Nodal distances for rooted phylogenetic trees

Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. For rooted phylogenetic trees, however, these vectors can only separate non-weighted binary trees, and therefore these dissimilarity measures are metrics only on this class of rooted phylogenetic trees. In this paper we overcome this problem, by splitting in a suitable way each path length between two taxa into two lengths. We prove that the resulting splitted path lengths matrices single out arbitrary rooted phylogenetic trees with nested taxa and arcs weighted in the set of positive real numbers. This allows the definition of metrics on this general class of rooted phylogenetic trees by comparing these matrices through metrics in spaces M_n(\mathbb R){\mathcal{M}_n(\mathbb {R})} of real-valued n × n matrices. We conclude this paper by establishing some basic facts about the metrics for non-weighted phylogenetic trees defined in this way using L ^p metrics on M_n(\mathbb R){\mathcal{M}_n(\mathbb {R})}, with ${p \in \mathbb {R}_{ >0 }}${p \in \mathbb {R}_{ >0 }}.     

A high-level 3D visualization API for Java and ImageJ

Background  

Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set.     

Applauding with Closed Hands: Neural Signature of Action-Sentence Compatibility Effects

Background

Behavioral studies have provided evidence for an action–sentence compatibility effect (ACE) that suggests a coupling of motor mechanisms and action-sentence comprehension. When both processes are concurrent, the action sentence primes the actual movement, and simultaneously, the action affects comprehension. The aim of the present study was to investigate brain markers of bidirectional impact of language comprehension and motor processes.

Methodology/Principal Findings

Participants listened to sentences describing an action that involved an open hand, a closed hand, or no manual action. Each participant was asked to press a button to indicate his/her understanding of the sentence. Each participant was assigned a hand-shape, either closed or open, which had to be used to activate the button. There were two groups (depending on the assigned hand-shape) and three categories (compatible, incompatible and neutral) defined according to the compatibility between the response and the sentence. ACEs were found in both groups. Brain markers of semantic processing exhibited an N400-like component around the Cz electrode position. This component distinguishes between compatible and incompatible, with a greater negative deflection for incompatible. Motor response elicited a motor potential (MP) and a re-afferent potential (RAP), which are both enhanced in the compatible condition.

Conclusions/Significance

The present findings provide the first ACE cortical measurements of semantic processing and the motor response. N400-like effects suggest that incompatibility with motor processes interferes in sentence comprehension in a semantic fashion. Modulation of motor potentials (MP and RAP) revealed a multimodal semantic facilitation of the motor response. Both results provide neural evidence of an action-sentence bidirectional relationship. Our results suggest that ACE is not an epiphenomenal post-sentence comprehension process. In contrast, motor-language integration occurring during the verb onset supports a genuine and ongoing brain motor-language interaction.     

Mathematical modeling of tuberculosis bacillary counts and cellular populations in the organs of infected mice

Background

Mycobacterium tuberculosis is a particularly aggressive microorganism and the host''s defense is based on the induction of cellular immunity, in which the creation of a granulomatous structure has an important role.

Methodology

We present here a new 2D cellular automata model based on the concept of a multifunctional process that includes key factors such as the chemokine attraction of the cells; the role of innate immunity triggered by natural killers; the presence of neutrophils; apoptosis and necrosis of infected macrophages; the removal of dead cells by macrophages, which induces the production of foamy macrophages (FMs); the life cycle of the bacilli as a determinant for the evolution of infected macrophages; and the immune response.

Results

The results obtained after the inclusion of two degrees of tolerance to the inflammatory response triggered by the infection shows that the model can cover a wide spectrum, ranging from highly-tolerant (i.e. mice) to poorly-tolerant hosts (i.e. mini-pigs or humans).

Conclusions

This model suggest that stopping bacillary growth at the onset of the infection might be difficult and the important role played by FMs in bacillary drainage in poorly-tolerant hosts together with apoptosis and innate lymphocytes. It also shows the poor ability of the cellular immunity to control the infection, provides a clear protective character to the granuloma, due its ability to attract a sufficient number of cells, and explains why an already infected host can be constantly reinfected.     

Intragranulomatous necrosis in lungs of mice infected by aerosol with Mycobacterium tuberculosis is related to bacterial load rather than to any one cytokine or T cell type

Low dose aerosol infection of C57BL/6 mice with a clinical strain of Mycobacterium tuberculosis (UTE 0335 R) induced intragranulomatous necrosis in pulmonary granulomas (INPG) at week 9 postinfection. Infection of different knockout (KO) mouse strains with UTE 0335 R induced INPG in all strains and established two histopathological patterns. The first pattern was seen in SCID mice and in mice with deleted alpha/beta T receptor, TNF R1, IL-12, IFN-gamma, or iNOS genes, and showed a massive INPG with a high granulomatous infiltration of the lung, a large and homogeneous eosinophilic necrosis full of acid-fast bacilli, with marked karyorrhexis, coarse basophilic necrosis, and surrounded by patches delimited by partially conserved alveolar septum full of PMNs. The second pattern was seen in mice with deleted IL-1 R1, IL-6, IL-10, CD4, CD8 or gamma/delta T cell receptor genes, and showed more discrete lesions with predominant homogeneous eosinophilic necrosis with few bacilli and surrounded by a well-defined lymphocyte-based ring. Local expression of IFN-gamma, iNOS, TNF and RANTES showed no significant differences between these mouse strains generating a discrete INPG. Mouse strains showing a massive INPG showed higher, lower or equal expression values compared to the control strain. In conclusion, the severity of the INPG pattern correlated with pulmonary CFU counts, irrespective of the genetic absence or the infection-induced levels of cytokine mediators.     

Trophic Cascades Uncoupled in a Coastal Marsh Ecosystem

The Mediterranean population of the exotic eastern mosquitofish Gambusia holbrooki (Agassiz 1859) (Osteichthyes, Poeciliidae) has been held responsible for causing eutrophication due to zooplankton removal and phytoplankton enhancement, however no experimental evidence exists of this. To test this allegation, an enclosure experiment was conducted in spring in an oligohaline coastal marsh. The manipulation of fish density had profound effects on zooplankton, whose density greatly decreased when the occurrence of mosquitofish increased. Cladocerans and ostracods were more affected by mosquitofish than cyclopoid copepods, whilst rotifer density was not modified. Changes in zooplankton density did not cascade to lower trophic levels as no differences were observed between the chlorophyll concentration in fish and fish-less enclosures. This is because zooplankton was dominated by species with low filter-feeding rates, such as small cladocerans. In consequence, the total macrophyte standing crop was not affected. The only benthic macroinvertebrate species whose density increased in the absence of eastern mosquitofish was the mud snail P. acuta. Higher numbers of snails explain why the standing crop of the filamentous green algae Oedogonium sp. decreased in fish-less enclosures. The density of chironomid midge larvae did not increase in fish-less enclosures, because eastern mosquitofish forage on them mainly during summer, when zooplankton has already been depleted; nor were damselflies, probably because they are too large. Nitrogen concentration decreased after fish exclusion, but phosphorus concentration remain unchanged. In conclusion, it was found that the eastern mosquitofish affect zooplankton of the Mediterranean oligohaline lagoons considerably, but they do not enhance phytoplankton growth, because the system is bottom-controlled by submerged macrophytes.     

Early emergence of the FtsH proteases involved in photosystem II repair

Efficient degradation of damaged D1 during the repair of PSII is carried out by a set of dedicated FtsH proteases in the thylakoid membrane. Here we investigated whether the evolution of FtsH could hold clues to the origin of oxygenic photosynthesis. A phylogenetic analysis of over 6000 FtsH protease sequences revealed that there are three major groups of FtsH proteases originating from gene duplication events in the last common ancestor of bacteria, and that the FtsH proteases involved in PSII repair form a distinct clade branching out before the divergence of FtsH proteases found in all groups of anoxygenic phototrophic bacteria. Furthermore, we showed that the phylogenetic tree of FtsH proteases in phototrophic bacteria is similar to that for Type I and Type II reaction centre proteins. We conclude that the phylogeny of FtsH proteases is consistent with an early origin of photosynthetic water oxidation chemistry.     

seco-iridoids from Calycophyllum spruceanum (Rubiaceae)

Three seco-iridoids 7-methoxydiderroside, 6'-O-acetyldiderroside and 8-O-tigloyldiderroside, were isolated from the wood bark of Calycophyllum spruceanum together with the known iridoids loganetin, loganin and the seco-iridoids secoxyloganin, kingiside and diderroside. Their structures were elucidated by means of NMR and MS spectral data analysis. Using NOE correlations and coupling constants, the relative stereochemistry of the new derivatives was established. 7-Methoxydiderroside, 6'-O-acetyldiderroside and the known secoxyloganin and diderroside showed in vitro activity against trypomastigote forms of Trypanosoma cruzi, with IC(50) values of 59.0, 90.2, 74,2 and 84.9 microg/mL, respectively and were compared to the standard gentian violet (IC(50) 7.5 microg/ml).     

Resistance to Thrips palmi (Thysanoptera: Thripidae) in beans

Resistance in beans, Phaseolus vulgaris L., to the melon thrips Thrips palmi Karny was studied under field conditions at two sites in Colombia. Genotypes were rated for resistance on the basis of visual damage scores, bean production ratings (a visual estimate of pod and seed set), and grain yields. Of 1,138 genotypes tested, only 60 (5.3%) were rated as resistant. Repeated testing allowed us to identify potential sources of resistance in five germplasm accessions (G 02402, G 02852, G 03177, G 03569, and G 04055), one commercial variety ('Brunca'), six elite breeding lines (A 216, DOR 714, EMP 486, FEB 115, FEB 161, and FEB 162), 41 recombinant inbred lines derived from the BAT 881 x G 21212 cross, and seven recombinant inbred lines derived from a cross between DOR 364 and BAT 477. Resistance was not associated with maturity, growth habit, pubescence, and seed color or seed size. In general, correlations between visual damage scores and bean production ratings and between damage scores and yield were high and significant meaning that selection on damage rating is useful to identify genotypes that may have tolerance as a mechanism of resistance. The continuous distribution of damage scores of 139 recombinant inbred lines suggested that the inheritance of resistance to the melon thrips might be quantitative. Overall, resistance levels in beans can be considered as moderate, because none of the genotypes tested received damage scores of <3 on a 1-9 scale and none was ever rated as highly resistant in terms of bean production ratings.     

Gamma/delta T cell-deficient mice exhibit reduced disease severity and decreased inflammatory response in the brain in murine neurocysticercosis

In a recently developed mouse model for neurocysticercosis, the immune response was characterized by a massive influx of gammadelta T cells and a type 1 pathway of cytokine expression. To understand the role of gammadelta T cells during this infection, the cellular and cytokine response was analyzed in mice that lack gammadelta T cells (TCRdelta(-/-)). In TCRdelta(-/-) mice, Mesocestoides corti metacestodes preferentially invaded the extraparenchymal areas of the brain. Furthermore, parasites were able to escape from the brain and establish a systemic infection with liver and peritoneal involvement. Immunopathological studies indicated that TCRdelta(-/-) mice develop little inflammatory response and less neurological symptomatology. Significantly reduced numbers of T cells, macrophages, dendritic cells, and mast cells were present in the brain. The cytokine response in the brain of TCRdelta(-/-) mice appears to be a mixed type1/type 2 response with low levels of IL-2, IL-4, IL-10, IL-12, IL-13, IL-15, and IFN-gamma. To further investigate the immunological significance of this cell population, gammadelta T cells were adoptively transferred into intracranially infected TCRdelta(-/-) mice. gammadelta T cells were specifically recruited into the CNS in response to this parasitic infection, and they were able to target the infected brain within 12 h after transfer. These results suggest that gammadelta T cells are key players in the immune response elicited during this CNS infection and direct a type 1 response in wild-type mice upon infection.