Genetics – Australian Science

How Modern Technology is Improving Health Care (Genome and Algorithms)

Josip — Fri, 04 Mar 2016 08:08:16 +0000

Genome Testing

According to an article that rates this year’s medical advances according to their importance, at the top of the list is a new Ebola vaccine that is expected to be available later this year. Genome-based testing, which has the potential to increase the speed and flexibility of clinical trials for life-saving experimental treatments, ranked at number two.

Within the field of genome testing, one of the most important recent discoveries in medicine is CRISPR, which scientists have learned to use as a genome editing tool. CRISPR, an acronym for clustered regularly interspaced short palindromic repeats, is a natural defense mechanism found in bacteria. In the 1980s, scientists began observing patterns of bacterial genomes and now understand more about how the process of preventing viruses from replicating works.

A viral microbe copies the genetic material in each spacer into an RNA molecule. Cas9 enzymes cradle the RNA molecule, and in combination, they explore a cell. If they find genetic material that matches the CRISPR RNA, the viral RNA attaches to it. The Cas9 enzymes cut the DNA in half, preventing it from multiplying. Scientists believe that CRISPR has the potential to revolutionize biology because it can identify and remove bad genes from a DNA strand at very little economic cost.

Health Algorithms

According to a recent study, a new computer-based test can help predict the likelihood of developing dementia. The test utilizes a complex algorithm based on information such as a person’s age, weight, gender, social habits and previous medical history. Those whose test results showed them to be at higher risk could then take additional preventive measures by increasing activities that have been proven to improve memory. The focus of this technology is prevention.

Researchers used the test to assess the medical records of over 226,000 people over the age of 60. The algorithm proved to be so accurate that the developers decided to share it freely with other researchers. Their goal is that it become available to the public and an important element of a national healthcare database. They predict that it may take a few years to reach those goals.

Integrated Health Care Software

Another technological advance in medicine are software services that enable those in the medical profession to deliver a higher level of care. From a patient’s perspective, that higher level of care is manifested at every level of the health care system. Doctors are able to develop superior treatment plans by quickly and securely sharing medical information with specialists. All the time saved by not having to make physical appointments and drive to them can be used to increase communication between doctors and their patients. Automated scheduling capabilities also give other medical staff more time to communicate with the patient, which results in providing the doctor with more useful information.

One of the most common complaints of health care professionals in the last decade is the growing amount of paperwork they are required to complete. Health care professionals choose their careers based on a desire to spend their time having human interactions that result in people feeling better, not learning complex insurance billing procedures. Clinical trials have shown that one of the benefits for health care providers is the simplification and automation of some of the most time and energy consuming billing processes.

The Future

Scientists and health care professionals predict that the next thing that will revolutionize health care is the concept of precision medicine. Rather than offering every patient the same treatment for the same illness or condition, this concept focuses on developing individual treatment plans based on a number of genetic and environmental factors. Research in the field of epigenetics has demonstrated that genes are not, as was once believed, fixed, but are in fact affected by the environment.

The Precision Medicine Initiative, which is currently being developed and is expected to be launched later this year, promises to change the way medical professionals are trained by incorporating many of the newest scientific discoveries. This will allow doctors to more easily develop and implement valuable new techniques into their practices. Scientific advancements in genetics, computer technology, and medicine are making the future of health care look very bright indeed.

Cite this article:
Ivanovic J (2016-03-04 08:08:16). How Modern Technology is Improving Health Care (Genome and Algorithms). Australian Science. Retrieved: May 07, 2024, from http://australianscience.com.au/genetics/how-modern-technology-is-improving-health-care-genome-and-algorithms/

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My Dog Speaks To Me With His Eyes – Evolution of Human/Dog Bonds

Lia Paola Zambetti — Mon, 11 May 2015 10:11:21 +0000

Puppy love – same as baby love? Yes, it seems so:

“My dog talks to me with his/her eyes

Cite this article:
Zambetti L (2015-05-11 10:11:21). My Dog Speaks To Me With His Eyes - Evolution of Human/Dog Bonds. Australian Science. Retrieved: May 07, 2024, from http://australianscience.com.au/news/my-dog-speaks-to-me-with-his-eyes-evolution-of-humandog-bonds/

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Bacon Fans United: The Pig Genome Sequenced

rayna.s — Sat, 17 Nov 2012 00:28:42 +0000

Breeding healthier and meatier piggies has been one of the many scientific challenges of the past decades; creating more reliable models to study human diseases is another. The swine disease model is indeed much better to use when studying human disorders than the (thus far) widely used murine models. Although pigs reproduce slower than mice and are more expensive to take care of, they are more similar to humans when it comes to anatomy and physiology. These common grounds have allowed the development of accurate swine models for diabetes, cystic fibrosis or retinitis pigmentosa (a cause of blindness). In its issue of 15 November, Nature published the fully sequenced and annotated pig genome. This is a major achievement, and will allow considerable progress to be made on both the yummy and the healthy fronts.

Sus scrofa domestica, by its official name, originates from South-East Asia and then went on a visit to Europe. A closer examination of the sequenced pig genome consistently shows a clear and deep split between Asian and European wild boars rooting some 1 My ago. More precisely, the analysis allowed to date the split between the two lineages in the mid-Pleistocene (1.6–0.8 My ago), a divergence the authors explain with possible colder climate prompting isolation between populations across Eurasia.

Demographic history of wild boars. Image from Groenen et al. (Nature, 2012). The default mutation rate for human (μ) was used, and the generation time (g) was estimated to 5 years. The Last Glacial Maximum (LGM) is highlighted in grey. WBnl, wild boar Netherlands; WBit, wild boar Italy; WBNch, wild boar north China; WBSch, wild boar south China.

As the authors explain it:

Our demographic analysis on the whole-genome sequences of European and Asian wild boars revealed an increase in the European population after pigs arrived from China. During the Last Glacial Maximum (LGM; ~20,000 years ago), however, Asian and European populations both suffered population bottlenecks. The drop in population size was more pronounced in Europe than Asia, suggesting a greater impact of the LGM in northern European regions and probably resulting in the observed lower genetic diversity in modern European wild boar.

Noticeably, pigs have been faithful companions to humans for 10,000 years now. Breeding piggies and selecting for some particular features of theirs has had an important impact on the swine genome. Authors thus identified a wide range of genes and gene families to have undergone fast-paced evolution. Immunity-related genes, already known to be actively evolving in Mammals, were for instance part of this subset, and further analysis revealed evidence for specific gene duplications and gene-family expansions. Lastly, a significant expansion of the porcine olfactory receptor gene family was described. The authors explain it by the importance smell has for pigs when scavenging for food.

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How Have Marsupials Evolved?

rayna.s — Thu, 08 Nov 2012 00:18:59 +0000

The phylogenetic relationships between two orders of marsupials have been intesively debated. Authors benefited from recent sequencing projects which provided two marsupial genomes: this of the South American opossum (Monodelphis domestica) and the one of a kangaroo, the Australian tammar wallaby (Macropus eugenii). Retroposons are suitable and homoplasy-free markers: their insertion sites are random; parallel insertions or exact excisions are very rare.

Thus, if one finds a retroposon in the homologous genomic loci of both species this indicates a common ancestry; on the contrary: if the marker is missing in one of the species, it means prior divergence. Moreover, one retroposon can insert into another: this situation is called transposition into transposition. These nested mobile elements insertions provide precious information about the relative times during which given retroposon families integrated into genomes: young elements can insert into older ones, but the reciprocal is impossible.

After complete screening of the opposum and kangaroo genomes, authors found ~8,000 and ~4,000 nested retroposon insertions, respectively. Then, the frequencies and time scales of SINEs (Short INterspersed Elements) were calculated (using TinT software) and 3 groups identified:

SINEs specific to the lineage leading to opossum => phylogenetically informative markers present in the opossum lineage;
SINEs specific to the lineage leading to kangaroo => phylogenetically informative markers present in the kangaroo lineage;
SINEs active in both species => phylogenetically informative markers present in both lineages .

Also, ~220,000 genomic loci containing retroposons were detected using three different strategies. After screening and experimental confirmation, a total of ~440 marsupial sequences were aligned and analyzed to reveal 53 informative markers. Ten of those confirmed again the monophyly of marsupials. The other 43 phylogenetically informative retroposon markers provide significant support for most of the basal splits within marsupials.

Phylogenetic tree of marsupials derived from retroposon data.

Authors did not find any loci containing elements present in opossum plus Paucituberculata but absent in kangaroo, which would have supported the alternative of a close relationship between Didelphimorphia and Paucituberculata. They screened for markers that would support the alternative hypothesis of Paucituberculata being the sister to all marsupials: experimental verification showed that all of the putative elements were also present in the order Paucituberculata (Rhyncholestes), thus supporting the monophyly of marsupials, but not the basal divergence.

Furthermore, 13 of the original 53 markers were present in the South American Microbiotheria and the 4 Australasian orders but not in either Didelphimorphia or Paucituberculata: this significantly supports the monophyly of Australidelphia. The branch separating Australidelphia from Didelphimorphia and Paucituberculata is one of the strongest supported as well. Nevertheless, poor fossil record from South America, Antarctica, and Australia does not allow to assess Australidelphian early realtionships and biogeography.

Two competing hypotheses exist regarding Microbiotheria: the latter are either excluded from the Australasian order (based on nuclear protein-coding genes) or embeded into it (completely or partially based on mitochondrial data). No reliable marsupial phylogeny is established up to now. In the present study, authors provide evidence for 4 independent diagnostic retroposon insertions which allow to place Microbiotheria within South America marsupials. Thus, authors propose the new name Euaustralidelphia for the monophyletic grouping of the four Australasian orders Notoryctemorphia, Dasyuromorphia, Peramelemorphia, and Diprotodontia. In total, 18 out of the initial 53 retroposon markers provide significant support for the monophyly of each of the five multi-species marsupial orders.

Authors conclude: “the retroposon marker system identified a clear separation between the South American and Australasian marsupials. Thus, the current findings support a simple paleobiogeographic hypothesis, indicating only a single effective migration from South America to Australia, which is remarkable given that South America, Antarctica, and Australia were connected in the South Gondwanan continent for a considerable time.”

Nilsson MA, Churakov G, Sommer M, Tran NV, Zemann A, Brosius J, & Schmitz J (2010). Tracking marsupial evolution using archaic genomic retroposon insertions. PLoS biology, 8 (7) PMID: 20668664

(This was originally published on the author’s personal blog. Image is from the original article.)

Cite this article:
Stamboliyska R (2012-11-08 00:18:59). How Have Marsupials Evolved?. Australian Science. Retrieved: May 07, 2024, from http://australianscience.com.au/genetics/how-have-marsupials-evolved/

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The evolution of human mortality

Charles Ebikeme — Mon, 15 Oct 2012 17:00:44 +0000

How long until we live forever?

The general consensus is that we are getting older and living longer. Despite consequences and kryptonite, it is getting easier to stay alive. Heaven can wait, it seems. Every year each baby born is expected to live 3 months longer than its predecessor of the previous year. This has been the case for the last 160 years. A stunning display of the ability we humans have to prolong the length of life. And it is this simple fact of life that economists and politicians are struggling to deal with — an ageing population and not enough resources to go around.

But outside of this there are some interesting and important questions to pose when thinking about human mortality. Does our mortality have a basis in our genetics? Researchers, publishing in PNAS, wanted to know if this reduction of mortality was as a result of a possible genetic shift or something much simpler. They wanted to understand the evolutionary context for variation in human mortality patterns — particularly comparing those of today to hunter-gatherer populations. Modern-day hunter-gatherer populations which are used as a proxy in evolutionary terms.

What they found was a significant decrease in human mortality. The vast majority of this mortality reduction has only occurred since 1900 and has been experienced by only about 4 of the 8,000 human generations that have ever lived. An astounding fact.

The average age-speci

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Weekly Science Picks

Kelly Burnes — Sun, 16 Sep 2012 03:01:39 +0000

So much science, so little time... - Photo credit, Leo Reynolds

Sigh, my photo caption sums it all up…

But here are the news stories that caught my eye and I hope you find them interesting as well. Maybe reading them will inspire your own work or to dig deeper for answers. In any case, enjoy!

This is one of my favorite topics because it offers up rampant debate on so many topics – society, education, cognition. You’re just going to have to read it for yourself.

This Is Your Brain on the Internet (Maybe) by Kyle Hill

So what is the Internet doing to our thinking? It is hard to say. Current research has a hard time keeping up with the break-neck pace of online culture, and only the more conventional mediums like television and newspapers have been evaluated in any rigorous sense.

Newspapers might be old school, but they do have an online media presence as well these days. This article was published in The Australian this week and concerns Australia’s own CSIRO. Genetically modified crops and foods have been a part of our collective diet for many years, whether or not some want to admit it. And they are here to stay. I am of the opinion that they play an important role in our food security given a number of ever changing variables in our environment. The usual characters are depicted in this piece and it will be interesting to follow this story and hear the response from CSIRO.

Scientists Wary of CSIRO GM Crop by Adam Cresswell

SCIENTISTS from three countries are warning a CSIRO-led push to make Australia the first nation in the world to introduce genetically modified wheat crops could pose a significant health threat to humans and other animals.

If you haven’t heard, NYC Mayor Mike Bloomberg has banned sugary soft drink sales in cups larger than 16 0z. in his efforts to personally tackle the obesity epidemic. I feel some disclaimers are in order: One, this story did appear on www.bloomberg.com, but you could have found it in a variety of online publications; and two, I serve on the Mayor’s Best Practices Partnership to identify strategies to combat childhood obesity. That being said, I find the details of the ban interesting as you can see in the quote below. I personally do not see the need for a a 32 oz. soda, but people who want their sugary fix will do some quick addition, carry more cans or bottles and walk to get more refills. Oh, how long must we wait for data on this?!

NYC Health Panel Backs Bloomberg Ban on Super-Size Sodas by Henry Goldman and Leslie Patton

Restaurants, movie theaters and other outlets have six months to comply or face a $200 fine each time there’s a violation, the health department said. The ban doesn’t apply to convenience stores and groceries that don’t act primarily as purveyors of prepared foods, which are regulated by New York state. The rules do allow consumers to buy as many of the smaller drinks as they want and to get refills.

To continue with the discussion on obesity, this is an interesting read which once again highlights the genetics vs. environment debate.

What’s the Main Cause of Obesity – Our Genes or the Environment? from ScienceDaily with resources from the BMJ (British Medical Journal)

The ongoing obesity epidemic is creating an unprecedented challenge for healthcare systems around the world, but what determines who gets fat?

And one last article that I thought was noteworthy, and a bit on the strange side by the title:

Chemists Develop Nose-Like Array to ‘Smell’ Cancer from ScienceDaily, findings appear in the current issue of the journal ACS Nano

The chemist says, “Smell ‘A’ generates a pattern in the nose, a unique set of activated receptors, and these are different for every smell we encounter. Smell ‘B’ has a different pattern. Your brain will instantly recognize each, even if the only time you ever smelled it was 40 years ago. In the same way, we can tune or teach our nanoparticle array to recognize many healthy tissues, so it can immediately recognize something that’s even a little bit ‘off,’ that is, very subtly different from normal. It’s like a ‘check engine’ light, and assigns a different pattern to each ‘wrong’ tissue. The sensitivity is exquisite, and very powerful.”

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The Devil’s Technology

Ross Chapman — Fri, 27 Jul 2012 00:44:57 +0000

Biotechnology is rarely considered to be good for the environment. In fact, environmental campaigners frequently claim that genetically modified organisms represent a major threat to biodiversity and ecosystems. However, the study of the Tasmanian Devil Facial Tumour disease (DFTD) using genetic technologies is an example where biotechnology has been used to create a definite environmental benefit.

The Tasmanian Devil (Sarcophilius harrisi) is Australia’s largest surviving carnivore and endemic to the island of Tasmania. DFTD induces cancerous tumours on the face and inside the mouth of affected animals which die within months. The condition was first observed in north-eastern Tasmania in 1996. DFTD, like other cancers, is caused when mutations within a cell prompt it to switch from normal function into tumorous growth. Cancers are considered non-contagious as the tumour is contained within the body and is unable to spread to alternative hosts. Furthermore, the immune system of any alternative host would normally recognise any foreign tumour cells that managed to invade the body, and quickly kill them before the disease becomes established. However, the DFTD is exceptional in that it is readily transmitted between individuals of the same species, and this has resulted in the disease rapidly sweeping across the island and threatening the entire species with extinction.

In order to better understand the DFTD, an international team of scientists has sequenced the entire genome of the Tasmanian Devil and identified mutations underlying DFTD. The results were recently published in the scientific journal Cell. This biotechnological research surprisingly identified that none of the tumours originated in any of the hosts examined. Instead, they were able to trace them all back to one cancerous cell from within a female devil, possibly in the early 1990s. This radical and unusual tumour had developed the ability to jump from individual to individual in a uniquely contagious manner, so spreading the disease across the species.

The Tasmanina devil facial tumour.

Using the genetic sequence information, the researchers were able to discount the involvement of a virus in the transmission of DFTD. Instead they were able to identify a new and radical form of transmission. Devils often bite each other in the face during eating and feeding behaviours. During biting, fragments of tumour from an affected individual become implanted in an almost vampiric manner in a new and healthy individual.

The scientists also discovered that the DFTD tumour carries a mutation in a gene that plays a critical role in regulating the host’s immune reaction. From this, they concluded that the tumour cells are able to interfere with the host’s immune system immediately after implantation, The disrupted immune system is unable to kill the tumour, thereby ensuring the survival of the disease in the new individual.

The results of this study have provided valuable insight into the management of the DFTD and the conservation of the Tasmanian Devil. Because the condition is only transmitted through the bite from a diseased individual, the disease can be effectively controlled by quarantining healthy populations from diseased. The condition will then be naturally eliminated as diseased individuals die off from within the affected population. Such a policy has already been implemented with the Tasmanian Department of Primary Industries, Water and Environment who have been identifying and quarantining disease free populations within the island. Individuals from the protected population may then be re-introduced into the Tasmanian Devil’s former habitat once the disease threat has passed.

Despite the frequently cited threats that biotechnology poses to the environment, the application of gene sequencing technologies to the DFTD is an example of how biotechnology might be adopted to solve major environmental problems. In fact, the outcome of this gene sequencing project has contributed to a management plan that might yet save the Tasmanian Devil from extinction and conserve an important component of Australia’s unique biodiversity.

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The clues to human uniqueness

Charles Ebikeme — Mon, 02 Jul 2012 00:52:17 +0000

Over 2 million years ago, before the emergence of the genus Homo, within the rift valleys and savannah grasslands of Africa during the Pliocene period, a unique event took place. One that, with some hyperbole, admittedly, shaped the course of human evolution. The event was on a molecular scale but had its bearings on what we now call and search for as the “human condition

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The EMBO Meeting 2012 – Call for Participation

Editorial Board — Fri, 29 Jun 2012 07:03:14 +0000

EARLY REGISTRATION & ABSTRACT SUBMISSION: 12 JUNE 2012
ON-LINE REGISTRATION: 4 SEPTEMBER 2012

UPDATE: Late abstract deadline 12 August 14:00 CEST (Berlin)

SUBMIT ABSTRACT | REGISTER

http://www.the-embo-meeting.org/

This annual conference attracts 1,500 scientists working in the life sciences. Featuring an impressive line-up of more than 120 world-class scientific speakers, including: Paul Nurse, Linda Partridge, Kari Alitalo, Steven Henikoff and Rob Singer. The programme includes three plenary lecture sessions devoted to genomics, RNA and oxygen sensing, vasculogenesis and disease. 20 concurrent sessions juxtapose classical fields of research with those exploring new frontiers in molecular biology. Daily meet the speaker lunches, giving access to leading researchers, and poster sessions extend the scientific programme.

Latest News:

Brisbane Times:

Scientists closer to elixir of youth

A FUTURE where Australians can pop a pill and significantly delay the effects of ageing – from hair loss to the onset of dementia – may be only about a decade away, one of the world’s leading evolutionary biologists predicts.

Professor Dame Linda Partridge, who heads research teams at University College London and is the founding director of the Max Planck Institute for Biology of Ageing in Cologne, has been selected to give the prestigious Graeme Clark Oration in Melbourne next month.

She predicts that at some point in the next 10 years drugs will be available that could keep us healthy in body and mind long into old age.

More: http://www.brisbanetimes.com.au/act-news/scientists-closer-to-elixir-of-youth-20120616-20h6o.html

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How Much is that Green Algae in the Window?

Kelly Burnes — Mon, 04 Jun 2012 00:36:02 +0000

Whoever thought you could make money in biology, right? Turns out, there is quite a bit of money to be made in this field. And I think we are realizing more than ever the importance of the life sciences and the contribution it offers to society and the economy.

“I think the biggest innovations of the 21^st Century will be the intersection of biology and technology. A new era is beginning, just like the digital one was when I was his age.

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