisms inhabiting aquatic environment near hydrothermal vents, can be better understood their relationship through metagenomics than in the laboratory because of restrictions.#

Metagenomics is also the theme of the 2014 Genetics Week (Harnessing Novel genes in thermal environments through Metagenomics). Started in 1986, the Genetics Week, which is a week-long event that presents recent advancements in the field of Genetics, is an annual event conducted every December of each year. Aside from presenting Genetic concepts, the event also showcases the history, membership and achievements of the organization in celebration of its founding anniversary. The events included in the Genetics week are the opening of the exhibit at the Institute of Biological Sciences Lobby (Wing C), a symposium, the IQlympics, orientation for interested applicants, Open Tambayan and Alumni Homecoming. Following the academic calendar shift which was implemented in AY 2014-2015, the annual Genetics Week was moved to October from its traditional schedule. 

BuCASan 2014: Commencing a new battle for domination

GENEWS October 2014 Issue

Perky chants that linger in the ears, drumrolls that thrill the crowd, dazzling lights that groove into the hype of music: everything was nothing but a spectacular gala.

BuCASan marks the beginning of a new PalaCASan season. Among the activities in the event
were Mr. & Ms. PalaCASan, Cheerdance and OrgGimik competition.

PalaCASan has become one of the most popular, most-awaited, and most talked about semester-long festivities of sports and action of the entire UPLB College of Arts and Sciences (CAS) athletic scene. Fifteen CAS-based academic organizations flock to the Baker Hall on September 13 for the annual BuCASan – the mark of the beginning of PalaCASan’s new season. With the theme “Champions of the Future”, space-age aura set the vibe as the hall was totally transformed into a futuristic wasteland where the contestants were its inhabitants fighting for domination.

Dynamic flips and torrential lifts jump-started the morning slice of the occasion as the cheerleading competition pushed through. Heart-pounding tosses and passion-poured routines of SAM-UP (Society of Applied Mathematics of UPLB) maneuvered their way to victory past UP Cells (UP Cell Biological Society) and COSS (UPLB Computer Science Society) who landed on the 2nd and 3rd spots, respectively.

Mr. & Ms. GeneSoc 2014. Bea Arrelano
and Paul Jhon Diezon.

Overflowing splendor outbreak preceded the afternoon rites of the program as each organization’s most delicate faces were showcased in Mr. and Ms. PalaCASan 2014. Spirit-boosting showdown between the candidates has been relayed to the nerves of their brods and sisses as the whole Baker Hall started to growl blended chants and cheers. Loudest efforts have been exerted but it was the chanters of “Gipodagan UP Cells…” and “Go red! Go White! Go chemsoc fight!” who won their lungs out. Mr. UPLB Chemical Society and Ms. UP Cell Biological Society were crowned Mr. & Ms. PalaCASan 2014 by the panel of judges headed by Mr. Mike Tan Lopez of the Department of Social Sciences.

Talking about the blue-blooded genomes, it was also a feasting celebration for The UPLB Genetics Society. Metallic blue pom-poms and GeneSoc letters sway side by side the victory of Beatriz Arellano (Riboprobeswho notched a Ms. PalaCASan 2014 3rd runner-up finish. Genes’ hearts pound to the beat of the drum as Batch Riboswitch’s stellar iridescent hand mime performance paid off bagging the title “Best Org Gimmick”.

Congtratulations Batch Riboswitch for winning 'Best Org Gimmick' in the recent BuCASan 2014!
Posted by The UPLB Genetics Society on Tuesday, September 16, 2014

The night was nothing but a blast. There were vibrant flashes and strobes of light everywhere, cheers echoing and spirits overflowing. The hype of every beat got the best of all spectators that it turned not into a usual competition but rather a colorful display of each organization’s finest. The aura, the environment, the rhythm was an epitome of an ultramodern inception.#

For more photos, visit the Official Facebook page of The UPLB Genetics Society (Link).