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New and Exciting in PLoS this week

Lots of cool papers today in 4 out of 7 PLoS journals! 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, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks – you go and look for your own favourites:

Charles Darwin’s Reception in Germany and What Followed:

In Germany, Charles Darwin’s thinking was accepted very quickly after the publication of On the Origin of Species in November, 1859. This was due, in no small measure, to the fact that a translation by the noted German paleontologist Heinrich Georg Bronn appeared in April, 1860, only months after the original publication [1]. Bronn’s own research led him to several insights that paralleled those of Darwin, resulting in a translation that was quite liberal and included the addition of numerous footnotes; but perhaps most importantly, Bronn added a new final chapter (chapter 15) to Darwin’s book [2]. In these final notes, Bronn summarized his assessments of and conclusions on Darwin’s Origin in 26 pages [2]. He outlined what he thought Darwin had meant to say, partly reinterpreted it, and critiqued it. Darwin welcomed this discussion, and 18 letters were exchanged between the two men. In subsequent editions of Origin, Darwin developed his theory further through such feedback. Bronn’s critical epilogue was partly inspired by his adherence to an idealistic–even romantic–and teleological Naturphilosophie that viewed evolution as a progressive development toward perfection; this has at least been long thought, explaining why Bronn used the word, in both text and title of the translation, vervollkommnet (perfected) for Darwin’s word “favored.” Bronn also freely translated Darwin’s “struggle for existence” into Kampf ums Dasein, which might be best translated back into English as “fight for existence or life,” a phrase that Darwin himself was not entirely happy with. New interpretations of Bronn’s work and his influence on Ernst Haeckel and evolutionary thought in Germany are presented in the new book by Sander Gliboff, H. G. Bronn, Ernst Haeckel, and the Origins of German Darwinism: A Study in Translation and Transformation [3].

Ethics Without Borders:

Many nongovernmental organizations (NGOs) provide medical care and humanitarian assistance to some of the most vulnerable populations on earth. Increasingly, such organizations are also important producers of health research, which can range from simple health surveys or interview studies, to complex clinical trials.

There is little doubt that the results of such research can be immensely valuable. First, they may be critical in informing the scale and type of interventions an NGO may need to deliver–for example, a survey of growth among children being treated for malnutrition [1]. Second, they may provide crucial data against which the effects of ongoing events can be monitored–for example, the effect on displaced populations of access to maternal health care [2]. Third, they may be used to inform health policy at the highest levels–for example, studies of anti-malarial efficacy among populations served by NGOs can inform recommendations for treatment regimens internationally (reviewed in [3]).

PLoS Neglected Tropical Diseases: Two Years of Providing Access to Innovation for the World’s Poor … and Counting:

It has been almost two years since PLoS Neglected Tropical Diseases was launched as the first open-access journal devoted to the neglected tropical diseases (NTDs). At that time we aspired to achieve multiple goals by creating a new journal for the NTD community. We believed that through an open-access format, we would provide an immediate and vital mechanism by which the community of NTD scientists, public health experts, and health care professionals would have access to the latest information about these conditions. Back in 2007, we were especially excited about reaching investigators in the disease-endemic countries, particularly those who often cannot afford the expense of some of the more traditional and established biomedical journals. To help realize these goals we went to great lengths to secure a high level of editorial board representation from disease-endemic countries in Latin America, Africa, and Asia. We also hoped that through our frontmatter articles that included viewpoints, commentaries, reviews, and editorials, PLoS Neglected Tropical Diseases would have an important role in advocacy and elevating the profile of the NTDs.

Compromise or Capitulation? US Food and Drug Administration Jurisdiction Over Tobacco Products:

On June 12, 2009, the United States Congress passed the Family Smoking Prevention and Tobacco Control Act (S. 982), granting the US Food and Drug Administration (FDA) authority regulating tobacco products. The idea of FDA regulation of tobacco has broad [1], but not unanimous, support among medical and public health professionals. This law has many strengths (Table 1): it grants the FDA general authority over tobacco products, including the ability to reduce (but not eliminate) nicotine, requires improved warning labels on cigarette and other tobacco packages, and implements the rules limiting marketing of tobacco products to youth that the FDA issued in 1996. It also repeals pre-emption of state and local regulation of tobacco marketing and advertising, and grants states and localities broad rights to regulate or prohibit the sale, distribution, possession, exposure to, access to, or use of tobacco products.

Bats, Emerging Diseases, and the Human Interface:

The tragic death of a Dutch patient due to Duvenhage virus infection acquired after bat exposure in Kenya during 2007 emphasizes the potential dangers associated with ecotourism, underscores the role of Chiroptera as reservoirs of emerging infectious diseases, and highlights modern attempts to prevent and treat these zoonotic diseases.

The patient in this incident, a physician from The Netherlands, was a visitor to a game park in eastern Kenya, and had not been previously vaccinated against rabies. Often, many travelers abroad may not be well versed in local environmental conditions. Well before expected departure, travel medicine consultants should discuss both generic and country-specific risks with their clients. For maximum benefit, several biologics require administration a month in advance of departure, such as rabies pre-exposure immunization. Besides primary vaccination suggestions, and health insurance considerations for emergency care abroad or medical evacuation as needed, basic education is necessary concerning realistic public health concerns, especially in developing countries. Selective positive social behaviors should be promoted, especially as related to personal interactions with animals, both domestic and wild. Greater appreciation of animals from a distance is ideal, rather than any personal provocations. If animal bites or scratches do occur, immediate thorough washing of wounds with soap and clean water is valuable, followed by careful biomedical evaluation. While the latter was attempted in this particular Kenyan incident, the global implications of bat rabies were not appreciated.

Fatal Human Rabies due to Duvenhage Virus from a Bat in Kenya: Failure of Treatment with Coma-Induction, Ketamine, and Antiviral Drugs:

Rabies, encephalitis caused by lyssaviruses, was considered universally fatal until a young, unvaccinated patient with bat rabies survived after a new therapeutic approach [1]. The long-term favourable outcome of this patient suggested that successful interventions may be possible [2]. However, 11 patients, subsequently treated in a similar way, have not survived (reviewed by Wilde et al. [3]). Of six of these patients, information is published [4]-[8]; the other five are mentioned in the review [3].

We report on a patient with rabies due to Duvenhage virus from a bat in Kenya. A very brief description of this case without clinical details and without results of virological and pathological investigations was reported in Eurosurveillance [7]. This report was included in the review of Wilde et al. [3]. We now present this patient in more detail and with results of virological and pathological investigations. We received written consent for publication of this case report from the patient’s husband.

Henipavirus RNA in African Bats:

Henipaviruses (Hendra and Nipah virus) are highly pathogenic members of the family Paramyxoviridae. Fruit-eating bats of the Pteropus genus have been suggested as their natural reservoir. Human Henipavirus infections have been reported in a region extending from Australia via Malaysia into Bangladesh, compatible with the geographic range of Pteropus. These bats do not occur in continental Africa, but a whole range of other fruit bats is encountered. One of the most abundant is Eidolon helvum, the African Straw-coloured fruit bat. Feces from E. helvum roosting in an urban setting in Kumasi/Ghana were tested for Henipavirus RNA. Sequences of three novel viruses in phylogenetic relationship to known Henipaviruses were detected. Virus RNA concentrations in feces were low. The finding of novel putative Henipaviruses outside Australia and Asia contributes a significant extension of the region of potential endemicity of one of the most pathogenic virus genera known in humans.

Bat Eyes Have Ultraviolet-Sensitive Cone Photoreceptors:

Mammalian retinae have rod photoreceptors for night vision and cone photoreceptors for daylight and colour vision. For colour discrimination, most mammals possess two cone populations with two visual pigments (opsins) that have absorption maxima at short wavelengths (blue or ultraviolet light) and long wavelengths (green or red light). Microchiropteran bats, which use echolocation to navigate and forage in complete darkness, have long been considered to have pure rod retinae. Here we use opsin immunohistochemistry to show that two phyllostomid microbats, Glossophaga soricina and Carollia perspicillata, possess a significant population of cones and express two cone opsins, a shortwave-sensitive (S) opsin and a longwave-sensitive (L) opsin. A substantial population of cones expresses S opsin exclusively, whereas the other cones mostly coexpress L and S opsin. S opsin gene analysis suggests ultraviolet (UV, wavelengths <400 nm) sensitivity, and corneal electroretinogram recordings reveal an elevated sensitivity to UV light which is mediated by an S cone visual pigment. Therefore bats have retained the ancestral UV tuning of the S cone pigment. We conclude that bats have the prerequisite for daylight vision, dichromatic colour vision, and UV vision. For bats, the UV-sensitive cones may be advantageous for visual orientation at twilight, predator avoidance, and detection of UV-reflecting flowers for those that feed on nectar.

Ancient DNA Resolves Identity and Phylogeny of New Zealand’s Extinct and Living Quail (Coturnix sp.):

The New Zealand quail, Coturnix novaezealandiae, was widespread throughout New Zealand until its rapid extinction in the 1870’s. To date, confusion continues to exist concerning the identity of C. novaezealandiae and its phylogenetic relationship to Coturnix species in neighbouring Australia, two of which, C. ypsilophora and C. pectoralis, were introduced into New Zealand as game birds. The Australian brown quail, C. ypsilophora, was the only species thought to establish with current populations distributed mainly in the northern part of the North Island of New Zealand. Owing to the similarities between C. ypsilophora, C. pectoralis, and C. novaezealandiae, uncertainty has arisen over whether the New Zealand quail is indeed extinct, with suggestions that remnant populations of C. novaezealandiae may have survived on offshore islands. Using fresh and historical samples of Coturnix sp. from New Zealand and Australia, DNA analysis of selected mitochondrial regions was carried out to determine phylogenetic relationships and species status. Results show that Coturnix sp. specimens from the New Zealand mainland and offshore island Tiritiri Matangi are not the New Zealand quail but are genetically identical to C. ypsilophora from Australia and can be classified as the same species. Furthermore, cytochrome b and COI barcoding analysis of the New Zealand quail and Australia’s C. pectoralis, often confused in museum collections, show that they are indeed separate species that diverged approximately 5 million years ago (mya). Gross morphological analysis of these birds suggests a parallel loss of sustained flight with very little change in other phenotypic characters such as plumage or skeletal structure. Ancient DNA has proved invaluable for the detailed analysis and identification of extinct and morphologically cryptic taxa such as that of quail and can provide insights into the timing of evolutionary changes that influence morphology.

Large Scale Application of Neural Network Based Semantic Role Labeling for Automated Relation Extraction from Biomedical Texts:

To reduce the increasing amount of time spent on literature search in the life sciences, several methods for automated knowledge extraction have been developed. Co-occurrence based approaches can deal with large text corpora like MEDLINE in an acceptable time but are not able to extract any specific type of semantic relation. Semantic relation extraction methods based on syntax trees, on the other hand, are computationally expensive and the interpretation of the generated trees is difficult. Several natural language processing (NLP) approaches for the biomedical domain exist focusing specifically on the detection of a limited set of relation types. For systems biology, generic approaches for the detection of a multitude of relation types which in addition are able to process large text corpora are needed but the number of systems meeting both requirements is very limited. We introduce the use of SENNA (“Semantic Extraction using a Neural Network Architecture”), a fast and accurate neural network based Semantic Role Labeling (SRL) program, for the large scale extraction of semantic relations from the biomedical literature. A comparison of processing times of SENNA and other SRL systems or syntactical parsers used in the biomedical domain revealed that SENNA is the fastest Proposition Bank (PropBank) conforming SRL program currently available. 89 million biomedical sentences were tagged with SENNA on a 100 node cluster within three days. The accuracy of the presented relation extraction approach was evaluated on two test sets of annotated sentences resulting in precision/recall values of 0.71/0.43. We show that the accuracy as well as processing speed of the proposed semantic relation extraction approach is sufficient for its large scale application on biomedical text. The proposed approach is highly generalizable regarding the supported relation types and appears to be especially suited for general-purpose, broad-scale text mining systems. The presented approach bridges the gap between fast, cooccurrence-based approaches lacking semantic relations and highly specialized and computationally demanding NLP approaches.

Sex Determination in the Squalius alburnoides Complex: An Initial Characterization of Sex Cascade Elements in the Context of a Hybrid Polyploid Genome:

Sex determination processes vary widely among different vertebrate taxa, but no group offers as much diversity for the study of the evolution of sex determination as teleost fish. However, the knowledge about sex determination gene cascades is scarce in this species-rich group and further difficulties arise when considering hybrid fish taxa, in which mechanisms exhibited by parental species are often disrupted. Even though hybridisation is frequent among teleosts, gene based approaches on sex determination have seldom been conducted in hybrid fish. The hybrid polyploid complex of Squalius alburnoides was used as a model to address this question. We have initiated the isolation and characterization of regulatory elements (dmrt1, wt1, dax1 and figla) potentially involved in sex determination in S. alburnoides and in the parental species S. pyrenaicus and analysed their expression patterns by in situ hybridisation. In adults, an overall conservation in the cellular localization of the gene transcripts was observed between the hybrids and parental species. Some novel features emerged, such as dmrt1 expression in adult ovaries, and the non-dimorphic expression of figla, an ovarian marker in other species, in gonads of both sexes in S. alburnoides and S. pyrenaicus. The potential contribution of each gene to the sex determination process was assessed based on the timing and location of expression. Dmrt1 and wt1 transcripts were found at early stages of male development in S. alburnoides and are most likely implicated in the process of gonad development. For the first time in the study of this hybrid complex, it was possible to directly compare the gene expression patterns between the bisexual parental species and the various hybrid forms, for an extended set of genes. The contribution of these genes to gonad integrity maintenance and functionality is apparently unaltered in the hybrids, suggesting that no abrupt shifts in gene expression occurred as a result of hybridisation.

Inheritance of Acquired Behaviour Adaptations and Brain Gene Expression in Chickens:

Environmental challenges may affect both the exposed individuals and their offspring. We investigated possible adaptive aspects of such cross-generation transmissions, and hypothesized that chronic unpredictable food access would cause chickens to show a more conservative feeding strategy and to be more dominant, and that these adaptations would be transmitted to the offspring. Parents were raised in an unpredictable (UL) or in predictable diurnal light rhythm (PL, 12:12 h light:dark). In a foraging test, UL birds pecked more at freely available, rather than at hidden and more attractive food, compared to birds from the PL group. Female offspring of UL birds, raised in predictable light conditions without parental contact, showed a similar foraging behavior, differing from offspring of PL birds. Furthermore, adult offspring of UL birds performed more food pecks in a dominance test, showed a higher preference for high energy food, survived better, and were heavier than offspring of PL parents. Using cDNA microarrays, we found that the differential brain gene expression caused by the challenge was mirrored in the offspring. In particular, several immunoglobulin genes seemed to be affected similarly in both UL parents and their offspring. Estradiol levels were significantly higher in egg yolk from UL birds, suggesting one possible mechanism for these effects. Our findings suggest that unpredictable food access caused seemingly adaptive responses in feeding behavior, which may have been transmitted to the offspring by means of epigenetic mechanisms, including regulation of immune genes. This may have prepared the offspring for coping with an unpredictable environment.

Comments

  1. #1 Michael D. Barton, FCD
    July 28, 2009

    I’ll have to share the Darwin piece on DOD!

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