Composition and activity of beta-Proteobacteria ammonia-oxidizing communities associated with intertidal rocky biofilms and sediments of the Douro River estuary, Portugal

AIMS: To characterize the phylogenetic composition of ammonia-oxidizing bacteria (AOB) of the beta-subclass of the class Proteobacteria in intertidal sediment and rocky biofilms of the Douro estuary, and evaluate relationships with environmental variables and N-biogeochemistry. METHODS AND RESULTS: Cluster analysis of denaturing gradient gel electrophoresis profiles showed differences in beta-Proteobacteria AOB assemblage composition between rocky biofilms and sediments. All sequences obtained from intertidal rocky biofilm sites exhibited phylogenetic affinity to Nitrosomonas sp. lineages, whereas a majority of the sequences from the sediment sites were most similar to marine Nitrosospira cluster 1. Hierarchical cluster analysis based on environmental variables identified two main groups of samples. The first contained samples from rocky biofilm sites characterized by high concentrations of NO2- and NH4+, and high organic matter and chlorophyll a content. The second group contained all of the sediment samples; these sites were characterized by lower values for the variables above. In addition, rocky biofilm sites exhibited higher nitrification rates. CONCLUSIONS: Intersite differences in environmental and/or physical conditions led to the selection of different populations of beta-Proteobacteria AOB, supporting different magnitudes of N-cycling regimes. SIGNIFICANCE AND IMPACT OF THE STUDY: This study represents an important step in establishing the influence of environmental factors on the distribution of beta-Proteobacteria AOB with possible consequences for N-biogeochemistry.     

HIV-1 VprB and C RNA cleavage by potent 10-23 DNAzymes that also cause reversal of G2 cell cycle arrest mediated by Vpr genes

Accessory Vpr protein of HIV-1 is known to influence several key cellular functions that also impacts on the HIV-1 replication cycle. Besides other activities, it alone causes cell cycle arrest at the G2 phase and thus potentially contribute to the overall pathology. We designed several 10-23 catalytic motifs containing DNAzymes (Dzs) against the full-length Vpr gene from subtype B and checked its activity against VprC gene from one of the Indian HIV-1 isolates. Among several Dzs that showed sequence-specific cleavage activities, Dz-94 was very potent and equally efficient in its ability to cleave full-length VprB and C RNA to completion under standard conditions of cleavage. Although Dz-90 target sequence was fully conserved between VprB and C genes, it was more effective on latter genes, suggesting that spatial structures of RNA at other regions of Vpr can also influence the cleavage activity for this Dz. HIV-1 VprB and C encoding genes under the powerful CMV promoter, when cotransfected into mammalian cells with Dz-94, a potent intracellular inhibition, was observed, which also resulted in reversing the G2 cell cycle arrest mediated by VprB and C proteins. Thus, Dz-94 could potentially be developed to prevent Vpr-mediated cytopathic effects caused by HIV-1 subtype B and C isolates.     

Expression of endothelin 1 and its receptors in the hypoxic pregnant rat

Endothelin 1 (EDN1) plays a primary role in the pathophysiology of hypoxia-induced fetal growth restriction in the rat. In this study we evaluated the effects of chronic maternal hypoxia on the expression of endothelin and its receptors and on receptor binding activity in the uterus and placenta of the rat, in order to elucidate their roles in hypoxia-induced fetal growth restriction. Timed-pregnant Sprague-Dawley rats were maintained in either a normoxic or a normobaric hypoxic (12% O(2)) atmosphere from Gestational Days 18-21. Uterine and placental tissues collected on Gestational Day 21 were assayed for Edn1, Ednra, and Ednrb (endothelin receptors) mRNA expression by real-time quantitative RT-PCR, for localization of EDN1 and its receptors by immunohistochemistry, for EDNRA and EDNRB protein expression by Western blot, and for receptor binding activity by homologous competitive binding assays. EDN1 mRNA expression was significantly increased in the hypoxic placenta, but not in the uterus, compared with normoxic controls. Immunohistochemistry revealed increased EDN1 specifically in the labyrinth of the placenta. Receptor mRNA levels were not significantly affected by hypoxia, but EDNRA protein expression was significantly decreased specifically in the uterine placental beds. Receptor binding decreased significantly in response to hypoxia in all tissues investigated, compared with controls. These results suggest that chronic maternal hypoxia results in increased expression of EDN1 in the placenta but not in the uterus, and that reduced binding activity, rather than regulation of receptor expression, is a mechanism by which these tissues regulate the local hemodynamic response to increased endogenous placental EDN1 in the setting of hypoxia.     

Depth distribution of microbial diversity in Mono Lake,a meromictic soda lake in California

We analyzed the variation with depth in the composition of members of the domain Bacteria in samples from alkaline, hypersaline, and currently meromictic Mono Lake in California. DNA samples were collected from the mixolimnion (2 m), the base of the oxycline (17.5 m), the upper chemocline (23 m), and the monimolimnion (35 m). Composition was assessed by sequencing randomly selected cloned fragments of 16S rRNA genes retrieved from the DNA samples. Most of the 212 sequences retrieved from the samples fell into five major lineages of the domain BACTERIA: alpha- and gamma-Proteobacteria (6 and 10%, respectively), Cytophaga-Flexibacter-Bacteroides (19%), high-G+C-content gram-positive organisms (Actinobacteria; 25%), and low-G+C-content gram-positive organisms (Bacillus and Clostridium; 19%). Twelve percent were identified as chloroplasts. The remaining 9% represented beta- and delta-Proteobacteria, Verrucomicrobiales, and candidate divisions. Mixolimnion and oxycline samples had low microbial diversity, with only 9 and 12 distinct phylotypes, respectively, whereas chemocline and monimolimnion samples were more diverse, containing 27 and 25 phylotypes, respectively. The compositions of microbial assemblages from the mixolimnion and oxycline were not significantly different from each other (P = 0.314 and 0.877), but they were significantly different from those of chemocline and monimolimnion assemblages (P < 0.001), and the compositions of chemocline and monimolimnion assemblages were not significantly different from each other (P = 0.006 and 0.124). The populations of sequences retrieved from the mixolimnion and oxycline samples were dominated by sequences related to high-G+C-content gram-positive bacteria (49 and 63%, respectively) distributed in only three distinct phylotypes, while the population of sequences retrieved from the monimolimnion sample was dominated (52%) by sequences related to low-G+C-content gram-positive bacteria distributed in 12 distinct phylotypes. Twelve and 28% of the sequences retrieved from the chemocline sample were also found in the mixolimnion and monimolimnion samples, respectively. None of the sequences retrieved from the monimolimnion sample were found in the mixolimnion or oxycline samples. Elevated diversity in anoxic bottom water samples relative to oxic surface water samples suggests a greater opportunity for niche differentiation in bottom versus surface waters of this lake.     

Effective control of yellow stem borer and rice leaf folder in transgenic rice indica varieties Basmati 370 and M 7 using the novel δ-endotoxin cry2A Bacillus thuringiensis gene

Transgenic rice indica varieties Basmati 370 and M 7 expressing the novel cry2A (Bt) insecticidal gene were generated by particle bombardment. Molecular and biochemical analyses in R0 and R1 populations confirmed stable integration and expression of this novel Bt transgene. We estimated that the gene product was expressed up to 5% of total leaf protein. Insect feeding bioassays demonstrated that the Cry2A protein was effective against the yellow stem borer and the rice leaf folder, two major rice pests in the Indian Subcontinent. This is the first report of the control of major rice pests using this specific Bt gene. The cry2A gene can now be used in combination with other insecticidal genes for pyramiding resistance against insect pests. This will delay, or perhaps in combination with integrated pest management practices, prevent evolution of insect populations resistant to single insecticidal genes.     

Impaired mitochondrial respiration promotes dendritic branching via the AMPK signaling pathway

Functional neuronal circuits require a constant remodeling of their network composed of highly interconnected neurons. The plasticity of synapses and the shaping of elaborated dendritic branches are energy demanding and therefore depend on an efficient mitochondrial oxidative phosphorylation (OXPHOS). The spatial and functional regulations of dendritic patterning occur also after cell fate specification; however, the molecular mechanisms underlying this complex process remain elusive. Here, we exploit the changes in dendritic architecture in highly branched neurons as a result of aberrant mitochondrial activity. In sensory neurons of Caenorhabditis elegans, genetic manipulations of mitochondrial complex I subunits cause an unexpected outgrowth of dendritic arbors and ectopic structures. The increased number of dendritic branches is coordinated through a specific signaling cascade rather than as a simple consequence of oxidative stress. On the basis of genetic and pharmacological evidence, we show that OXPHOS deficiency promotes branching through the activation of the AMP-activated protein kinase AMPK and the downstream target phosphoinositide 3-kinase PI3K. Taken together, our findings describe a well-defined signaling pathway that regulates dendritic outgrowth in conditions of compromised OXPHOS and the resulting AMPK activation.     

Mitigating Strategies of Gibberellins in Various Environmental Cues and Their Crosstalk with Other Hormonal Pathways in Plants: a Review

Plant Molecular Biology Reporter - Phytohormones are chemical substances that in minute concentration instruct a plethora of developmental and physiological responses in plants. These signal...     

Direct, genome-wide assessment of DNA mutations in single cells

DNA mutations are the inevitable consequences of errors that arise during replication and repair of DNA damage. Because of their random and infrequent occurrence, quantification and characterization of DNA mutations in the genome of somatic cells has been difficult. Random, low-abundance mutations are currently inaccessible by standard high-throughput sequencing approaches because they cannot be distinguished from sequencing errors. One way to circumvent this problem and simultaneously account for the mutational heterogeneity within tissues is whole genome sequencing of a representative number of single cells. Here, we show elevated mutation levels in single cells from Drosophila melanogaster S2 and mouse embryonic fibroblast populations after treatment with the powerful mutagen N-ethyl-N-nitrosourea. This method can be applied as a direct measure of exposure to mutagenic agents and for assessing genotypic heterogeneity within tissues or cell populations.