Terminal-repeat retrotransposons with GAG domain in plant genomes: a new testimony on the complex world of transposable elements

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

High rate of chimeric gene origination by retroposition in plant genomes

Retroposition is widely found to play essential roles in origination of new mammalian and other animal genes. However, the scarcity of retrogenes in plants has led to the assumption that plant genomes rarely evolve new gene duplicates by retroposition, de

Control of meiotic recombination frequency in plant genomes.

Sexual eukaryotes reproduce via the meiotic cell division, where ploidy is halved and homologous chromosomes undergo reciprocal genetic exchange, termed crossover (CO). CO frequency has a profound effect on patterns of genetic variation and species evolution. Relative CO rates vary extensively both within and between plant genomes. Plant genome size varies by over 1000-fold, largely due to differential expansion of repetitive sequences, and increased genome size is associated with reduced CO frequency. Gene versus repeat sequences associate with distinct chromatin modifications, and evidence from plant genomes indicates that this epigenetic information influences CO patterns. This is consistent with data from diverse eukaryotes that demonstrate the importance of chromatin structure for control of meiotic recombination. In this review I will discuss CO frequency patterns in plant genomes and recent advances in understanding recombination distributions.

The non-timber forest products sector in nepal : policy issues in plant conservation and utilization

The non-timber forest products (NTFPs) sector in Nepal is being promoted with the concept of sustainable management as articulated by the Convention on Biological Diversity. To promote and regulate this sector, Nepal adopted the Herbs and NTFP Development Policy in 2004. The goal of this thesis was to assess the effectiveness of this policy along with other forestry and natural resource policies in Nepal concerning the conservation and sustainable use of NTFPs. I conducted open-ended semi-structured interviews with 28 key informants in summer 2006 in Nepal where I also collected relevant documents and publications. I did qualitative analysis of data obtained from interviews and document review. The research found many important issues that need to be addressed to promote the NTFP sector as envisioned by the Government of Nepal. The findings of this research will help to further implement the policy and promote the NTFP sector through sustainable management practices.

Exploring plant genomes by RNA-induced gene silencing

The nucleotide sequences of several animal, plant and bacterial genomes are now known, but the functions of many of the proteins that they are predicted to encode remain unclear. RNA interference is a gene-silencing technology that is being used successfully to investigate gene function in several organisms - for example, Caenorhabditis elegans. We discuss here that RNA-induced gene silencing approaches are also likely to be effective for investigating plant gene function in a high-throughput, genome-wide manner.

Coincident sequence-specific RNA degradation of linked transgenes in the plant genome

The expression of transgenes in plant genomes can be inhibited by either transcriptional gene silencing or posttranscriptional gene silencing (PTGS). Overexpression of the chalcone synthase-A (CHS-A) transgene triggers PTGS of CHS-A and thus results in loss of flower pigmentation in petunia. We previously demonstrated that epigenetic inactivation of CHS-A transgene transcription leads to a reversion of the PTGS phenotype. Although neomycin phosphotransferase II (nptII), a marker gene co-introduced into the genome with the CHS-A transgene, is not normally silenced in petunia, even when CHS-A is silenced, here we found that nptII was silenced in a petunia line in which CHS-A PTGS was induced, but not in the revertant plants that had no PTGS of CHS-A. Transcriptional activity, accumulation of short interfering RNAs, and restoration of mRNA level after infection with viruses that had suppressor proteins of gene silencing indicated that the mechanism for nptII silencing was posttranscriptional. Read-through transcripts of the CHS-A gene toward the nptII gene were detected. Deep-sequencing analysis revealed a striking difference between the predominant size class of small RNAs produced from the read-through transcripts (22 nt) and that from the CHS-A RNAs (21 nt). These results implicate the involvement of read-through transcription and distinct phases of RNA degradation in the coincident PTGS of linked transgenes and provide new insights into the destabilization of transgene expression.

Role of RNA polymerase IV in plant small RNA metabolism.

In addition to the three RNA polymerases (RNAP I-III) shared by all eukaryotic organisms, plant genomes encode a fourth RNAP (RNAP IV) that appears to be specialized in the production of siRNAs. Available data support a model in which dsRNAs are generated by RNAP IV and RNA-dependent RNAP 2 (RDR2) and processed by DICER (DCL) enzymes into 21- to 24-nt siRNAs, which are associated with different ARGONAUTE (AGO) proteins for transcriptional or posttranscriptional gene silencing. However, it is not yet clear what fraction of genomic siRNA production is RNAP IV-dependent, and to what extent these siRNAs are preferentially processed by certain DCL(s) or associated with specific AGOs for distinct downstream functions. To address these questions on a genome-wide scale, we sequenced approximately 335,000 siRNAs from wild-type and RNAP IV mutant Arabidopsis plants by using 454 technology. The results show that RNAP IV is required for the production of >90% of all siRNAs, which are faithfully produced from a discrete set of genomic loci. Comparisons of these siRNAs with those accumulated in rdr2 and dcl2 dcl3 dcl4 and those associated with AGO1 and AGO4 provide important information regarding the processing, channeling, and functions of plant siRNAs. We also describe a class of RNAP IV-independent siRNAs produced from endogenous single-stranded hairpin RNA precursors.

Phycobilisomes linker family in cyanobacterial genomes: divergence and evolution

Cyanobacteria are the oldest life form making important contributions to global CO2 fixation on the Earth. Phycobilisomes (PBSs) are the major light harvesting systems of most cyanobacteria species. Recent availability of the whole genome database of cyanobacteria provides us a global and further view on the complex structural PBSs. A PBSs linker family is crucial in structure and function of major light-harvesting PBSs complexes. Linker polypeptides are considered to have the same ancestor with other phycobiliproteins (PBPs), and might have been diverged and evolved under particularly selective forces together. In this paper, a total of 192 putative linkers including 167 putative PBSs-associated linker genes and 25 Ferredoxin-NADP oxidoreductase (FNR) genes were detected through whole genome analysis of all 25 cyanobacterial genomes (20 finished and 5 in draft state). We compared the PBSs linker family of cyanobacteria in terms of gene structure, chromosome location, conservation domain, and polymorphic variants, and discussed the features and functions of the PBSs linker family. Most of PBSs-associated linkers in PBSs linker family are assembled into gene clusters with PBPs. A phylogenetic analysis based on protein data demonstrates a possibility of six classes of the linker family in cyanobacteria. Emergence, divergence, and disappearance of PBSs linkers among cyanobacterial species were due to speciation, gene duplication, gene transfer, or gene loss, and acclimation to various environmental selective pressures especially light.

Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes

BACKGROUND:Recent advances in genome sequencing suggest a remarkable conservation in gene content of mammalian organisms. The similarity in gene repertoire present in different organisms has increased interest in studying regulatory mechanisms of gene expression aimed at elucidating the differences in phenotypes. In particular, a proximal promoter region contains a large number of regulatory elements that control the expression of its downstream gene. Although many studies have focused on identification of these elements, a broader picture on the complexity of transcriptional regulation of different biological processes has not been addressed in mammals. The regulatory complexity may strongly correlate with gene function, as different evolutionary forces must act on the regulatory systems under different biological conditions. We investigate this hypothesis by comparing the conservation of promoters upstream of genes classified in different functional categories.RESULTS:By conducting a rank correlation analysis between functional annotation and upstream sequence alignment scores obtained by human-mouse and human-dog comparison, we found a significantly greater conservation of the upstream sequence of genes involved in development, cell communication, neural functions and signaling processes than those involved in more basic processes shared with unicellular organisms such as metabolism and ribosomal function. This observation persists after controlling for G+C content. Considering conservation as a functional signature, we hypothesize a higher density of cis-regulatory elements upstream of genes participating in complex and adaptive processes.CONCLUSION:We identified a class of functions that are associated with either high or low promoter conservation in mammals. We detected a significant tendency that points to complex and adaptive processes were associated with higher promoter conservation, despite the fact that they have emerged relatively recently during evolution. We described and contrasted several hypotheses that provide a deeper insight into how transcriptional complexity might have been emerged during evolution.

Chloroplast microsatellites: new tools for studies in plant ecology and systematics

The nonrecombinant, uniparentally inherited nature of organelle genomes
makes them useful tools for evolutionary studies. However, in plants, detecting
useful polymorphism at the population level is often difficult because of the
low level of substitutions in the chloroplast genome, and because of the slow
substitution rates and intramolecular recombination of mtDNA. Chloroplast
microsatellites represent potentially useful markers to circumvent this problem
and, to date, studies have demonstrated high levels of intraspecific variability.
Here,we discuss the use of these markers in ecological and evolutionary
studies of plants, as well as highlighting some of the potential problems
associated with such use.

Getting to the root of neuronal signalling in plant-parasitic nematodes using RNA interference

A variety of genes expressed in preparasitic second-stage juveniles (J2) of plant-parasitic nematodes appear to be vulnerable to RNA interference (RNAi) in vitro by coupling double-stranded (ds)RNA soaking with the artificial stimulation of pharyngeal pumping. Also, there is mounting evidence that the in planta generation of nematode-specific double-stranded RNAs (dsRNAs) has real utility in the control of these pests. Although neuronally-expressed genes in Caenorhabditis elegans are commonly refractory to RNAi, we have discovered that neuronally-expressed genes in plant-parasitic nematodes are highly susceptible to RNAi and that silencing can be induced by simple soaking procedures without the need for pharyngeal stimulation. Since most front-line anthelmintics that are used for the control of nematode parasites of animals and humans act to disrupt neuromuscular coordination, we argue that intercellular signalling processes associated with neurons have much appeal as targets for transgenic plant-based control strategies for plant-parasitic nematodes. FMRFamide-like peptides (FLPs) are a large family of neuropeptides which are intimately associated with neuromuscular regulation, and our studies on flp gene function in plant-parasitic nematodes have revealed that their expression is central to coordinated locomotory activities. We propose that the high level of conservation in nervous systems across nematodes coupled with the RNAi-susceptibility of neuronally-expressed genes in plant-parasitic nematodes provides a valuable research tool which could be used to interrogate neuronal signalling processes in nematodes.

Assessment of Energy Conservation in Indian Cement Industry and Forecasting of Co2 Emissions

Cement industry ranks 2nd in energy consumption among the industries in India. It is one of the major emitter of CO2, due to combustion of fossil fuel and calcination process. As the huge amount of CO2 emissions cause severe environment problems, the efficient and effective utilization of energy is a major concern in Indian cement industry. The main objective of the research work is to assess the energy cosumption and energy conservation of the Indian cement industry and to predict future trends in cement production and reduction of CO2 emissions. In order to achieve this objective, a detailed energy and exergy analysis of a typical cement plant in Kerala was carried out. The data on fuel usage, electricity consumption, amount of clinker and cement production were also collected from a few selected cement industries in India for the period 2001 - 2010 and the CO2 emissions were estimated. A complete decomposition method was used for the analysis of change in CO2 emissions during the period 2001 - 2010 by categorising the cement industries according to the specific thermal energy consumption. A basic forecasting model for the cement production trend was developed by using the system dynamic approach and the model was validated with the data collected from the selected cement industries. The cement production and CO2 emissions from the industries were also predicted with the base year as 2010. The sensitivity analysis of the forecasting model was conducted and found satisfactory. The model was then modified for the total cement production in India to predict the cement production and CO2 emissions for the next 21 years under three different scenarios. The parmeters that influence CO2 emissions like population and GDP growth rate, demand of cement and its production, clinker consumption and energy utilization are incorporated in these scenarios. The existing growth rate of the population and cement production in the year 2010 were used in the baseline scenario. In the scenario-1 (S1) the growth rate of population was assumed to be gradually decreasing and finally reach zero by the year 2030, while in scenario-2 (S2) a faster decline in the growth rate was assumed such that zero growth rate is achieved in the year 2020. The mitigation strategiesfor the reduction of CO2 emissions from the cement production were identified and analyzed in the energy management scenarioThe energy and exergy analysis of the raw mill of the cement plant revealed that the exergy utilization was worse than energy utilization. The energy analysis of the kiln system showed that around 38% of heat energy is wasted through exhaust gases of the preheater and cooler of the kiln sysetm. This could be recovered by the waste heat recovery system. A secondary insulation shell was also recommended for the kiln in the plant in order to prevent heat loss and enhance the efficiency of the plant. The decomposition analysis of the change in CO2 emissions during 2001- 2010 showed that the activity effect was the main factor for CO2 emissions for the cement industries since it is directly dependent on economic growth of the country. The forecasting model showed that 15.22% and 29.44% of CO2 emissions reduction can be achieved by the year 2030 in scenario- (S1) and scenario-2 (S2) respectively. In analysing the energy management scenario, it was assumed that 25% of electrical energy supply to the cement plants is replaced by renewable energy. The analysis revealed that the recovery of waste heat and the use of renewable energy could lead to decline in CO2 emissions 7.1% for baseline scenario, 10.9 % in scenario-1 (S1) and 11.16% in scenario-2 (S2) in 2030. The combined scenario considering population stabilization by the year 2020, 25% of contribution from renewable energy sources of the cement industry and 38% thermal energy from the waste heat streams shows that CO2 emissions from Indian cement industry could be reduced by nearly 37% in the year 2030. This would reduce a substantial level of greenhouse gas load to the environment. The cement industry will remain one of the critical sectors for India to meet its CO2 emissions reduction target. India’s cement production will continue to grow in the near future due to its GDP growth. The control of population, improvement in plant efficiency and use of renewable energy are the important options for the mitigation of CO2 emissions from Indian cement industries

Noise levels and hearing conservation in a water treatment facility

This paper describes a study assessing the sound levels and noise exposures of a municipal water treatment plant to determine the level of employee noise exposure dosages and to make any necessary recommendations regarding reducing the risk of noise induced hearing loss in employees.