Large Continuous Regions Research Articles

Production and visualization of quaternary combinatorial thin films

A new method for the production of four-component (element or compound) combinatorial thin films is presented. The combinatorial thin film consists of nine continuous four-component regions producing planes in quaternary composition space. The method allows for the coverage of large continuous regions of quaternary or pseudoquaternary systems. The magnetron sputtering deposition method is mechanically simple and uses existing infrastructure. New software for the visualization of quaternary data is also presented. This software allows the straightforward identification of composition-dependent properties such as x-ray diffraction intensities. The new production method and software are demonstrated with a four-element combinatorial thin film containing Si, Sn, Co and C.

Sequence Analysis of the 144-Kilobase Accessory Plasmid pSmeSM11a, Isolated from a DominantSinorhizobium melilotiStrain Identified during a Long-Term Field Release Experiment

The genome of Sinorhizobium meliloti type strain Rm1021 consists of three replicons: the chromosome and two megaplasmids, pSymA and pSymB. Additionally, many indigenous S. meliloti strains possess one or more smaller plasmids, which represent the accessory genome of this species. Here we describe the complete nucleotide sequence of an accessory plasmid, designated pSmeSM11a, that was isolated from a dominant indigenous S. meliloti subpopulation in the context of a long-term field release experiment with genetically modified S. meliloti strains. Sequence analysis of plasmid pSmeSM11a revealed that it is 144,170 bp long and has a mean G+C content of 59.5 mol%. Annotation of the sequence resulted in a total of 160 coding sequences. Functional predictions could be made for 43% of the genes, whereas 57% of the genes encode hypothetical or unknown gene products. Two plasmid replication modules, one belonging to the repABC replicon family and the other belonging to the plasmid type A replicator region family, were identified. Plasmid pSmeSM11a contains a mobilization (mob) module composed of the type IV secretion system-related genes traG and traA and a putative mobC gene. A large continuous region that is about 42 kb long is very similar to a corresponding region located on S. meliloti Rm1021 megaplasmid pSymA. Single-base-pair deletions in the homologous regions are responsible for frameshifts that result in nonparalogous coding sequences. Plasmid pSmeSM11a carries additional copies of the nodulation genes nodP and nodQ that are responsible for Nod factor sulfation. Furthermore, a tauD gene encoding a putative taurine dioxygenase was identified on pSmeSM11a. An acdS gene located on pSmeSM11a is the first example of such a gene in S. meliloti. The deduced acdS gene product is able to deaminate 1-aminocyclopropane-1-carboxylate and is proposed to be involved in reducing the phytohormone ethylene, thus influencing nodulation events. The presence of numerous insertion sequences suggests that these elements mediated acquisition of accessory plasmid modules.

Gene array profiling of large hypothalamic CNS regions in lactating and randomly cycling virgin mice

A dramatic example of neuronal and physiological plasticity in adult mammals occurs during the transition from a non-maternal to a maternal, lactating state. In this study, we compared gene expression within a large continuous region of the CNS involved in maternal behaviors (hypothalamus, preoptic regions, and nucleus accumbens) between lactating (L) (postpartum Day 7) and randomly cycling virgin (V) outbred mice. Using high-density oligonucleotide arrays representing 11,904 genes, two statistical algorithms were used to identify significant differences in gene expression: robust multiarray ( P < 0.001) ( n = 92 genes) and significance analysis of microarrays using a 10% false discover rate ( n = 114 genes). 27 common genes were identified as significant using both techniques. A subset of genes ( n = 5) were selected and examined by real-time PCR. Our findings were consistent with previous published work. For example, neuropeptide Y (NPY) and proenkephalin were elevated in L mice, whereas POMC was decreased. Increased levels of NPY Y2 receptor and polo-like kinase and decreased levels of endothelin receptor type b in L mice are examples of novel gene expression changes not previously identified. Expression differences occurred in broad classes. Together, our findings provide possible new material on gene expression changes that may support maternal behaviors. The advantages and drawbacks of sampling large CNS regions using arrays are discussed.

How parasitism affects critical patch-size in a host–parasitoid model: application to the forest tent caterpillar

Habitat structure has broad impacts on many biological systems. In particular, habitat fragmentation can increase the probability of species extinction and on the other hand it can lead to population outbreaks in response to a decline in natural enemies. An extreme consequence of fragmentation is the isolation of small regions of suitable habitat surrounded by a large region of hostile matrix. This scenario can be interpreted as a critical patch-size problem, well studied in a continuous time framework, but relatively new to discrete time models. In this paper we present an integrodifference host–parasitoid model, discrete in time and continuous in space, to study how the critical habitat-size necessary for parasitoid survival changes in response to parasitoid life history traits, such as emergence time. We show that early emerging parasitoids may be able to persist in smaller habitats than late emerging species. The model predicts that these early emerging parasitoids lead to more severe host outbreaks. We hypothesise that promoting efficient late emerging parasitoids may be key in reducing outbreak severity, an approach requiring large continuous regions of suitable habitat. We parameterise the model for the host species of the forest tent caterpillar Malacosoma disstria Hbn., a pest insect for which fragmented landscape increases the severity of outbreaks. This host is known to have several parasitoids, due to paucity of data and as a first step in the modelling we consider a single generic parasitoid. The model findings are related to observations of the forest tent caterpillar offering insight into this host–parasitoid response to habitat structure.

Microstructure transitions derived from solubilization of lutein and lutein esters in food microemulsions

Solubilization and structural transformations in nonionic food microemulsions, characterized by large continuous isotropic region, containing solubilized lutein, and lutein ester were studied. The preparations are of oil-based concentrates composed of solubilized lutein or lutein ester in reverse micelles constructed from hydrophilic surfactant, alcohol and R(+)-limonene. The reverse micelles are diluted along a 60/40 surfactant/oil dilution line with aqueous phase (containing water and glycerol) up to the opposite corner of the diagram where o/w microemulsions are formed passing through a bicontinuous phase, without any visual phase separation. The dilution goes through two structural transitions that were determined in empty (reference) and solubilized systems. The solubilization capacity of both free lutein (FL) and lutein ester (LE) is considerably higher (as expected) in the reverse micelles (no aqueous phase), and in the W/O microemulsions than in the O/W microemulsions, but the highest solubilization was obtained within the bicontinuous phase. The solubilization was found to be affected by the lipophilicity of the surfactant and is also concentration-dependent throughout all the microemulsions structures, but the most pronounced surfactant effect was shown to be in the bicontinuous region. Structural transitions w/o→bicontinuous occurred at 30 wt.% aqueous phase in ‘empty’ (reference) microemulsions as well as in microemulsions containing solubilized free and esterified lutein (at the maximum solubilization levels). However, the transitions bicontinuous→o/w occurred at higher aqueous phase contents of 50 and 60 wt.% aqueous phase for FL and LE, respectively, in comparison to a transition at 40 wt.% for the empty microemulsion. As a result, the bicontinuous region in the presence of the guest molecules becomes much broader. The results indicate that in the reverse swollen micelles the guest molecules, being practically lipophilic will be easily accommodated at the concaved water interfaces (in the w/o region), which will enable high solubilization capacities, and without significant modifications of the interface. It becomes also evident that at zero curvature interfaces (bicontinuous) and in convex interfaces (oil/water) the lutein ester (the more lipophilic molecule) penetrates into the interface and swells both the bicontinuous interface and the droplets, similarly to most guest molecules. However, free lutein is poorly accommodated at the interface and interferes with the interfacial organization and modifies the flattened curvature, affecting the transformation from bicontinuous to o/w droplets.

An unusual chemical reactivity of Sm site adenosines strongly correlates with proper assembly of core U snRNP particles

The small nuclear ribonucleoprotein particles (snRNP) U1, U2, U4, and U5 contain a common set of eight Sm proteins that bind to the conserved single-stranded 5′-PuAU3–6GPu-3′ (Sm binding site) region of their constituent U snRNA (small nuclear RNA), forming the Sm core RNP. Using native and in vitro reconstituted U1 snRNPs, accessibility of the RNA within the Sm core RNP to chemical structure probes was analyzed. Hydroxyl radical footprinting of in vitro reconstituted U1 snRNP demonstrated that riboses within a large continuous RNA region, including the Sm binding site, were protected. This protection was dependent on the binding of the Sm proteins. In contrast with the riboses, the phosphate groups within the Sm core site were accessible to modifying reagents. The invariant adenosine residue at the 5′ end, as well as an adenosine two nucleotides downstream of the Sm binding site, showed an unexpected reactivity with dimethyl sulfate. This novel reactivity could be attributed to N7-methylation of the adenosine and was not observed in naked RNA, indicating that it is an intrinsic property of the RNA- protein interactions within the Sm core RNP. Further, this reactivity was observed concomitantly with formation of the Sm subcore intermediate during Sm core RNP assembly. As the Sm subcore can be viewed as the commitment complex in this assembly pathway, these results suggest that the peculiar reactivity of the Sm site adenosine bases may be diagnostic for proper assembly of the Sm core RNP. Consistent with this idea, a strong correlation was found between the unusual N7-A methylation sensitivity of the Sm core RNP and its ability to be imported into the nucleus of Xenopus laevis oocytes.

The preparation and study of a holey polymer film

A holey carbon grid (HCG) consists of a TEM grid with a holey polymer film (HPF) attached to its surface and a carbon coating to provide mechanical stability and electrical conductivity. HCGs have found wide use in the preparation of liquid samples for cryo-TEM. These grids increase the number of sample sites by as much as three orders of magnitude and aid in the formation of fairly uniform, thin specimen films (&lt; 250 nm). Several methods have been reported for the production of HPFs for specimen support. Unfortunately, most methods are unreliable, often producing films with pseudo-holes and large continuous film regions. Essential to improving any technique is an understanding of the process mechanisms involved. This paper describes a technique, modified from Refs. 1 and 2, for preparing HPFs and suggests a drying mechanism to explain the results.

Sequences of two kinetoplast DNA minicircles of Tryptanosoma brucei.

Kinetoplast DNA of Trypanosoma brucei is composed of a network of about 10,000 interlocked minicircle DNA molecules (1.0 kilobase) that are catenated with about 50 maxicircle DNA molecules (23 kilobases). Several different DNA . DNA hybridization techniques using individual minicircle DNA sequences cloned in Escherichia coli have indicated that each minicircle molecule contains about one-fourth of its sequence in common with most other minicircles and the remaining three-fourths in common with about 1 out of every 300 minicircles. We have determined the complete sequence of two cloned minicircle DNA molecules that were released from the total kinetoplast DNA network by different restriction enzymes; one minicircle is 1004 base pairs long, the other is 983 base pairs. Both are about 72% dA + dT. They share about 27% of their sequences; the largest continuous region in common is 122 base pairs of near-perfect homology. Twelve other regions of perfect homology equal to or greater than 10 base pairs are also present. Both sequences contain a large number of translation termination codons in all potential translation reading frames. The largest oligopeptide potentially specified by one minicircle sequence is 52 amino acids; the largest by the other minicircle sequence is 71 amino acids. One minicircle contains a decanucleotide sequence that is repeated in tandem five times. It is proposed that massive recombination among the interlocked minicircles in the kinetoplast DNA network may account for much of the homology observed in the two minicirce sequences.

The structure of the mitochondrial cloud of Xenopus laevis oocytes

The ultrastructure of the mitochondrial cloud (Balbiani body) of the pre-vitellogenic oocytes of Xenopus laevis has been examined using transmission and stereoscan electron microscopy. Examination of conventional thin sections confirm previous observations which suggest that the cloud consists essentially of many thousands mitochondria and numerous small vesicles; larger clouds, in oocytes greater than 200 mum in diameter, contain relatively more vesicles. Using a standard electron microscope at 100 kV very long and coursing arrays of mitochondrial profiles can be detected. The presence of very long mitochondrial elements has been confirmed using a high voltage microscope operating at 500-1000 kV. Stereoscan preparations, isolated from pre-vitellogenic oocytes, lend some support to the view that the mitochondrial cloud amy consist of a mass of long filamentous mitochondria and the possibility that there are large continuous regions of mitochondrial material cannot be ruled out.