Oldest Fossils of Large Seaweeds, Possible Animals Tell Story About Oxygen in an Ancient Ocean

These images are part and counterpart of a macroscopic Lantian fossil, probably a seaweed, with differentiated morphologies including a distinct root-like holdfast to secure the organism on sea bottom, a conical stem, and a crown of ribbon-like structures. Scale bar is 1 centimeter. 

Almost 600 million years ago, before the rampant evolution of diverse life forms known as the Cambrian explosion, a community of seaweeds and worm-like animals lived in a quiet deep-water niche under the sea near what is now Lantian, a small village in Anhui Province of South China. Then they simply died, leaving some 3,000 nearly pristine fossils preserved between beds of black shale deposited in oxygen-free waters.

Scientists from the Chinese Academy of Sciences, Virginia Tech in the U.S., and Northwest University in Xi'an, China report the discovery of the fossils and the mystery in the Feb. 17 issue of Nature.
In addition to perhaps ancient versions of algae and worms, the Lantian biota -- named for its location -- included macrofossils with complex and puzzling structures. In all, scientists identified about 15 different species at the site.
The fossils suggest that morphological diversification of macroscopic eukaryotes -- the earliest versions of organisms with complex cell structures -- may have occurred only tens of millions of years after the snowball earth event that ended 635 million years ago, just before the Ediacaran Period. And their presence in the highly organic-rich black shale suggests that, despite the overall oxygen-free conditions, brief oxygenation of the oceans did come and go.
"So there are two questions," said Shuhai Xiao, professor of geobiology in the College of Science at Virginia Tech. "Why did this community evolve when and where it did? It is clearly different in terms of the number of species compared to biotas preserved in older rocks. There are more species here and they are more complex and larger than what evolved before. These rocks were formed shortly after the largest ice age ever, when much of the global ocean was frozen. By 635 million years ago, the snowball earth event ended and oceans were clear of ice. Perhaps that prepared the ground for the evolution of complex eukaryotes."
The team was examining the black shale rocks because, although they were laid down in waters that were not good for oxygen-dependent organisms, "they are known to be able to preserve fossils very well," said Shuhai. "In most cases, dead organisms were washed in and preserved in black shales. In this case, we discovered fossils that were preserved in pristine condition where they had lived -- some seaweeds still rooted."
The conclusion that the environment would have been poisonous is derived from geochemical data, "but the bedding surfaces where these fossils were found represent moments of geological time during which free oxygen was available and conditions were favorable. They are very brief moments to a geologist," said Xiao. "but long enough for the oxygen-demanding organisms to colonize the Lantian basin and capture the rare opportunities."
The research team suggests in the article in Nature that the Lantian basin was largely without oxygen but was punctuated by brief oxic episodes that were opportunistically populated by complex new life forms, which were subsequently killed and preserved when the oxygen disappeared. "Such brief oxic intervals demand high-resolution sampling for geochemical analysis to capture the dynamic and complex nature of oxygen history in the Ediacaran Period," said lead author Xunlai Yuan, professor of palaeontology with the Chinese Academy of Sciences.
Proving that hypothesis awaits further study. The rocks in the study region are deposited in layered beds. The nature of the rock changes subtly and there are finer and finer layers that can be recognized within each bed. "We will need to sample each layer to see whether there is any difference in oxygen contents between layers with fossils and those without" said co-author Chuanming Zhou, professor of palaeontology with the Chinese Academy of Sciences.
The research was supported by Chinese Academy of Sciences, National Natural Science Foundation of China, Chinese Ministry of Science and Technology, National Science Foundation, NASA Exobiology and Evolutionary Biology Program, and a Guggenheim fellowship to Xiao

Primates' Unique Gene Regulation Mechanism

Three baby orangutans from Tanjung Putting Orangutan Rehab Center in Borneo Indonesia. Scientists have discovered a new way genes are regulated that is unique to primates, including humans and monkeys. 

Scientists have discovered a new way genes are regulated that is unique to primates, including humans and monkeys. Though the human genome -- all the genes that an individual possesses -- was sequenced 10 years ago, greater understanding of how genes function and are regulated is needed to make advances in medicine, including changing the way we diagnose, treat and prevent a wide range of diseases.
"It's extremely valuable that we've sequenced a large bulk of the human genome, but sequence without function doesn't get us very far, which is why our finding is so important," said Lynne E. Maquat, Ph.D., lead author of the new study published February 9 in the journal Nature.
When our genes go awry, many diseases, such as cancer, Alzheimer's and cystic fibrosis can result. The study introduces a unique regulatory mechanism that could prove to be a valuable treatment target as researchers seek to manipulate gene expression -- the conversion of genetic information into proteins that make up the body and perform most life functions -- to improve human health.
The newly identified mechanism involves Alu elements, repetitive DNA elements that spread throughout the genome as primates evolved. While scientists have known about the existence of Alu elements for many years, their function, if any, was largely unknown.
Maquat discovered that Alu elements team up with molecules called long noncoding RNAs (lncRNAs) to regulate protein production. They do this by ensuring messenger RNAs (mRNAs), which take genetic instructions from DNA and use it to create proteins, stay on track and create the right number of proteins. If left unchecked, protein production can spiral out of control, leading to the proliferation or multiplication of cells, which is characteristic of diseases such as cancer.
"Previously, no one knew what Alu elements and long noncoding RNAs did, whether they were junk or if they had any purpose. Now, we've shown that they actually have important roles in regulating protein production," said Maquat, the J. Lowell Orbison Chair, professor of Biochemistry and Biophysics and director of the Center for RNA Biology at the University of Rochester Medical Center.
The expression of genes that call for the development of proteins involves numerous steps, all of which are required to occur in a precise order to achieve the appropriate timing and amount of protein production. Each of these steps is regulated, and the pathway discovered is one of only a few pathways known to regulate mRNAs directly in the midst of the protein production process.
Regulating mRNAs is one of several ways cells control gene expression, and researchers from institutions and companies around the world are honing in on this regulatory landscape in search of new ways to manage and treat disease.
According to Maquat, "This new mechanism is really a surprise. We continue to be amazed by all the different ways mRNAs can be regulated."
Maquat and the study's first author, Chenguang Gong, a graduate student in the Department of Biochemistry and Biophysics at the Medical Center, found that long noncoding RNAs and Alu elements work together to trigger a process known as SMD (Staufen 1-mediated mRNA decay). SMD conditionally destroys mRNAs after they orchestrate the production of a certain amount of proteins, preventing the creation of excessive, unwanted proteins in the body that can disrupt normal processes and initiate disease.
Specifically, long noncoding RNAs and Alu elements recruit the protein Staufen-1 to bind to numerous mRNAs. Once an mRNA finishes directing a round of protein production, Staufen-1 works with another regulatory protein previously identified by Maquat, UPF1, to initiate the degradation or decay of the mRNA so that it cannot create any more proteins.
While the research fills in a piece of the puzzle as to how our genes operate, it also accentuates the overwhelming complexity of how our DNA shapes us and the many known and unknown players involved. Maquat and Gong plan on exploring the newly identified pathway in future research.
This research was supported by a grant from the General Medical Sciences Division of the National Institutes of Health and an Elon Huntington Hooker Graduate Student Fellowship.