Spring Insider 2018

CONTENT

SQ INSIDER

SQ High School Essay Contest Winner Amy Le La Jolla High School

In the fourth annual High School Essay Contest, the SQ Community Outreach team asked high school students to write a 500-750 word piece about biotechnological advances and possible ethical and societal implications of a biotechnological advance.

SQ hopes this experience will encourage and celebrate science communication among future scientists and inspire them to think about biology in a broader context.

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Job on the Rise

Illustration by Qiuwan Liu | Staff Illustrator

ne organ donor can save eight lives. Yet, the number of organ donors is not sufficient to supply hospitals with what they require for every patient on a transplant list. Why is this the case? Because only 52% of the nation is enrolled to donate organs, while there are 120,000 people in the US waiting for a transplant, not to mention the fact that every 10 minutes, another name is added to the transplant list.

The 3D printer remedies these problems. The first 3D printer was made in 1986 by Charles Hull. The printer works by creating objects in slices.

Filament is used and liquified, similar to a hot glue gun, which is then placed in layers by the machine. The machine intricately layers the plastic in order to allow for movement once the object

is made. Originally, 3D printers were used to manufacture everyday appliances such as forks and spoons. This slowly developed into creating larger items like a guitar, a gun, or a camera, and eventually biological parts.

Although currently only body parts such as ears, skin, or a trachea can be created, scientists are attempting to create organs out of the patients’ own cells therefore automatically creating an organ that “SCIENTISTS ARE ATTEMPTING TO CREATE ORGANS matches the patient.

OUT OF THE PATIENTS’ OWN CELLS THEREFORE Since organ rejection is AUTOMATICALLY CREATING AN ORGAN THAT MATCHES THE PATIENT” likely, creating an organ out of the patient’s cells will lead to a higher sucthe number of jobs that can be process rate and no wasted organs. duced as a result of the introduction of In the medical world, 3D printing is 3D printers to the medical field. referred to as bioprinting. Bioprinting Not only will bioprinting create new is not only helping save the lives of jobs but it will also open up positions thousands of people but will be creatin current ones. 3D printing is projecting more jobs as well. Once an organ ed to be a seven billion dollar industry is made, it will need to be assessed by 2025, with nearly half of the profits before placed into the patient. Nurses coming from the bioprinting industry. and doctors are extremely busy people The industry has a large projected who must monitor their patients, so growth percentage making room for they will need an organ assessor. more jobs. Positions for engineering, The assessor will evaluate the organ 3D designing, and modeling machinery by asking questions like “Is the orwill rise. Organ assessors will need to gan working?” or “Does it have any have a strong background in technoldefects?” After these questions are ogy and science to better understand addressed, the assessor will further the limitations and requirements that evaluate it by their standards. More a bioprinting machine must have in specifically, the assessor will run tests order to function correctly. to determine the functionality of the We are still a long way from creating organ. Furthermore, the 3D printer has a living and working organ that can be the potential not only to create organs used in a person’s body, but as doctors but also dental crowns or prosthetics. have successfully created limbs for A 3D printer will not be easy to work amputees, organs are only a few steps with, therefore each dentist or orthope- away. Once this is done, the position of dic office will require a technician who an organ assessor will open up. Maybe can operate it at all times. This adds to this will be the job for you!

Saltman Quarterly

Volume 8 | Spring 2018

Science of Unwinding pg 2

23andMe pg 3

Al and the Genome pg 3

SQ High School Essay Contest pg 4

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The term ‘genetic testing’ may sound unfamiliar, but almost all Americans have been exposed to it through either personal experience or media coverage. In fact, since the introduction to public genetic testing in the ‘70s and ‘80s, the world has become increasingly fascinated..... (Continue on page 2) Illustration by Vicky Hoznek | Staff Illustrator

SQ INSIDER

THE SCIENCE OF UNWINDING

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his interest has even leaked into entertainment, with labs on crime TV shows running forensic tests to solve cases, men on talk shows impromptu dancing after paternity tests come back negative and, most recently, privatized companies like 23andMe releasing affordable genealogical testing to determine ancestry.

Genetic testing and counseling is, as we know it today, a process of deriving and analyzing one’s DNA. It is very useful in medical settings, especially for those with a history of genetic disease in their family and women who are pregnant or planning to become pregnant. However, it can also be used as a tool to analyze the code which both distinguishes us as individuals and joins life together under common themes.

Genetic material for analysis is easy to obtain, it can come from a blood test, cheek tissues from a swab, spit collected in a tube, or a tuft of hair. The collected sample is then sent to a lab where it is analyzed in a multitude of different ways, depending on what the researchers are looking for. A genetic counselor could look at the chromosomes by examining a cell frozen in mitosis, sequence a specific part of DNA using primers to find mutations, or even look at the levels of certain molecules. Methyl groups may be examined, molecules which can bend the DNA to inactivate segments and ultimately code for a different protein expression.

This data can then be used to look for many different things in the genome, some of which you may have heard of or even undergone without realizing. For example, everyone born in California after 1966 must undergo newborn screening to test babies for treatable genetic disorders. Carrier testing is taken by individuals who want to see if they carry recessive genes for serious genetic disorders like cystic fibrosis that could potentially be passed on to their offspring.

There is also predictive genetic testing to see if a person will develop a serious disease later in life, such as Huntington’s, Alzheimer’s, and other genetically inherited cancers.

A rapidly growing field is pharmacogenomic testing, where a laboratory examines variations that certain individuals might have in their genes that change their responsiveness to specific, individualized

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Written by

CATHERINE FRUSETTA

UTS STAFF WRITER

Illustration by

VICKY HOZNEK

STAFF ILLUSTRATOR

medications. Research in this field may be able to identify individuals who will react especially badly to cancer medications, for example.

The processes for genetically analyzing people have already become progressively cheaper and more accessible. In fact, the cultural phenomenon of the “$1,000 Genome”, or the commercially available sequencing of an entire genome for $1,000, was already achieved by Veritas Genetics in 2015.

With this, more people than ever are starting to record their genetic information into both private and public databases, which can then be used by scientists to study not only individual genomes, but “MORE PEOPLE THAN EVER ARE STARTING TO RECORD the genetic data of entire THEIR GENETIC INFORMATION... WHICH CAN THEN BE populations.

USED BY SCIENTISTS TO STUDY NOT ONLY INDIVIDUAL Our joined web of GENOMES, BUT THE GENETIC DATA OF ENTIRE genomic information has POPULATIONS” the possibility to be used to improve fields other than medicine as well. In Computer Science, the use of artificial intelligence can be used to obtain genetic data and in Sociology, a greater understanding of equality between individuals of different Editor-in-Chief: Cade Oost backgrounds can be reached.

Executive Editor: Madalyn De Viso Even today, however, access to genetic Head Production Editor: Tushara Govind sequencing allows us to know more about UTS Production Editor: Dominique Sy ourselves than we could have known otherProduction Team: Lee Diego Lacasa, Zarina wise. To sequence the DNA of each person Gallardo, Arya Natarajan, Nina Shi is to put another piece in the puzzle that is Online Editor: Sharada Saraf our joint understanding of the human race.

SQ Features Editor: Rithvik Shankar As genetic testing and counseling become UTS Features Editor: Samreen Haque integrated into our everyday lives, we will not Staff Writers: Catherine Frusetta, Michael only better get to know what makes us indiHerron, Peter Chew viduals, but understand that life is simply a Staff Illustrator: Varsha Rajesh, Vicky Hoznek, line of genetic code which has been edited Qiuwan Liu Head Advisers: for billions of years. To have power over James Cooke, Ph.D this code, it may become possible to obtain Assistant Teaching Professor of Neurobiology complete power over both oneself and the Hermila Torres possibilities of life beyond us.

Manager, do/bio Center

sqonline.ucsd.edu

Building a Homo sapiens’ Network of Heredity

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Written by MICHAEL HERRON | SQ STAFF WRITER Illustration by VARSHA RAJESH | STAFF ILLUSTRATOR

urrently used in over 500 laboratories worldwide to diagnose over 2,000 human conditions, genetic testing has gained significant popularity over the past few years, particularly with the advent of companies such as 23andMe. Founded in 2006, 23andMe sequences customers’ submitted saliva samples and compares them with accumulated data of different ethnic groups to determine ancestry.

Currently, the company has attracted over 2 million customers that have been drawn to 23andMe’s two listed $99 and $199 genetic testing packages. Both packages offer genetics testing, the $99 test solely identifying genetic markers to highlight ancestral origins and the $199 test having an additional health service component to assess one’s potential risk of developing certain hereditary diseases.

The public’s interest in 23andMe has led to its collaboration with other repu-

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he turn of the 21st century saw the completion of the ambitious Human Genome Project, which set out to sequence the entire human genome. Since then, great strides have been taken to make the sequencing process faster and more cost-effective. Behind such advances are artificial intelligence methods such as “deep learning” approaches to data processing.

“DEEP LEARNING ALGORITHMS ARE MODELED AFTER NEURONAL CONNECTIONS FOUND IN BIOLOGICAL BRAINS”

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table companies, such as Genentech.

By default, 23andMe’s tests only search for known genomic variations. However, Genentech’s $10 million partnership goal is to incorporate full genome sequencing of customers in order to discover new targets for drugs and diagnostic tests. One project currently underway is Parkinson’s disease research, with 12,000 Parkinson’s patients signed up via the Michael J. Fox Foundation. This ongoing study is aimed at shedding light on the genetic variation expressed in those afflicted with the disease.

23andMe not only answers questions regarding ancestry, but it also enables consumers to participate in research through providing consent of their genetic information use. Alex Schuth of Genentech and 23andMe’s CEO Anne Wojcicki’s marked partnership is expected to increase mass collection of consumer

“23ANDME NOT ONLY ANSWERS QUESTIONS REGARDING ANCESTRY, BUT IT ALSO ENABLES CONSUMERS TO PARTICIPATE IN RESEARCH”

genetic information, estimated at 10 million. This stark increase in consumers will accumulate data collection that may provide crucial insight for research and patient treatment strategies, such as personalized gene therapy for patients, and understanding genetic variations amongst minority groups for potential cancer treatment. This, in turn, will also lead to a larger database of genetic variety for future studies, which may be useful in determining genetic markers for disease drug targets.

Written by PETER CHEW | UTS STAFF WRITER Illustration by QIUWAN LIU | STAFF ILLUSTRATOR Deep learning, a subset of machine learning, utilizes algorithms recognize patterns in large data sets. Interestingly, deep learning algorithms are modeled after neuronal connections found in biological brains. The algorithms simulate individual processing units analogous to neurons and communication between them. Such networks are often “trained” with easier data sets and human supervision, allowing the network to adjust how its virtual neurons fire and produce a correct result in subsequent trials. After the training period, the artificial neural network can be used to rapidly parse through vast amounts of experimental data for complex patterns that would have taken human researchers years to analyze.

Biologists utilize deep learning in the development of algorithms designed to assemble a multitude of individually-sequenced DNA fragments back into a full genome. Since a full, uncoiled genome is much too unwieldy to work with, many

base pair sequencing techniques analyze miniscule fragments at a time. Assembling the fragments back together was previously the costliest task in sequencing. Advancements in deep learning play a significant part in making genome sequencing as affordable as it is today, since neural nets allow fast and efficient reconstruction of patient genomes while reducing the need for repetition of laboratory procedures. This has allowed personalized medicine to become goal that many hospitals and clinics now strive toward. Rather than standard treatments for illness, a patient’s genome can be analyzed to detect predisposition towards disease and serve as a blueprint for drugs that are specially designed to be extremely effective for an individual. While very technologically demanding, personalized medicine is projected to lower healthcare costs and improve treatment efficacy in the long run.

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