Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

Background

Although it has proven to be an important foundation for investigations of carnivoran ecology, biology and evolution, the complete species-level supertree for Carnivora of Bininda-Emonds et al. is showing its age. Additional, largely molecular sequence data are now available for many species and the advancement of computer technology means that many of the limitations of the original analysis can now be avoided. We therefore sought to provide an updated estimate of the phylogenetic relationships within all extant Carnivora, again using supertree analysis to be able to analyze as much of the global phylogenetic database for the group as possible.

Results

In total, 188 source trees were combined, representing 114 trees from the literature together with 74 newly constructed gene trees derived from nearly 45,000 bp of sequence data from GenBank. The greater availability of sequence data means that the new supertree is almost completely resolved and also better reflects current phylogenetic opinion (for example, supporting a monophyletic Mephitidae, Eupleridae and Prionodontidae; placing Nandinia binotata as sister to the remaining Feliformia). Following an initial rapid radiation, diversification rate analyses indicate a downturn in the net speciation rate within the past three million years as well as a possible increase some 18.0 million years ago; numerous diversification rate shifts within the order were also identified.

Conclusions

Together, the two carnivore supertrees remain the only complete phylogenetic estimates for all extant species and the new supertree, like the old one, will form a key tool in helping us to further understand the biology of this charismatic group of carnivores.     

Electromechanical Models of the Outer Hair Cell Composite Membrane

The outer hair cell (OHC) is an extremely specialized cell and its proper functioning is essential for normal mammalian hearing. This article reviews recent developments in theoretical modeling that have increased our knowledge of the operation of this fascinating cell. The earliest models aimed at capturing experimental observations on voltage-induced cellular length changes and capacitance were based on isotropic elasticity and a two-state Boltzmann function. Recent advances in modeling based on the thermodynamics of orthotropic electroelastic materials better capture the cell’s voltage-dependent stiffness, capacitance, interaction with its environment and ability to generate force at high frequencies. While complete models are crucial, simpler continuum models can be derived that retain fidelity over small changes in transmembrane voltage and strains occurring in vivo. By its function in the cochlea, the OHC behaves like a piezoelectric-like actuator, and the main cellular features can be described by piezoelectric models. However, a finer characterization of the cell’s composite wall requires understanding the local mechanical and electrical fields. One of the key questions is the relative contribution of the in-plane and bending modes of electromechanical strains and forces (moments). The latter mode is associated with the flexoelectric effect in curved membranes. New data, including a novel experiment with tethers pulled from the cell membrane, can help in estimating the role of different modes of electromechanical coupling. Despite considerable progress, many problems still confound modelers. Thus, this article will conclude with a discussion of unanswered questions and highlight directions for future research.     

Solvers for the cardiac bidomain equations

The bidomain equations are widely used for the simulation of electrical activity in cardiac tissue. They are especially important for accurately modeling extracellular stimulation, as evidenced by their prediction of virtual electrode polarization before experimental verification. However, solution of the equations is computationally expensive due to the fine spatial and temporal discretization needed. This limits the size and duration of the problem which can be modeled. Regardless of the specific form into which they are cast, the computational bottleneck becomes the repeated solution of a large, linear system. The purpose of this review is to give an overview of the equations and the methods by which they have been solved. Of particular note are recent developments in multigrid methods, which have proven to be the most efficient.     

Fermentation characterization and flux analysis of recombinant strains of Clostridium acetobutylicum with an inactivated solR gene

The effect of solR inactivation on the metabolism of Clostridium acetobutylicum was examined using fermentation characterization and metabolic flux analysis. The solR-inactivated strain (SolRH) of this study had a higher rate of glucose utilization and produced higher solvent concentrations (by 25%, 14%, and 81%, respectively, for butanol, acetone, and ethanol) compared to the wild type. Strain SolRH(pTAAD), carrying a plasmid-encoded copy of the bifunctional alcohol/aldehyde dehydrogenase gene (aad) used in butanol production, produced even higher concentrations of solvents (by 21%, 45%, and 62%, respectively, for butanol, acetone, and ethanol) than strain SolRH. Clarithromycin used for strain SolRH maintenance during SolRH(pTAAD) fermentations did not alter product formation; however, tetracycline used for pTAAD maintenance resulted in 90% lower solvent production. Journal of Industrial Microbiology & Biotechnology (2001) 27, 322–328. Received 12 September 2000/ Accepted in revised form 21 July 2001     

Polygalacturonase Inhibiting Proteins (PGIPs) of Plants

Polygalacturonase inhibiting proteins (PGIPs) are widely distributed in plants and appear to play an important role in protection of plants from fungal infection and also in maturation and ripening of fruits. They are leucine rich thermostable glycoproteins of about 40 kD and exhibit differential inhibition of polygalacturonases from different sources. A lot of attention is now being paid to these proteins with respect to their physicochemical and biological properties and also to their genes. These proteins show a lot of sequence homology to several signal transduction molecules from diverse species and have been suggested to play a similar role in plants. These proteins are also potentially important from biotechnological perspective. This review focuses on the recent work carried on PGIPs and its implications.     

Rotifera from Burundi: the Lepadellidae (Rotifera: Monogononta)

We studied the distribution of Lepadellidae (Rotifera) in freshwater habitats in the floodplain of the River Rusizi in northwest Burundi. Twenty-three species belonging to ColurellaBory de St. Vincent, 1824 (3 species), Lepadella Bory de St. Vincent, 1826 (18 species) and Squatinella Bory de St. Vincent, 1826 (2 species) are recorded, 22 of them are new to Burundi. One of the taxa encountered probably represents an unnamed species. Lepadella arabicaSegers & Dumont, 1993 is recognised as junior subjective synonym of Lepadella eurysterna Myers, 1942 (syn. nov.). Most of the taxa recorded are cosmopolitan or tropicopolitan, two are restricted to the tropical regions of the Old World and Australia, and one, Squatinella lunata Segers, 1993 is an Ethiopian endemic.     

Thermocyclops dumonti sp. n. (Crustacea,Copepoda), from a Temporary Waterbody in China

Six species of the genus Thermocyclops have hitherto been known from Chinese freshwaters. A new species is here recorded from a sample collected from an eutrophic pool in central China. It is described and compared using classical morphology and mapping of its pore signature. Thermocyclops dumonti differs from T. kawamurai by absence of ornamentation on prominences of intercoxal plates of P₁‐P₃, by relative length of apical spines of Enp₃P₄ and caudal ramus. It differs from T. dybowskii by ornamentation of P₄ intercoxal plate, relative length of Enp₃P₄ and caudal ramus, by shape of Tmi. As in other species of Thermocyclops, the perforations are bilaterally symmetrical and, species‐specific patterns occur on the cephalosome, metasome, and urosome. Conserved patterns are found elsewhere on the rostrum, cephalosome, metasome, and furcal branches. Based on pore pattern, Thermocyclops dumonti is separated from two close relatives, T. schmeili and T. dybowskii.     

C-terminal and n-terminal fusions of aequorin with small peptides in immunoassay development

Aequorin fusion proteins have been used extensively in intracellular Ca2+ measurements and in the development of binding assays. Gene fusions to aequorin for production of fusion proteins have been so far limited to its N-terminus, as previous studies have indicated that aequorin loses its activity upon modification of its C-terminus. To further investigate this, two model peptides, an octapeptide (DTLDDDDL), and leu-enkephalin (TGGFL), an opioid peptide, were fused to the C-terminus of a cysteine-free mutant of aequorin through genetic engineering. The octapeptide was also fused to the N-terminus of the aequorin-leu-enkephalin fusion protein, which enables its affinity purification. Contrary to reports of earlier studies, we found that aequorin retains its bioluminescence activity after modification of the C-terminus. The half-life of light emission and the calibration curves obtained with the fusion proteins were comparable to those of the cysteine-free mutant of aequorin. Dose-response curves for the octapeptide were generated using two aequorin-octapeptide fusion proteins with the octapeptide fused to the N-terminus in one case, and to the C-terminus in the other. Similar detection limits for the octapeptide were obtained using both fusion proteins. The C-terminal fusion system has advantages in cases where antibodies recognize only the C-terminus of the peptide, as well as in cases where the functionality of the peptide lies in its C-terminus. The purification is also simplified as the affinity tag can be engineered at one terminus and the peptide of interest at the other.     

Transgenic indica rice expressing Mirabilis jalapa antimicrobial protein (Mj-AMP2) shows enhanced resistance to the rice blast fungus Magnaporthe oryzae

Mj-AMP2, a knottin-type antimicrobial peptide, in vitro inhibits the growth of several plant pathogenic fungi including Magnaporthe oryzae. We demonstrate that transgenic rice (Oryza sativa L.) plants expressing the Mj-AMP2 gene show enhanced resistance to M. grisea, the causal agent of the rice blast disease. Mj-AMP2 was efficiently expressed and the level of Mj-AMP2 ranged from 0.32% to 0.38% of the total protein in the transgenic rice plants. In vitro inhibitory activity assays with the crude protein extract from transgenic rice indicated that the Mj-AMP2 protein produced was biologically active. Constitutive expression of Mj-AMP2 in transgenic rice reduces the growth of M. grisea by 63% with respect to untransformed control plant, and no effect on plant phenotype was observed. Transgene expression of Mj-AMP2 gene was not accompanied by an induction of pathogenesis-related (PR) gene expression indicating that the transgene product itself is directly active against the pathogen. The results presented in this study suggest that the Mj-AMP2 gene could be a useful candidate for protection of rice plants against the rice blast fungus M. grisea.     

Type 1 and Type 2 Epstein-Barr viruses induce proliferation,and inhibit differentiation,in infected telomerase-immortalized normal oral keratinocytes

Differentiated epithelial cells are an important source of infectious EBV virions in human saliva, and latent Epstein-Barr virus (EBV) infection is strongly associated with the epithelial cell tumor, nasopharyngeal carcinoma (NPC). However, it has been difficult to model how EBV contributes to NPC, since EBV has not been shown to enhance proliferation of epithelial cells in monolayer culture in vitro and is not stably maintained in epithelial cells without antibiotic selection. In addition, although there are two major types of EBV (type 1 (T1) and type 2 (T2)), it is currently unknown whether T1 and T2 EBV behave differently in epithelial cells. Here we inserted a G418 resistance gene into the T2 EBV strain, AG876, allowing us to compare the phenotypes of T1 Akata virus versus T2 AG876 virus in a telomerase-immortalized normal oral keratinocyte cell line (NOKs) using a variety of different methods, including RNA-seq analysis, proliferation assays, immunoblot analyses, and air-liquid interface culture. We show that both T1 Akata virus infection and T2 AG876 virus infection of NOKs induce cellular proliferation, and inhibit spontaneous differentiation, in comparison to the uninfected cells when cells are grown without supplemental growth factors in monolayer culture. T1 EBV and T2 EBV also have a similar ability to induce epithelial-to-mesenchymal (EMT) transition and activate canonical and non-canonical NF-κB signaling in infected NOKs. In contrast to our recent results in EBV-infected lymphoblastoid cells (in which T2 EBV infection is much more lytic than T1 EBV infection), we find that NOKs infected with T1 and T2 EBV respond similarly to lytic inducing agents such as TPA treatment or differentiation. These results suggest that T1 and T2 EBV have similar phenotypes in infected epithelial cells, with both EBV types enhancing cellular proliferation and inhibiting differentiation when growth factors are limiting.