Agrobacterium-mediated transformation and inbred line development in the model grass Brachypodium distachyon

Brachypodium distachyon (Brachypodium) has been proposed as a model temperate grass because its physical, genetic, and genome attributes (small stature, simple growth requirements, small genome size, availability of diploid ecotypes, annual lifecycle and self fertility) are suitable for a model plant system. Two additional requirements that are necessary before Brachypodium can be widely accepted as a model system are an efficient transformation system and homogeneous inbred reference genotypes. Here we describe the development of inbred lines from 27 accessions of Brachypodium. Determination of c-values indicated that five of the source accessions were diploid. These diploid lines exhibit variation for a variety of morphological traits. Conditions were identified that allow generation times as fast as two months in the diploids. An Agrobacterium-mediated transformation protocol was developed and used to successfully transform 10 of the 19 lines tested with efficiencies ranging from 0.4% to 15%. The diploid accession Bd21 was readily transformed. Segregation of transgenes in the T ₁ generation indicated that most of the lines contained an insertion at a single genetic locus. The new resources and methodologies reported here will advance the development and utilization of Brachypodium as a new model system for grass genomics.     

In vitro regeneration of Vigna unguiculata (L.) Walp. cv. Blackeye cowpea via shoot organogenesis

An in vitro regeneration system was developed in cowpea [Vigna unguiculata (L.) Walp.] Blackeye. Among several explants studied, shoot initiation response was observed from shoot apices of 3–5-day-old seedlings. The optimal medium for maximum shoot initiation comprised MS salts, B₅ vitamins, 8.88 μM N ⁶-benzylaminopurine, 1 gl^-1 casein hydrolysate, 342 μM L-glutamine, 3% sucrose, 0.3% phytagel, adjusted to pH 5.8. A shift in pH from 5.8 to 7.0 had no effect on shoot initiation and on number of shoots per explant. The highest shoot initiation frequency (77%) was obtained using this preferred medium, reaching a maximum of eight shoots per explant. For shoot elongation, 14 μM gibberellic acid was supplemented in the shoot initiation medium. Presence of indolebutyric acid in the rooting medium had no effect on root induction. The regenerated plants were fertile and developed normally.     

Patterns in cumulative increase in live and dead species from foraminiferal time series of Cowpen Marsh, Tees Estuary, UK: Implications for sea-level studies

We have collected live and dead foraminiferal times-series data at 2-weekly intervals for a 12-month period from the intertidal zone of Cowpen Marsh, Tees Estuary, UK. The data from the 689 samples show profound differences between live and dead assemblages, although assemblages are dominated by just three species, Haynesina germanica, Jadammina macrescens and Trochammina inflata, which represent over 70% of the assemblage. The cumulative increase in species of most environments approximates to a lognormal or log series. None of the datasets show a broken stick pattern. The cumulative maximum number of species, which represents the species carrying capacity of the environment, is recorded earlier in the life assemblages than the dead counterparts. The dead assemblage of Cowpen Marsh is found to have a higher abundance (435 compared to 163 individuals/10 cm³) and number of species (52 compared to 28) than its live counterpart because the dead assemblage represents many generations added over a long period of time. In contrast, some species are recorded in the live dataset that were not found in the dead assemblage, indicating the dead record is either incomplete (e.g. taphonomic change) or inadequately sampled.We investigated the influence of patterns in cumulative increase on dead assemblages for sea-level reconstructions through the development of foraminiferal-based transfer functions. The cumulative transfer functions suggest that the performance improves during the first six sample intervals of the time-series dataset with reconstruction differing by 1.2 m and remains constant thereafter.     

Relationships of Exodontiella, a non-alysiine, exodont member of the family Braconidae (Insecta, Hymenoptera)

The placement of Exodontiella Wharton is re-examined in light of the discovery of four additional individuals. Genomic DNA was extracted from one of the individuals, the D2 expansion segment of the 28S rRNA gene was sequenced, and the sequence compared to selected taxa within the Braconidae. Based on the molecular data and the morphological study, Exodontiella is formally transferred from the Opiinae to the Gnamptodontinae. The genus and its included species are redescribed.     

Identifying Conservation Priority Zones for Effective Management of Tropical Forests in Eastern Ghats of India

There are thousands of protected forest areas existing on earth, yet the deforestation rate continues unabated both inside and outside the protected areas especially in the tropical forests. It identifies the less effectiveness of the current conservation strategies, which is normally oriented around the forest area cover rather than the quality of the protected areas. This calls for realistic and effective management strategies for forests. Based on the drawbacks the present study aims at identifying conservation priority sites within the protected areas (Reserved Forests) of Shervarayan hills, Eastern Ghats of Tamil Nadu, India. The remnant forest patches having less effective management/protection is identified and analysed for its qualitative contribution to the ecosystem. Quadrats of 20 × 20 m were laid in different vegetation based on the percentage of forest cover and assess the species diversity pertaining the richness, Endemism and Red list categories. Thematic layers (maps) such as vegetation type, floristic species richness, floristic endemism, and red list flora are created and categorized according to their weightage classes and overlaid in GIS domain to demarcate the Conservation Priority Zones (CPZ). The CPZ are classified according to the priority status i.e., high, moderate and low based on the contributing species richness, levels of endemism and concentration of Red listed plants.     

The Spatial Structure of Variability in a Semi-arid, Fluvial Ecosystem

The arrangement and composition of flowpath types within a given network are thought to govern its functioning. This concept assumes that different flowpath types are functionally distinct. We investigated this assumption in a fluvial ecosystem by comparing the riparian zone, parafluvial zone (in-channel gravel bars), and surface stream. We hypothesized that differences in advection, uptake, and sorption would render material cycles more (a) open and (b) mutable in the surface stream, whereas the converse would occur in the riparian zone, and an intermediate state would be seen in the intervening parafluvial zone. To test our first hypothesis, we predicted that spatial heterogeneity in solute concentrations would be least in the surface stream, greater in the parafluvial zone, and greatest in the riparian zone. Using a null model, we ascertained that this pattern was shown by all solute species we examined (nitrate, ammonium, total dissolved inorganic nitrogen [DIN], dissolved organic N, total dissolved N, soluble reactive phosphorus, dissolved organic carbon, and chloride). To test our second hypothesis, we predicted that temporal change in spatial heterogeneity would be greatest in the surface stream, less in the parafluvial zone, and least in the riparian zone. Nitrate, DIN, and chloride showed this pattern. In particular, surface stream inorganic N was less spatially variable following months of high rainfall. According to an extant hypothesis, these results suggest that inorganic N processing may be a stable function in this ecosystem. Other solute species did not support our second prediction, perhaps because their retention and release dynamics are influenced principally by geochemistry. Generally, our findings indicate that a geomorphic template can generate spatial patterns in ecosystem function, warranting an expansion of the spiraling framework to a variety of flowpath types.     

Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons

Background  

While all codons that specify amino acids are universally recognized by tRNA molecules, codons signaling termination of translation are recognized by proteins known as class-I release factors (RF). In most eukaryotes and archaea a single RF accomplishes termination at all three stop codons. In most bacteria, there are two RFs with overlapping specificity, RF1 recognizes UA(A/G) and RF2 recognizes U(A/G)A.     

Role of the EXPO ’70 forest project in forest restoration in urban areas

The forest-restoration project of EXPO ’70 Commemorative Park, Japan, is an epoch-making attempt to restore a nature-oriented forest park in an urban area in which large-scale land reclamation had occurred. The objective of this paper is to review the concept, planning, and design, and the outcome so far, and discuss current aspects of creating a core natural habitat in the city of Osaka. Innovative planning policy and design methods have been used for construction of the forest-restoration project of EXPO Park. Unexpected troubles have occurred, however. After approximately 10 years severe effects of poor drainage and soil compaction on the establishment of the forest have been revealed by intensive monitoring. Partial redevelopment and soil-amendment work has therefore been conducted. These improvements seemed to have resulted in “a self-sustaining forest”, the original objective of the planning policy. After approximately 25 years, however, a second intensive monitoring program has revealed that the status of nature restoration is generally favorable in quantity but not in structure of forest communities or biodiversity. The major issues identified are excessive tree density with a single foliage layer caused by the single generation of immature forest stand, and ecological isolation from the source of nature. The EXPO forest is currently in the “Second Generation” stage; this involves management, including artificial gap regeneration, and soil seed bank introduction, with careful monitoring. The project is expected to be an ideal example of a core habitat of nature-oriented forest in urban areas achieved by adaptive management.     

Predisposition for venoconstriction in the equine laminar dermis: implications in equine laminitis.

Equine laminitis is a crippling condition associated with a variety of systemic diseases. Although it is apparent that the prodromal stages of laminitis involve microvascular dysfunction, little is known regarding the physiology of this vasculature. The aim of the present study was to determine the relative responses of equine laminar arteries and veins to the vasoconstrictor agonists phenylephrine (1 nM-10 microM), 5-HT (1 nM-10 microM), PGF2alpha (1 nM-100 microM), and endothelin-1 (1 pM-1 microM). We have determined that laminar veins were more sensitive, with respect to the concentration of agonist required to initiate a contractile response and to achieve EC(50), for all agonists tested. EC50 values, for veins and arteries, respectively, were 84+/-7 vs. 688+/-42 nM for phenylephrine, 35+/-6 vs. 224+/-13 nM for 5-HT, 496+/-43 nM vs. 3.0+/-0.6 microM for PGF2alpha, and 467+/-38 pM vs. 70.6+/-6.4 nM for endothelin-1. Moreover, when expressed as a percentage of the response to a depolarizing stimulus (80 mM potassium), the maximal contractile response of laminar veins exceeded that for the laminar arteries for each agonist. These results indicate that there may be a predisposition for venoconstriction within the vasculature of the equine digit. While this physiological predisposition for venoconstriction may be important in the regulation of blood flow during exercise, it also may help to explain why laminitis can result from a variety of pathological systemic conditions.