BaseSciences.com Latest Blog Posts

Cell biology: Collagen secretion explained

Thu, 23 Feb 2012 11:29:15 GMT

Cells package proteins into vesicles for secretion to the extracellular milieu. A study has now identified an enzyme that modifies the packaging machinery to encapsulate unusually large proteins, such as collagen. See Article p.495

Molecular biology: RNA discrimination

Thu, 16 Feb 2012 09:06:24 GMT

In the cell, genomic DNA is transcribed into various types of RNA. But not all RNAs are translated into proteins. Does this give protein-coding RNAs greater credibility in terms of function? Views differ.

Physicists find dark matter: It's everywhere

Wed, 15 Feb 2012 09:06:44 GMT

A group of Japanese physicists has revealed where dark matter is — though not what it is — for the first time. As it turns out, the mysterious substance is almost everywhere, drooping throughout intergalactic space to form an all-encompassing web of matter.

Dark matter is invisible: It doesn't interact with light, so astronomers cannot actually see it. So far, it has only been observed indirectly by way of the gravitational force it exerts on ordinary, visible matter. On the basis of this gravitational interaction, physicists have inferred that dark matter constitutes 22 percent of the matter-energy content of the universe, while ordinary detectable matter constitutes just 4.5 percent.

Shogo Masaki at Nagoya University and colleagues at the University of Tokyo’s Institute for the Physics and Mathematics of the Universe used computer simulations to model recent observational data of 24 million galaxies. By determining how light from the galaxies was bending slightly as it passed through space en route to Earth — an effect known as gravitational lensing — the researchers were able to work out the location of the dark matter that was bending it.

As detailed in a study published online Friday in The Astrophysical Journal, their model shows that dark matter extends from each galaxy far into intergalactic space, overlapping with the dark matter from adjacent galaxies to form a pervasive web that envelops the whole universe.

In fact, "intergalactic space" is a misnomer; the research shows that galaxies aren't contained regions with well-defined edges that are separated from one another by millions of light-years. Instead, they are composed of a central clump of ordinary, visible matter surrounded by a web of dark matter that extends "in an organized way halfway to the neighboring galaxy, so that the universe is filled with the material associated with … galaxies," the researchers wrote in a statement.

Furthermore, what we call "galaxies" are merely the peaks of this continuous matter distribution, the researchers explained. The group mapped the distribution of dark matter over a distance of 100 million light-years from the center of each galaxy. "Its distribution," they noted, "is never random or uniform, but is well-organized."

Numerous dark matter searches are being conducted around the world. Scientists suspect the elusive material consists of WIMPs ("weakly interacting massive particles"), particles that are many times heavier than protons and only interact through gravity and the weak nuclear force.

Plants use circadian rhythms to prepare for battle with insects

Tue, 14 Feb 2012 09:18:02 GMT

"When you walk past plants, they don't look like they're doing anything," said Janet Braam, an investigator on the new study, which appears this week in the Proceedings of the National Academy of Sciences. "It's intriguing to see all of this activity down at the genetic level. It's like watching a besieged fortress go on full alert."

Braam, professor and chair of Rice's Department of Biochemistry and Cell Biology, said scientists have long known that plants have an internal clock that allows them to measure time regardless of light conditions. For example, some plants that track the sun with their leaves during the day are known to "reset" their leaves at night and move them back toward the east in anticipation of sunrise.

In recent years, scientists have begun to apply powerful genetic tools to the study of plant circadian rhythms. Researchers have found that as many as one-third of the genes in Arabidopsis thaliana -- a widely studied species in plant biology -- are activated by the circadian cycle. Rice biochemist Michael Covington found that some of these circadian-regulated genes were also connected to wounding responses.

"We wondered whether some of these circadian-regulated genes might allow plants to anticipate attacks from insects, in much the same way that they anticipate the sunrise," said Covington, now at the University of California, Davis.

Danielle Goodspeed, a graduate student in biochemistry and cell biology, designed a clever experiment to answer the question. She used 12-hour light cycles to entrain the circadian clocks of both Arabidopsis plants and cabbage loopers, a type of caterpillar that eats Arabidopsis. Half of the plants were placed with caterpillars on a regular day-night cycle, and the other half were placed with "out-of-phase" caterpillars whose internal clocks were set to daytime mode during the hours that the plants were in nighttime mode.
"We found that the plants whose clocks were in phase with the insects were relatively resistant, whereas the plants whose clocks were out of phase were decimated by the insects feeding on them," Goodspeed said.

Wassim Chehab, a Rice faculty fellow in biochemistry and cell biology, helped Goodspeed design a follow-up experiment to understand how plants used their internal clocks to resist insect attacks. Chehab and Goodspeed examined the accumulation of the hormone jasmonate, which plants use to regulate the production of metabolites that interfere with insect digestion.

They found that Arabidopsis uses its circadian clock to increase jasmonate production during the day, when insects like cabbage loopers feed the most. They also found that the plants used their internal clocks to regulate the production of other chemical defenses, including those that protect against bacterial infections.

"Jasmonate defenses are employed by virtually all plants, including tomatoes, rice and corn," Chehab said. "Understanding how plants regulate these hormones could be important for understanding why some pests are more damaging than others, and it could help suggest new strategies for insect resistance."

Biologists worry about fate of endangered toad

Mon, 13 Feb 2012 09:12:46 GMT

BASTROP, Texas (AP) — Mike Forstner tromps along the mucky edge of a pond, trilling loudly as he sweeps the beam of his flashlight over the bank.

He's hoping for an answering call from an endangered Houston toad, but he hears nothing. The tea-colored watering holes around Bastrop are the last stronghold of the endangered amphibian, which is about the size of a partially flattened apricot. But after years of drought and development, topped five months ago by searing wildfires, Forstner fears the worst.

"I believe the Houston toad effectively ceased to exist as a purely wild species on Sept. 5, 2011," said Forstner, 47, a biology professor at Texas State University who is spearheading the Houston toad recovery effort. "We've had the most rain since 2002, and it was insignificant to motivate the Houston toad to chorus. That's not good."

A week after that late January hunt on Griffith League Scout Ranch, though, when temperatures warmed slightly, Forstner and his crews heard three of the grayish-brown toads chorusing in Bastrop County. The next night, they detected three more. Crews from the Texas Cooperative Wildlife Collection at Texas A&M University and the herpetology department of the Houston Zoo heard a few in Austin County, farther east, too.

The activity triggered a requirement that wildlife biologists inspect construction and debris removal sites inside areas that burned for toads before work can continue. The croaking is a hopeful sign, but Forstner said long-term prospects remain grim.

Scientists monitoring the toads for the past five decades have observed a slow, steady decline in their numbers. The toads live in an increasingly fragmented habitat, their annual treks to breeding ponds bisected by roads. A fungus that affects toads and frogs and is suspected in a worldwide decline in amphibian populations might be partly to blame, too. Those forces, coupled with the drought and fires, probably have caused the collapse in population, Forstner said.

The Houston toad, the first amphibian placed on the endangered species list in 1970, is one of 10 species of toads found in Texas and the only one that lives solely in the Lone Star State. Once spread across 12 east-central Texas counties, they're now found mainly in Austin, Bastrop and Leon counties.

"It's a native species, a native Texan that needs help," said Paul Crumb, head of a captive breeding program at the Houston Zoo. "It illustrates the plight of what's going on with habitat and endangered species in the state."

The zoo has about 3,000 of the amphibians and has released more than 20,000 captive-bred toads into the wild to augment the population. Some are embedded with microchips readable by a scanner that can detect them up to a foot underground.

During breeding, the males "chorus" to draw in females, which lay gelatinous strands containing thousands of eggs. But they're finicky, chorusing only on warm, humid and still nights, usually after heavy rainfalls.

In monitoring surveys a decade and more ago, researchers detected hundreds of Houston toads in Bastrop County during breeding season. Numbers have dipped precipitously since then. After several years of finding nearly none, researchers detected 110 toads in 2010. Last year, in the midst of drought, they recorded just eight. Three of those were on the Griffith League ranch.

Then the September wildfires burned about 40,000 acres, damaging up to 40 percent of the toads' best habitat. The blow comes on the heels of a lingering drought Forstner estimates already had killed 80 percent of the toads. The fire, he said, might have finished off half of the toads that survived the drought.

Researchers monitor the numbers in the wild through audio surveys, driving designated routes and pausing periodically to roll down the windows and listen for the toads' loud, high-pitched trill, which some compare to the sound of chirping crickets or tinkling bells. It lasts 12 to 14 seconds.

Forstner begins his surveys as night falls and wraps them up about 2 a.m. Similar surveys take place across the toads' territory, about 30 times a year during breeding season, between January and June.

When breeding does occur, tadpoles develop in a few months, crawl out of the water and scatter into the landscape, sometimes moving several miles from where they were born. As they move, they're picked off by everything from scorpions and birds to feral hogs. "It's Normandy. They come out of the water; they hit the beach; they stay a couple of days while they transition from aquatic to terrestrial," Forstner said.

In the wild, just 1 percent of eggs survive to toadlet. The September wildfires made those odds even worse. They depleted the toads' cover, leaving them more vulnerable to predators, which at the same time have less available food.

On a recent night, Forstner and two doctoral candidates who help with the monitoring surveys pull up at Pond 5. He rolls down the windows of his truck, kills the engine and holds up a device that measures weather conditions. He records the data: It's 56 degrees and 80 percent humidity, with winds at 1.8 miles per hour.

It's a little cooler than ideal but within the toads' window. If they're out there, they should be chirping. He climbs out of his truck and heads to a nearby pond, as coyotes yip in the distance. He emits another trill, scanning the shoreline for toads.

Forstner listens, identifying the distant call of a spade foot toad. Leopard and cricket frogs have also been heard inside the burn zone, indicating that at least some amphibians survived the fires. "The forest is still here. There are fragmented patches. There's a shot," he said.

Computational Biology Illuminates How Cells Change Gears

Sat, 11 Feb 2012 09:38:31 GMT

Bioinformatics researchers from UC San Diego just moved closer to unlocking the mystery of how human cells switch from “proliferation mode” to “specialization mode.” This computational biology work from the Jacobs School of Engineering’s bioengineering department could lead to new ideas for curbing unwanted cell proliferation—including some cancers.

This research, published in Nature Genetics, could also improve our understanding of how organs and other complex tissues develop.

The UC San Diego bioengineers are part of a Japan-based global research consortium, the Genome Network Project, which generated one of the first close-to-comprehensive looks at a human cell’s entire network of proteins called “transcription factors.” Each human cell contains approximately 2,000 transcription factors, which are proteins that bind to specific locations on the cell’s DNA. Once bound to DNA, transcription factors work to either encourage or prevent “transcription”—the process by which messenger RNA is generated from DNA. These messenger RNA strands then travel to cellular factories called ribosomes which churn out proteins based on the specifications of the mRNA.

“Transcription is one of the most important events in the cell…it determines cell morphology and cell function,” said Timothy Ravasi, a UC San Diego research scientist from the bioengineering department and author on the new Nature Genetics paper.

Researchers have long understood that most transcription factors in human cells do not work alone, but studying the entire network of transcription factors within a cell has been difficult until now. In the new study, the researchers used a series of computational and integrative biology approaches in order to look at how the activity of the network of transcription factors in a myeloid leukemia cell line changes over time.

“Leukemia” refers to a variety of pathologies involving uncontrolled proliferation of white blood cells. Understanding the role of the transcriptional network during differentiation in leukemia cells could offer a glimpse into the cause of leukemia, or offer possible approaches for treating leukemia, according to Ravasi.

During the laboratory phase of the project, researchers introduced a compound that stopped cell proliferation in the myeloid leukemia cell line. Next, they collected as much information as possible regarding the activity of the transcription factor network during the processes of differentiation and maturation into immune cells known as monocytes and macrophages. Computational work performed at UC San Diego after all the laboratory data had been collected allowed the researchers to identify specific subnetworks of transcription factors that were activated at particular time points.

Integrative Biology
The UCSD researchers were challenged to integrate different but related data sets in order to tease out real signals from noise. This is known as “integrative biology.”

“We take lots of measurements of the same thing…we integrate them together,” which leads to higher confidence in experimental results, Ravasi explained. Measuring both messenger RNA and protein levels, is one example. Detection of both signals provides two independent data points indicating the presence of the same protein.

“Getting to be the first to analyze and make sense of this large and fascinating data set was a huge opportunity,” said Ravasi. The UC San Diego bioinformatics team working on this project included Ravasi and two post-doctoral researchers from Trey Ideker’s bioengineering laboratory, Ariel Schwartz, now at Synthetic Genomics, and Kai Tan, now an assistant professor of internal medicine and biomedical engineering at the University of Iowa.

By monitoring the activity of the transcriptional network one hour after the onset of differentiation, the researchers identified a gene that appears to play an important role in cell differentiation in white blood cells. “It’s a long shot, but if you found a compound that inhibits this gene, you could make the cells begin to differentiate towards a normal monoblast line rather than continue unchecked cell proliferation,” said Ravasi.

Resilient and Redundant
Based on the new research, it appears that the network of transcription factors from the human myeloid leukemia cell line is redundant and resilient, explained Ravasi. The researchers turned-off or “knocked down” 52 transcription factors, one at a time, in order to study their individual role within the network. Most of the single knock-downs did not result in changes to cell differentiation or cell shape.

“The transcriptional network for this cell type appears quite redundant which likely makes the network resilient to mutations or environmental agents that could interfere with transcription factor function,” said Ravasi. “My guess is that we will find similar redundancy in the transcription networks of other cell lines, and in the transcription networks that regulate other aspects of cell function, but we can’t say that from these data.”

Magnetosphereic & Ionosphere / Thermosphere Physics

Thu, 09 Feb 2012 09:06:14 GMT

The Earth’s magnetosphere is a bubble of space around our planet dominated by the magnetic field produced within the Earth’s outer core. Furthermore, the Earth’s upper atmosphere, called the thermosphere, is ionized by EUV photons from the Sun as well as energetic particles raining down from the magnetosphere (creating the ionosphere).

This whole system of the magnetosphere, ionosphere, and thermosphere is called geospace, and is continuously impacted by the supersonic solar wind, a magnetic and electrically charged gas streaming away from the Sun. In AOSS, research on magnetosphere-ionosphere-thermosphere physics includes experimental, data analysis, and numerical studies on a wide range of topics within this field. Areas of interest include the solar wind control of magnetospheric topology and dynamics, ionospheric outflow and solar wind entry, electrodynamic coupling between the magnetosphere and ionosphere, inner magnetospheric dynamics and radiation belt formation, magnetic storm and substorm physics, solar flare and high-latitude heating of the ionosphere and thermosphere, auroral physics, and the influence of the magnetospheric energetic particles on the Earth’s middle and upper atmosphere.

BIOL 102: Introductory Biology of Cells

Wed, 08 Feb 2012 09:22:25 GMT

Term and Exam Dates

Summer term (May-June): May 7 - June 18, 2012
Final examinations held: June 21 - 22, 2012

Course Description

An introduction to the basic themes and concepts of modern biology spanning organizational levels from molecules to cells in an evolutionary context.

BIOL 103, Introductory Biology of Organism, for which BIOL 102 is a prerequisite, is offered in the July-August term. BIOL 102 Online has a significant level of interaction with the instructor and TAs to help students master the course material.

This course is intended primarily for students in biological and life sciences, for those considering pursuing careers in the health sciences/medical sector, and those with a general interest in Biology and plans to take further Biology courses. The Biology Department at Queen’s has two other courses, BIOL110 and BIOL111, that are intended for students who plan to take only one or two Biology courses.

This course may be used by Queen’s students towards the degree requirements of programs in the biological and life sciences. Students from other institutions pursuing chemistry, biochemistry or similar programs should check with their home institution regarding the suitability of this course towards their degree programs.

Method of Delivery

e-Learning through Moodle with online tutorials given by TAs and the Course Instructor and regular quizzes to help you reach your learning goals. As well, you will engage in interactive learning through Pearson’sMasteringBiology, which is the portal for the virtual laboratory modules.

Exam

BIOL 102 Online requires you to write a supervised examination at an established exam centre. Queen's has exam centres around the world. When you register indicate where you would like to write your exam by checking the online list of current exam locations.

Course Objectives / Topics Covered

The Molecules of Life

Biology and the Tree of Life
Water and Carbon: The Chemical Basis of Life
Structure and Function of Proteins, Nucleic Acids, Carbohydrates and Lipids
Cell Structure and Function

Cell Biology
Cell-Cell Interactions
Respiration and Photosynthesis
Cell Cycle and Meiosis
Gene Structure and Expression

Patterns of Inheritance
DNA and the Gene: Synthesis and Repair
Control of Transcription, Translation in Bacteria and Eukaryotes
Genetic and Genomic Technologies

The Chemistry Degree: Is it Losing Substance?

Tue, 07 Feb 2012 09:01:43 GMT

What is Chemistry?
Air, water, notebooks and computers. What do all of these things have in common? They are all considered to be that which is known as matter. What is matter? It is a term which describes the substance that all objects consist of. There are four states of matter: solid, liquid, gas and plasma. At the atomic level, the states of matter range from a smaller distance between particles to a larger expanse between atoms from solid to plasma. Chemistry is the study of these four states of matter, specifically concerning its behavior, composition, interactions, properties, structures and reactions. Chemistry is often referred to as the central science because it branches the physical sciences with the natural sciences.

What Can You Do With a Chemistry Degree?
A chemistry degree opens the door to a wide variety of possibilities, but it depends on the education level achieved in the degree. Jobs for chemistry degree holders are becoming increasingly selective and searching for candidates with higher levels of education. An Associate’s degree in chemistry is generally not enough to land a serious position in the field and a Bachelor’s degree may only be enough for a bench job (one in which you run equipment and prepare chemicals for experiments, essentially an assistant chemist). A Master’s degree or a terminal degree in chemistry (doctor of philosophy or medical doctor in chemistry) opens the door to many more possibilities. Some of the career options available to chemistry majors include:

Chemist
Technical Writer
Ceramics
Plastics
Chemical Engineering
Geochemist
Agrochemist
Materials Scientist
Military Systems
What is the Job Outlook for Chemists?
The United States of America has an organization which tracks employment growth and long term prospects for a variety of careers in the country. This organization is called the Bureau of Labor Statistics and it provides research on the outlook for chemists and materials scientists. The Bureau of Labor Statistics projects that job growth will be slower than the average of all occupations. The employment of chemists and materials scientists is expected to grow by 3 percent between 2008-2018. This growth projection is affected by the growth of chemist and materials scientist job openings, and these are expected to grow at a rate of two and twelve percent respectively.

What are the Returns for a Chemistry Degree?
While job prospects for chemistry degree holders are decreasing, those who find employment will find considerable rewards in their profession. The median annual wages of chemists in May 2008 were $66,230 according t the Bureau of Labor Statistics. The middle 50 percent earned between $48,630 and $89,660. The lowest 10 percent earned less than $37,840, and the highest 10 percent earned more than $113,080.

Should You Become a Chemistry Major?
Job prospects may be declining somewhat, but growth still exists for chemistry jobs. If you are interested in the field and feel it is your passion, do not hesitate to pursue the degree. The most important thing in life is to be happy with what you do, and if chemistry is your passion you should certainly pursue it.

Cell-Cell Communication and Cell Signaling

Mon, 06 Feb 2012 09:35:18 GMT

Members of the Department are active participants in an inter-departmental Gap Junction Group. The research efforts of the Group are designed to examine the role of gap junctions in health in disease with special interests in human diseases linked to connexin mutations, male and female reproduction, development, endothelial barrier integrity, peripheral neuropathies, breast cancer and carcinogenesis. Research interests extend beyond the Group and include intracellular signaling as linked to chondrocyte differentiation and arthritis, osteoblast differentiation in bone development and small GTPases in cell migration, as well as cellular and molecular events in fetal-maternal interactions during placental development.