Low frequency of zinc-finger nuclease-induced mutagenesis in <Emphasis Type="Italic">Populus</Emphasis>

Gene flow from recombinant-DNA-modified (GMO) trees is a major barrier to their public acceptance and regulatory approval. Because many intensively grown trees are vegetatively propagated, complete sexual sterility could be a powerful means to mitigate or prevent gene flow. We tested four pairs of zinc-finger nucleases (ZFNs) as mutagenic agents against the LEAFY and AGAMOUS orthologs in poplar that are expected to be required for sexual fertility. To reduce the potential for pleiotropic effects from mutagenesis, each of the pairs was functionally linked to a heat shock promoter to provide inducible ZFN expression. Using Agrobacterium tumefaciens, we transformed more than 21,000 total explants compromised of both male and female hybrid poplar. The rate of transformation for the ZFN constructs (2 %) was generally reduced compared to the transgenic control (8 %). We produced 391 ZFN transgenic shoots of which only two developed into plants with mutations in a target gene; both were 7-bp deletions in one allele of the PtAG2 locus. No mutations were observed in the PtAG1 or PtLFY loci. Our results indicate a mutation rate of zero to 0.3 % per explant per allele, among the lowest reported for ZFN mutagenesis in plants. The combined effects of low recovery of transgenic plants, a modest mutation frequency, and much higher reported rates of directed mutation for other gene editing methods suggest that the efficient use of ZFNs in poplar requires further technical improvements.     

Polyamine biosynthesis during somatic embryogenesis in interior spruce (Picea glauca x Picea engelmannii complex)

Putrescine, spermidine, and spermine levels during somatic embryogenesis of interior spruce (Picea glauca x Picea engelmannii complex) were quantified On abscisic acid supplemented growth medium putrescine and spermidine levels increased two-fold coinciding with maturation of the early somatic embryos to globular embryos. Polyclonal antibodies raised against Escherichia coli arginine decarboxylase (ADC) and ornithine decarboxylase (ODC), following affinity purification specifically recognized spruce ADC and ODC, which corresponded to 85kD and 65kD bands on western blots of total protein extracts from embryogenic masses, Immunoassays using these antibodies showed increased ADC levels corresponding to embryo maturation while ODC levels remained the same. From these results it is concluded that polyamines are involved in the maturation of somatic embryos of interior spruce.Abbreviations ADC arginine decarboxylase - BSA bovine serum albumin - ODC ornithine decarboxylase - PBS phosphate buffered saline - PCA perchloric acid - SDS-PAGE sodium dodecyl sulfateporyacrylamide gel electrophoresis     

Preliminary karyotype and chromosomal localization of ribosomal DNA sites in white spruce using fluorescence in situ hybridization.

We have localized the major ribosomal DNA (rDNA) loci on metaphase chromosomes and in interphase nuclei of white spruce (2n = 24) by fluorescence in situ hybridization. Hybridization sites of the biotin-labelled rDNA probe were detected using antibody-fluorochrome conjugates and a confocal laser scanning microscope. White spruce has at least 12, and possibly as many as 14, rDNA sites, 1 site present on each of seven separate chromosome pairs. This is one of the highest numbers of rDNA loci yet reported among plant species. The position of the rDNA loci together with secondary constriction patterns permit, for the first time, all homologous pairs of white spruce chromosomes to be distinguished. We discuss the application of molecular cytogenetics in studies relating to the organization and evolution of DNA sequences within conifer genomes.     

Ammonia assimilation and glutamate formation in Caulobacter crescentus.

In the dimorphic bacterium Caulobacter crescentus, ammonia assimilation occurs only via the combined action of the enzymes glutamine synthetase and glutamate synthase. Mutants auxotrophic for glutamate lacked glutamate synthase activity, and the mutations leading to the glutamate auxotrophy appeared to lie at two distinct genetic loci. Both glutamate synthase and glutamine synthetase activities were subject to regulation by repression. Glutamate synthase activity was highest in cultures grown in minimal medium with ammonia as sole nitrogen source and was about fivefold lower in rich broth. Glutamine synthetase activity was highest in cells grown with growth-rate-limiting amounts of ammonia as nitrogen source and was about fourfold lower in rich broth. In addition, glutamine synthetase activity appeared to be regulated by an adenylylation system like that described for Escherichia coli.     

Design and synthesis of potent, non-peptidic inhibitors of HPTPbeta

The sulfamic acid phosphotyrosine mimetic was coupled with a previously known malonate template to obtain highly selective and potent inhibitors of HPTPbeta. Potentially hydrolyzable malonate ester functionalities were replaced with 1,2,4-oxadiazoles without a significant effect on HPTPbeta potency.     

Stunting in Oreochromis mossambicus (Peters) (Pisces, Cichlidae): An evaluation of past and recent data from Sri Lankan reservoir populations

Tilapiine fish are known to become stunted under different environmental conditions. Of the tilapia, Oreochromis mossambicus (Peters), once considered to be the aquatic chicken, is now treated as a nuisance species in some countries because of its tendency to stunt easily. O. mossambicus is the mainstay of the commercial gillnet fishery in existence in the multitude of reservoirs in Sri Lanka for over 35 years. Published and new evidence on O. mossambicus population traits are presented with a view to evaluating whether the populations in Sri Lankan reservoirs are stunted or not. The main lines of evidence considered are the mean size at maturity (Lm), the proportion of individuals below 20 cm total length in the commercial landings, and growth performance of the individual reservoir populations. Statistically valid inter-relationships exist between the mean length at maturity and the proportion of undersized individuals (below 20 cm) in the landings, and the ratio of the reservoir catchment or watershed area to surface area. Evidence on Lm indicate that there is a tendency for O. mossambicus populations to stunt, however, evidence on growth and mean landing size do not indicate stunting.     

NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition

The RNA genome of the human immunodeficiency virus type-1 (HIV-1) contains a approximately 120 nucleotide Psi-packaging signal that is recognized by the nucleocapsid (NC) domain of the Gag polyprotein during virus assembly. The Psi-site contains four stem-loops (SL1-SL4) that possess overlapping and possibly redundant functions. The present studies demonstrate that the 19 residue SL2 stem-loop binds NC with affinity (K(d)=110(+/-50) nM) similar to that observed for NC binding to SL3 (K(d)=170(+/-65) nM) and tighter than expected on the basis of earlier work, suggesting that NC-SL2 interactions probably play a direct role in the specific recognition and packaging of the full-length, unspliced genome. The structure of the NC-SL2 complex was determined by heteronuclear NMR methods using (15)N,(13)C-isotopically labeled NC protein and SL2 RNA. The N and C-terminal "zinc knuckles" (Cys-X(2)-Cys-X(4)-His-X(4)-Cys; X=variable amino acid) of HIV-1 NC bind to exposed guanosine bases G9 and G11, respectively, of the G8-G9-U10-G11 tetraloop, and residues Lys3-Lys11 of the N-terminal tail forms a 3(10) helix that packs against the proximal zinc knuckle and interacts with the RNA stem. These structural features are similar to those observed previously in the NMR structure of NC bound to SL3. Other features of the complex are substantially different. In particular, the N-terminal zinc knuckle interacts with an A-U-A base triple platform in the minor groove of the SL2 RNA stem, but binds to the major groove of SL3. In addition, the relative orientations of the N and C-terminal zinc knuckles differ in the NC-SL2 and NC-SL3 complexes, and the side-chain of Phe6 makes minor groove hydrophobic contacts with G11 in the NC-SL2 complex but does not interact with RNA in the NC-SL3 complex. Finally, the N-terminal helix of NC interacts with the phosphodiester backbone of the SL2 RNA stem mainly via electrostatic interactions, but does not bind in the major groove or make specific H-bonding contacts as observed in the NC-SL3 structure. These findings demonstrate that NC binds in an adaptive manner to SL2 and SL3 via different subsets of inter and intra-molecular interactions, and support a genome recognition/packaging mechanism that involves interactions of two or more NC domains of assembling HIV-1 Gag molecules with multiple Psi-site stem-loop packaging elements during the early stages of retrovirus assembly.     

Obtaining Large Columnar CdTe Grains and Long Lifetime on Nanocrystalline CdSe,MgZnO, or CdS Layers

CdTe solar cells have reached efficiencies comparable to multicrystalline silicon and produce electricity at costs competitive with traditional energy sources. Recent efficiency gains have come partly from shifting from the traditional CdS window layer to new materials such as CdSe and MgZnO, yet substantial headroom still exists to improve performance. Thin film technologies including Cu(In,Ga)Se₂, perovskites, Cu₂ZnSn(S,Se)₄, and CdTe inherently have many grain boundaries that can form recombination centers and impede carrier transport; however, grain boundary engineering has been difficult and not practical. In this work, it is demonstrated that wide columnar grains reaching through the entire CdTe layer can be achieved by aggressive postdeposition CdTe recrystallization. This reduces the grain structure constraints imposed by nucleation on nanocrystalline window layers and enables diverse window layers to be selected for other properties critical for electro‐optical applications. Computational simulations indicate that increasing grain size from 1 to 7 µm can be equivalent to decreasing grain‐boundary recombination velocity by three orders of magnitude. Here, large high‐quality grains enable CdTe lifetimes exceeding 50 ns.     

Sexual dimorphism in digital dermatoglyphic traits among Sinhalese people in Sri Lanka

Background

The purpose of this study was to evaluate gender-wise diversity of digital dermatoglyphic traits in a sample of Sinhalese people in Sri Lanka.

Findings

Four thousand and thirty-four digital prints of 434 Sinhalese individuals (217 males and 217 females) were examined for their digital dermatoglyphic pattern distribution. The mean age for the entire group was 23.66 years (standard deviation = 4.93 years). The loop pattern is observed more frequently (n = 2,592, 59.72%) compared to whorl (n = 1,542, 35.53%) and arch (n = 206, 4.75%) in the Sinhalese population. Females (n = 1,274, 58.71%) have a more ulnar loop pattern than males (n = 1,231, 56.73%). The plain whorl pattern is observed more frequently in males (n = 560, 25.81%) compared to females (n = 514, 23.69%).The double loop pattern is observed more frequently on the right and left thumb (digit 1) of both males and females. Pattern intensity index, Dankmeijer index and Furuhata index are higher in males.

Conclusions

Ulnar loop is the most frequently occurring digital dermatoglyphic pattern among the Sinhalese. All pattern indices are higher in males. To some extent, dermatoglyphic patterns of Sinhalese are similar to North Indians and other Caucasoid populations. Further studies with larger sample sizes are recommended to confirm our findings.     

Seasonality in Dietary Shifts in Size-Structured Freshwater Fish Assemblages in Three Reservoirs of Sri Lanka

We studied seasonal changes in feeding habits of size-structured fish assemblages in three freshwater reservoirs in Sri Lanka. We obtained fish samples for diet analysis from three reservoirs during the months of rising water level (RIWL) and receding water level (REWL). During RIWL, peripheral areas with terrestrial/semi-terrestrial macrophytes get inundated, which resulted in increased food availability for macrophyte feeding fish. During REWL, detrital food sources increase due to decaying terrestrial plant material, which has inundated. Based on the dietary habits of individual species in the three reservoirs during RIWL and REWL, it is evident that detritivorous and phytoplanktivorous fish species, which belong to low trophic levels do not show significant variation in dietary habits between the two seasons (e.g. Oreochromis mossambicus, Oreochromis niloticus and Amblypharyngodon melettinus). Stenophagous species such as benthic invertebrate predators (Puntius chola and Puntius dorsalis), macrophytophagous species (Etroplus suratensis and Tilapia rendalli) and zooplanktivorous Hemirhamphus limbatus do not exhibit significant variation in dietary habits between seasons. Also their feeding habits do not vary with body size. Euryphagous species such as Puntius filamentosus on the other hand, exhibit variations in dietary habits between seasons as well as with body size. Stenophagous species, which feed on detritus and phytoplankton and euryphagous species, which exhibit temporal dietary plasticity, are therefore abundant in fish assemblages of these reservoirs.