Chromatin,gene silencing and HIV latency

One of the cellular defenses against virus infection is the silencing of viral gene expression. There is evidence that at least two gene-silencing mechanisms are used against the human immuno-deficiency virus (HIV). Paradoxically, this cellular defense mechanism contributes to viral latency and persistence, and we review here the relationship of viral latency to gene-silencing mechanisms.     

Bark Beetle-Affected Forests Provide Elk Only a Marginal Refuge from Hunters

For nearly 2 decades, the forests of the Rocky Mountains in the United States experienced a bark-beetle (Dendoctronus ponderosae) epidemic. The number of dead and falling trees from this epidemic likely will affect how elk (Cervus canadensis) and hunters use the forest and their interactions. Downed trees potentially create a component of refuge habitat that could affect the effectiveness of hunting to regulate abundance of growing elk populations. We evaluated how forests affected by bark beetles in south-central Wyoming, USA, influenced resource selection of 50 female elk and 374 hunters in 2012–2016, and interactions between elk and hunters. We employed global positioning system (GPS) technology on elk and hunters, and developed a satellite-derived land classification specifically depicting beetle-affected forests. We tested the predictions that elk would increase use of beetle-killed areas from summer to the hunting season, and that hunters would avoid beetle-killed areas regardless of elk use. Elk increased use of beetle-killed areas during hunting seasons as did hunters during the archery season; however, during the rifle season, hunters avoided beetle-killed areas. Nevertheless, during the rifle season, areas of beetle-kill with a high probability of elk occurrence dampened the aversion hunters had towards beetle-killed areas. Therefore, in contrast to our expectations, forests that have been altered by the bark-beetle epidemic may only function marginally as a refuge for elk. Our study area was at the beginning of the tree-fall phase (i.e., ~3–7 yr after peak infestation) of the bark-beetle epidemic; thus, future research efforts should focus on how a continued increase in downed trees will influence interactions between elk and hunters. At current levels of tree fall, however, beetle-kill should not limit the ability of managers to regulate elk herds through harvest. © 2020 The Wildlife Society.     

Expression of foreign genes in transgenic yellow-poplar plants

Cells of yellow-poplar (Liriodendron tulipifera L.) were transformed by direct gene transfer and regenerated into plants by somatic embryogenesis. Plasmid DNA bearing marker genes encoding β-glucuronidase (GUS) and neomycin phosphotransferase (NPT II) were introduced by microprojectile bombardment into single cells and small cell clusters isolated from embryogenic suspension cultures. The number of full-length copies of the GUS gene in independently transformed callus lines ranged from approximately 3 to 30. An enzyme-linked immunosorbent assay for NPT II and a fluorometric assay for GUS showed that the expression of both enzymes varied by less than fourfold among callus lines. A histochemical assay for GUS activity revealed a heterogeneous pattern of staining with the substrate 5-bromo-4-chloro-3-indoyl-β-d-glucuronic acid in some transformed cell cultures. However, cell clusters reacting positively (blue) or negatively (white) with 5-bromo-4-chloro-3-indoyl-β-d-glucuronic acid demonstrated both GUS activity and NPT II expression in quantitative assays. Somatic embryos induced from transformed cell cultures were found to be uniformly GUS positive by histochemical analysis. All transgenic plants sampled expressed the two marker genes in both root and shoot tissues. GUS activity was found to be higher in leaves than roots by fluorometric and histochemical assays. Conversely, roots expressed higher levels of NPT II than leaves.     

Characterization of an S-type lectin purified from porcine heart

We have purified a carbohydrate-binding protein from porcine heart by affinity chromatography on asialofetuin-Sepharose and have characterized this protein with respect to its size, amino acid composition, partial amino acid sequence, and carbohydrate-binding specificity. Porcine heart lectin (PHL) has a subunit molecular mass of 14,700 and is immunologically cross-reactive with a polyclonal antibody raised against a lectin isolated from calf heart. The amino acid composition of PHL is similar to that of lectins that have been isolated from calf heart, bovine brain, and rat lung. Moreover, the primary sequences of four tryptic fragments (52 amino acids total) derived from PHL are closely related to sequences previously determined for 10 other vertebrate-derived lectins. The ability of PHL to agglutinate rabbit erythrocytes was inhibited only by oligosaccharides containing terminal beta-galactosyl residues. These data indicate that PHL is a vertebrate "S-type" lectin and provide further evidence that the structures and carbohydrate-binding specificities of these lectins are highly conserved across diverse vertebrate genera.     

Expression of organomercurial lyase in eastern cottonwood enhances organomercury resistance

Summary Release of inorganic mercury pollutants into shallow aquatic environments has resulted in the bacterial production of a more toxic organic mercury species, methylmercury. The bacterial organomercurial lyase (MerB) catalyses the protonolysis of the carbon-mercury bond and releases Hg(II), a less toxic, non-biomagnified form of mercury. Our objective was to engineer eastern cottonwood (Populus deltoides), a fast-growing tree adapted to growth in riparian environments, with the merB gene to explore its potential for phytoremediation of mercury. We produced multiple eastern cottonwood clones expressing a modified bacterial merB gene, confirmed that the gene was expressed in the transclones and tested the regenerated plants for their ability to tolerate exposure to an organic mercury source, phenylmercuric acetate (PMA), in vitro and in hydroponic culture, compared to wild-type control trees. Transgenic merB plants expressed high levels of MerB protein and showed some evidence of higher resistance to the organic mercury than wild-type plants, producing longer roots under exposure to PMA in vitro, although hydroponic culture results were inconclusive. Our results indicate that in order for merB to be useful in eastern cottonwood trees designed to degrade methylmercury at mercury-contaminated aquatic sites, it will probably need to be combined with other genes such as merA.     

Using median sets for inferring phylogenetic trees

MOTIVATION: Algorithms for phylogenetic tree reconstruction based on gene order data typically repeatedly solve instances of the reversal median problem (RMP) which is to find for three given gene orders a fourth gene order (called median) with a minimal sum of reversal distances. All existing algorithms of this type consider only one median for each RMP instance even when a large number of medians exist. A careful selection of one of the medians might lead to better phylogenetic trees. RESULTS: We propose a heuristic algorithm amGRP for solving the multiple genome rearrangement problem (MGRP) by repeatedly solving instances of the RMP taking all medians into account. Algorithm amGRP uses a branch-and-bound method that branches over medians from a selected subset of all medians for each RMP instance. Different heuristics for selecting the subsets have been investigated. To show that the medians for RMP vary strongly with respect to different properties that are likely to be relevant for phylogenetic tree reconstruction, the set of all medians has been investigated for artificial datasets and mitochondrial DNA (mtDNA) gene orders. Phylogenetic trees have been computed for a large set of randomly generated gene orders and two sets of mtDNA gene order data for different animal taxa with amGRP and with two standard approaches for solving the MGRP (GRAPPA-DCM and MGR). The results show that amGRP outperforms both other methods with respect to solution quality and computation time on the test data. AVAILABILITY: The source code of amGRP, additional results and the test instances used in this paper are freely available from the authors.     

Landmark cues can change the motivational state of desert ant foragers

Desert ants of the genus Cataglyphis rely on path integration vectors to return to the nest (inbound runs) and back to frequently visited feeding sites (outbound runs). If disturbed, e.g., experimentally displaced on their inbound runs, they continue to run off their home-bound vector, but if disturbed in the same way on their outbound runs, they do not continue their feeder-based vector, but immediately switch on the home-bound state of their path integration vector and return to the nest. Here we show that familiar landmarks encountered by the ants during their run towards the feeder can change the ants’ motivational state insofar that the ants even if disturbed continue to run in the nest-to-feeder direction rather than reverse their courses, as they do in landmark-free situations. Hence, landmark cues can cause the ants to change their motivational state from homing to foraging.     

Isolation and characterization of a Chlamydomonas gene that encodes a putative blue-light photoreceptor of the phototropin family

In the search for a Chlamydomonas reinhardtii photoreceptor that may mediate blue-light-induced responses we identified a gene that encodes a protein with a structure typical for that of members of the phototropin family, i.e. two LOV domains that may function in flavin mononucleotide binding and a ser/thr kinase domain. The amino acid sequences of these domains are closely related to those of higher plant phototropins. This single-copy gene ( Phot ) encodes a protein with a calculated molecular mass of 81.4 kDa which is distinctly smaller than the homologous proteins of higher plants that exhibit molecular masses around 120 kDa. Expression analyses revealed rather constant levels of Phot mRNA and Phot protein in vegetative cells incubated in the dark and in cells undergoing gametogenesis. Only vegetative cells in the light showed a reduced expression of the Phot gene. Cell fractionation studies revealed that the protein is membrane-associated. In higher plants, phototropins were shown to be bound to the plasma membrane. However, the expression of a Phot-GFP gene fusion in tobacco protoplasts revealed an association of the fusion protein with the endogenous membrane network of the cell.