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At least 415 records · Page 23Linked to original sources
PubMed2006

Comparative genomics reveals long, evolutionarily conserved, low-complexity islands in yeast proteins.

Eukaryotic proteomes abound in low-complexity sequences, including tandem repeats and regions with significantly biased amino acid compositions. We assessed the functional importance of compositionally biased sequences in the yeast proteome using an evolutionary analysis of 2838 orthologous open reading frame (ORF) families from three Saccharomyces species (S. cerevisiae, S. bayanus, and S. paradoxus). Sequence conservation was measured by the amino acid sequence variability and by the ratio of nonsynonymous-to-synonymous nucleotide substitutions (K(a)/K(s)) between pairs of orthologous ORFs. A total of 1033 ORF families contained one or more long (at least 45 residues), low-complexity islands as defined by a measure based on the Shannon information index. Low-complexity islands were generally less conserved than ORFs as a whole; on average they were 50% more variable in amino acid sequences and 50% higher in K(a)/K(s) ratios. Fast-evolving low-complexity sequences outnumbered conserved low-complexity sequences by a ratio of 10 to 1. Sequence differences between orthologous ORFs fit well to a selectively neutral Poisson model of sequence divergence. We therefore used the Poisson model to identify conserved low-complexity sequences. ORFs containing the 33 most conserved low-complexity sequences were overrepresented by those encoding nucleic acid binding proteins, cytoskeleton components, and intracellular transporters. While a few conserved low-complexity islands were known functional domains (e.g., DNA/RNA-binding domains), most were uncharacterized. We discuss how comparative genomics of closely related species can be employed further to distinguish functionally important, shorter, low-complexity sequences from the vast majority of such sequences likely maintained by neutral processes.

Amino Acid Sequence↗
PubMed2005

Evolutionary conservation and characterization of the bare lymphocyte syndrome transcription factor RFX-B and its paralogue ANKRA2.

The extraordinary homology between major histocompatibility complex class II (MHC II) proteins across species from human to bony fish suggests that transcription factors that regulate these proteins might be conserved as well. Deficiencies in four proteins that regulate MHC II genes in humans (RFX-B, RFX5, RFXAP, and CIITA) cause an inherited immunodeficiency disorder known as the bare lymphocyte syndrome (BLS). To understand the structure and mechanism of function of the BLS transcription factors, we analyzed the evolutionary history of RFX-B, the factor deficient in the majority of patients with BLS. Sequence comparison and analysis of the RFX-B proteins showed that RFX-B and a closely related protein, ANKRA2, are present in humans to bony fish and that specific domains are highly conserved. In addition to sequence conservation, functional conservation exists, as mouse and Xenopus RFX-B orthologues, but not the paralogous protein ANKRA2, were able to complement the MHC II deficiency in a BLS-patient-derived cell line deficient in RFX-B. The remarkable conservation of the RFX-B lineage attests to the conservation of the regulation mechanism for this gene system and its importance to precisely regulate MHC class II molecules in both the developing and active immune response.

Amino Acid Sequence↗
PubMed2005

Measuring and incorporating vulnerability into conservation planning.

Conservation planning is the process of locating and designing conservation areas to promote the persistence of biodiversity in situ. To do this, conservation areas must be able to mitigate at least some of the proximate threats to biodiversity. Information on threatening processes and the relative vulnerability of areas and natural features to these processes is therefore crucial for effective conservation planning. However, measuring and incorporating vulnerability into conservation planning have been problematic. We develop a conceptual framework of the role of vulnerability assessments in conservation planning and propose a definition of vulnerability that incorporates three dimensions: exposure, intensity, and impact. We review and categorize methods for assessing the vulnerability of areas and the features they contain and identify the relative strengths and weaknesses of each broad approach. Our review highlights the need for further development and evaluation of approaches to assess vulnerability and for comparisons of their relative effectiveness.

Animals↗
PubMed2006

Incentive-based conservation programs in developing countries: a review of some key issues and suggestions for improvements.

Biodiversity conservation in developing countries has been a challenge because of the combination of rising human populations, rapid technological advances, severe social hardships, and extreme poverty. To address the social, economic, and ecological limitations of people-free parks and reserves, incentives have been incorporated into conservation programs in the hopes of making conservation meaningful to local people. However, such incentive-based programs have been implemented with little consideration for their ability to fulfill promises of greater protection of biodiversity. Evaluations of incentive-based conservation programs indicate that the approach continually falls short of the rhetoric. This article provides an overview of the problems associated with incentive-based conservation approaches in developing countries. It argues that existing incentive-based programs (IBPs) have yet to realize that benefits vary greatly at different "community" scales and that a holistic conceptualization of a community is essential to incorporate the complexities of a heterogeneous community when designing and implementing the IBPs. The spatial complexities involved in correctly identifying the beneficiaries in a community and the short-term focus of IBPs are two major challenges for sustaining conservation efforts. The article suggests improvements in three key areas: accurate identification of "target" beneficiaries, greater inclusion of marginal communities, and efforts to enhance community aptitudes.

Biodiversity↗
PubMed2006

Even conservation rules are made to be broken: implications for biodiversity.

Despite efforts to enclose and control conservation zones around the world, direct human impacts in conservation areas continue, often resulting from clandestine violations of conservation rules through outright poaching, strategic agricultural encroachment, or noncompliance. Nevertheless, next to nothing is actually known about the spatially and temporally explicit patterns of anthropogenic disturbance resulting from such noncompliance. This article reviews current understandings of ecological disturbance and conservation noncompliance, concluding that differing forms of noncompliance hold differing implications for diversity. The authors suggest that forms of anthropogenic patchy disturbance resulting from violation may maintain, if not enhance, floral diversity. They therefore argue for extended empirical investigation of such activities and call for conservation biologists to work with social scientists to assess this conservation reality by analyzing how and when incomplete enforcement and rule-breaking drive ecological change.

Biodiversity↗
PubMed2006

Integrating human impacts and ecological integrity into a risk-based protocol for conservation planning.

Conservation planning aims to protect biodiversity by sustainng the natural physical, chemical, and biological processes within representative ecosystems. Often data to measure these components are inadequate or unavailable. The impact of human activities on ecosystem processes complicates integrity assessments and might alter ecosystem organization at multiple spatial scales. Freshwater conservation targets, such as populations and communities, are influenced by both intrinsic aquatic properties and the surrounding landscape, and locally collected data might not accurately reflect potential impacts. We suggest that changes in five major biotic drivers-energy sources, physical habitat, flow regime, water quality, and biotic interactions-might be used as surrogates to inform conservation planners of the ecological integrity of freshwater ecosystems. Threats to freshwater systems might be evaluated based on their impact to these drivers to provide an overview of potential risk to conservation targets. We developed a risk-based protocol, the Ecological Risk Index (ERI), to identify watersheds with least/most risk to conservation targets. Our protocol combines risk-based components, specifically the frequency and severity of human-induced stressors, with biotic drivers and mappable land- and water-use data to provide a summary of relative risk to watersheds. We illustrate application of our protocol with a case study of the upper Tennessee River basin, USA. Differences in risk patterns among the major drainages in the basin reflect dominant land uses, such as mining and agriculture. A principal components analysis showed that localized, moderately severe threats accounted for most of the threat composition differences among our watersheds. We also found that the relative importance of threats is sensitive to the spatial grain of the analysis. Our case study demonstrates that the ERI is useful for evaluating the frequency and severity of ecosystem-wide risk, which can inform local and regional conservation planning.

Agriculture↗
PubMed2001

Does community-based conservation shape favorable attitudes among locals? an empirical study from nepal.

Like many developing countries, Nepal has adopted a community-based conservation (CBC) approach in recent years to manage its protected areas mainly in response to poor park-people relations. Among other things, under this approach the government has created new "people-oriented" conservation areas, formed and devolved legal authority to grassroots-level institutions to manage local resources, fostered infrastructure development, promoted tourism, and provided income-generating trainings to local people. Of interest to policy-makers and resource managers in Nepal and worldwide is whether this approach to conservation leads to improved attitudes on the part of local people. It is also important to know if personal costs and benefits associated with various intervention programs, and socioeconomic and demographic characteristics influence these attitudes. We explore these questions by looking at the experiences in Annapurna and Makalu-Barun Conservation Areas, Nepal, which have largely adopted a CBC approach in policy formulation, planning, and management. The research was conducted during 1996 and 1997; the data collection methods included random household questionnaire surveys, informal interviews, and review of official records and published literature. The results indicated that the majority of local people held favorable attitudes toward these conservation areas. Logistic regression results revealed that participation in training, benefit from tourism, wildlife depredation issue, ethnicity, gender, and education level were the significant predictors of local attitudes in one or the other conservation area. We conclude that the CBC approach has potential to shape favorable local attitudes and that these attitudes will be mediated by some personal attributes.

Adolescent↗
PubMed2003

Strong conservation of the human NF2 locus based on sequence comparison in five species.

We analyzed 137 kb covering human neurofibromatosis 2 ( NF2) tumor suppressor locus and orthologous loci from baboon, mouse, rat, and pufferfish Takifugu rubripes. A predominant feature of human-rodent conservation is a very similar distribution of conserved islands, regarding length, position, and degree of identity. By use of a threshold of 75% identity over > or =100 bp of gap-free alignment, comparisons of human-mouse sequences resulted in 3.58% for extra-exonic conservation, which can be compared to 4.5% of exonic sequence content within the human locus. We identified a duplication of neurofibromin 2 in pufferfish, which resulted in two putative proteins with 74% and 76% identity to the human protein. One distinct island (called inter 1), conserved between all analyzed species, was located between promoters of the NIPSNAP1 and NF2 genes. Inter 1 might represent a novel regulatory element, important for the function of this locus. The high level of intronic conservation in the NF2 locus suggests that a number of unknown regulatory elements might exist within this gene. These elements could be affected by disease-causing mutations in NF2 patients and NF2-associated tumors. Alternatively, this conservation might be explained by presence of not yet characterized transcriptional unit(s) within this locus.

Amino Acid Sequence↗
PubMed1995

The extra sex combs protein is highly conserved between Drosophila virilis and Drosophila melanogaster.

Extra sex combs (esc) is one of the Polycomb Group genes, whose products are required for long term maintenance of the spatially restricted domains of homeotic gene expression initially established by the products of the segmentation genes. We recently showed that the esc protein contains five copies of the WD motif, which in other proteins has been directly implicated in protein-protein interactions. Mutations affecting the WD repeats of the esc protein indicate that they are essential for its function as a repressor of the homeotic genes. We proposed that they may mediate interactions between esc and other Polycomb Group proteins, recruiting them to their target genes, perhaps by additional interactions with transiently expressed repressors such as hunchback. To further investigate the functional importance of the WD motifs and identify other functionally important regions of the esc protein, we have begun to determine its evolutionary conservation by characterizing the esc gene from Drosophila virilis, a distantly related Drosophila species. We show that the esc protein is highly conserved between these species, particularly its WD motifs. Their high degree of conservation, particularly at positions which are not conserved in the WD consensus derived from alignment of all known WD motifs, suggests that each of the WD repeats in the esc protein is functionally specialized and that this specialization has been highly conserved during evolution. Its highly charged N-terminus exhibits the greatest divergence, but even these differences are conservative of its predicted physical properties. These observations suggest that the esc protein is functionally compact, nearly every residue making an important contribution to its function.

Amino Acid Sequence↗
PubMed2006

A new method for quantifying residue conservation and its applications to the protein folding nucleus.

The conservation of residues in columns of a multiple sequence alignment (MSA) reflects the importance of these residues for maintaining the structure and function of a protein. To date, many scores have been suggested for quantifying residue conservation, but none has achieved the full rigor both in biology and statistics. In this paper, we present a new approach for measuring the evolutionary conservation at aligned positions. Our conservation measure is related to the logarithmic probabilities for aligned positions, and combines the physicochemical properties and the frequencies of amino acids. Such a measure is both biologically and statistically meaningful. For testing the relationship between an amino acid's evolutionary conservation and its role in the Phi-value defined protein folding kinetics, our results indicate that the folding nucleus residues may not be significantly more conserved than other residues by using the biological-relevance weighted statistical scoring method suggested in this paper as an alternative to entropy-based procedures.

Amino Acid Sequence↗
PubMed2003

Local people's attitudes towards conservation and wildlife tourism around Sariska Tiger Reserve, India.

Conservationists in the recent years view local peoples' support for protected areas management as an important element of biodiversity conservation. This is often linked to the direct benefits, which local communities get from the protected areas. These benefits could be in the form of biomass resources, park funds diverted to local villages by state agencies and revenue from wildlife tourism. There are a very few studies which have attempted to study the direct relationship between benefits from wildlife tourism and local support for conservation. In India, wildlife tourism is restricted, and mostly controlled by state and private agencies. Wildlife conservation policy does not view tourism in protected areas as a source of revenue for the local communities. The present study examines the local people's attitudes towards wildlife tourism and the impact of benefits from tourism on the local support for Sariska Tiger Reserve (STR), India. STR is a flagship for tourism where protected areas are increasingly being visited and where local support for wildlife tourism has not been studied adequately. Results indicate that two-thirds of the respondents were positive towards tourism and support for conservation. The respondents were aware that more tourism benefits are possible from a well-conserved protected area. There appears to be correlation between benefits obtained by local people from wildlife tourism and other sources, and support for protected area existence, suggesting that benefits impact people's attitudes towards conservation. Some of the main problems are the unequal distribution of tourism benefits, lack of locals' involvement in tourism and development. There is a need to clearly address these issues, so that protected areas may get the support of local people, which may lead to sustainable development.

Animals↗
PubMed2005

The conservation benefits of cost-effective land acquisition: a case study in Maryland.

Economic theory asserts that to achieve maximum conservation benefits land acquisition needs to be cost effective. Yet the most common planning technique used by land conservation organizations is 'benefit-targeting' that focuses only on acquiring parcels with the highest benefits and ignores costs. Unlike most of the literature which focuses on covering problems, this research applies optimization techniques to achieve maximum aggregate conservation benefits for an ongoing land acquisition effort in the Catoctin Mountain Region in central Maryland. For this case study, optimization yields additional conservation benefits worth an estimated 3.1-3.9 million US dollars or achieves the same level of conservation benefits but at a cost savings ranging from 0.9 to 3.5 million US dollars, depending on the initial budget size. Finally, the highest efficiencies are achieved in low budget scenarios, like those most prevalent in conservation efforts.

Budgets↗
PubMed2005

PEDF and the serpins: phylogeny, sequence conservation, and functional domains.

Pigment epithelium derived factor (PEDF) is non-inhibitory serpin with neurotrophic and antiangiogenic functions. In this study, we have assembled PEDF sequences for 9 additional species by data base mining and performed cross-species alignment for 14 PEDF sequences to identify conserved structural domains. We found evolutionary conservation of a leader sequence, a single C-terminal glycosylation site, collagen-binding residues, and four specific conserved PEDF peptides. The C-terminus, 384--415 and an N-terminal region 78--95, show close homology with many other serpins, and there is strong conservation of 39 of 51 consensus key residues involved in serpin structure and function. Two peptide regions, 40--67 and 277--301, are unique to PEDF but conserved in all species. Conserved residues at the N-terminus, helix d (hD), and helix A (hA) of PEDF form a structure similar to the heparin-binding groove of other serpins. We identified a motif in PEDF that is homologous to the nuclear localization signals of other proteins. A bitopographical localization of PEDF was confirmed by immunocytochemistry and Western blots. Our results suggest that secretion is required for PEDF's activity, that PEDF can migrate to the nucleus, and that PEDF has structural and functional features more common with inhibitory serpins.

Amino Acid Motifs↗
PubMed2004

Computational prediction of conserved operons and phylogenetic footprinting of transcription regulatory elements in the metal-reducing bacterial family Geobacteraceae.

Members of the family Geobacteraceae are an important group of microorganisms from the delta subdivision of Proteobacteria that couple the oxidation of organic compounds to metal reduction. In order to uncover transcription regulatory interactions in these organisms, we used computational methods to identify conserved operons and putative cis-regulatory transcription elements. We identified 26 putative operons with gene order and function conserved among two species of Geobacteraceae, Geobacter sulfurreducens and Geobacter metallireducens. Most of these operons were also conserved in Desulfovibrio vulgaris, an additional metal reducing organism from family Desulfovibrionaceae of the delta subdivision of Proteobacteria. The predicted conserved operons were investigated for the presence of transcription factor binding sites by two different methods, (i) comparison of non-coding regions in conserved operons, and (ii) neural network promoter prediction. Predicted motifs were screened to identify most likely transcription factor binding sites and ribosome-binding sites. We provide information on motifs in Geobacteraceae similar to known transcription factor binding sites in Escherichia coli, conserved motifs in other bacterial species, putative palindromic sites, and predicted ribosome-binding sites. These predictions will aid in further elucidation of regulatory networks of gene interactions in Geobacteraceae.

Animals↗
PubMed2005

Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function.

The mammalian transcriptome contains many non-protein-coding RNAs (ncRNAs), but most of these are of unclear significance and lack strong sequence conservation, prompting suggestions that they might be non-functional. However, certain long functional ncRNAs such as Air and Xist are also poorly conserved. In this article, we systematically analyzed the conservation of several groups of functional ncRNAs, including miRNAs, snoRNAs and longer ncRNAs whose function has been either documented or confidently predicted. As expected, miRNAs and snoRNAs were highly conserved. By contrast, the longer functional non-micro, non-sno ncRNAs were much less conserved with many displaying rapid sequence evolution. Our findings suggest that longer ncRNAs are under the influence of different evolutionary constraints and that the lack of conservation displayed by the thousands of candidate ncRNAs does not necessarily signify an absence of function.

Animals↗
PubMed2000

Mutational analysis of the highly conserved C-terminal residues of the XylS protein, a member of the AraC family of transcriptional regulators.

The XylS protein of the TOL plasmid of Pseudomonas putida belongs to the so-called AraC/XylS family of regulators, that includes more than 100 different bacterial proteins. A conserved stretch of about 100 amino acids is present at the C-terminal end. This conserved region is believed to contain seven alpha-helices, including two helix-turn-helix (HTH) DNA binding motifs (alpha(2)-T-alpha(3) and alpha(5)-Talpha-(6)), connected by a linker alpha-helix (alpha(4)), and two flanking alpha-helices (alpha(1) and alpha(7)). The second HTH motif is the region with the highest homology in the proteins of the family, with certain residues showing almost 90% identity. We have constructed XylS single mutants in the most conserved residues and have analysed their ability to stimulate transcription from its cognate promoter, Pm, fused to 'lacZ. The analysis revealed that mutations in the alpha(5)-helix conserved residues had little effect on the XylS transcriptional activity, whereas the distribution of polarity in the alpha(6)-helix was important for the activity. The strongest effect of the mutations was observed in conserved residues located outside the DNA binding domain, namely, Gly-290 in the turn between the two helices, Pro-309 located downstream of alpha(6), and Leu-313, in the small last helix alpha(7), that seems to play an important role in the activation of RNA-polymerase. Our analysis shows that conservation of amino acids in the family reflects structural requirements rather than functionality in specific DNA interactions.

Amino Acid Sequence↗
PubMed2000

The role of conserved extracellular cysteine residues in vasopressin V2 receptor function and properties of two naturally occurring mutant receptors with additional extracellular cysteine residues.

The G protein-coupled vasopressin V2 receptor (V2 receptor) contains a pair of conserved cysteine residues (C112 and C192) which are thought to form a disulfide bond between the first and second extracellular loops. The conserved cysteine residues were found to be important for the correct formation of the ligand binding domain of some G protein-coupled receptors. Here we have assessed the properties of the V2 receptor after site-directed mutagenesis of its conserved cysteine residues in transiently transfected human embryonic kidney (HEK 293) cells. Mutant receptors (C112S, C112A and C192S, C192A) were non-functional and located mostly in the cell's interior. The conserved cysteine residues of the V2 receptor are thus not only important for the structure of the ligand binding domain but also for efficient intracellular receptor transport. In addition to the functional significance of the conserved cysteine residues, we have also analyzed the defects of two mutant V2 receptors which cause X-linked nephrogenic diabetes insipidus (NDI) by the introduction of additional cysteine residues into the second extracellular loop (mutants G185C, R202C). These mutations are assumed to impair normal disulfide bond formation. Mutant receptor G185C and R202C were efficiently transported to the plasma membrane but were defective in ligand binding. Only in the case of the mutant receptor R202C, the more sensitive adenylyl cyclase activity assay revealed vasopressin-stimulated cAMP formation with a 35-fold increased EC(50) value and with a reduced EC(max), indicating that ligand binding is not completely abolished. Taking the unaffected intracellular transport of both NDI-causing mutant receptors into account, our results indicate that the observed impairment of ligand binding by the additional cysteine residues is not due to the prevention of disulfide bond formation between the conserved cysteine residues.

Amino Acid Sequence↗
PubMed2002

Sequence and structural conservation in RNA ribose zippers.

The "ribose zipper", an important element of RNA tertiary structure, is characterized by consecutive hydrogen-bonding interactions between ribose 2'-hydroxyls from different regions of an RNA chain or between RNA chains. These tertiary contacts have previously been observed to also involve base-backbone and base-base interactions (A-minor type). We searched for ribose zipper tertiary interactions in the crystal structures of the large ribosomal subunit RNAs of Haloarcula marismortui and Deinococcus radiodurans, and the small ribosomal subunit RNA of Thermus thermophilus and identified a total of 97 ribose zippers. Of these, 20 were found in T. thermophilus 16 S rRNA, 44 in H. marismortui 23 S rRNA (plus 2 bridging 5 S and 23 S rRNAs) and 30 in D. radiodurans 23 S rRNA (plus 1 bridging 5 S and 23 S rRNAs). These were analyzed in terms of sequence conservation, structural conservation and stability, location in secondary structure, and phylogenetic conservation. Eleven types of ribose zippers were defined based on ribose-base interactions. Of these 11, seven were observed in the ribosomal RNAs. The most common of these is the canonical ribose zipper, originally observed in the P4-P6 group I intron fragment. All ribose zippers were formed by antiparallel chain interactions and only a single example extended beyond two residues, forming an overlapping ribose zipper of three consecutive residues near the small subunit A-site. Almost all ribose zippers link stem (Watson-Crick duplex) or stem-like (base-paired), with loop (external, internal, or junction) chain segments. About two-thirds of the observed ribose zippers interact with ribosomal proteins. Most of these ribosomal proteins bridge the ribose zipper chain segments with basic amino acid residues hydrogen bonding to the RNA backbone. Proteins involved in crucial ribosome function and in early stages of ribosomal assembly also stabilize ribose zipper interactions. All ribose zippers show strong sequence conservation both within these three ribosomal RNA structures and in a large database of aligned prokaryotic sequences. The physical basis of the sequence conservation is stacked base triples formed between consecutive base-pairs on the stem or stem-like segment with bases (often adenines) from the loop-side segment. These triples have previously been characterized as Type I and Type II A-minor motifs and are stabilized by base-base and base-ribose hydrogen bonds. The sequence and structure conservation of ribose zippers can be directly used in tertiary structure prediction and may have applications in molecular modeling and design.

Bacteria↗