The expanding world of DNA and RNA

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Meeting water requirements of an expanding world population

Water availability in the root zone (green water) is a critical component of plant production, but is often deficient in many Third World regions. When deficient, runoff water (blue water) can be added. Focusing on ten physiographic regions in Africa and Asia, characterized by mainly or partly dry climates and rapid population growth, this study analyses whether in a 30-years'' perspective enough blue water could be provided to allow food self-sufficiency. It is assumed that for food self-sufficiency some 900 cubic metres of water per person per year has to be provided. In judging the realism it is assumed that a maximum 25 per cent increase in water mobilization rate would be manageable in a 30-year period. The study suggests that by 2025, water scarcity will make regions populated by some 55 per cent of the world''s population dependent on food imports. For water-wasting regions in Central Asia, water saving might, however, free the water needed. The paper closes by proposing some urgent measures. <br>     

The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus

Archaeal L7Ae is a multifunctional protein that binds to a distinctive K-turn motif in RNA and is found as a component in the large subunit of the ribosome, and in ribose methylation and pseudouridylation guide RNP particles. A collection of L7Ae-associated small RNAs were isolated from Sulfolobus solfataricus cell extracts and used to construct a cDNA library; 45 distinct cDNA sequences were characterized and divided into six groups. Group 1 contained six RNAs that exhibited the features characteristic of the canonical C/D box archaeal sRNAs, two RNAs that were atypical C/D box sRNAs and one RNA representative of archaeal H/ACA sRNA family. Group 2 contained 13 sense strand RNA sequences that were encoded either within, or overlapping annotated open reading frames (ORFs). Group 3 contained three sequences form intergenic regions. Group 4 contained antisense sequences from within or overlapping sense strand ORFs or antisense sequences to C/D box sRNAs. More than two-thirds of these sequences possessed K-turn motifs. Group 5 contained two sequences corresponding to internal regions of 7S RNA. Group 6 consisted of 11 sequences that were fragments from the 5' or 3' ends of 16S and 23S ribosomal RNA and from seven different tRNAs. Our data suggest that S. solfataricus contains a plethora of small RNAs. Most of these are bound directly by the L7Ae protein; the others may well be part of larger, transiently stable RNP complexes that contain the L7Ae protein as core component.     

Ribonucleases P/MRP and the expanding ribonucleoprotein world

One of the hallmarks of life is the widespread use of certain essential ribozymes. The ubiquitous ribonuclease P (RNase P) and eukaryotic RNase MRP are essential complexes where a structured, noncoding RNA acts in catalysis. Recent discoveries have elucidated the three-dimensional structure of the ancestral ribonucleoprotein complex, suggested the possibility of a protein-only composition in organelles, and even noted the absence of RNase P in a non-free-living organism. With respect to these last two findings, import mechanisms for RNases P/MRP into mitochondria have been demonstrated, and RNase P is present in organisms with some of the smallest known genomes. Together, these results have led to an ongoing debate regarding the precise definition of how "essential" these ribozymes truly are.     

植物snoRNA

植物体含有的小分子核仁RNA(small nucleolar RNA,snoRNA)是一类典型的非编码RNA,参与rRNA的加工与修饰.该文就植物snoRNA的结构、功能、生物合成与调控研究进展作介绍.     

植物核仁小分子RNA的研究进展

20世纪60年代末Weinberg等在哺乳动物中发现了第一个核仁小分子RNA(small nucleolar RNA,snoRNA)U3,在这一领域的研究特别是在20世纪90年代以来,陆续发现许多新的核仁小分子RNA。近几年对动物、酵母和植物方面snoRNA的研究进展,使人们大大地加深了对于rRNA加工和转录以及一系列生物调控过程和机制的认识,正如Smith和Steitz所说的那样：“核仁中sno风暴”引起生物界极大的震动。本文重点介绍植物snoRNA的研究。     

Recent structural insights into the expanding world of carbohydrate-active enzymes

Enzymes that catalyse the synthesis and breakdown of glycosidic bonds account for 1-3% of the proteins encoded by the genomes of most organisms. At the current rate, over 12 000 glycosyltransferase and glycoside hydrolase open reading frames will appear during 2006. Recent advances in the study of the structure and mechanism of these carbohydrate-active enzymes reveal that glycoside hydrolases continue to display a wide variety of scaffolds, whereas nucleotide-sugar-dependent glycosyltransferases tend to be grafted onto just two protein folds. The past two years have seen significant advances, including the discovery of a novel NAD+-dependent glycosidase mechanism, the dissection of the reaction coordinate of sialidases and a better understanding of the expanding roles of auxiliary carbohydrate-binding domains.     

Oxymoron no more: the expanding world of heterochromatic genes

Heterochromatin has been oversimplified and even misunderstood. In particular, the existence of heterochromatic genes is often overlooked. Diverse types of genes reside within regions classified as constitutive heterochromatin and activating influences of heterochromatin on gene expression in Drosophila are well documented. These properties are usually considered paradoxical because heterochromatin is commonly portrayed as "silent chromatin". In the past, studies of heterochromatic genes were limited to a few Drosophila genes. However, the recent discovery of several hundred heterochromatic genes in Drosophila, plants and mammals through sequencing projects offers new opportunities to examine the variety of ways in which heterochromatin influences gene expression. Comparative genomics is revealing diverse origins of heterochromatic genes and remarkable evolutionary fluidity between heterochromatic and euchromatic domains. These features justify a broader view of heterochromatin, one that accommodates repressive, permissive and activating effects on gene expression, and recognizes chromosomal and evolutionary transitional states between heterochromatin and euchromatin.     

Plant snoRNA database

The Plant snoRNA database (http://www.scri.sari.ac.uk/plant_snoRNA/) provides information on small nucleolar RNAs from Arabidopsis and eighteen other plant species. Information includes sequences, expression data, methylation and pseudouridylation target modification sites, initial gene organization (polycistronic, single gene and intronic) and the number of gene variants. The Arabidopsis information is divided into box C/D and box H/ACA snoRNAs, and within each of these groups, by target sites in rRNA, snRNA or unknown. Alignments of orthologous genes and gene variants from different plant species are available for many snoRNA genes. Plant snoRNA genes have been given a standard nomenclature, designed wherever possible, to provide a consistent identity with yeast and human orthologues.     

Changes in non-randomness in the expanding introduced avifauna of the world

The identities of bird species introduced to areas beyond the limits of their native geographic ranges have historically depended on a combination of societal demands for species with certain characteristics, and the availability of species for capture, transport and release. However, both societal demands and availability have changed over time, which should also change the characteristics of species more recently added to the list of introduced birds. Here, we quantify temporal changes in selectivity of introduced bird species by comparing the characteristics of 423 species listed in the seminal catalogue of introduced birds (Long, J. L. 1981 . Introduced birds of the world. – David and Charles, London) with those of 122 species that have been introduced but are not listed in Long (1981) . We demonstrate differences between these two groups of species in the frequencies with which different taxa are represented, in the geographic range sizes of species, and in their biogeographic regions of origin, but not in body mass. Both groups also differ from bird species in general in terms of geographic range sizes, body masses, and taxonomic composition. We relate the observed differences in the characteristics of species listed or unlisted in Long (1981) to changes in the changes in attitudes, legislation and vectors of transport relating to exotic species. We conclude by noting that the utility of published catalogues of introduced bird species is increasingly being eroded by the continued liberation and establishment of bird species.     

The expanding cell

The final size of a plant depends far less on the number ofcells produced by division than on the massive expansion ofthose cells once they have stopped dividing. Even in the tallestplant the apical meristems that ride this wave of cell expansiononly measure millimetres and, in more modest plants, micrometres.It is the swelling produced by the entry of water into the vacuoleof the non-dividing cells just behind the apex that drives thegrowing point further into its surroundings. This separationbetween division and expansion has been known since the     

The expanding polymerase universe

Over the past year, the number of known prokaryotic and eukaryotic DNA polymerases has exploded. Many of these newly discovered enzymes copy aberrant bases in the DNA template over which 'respectable' polymerases fear to tread. The next step is to unravel their functions, which are thought to range from error-prone copying of DNA lesions, somatic hypermutation and avoidance of skin cancer, to restarting stalled replication forks and repairing double-stranded DNA breaks.     

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing

Background

In recent years, a variety of small RNAs derived from other RNAs with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance of these RNAs is largely unknown. To gain insight into the complexity of snoRNA processing and the functional relevance of snoRNA-derived small RNAs, we sequence long and short RNAs, small RNAs that co-precipitate with the Argonaute 2 protein and RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of core snoRNA-associated proteins.

Results

Analysis of these data sets reveals that many loci in the human genome reproducibly give rise to C/D box-like snoRNAs, whose expression and evolutionary conservation are typically less pronounced relative to the snoRNAs that are currently cataloged. We further find that virtually all C/D box snoRNAs are specifically processed inside the regions of terminal complementarity, retaining in the mature form only 4-5 nucleotides upstream of the C box and 2-5 nucleotides downstream of the D box. Sequencing of the total and Argonaute 2-associated populations of small RNAs reveals that despite their cellular abundance, C/D box-derived small RNAs are not efficiently incorporated into the Ago2 protein.

Conclusions

We conclude that the human genome encodes a large number of snoRNAs that are processed along the canonical pathway and expressed at relatively low levels. Generation of snoRNA-derived processing products with alternative, particularly miRNA-like, functions appears to be uncommon.     

The box C/D motif directs snoRNA 5'-cap hypermethylation

The 5′-cap structure of most spliceosomal small nuclear RNAs (snRNAs) and certain small nucleolar RNAs (snoRNAs) undergoes hypermethylation from a 7-methylguanosine to a 2,2,7-trimethylguanosine structure. 5′-Cap hypermethylation of snRNAs is dependent upon a conserved sequence element known as the Sm site common to most snRNAs. Here we have performed a mutational analysis of U3 and U14 to determine the cis-acting sequences required for 5′-cap hypermethylation of Box C/D snoRNAs. We have found that both the conserved sequence elements Box C (termed C′ in U3) and Box D are necessary for cap hypermethylation. Furthermore, the terminal stem structure that is formed by sequences that flank Box C (C′ in U3) and Box D is also required. However, mutation of other conserved sequences has no effect on hypermethylation of the cap. Finally, the analysis of fragments of U3 and U14 RNAs indicates that the Box C/D motif, including Box C (C′ in U3), Box D and the terminal stem, is capable of directing cap hypermethylation. Thus, the Box C/D motif, which is important for snoRNA processing, stability, nuclear retention, protein binding, nucleolar localization and function, is also necessary and sufficient for cap hypermethylation of these RNAs.     

The expanding prisoner reentry industry

The prisoner reentry industry (PRI) has become a major part of the Social Control Industrial Complex. As with the Prison Industrial Complex, the PRI is not just a collection of institutions, organizations, and interest groups (both public and private); it is also a state of mind. Developing and facilitating programs and services for the formerly incarcerated have become a huge “cash-cow,” producing profits for the PRI at the expense of the taxpayer, while doing little to link the formerly incarcerated person to the social capital and human skills necessary to become a “citizen.” Data that include the voices of the formerly incarcerated, members of their families, and criminal justice practitioners suggest that a person’s level of success during their “personal reentry experience” varies in large part, by the individual parole officer they are assigned to and the number and types of programs they are required to participate in. Furthermore, their quality of life after release and their level of success is determined in large part by the program administrators managing those “for-profit companies” and “non-profit/for-profit agencies,” that supervise parolee programs. The argument here is that there must be a better system for monitoring the activities of those organizations that are in the business of facilitating prisoner reentry-related services. A process of accountability that will ensure that organizations part of the PRI are in fact providing services in the manner that was stated and agreed upon during their request for funding. The most important tool for ending this cycle lies in creating employment opportunities for the formerly incarcerated and empowering them to access those resources afforded all citizens. Consequently, if those agencies and organizations in the business of facilitating prisoner reentry were successful at making available the services they argue they do provide, members of these organizations would work themselves out of a job; that would be a valid indicator of organizational success.