The Entamoeba histolytica genome: something old,something new,something borrowed and sex too?

The recent publication of the protozoan parasite Entamoeba histolytica genome provides new insights into eukaryotic evolution, the role of lateral gene transfer in amebic biology and the adaptations required for eukaryotes that reside within the human intestine.     

Something old, something transgenic, or something fungal for mosquito control?

In spite of the current research emphasis on the use of transgenic mosquitoes, insecticides are still the main method for controlling malarial mosquitoes. Although pyrethroids are the compounds of choice, insecticide resistance is now threatening the effective life of these invaluable compounds. Two recent studies have re-focused interest on entomopathogenic fungi as useful alternatives to conventional insecticides, suggesting that these fungi could be used as alternative control methods, which would thus also prolong the effective lifetime of pyrethroids.     

Pertussis control: time for something new?

Childhood acellular pertussis vaccines were licensed and implemented in the US in the 1990s following an effort to improve on the safety profile of whole-cell vaccines. However, waning of immunity from acellular vaccines may be driving the recent resurgence of pertussis, raising the need to consider new prevention strategies.     

Primary auditory cortex of cats: feature detection or something else?

Neurons in sensory cortices are often assumed to be feature detectors, computing simple and then successively more complex features out of the incoming sensory stream. These features are somehow integrated into percepts. Despite many years of research, a convincing candidate for such a feature in primary auditory cortex has not been found. We argue that feature detection is actually a secondary issue in understanding the role of primary auditory cortex. Instead, the major contribution of primary auditory cortex to auditory perception is in processing previously derived features on a number of different timescales. We hypothesize that, as a result, neurons in primary auditory cortex represent sounds in terms of auditory objects rather than in terms of feature maps. According to this hypothesis, primary auditory cortex has a pivotal role in the auditory system in that it generates the representation of auditory objects to which higher auditory centers assign properties such as spatial location, source identity, and meaning.Abbreviations A1 primary auditory cortex - MGB medical geniculate body - IC inferior coliculus - STRF spectrotemporal receptive field     

Missing something? Codon aversion as a new character system in phylogenetics

Although many studies have documented codon usage bias in different species, the importance of codon usage in a phylogenetic framework remains largely unknown. We demonstrate that a phylogenetic signal is present in the codon usage and non‐usage biases of 17 717 orthologues evaluated across 72 tetrapod species using a simple parsimony analysis of a binary matrix of codon characters. Phylogenies estimated using stop codons were more congruent with previous hypotheses than phylogenies based on any other single codon or a combination of codons. Although each codon is present in every species, specific genes have different codon preferences and may or may not use every possible codon. This observation allowed us to map the pattern of codon usage and non‐usage across the topology. These results suggest that codon usage is phylogenetically conserved across shallow and deep levels within tetrapods.     

Ion channels: does each subunit do something on its own?

The advent of the patch-clamp technique 25 years ago revolutionized the study of ion channels. This method also made it possible to measure the kinetic behavior of single protein molecules. The low-noise recordings of ionic currents through single channels, coupled with other cutting-edge technologies, have revealed a rich complexity of functional states that are not readily explained by simple allosteric protein models such as the popular concerted model and the sequential model. Although these models can each account for elements of ion channel function, we propose that variations or extensions of the lesser-known general allosteric model provide a more promising framework for explaining the intricate behaviors of ion channels.     

Inflammatory bowel disease - is there something new in the immunological background?

In the present paper we correlate clinical data, as well as histopathological, immunohistochemical and molecular biology methods, with the occurrence of both forms of inflammatory bowel disease (IBD) i.e. ulcerative colitis and Crohn's disease. We found that patients with a history of Epstein-Barr virus (EBV) or cytomegalovirus (CMV) infections, as well as steroid treatment, had increased susceptibility to the development of IBD. The diagnosis of IBD was confirmed by histopathology. Previous infections by EBV and CMV, as well as M. tuberculosis, were proved by PCR-based techniques and in situ hybridization. We found PCR-proved latent viral infections in 30-50% of the IBD patients we studied. However, we were unable to prove the presence of viral antigens by immunohistochemistry for EBV or CMV. We found positive correlations between the presence of anti-CMV IgG, as well as PCR-positive results for M. tuberculosis with an ulcerative colitis diagnosis. Additionally, up to 80% of IBD patients used steroids, which was found to be correlated with a diagnosis of Crohn's disease. Our data may support the theory that IBD could be related to previous viral infections and the use of steroids.     

Early events in protein folding: Is there something more than hydrophobic burst?

The presence of native contacts in the denatured state of many proteins suggests that elements of the biologically active structure of these molecules are formed during the initial stage of the folding process. The rapidity with which these events take place makes it difficult to study them in vitro, but, by the same token, suitable for studies in silico. With the help of all-atom, explicit solvent, molecular dynamics simulations we have followed in time, starting from elongated structureless conformations, the early events in the folding of src-SH3 domain and of proteins G, L, and CI2. It is observed that within the first 50 ns two important events take place, essentially independent of each other: hydrophobic collapse and formation of a few selected native contacts. The same contacts are also found in simulations carried out in the presence of guanidinium chloride in order to reproduce the conditions used to characterize experimentally the denatured state and testify to the fact that these contacts are to be considered a resilient characterizing property of the denaturated state.     

Antipredator behavior in lemurs: Evidence of an extinct eagle on Madagascar or something else?

Goodman (1994) related the antipredator response exhibited by two species of lemurs from southwestern Madagascar against extant birds of prey to the predatory efforts of an extinct eagle, inhabiting the same region about 4000 years ago. He argued that today’s smaller raptors, hunting young individuals perhaps only occasionally, represent marginal danger to lemurs. Nevertheless,their activity would be sufficient to impose a continuous reinforcement to a strong antipredator response. I question such an interpretation and instead suggest that extant birds of prey may indeed represent a strong threat to lemurs and that the same might not have been necessarily true for the extinct eagle. In addition, I propose four optional hypotheses, all of which encompass a marginal role for the extinct eagle.     

Fission and fusion in island taxa – serendipity,or something to be expected?

A well‐used metaphor for oceanic islands is that they act as ‘natural laboratories’ for the study of evolution. But how can islands or archipelagos be considered analogues of laboratories for understanding the evolutionary process itself? It is not necessarily the case that just because two or more related species occur on an island or archipelago, somehow, this can help us understand more about their evolutionary history. But in some cases, it can. In this issue of Molecular Ecology, Garrick et al. ( 2014 ) use population‐level sampling within closely related taxa of Galapagos giant tortoises to reveal a complex demographic history of the species Chelonoidis becki – a species endemic to Isabela Island, and geographically restricted to Wolf Volcano. Using microsatellite genotyping and mitochondrial DNA sequencing, they provide a strong case for C. becki being derived from C. darwini from the neighbouring island of Santiago. But the interest here is that colonization did not happen only once. Garrick et al. ( 2014 ) reveal C. becki to be the product of a double colonization event, and their data reveal these two founding lineages to be now fusing back into one. Their results are compelling and add to a limited literature describing the evolutionary consequences of double colonization events. Here, we look at the broader implications of the findings of Garrick et al. ( 2014 ) and suggest genomic admixture among multiple founding populations may be a characteristic feature within insular taxa.     

Biased codon usage near intron-exon junctions: selection on splicing enhancers, splice-site recognition or something else?

Two groups recently argued that, in human genes, synonymous sites near intron-exon junctions undergo selection for correct splicing. However, neither study controlled for the possibility of an underlying nucleotide bias at the ends of exons. In this article, we show that generalized A and T enrichment exists, which could be independent of splicing regulation. Evidence for selection between synonymous codons that are associated with splicing enhancers remains after controlling for this bias, whereas support for cryptic splice-site avoidance is diminished.     

Something old,something new: do genetic studies of contemporary populations reliably represent prehistoric populations of Pacific Rattus exulans?

Through our research focusing on genetic studies of both ancient and extant commensal animals in the Pacific for addressing issues of population origins and mobility in the region, we have been able to process a large number of archaeological faunal remains that we can compare to modern samples from the same islands. These comparisons shed light on and provide specific evidence for Rattus exulans population change through time. This information may provide a model for understanding human populations in the region and will illustrate the complexities of using data obtained from modern populations to infer prehistoric relationships. Two case studies are presented here-analyses of modern and archaeological populations of R. exulans from both Chatham Island and New Zealand. These two cases provide very different pictures regarding the relationship between the archaeological and the extant populations.     

Can biophysics tell us something about the weak equivalence principle vis a vis the thought experiment of Einstein involving human subjects?

Over a period of several decades it has been noticed that most astronauts, either orbiting the earth or on trips to the moon, have observed phosphenes or light flashes (LF) including streaks, spots and clouds of light when their eyes are closed or they are in a darkened cabin. Scientists suspect that two separate components of cosmic rays cause these flashes due to direct interaction with the retina. This phenomenon is not noticed on the ground because of cosmic ray interaction with the atmosphere. The argument is advanced that this effect may provide us with a new method of exploring the weak equivalence principle from the standpoint of Einstein's original thought experiment involving human subjects. This can be done, utilizing the retina only, as an animate quantum mechanical measuring device or, in conjunction with the Anomalous Long Term Effects on Astronauts (ALTEA) facility.     

Maternal age and non‐chromosomal birth defects,Atlanta—1968–2000: Teenager or thirty‐something,who is at risk?

OBJECTIVE: This investigation explored the association between maternal age and non-chromosomal birth defects to assess any increased risk associated with maternal age. METHODS: Birth defect cases were ascertained by the Metropolitan Atlanta Congenital Defects Program (MACDP), denominator information was obtained using birth certificate data. Infants with any chromosomal diagnosis were excluded. Effect estimates were calculated using 5-year maternal age categories with 25-29 years as the referent. Multiple logistic regression was used to adjust for maternal race, parity, infant sex, and birth year. RESULTS: A total of 1,050,616 singleton infants, born after > or = 20 weeks gestation in the five counties of metropolitan Atlanta from 1968 through 2000 who did not have a chromosomal abnormality and whose mother was 14 to 40 years old, were included in the analyses, 32,816 of them were identified with birth defects by the MACDP. Young maternal age (14-19 years) was associated with anencephaly (OR = 1.81, 95% CI = 1.30-2.52), hydrocephaly without neural tube defect (OR = 1.56, 95% CI = 1.23-1.96), all ear defects (OR = 1.28, 95% CI = 1.10-1.49), cleft lip (OR = 1.88, 95% CI = 1.30-2.73), female genital defects (OR = 1.57, 95% CI = 1.12-2.19), hydronephrosis (OR = 1.42, 95% CI = 1.11-1.82), polydactyly (OR = 1.29, 95% CI = 1.09-1.52), omphalocele (OR = 2.08, 95% CI = 1.39-3.12), and gastroschisis (OR = 7.18, 95% CI = 4.39-11.75). Advanced maternal age (35-40 years) was associated with all heart defects (OR = 1.12, 95% CI = 1.03-1.22), tricuspid atresia (OR = 1.24, 95% CI = 1.02-1.50), right outflow tract defects (OR = 1.28, 95% CI = 1.10-1.49), hypospadias 2nd degree or higher (OR = 1.85, 95% CI = 1.33-2.58), male genital defects excluding hypospadias (OR = 1.25, 95% CI = 1.08-1.45) and craniosynostosis (OR = 1.65, 95% CI = 1.18-2.30). CONCLUSIONS: Young and advanced maternal ages are associated with different types of birth defects. Underlying causes for these associations are not clear.