Is There a Phylogenetic Signal in Prokaryote Proteins?

Using the sequence information from nine completely sequenced bacterial genomes, we extract 32 protein families that are thought to contain orthologous proteins from each genome. The alignments of these 32 families are used to construct a phylogeny with the neighbor-joining algorithm. This tree has several topological features that are different from the conventional phylogeny, yet it is highly reliable according to its bootstrap values. Upon closer study of the individual families used, it is clear that the strong phylogenetic signal comes from three families, at least two of which are good candidates for horizontal transfer. The tree from the remaining 29 families consists almost entirely of noise at the level of bacterial phylum divisions, indicating that, even with large amounts of data, it may not be possible to reconstruct the prokaryote phylogeny using standard sequence-based methods. Received: 22 November 1998 / Accepted: 17 February 1999     

High interannual variation in the hatching sex ratio of Tengmalm’s owl broods during a vole cycle

The sex ratio at hatching in broods of Tengmalms owl (Aegolius funereus) in northern Sweden was investigated for 3 years characterized by different phases of the vole and owl cycle. Previous work showed the sex ratio in this species to be male-biased for 1 year with a favourable food supply, and that in feeding experiments male nestlings (but not females) suffered higher mortality when food was limited, but not otherwise. Here we present data from a complete 3-year owl cycle, showing that mean brood sex ratio varied significantly among years, being male-biased (65% males) in the first year of high owl breeding density, unbiased (49%) in the second year of high owl breeding density, and female-biased (33% males) in the owls low year. Brood sex ratio did not vary significantly within years with laying date or parental age. Vole availability, and therefore the owls food supply, declined during the 3 years studied. Tengmalms owl parents thus appear to adaptively adjust the sex ratio of their broods according to the expected annual mortality risk of sons.     

Useless Hearing in Male Emblemasoma auditrix (Diptera,Sarcophagidae) – A Case of Intralocus Sexual Conflict during Evolution of a Complex Sense Organ?

Sensory modalities typically are important for both sexes, although sex-specific functional adaptations may occur frequently. This is true for hearing as well. Consequently, distinct behavioural functions were identified for the different insect hearing systems. Here we describe a first case, where a trait of an evolutionary novelty and a highly specialized hearing organ is adaptive in only one sex. The main function of hearing of the parasitoid fly Emblemasoma auditrix is to locate the host, males of the cicada species Okanagana rimosa, by their calling song. This task is performed by female flies, which deposit larvae into the host. We show that male E. auditrix possess a hearing sense as well. The morphology of the tympanal organ of male E. auditrix is rather similar to the female ear, which is 8% broader than the male ear. In both sexes the physiological hearing threshold is tuned to 5 kHz. Behavioural tests show that males are able to orient towards the host calling song, although phonotaxis often is incomplete. However, despite extensive observations in the field and substantial knowledge of the biology of E. auditrix, no potentially adaptive function of the male auditory sense has been identified. This unique hearing system might represent an intralocus sexual conflict, as the complex sense organ and the behavioural relevant neuronal network is adaptive for only one sex. The correlated evolution of the sense organ in both sexes might impose substantial constraints on the sensory properties of the ear. Similar constraints, although hidden, might also apply to other sensory systems in which behavioural functions differ between sexes.     

Does Human Body Odor Represent a Significant and Rewarding Social Signal to Individuals High in Social Openness?

Across a wide variety of domains, experts differ from novices in their response to stimuli linked to their respective field of expertise. It is currently unknown whether similar patterns can be observed with regard to social expertise. The current study therefore focuses on social openness, a central social skill necessary to initiate social contact. Human body odors were used as social cues, as they inherently signal the presence of another human being. Using functional MRI, hemodynamic brain responses to body odors of women reporting a high (n = 14) or a low (n = 12) level of social openness were compared. Greater activation within the inferior frontal gyrus and the caudate nucleus was observed in high socially open individuals compared to individuals low in social openness. With the inferior frontal gyrus being a crucial part of the human mirror neuron system, and the caudate nucleus being implicated in social reward, it is discussed whether human body odor might constitute more of a significant and rewarding social signal to individuals high in social openness compared to individuals low in social openness process.     

Evolution in Action-Peacock-Feather Like Supraocular Tentacles of the Lionfish, Pterois volitans – the Distribution of a New Signal

Synopsis Observations on populations of the lionfish, Pterois volitans (Scorpaenidae), in the Red Sea revealed that during the last four decades a novel phenotype of this species has started to evolve, which instead of the typical ray-like supraocular tentacles bears a pair of feather-like tentacles, one or both of which bear a sharply defined eye-mark, previously noted in this fish in the eastern Indian ocean. During the ongoing studies of the last 25 years it has become clear that this ornamentation, possibly first observed in the Red Sea at the southern tip of Sinai, had gradually extended both westward to the Egyptian shores, and eastward, along the 180 km of the Gulf of Aqaba. In the last decade such ornamented specimens have begun to appear and multiply at the northern tip of the Gulf, within the large population of ‘regular’ lionfish bearing ray-like tentacles. The evolutionary basis for this development, and the possible usefulness of this novel signal are discussed.     

The reef coral Goniastrea aspera: a ‘winner’ becomes a ‘loser’ during a severe bleaching event in Thailand

The reef coral Goniastrea aspera is regarded as one of the most environmentally tolerant species on Indo-Pacific reefs. Its demise, following a severe bleaching event in the Andaman Sea in the north-eastern Indian Ocean in 2010, was surprising in view of the rapid recovery of co-existing species such as Porites lutea. Demographic studies of G. aspera at this site showed the population was mainly composed of large individuals, which recruited in the early 1990s. These results, and size-specific mortality observed in G. aspera, post-bleaching, suggest that factors, related to size and age, may have contributed to the coral’s marked decline.     

Nitrogen fixation in the High Arctic: a source of ‘new’ nitrogen?

Biological nitrogen (N₂) fixation performed by diazotrophs (N₂ fixing bacteria) is thought to be one of the main sources of plant available N in pristine ecosystems like arctic tundra. However, direct evidence of a transfer of fixed N₂ to non-diazotroph associated plants is lacking to date. Here, we present results from an in situ ¹⁵N–N₂ labelling study in the High Arctic. Three dominant vegetation types (organic crust composed of free-living cyanobacteria, mosses, cotton grass) were subjected to acetylene reduction assays (ARA) performed regularly throughout the growing season, as well as ¹⁵N–N₂ incubations. The ¹⁵N-label was followed into the dominant N₂ fixer associations, soil, soil microbial biomass and non-diazotroph associated plants three days and three weeks after labelling. Mosses contributed most to habitat N₂ fixation throughout the measuring campaigns, and N₂ fixation activity was highest at the beginning of the growing season in all plots. Fixed ¹⁵N–N₂ became quickly (within 3 days) available to non-diazotroph associated plants in all investigated vegetation types, proving that N₂ fixation is an actual source of available N in pristine ecosystems.     

Behaviour of dehydrated baker’s yeast during reduction reactions in a biphasic medium

The behaviour of dry bakers yeast (Saccharomyces cerevisiae type II, Sigma) used as biocatalyst without preliminary growth for the synthesis of 2-heptanol from 2-heptanone in a biphasic system is presented. Cells undergo intracellular trehalose consumption with a stoichiometric ethanol production during the first 15 h of the process. This metabolism is then replaced by acetate accumulation. These reactions are disconnected from the biocatalytic reaction and do not provide reduced cofactors. 2-Heptanone is metabolised by two pathways. The first leads to 2-heptanol (molar yield close to 55%, enantioselectivity higher than 99%, with a slight decrease at the end of the process) and the second corresponds to material incorporation into the biomass. This latter phenomenon is assumed to provide the biocatalyst with the reduced cofactors needed for the reduction process. Overall, the process yielded ca. 1.4 g/l 2-heptanol in 50 h reaction, which is close to that observed with fresh cells previously grown for 15 h.     

Implementation of a National Measles Elimination Program in Iran: Phylogenetic Analysis of Measles Virus Strains Isolated during 2010–2012 Outbreaks

Measles virus (MV) causes small and large outbreaks in Iran. Molecular assays allow identifying and the sources of measles imported from neighboring countries. We carried out a phylogenetic analysis of measles virus circulating in Iran over the period 2010–2012. Specimens from suspected cases of measles were collected from different regions of Iran. Virus isolation was performed on urine and throat swabs. Partial nucleoprotein gene segments of MV were amplified by RT-PCR. PCR products of 173 samples were sequenced and analyzed. The median age of confirmed cases was 2 years. Among all confirmed cases, 32% had unknown vaccination status, 20% had been vaccinated, and 48% had not been vaccinated. Genotypes B3 and D8 (for the first time), H1 and D4 were detected mainly in unvaccinated toddlers and young children. Genotype B3 became predominant in 2012 and was closely related to African strains. H1 strains were also found in small and large outbreaks during 2012 but were not identical to Iranian H1-2009 strains. A majority of the Iranian D4 strains during 2010–2012 outbreaks were linked to the D4 strain identified in the Pakistan in 2007. We identified a single case in 2010 belonging to D8 genotype with 99.7% identity to Indian isolates. Although the vaccination program is currently good enough to prevent nationwide epidemics and successfully decreased measles incidence in Iran, the fraction of protected individuals in the population was not high enough to prevent continuous introduction of cases from abroad. Due to increasing number of susceptible individuals in some areas, sustained transmission of the newly introduced viral genotype remains possible.     

Changes in Meningococcal Strains in the Era of a Serogroup C Vaccination Campaign: Trends and Evolution in Belgium during the Period 1997–2012

Background

Invasive meningococcal disease (IMD) is a major cause of bacterial meningitides and septicaemia. This study shows the results of the laboratory-based surveillance of IMD in Belgium over the period 1997–2012.

Methods

The results are based on microbiological and molecular laboratory surveillance of 2997 clinical isolates of N. meningitides received by the Belgian Meningococcal Reference Centre (BMRC) over the period 1997–2012.

Results

Serogroup B has always been a major cause of meningococcal disease in Belgium, with P3.4 as most frequent serotype till 2008, while an increase in non-serotypable strains has been observed in the last few years. Clonal complexes cc-41/44 and cc-269 are most frequently observed in serogroup B strains. In the late nineties, the incidence of serogroup C disease increased considerably and peaked in 2001, mainly associated with phenotypes C:2a:P1.5,2, C:2a:P1.5 and C:2a:P1.2 (ST-11/ET-37 clonal complex). The introduction of the meningococcal C conjugate vaccine has been followed by an 88% significant decrease in serogroup C disease from 2001 to 2004 nationally, yet sharper in Flanders (92%) compared to Wallonia (77%). Since 2008 a difference in incidence of serogroup C was observed in Flanders (0–0.1/100,000) versus Wallonia (0.1–0.3/100,000).

Conclusion

This study showed the change in epidemiology and strain population over a 16 years period spanning an exhaustive vaccination campaign and highlights the influence of regional vaccination policies with different cohorts sizes on short and long-term IMD incidences.     

Monitoring Arthrobacter protophormiae RKJ100 in a ‘tag and chase’ method during p-nitrophenol bio-remediation in soil microcosms

Monitoring of micro-organisms released deliberately into the environment is essential to assess their movement during the bio-remediation process. During the last few years, DNA-based genetic methods have emerged as the preferred method for such monitoring; however, their use is restricted in cases where organisms used for bio-remediation are not well characterized or where the public domain databases do not provide sufficient information regarding their sequence. For monitoring of such micro-organisms, alternate approaches have to be undertaken. In this study, we have specifically monitored a p-nitrophenol (PNP)-degrading organism, Arthrobacter protophormiae RKJ100, using molecular methods during PNP degradation in soil microcosm. Cells were tagged with a transposon-based foreign DNA sequence prior to their introduction into PNP-contaminated microcosms. Later, this artificially introduced DNA sequence was PCR-amplified to distinguish the bio-augmented organism from the indigenous microflora during PNP bio-remediation.     

Hypoxia Promotes Dopaminergic Differentiation of Mesenchymal Stem Cells and Shows Benefits for Transplantation in a Rat Model of Parkinson’s Disease

Mesenchymal stem cells (MSCs) are multipotent cells capable of differentiating into dopaminergic (DAergic) neurons, which is one of the major cell types damaged in Parkinson’s disease (PD). For this reason, MSCs are considered a potential cell source for PD therapy. It has been proved that hypoxia is involved in the proliferation and differentiation of stem cells. In this study, we investigated the effect of hypoxia on MSC proliferation and DAergic neuronal differentiation. Our results demonstrate that 3% O₂ treatment can enhance rat MSC proliferation by upregulation of phosphorylated p38 MAPK and subsequent nuclear translocation of hypoxia inducible factor (HIF)-1α. During neural differentiation, 3% O₂ treatment increases the expression of HIF-1α, phosphorylated ERK and p38 MAPK. These changes are followed by promotion of neurosphere formation and further DAergic neuronal differentiation. Furthermore, we explored the physiological function of hypoxia-induced DAergic neurons from human fetal MSCs by transplanting them into parkinsonian rats. Grafts induced with hypoxia display more survival of DAergic neurons and greater amelioration of behavioral impairments. Altogether, these results suggest that hypoxia can promote MSC proliferation and DAergic neuronal differentiation, and benefit for intrastriatal transplantation. Therefore, this study may provide new perspectives in application of MSCs to clinical PD therapy.     

‘Testing Together Challenges the Relationship’: Consequences of HIV Testing as a Couple in a High HIV Prevalence Setting in Rural South Africa

Objective

We conducted qualitative individual and combined interviews with couples to explore their experiences since the time of taking an HIV test and receiving the test result together, as part of a home-based HIV counselling and testing intervention.

Methods

This study was conducted in October 2011 in rural KwaZulu-Natal, South Africa, about 2 years after couples tested and received results together. Fourteen couples were purposively sampled: discordant, concordant negative and concordant positive couples.

Findings

Learning about each other’s status together challenged relationships of the couples in different ways depending on HIV status and gender. The mutual information confirmed suspected infidelity that had not been discussed before. Negative women in discordant partnerships remained with their positive partner due to social pressure and struggled to maintain their HIV negative status. Most of the couple relationships were characterized by silence and mistrust. Knowledge of sero-status also led to loss of sexual intimacy in some couples especially the discordant. For most men in concordant negative couples, knowledge of status was an awakening of the importance of fidelity and an opportunity for behaviour change, while for concordant positive and discordant couples, it was seen as proof of infidelity. Although positive HIV status was perceived as confirmation of infidelity, couples continued their relationship and offered some support for each other, living and managing life together. Sexual life in these couples was characterized by conflict and sometimes violence. In the concordant negative couples, trust was enhanced and behaviour change was promised.

Conclusions

Findings suggest that testing together as couples challenged relationships in both negative and positive ways. Further, knowledge of HIV status indicated potential to influence behaviour change especially among concordant negatives. In the discordant and concordant positive couples, traditional gender roles exposed women’s vulnerability and their lack of decision-making power.     

Does Village Water Supply Affect Children’s Length of Stay in a Therapeutic Feeding Program in Niger? Lessons from a Médecins Sans Frontières Program

Objective

With an increasing move towards outpatient therapeutic feeding for moderately and severely malnourished children, the home environment has become an increasingly important factor in achieving good program outcomes. Infections, including those water-borne, may significantly delay weight gain in a therapeutic feeding program. This study examined the relationship between adequacy of water supply and children’s length of stay in a therapeutic feeding program in Niger.

Methods

The length of stay in a therapeutic feeding program of Médecins Sans Frontières in Niger was registered for 1518 children from 20 villages in the region. In parallel, the quality and quantity of the water source in each village were documented, and the association between adequacy of the water supply and length of stay in the program was assessed through Generalized Estimating Equation analysis.

Results

36% of the children presented with a secondary infection, 69% of which were water-related. When stratified by the adequacy of the quantity and/or quality of the water supply in their village of origin, non-adequacy of the water supply was clearly associated with a higher prevalence of secondary water-related infections and with much longer lengths of stay of malnourished children in the therapeutic feeding program.

Conclusion

This study suggests that therapeutic feeding programs using an outpatient model should routinely evaluate the water supply in their target children’s villages if they are to provide optimal care.     

Signal alterations of the basal ganglia in the differential diagnosis of Parkinson’s disease: a retrospective case-controlled MRI data bank analysis

Background

Based upon the acquainted loss of dopaminergic neurons in the substantia nigra in Parkinson’s disease (PD), we hypothesised changes in magnetic resonance imaging signal intensities of the basal ganglia to be useful as an additional technical tool in the diagnostic work-up.

Methods

Region-of-interest analyses (substantia nigra and globus pallidus internus) of T2-weighted scans were performed in seventy subjects with PD, 170 age- and gender-matched controls and 38 patients with an atypical form of neurodegenerative Parkinsonian syndrome (N?=?11 multisystem atrophy, N?=?22 progressive supranuclear palsy, N?=?5 corticobasal syndrome).

Results

In patients with PD, significant changes in signal intensities within the substantia nigra were observed compared to controls at p?<?0.001. For the globus pallidus internus, signal alterations in PD and progressive supranuclear palsy were found to be significant (p?<?0.001) if compared to controls. Furthermore, signal changes of substantia nigra correlated with signal intensities of globus pallidus internus in the ipsilateral hemisphere in both groups. Sensitivity was 86% and specificity was 90% for the combined analysis of substantia nigra and globus pallidus internus in the complete patient sample versus controls.

Conclusions

Signal alterations of substantia nigra and globus pallidus internus in routine magnetic resonance imaging were useful to distinguish patients with PD from controls. In addition, signal changes in globus pallidus internus could be used to differentiate progressive supranuclear palsy patients from controls. These analyses have the potential to serve as an additional non-invasive technical tool to support the individual differential diagnosis of PD.

     

Variability of Stepping during a Virtual Reality Paradigm in Parkinson’s Disease Patients with and without Freezing of Gait

Background

Freezing of gait is a common and debilitating symptom affecting many patients with advanced Parkinson’s disease. Although the pathophysiology of freezing of gait is not fully understood, a number of observations regarding the pattern of gait in patients with this symptom have been made. Increased ‘Stride Time Variability’ has been one of the most robust of these features. In this study we sought to identify whether patients with freezing of gait demonstrated similar fluctuations in their stepping rhythm whilst performing a seated virtual reality gait task that has recently been used to demonstrate the neural correlate of the freezing phenomenon.

Methods

Seventeen patients with freezing and eleven non-freezers performed the virtual reality task twice, once whilst ‘On’ their regular Parkinsonian medication and once in their practically defined ‘Off’ state.

Results

All patients displayed greater step time variability during their ‘Off’ state assessment compared to when medicated. Additionally, in the ‘Off’ state, patients with freezing of gait had greater step time variability compared to non-freezers. The five steps leading up to a freezing episode in the virtual reality environment showed a significant increase in step time variability although the final three steps preceding the freeze were not characterized by a progressive shortening of latency.

Conclusions

The results of this study suggest that characteristic features of gait disturbance observed in patients with freezing of gait can also be demonstrated with a virtual reality paradigm. These findings suggest that virtual reality may offer the potential to further explore the freezing phenomenon in Parkinson’s disease.     

Prolactin Receptor Gene Diversity in Azara’s Owl Monkeys (Aotus azarai) and Humans (Homo sapiens) Suggests a Non-Neutral Evolutionary History among Primates

Although paternal care is rare in mammals, males of several primate taxa exhibit high degrees of this behavior. Studies a number of vertebrate species found a positive correlation between prolactin (PRL) levels and paternal care. Studies of maternal care in knockout mice also indicate that the prolactin receptor (PRLR) plays a critical role in the neural regulation of parental care. To better understand the extent of PRLR genetic variation within primates, we characterized intraspecific coding variation in Azara’s owl monkeys (Aotus azarai) from northern Argentina, a species with intensive paternal care. We then examined PRLR variation in 1088 humans (Homo sapiens) from the 1000 Genomes Project. Lastly, we assessed interspecific variation in PRLR in 4 different Aotus spp. and 12 phylogenetically (and behaviorally) disparate primate taxa. Our analyses revealed that the coding region of PRLR exhibits significant variation in all species of primates, with nonsynonymous amino acid substitutions being enriched in the intracellular domain, a region responsible for activation of downstream targets in the PRL pathway. In addition, several species exhibit entire codon deletions in this region. These results suggest a non-neutral evolutionary history of the PRLR locus within different primate lineages, and further imply that the translated PRLR protein has undergone considerable change throughout primate evolution. Such changes may be driven by selection for different behaviors and physiologies resulting from modulations of the pleiotropic prolactin pathway. Yet, the genetic variants in PRLR among primate taxa do not discretely cluster with species-level differences in paternal care behaviors. These observations imply that other mechanisms must be involved in the regulation of paternal care in primates.     

A laboratory captured ‘giving way’ episode during a single-leg landing task in an individual with unilateral chronic ankle instability

An episode of ‘giving way’ at the ankle is described as excessive inversion of the rearfoot that does not result in an acute ankle sprain and is a unique feature associated with chronic ankle instability (CAI). Limited data currently exists describing the preparatory movement patterns and those that occur during an episode of ‘giving way. Therefore, this case report describes the movement patterns and the forces generated during an unintentional ‘giving way’ captured while an individual with unilateral CAI was performing a single-leg landing task in a research laboratory. The participant completed five single-leg landing trials for both limbs. 3D lower extremity kinematics and kinetics for the sagittal and frontal plane were extracted from 200 ms before and after initial contact (IC). Relative to the affected and un-affected single-leg landing trials, the ‘giving way’ episode was characterized by an increase in plantarflexion and hip extension moments before and after IC. The plantarflexion deviation dissipated (50 ms post-IC) and was followed by excessive ankle inversion. The ankle began to plantarflex again (150 ms post-IC) and the knee extended (50 ms post-IC) and adducted (100 ms post-IC). As a result, the ankle inversion angle plateaued at 150 ms post-IC. Furthermore, large sagittal plane internal joint moments were observed. In the frontal plane, the ‘giving way’ trial generated a large inversion joint moment which was counteracted by a large internal eversion joint moment. The observed plantarflexion and knee extension and adduction after initial contact likely contributed to preventing the ankle from continuing to invert and avoid an ankle sprain.     

Parasitic ‘Candidatus Aquarickettsia rohweri’ is a marker of disease susceptibility in Acropora cervicornis but is lost during thermal stress

Holobiont phenotype results from a combination of host and symbiont genotypes as well as from prevailing environmental conditions that alter the relationships among symbiotic members. Corals exemplify this concept, where shifts in the algal symbiont community can lead to some corals becoming more or less thermally tolerant. Despite linkage between coral bleaching and disease, the roles of symbiotic bacteria in holobiont resistance and susceptibility to disease remains less well understood. This study thus characterizes the microbiome of disease-resistant and -susceptible Acropora cervicornis coral genotypes (hereafter referred to simply as ‘genotypes’) before and after high temperature-mediated bleaching. We found that the intracellular bacterial parasite ‘Ca. Aquarickettsia rohweri’ was strikingly abundant in disease-susceptible genotypes. Disease-resistant genotypes, however, had notably more diverse and even communities, with correspondingly low abundances of ‘Ca. Aquarickettsia’. Bleaching caused a dramatic reduction of ‘Ca. Aquarickettsia’ within disease-susceptible corals and led to an increase in bacterial community dispersion, as well as the proliferation of opportunists. Our data support the hypothesis that ‘Ca. Aquarickettsia’ species increase coral disease risk through two mechanisms: (i) the creation of host nutritional deficiencies leading to a compromised host-symbiont state and (ii) the opening of niche space for potential pathogens during thermal stress.