Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1

Splicing patterns in human immunodeficiency virus type 1 (HIV-1) are maintained through cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of the 3′ acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b), and an exonic splicing enhancer (ESE3). Because HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge, and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate that the UP1 domain of heterogeneous nuclear ribonucleoprotein A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Collectively, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA-binding protein.     

Flight loss linked to faster molecular evolution in insects

The loss of flight ability has occurred thousands of times independently during insect evolution. Flight loss may be linked to higher molecular evolutionary rates because of reductions in effective population sizes (N_e) and relaxed selective constraints. Reduced dispersal ability increases population subdivision, may decrease geographical range size and increases (sub)population extinction risk, thus leading to an expected reduction in N_e. Additionally, flight loss in birds has been linked to higher molecular rates of energy-related genes, probably owing to relaxed selective constraints on energy metabolism. We tested for an association between insect flight loss and molecular rates through comparative analysis in 49 phylogenetically independent transitions spanning multiple taxa, including moths, flies, beetles, mayflies, stick insects, stoneflies, scorpionflies and caddisflies, using available nuclear and mitochondrial protein-coding DNA sequences. We estimated the rate of molecular evolution of flightless (FL) and related flight-capable lineages by ratios of non-synonymous-to-synonymous substitutions (dN/dS) and overall substitution rates (OSRs). Across multiple instances of flight loss, we show a significant pattern of higher dN/dS ratios and OSRs in FL lineages in mitochondrial but not nuclear genes. These patterns may be explained by relaxed selective constraints in FL ectotherms relating to energy metabolism, possibly in combination with reduced N_e.     

5S ribosomal gene clusters in wheat: pulsed field gel electrophoresis reveals a high degree of polymorphism

Summary The long-range structure of 5S rRNA gene clusters has been investigated in wheat (Triticum aestivum L.) by means of pulsed field gel electrophoresis. Using aneuploid stocks, 5S rRNA gene clusters were assigned to sites on chromosomes 1B, 1D, 513 and 5D. Cluster sizes were evaluated and the copy number of 5S DNA repeats was estimated at 4700-5200 copies for the short repeating unit (410 bp) and about 3100 copies for the long repeat (500 bp) per haploid genome. A comparison of wheat cultivars revealed extremely high levels of polymorphism in the 5S rRNA gene clusters. With one restriction enzyme digest all varieties tested gave unique banding patterns and, on a per fragment basis, 21-fold more polymorphism was detected among cultivars for 5S DNA compared to standard restriction fragment length polymorphisms (RFLPs) detected with single copy clones. Experiments with aneuploid stocks suggest that the 5S rRNA gene clusters at several chromosomal sites contribute to this polymorphism. A number of previous reports have shown that wheat cultivars are not easily distinguished by isozymes or RFLPs. The high level of variation detected in 5S rRNA gene clusters therefore offers the possibility of a sensitive fingerprinting method for wheat. 5S DNA and other macro-satellite sequences may also serve as hypervariable Mendelian markers for genetic and breeding experiments in wheat.     

The goatfish Pseudupeneus maculatus and its follower fishes at an oceanic island in the tropical west Atlantic

The influence of a substratum-disturbing forager, the spotted goatfish Pseudupeneus maculatus on the assemblage of its escorting, opportunistic-feeding fishes was examined at Fernando de Noronha Archipelago (tropical west Atlantic). Followers attracted to spotted goatfish foraging singly differed from followers of spotted goatfish foraging in groups in several characteristics. The larger the nuclear fish group, the greater the species richness and number of individuals of followers. Moreover, groups of foraging spotted goatfish attracted herbivores, not recorded for spotted goatfish foraging singly. The size of follower individuals increased with the size and the number of foraging spotted goatfish. The zoobenthivorous habits of the spotted goatfish and its ability to disturb a variety of soft substrata render it an important nuclear fish for several follower species of the reef fish assemblage at Fernando de Noronha.     

Regressive evolution: ontogeny and genetics of cavefish eye rudimentation

Two hypotheses exist to explain ontogenetic eye reduction in Astyanax cave fish: first, after lens induction by the primordial eye cup, the lens plays the role of a central regulator of eye and retina regression or, second, the retina itself is an independent unit of eye development. A comparative study of five blind cave fish populations and their surface sister form was performed to investigate the differences of ontogenetic eye regression between the cave populations during different stages of development. The study revealed that, in addition to the initial formation of smaller primordia, eye regression is also caused during later ontogeny by different relative growth and specific histological characteristics. Whereas the cave fish lens never properly differentiates, the regressive process of the retina is transitorily interrupted by ongoing differentiation. In the newly-discovered Molino cave population, even visual cells with well-organized outer segments develop, which are secondarily reduced at a later ontogenetic stage. This result shows that the retina and lens are independent developmental units within the eye ball. Presumably, the genetic systems responsible for both show independent inheritance, which is also corroborated by hybrids of F ₂-crosses between the cave and surface fish, in which lens and retina development do not correlate. During ontogeny, the eye size differs between the cave populations. In Pachón cave fish, the relatively large eye size correlates with an ancient introgression from a surface population, which may have delayed eye regression.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 287–296.     

Do borderline nuclear changes in gynaecological cytlogy constitute a reliable reporting category?

Fourteen laboratories participated in a national slide exchange study to investigate whether borderline nuclear changes (BNC) constitute a reliable reporting category. Slides were submitted by participating laboratories, having achieved a 100% intralaboratory consensus at the primary screener, checker, and medical levels. Sets of seven slides were examined in laboratories for 1 week, and exchanges were undertaken over a 6-month period. Each laboratory was requested to submit three consensus opinions on each slide at the primary screener, checker, and medical levels.
Response patterns for submitted slides achieving a reporting category consensus at the 50 and 80% consensus levels indicated that negative, BNC, and mild dyskaryosis are distinct and comparable categories. Similarly, the two subcategories of BNC with or without human papillomavirus (HPV) are nearly as distinct as the overall BNC category.
The percentage of submitted slides achieving consensus at consensus levels between 50 and 80% produced variable findings with regard to the practical success of the main reporting categories. The negative category was reasonably successful, whereas mild dyskaryosis was consistently poor. Borderline nuclear changes were successful at the 50% consensus level but showed a rapid decline by the 65% consensus level. The reason(s) for this remains speculative but indicates a possible potential of BNC to work successfully with additional training and education.
Reporting practices were not consistent among the laboratories and differences were identified between medical and nonmedical staff. A high use of the BNC category was noted in slides that failed to achieve consensus. A national study assessing all grades of abnormalities would appear essential.     

The use of clip cages to restrain insects reduces leaf expansion systemically in Rumex obtusifolius

Abstract. 1. Clip cages have been used widely by experimental ecologists to contain insects on plants.
2. Under controlled conditions, the effect of applying clip cages alone and clip cages and the chrysomelid beetle Gastrophysa viridula on systemic leaf expansion of Rumex obtusifolius was investigated. Treatments were applied to the fully expanded fourth leaf and expansion of leaf 8 was measured over a period of 22 days.
3. The application of clip cages reduced the rate at which leaf area increased and led to reductions in final leaf areas.
4. Clip cages have systemic effects on plant development and these effects are sustained even after the clip cage is removed. Investigators should take this into account in designing experiments.     

Mercury in blood cells—Altered elemental profiles

The study was composed of 27 persons that displayed vague symptoms similar to those of the victims of Minamata and Iraq. Skew distributions of mercury were observed in individual erythrocytes and neutrophil granulocytes when measured by PIXE. Mercury could not be detected in the platelets. The erythrocytes also displayed lowered concentrations of magnesium and zinc, together with increased concentrations of calcium and strontium. The neutrophils displayed decreased concentrations of magnesium and zinc and increased concentrations of calcium, strontium, and iron. The presence of mercury and the altered elemental profiles in the erythrocytes and the neutrophil granulocytes are suggested as early signs of exposure.