Variation in genome organization of the plant pathogenic fungus Colletotrichum lindemuthianum

The genome structure of Colletotrichum lindemuthianum in a set of diverse isolates was investigated using a combination of physical and molecular approaches. Flow cytometric measurement of genome size revealed significant variation between strains, with the smallest genome representing 59% of the largest. Southern-blot profiles of a cloned fungal telomere revealed a total chromosome number varying from 9 to 12. Chromosome separations using pulsed-field gel electrophoresis (PFGE) showed that these chromosomes belong to two distinct size classes: a variable number of small (< 2.5 Mb) polymorphic chromosomes and a set of unresolved chromosomes larger than 7 Mb. Two dispersed repeat elements were shown to cluster on distinct polymorphic minichromosomes. Single-copy flanking sequences from these repeat-containing clones specifically marked distinct small chromosomes. These markers were absent in some strains, indicating that part of the observed variability in genome organization may be explained by the presence or absence, in a given strain, of dispensable genomic regions and/or chromosomes.

Flexibility of representational states in working memory

The relationship between working memory (WM) and attention is a highly interdependent one, with evidence that attention determines the state in which items in WM are retained. Through focusing of attention, an item might be held in a more prioritized state, commonly termed as the focus of attention (FOA). The remaining items, although still retrievable, are considered to be in a different representational state. One means to bring an item into the FOA is to use retrospective cues (‘retro-cues’) which direct attention to one of the objects retained in WM. Alternatively, an item can enter a privileged state once attention is directed towards it through bottom-up influences (e.g. recency effect) or by performing an action on one of the retained items (‘incidental’ cueing). In all these cases, the item in the FOA is recalled with better accuracy compared to the other items in WM. Far less is known about the nature of the other items in WM and whether they can be flexibly manipulated in and out of the FOA. We present data from three types of experiments as well as transcranial magnetic stimulation to early visual cortex to manipulate the item inside FOA. Taken together, our results suggest that the context in which items are retained in WM matters. When an item remains behaviourally relevant, despite not being inside the FOA, re-focusing attention upon it can increase its recall precision. This suggests that a non-FOA item can be held in a state in which it can be later retrieved. However, if an item is rendered behaviourally unimportant because it is very unlikely to be probed, it cannot be brought back into the FOA, nor recalled with high precision. Under such conditions, some information appears to be irretrievably lost from WM. These findings, obtained from several different methods, demonstrate quite considerable flexibility with which items in WM can be represented depending upon context. They have important consequences for emerging state-dependent models of WM.

Geographical distribution of American cutaneous leishmaniasis and its phlebotomine vectors (Diptera: Psychodidae) in the state of Sao Paulo, Brazil

Background: American cutaneous leishmaniasis (ACL) is a re-emerging disease in the state of Sao Paulo, Brazil. It is important to understand both the vector and disease distribution to help design control strategies. As an initial step in applying geographic information systems (GIS) and remote sensing (RS) tools to map disease-risk, the objectives of the present work were to: (i) produce a single database of species distributions of the sand fly vectors in the state of Sao Paulo, (ii) create combined distributional maps of both the incidence of ACL and its sand fly vectors, and (iii) thereby provide individual municipalities with a source of reference material for work carried out in their area. Results: A database containing 910 individual records of sand fly occurrence in the state of Sao Paulo, from 37 different sources, was compiled. These records date from between 1943 to 2009, and describe the presence of at least one of the six incriminated or suspected sand fly vector species in 183/645 (28.4%) municipalities. For the remaining 462 (71.6%) municipalities, we were unable to locate records of any of the six incriminated or suspected sand fly vector species (Nyssomyia intermedia, N. neivai, N. whitmani, Pintomyia fischeri, P. pessoai and Migonemyia migonei). The distribution of each of the six incriminated or suspected vector species of ACL in the state of Sao Paulo were individually mapped and overlaid on the incidence of ACL for the period 1993 to 1995 and 1998 to 2007. Overall, the maps reveal that the six sand fly vector species analyzed have unique and heterogeneous, although often overlapping, distributions. Several sand fly species - Nyssomyia intermedia and N. neivai - are highly localized, while the other sand fly species - N. whitmani, M. migonei, P. fischeri and P. pessoai - are much more broadly distributed. ACL has been reported in 160/183 (87.4%) of the municipalities with records for at least one of the six incriminated or suspected sand fly vector species, while there are no records of any of these sand fly species in 318/478 (66.5%) municipalities with ACL. Conclusions: The maps produced in this work provide basic data on the distribution of the six incriminated or suspected sand fly vectors of ACL in the state of Sao Paulo, and highlight the complex and geographically heterogeneous pattern of ACL transmission in the region. Further studies are required to clarify the role of each of the six suspected sand fly vector species in different regions of the state of Sao Paulo, especially in the majority of municipalities where ACL is present but sand fly vectors have not yet been identified.

Survival, Population Size, and Gonotrophic Cycle Duration of Nyssomyia neivai (Diptera: Psychodidae) at an Endemic Area of American Cutaneous Leishmaniasis in Southeastern Brazil

The survival, absolute population size, gonotrophic cycle duration, and temporal and spatial abundance of Nyssomyia neivai (Pinto) were studied in a rural area endemic for American cutaneous leishmaniasis (ACL) in Conchal, Sao Paulo State, southeastern Brazil, using mark-release-recapture techniques and by monitoring population fluctuation. The monthly abundance exhibited a unimodal pattern, with forest and domicile habitats having the highest relative abundances. A total of 1,873 males and 3,557 females were marked and released during the six experiments, of which 4.1-13.0% of males and 4.1-11.8% of females were recaptured. Daily survivorship estimated from the decline in recaptures per day was 0.681 for males and 0.667 for females. Gonotrophic cycle duration was estimated to be 4.0 d. Absolute population size was calculated using the Lincoln Index and ranged from 861 to 4,612 males and from 2,187 to 19,739 females. The low proportion of females that reach the age when they are potentially infective suggests that N. neivai has a low biological capacity to serve as a vector and that factors such as high biting rates and opportunistic feeding behavior would be needed to enable Leishmania (Viannia) braziliensis Vianna transmission. This agreed with the epidemiological pattern of ACL in southeastern Brazil that is characterized by low incidence, with isolated cases acquired principally within domiciliary habitats.

Social organization of marine Tucuxi dolphins, Sotalia guianensis, in the Cananeia Estuary of southeastern Brazil

Social organization is an important component of the population biology of a species that influences gene flow, the spatial pattern and scale of movements, and the effects of predation or exploitation by humans. An important element of social structure in mammals is group fidelity, which can be quantified through association indices. To describe the social organization of marine tucuxi dolphins (Sotalia guianensis) found in the Cananeia estuary, southeastern Brazil, association indices were applied to photo-identification data to characterize the temporal stability of relationships among members of this population. Eighty-seven days of fieldwork were conducted from May 2000 to July 2003, resulting in direct observations of 374 distinct groups. A total of 138 dolphins were identified on 1-38 distinct field days. Lone dolphins were rarely seen, whereas groups were composed of up to 60 individuals (mean +/- 1 SD = 12.4 +/- 11.4 individuals per group). A total of 29,327 photographs were analyzed, of which 6,312 (21.5%) were considered useful for identifying individuals. Half-weight and simple ratio indices were used to investigate associations among S. guianensis as revealed by the entire data set, data from the core study site, and data from groups composed of <= 10 individuals. Monte Carlo methods indicated that only 3 (9.3%) of 32 association matrices differed significantly from expectations based on random association. Thus, our study suggests that stable associations are not characteristic of S. guianensis in the Cananeia estuary.

A real-time polymerase chain reaction assay for the identification and quantification of American Leishmania species on the basis of glucose-6-phosphate dehydrogenase

A real-time polymerase chain reaction (PCR) test was developed on the basis of the Leishmania glucose-6-phosphate dehydrogenase locus that enables identification and quantification of parasites. Using two independent pairs of primers in SYBR-Green assays, the test identified etiologic agents of cutaneous leishmaniasis belonging to both subgenera, Leishmania (Viannia) and Leishmania (Leishmania) in the Americas. Furthermore, use of TaqMan probes enables distinction between L. (V.) braziliensis or L. (V.) peruviania from the other L. (Viannia) species. All assays were negative with DNA of related trypanosomatids, humans, and mice. The parasite burden was estimated by normalizing the number of organisms per total amount of DNA in the sample or per host glyceraldehyde-3-phosphate dehydrogenase copies. The real-time PCR assay for L. (Leishmania) subgenus showed a good linear correlation with quantification on the basis of a limiting dilution assay in experimentally infected mice. The test successfully identifies and quantifies Leishmania in human biopsy specimens and represents a new tool to study leishmaniasis.

Organization of ventral tegmental area projections to the ventral tegmental area-nigral complex in the rat

The ventral tegmental area (VTA) is a nodal link in reward circuitry. Based on its striatal output, it has been subdivided in a caudomedial part which targets the ventromedial striatum, and a lateral part which targets the ventrolateral striatum [Ikemoto S (2007) Dopamine reward circuitry: two projection systems from the ventral midbrain to the nucleus accumbens-olfactory tubercle complex. Brain Res Rev 56:27-78]. Whether these two VTA parts are interconnected and to what extent the VTA innervates the substantia nigra compacta (SNc) and retrorubral nucleus (RR) are critical issues for understanding information processing in the basal ganglia. Here, VTA projections to the VTA-nigral complex were examined in rats, using Phaseolus vulgaris leucoagglutinin (PHA-L) as anterograde tracer. The results show that the dorsolateral VTA projects to itself, as well as to the dorsal tier of the SNc and RR, largely avoiding the caudomedial VTA. The ventrolateral VTA innervates mainly the interfascicular nucleus. The components of the caudomedial VTA (the interfascicular, paranigral and caudal linear nuclei) are connected with each other. In addition, the caudomedial VTA (especially the paranigral and caudal linear nuclei) innervates the lateral VTA, and, to a lesser degree, the SNc and RR. The caudal pole of the VTA sends robust, bilateral projections to virtually all the VTA-nigral complex, which terminate in the dorsal and ventral tiers. Modest inputs from the medial supramammillary nucleus to ventromedial parts of the VTA-nigral complex were also identified. In double-immunostained sections, PHA-L-labeled varicosities were sometimes found apposed to tyrosine hydroxylase-positive neurons in the ventral mesencephalon. Overall, the results underscore that VTA projections to the VTA-nigral complex are substantial and topically organized. In general, these projections, like the spiralated striato-nigro-striatal loops, display a medial-to-lateral organization. This anatomical arrangement conceivably permits the ventromedial striatum to influence the activity of the lateral striatum. The caudal pole of the VTA appears to be a critical site for a global recruitment of the mesotelencephalic system. (C) 2008 IBRO. Published by Elsevier Ltd. All rights reserved.

CALCULATION OF MAGNETODONOR STATES IN InP AND POLARON EFFECTS

Far-infrared transitions in polar semiconductors are known to be affected by the presence of shallow donor impurities, external magnetic fields and the electron-LO-phonon interaction. We calculate the magnetodonor states in indium phosphide by a diagonalization procedure, and introduce the electron-phonon interaction by the Frohlich term. The main effects of this perturbation are calculated by a multi-level version of the Wigner-Brillouin theory. We determine the transition energies, from the ground state to excited states, and find good qualitative agreement with recently reported absorption-spectroscopy measurements in the 100-800 cm(-1) range, with applied magnetic fields up to 30 T. Our calculations suggest that experimental peak splittings in the 400-450 cm(-1) range are due to the electron-phonon interaction.

Hierarchical spatial organization of geographical networks

In this work, we propose a hierarchical extension of the polygonality index as the means to characterize geographical planar networks. By considering successive neighborhoods around each node, it is possible to obtain more complete information about the spatial order of the network at progressive spatial scales. The potential of the methodology is illustrated with respect to synthetic and real geographical networks.

Spectroscopic evidence of extended states in quantized Hall phase of weakly coupled GaAs/AlGaAs multi-layers

The influence of the interlayer coupling on formation of the quantized Hall conductor phase at the filling factor v = 2 was studied in the multi-layer GaAs/AlGaAs heterostructures. The disorder broadened Gaussian photoluminescence line due to the localized electrons was found in the quantized Hall phase of the isolated multi-quantum well structure. On the other hand, the quantized Hall phase of the weakly coupled multi-layers emitted an unexpected asymmetrical line similar to that one observed in the metallic electron systems. We demonstrated that the observed asymmetry is caused by a partial population of the extended electron states formed in the quantized Hall conductor phase due to the interlayer percolation. A sharp decrease of the single-particle scattering time associated with these extended states was observed at the filling factor v = 2. (c) 2007 Elsevier B.V. All rights reserved.

Spontaneous recoherence of quantum states after decoherence

In this work, we identify the set of time-dependent pure states building the statistical mixture to which a system, initially in a pure state, is driven by the reservoir. This set of time-dependent pure states, composing what we term a pure basis, are those that diagonalize the reduced density operator of the system. Next, we show that the evolution of the pure-basis states reveals an interesting phenomenon as the system, after decoherence, evolves toward the equilibrium: the spontaneous recoherence of quantum states. Around our defined recoherence time, the statistical mixture associated with a special kind of initial states termed even-symmetric, spontaneously undergoes a recoherence process, by which the initial state of the system emerges from the mixture except for its reduced excitation drained into the reservoir. This phenomenon reveals that the reservoir only shuffle the original information carried out by the initial state of the system instead of erasing it. Moreover, as the spontaneously recohered state occurs only for asymptotic time, we also present a protocol to extract it from the mixture through specific projective measurements. The password to retrieve the original information stems is the knowledge of both the initial state itself and the associated pure basis. A definition of the decoherence time of an N-state superposition is also presented.

Quenching of excited states of red-pigment zinc protoporphyrin IX by hemin and natural reductors in dry-cured hams

Zinc protoporphyrin IX (ZnPP), the major red pigment in hams dry-cured without nitrates/nitrites, is an efficient photosensitizer, which upon absorption of visible light forms short-lived excited singlet state ((1)ZnPP*) and by intersystem crossing yields the very reactive triplet-excited state ((3)ZnPP*). Using nano-second laser flash photolysis and transient absorption spectroscopy NADH, ascorbic acid, hemin and dehydroascorbic acid were each found to be efficient quenchers of (3)ZnPP*. The deactivation followed, in homogeneous dimethyl sulfoxide (DMSO) or DMSO:water (1:1) solutions, second-order kinetics. The rate constant for ascorbic acid and NADH for reductive quenching of (3)ZnPP* was at 25 A degrees C found to be 7.5 +/- A 0.1 x 10(4) L mol(-1) s(-1) and 6.3 +/- A 0.1 x 10(5) L mol(-1) s(-1), respectively. The polyphenols catechin and quercetin had no effect on (3)ZnPP*. The quenching rate constant for oxidative deactivation of (3)ZnPP* by dehydroascorbic acid and hemin was at 25 A degrees C: 1.6 +/- A 0.1 x 10(5) L mol(-1) s(-1) and 1.47 +/- A 0.1 x 10(9) L mol(-1) s(-1), respectively. Oxidized glutathione did not act as an oxidative quencher for (3)ZnPP*. After photoexcitation of ZnPP to (1)ZnPP*, fluorescence was only found to be quenched by the presence of hemin in a diffusion-controlled reaction. The efficient deactivation of (3)ZnPP* and (1)ZnPP* by the metalloporphyrin (hemin) naturally present in meat may accordingly inherently protect meat proteins and lipids against ZnPP photosensitized oxidation.