Energy Eating Bacteria

There has been a discovery that certain bacteria are able to take up energy in terms of electrons for photosynthesis purposes. A form of photosynthesis where bacteria utilize varieties of ferrous iron as the source of electrons to fix carbon dioxide is called photoferrotrophy. A study performed by Washington University in St. Louis at Arpita Bose’s laboratory, unveils the pathway in which these bacteria accomplish this task which previously has been poorly misunderstood.





Read More




Rice Genome Sequencing Project

Rice (Oriza sativa) is the second most cultivated cereal crop worldwide after maize.  It is the staple food for over half of the world’s population, mainly in Asia, South America and Africa. Rice is an annual crop and grows in a warm and humid climate where plenty of rain/water is available.  Although there are several species of rice, the Asian rice (Oriza sativa) is the most commonly cultivated rice. The Asian rice has two subspecies, one is indica and the other one is japonica. Worldwide, there are over 40,000 varieties of rice.

Rice has the smallest genome size among all cereal crops with its genome size at around 430MB. The next largest genome of any cereal crop is of sorghum which is at around 750Mb. When the genome size of wheat is compared with the rice genome, the wheat genome is over 37 times larger than the rice genome. The human genome is about 8 times larger than the rice genome.  Because of its importance in food supply worldwide and its smaller genome size, scientist selected rice for sequencing as a model for cereal crops. Sequencing of rice genome started in 1998 by International Rice Genome Sequence Project (IRGSP) with the involvement of 10 rice producing countries that included Brazil, Canada, China, France, India, Japan, Korea, Thailand, Vietnam and the USA.  Rice genome project was the last major genome sequencing project that used the Sanger sequencing method.  Before the completion of the rice genome sequencing project under IRGSP, private companies Monsanto and Syngenta published the rice genome sequence in 2000 and 2002, respectively.  It was the first ever genome sequencing done by private companies. IRGSP revealed map-based high quality genome of rice in 2005. The rice genome was the second plant genome sequenced after Arabidopsis






Read More




Mother's Immune System May Be Key to Delivery Date

In a study published in the American Journal of Obstetrics and Gynecology, an estimated 98% of all prematurely born infants survive their infancy, however approximately 44% of the ones born severely premature do not survive. If a child is born premature, not only do the immediate complications exist but long-term complications do as well, varying in different degrees from minor to life-long disabilities. There exist several groups of scientists currently each with different research driven approaches having the same overall goal in mind: to elucidate the conditions indicative of pre-term labor so that it can be avoided or in the very least so that steps may taken to increase the gestational age of the infant before delivery, decreasing avoidable complications and increasing the baby’s viability.

While a mother is pregnant with an unborn baby, throughout the stages of her pregnancy her body’s immune system is a symphony of give and take: certain aspects of the immune system must be lowered, so that the system does not view the infant as a foreign pathogen and pre-term labor induced as a result, and other aspects of the immune system must be increased so that throughout the gestation the mother’s body as well as the unborn’s are protected from externally introduced viral and bacterial pathogens. In an article published in Science Immunology, An Immune Clock of Human Pregnancy, the authors research and observe the maternal immune system for the complete duration of the gestation and post-natal by way of whole blood sampling of a sampling of pregnant women. High dimensional Mass cytometry was their method of bench research and had the benefit of allowing the scientists to observe over nine hundred and eighty four immunity features of the gestational immune response as well as a subset of twenty-four immune system cells directly in whole blood samples. Whole blood sampling is an advantageous medium in that it allowed the scientists to observe all immune cells present and their interactions with minimal disturbance to the balances of those cells from unnecessary laboratory method handling.








Read More




Sequencing Ancient DNA

The DNA recovered from the ancient specimens is called ancient DNA (aDNA). The time period of the aDNA collected from the target specimen can range from 100 years to million years. Some of the sources of aDNA are: mummified tissues, archeological skeletons, iced animal and plant remains, and sediments from oceans, rivers and lakes. The major advantage of studying aDNA is that it will provide insights into the history. With that it can help to resolve long standing disputes, confusions or curiosities. For example, comprehending evolutionary processes, determining how humans migrated from one continent to others, and understanding interactions between diseases and humans.

There are two main challenges of investigating aDNA, i.e. degradation and contamination of the genetic material. Degradation of aDNA is caused by the time lapses after the individual was dead, and the environment it was recovered from. Scientists have found a correlation between the age of specimen and degradation of aDNA. With the same age the rate of degradation can vary depending on the environmental conditions, for example, the rate of degradation is slow in a frozen condition, while it is accelerated in the hot and humid conditions. The other important factor to consider about degradation of aDNA is the type of DNA. The rate of degradation is twice as much higher for nuclear DNA (nDNA) than that for mitochondrial DNA (mtDNA). There are two main reasons behind the slower degradation rate of mtDNA as compared to the nDNA. One is due to the double membrane cover of mitochondria as opposed to the single membrane cover of nucleus. The membranes are known for protecting DNA from autolysis. The other reason is that the mtDNA occurs in a higher copy numbers than the nDNA. Because of the lower degradation rate, most of the studies about ancient samples are based on mtDNA.





Read More




Does Genome Size Matter?

Total amount of DNA within a single set of chromosomes in a cell is called genome size or C-value. Commonly, genome size is measured in picograms or the number of nucleotide base pairs (one picogram of DNA is equal to 978 megabases of DNA). The common methods for determining genome size are: flow cytometry, computerized image analysis, densitometric measurement after Feulgen staining. Recently, due to rapid advancement in sequencing technology and the reduction in cost of sequencing, whole genome sequencing method is getting popular for the genome size determination tasks. Knowing genome size is important to plan genetic studies of the targeted species. Also, if someone is interested in sequencing the whole genome of a particular species, knowing the genome size can help to estimate the time and costs of such project. The information about the genome size can provide insights into the evolutionary history of the species.




Read More




Genetic History of Rome

Rome wasn't built in a day. Rome known as the Eternal City was the first in the ancient world to reach 1 Million residents. Ancient Rome was the capital of an empire of ~70 millions inhabitants, but little is known about the ancestral origins of ancient Romans and expansion of Roman empire across ancient Europe, Asia and the Mediterranean region. Contemporary accounts and archaeological evidence indicated that with the expansion of empire, tight connections between Rome and other parts of the empire built through trade, military campaigns, new roads and slavery. However, those records provide limited information about the genetic constituents of the population. Ancient skeleton’s DNA samples and next generation sequencing technologies have been used previously to fill gaps in other regions of the world related to human history. Rome presented an interesting opportunity to use the same ancient DNA techniques and sequencing technologies to fill in details related to human history. Using ancient DNA and next generation sequencing technologies, an international team from US, Austria and Italy studied the genetic ancestry of individuals migrated through Rome since the Mesolithic period. In just few centuries the Roman Empire had expanded west to Britain, south into North Africa and east into Syria and Iraq. The study, published in Science, involved the sequencing of genomes of ancient individuals from various archaeological sites in Rome and other parts of central Italy spanning the past 12000 years. The investigators observed two major prehistoric ancestry transitions, one with the introduction of farming and other prior to the Iron Age. The sequencing data revealed individuals with ancestry from other parts of Europe, the Near East, North Africa, coinciding with trade and an increased movement of populations. Data also revealed a major shift in the Neolithic between hunter gatherers and farmers. Before founding of Rome, the genetic composition of the region approximated that of modern Mediterranean populations. During the Imperial period, there was net immigration from the Near East, followed by an increase in genetic contributions from Europe.




Read More




Is Biofilm Keeping You Awake?

 There are many television commercials and Internet advertisements recently all stating that they have instruments detrimental to the cleanliness of CPAP machines. A CPAP machine is a medical grade device used for the delivery of constant positive air pressure for the treatment and relief of sleep apnea (a type of respiratory ventilation).  Anything such as this instrument used to improve quality of life should certainly be kept clean in order to avoid the introduction of infectious material into the lungs, an organ whose functional environment is of vital importance and sterility is paramount. Yet what is exactly is this infectious material that is able to survive in the plastic hoses and masks of the CPAP machine? Simply stated, the instrument plastics surfaces are susceptible to biofilms, a complex of microorganism cells that attach and proliferate on many different surfaces, both organic and inorganic, that are extremely difficult, and in some instances impossible, to remove from their attached surface. A biofilm is a cluster of cells encompassed by a matrix (predominantly a polysaccharide matrix) as opposed to cells that are planktonic, in that planktonic cells are able to float freely in their suspension and are easily rinsed away from their surrounding environments. A biofilm can consist of a single type of cell or several different types inhabiting a single matrix, studies lending strength to the hypothesis that biofilms tend to be thicker and stronger when there are more than one type of bacteria present, in that the different types of colonies lend their different strengths to the overall strength of the biofilm matrix.





Read More




Whole Exome Sequencing Sheds Light on Cervical Cancer

The Cervix is lower part of the uterus and cervical cancer occurs in the cells of the cervix. In cervical cancer, the cells of the cervix grow abnormally and invade other tissues and organs of the body including lungs, liver, bladder, vagina, and rectum. All women are at risk for cervical cancer and occurs most often in women over age 30. What is the exact cause of the cancer? no one knows. Research suggests that the main cause of cervical cancer is the infection with certain types of human papillomavirus (HPV). HPV is a virus that is passed from one person to another during sex. When a person gets exposed to HPV, the immune system fights with the virus and kills it before it can do any harm. However, in some people the virus survives for years and causes cervical cells to become cancer cells. Early detected cervical cancer is treatable and associated with long survival rate. Cervical cancer is the fourth most common type of cancer for women worldwide. More than 13,000 women in the United States will be diagnosed with cervical cancer each year, and more than 4,000 of women will die. Pap tests can detect cervical precancer before it turns into cancer. Because many women getting regular Pap tests, the number of deaths from cervical cancer have decreased significantly. There are different treatment options and survival outcomes for cervical cancer patients with early versus advanced stage. Treatment may include surgery, radiation therapy, chemotherapy, or a combination. Despite advancement in technologies the prognosis of advanced/recurrent cervical cancer patients remains poor. The development of effective treatments for patients with  advanced/recurrent cervical cancer remains a medical need.




Read More