Diversity of Archaea in Brazilian savanna soils

Although the richness of Bacteria and Fungi in Cerrado’ soils has been reported, here we report, for the first time, the archaeal community in Cerrado’s soils. DNA extracted from soil of two distinct vegetation types, a dense subtype of sensu strict (cerrado denso) and riverbank forest (mata de galeria), was used to amplify Archaea-specific 16S rRNA gene. All of the fragments sequenced were classified as Archaea into the phylum Thaumarchaeota, predominantly affiliated to groups I.1b and I.1c. Sequences affiliated to the group I.1a were found only in the soil from riverbank forest. Soils from ‘cerrado denso’ had greater Archaea richness than those from ‘mata de galeria’ based on the richness indexes and on the rarefaction curve. β-Diversity analysis showed significant differences between the sequences from the two soil areas studied because of their different thaumarchaeal group composition. These results provide information about the third domain of life from Cerrado soils.     

Local NO synthase inhibition produces histological and functional recovery in Achilles tendon of rats after tenotomy

Repair of injured tendon is a very slow process and involves the release of many molecules, including nitric oxide. We investigate the influence of local nitrergic inhibition in histological and functional recovery of injured Achilles tendon. A standard murine model of tendon injury by rupture was used. The animals were divided into three experimental groups: control, injury + vehicle (normal saline) and injury + Nω-nitro-L-arginine methyl ester (L-NAME). The products were injected into the paratendinous region every 2 days and body weight gain and Achilles functional index (AFI) were evaluated on days 0, 7, 14 and 21 after tendon injury. On day 21 post-injury, the animals were killed to evaluate nitric oxide production and tissue organization. We observed that tendon surgical division led to increased tissue nitrite levels, which were reduced in L-NAME-treated rats. The AFI revealed functional recovery of L-NAME-treated animals on day 21 post-injury, which was not observed in the saline-treated group. Microscopic analysis of hematoxylin-eosin staining and collagen autofluorescence showed that L-NAME-treated rats had more aligned areas of collagen fibers and that the diameter of newly organized collagen in this group was also greater than that in the vehicle-treated one. We demonstrate that local treatment with L-NAME significantly improves the functional parameters and accelerates histomorphological recovery.     

Integrin participates in the effect of thyroxine on plasma membrane in immature rat testis

Background

The secretory activity of Sertoli cells (SC) is dependent on ion channel functions and protein synthesis and is critical to ongoing spermatogenesis. The aim of this study was to investigate the mechanism of action associated with a non-metabolizable amino acid [¹⁴C]-MeAIB (α-(methyl-amino)isobutyric acid) accumulation stimulated by T₄ and the role of the integrin receptor in this event, and also to clarify whether the T₄ effect on MeAIB accumulation and on Ca²⁺ influx culminates in cell secretion.

Methods

We have studied the rapid and plasma membrane initiated effects of T₄ by using ⁴⁵Ca²⁺ uptake and [⁴⁵C]-MeAIB accumulation assays, respectively. Thymidine incorporation into DNA was used to monitor nuclear activity and quinacrine to analyze the secretory activity on SC.

Results

The stimulation of MeAIB accumulation by T₄ appears to be mediated by the integrin receptor in the plasma membrane since tetrac and RGD peptide were able to nullify the effect of this hormone. In addition, T₄ increases extracellular Ca²⁺ uptake and Ca²⁺ from intracellular stocks to enhance nuclear activity, but this genomic action seems not to influence SC secretion mediated by T₄. Also, the cytoskeleton and ClC-3 chloride channel contribute to the membrane-associated responses of SC.

Conclusions

T₄ integrin receptor activation ultimately determines the plasma membrane responses on amino acid transport in SC, but it is not involved in calcium influx, cell secretion or the nuclear effect of the hormone.

General significance

The integrin receptor activation by T₄ may take a role in plasma membrane processes involved in the male reproductive system.     

Polymerase manager protein UmuD directly regulates Escherichia coli DNA polymerase III α binding to ssDNA

Replication by Escherichia coli DNA polymerase III is disrupted on encountering DNA damage. Consequently, specialized Y-family DNA polymerases are used to bypass DNA damage. The protein UmuD is extensively involved in modulating cellular responses to DNA damage and may play a role in DNA polymerase exchange for damage tolerance. In the absence of DNA, UmuD interacts with the α subunit of DNA polymerase III at two distinct binding sites, one of which is adjacent to the single-stranded DNA-binding site of α. Here, we use single molecule DNA stretching experiments to demonstrate that UmuD specifically inhibits binding of α to ssDNA. We predict using molecular modeling that UmuD residues D91 and G92 are involved in this interaction and demonstrate that mutation of these residues disrupts the interaction. Our results suggest that competition between UmuD and ssDNA for α binding is a new mechanism for polymerase exchange.     

Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques

Multiple sequence alignments (MSAs) have become one of the most studied approaches in bioinformatics to perform other outstanding tasks such as structure prediction, biological function analysis or next-generation sequencing. However, current MSA algorithms do not always provide consistent solutions, since alignments become increasingly difficult when dealing with low similarity sequences. As widely known, these algorithms directly depend on specific features of the sequences, causing relevant influence on the alignment accuracy. Many MSA tools have been recently designed but it is not possible to know in advance which one is the most suitable for a particular set of sequences. In this work, we analyze some of the most used algorithms presented in the bibliography and their dependences on several features. A novel intelligent algorithm based on least square support vector machine is then developed to predict how accurate each alignment could be, depending on its analyzed features. This algorithm is performed with a dataset of 2180 MSAs. The proposed system first estimates the accuracy of possible alignments. The most promising methodologies are then selected in order to align each set of sequences. Since only one selected algorithm is run, the computational time is not excessively increased.     

Continental estimates of forest cover and forest cover changes in the dry ecosystems of Africa between 1990 and 2000

Aim

This study provides regional estimates of forest cover in dry African ecoregions and the changes in forest cover that occurred there between 1990 and 2000, using a systematic sample of medium‐resolution satellite imagery which was processed consistently across the continent.

Location

The study area corresponds to the dry forests and woodlands of Africa between the humid forests and the semi‐arid regions. This area covers the Sudanian and Zambezian ecoregions.

Methods

A systematic sample of 1600 Landsat satellite imagery subsets, each 20 km × 20 km in size, were analysed for two reference years: 1990 and 2000. At each sample site and for both years, dense tree cover, open tree cover, other wooded land and other vegetation cover were identified from the analysis of satellite imagery, which comprised multidate segmentation and automatic classification steps followed by visual control by national forestry experts.

Results

Land cover and land‐cover changes were estimated at continental and ecoregion scales and compared with existing pan‐continental, regional and local studies. The overall accuracy of our land‐cover maps was estimated at 87%. Between 1990 and 2000, 3.3 million hectares (Mha) of dense tree cover, 5.8 Mha of open tree cover and 8.9 Mha of other wooded land were lost, with a further 3.9 Mha degraded from dense to open tree cover. These results are substantially lower than the 34 Mha of forest loss reported in the FAO's 2010 Global Forest Resources Assessment for the same period and area.

Main conclusions

Our method generates the first consistent and robust estimates of forest cover and change in dry Africa with known statistical precision at continental and ecoregion scales. These results reduce the uncertainty regarding vegetation cover and its dynamics in these previously poorly studied ecosystems and provide crucial information for both science and environmental policies.     

Sequence verification of synthetic DNA by assembly of sequencing reads

Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.org.     

The role of short-tongued insects in floral variation across the range of a style-dimorphic plant

Background and Aims

Heterostyly and related style polymorphisms are suitable model systems to evaluate the importance of functional pollinators in the maintenance of population variability. In Narcissus papyraceus different functional pollinators, incompatibility system and flower morphology have been proposed to influence the maintenance of polymorphism through their effect on disassortative mating. Here a test is done to find out if the visitation rate of long- versus short-tongued pollinators correlates with the morph ratio and if the latter is related to other flower traits of the species across its main geographic range.

Methods

Floral traits from 34 populations in the south-west of the Iberian Peninsula and in north-west Africa were measured, perianth variation was described and a comparison was made of allometric relationships between sex organs and floral tube. Correlations between pollinator guilds, stigma–anther separation of reciprocal morphs (our proxy for disassortative mating) and morph-ratio variation were analysed. Finally, the incompatibility system of the species in the northern and southern borders of its distribution are described.

Key Results

Flowers from southern populations were significantly larger than flowers from centre and northern populations. The abundance of short-styled plants decreased gradually with increasing distance from the core region (the Strait of Gibraltar), with these disappearing only in the northern range. Although there was a significant difference in stigma–anther separation among populations, morph ratio was not associated with reciprocity or floral tube length. Long-style morph frequency increased with short-tongued pollinator visitation rate. Populations from both edges of the distribution range were self-incompatible and within- and between-morph compatible.

Conclusions

The style morph ratio changed gradually, whereas perianth trait variation showed abrupt changes with two morphotypes across the range. The positive relationship between the visitation rate of short-tongued pollinators and the decrease of the short-style morph supports our initial hypothesis. The results highlight the importance of different pollinators in determining the presence of style polymorphism.     

Effects of arbuscular mycorrhizal fungal species and the medium pH on the growth of Pueraria phaseoloides (Roxb.) Benth

Soil conditions may change the response of plants to inoculation with arbuscular mycorrhizal fungi (AMF). This, in turn, may influence the development of mycorrhizal associations. The effect of AM species isolated from different ecosystems was evaluated on Pueraria phaseoloides (kudzu). Experiments were conducted under controlled conditions in Leonard jars, on a substrate made of peat, rice husk, and vermiculite (1-1-1) enriched with rock phosphate plus a modified Hoagland nutrient solution. In the first experiment the initial pH of the substrate (8.0) was reduced by approximately one unit by inoculation with Kuklospora colombiana, Glomus clarum, and Glomus manihotis. The result was the same for Acaulospora longula species when 4-morpholine ethanesulphonic acid (MES) buffer was used. The final pH of the substrate was correlated with the above-ground plant biomass production suggesting that the most effective fungus regulated the pH of the substrate. This positive interaction leads to a higher concentration of P and K in plants. When the pH of the substrate was buffered with MES, in the second experiment, the efficiency of K. colombiana was reduced, even though plants inoculated with this fungus yielded more than non-inoculated plants. G. intraradices and A. longula were favoured by buffer addition. Beneficial buffer effects on this plant resulted in lower pH, better plant P and K uptake, and higher biomass production. The best plant yield was obtained at pH 7.0 in both experiments. G. clarum and G. manihotis yielded the highest biomass production. Under the proposed conditions, AMF improved P. phaseoloides growth and pH regulation. These growth conditions may be used for the evaluation and propagation of some AMF species adding MES buffer in the nutrient solution.