BioHacking...a talk

Quadruplex DNA Observed in Cells

There is no more iconic image in biology than that of DNA's double-stranded helix, which coils and supercoils on itself to form dense chromosomes.

But a quite different, square-shaped type of DNA structure can easily be created in the laboratory by the folding of synthetic DNA strands rich in guanine, one of the building blocks of DNA. Scientists have long believed that these so-called 'G-quadruplex structures' may occasionally form in the DNA of living cells. A G-quadruplex comprises four guanines from different places along a G-rich strand held together by a special type of hydrogen bonding to form a compact square structure that interrupts the DNA helix.

In a paper published online today in Nature Chemistry, researchers led by Shankar Balasubramanian at the University of Cambridge, UK, provide strong evidence that G-quadruplexes do occur in cells — and that these unusual structures may have important biological functions.

Multi stranded DNA molecules can no longer be called alien.

Estimating Divergence Times in Large Molecular Phylogenies

Estimating divergence times in large molecular phylogenies

Authors:

1. Koichiro Tamura (a)
2. Fabia Ursula Battistuzzi (b,c)
3. Paul Billing-Ross (b)
4. Oscar Murillo (b)
5. Alan Filipski (b)
6. Sudhir Kumar (b,d,*)

Author Affiliations:

a. Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan

b. Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5301

c. Department of Biological Sciences, Oakland University, Rochester, MI 48309

d. School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501

*. To whom correspondence should be addressed. E-mail: s.kumar@asu.edu.

Abstract:

Molecular dating of species divergences has become an important means to add a temporal dimension to the Tree of Life. Increasingly larger datasets encompassing greater taxonomic diversity are becoming available to generate molecular timetrees by using sophisticated methods that model rate variation among lineages. However, the practical application of these methods is challenging because of the exorbitant calculation times required by current methods for contemporary data sizes, the difficulty in correctly modeling the rate heterogeneity in highly diverse taxonomic groups, and the lack of reliable clock calibrations and their uncertainty distributions for most groups of species. Here, we present a method that estimates relative times of divergences for all branching points (nodes) in very large phylogenetic trees without assuming a specific model for lineage rate variation or specifying any clock calibrations. The method (RelTime) performed better than existing methods when applied to very large computer simulated datasets where evolutionary rates were varied extensively among lineages by following autocorrelated and uncorrelated models. On average, RelTime completed calculations 1,000 times faster than the fastest Bayesian method, with even greater speed difference for larger number of sequences. This speed and accuracy will enable molecular dating analysis of very large datasets. Relative time estimates will be useful for determining the relative ordering and spacing of speciation events, identifying lineages with significantly slower or faster evolutionary rates, diagnosing the effect of selected calibrations on absolute divergence times, and estimating absolute times of divergence when highly reliable calibration points are available.

Dinosaur Proteins From Fossils Confirmed

Caption: T.rex (B), B. canadensis (E) and ostrich osteocytes (H) showing positive response to propidium iodide, a DNA intercalating dye.

A team of researchers from North Carolina State University and the Palo Alto Research Center (PARC) has found more evidence for the preservation of ancient dinosaur proteins, including reactivity to antibodies that target specific proteins normally found in bone cells of vertebrates. These results further rule out sample contamination, and help solidify the case for preservation of cells – and possibly DNA – in ancient remains.

Dr. Mary Schweitzer, professor of marine, earth and atmospheric sciences with a joint appointment at the North Carolina Museum of Natural Sciences, first discovered what appeared to be preserved soft tissue in a 67-million-year-old Tyrannosaurus Rex in 2005. Subsequent research revealed similar preservation in an even older (about 80-million-year-old)Brachylophosaurus canadensis. In 2007 and again in 2009, Schweitzer and colleagues used chemical and molecular analyses to confirm that the fibrous material collected from the specimens was collagen.

Schweitzer's next step was to find out if the star-shaped cellular structures within the fibrous matrix were osteocytes, or bone cells. Using techniques including microscopy, histochemistry and mass spectrometry, Schweitzer demonstrates that these cellular structures react to specific antibodies, including one – a protein known as PHEX – that is found in the osteocytes of living birds. The findings appear online in Bone and were presented last week at the annual meeting of the Society of Vertebrate Paleontology.

"The PHEX finding is important because it helps to rule out sample contamination," Schweitzer says. "Some of the antibodies that we used will react to proteins found in other vertebrate cells, but none of the antibodies react to microbes, which supports our theory that these structures are surviving osteocytes. Additionally, the antibody to PHEX will only recognize and bind to one specific site only found in mature bone cells from birds. These antibodies don't react to other proteins or cells. Because so many other lines of evidence support the dinosaur/bird relationship, finding these proteins helps make the case that these structures are dinosaurian in origin."

Schweitzer and her team also tested for the presence of DNA within the cellular structures, using an antibody that only binds to the "backbone" of DNA. The antibody reacted to small amounts of material within the "cells" of both the T. rex and the B. canadensis. To rule out the presence of microbes, they used an antibody that binds histone proteins, which bind tightly to the DNA of everything except microbes, and got another positive result. They then ran two other histochemical stains which fluoresce when they attach to DNA molecules. Those tests were also positive. These data strongly suggest that the DNA is original, but without sequence data, it is impossible to confirm that the DNA is dinosaurian.

Fungal Carnivorism : Evolved Due to Mass Exctinctions? Or Not?

Origin and evolution of carnivorism in the Ascomycota (fungi)


1. Ence Yang (a)
2. Lingling Xu (a,b)
3. Ying Yang (a)
4. Xinyu Zhang (a)
5. Meichun Xiang (a)
6. Chengshu Wang (c)
7. Zhiqiang An (d, *)
8. Xingzhong Liu (a, *)

a. State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China

b. College of Biotechnology, Xi'an University of Arts and Science, Xi'an 710065, China

c. Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China

d. Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030

*. To whom correspondence may be addressed. E-mail: zhiqiang.an@uth.tmc.edu or liuxz@im.ac.cn.

Abstract:

Carnivorism is one of the basic life strategies of fungi. Carnivorous fungi possess the ability to trap and digest their preys by sophisticated trapping devices. However, the origin and development of fungal carnivorism remains a gap in evolution biology. In this study, five protein-encoding genes were used to construct the phylogeny of the carnivorous fungi in the phylum Ascomycota; these fungi prey on nematodes by means of specialized trapping structures such as constricting rings and adhesive traps. Our analysis revealed a definitive pattern of evolutionary development for these trapping structures. Molecular clock calibration based on two fossil records revealed that fungal carnivorism diverged from saprophytism about 419 Mya, which was after the origin of nematodes about 550–600 Mya. Active carnivorism (fungi with constricting rings) and passive carnivorism (fungi with adhesive traps) diverged from each other around 246 Mya, shortly after the occurrence of the Permian–Triassic extinction event about 251.4 Mya. The major adhesive traps evolved around 198–208 Mya, which was within the time frame of the Triassic–Jurassic extinction event about 201.4 Mya. However, no major carnivorous ascomycetes divergence was correlated to the Cretaceous–Tertiary extinction event, which occurred more recently (about 65.5 Mya). Therefore, a causal relationship between mass extinction events and fungal carnivorism evolution is not validated in this study. More evidence including additional fossil records is needed to establish if fungal carnivorism evolution was a response to mass extinction events.

No time & link.  Perhaps they ought to consider whether or not the KT Extinction was uniquely different than the PT/TJ and whether or not that might have some important bits.

Turtles: Back to Parareptilia You Go!

The position of turtles based on molecular (1: e.g. Hugall et al. 2007) and morphological datasets (2: e.g. deBraga & Rieppel 1997; 3: Gauthier et al. 1988). The addition of key fossils eliminates the apparent disagreement among morphological datasets in support of turtles outside Diapsida (3). The Permian ‘parareptile’ Eunotosaurus shares uniquely derived features with turtles that help fill important gaps in the evolutionary origin of the turtle shell. Bootstrap (top) and Bremer (bottom) support values are provided for the Eunotosaurus-turtle clade. Star indicates complete shell.

Transitional fossils and the origin of turtles

1. Tyler R. Lyson (a,*)
2. Gabe S. Bever (a)
3. Bhart-Anjan S. Bhullar (b)
4. Walter G. Joyce (c)
5. Jacques A. Gauthier (a)

a. Department of Geology and Geophysics, Yale University, New Haven, CT 06511, USA

b. Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA

c. Institut für Geowissenschaften, University of Tübingen, 72076 Tübingen, Germany

* Author for correspondence (tyler.lyson@yale.edu).

Abstract:

The origin of turtles is one of the most contentious issues in systematics with three currently viable hypotheses: turtles as the extant sister to (i) the crocodile–bird clade, (ii) the lizard–tuatara clade, or (iii) Diapsida (a clade composed of (i) and (ii)). We reanalysed a recent dataset that allied turtles with the lizard–tuatara clade and found that the inclusion of the stem turtle Proganochelys quenstedti and the ‘parareptile’ Eunotosaurus africanus results in a single overriding morphological signal, with turtles outside Diapsida. This result reflects the importance of transitional fossils when long branches separate crown clades, and highlights unexplored issues such as the role of topological congruence when using fossils to calibrate molecular clocks.

The tug of war continues over the turtles! Once anapsida then parareptilia, then diapsida and back once more into parareptilia! Oy!

That said, I am beginning to think that the molecular clock isn't nearly as regular as is often assumed. I get the distinct feeling that there are bursty times of rapid mutation and other quieter moments of stasis and little change. Perhaps the molecular clock just needs more fiber in its diet, eh?

Recreating a Functional Ancestral Archosaur Visual Pigment

Recreating a Functional Ancestral Archosaur Visual Pigment

1. Belinda S. W. Chang (A)

2. Karolina Jönsson (A)

3. Manija A. Kazmi (A)

4. Michael J. Donoghue (B)

5. Thomas P. Sakmar (A)

A. Laboratory of Molecular Biology & Biochemistry, The Rockefeller University, New York;

B. Department of Ecology & Evolutionary Biology, Yale University

Abstract:
The ancestors of the archosaurs, a major branch of the diapsid reptiles, originated more than 240 MYA near the dawn of the Triassic Period. We used maximum likelihood phylogenetic ancestral reconstruction methods and explored different models of evolution for inferring the amino acid sequence of a putative ancestral archosaur visual pigment. Three different types of maximum likelihood models were used: nucleotide-based, amino acid–based, and codon-based models. Where possible, within each type of model, likelihood ratio tests were used to determine which model best fit the data. Ancestral reconstructions of the ancestral archosaur node using the best-fitting models of each type were found to be in agreement, except for three amino acid residues at which one reconstruction differed from the other two. To determine if these ancestral pigments would be functionally active, the corresponding genes were chemically synthesized and then expressed in a mammalian cell line in tissue culture. The expressed artificial genes were all found to bind to 11-cis-retinal to yield stable photoactive pigments with {lambda}max values of about 508 nm, which is slightly redshifted relative to that of extant vertebrate pigments. The ancestral archosaur pigments also activated the retinal G protein transducin, as measured in a fluorescence assay. Our results show that ancestral genes from ancient organisms can be reconstructed de novo and tested for function using a combination of phylogenetic and biochemical methods.

Cited in the parareptile paper in reference to the nocturnalness of the ancestry of archosaurs.