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There are 10 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Resurrection of a Bull by Cloning from Organs Frozen without Cryoprotectant in a −80°C Freezer for a Decade:

Frozen animal tissues without cryoprotectant have been thought to be inappropriate for use as a nuclear donor for somatic cell nuclear transfer (SCNT). We report the cloning of a bull using cells retrieved from testicles that had been taken from a dead animal and frozen without cryoprotectant in a −80°C freezer for 10 years. We obtained live cells from defrosted pieces of the spermatic cords of frozen testicles. The cells proliferated actively in culture and were apparently normal. We transferred 16 SCNT embryos from these cells into 16 synchronized recipient animals. We obtained five pregnancies and four cloned calves developed to term. Our results indicate that complete genome sets are maintained in mammalian organs even after long-term frozen-storage without cryoprotectant, and that live clones can be produced from the recovered cells.

Adaptation of the Spore Discharge Mechanism in the Basidiomycota:

Spore discharge in the majority of the 30,000 described species of Basidiomycota is powered by the rapid motion of a fluid droplet, called Buller’s drop, over the spore surface. In basidiomycete yeasts, and phytopathogenic rusts and smuts, spores are discharged directly into the airflow around the fungal colony. Maximum discharge distances of 1-2 mm have been reported for these fungi. In mushroom-forming species, however, spores are propelled over much shorter ranges. In gilled mushrooms, for example, discharge distances of <0.1 mm ensure that spores do not collide with opposing gill surfaces. The way in which the range of the mechanism is controlled has not been studied previously. In this study, we report high-speed video analysis of spore discharge in selected basidiomycetes ranging from yeasts to wood-decay fungi with poroid fruiting bodies. Analysis of these video data and mathematical modeling show that discharge distance is determined by both spore size and the size of the Buller's drop. Furthermore, because the size of Buller's drop is controlled by spore shape, these experiments suggest that seemingly minor changes in spore morphology exert major effects upon discharge distance. This biomechanical analysis of spore discharge mechanisms in mushroom-forming fungi and their relatives is the first of its kind and provides a novel view of the incredible variety of spore morphology that has been catalogued by traditional taxonomists for more than 200 years. Rather than representing non-selected variations in micromorphology, the new experiments show that changes in spore architecture have adaptive significance because they control the distance that the spores are shot through air. For this reason, evolutionary modifications to fruiting body architecture, including changes in gill separation and tube diameter in mushrooms, must be tightly linked to alterations in spore morphology.

Rapid Effects of Marine Reserves via Larval Dispersal:

Marine reserves have been advocated worldwide as conservation and fishery management tools. It is argued that they can protect ecosystems and also benefit fisheries via density-dependent spillover of adults and enhanced larval dispersal into fishing areas. However, while evidence has shown that marine reserves can meet conservation targets, their effects on fisheries are less understood. In particular, the basic question of if and over what temporal and spatial scales reserves can benefit fished populations via larval dispersal remains unanswered. We tested predictions of a larval transport model for a marine reserve network in the Gulf of California, Mexico, via field oceanography and repeated density counts of recently settled juvenile commercial mollusks before and after reserve establishment. We show that local retention of larvae within a reserve network can take place with enhanced, but spatially-explicit, recruitment to local fisheries. Enhancement occurred rapidly (2 yrs), with up to a three-fold increase in density of juveniles found in fished areas at the downstream edge of the reserve network, but other fishing areas within the network were unaffected. These findings were consistent with our model predictions. Our findings underscore the potential benefits of protecting larval sources and show that enhancement in recruitment can be manifested rapidly. However, benefits can be markedly variable within a local seascape. Hence, effects of marine reserve networks, positive or negative, may be overlooked when only focusing on overall responses and not considering finer spatially-explicit responses within a reserve network and its adjacent fishing grounds. Our results therefore call for future research on marine reserves that addresses this variability in order to help frame appropriate scenarios for the spatial management scales of interest.

A Trouble Shared Is a Trouble Halved: Social Context and Status Affect Pain in Mouse Dyads:

In mice behavioral response to pain is modulated by social status. Recently, social context also has been shown to affect pain sensitivity. In our study, we aimed to investigate the effects of interaction between status and social context in dyads of outbred CD-1 male mice in which the dominance/submission relationship was stable. Mice were assessed for pain response in a formalin (1% concentration) test either alone (individually tested-IT), or in pairs of dominant and subordinate mice. In the latter condition, they could be either both injected (BI) or only one injected (OI) with formalin. We observed a remarkable influence of social context on behavioral response to painful stimuli regardless of the social status of the mice. In the absence of differences between OI and IT conditions, BI mice exhibited half as much Paw-licking behavior than OI group. As expected, subordinates were hypoalgesic in response to the early phase of the formalin effects compared to dominants. Clear cut-differences in coping strategies of dominants and subordinates appeared. The former were more active, whereas the latter were more passive. Finally, analysis of behavior of the non-injected subjects (the observers) in the OI dyads revealed that dominant observers were more often involved in Self-grooming behavior upon observation of their subordinate partner in pain. This was not the case for subordinate mice observing the pain response of their dominant partner. In contrast, subordinate observers Stared at the dominant significantly more frequently compared to observer dominants in other dyads. The observation of a cagemate in pain significantly affected the observer’s behavior. Additionally, the quality of observer’s response was also modulated by the dominance/submission relationship.

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There are 18 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the day – so many today! – but you go and look for your own favourites:
Can Playing the Computer Game “Tetris” Reduce the Build-Up of Flashbacks for Trauma? A Proposal from Cognitive Science:

Flashbacks are the hallmark symptom of Posttraumatic Stress Disorder (PTSD). Although we have successful treatments for full-blown PTSD, early interventions are lacking. We propose the utility of developing a ‘cognitive vaccine’ to prevent PTSD flashback development following exposure to trauma. Our theory is based on two key findings: 1) Cognitive science suggests that the brain has selective resources with limited capacity; 2) The neurobiology of memory suggests a 6-hr window to disrupt memory consolidation. The rationale for a ‘cognitive vaccine’ approach is as follows: Trauma flashbacks are sensory-perceptual, visuospatial mental images. Visuospatial cognitive tasks selectively compete for resources required to generate mental images. Thus, a visuospatial computer game (e.g. “Tetris”) will interfere with flashbacks. Visuospatial tasks post-trauma, performed within the time window for memory consolidation, will reduce subsequent flashbacks. We predicted that playing “Tetris” half an hour after viewing trauma would reduce flashback frequency over 1-week. The Trauma Film paradigm was used as a well-established experimental analog for Post-traumatic Stress. All participants viewed a traumatic film consisting of scenes of real injury and death followed by a 30-min structured break. Participants were then randomly allocated to either a no-task or visuospatial (“Tetris”) condition which they undertook for 10-min. Flashbacks were monitored for 1-week. Results indicated that compared to the no-task condition, the “Tetris” condition produced a significant reduction in flashback frequency over 1-week. Convergent results were found on a clinical measure of PTSD symptomatology at 1-week. Recognition memory between groups did not differ significantly. Playing “Tetris” after viewing traumatic material reduces unwanted, involuntary memory flashbacks to that traumatic film, leaving deliberate memory recall of the event intact. Pathological aspects of human memory in the aftermath of trauma may be malleable using non-invasive, cognitive interventions. This has implications for a novel avenue of preventative treatment development, much-needed as a crisis intervention for the aftermath of traumatic events.

Olfactory Sex Recognition Investigated in Antarctic Prions:

Chemical signals can yield information about an animal such as its identity, social status or sex. Such signals have rarely been considered in birds, but recent results have shown that chemical signals are actually used by different bird species to find food and to recognize their home and nest. This is particularly true in petrels whose olfactory anatomy is among the most developed in birds. Recently, we have demonstrated that Antarctic prions, Pachyptila desolata, are also able to recognize and follow the odour of their partner in a Y-maze. However, the experimental protocol left unclear whether this choice reflected an olfactory recognition of a particular individual (i.e. partner) or a more general sex recognition mechanism. To test this second hypothesis, male and female birds’ odours were presented simultaneously to 54 Antarctic prions in a Y-maze. Results showed random behaviour by the tested bird, independent of its sex or reproductive status. Present results do not support the possibility that Antarctic prions can distinguish the sex of a conspecific through its odour but indirectly support the hypothesis that they can distinguish individual odours.

Giant Panda Genomic Data Provide Insight into the Birth-and-Death Process of Mammalian Major Histocompatibility Complex Class II Genes:

To gain an understanding of the genomic structure and evolutionary history of the giant panda major histocompatibility complex (MHC) genes, we determined a 636,503-bp nucleotide sequence spanning the MHC class II region. Analysis revealed that the MHC class II region from this rare species contained 26 loci (17 predicted to be expressed), of which 10 are classical class II genes (1 DRA, 2 DRB, 2 DQA, 3 DQB, 1 DYB, 1 DPA, and 2 DPB) and 4 are non-classical class II genes (1 DOA, 1 DOB, 1 DMA, and 1 DMB). The presence of DYB, a gene specific to ruminants, prompted a comparison of the giant panda class II sequence with those of humans, cats, dogs, cattle, pigs, and mice. The results indicated that birth and death events within the DQ and DRB-DY regions led to major lineage differences, with absence of these regions in the cat and in humans and mice respectively. The phylogenetic trees constructed using all expressed alpha and beta genes from marsupials and placental mammals showed that: (1) because marsupials carry loci corresponding to DR, DP, DO and DM genes, those subregions most likely developed before the divergence of marsupials and placental mammals, approximately 150 million years ago (MYA); (2) conversely, the DQ and DY regions must have evolved later, but before the radiation of placental mammals (100 MYA). As a result, the typical genomic structure of MHC class II genes for the giant panda is similar to that of the other placental mammals and corresponds to BTNL2~DR1~DQ~DR2~DY~DO_box~DP~COL11A2. Over the past 100 million years, there has been birth and death of mammalian DR, DQ, DY, and DP genes, an evolutionary process that has brought about the current species-specific genomic structure of the MHC class II region. Furthermore, facing certain similar pathogens, mammals have adopted intra-subregion (DR and DQ) and inter-subregion (between DQ and DP) convergent evolutionary strategies for their alpha and beta genes, respectively.

Gonadal Transcriptome Alterations in Response to Dietary Energy Intake: Sensing the Reproductive Environment:

Reproductive capacity and nutritional input are tightly linked and animals’ specific responses to alterations in their physical environment and food availability are crucial to ensuring sustainability of that species. We have assessed how alterations in dietary energy intake (both reductions and excess), as well as in food availability, via intermittent fasting (IF), affect the gonadal transcriptome of both male and female rats. Starting at four months of age, male and female rats were subjected to a 20% or 40% caloric restriction (CR) dietary regime, every other day feeding (IF) or a high fat-high glucose (HFG) diet for six months. The transcriptional activity of the gonadal response to these variations in dietary energy intake was assessed at the individual gene level as well as at the parametric functional level. At the individual gene level, the females showed a higher degree of coherency in gonadal gene alterations to CR than the males. The gonadal transcriptional and hormonal response to IF was also significantly different between the male and female rats. The number of genes significantly regulated by IF in male animals was almost 5 times greater than in the females. These IF males also showed the highest testosterone to estrogen ratio in their plasma. Our data show that at the level of gonadal gene responses, the male rats on the IF regime adapt to their environment in a manner that is expected to increase the probability of eventual fertilization of females that the males predict are likely to be sub-fertile due to their perception of a food deficient environment.

Allele-Specific Gene Expression Is Widespread Across the Genome and Biological Processes:

Allelic specific gene expression (ASGE) appears to be an important factor in human phenotypic variability and as a consequence, for the development of complex traits and diseases. In order to study ASGE across the human genome, we have performed a study in which genotyping was coupled with an analysis of ASGE by screening 11,500 SNPs using the Mapping 10 K Array to identify differential allelic expression. We found that from the 5,133 SNPs that were suitable for analysis (heterozygous in our sample and expressed in peripheral blood mononuclear cells), 2,934 (57%) SNPs had differential allelic expression. Such SNPs were equally distributed along human chromosomes and biological processes. We validated the presence or absence of ASGE in 18 out 20 SNPs (90%) randomly selected by real time PCR in 48 human subjects. In addition, we observed that SNPs close to -but not included in- segmental duplications had increased levels of ASGE. Finally, we found that transcripts of unknown function or non-coding RNAs, also display ASGE: from a total of 2,308 intronic SNPs, 1510 (65%) SNPs underwent differential allelic expression. In summary, ASGE is a widespread mechanism in the human genome whose regulation seems to be far more complex than expected.

Endemicity, Biogeograhy, Composition, and Community Structure On a Northeast Pacific Seamount:

The deep ocean greater than 1 km covers the majority of the earth’s surface. Interspersed on the abyssal plains and continental slope are an estimated 14000 seamounts, topographic features extending 1000 m off the seafloor. A variety of hypotheses are posited that suggest the ecological, evolutionary, and oceanographic processes on seamounts differ from those governing the surrounding deep sea. The most prominent and oldest of these hypotheses, the seamount endemicity hypothesis (SMEH), states that seamounts possess a set of isolating mechanisms that produce highly endemic faunas. Here, we constructed a faunal inventory for Davidson Seamount, the first bathymetric feature to be characterized as a ‘seamount’, residing 120 km off the central California coast in approximately 3600 m of water (Fig 1). We find little support for the SMEH among megafauna of a Northeast Pacific seamount; instead, finding an assemblage of species that also occurs on adjacent continental margins. A large percentage of these species are also cosmopolitan with ranges extending over much of the Pacific Ocean Basin. Despite the similarity in composition between the seamount and non-seamount communities, we provide preliminary evidence that seamount communities may be structured differently and potentially serve as source of larvae for suboptimal, non-seamount habitats.

Atmospheric Hypoxia Limits Selection for Large Body Size in Insects:

The correlations between Phanerozoic atmospheric oxygen fluctuations and insect body size suggest that higher oxygen levels facilitate the evolution of larger size in insects. Testing this hypothesis we selected Drosophila melanogaster for large size in three oxygen atmospheric partial pressures (aPO2). Fly body sizes increased by 15% during 11 generations of size selection in 21 and 40 kPa aPO2. However, in 10 kPa aPO2, sizes were strongly reduced. Beginning at the 12th generation, flies were returned to normoxia. All flies had similar, enlarged sizes relative to the starting populations, demonstrating that selection for large size had functionally equivalent genetic effects on size that were independent of aPO2. Hypoxia provided a physical constraint on body size even in a tiny insect strongly selected for larger mass, supporting the hypothesis that Triassic hypoxia may have contributed to a reduction in insect size.

The Sleeping Brain’s Influence on Verbal Memory: Boosting Resistance to Interference:

Memories evolve. After learning something new, the brain initiates a complex set of post-learning processing that facilitates recall (i.e., consolidation). Evidence points to sleep as one of the determinants of that change. But whenever a behavioral study of episodic memory shows a benefit of sleep, critics assert that sleep only leads to a temporary shelter from the damaging effects of interference that would otherwise accrue during wakefulness. To evaluate the potentially active role of sleep for verbal memory, we compared memory recall after sleep, with and without interference before testing. We demonstrated that recall performance for verbal memory was greater after sleep than after wakefulness. And when using interference testing, that difference was even more pronounced. By introducing interference after sleep, this study confirms an experimental paradigm that demonstrates the active role of sleep in consolidating memory, and unmasks the large magnitude of that benefit.

Molecular Identification of Birds: Performance of Distance-Based DNA Barcoding in Three Genes to Delimit Parapatric Species:

DNA barcoding based on the mitochondrial cytochrome oxidase subunit I gene (cox1 or COI) has been successful in species identification across a wide array of taxa but in some cases failed to delimit the species boundaries of closely allied allopatric species or of hybridising sister species. In this study we extend the sample size of prior studies in birds for cox1 (2776 sequences, 756 species) and target especially species that are known to occur parapatrically, and/or are known to hybridise, on a Holarctic scale. In order to obtain a larger set of taxa (altogether 2719 species), we include also DNA sequences of two other mitochondrial genes: cytochrome b (cob) (4614 sequences, 2087 species) and 16S (708 sequences, 498 species). Our results confirm the existence of a wide gap between intra- and interspecies divergences for both cox1 and cob, and indicate that distance-based DNA barcoding provides sufficient information to identify and delineate bird species in 98% of all possible pairwise comparisons. This DNA barcoding gap was not statistically influenced by the number of individuals sequenced per species. However, most of the hybridising parapatric species pairs have average divergences intermediate between intraspecific and interspecific distances for both cox1 and cob. DNA barcoding, if used as a tool for species discovery, would thus fail to identify hybridising parapatric species pairs. However, most of them can probably still assigned to known species by character-based approaches, although development of complementary nuclear markers will be necessary to account for mitochondrial introgression in hybridising species.

Preferences across the Menstrual Cycle for Masculinity and Symmetry in Photographs of Male Faces and Bodies:

Previous studies have shown that women increase their preference for masculinity during the fertile phase of the menstrual cycle. Evidence for a similar preference shift for symmetry is equivocal. These studies have required participants to choose between subtle variations in computer-generated stimuli, and preferences for more natural stimuli have not been investigated. Our study employed photographs of individual males to investigate women’s preferences for face and body masculinity and symmetry across the menstrual cycle. We collected attractiveness ratings from 25 normally cycling women at high- and low-fertility days of the menstrual cycle. Attractiveness ratings made by these women were correlated with independent ratings of masculinity and symmetry provided by different sets of raters. We found no evidence for any cyclic shift in female preferences. Correlations between attractiveness and masculinity, and attractiveness and symmetry did not differ significantly between high- and low-fertility test sessions. Furthermore, there was no significant difference between high- and low-fertility ratings of attractiveness. These results suggest that a menstrual cycle shift in visual preferences for masculinity and symmetry may be too subtle to influence responses to real faces and bodies, and subsequent mate-choice decisions.

Neighbourhood Socioeconomics Status Predicts Non-Cardiovascular Mortality in Cardiac Patients with Access to Universal Health Care:

Although the Canadian health care system provides essential services to all residents, evidence suggests that socioeconomic gradients in disease outcomes still persist. The main objective of our study was to investigate whether mortality, from cardiovascular disease or other causes, varies by neighbourhood socioeconomic gradients in patients accessing the healthcare system for cardiovascular disease management. A cohort of 485 patients with angiographic evidence of coronary artery disease (CAD) and neighbourhood socioeconomic status information was followed for 13.3 years. Survival analyses were completed with adjustment for potentially confounding risk factors. There were 64 cases of cardiovascular mortality and 66 deaths from non-cardiovascular chronic diseases. No socioeconomic differentials in cardiovascular mortality were observed. However, lower neighbourhood employment, education, and median family income did predict an increased risk of mortality from non-cardiovascular chronic diseases. For each quintile decrease in neighbourhood socioeconomic status, non-cardiovascular mortality risk rose by 21-30%. Covariate-adjusted hazard ratios (95% confidence interval) for non-cardiovascular mortality were 1.21 (1.02-1.42), 1.21 (1.01-1.46), and 1.30 (1.06-1.60), for each quintile decrease in neighbourhood education, employment, and income, respectively. These patterns were primarily attributable to mortality from cancer. Estimated risks for mortality from cancer rose by 42% and 62% for each one quintile decrease in neighbourhood median income and employment rate, respectively. Although only baseline clinical information was collected and patient-level socioeconomic data were not available, our results suggest that environmental socioeconomic factors have a significant impact on CAD patient survival. Despite public health care access, CAD patients who reside in lower-socioeconomic neighbourhoods show increased vulnerability to non-cardiovascular chronic disease mortality, particularly in the domain of cancer. These findings prompt further research exploring mechanisms of neighbourhood effects on health, and ways they may be ameliorated.

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There are 9 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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Longstanding Theory Of Origin Of Species In Oceans Challenged:

New evidence uncovered by oceanographers challenges one of the most long-standing theories about how species evolve in the oceans. Most scientists believe that allopatric speciation, where different species arise from an ancestral species only after breeding populations have become physically isolated from each other, is the dominant mode of speciation both on land and in the sea. The key to this theory is the existence of some kind of physical barrier that operates to restrict interbreeding (gene flow) between populations so that, given enough time, such populations diverge until they’re considered separate species.
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Sexton and Norris’ findings augment a growing body of evidence which support the idea that sympatric speciation, where different species arise from a parent species without the presence of physical barriers, is more common than previously thought. In this mode of speciation, the necessary isolation might instead be achieved through shifts in the timing or depth of reproduction. However, until more research offers a clearer picture of how speciation occurs in the oceans, Sexton and Norris’ contention that sympatric and other similar processes are the “prevalent modes of marine speciation” will, no doubt, remain at odds with prevailing theories.

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