Improvements in the Assessment of Bacterial Viability and Killing

It is axiomatic that our planet is extensively inhabited by diverse micro-organisms such as bacteria, yet the absolute diversity of different bacterial species is widely held to be unknown. Different bacteria can be found from the depths of the oceans to the top of the mountains; even the air is more or less colonized by bacteria. Most bacteria are either harmless or even advantageous to human beings but there are also bacteria, which can cause severe infectious diseases or spoil the supplies intended for human consumption. Therefore, it is vitally important not only to be able to detect and enumerate bacteria but also to assess their viability and possible harmfulness. Whilst the growth of bacteria is remarkably fast under optimum conditions and easy to detect by cultural methods, most bacteria are believed to lie in stationary phase of growth in which the actual growth is ceased and thus bacteria may simply be undetectable by cultural techniques. Additionally, several injurious factors such as low and high temperature or deficiency of nutrients can turn bacteria into a viable but non-culturable state (VBNC) that cannot be detected by cultural methods. Thereby, various noncultural techniques developed for the assessment of bacterial viability and killing have widely been exploited in modern microbiology. However, only a few methods are suitable for kinetic measurements, which enable the real-time detection of bacterial growth and viability. The present study describes alternative methods for measuring bacterial viability and killing as well as detecting the effects of various antimicrobial agents on bacteria on a real-time basis. The suitability of bacterial (lux) and beetle (luc) luciferases as well as green fluorescent protein (GFP) to act as a marker of bacterial viability and cell growth was tested. In particular, a multiparameter microplate assay based on GFP-luciferase combination as well as a flow cytometric measurement based on GFP-PI combination were developed to perform divergent viability analyses. The results obtained suggest that the antimicrobial activities of various drugs against bacteria could be successfully measured using both of these methods. Specifically, the data reliability of flow cytometric viability analysis was notably improved as GFP was utilized in the assay. A fluoro-luminometric microplate assay enabled kinetic measurements, which significantly improved and accelerated the assessment of bacterial viability compared to more conventional viability assays such as plate counting. Moreover, the multiparameter assay made simultaneous detection of GFP fluorescence and luciferase bioluminescence possible and provided extensive information about multiple cellular parameters in single assay, thereby increasing the accuracy of the assessment of the kinetics of antimicrobial activities on target bacteria.

Phylogenetic relationships of Apodemus Kaup, 1829 (Rodentia: Muridae) species in the Eastern Mediterranean inferred from mitochondrial DNA, with emphasis on iranian species

Wood mice of the genus Apodemus are widely distributed in Eurasia, with the Eastern Mediterranean being considered as a hotspot. Indeed, numerous species have been documented in Iran, including A. witherbyi, A. hyrcanicus, A. uralensis, A. avicennicus, A. hermonensis, and A. arianus. In this study, 129 specimens were collected from different Iranian localities and two specimens from Afghanistan. The animals were identified taxonomically and their phylogenetic relationships were investigated using cytochrome b mitochondrial DNA sequences. Five species of the genus Apodemus were identified in Iran, including A. hyrcanicus, A. witherbyi, A. cf. ponticus, A. uralensis, and A. mystacinus, beside, A. pallipes from Afghanistan. This study found no evidence of A. flavicollis or A. sylvaticus in Iran, despite their occurrence in Turkey, shedding doubt on the status of A. flavicollis in Iran, Asia Minor, and the Levant. Phylogenetic analyses imply that A. witherbyi has priority over A. avicennicus, A. hermonensis, and A. iconicus. Estimation of the divergence time for these taxa suggests a separation at around 7.2 Ma for the subgenera Karstomys (including A. mystacinus and A. epimelas) and Sylvaemus (including A. flavicollis, A. sylvaticus, A. uralensis, A. pallipes, A. hyrcanicus, A. witherbyi, and A. cf. ponticus). Within the subgenus Karstomys, the divergence times for A. mystacinus and A. epimelas were between 3.0 and 6.1 Ma, and divergence times within the subgenus Sylvaemus were between 5.2 and 6.9 Ma for A. witherbyi and other species in this subgenus. It is postulated that vicariance events including the uplifting of the Zagros Mountains and Anatolian Plateau in the middle Miocene and climate oscillations during the Messinian Salinity Crisis besides formation of the Hyrcanian tertiary forests during the Neogene probably played substantial roles in the radiation and distribution of the genus Apodemus in the Eastern Mediterranean.

Landscape Systems and Human Land-Use Interactions in Mediterranean Highlands and Littoral Plains during the Late Holocene: Integrated Analysis from the InterAmbAr Project (North-Eastern Catalonia).

The main goal of the InterAmbAr reseach project is to analyze the relationships between landscape systems and human land-use strategies on mountains and littoral plains from a long-term perspective. The study adopts a high resolution analysis of small-scale study areas located in the Mediterranean region of north-eastern Catalonia. The study areas are distributed along an altitudinal transect from the high mountain (above 2000m a.s.l.) to the littoral plain of Empordà (Fig. 1). High resolution interdisciplinary research has been carried out from 2010, based on the integration of palaeoenvironmental and archaeological data. The micro-scale approach is used to understand human-environmental relationships. It allows better understanding of the local-regional nature of environmental changes and the synergies between catchment-based systems, hydro-sedimentary regimes, human mobility, land-uses, human environments, demography, etc.

Divergence with gene flow and fine-scale phylogeographical structure in the wedge-billed woodcreeper, Glyphorynchus spirurus, a Neotropical rainforest bird.

Determining the relative roles of vicariance and selection in restricting gene flow between populations is of central importance to the evolutionary process of population divergence and speciation. Here we use molecular and morphological data to contrast the effect of isolation (by mountains and geographical distance) with that of ecological factors (altitudinal gradients) in promoting differentiation in the wedge-billed woodcreeper, Glyphorynchus spirurus, a tropical forest bird, in Ecuador. Tarsus length and beak size increased relative to body size with altitude on both sides of the Andes, and were correlated with the amount of moss on tree trunks, suggesting the role of selection in driving adaptive divergence. In contrast, molecular data revealed a considerable degree of admixture along these altitudinal gradients, suggesting that adaptive divergence in morphological traits has occurred in the presence of gene flow. As suggested by mitochondrial DNA sequence data, the Andes act as a barrier to gene flow between ancient subspecific lineages. Genome-wide amplified fragment length polymorphism markers reflected more recent patterns of gene flow and revealed fine-scale patterns of population differentiation that were not detectable with mitochondrial DNA, including the differentiation of isolated coastal populations west of the Andes. Our results support the predominant role of geographical isolation in driving genetic differentiation in G. spirurus, yet suggest the role of selection in driving parallel morphological divergence along ecological gradients.

Aportació al coneixement florístic de les Guilleries i del Collsacabra (Catalunya Oriental), III

En la present nota indiquem un seguit de novetats corològiques per a la flora vascular dels massissos de les Guilleries i del Collsacabra.

New sample of drosophilids from the Font Groga site, Barcelona (Spain)

A new sample of drosophilids was obtained from Font Groga (Barcelona) on 9th October 2013. Flies were netted over 12 baits containing fermenting bananas placed along a trail from 4 to 7 pm. The number of flies classified according to species and sex is presented in Table 1. The most abundant species is D. subobscura (62.60%). This is expected because the sample was obtained during its autumn peak of expansion. Also interesting is to find again D. suzukii, and in a percentage similar (9.20%) to that obtained in 2012 sample. This species invaded recently many European regions and seems it is well established. We have finally estimated the species diversity using H" (Shannon diversity index) and J (Shannon uniformity index). The values obtained were 0.990 and 0.615, respectively. They are similar to those estimates obtained in the same site by Calabria in autumn 2007 and higher than those of Canals et al. in late autumn 2012.

Arcàdia

Postprint (published version)

Clave para la determinación de exuvias pupales de los quironómidos (Diptera: Chironomidae) de ríos altoandinos tropicales

The Chironomidae is a cosmopolitan family of Nematoceran flies with more than 20 000 species described. However the diversity of genera and species of the family in the Andean region beyond the 2 000m.a.s.l are scarcely known. We conducted faunal surveys and biomonitoring research in different streams of Colombia, Ecuador and Peru from May 2005 to October 2011. Based on specimens collections, and a taxonomic key was developed to identify pupae and pupal exuviae of 46 genera of midges (Diptera, Chironomidae) collected from streams at high altitude areas on the Andean tropical mountains. We included illustrations and brief taxonomic descriptions for all genera, of which several ones have not yet been formally described; in this latter case we used the nomenclature of Roback & Coffman (1983). For two genera, Cricotopus and Genus 1, keys to the most common morphospecies were provided. Results showed that in this area the chironomid assemblages are dominated by the members of the subfamily Orthocladiinae (22 genera) followed by the Chironominae (13). Six genera of Tanypodinae were identified, while only three and two genera were present from subfamilies Podonominae and Diamesinae. This key may be very useful for both studies about drift in streams, and for biomonitoring purposes.

Transformation of a Rural Landscape in the Eastern Pyrenees Between 1953 and 2000

In the mid-20th century, the southern parts of the Madres and Mont Coronat massif (Eastern Pyrenees, France) were characterized by a Mediterranean landscape shaped by human activity. Long-term use of these mountains for crops, livestock, and forestry led to an increase in grassland areas at the expense of forest. However, socioeconomic transformation (abandonment of agriculture and a decrease in the rural population) in recent decades has caused profound changes in this massif. Interpretation of aerial photographs (1953, 1969, 1988, and 2000) made it possible to detect and analyze the changes produced in the study area (6787 ha) during this period. In 1953 most of the massif landscape consisted of grasslands (38%) and open forests (18%), with some areas of dense forest (15%). By 2000, dense forest cover had doubled in size (31%), and grassland had decreased considerably (by 73% of the initial area). Since 1953, the study area has become more homogeneous, with a few local exceptions. The results of this study suggest that socioeconomic factors might be the main cause of landscape transformations in this period of approximately 50 years.

Caracterización de las amterias primas líticas del yacimiento paleolítico de la Dolina de l'Esquerda de ls Alzines (macizo del Garraf, Barcelona)

[spa] El presente estudio se centra en la caracterización macroscópica y microscópica de las materias primas silíceas del yacimiento de la Dolina de l'Esquerda de les Alzines, un yacimiento del Pleistoceno superior ubicado en el macizo del Garraf. El objetivo ha sido establecer distintas variedades de sílex, mediante la descripción macroscópica y microscópica de los elementos del conjunto lítico, para disponer, por vez primera, de unas categorías definidas de los recursos abióticos silíceos disponibles y explotados durante la prehistoria en este macizo. Además, mediante el presente estudio se ha evaluado también la posible procedencia y el área captación de dichas materias. [eng]The present study focuses on the macroscopic and microscopic characterization of siliceous raw materials from the archeological site of Dolina de l'Esquerda de les Alzines, an Upper Pleistocene deposit located in the Garraf Massif. The aim of this study has been to establish different varieties of chert, by a precise description of the elements of the lithic assemblage, to provide for the first time a few categories defined from the siliceous abiotic resources available and exploited during Prehistory in the massif. Furthermore, through the present study we also assessed the possible origin and procurement area of such materials.

Opus Dein perustajan elämä sarjakuvana

Kirjallisuusarvostelu

Unexpected effects of pigeon-peas (Cajanus cajan) in the restoration of rupestrian fields

Several degraded areas can be found along the Highway MG-010 that crosses the Espinhaço Mountain Biosphere Reserve in the Brazilian state of Minas Gerais. Restoration by planting the legume Cajanus cajan was implemented in some of these areas. The present study compares plant species richness, diversity, abundance, equitability, similarity, and soil composition between restored and non-restored areas, in an attempt to evaluate the effectiveness of the use of C. cajan in the restoration process in the mountain environment. Each treatment (restored and non-restored) had four sampling areas, each with three 300 m² plots. We counted and identified every individual plant found within these plots. We also collected soil from the superficial layer (0-10 cm) of each sampling area in both treatments. The areas where C. cajan was planted revealed lower species richness, diversity, and plant abundance. The soil of these areas also contained higher levels of Phosphorus and Magnesium. Plant equitability and similarity between plots and other soil components (pH, Nitrogen, Aluminum, Calcium, Potassium, H+Al, sum of bases - SB, cation exchange capacity - CTC, base saturation - V%, aluminum saturation - M%) did not differ between the two treatments. Contrary to the expectations, soil enhancement in the quartzitic soil poor in nutrients in the rupestrian fields can facilitate the invasion by exotic plants, which are not adapted to the lack of nutrients. As it appears, the use of C. cajan in restoration projects represents a mistake and future restoration plans should avoid the use of exotic species, given that they may cause negative effects on the native plant community, as demonstrated here in the rupestrian fields.

Rock outcrop vegetation in Brazil: a brief overview

This paper overviews the special issue of the Brazilian Journal of Botany dedicated to "Rock outcrop vegetation in Brazil". The main topics covered by this issue are phytogeography and vegetation ecology, plant life on shallow soils, plant reproduction and auto-ecology, morpho-physiology and plant adaptation, and finally conservation and global change. This collection of studies, in addition to other recent publications on Brazilian rocky outcrop vegetation, show that measurements of most of the relevant ecological and evolutionary parameters are under way and that scientific attention is now given to most Brazilian regions. However, there are still several gaps to be bridged: 1) inselbergs and high mountains in the Amazon and the Brazilian northeast, in particular, are still largely unknown to science; 2) long-term studies are almost totally unavailable, which hinders global change monitoring and assessment; 3) national and international networking are urgently needed to speed up scientific production about such habitats.

Mountain biodiversity in Brazil

The high species richness and diversity found in tropical montane habitats are often related to: 1) an effect of climatic and geological history on biotic evolution; 2) the various environmental impacts on species adaptation mechanisms; and 3) the continuous dispersal of fauna and flora in time. However, little is known about how these factors shaped species richness in Brazilian mountains. Official documents on biodiversity in Brazil make no explicit reference to mountains, even though there is a mountain work programme of the Convention on Biological Diversity, which Brazil is a signatory of. This paper discusses the importance of mountain ecosystems in Brazil to show the urgent need to include mountain biodiversity in the national agenda of biodiversity research and conservation.

Appleton's northern and eastern Traveller's guide

Full Title: Appleton's northern and eastern Traveller's guide : with new and authentic maps, illustrating those divisions of the country; forming likewise a complete guide to the Middle States, Canada, New Brunswick, and Nova Scotia, the White Mountains, Catskill Mountains, Niagara and Trenton Falls, Saratoga and Virginia Springs andc.; with the fashionable and healthful resort, and full and accurate descriptions of the principal cities, towns, villages; with distances, fares, andc.; illustrated with numerous maps and plans of cities, engraved on steel, and several wood engravings