Biology

The latest articles from Biology Direct (ISSN 1745-6150) published by BioMed Central

Total news: 10
Last news: November 30, 1999 00:00:00

The latest articles from Journal of Biology (ISSN 1475-4924) published by BioMed Central

Total news: 10
Last news: November 30, 1999 00:00:00

New article alert from biology-blog.com, the place for biology information.

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The latest research articles published by BioMed Central

Total news: 21
Last news: November 30, 1999 00:00:00

Heres a pollution-control tip from nature: Deep inside a flooded mine in Wisconsin, researchers from several institutions including the U.S. Department of Energys Lawrence Berkeley National Laboratory (Berkeley Lab) have discovered a world in which bacteria emit proteins that sweep up metal nanoparticles into immobile clumps. Their finding may lead to innovative ways to remediate subsurface metal toxins........ - [Read more]

Not so long ago, the difficult-to-sequence, highly repetitive, gene-poor DNA found in regions of chromosomes known as heterochromatin was called "junk." Like dark matter in the universe, the true nature of heterochromatin was unknown. Now members of the Drosophila Heterochromatin Genome Project (DHGP), headed by Gary Karpen of the Department of Energys Lawrence Berkeley National Laboratory, are approaching a complete assembly, mapping, and functional analysis of those portions (other than simple repeats) of the heterochromatic DNA of Drosophila melanogaster, the fruit fly. The results confirm that heterochromatin is far from mere junk........ - [Read more]

Four swarms of Asian bees found in Cairns have been cleared of carrying the dreaded Varroa destructor mite but the intruders themselves could pose the beginning of a serious threat to Australian honey bee populations. Asian bees are known to have found their way into Australian ports at least half a dozen times in the last decade........ - [Read more]

The mammalian order bats (Chiroptera) has two suborders, microbats (Microchiroptera) and fruit bats or flying foxes (Megachiroptera). In contrast to microbats, fruit bats (Fig. 1) do not echolocate. They have large eyes and pronounced visual centres in the brain. Fruit bats need a good sense of vision, because when they forage at night for nectar and fruit, they orient by vision and the sense of smell. During the flights to the foraging grounds at dusk and the return to the daytime roost at dawn, the animals navigate solely by vision. On moonless nights, fruit bats cannot fly and stay hungry. Visual navigation at twilight and sometimes also during the daytime did not fit the older view that fruit bats only possess rods, the photoreceptors for night vision. This prompted Brigitte Müller and Leo Peichl of the Max Planck Institute for Brain Research in Frankfurt/Main and Steven Goodman from The Field Museum for Natural History in Chicago to study the photoreceptors of fruit bats with modern histological methods........ - [Read more]

Mothers know best when it comes to dressing their children, at least among side-blotched lizards, a common species in the western United States. Scientists at the University of California, Santa Cruz, have observed that female side-blotched lizards are able to induce different color patterns in their offspring in response to social cues, "dressing" their progeny in patterns they will wear for the rest of their lives. The mothers influence gives her progeny the patterns most likely to ensure success under the conditions they will encounter as adults........ - [Read more]

Seen thundering across the landscape during an aerial survey, more than 1.3 million white-eared kob, tiang (African antelope), and mongalla gazelle are thriving in Southern Sudan, despite all odds. An estimated 8,000 elephants, concentrated mainly in the Sudd, the largest freshwater wetland in Africa, have also been observed. Researchers are astonished at the latest news: Based on experiences in other war-torn regions such as Mozambique and Angola, they believed wildlife had vanished from this area........ - [Read more]

New research from the University of Alberta and the Canadian Forest Service has revealed the humble rove beetle may actually have a lot to tell us about the effects of harvesting on forests species. Rove beetles can be used as indicators of clear-cut harvesting and regeneration practices and can be used as an example as to how species react to harvesting. It has been observed that after an area of forest was harvested, the a number of forest species, including rove beetles, decreased dramatically. As the forest regenerated, it never fully replicated the full characteristics of the older forest it replaced........ - [Read more]

Research on one of the oldest-living mammals - the bowhead whale - has helped preserve a primary food source for Eskimos in the far reaches of Alaska, and also may provide a useful tool for studying genetic variation in other migratory animals. The bowhead whale, devastated in the 19th and early 20th centuries by commercial whaling fleets, has been a food staple for Eskimos and other indigenous arctic peoples dating to prehistoric times. Due in part to research done by Purdue University professor John Bickham, the International Whaling Commission ruled last week to allow Eskimos to harvest 56 whales per year, the same quota that had been in place but had expired........ - [Read more]

Being a devoted husband and father is not enough to keep an avian marriage together for the Nazca booby, a long-lived seabird found in the Galapagos Islands off the coast of Ecuador. A number of Nazca booby females switch mates after successfully raising a chick, as per a Wake Forest University study scheduled for publication in the journal Proceedings of the Royal Society B: Biological Sciences June 13........ - [Read more]

It could be an artists depiction of someones stomach before and after a rather decadent meal. But it is a 3-D cryoelectron microscope reconstruction of the cross-section of a virus, before and after cramming itself full of its own DNA. The virus, phi29, has a tiny motor that pumps its DNA into the capsid-outer shell-during the assembly process. The potential energy of the tightly coiled DNA may help phi29 inject its genetic material into the bacterial cells it infects. Now a team led by physicists at the University of California, San Diego has used laser tweezers to measure the forces exerted by the motor as it pushes the DNA into the capsid........ - [Read more]

Global warming and the destruction of natural habitats will lead to significant declines and extinctions in the worlds 8,750 terrestrial bird species over the next century, as per a research studyconducted by biologists at the University of California, San Diego and Princeton University. Their study, the first global assessment of how climate change and habitat destruction may interact to impact the distribution of a large group of vertebrates over the next century, appears in the June 5 issue of the journal PLoS Biology........ - [Read more]

In flowers called columbines, evolution of the length of nectar spurs--the long tubes leading to plants nectar--happens in a way that allows flowers to match the tongue lengths of the pollinators that drink their nectar, biologists have found. The scientists were Justen Whittall of the University of California at Davis and Scott Hodges of the University of California at Santa Barbara. They were funded by the National Science Foundation (NSF). Their results appear in this weeks issue of the journal Nature........ - [Read more]

Nearly all of the 162 land-breeding frog species on Caribbean islands, including the coqui frogs of Puerto Rico, originated from a single frog species that arrived on a sea voyage from South America. They came 30 to 50 million years ago, as per DNA-sequence analyses by researchers at Penn State. Similarly, the researchers observed that the Central American relatives of these Caribbean amphibians also arose from a single species that arrived by raft from South America........ - [Read more]

A simple, cheap therapy using just oxygen could allow growers to store organic produce for longer and go a long way towards reducing the price of organic fruit and vegetables, reports Lisa Richards in Chemistry and Industry, the magazine of the SCI. Currently UK shoppers have to pay twice as much for some organic products. Organic apples, for example, are around double the price of conventionally grown apples in Sainburys, Waitrose and Tesco........ - [Read more]

Researchers have long wondered if local animal cultures exist, and now, based on findings by scientists at the Yerkes National Primate Research Center at Emory University, the University of Texas and St. Andrews University, Scotland, they have their answer: Yes. The study, available in todays online edition of Current Biology, confirms captive chimpanzees have the capacity to sustain the same kind of multiple-tradition cultures a number of scientists believe exist in the wild, providing further evidence chimpanzees and humans shared a common ancestor five to six million years ago who had a similar level of cultural complexity........ - [Read more]

Background: Oligonucleotide probes that are sequence identical may have different identifiers between manufacturers and even between different versions of the same companys microarray; and sometimes the same identifier is reused and represents a completely different oligonucleotide, resulting in ambiguity and potentially mis-identification of the genes hybridizing to that probe. Results: We have devised a unique, non-degenerate encoding scheme that can be used as a universal representation to identify an oligonucleotide across manufacturers. We have named the encoded representation nuID, for nucleotide universal identifier. Inspired by the fact that the raw sequence of the oligonucleotide is the true definition of identity for a probe, the encoding algorithm uniquely and non-degenerately transforms the sequence itself into a compact identifier (a lossless compression). In addition, we added a redundancy check (checksum) to validate the integrity of the identifier. These two steps, encoding plus checksum, result in an nuID, which is a unique, non-degenerate, permanent, robust and efficient representation of the probe sequence. For commercial applications that require the sequence identity to be confidential, we have an encryption schema for nuID. We demonstrate the utility of nuIDs for the annotation of Illumina microarrays, and we believe it has universal applicability as a source-independent naming convention for oligomers.ReviewersThis article was reviewed by Itai Yanai, Rong Chen (nominated by Mark Gerstein), and Gregory Schuler (nominated by David Lipman). - [Read more]

Background: Recent developments in cosmology radically change the conception of the universe as well as the very notions of "probable" and "possible". The model of eternal inflation implies that all macroscopic histories permitted by laws of physics are repeated an infinite number of times in the infinite multiverse. In contrast to the traditional cosmological models of a single, finite universe, this worldview provides for the origin of an infinite number of complex systems by chance, even as the probability of complexity emerging in any given region of the multiverse is extremely low. This change in perspective has profound implications for the history of any phenomenon, and life on earth cannot be an exception.HypothesisOrigin of life is a chicken and egg problem: for biological evolution that is governed, primarily, by natural selection, to take off, efficient systems for replication and translation are required, but even barebones cores of these systems appear to be products of extensive selection. The currently favored (partial) solution is an RNA world without proteins in which replication is catalyzed by ribozymes and which serves as the cradle for the translation system. However, the RNA world faces its own hard problems as ribozyme-catalyzed RNA replication remains a hypothesis and the selective pressures behind the origin of translation remain mysterious. Eternal inflation offers a viable alternative that is untenable in a finite universe, i.e., that a coupled system of translation and replication emerged by chance, and became the breakthrough stage from which biological evolution, centered around Darwinian selection, took off. A corollary of this hypothesis is that an RNA world, as a diverse population of replicating RNA molecules, might have never existed. In this model, the stage for Darwinian selection is set by anthropic selection of complex systems that rarely but inevitably emerge by chance in the infinite universe (multiverse). Conclusion: The plausibility of different models for the origin of life on earth directly depends on the adopted cosmological scenario. In an infinite universe (multiverse), emergence of highly complex systems by chance is inevitable. Therefore, under this cosmology, an entity as complex as a coupled translation-replication system should be considered a viable breakthrough stage for the onset of biological evolution.ReviewersThis article was reviewed by Eric Bapteste, David Krakauer, Sergei Maslov, and Itai Yanai. - [Read more]

Background: The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch 22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system. The origin of the genetic code and whether it evolved on the basis of a stereochemical correspondence between amino acids and their cognate codons (or anticodons), through selectional optimization of the code vocabulary, as a "frozen accident" or via a combination of all these routes is another wide open problem despite extensive theoretical and experimental studies. Here we combine the results of comparative genomics of translation system components, data on interaction of amino acids with their cognate codons and anticodons, and data on catalytic activities of ribozymes to develop conceptual models for the origins of the translation system and the genetic code. Results: Our main guide in constructing the models is the Darwinian Continuity Principle whereby a scenario for the evolution of a complex system must consist of plausible elementary steps, each conferring a distinct advantage on the evolving ensemble of genetic elements. Evolution of the translation system is envisaged to occur in a compartmentalized ensemble of replicating, co-selected RNA segments, i.e., in a RNA World containing ribozymes with versatile activities. Since evolution has no foresight, the translation system could not evolve in the RNA World as the result of selection for protein synthesis and must have been a by-product of evolution drive by selection for another function, i.e., the translation system evolved via the exaptation route. It is proposed that the evolutionary process that eventually led to the emergence of translation started with the selection for ribozymes binding abiogenic amino acids that stimulated ribozyme-catalyzed reactions. The proposed scenario for the evolution of translation consists of the following steps: binding of amino acids to a ribozyme resulting in an enhancement of its catalytic activity; evolution of the amino-acid-stimulated ribozyme into a peptide ligase (predecessor of the large ribosomal subunit) yielding, initially, a unique peptide activating the original ribozyme and, possibly, other ribozymes in the ensemble; evolution of self-charging proto-tRNAs that were selected, initially, for accumulation of amino acids, and subsequently, for delivery of amino acids to the peptide ligase; joining of the peptide ligase with a distinct RNA molecule (predecessor of the small ribosomal subunit) carrying a built-in template for more efficient, complementary binding of charged proto-tRNAs; evolution of the ability of the peptide ligase to assemble peptides using exogenous RNAs as template for complementary binding of charged proteo-tRNAs, yielding peptides with the potential to activate different ribozymes; evolution of the translocation function of the protoribosome leading to the production of increasingly longer peptides (the first proteins), i.e., the origin of translation. The specifics of the recognition of amino acids by proto-tRNAs and the origin of the genetic code depend on whether or not there is a physical affinity between amino acids and their cognate codons or anticodons, a problem that remains unresolved. Conclusions: We describe a stepwise model for the origin of the translation system in the ancient RNA world such that each step confers a distinct advantage onto an ensemble of co-evolving genetic elements. Under this scenario, the primary cause for the emergence of translation was the ability of amino acids and peptides to stimulate reactions catalyzed by ribozymes. Thus, the translation system might have evolved as the result of selection for ribozymes capable of, initially, efficient amino acid binding, and subsequently, synthesis of increasingly versatile peptides. Several aspects of this scenario are amenable to experimental testing. Reviewers: This article was reviewed by Rob Knight, Doron Lancet, Alexander Mankin (nominated by Arcady Mushegian), and Arcady Mushegian. - [Read more]

Background: Using a statistical physics approach, we study the stochastic switching behavior of a model circuit of multisite phosphorylation and dephosphorylation with feedback. The circuit consists of a kinase and phosphatase acting on multiple sites of a substrate that, contingent on its modification state, catalyzes its own phosphorylation and, in a symmetric scenario, dephosphorylation. The symmetric case is viewed as a cartoon of conflicting feedback that could result from antagonistic pathways impinging on the state of a shared component. Results: Multisite phosphorylation is sufficient for bistable behavior under feedback even when catalysis is linear in substrate concentration, which is the case we consider. We compute the phase diagram, fluctuation spectrum and large-deviation properties related to switch memory within a statistical mechanics framework. Bistability occurs as either a first-order or second-order non-equilibrium phase transition, depending on the network symmetries and the ratio of phosphatase to kinase numbers. In the second-order case, the circuit never leaves the bistable regime upon increasing the number of substrate molecules at constant kinase to phosphatase ratio. Conclusions: The number of substrate molecules is a key parameter controlling both the onset of the bistable regime, fluctuation intensity, and the residence time in a switched state. The relevance of the concept of memory depends on the degree of switch symmetry, as memory presupposes information to be remembered, which is highest for equal residence times in the switched states. Reviewers: This article was reviewed by Artem Novozhilov (nominated by Eugene Koonin), Sergei Maslov and Ned Wingreen. - [Read more]

Background: It is generally believed that life first evolved from single-stranded RNA (ssRNA) that both stored genetic information and catalyzed the reactions required for self-replication.Presentation of the hypothesisBy modeling early genome evolution on the engineering paradigm design-by-contract, an alternative scenario is presented in which life started with the appearance of double-stranded RNA (dsRNA) as an informational storage molecule while catalytic single-stranded RNA was derived from this dsRNA template later in evolution.Testing the hypothesisIt was investigated whether this scenario could be implemented mechanistically by starting with abiotic processes. Double-stranded RNA could be formed abiotically by hybridization of oligoribonucleotides that are subsequently non-enzymatically ligated into a double-stranded chain. Thermal cycling driven by the diurnal temperature cycles could then replicate this dsRNA when strands of dsRNA separate and later rehybridize and ligate to reform dsRNA. A temperature-dependent partial replication of specific regions of dsRNA could produce the first template-based generation of catalytic ssRNA, similar to the developmental gene transcription process. Replacement of these abiotic processes by enzymatic processes would guarantee functional continuity. Further transition from a dsRNA to a dsDNA world could be based on minor mutations in template and substrate recognition sites of an RNA polymerase and would leave all existing processes intact.Implications of the hypothesisModeling evolution on a design pattern, the dsRNA first hypothesis can provide an alternative mechanistic evolutionary scenario for the origin of our genome that preserves functional continuity.ReviewersThis article was reviewed by Anthony Poole, Eugene Koonin and Eugene Shakhnovich - [Read more]