New Insights into Old Lemurs: The Trophic Adaptations of the Archaeolemuridae

Modern tools of paleoecological and ecomorphological research have enabled researchers to reconstruct the lifeways of extinct species more thoroughly than ever before. We apply a variety of tools in an attempt to reconstruct the diets of the extinct archaeolemurids of Madagascar. Our data include dental use wear (examined across species and across ontogenetic series of single species), enamel microstructure, enamel thickness, and δ¹³C. The data are complemented by field data on the environmental contexts in which the species lived and ¹⁴C determinations that demonstrate the surprisingly late survival of archaeolemurids. Several lines of evidence converge to suggest that all archaeolemurid species were hard-object processors, but with different diets and different methods of food processing. Past reconstructions of the diet of Hadropithecus as a specialized grass consumer fail under the scrutiny of multiple lines of evidence.     

Robust Unidirectional Airflow through Avian Lungs: New Insights from a Piecewise Linear Mathematical Model

Avian lungs are remarkably different from mammalian lungs in that air flows unidirectionally through rigid tubes in which gas exchange occurs. Experimental observations have been able to determine the pattern of gas flow in the respiratory system, but understanding how the flow pattern is generated and determining the factors contributing to the observed dynamics remains elusive. It has been hypothesized that the unidirectional flow is due to aerodynamic valving during inspiration and expiration, resulting from the anatomical structure and the fluid dynamics involved, however, theoretical studies to back up this hypothesis are lacking. We have constructed a novel mathematical model of the airflow in the avian respiratory system that can produce unidirectional flow which is robust to changes in model parameters, breathing frequency and breathing amplitude. The model consists of two piecewise linear ordinary differential equations with lumped parameters and discontinuous, flow-dependent resistances that mimic the experimental observations. Using dynamical systems techniques and numerical analysis, we show that unidirectional flow can be produced by either effective inspiratory or effective expiratory valving, but that both inspiratory and expiratory valving are required to produce the high efficiencies of flows observed in avian lungs. We further show that the efficacy of the inspiratory and expiratory valving depends on airsac compliances and airflow resistances that may not be located in the immediate area of the valving. Our model provides additional novel insights; for example, we show that physiologically realistic resistance values lead to efficiencies that are close to maximum, and that when the relative lumped compliances of the caudal and cranial airsacs vary, it affects the timing of the airflow across the gas exchange area. These and other insights obtained by our study significantly enhance our understanding of the operation of the avian respiratory system.     

Mechano-electrical Transduction: New Insights into Old Ideas

The gating-spring theory of hair cell mechanotransduction channel activation was first postulated over twenty years ago. The basic tenets of this hypothesis have been reaffirmed in hair cells from both auditory and vestibular systems and across species. In fact, the basic findings have been reproduced in every hair cell type tested. A great deal of information regarding the structural, mechanical, molecular and biophysical properties of the sensory hair bundle and the mechanotransducer channel has accumulated over the past twenty years. The goal of this review is to investigate new data, using the gating spring hypothesis as the framework for discussion. Mechanisms of channel gating are presented in reference to the need for a molecular gating spring or for tethering to the intra- or extracellular compartments. Dynamics of the sensory hair bundle and the presence of motor proteins are discussed in reference to passive contributions of the hair bundle to gating compliance. And finally, the molecular identity of the channel is discussed in reference to known intrinsic properties of the native transducer channel.     

New Insights into the Ligninolytic Capability of a Wood Decay Ascomycete

Wood-grown cultures of Daldinia concentrica oxidized a permethylated β-¹⁴C-labeled synthetic lignin to ¹⁴CO₂ and also cleaved a permethylated α-¹³C-labeled synthetic lignin to give C_α-C_β cleavage products that were detected by ¹³C nuclear magnetic resonance spectrometry. Therefore, this ascomycete resembles white-rot basidiomycetes in attacking the recalcitrant nonphenolic structures that predominate in lignin.     

New Insights into the Diversity of Marine Picoeukaryotes

Over the last decade, culture-independent surveys of marine picoeukaryotic diversity based on 18S ribosomal DNA clone libraries have unveiled numerous sequences of novel high-rank taxa. This newfound diversity has significantly altered our understanding of marine microbial food webs and the evolution of eukaryotes. However, the current picture of marine eukaryotic biodiversity may be significantly skewed by PCR amplification biases, occurrence of rDNA genes in multiple copies within a single cell, and the capacity of DNA to persist as extracellular material. In this study we performed an analysis of the metagenomic dataset from the Global Ocean Survey (GOS) expedition, seeking eukaryotic ribosomal signatures. This PCR-free approach revealed similar phylogenetic patterns to clone library surveys, suggesting that PCR steps do not impose major biases in the exploration of environmental DNA. The different cell size fractions within the GOS dataset, however, displayed a distinct picture. High protistan diversity in the <0.8 µm size fraction, in particular sequences from radiolarians and ciliates (and their absence in the 0.8–3 µm fraction), suggest that most of the DNA in this fraction comes from extracellular material from larger cells. In addition, we compared the phylogenetic patterns from rDNA and reverse transcribed rRNA 18S clone libraries from the same sample harvested in the Mediterranean Sea. The libraries revealed major differences, with taxa such as pelagophytes or picobiliphytes only detected in the 18S rRNA library. MAST (Marine Stramenopiles) appeared as potentially prominent grazers and we observed a significant decrease in the contribution of alveolate and radiolarian sequences, which overwhelmingly dominated rDNA libraries. The rRNA approach appears to be less affected by taxon-specific rDNA copy number and likely better depicts the biogeochemical significance of marine protists.     

Integrating Ontogeny of Echolocation and Locomotion Gives Unique Insights into the Origin of Bats

The evolutionary sequence of events that led to flight and echolocation in bats is a compelling question in biology. Fundamentally lacking from this discussion is the ontogeny of how these two systems become functionally integrated producing an evolutionary developmental model. We build such a model by integrating growth and development of the cochlea, larynx, and sound production with the ontogeny of locomotion in newborn bats. In addition, we use available fossil and molecular data along with patterns of high frequency vocalization in extant mammals to model probable evolutionary transitions in bats. We find clear evidence that the ability to hear high frequency echolocation-like sounds preceded the ability to produce it and that a simple echolocation system was likely inherited from a shrew-like ancestor and was not an in situ evolutionary innovation of bats. Refinement of this system coevolved with sustained flight, both ontogenetically and evolutionarily, leading to the sophisticated echolocation observed today.     

Discovery of Unique Lanthionine Synthetases Reveals New Mechanistic and Evolutionary Insights

Lantibiotic synthetases are remarkable biocatalysts generating conformationally constrained peptides with a variety of biological activities by repeatedly utilizing two simple posttranslational modification reactions: dehydration of Ser/Thr residues and intramolecular addition of Cys thiols to the resulting dehydro amino acids. Since previously reported lantibiotic synthetases show no apparent homology with any other known protein families, the molecular mechanisms and evolutionary origin of these enzymes are unknown. In this study, we present a novel class of lanthionine synthetases, termed LanL, that consist of three distinct catalytic domains and demonstrate in vitro enzyme activity of a family member from Streptomyces venezuelae. Analysis of individually expressed and purified domains shows that LanL enzymes install dehydroamino acids via phosphorylation of Ser/Thr residues by a protein kinase domain and subsequent elimination of the phosphate by a phosphoSer/Thr lyase domain. The latter has sequence homology with the phosphothreonine lyases found in various pathogenic bacteria that inactivate host mitogen activated protein kinases. A LanC-like cyclase domain then catalyzes the addition of Cys residues to the dehydro amino acids to form the characteristic thioether rings. We propose that LanL enzymes have evolved from stand-alone protein Ser/Thr kinases, phosphoSer/Thr lyases, and enzymes catalyzing thiol alkylation. We also demonstrate that the genes for all three pathways to lanthionine-containing peptides are widespread in Nature. Given the remarkable efficiency of formation of lanthionine-containing polycyclic peptides and the latter''s high degree of specificity for their cognate cellular targets, it is perhaps not surprising that (at least) three distinct families of polypeptide sequences have evolved to access this structurally and functionally diverse class of compounds.     

Population Genetics of the Filarial Worm Wuchereria bancrofti in a Post-treatment Region of Papua New Guinea: Insights into Diversity and Life History

Background

Wuchereria bancrofti (Wb) is the primary causative agent of lymphatic filariasis (LF). Our studies of LF in Papua New Guinea (PNG) have shown that it is possible to reduce the prevalence of Wb in humans and mosquitoes through mass drug administration (MDA; diethylcarbamazine with/without ivermectin). While MDAs in the Dreikikir region through 1998 significantly reduced prevalence of Wb infection, parasites continue to be transmitted in the area.

Methods

We sequenced the Wb mitochondrial Cytochrome Oxidase 1 (CO1) gene from 16 people infected with Wb. Patients were selected from 7 villages encompassing both high and moderate annual transmission potentials (ATP). We collected genetic data with the objectives to (i) document contemporary levels of genetic diversity and (ii) distinguish between populations of parasites and hosts across the study area.

Principle Findings

We discovered 109 unique haplotypes currently segregating in the Wb parasite population, with one common haplotype present in 15 out of 16 infections. We found that parasite diversity was similar among people residing within the same village and clustered within transmission zones. For example, in the high transmission area, diversity tended to be more similar between neighboring villages, while in the moderate transmission area, diversity tended to be less similar.

Conclusions

In the Dreikikir region of PNG there are currently high levels of genetic diversity in populations of Wb. High levels of genetic diversity may complicate future MDAs in this region and the presence of dominant haplotypes will require adjustments to current elimination strategies.     

First Passage Time Analysis of Animal Movement and Insights into the Functional Response

Movement plays a role in structuring the interactions between individuals, their environment, and other species. Although movement models coupled with empirical data are widely used to study animal distribution, they have seldom been used to study search time. This paper proposes first passage time as a novel approach for understanding the effect of the landscape on animal movement and search time. In the context of animal movement, first passage time is the time taken for an animal to reach a specified site for the first time. We synthesize current first passage time theory and derive a general first passage time equation for animal movement. This equation is related to the Fokker–Planck equation, which is used to describe the distribution of animals in the landscape. We illustrate the first passage time method by analyzing the effect of territorial behavior on the time required for a red fox to locate prey throughout its home range. Using first passage time to compute search times, we consider the effect of two different searching modes on a functional response. We show that random searching leads to a Holling type III functional response. First passage time analysis provides a new tool for studying how animal movement may influence ecological processes.     

Single-Molecule Fluorescence Studies of a PH Domain: New Insights into the Membrane Docking Reaction

Proteins containing membrane targeting domains play essential roles in many cellular signaling pathways. However, important features of the membrane-bound state are invisible to bulk methods, thereby hindering mechanistic analysis of membrane targeting reactions. Here we use total internal reflection fluorescence microscopy (TIRFM), combined with single particle tracking, to probe the membrane docking mechanism of a representative pleckstrin homology (PH) domain isolated from the general receptor for phosphoinositides, isoform 1 (GRP1). The findings show three previously undescribed features of GRP1 PH domain docking to membranes containing its rare target lipid, phosphatidylinositol (3,4,5)-trisphosphate [PI(3,4,5)P₃]. First, analysis of surface diffusion kinetics on supported lipid bilayers shows that in the absence of other anionic lipids, the PI(3,4,5)P₃-bound protein exhibits the same diffusion constant as a single lipid molecule. Second, the binding of the anionic lipid phosphatidylserine to a previously unidentified secondary binding site slows both diffusion and dissociation kinetics. Third, TIRFM enables direct observation of rare events in which dissociation from the membrane surface is followed by transient diffusion through solution and rapid rebinding to a nearby, membrane-associated target lipid. Overall, this study shows that in vitro single-molecule TIRFM provides a new window into the molecular mechanisms of membrane docking reactions.     

Structural Insights into the Low pH Adaptation of a Unique Carboxylesterase from Ferroplasma: ALTERING THE pH OPTIMA OF TWO CARBOXYLESTERASES

To investigate the mechanism for low pH adaptation by a carboxylesterase, structural and biochemical analyses of EstFa_R (a recombinant, slightly acidophilic carboxylesterase from Ferroplasma acidiphilum) and SshEstI (an alkaliphilic carboxylesterase from Sulfolobus shibatae DSM5389) were performed. Although a previous proteomics study by another group showed that the enzyme purified from F. acidiphilum contained an iron atom, EstFa_R did not bind to iron as analyzed by inductively coupled plasma MS and isothermal titration calorimetry. The crystal structures of EstFa_R and SshEstI were determined at 1.6- and 1.5-Å resolutions, respectively. EstFa_R had a catalytic triad with an extended hydrogen bond network that was not observed in SshEstI. Quadruple mutants of both proteins were created to remove or introduce the extended hydrogen bond network. The mutation on EstFa_R enhanced its catalytic efficiency and gave it an alkaline pH optimum, whereas the mutation on SshEstI resulted in opposite effects (i.e. a decrease in the catalytic efficiency and a downward shift in the optimum pH). Our experimental results suggest that the low pH optimum of EstFa_R activity was a result of the unique extended hydrogen bond network in the catalytic triad and the highly negatively charged surface around the active site. The change in the pH optimum of EstFa_R happened simultaneously with a change in the catalytic efficiency, suggesting that the local flexibility of the active site in EstFa_R could be modified by quadruple mutation. These observations may provide a novel strategy to elucidate the low pH adaptation of serine hydrolases.     

New Insights into the Methodology of L-Arginine-Induced Acute Pancreatitis

Animal models are ideal to study the pathomechanism and therapy of acute pancreatitis (AP). The use of L-arginine-induced AP model is nowadays becoming increasingly popular in mice. However, carefully looking through the literature, marked differences in disease severity could be observed. In fact, while setting up the L-arginine (2×4 g/kg i.p.)-induced AP model in BALB/c mice, we found a relatively low rate (around 15%) of pancreatic necrosis, whereas others have detected much higher rates (up to 55%). We suspected that this may be due to differences between mouse strains. We administered various concentrations (5–30%, pH = 7.4) and doses (2×4, 3×3, or 4×2.5 g/kg) of L-arginine-HCl in BALB/c, FVB/n and C57BL/6 mice. The potential gender-specific effect of L-arginine was investigated in C57BL/6 mice. The fate of mice in response to the i.p. injections of L arginine followed one of three courses. Some mice (1) developed severe AP or (2) remained AP-free by 72 h, whereas others (3) had to be euthanized (to avoid their death, which was caused by the high dose of L-arginine and not AP) within 12 h., In FVB/n and C57BL/6 mice, the pancreatic necrosis rate (about 50%) was significantly higher than that observed in BALB/c mice using 2×4 g/kg 10% L–arginine, but euthanasia was necessary in a large proportion of animals, The i.p. injection of lower L-arginine concentrations (e.g. 5–8%) in case of the 2×4 g/kg dose, or other L-arginine doses (3×3 or 4×2.5 g/kg, 10%) were better for inducing AP. We could not detect any significant differences between the AP severity of male and female mice. Taken together, when setting up the L-arginine-induced AP model, there are several important factors that are worth consideration such as the dose and concentration of the administered L arginine-HCl solution and also the strain of mice.     

Insights into a mummy: a paleoradiological analysis

The aim of the study was to analyze possible human skeletal remains within the wrappings of a mummy from the Archaeological Museum, Zagreb, Croatia through the use of the multidetector CT (MDCT) technology. Plain X-ray films and MDCT images of the mummy were taken in both frontal and lateral views. In a single volumetric acquisition of the whole body by MDCT 0.75 mm axial slices were obtained and combined with sagittal and coronal reformatting and three-dimensional (3D) reconstruction. Sex and age was assessed visually using standard anthropological methods. The results suggest that the mummy was of an adult female, most likely over 40 years of age at death. Pathologies observed included degenerative changes on the vertebral column and healed fractures of the lower right arm. Damage of the ethmoid bone at the roof of the nasal cavity was most likely caused by mortuary brain removal practice. Remnants of a resin and an unusual object were found inside the cranial cavity. An elongated metal object and additional three metal "belts" can be seen on the lower portion of the body. All internal organs were removed and thoracic and abdominal cavities were filled with various substances, most likely mud and pieces of linen cloth. Our results show that the MDCT is a very useful technique for assessing the human remains in archeological samples, especially in comparison to the use of plain film (X-ray), where important details are obscured and 3D imaging impossible.