Protocol to quantify bird nest morphology via image analyses using linear measurements and geometric landmarks.

Here, we present a protocol to quantify bird nest morphology via image analyses. We describe steps for collecting linear size measurements, placing geometric landmarks, and undertaking generalized Procrustes analysis to extract coordinate data. This protocol was designed to measure within- and among-individual variation in the morphology of dome nests built by captive zebra finches using coconut fiber in a laboratory environment. For complete details on the use and execution of this protocol, please refer to Whittaker et al.1.

The roles of social information, asocial information, and initial bias in nest-building decisions.

Animals can use asocial (e.g., environmental cues) or social (e.g., conspecific behavior) information when making decisions. We investigated decisions made by zebra finches when asocial and social sources conveyed agreeing or conflicting information, and assessed the influence of initial bias on decision making. Finches completed an initial preference test ranking preference for three colors of nest-building material. Birds in the agree group (n = 14) then observed demonstrators build nests using nonpreferred color material (social information) that matched the environment color (asocial information). Birds in the conflict group (n = 15) observed demonstrators build nests with nonpreferred color material that did not match the cage environment (another nonpreferred color). A final preference test assessed any changes in color preference. The agree group reduced average preference for their initially preferred color, but did not significantly increase average preference for the asocial/social colors. The conflict group also reduced average preference for the initially preferred color and also increased preference for the socially demonstrated color. Observers with stronger initial bias were less likely to choose the socially demonstrated color than observers with weaker initial bias. This shows that social information informs nest-building decisions, even when in conflict with asocial information. However, bias influences social information use and adds nuance to how different individuals use information when making decisions. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Zebra finches have style: Nest morphology is repeatable and associated with experience.

We investigated whether birds build nests in repeatable styles and, if so, whether styles were associated with past nest-building experience. Laboratory, captive bred zebra finches in an Experimental group were given nest-building experience, whereas, birds in a Control group were not. Each pair (n = 20) then built four nests that underwent image analyses for nest size, geometric shape and entrance orientation. Birds built nests in repeatable styles, with lower morphometric variation among nests built by the same pair and higher morphometric variation among nests built by different pairs. Morphology was not associated with construction time, body weight, nor age of birds. We found lower morphometric variation among nests built by the Experimental group, which also used less material to build nests compared to the Control group. Prior experience may therefore have been advantageous, as learning to reduce material usage while achieving a similar product (nest) may have lowered building costs.

Global, regional, and cryptic population structure in a high gene-flow transatlantic fish.

Lumpfish (Cyclopterus lumpus) is a transatlantic marine fish displaying large population sizes and a high potential for dispersal and gene-flow. These features are expected to result in weak population structure. Here, we investigated population genetic structure of lumpfish throughout its natural distribution in the North Atlantic using two approaches: I) 4,393 genome wide SNPs and 95 individuals from 10 locations, and II) 139 discriminatory SNPs and 1,669 individuals from 40 locations. Both approaches identified extensive population genetic structuring with a major split between the East and West Atlantic and a distinct Baltic Sea population, as well as further differentiation of lumpfish from the English Channel, Iceland, and Greenland. The discriminatory loci displayed ~2-5 times higher divergence than the genome wide approach, revealing further evidence of local population substructures. Lumpfish from Isfjorden in Svalbard were highly distinct but resembled most fish from Greenland. The Kattegat area in the Baltic transition zone, formed a previously undescribed distinct genetic group. Also, further subdivision was detected within North America, Iceland, West Greenland, Barents Sea, and Norway. Although lumpfish have considerable potential for dispersal and gene-flow, the observed high levels of population structuring throughout the Atlantic suggests that this species may have a natal homing behavior and local populations with adaptive differences. This fine-scale population structure calls for consideration when defining management units for exploitation of lumpfish stocks and in decisions related to sourcing and moving lumpfish for cleaner fish use in salmonid aquaculture.

Genetic divergence and evidence of human-mediated translocation of two-fingered sloths (Choloepus hoffmanni) in Costa Rica.

Sloths are notoriously slow and consequently have limited dispersal ability, which makes them particularly vulnerable to the effects of habitat fragmentation and degradation. Sloths in Costa Rica are considered of conservation concern due to habitat loss, livestock production and increasing urbanization. Reintroductions from rescue centres are commonplace across the country, yet their genetic diversity and population structure are unknown, and there is currently little consideration of the genetic background prior to intervention or releases. We used microsatellite analysis to undertake the first exploratory investigation into sloth population genetics in Costa Rica. Using data from 98 two-fingered sloths (Choloepus hoffmanni) from four different geographic regions, we determined the presence of four potential genetic groups, three of them with minimal population structuring despite the limited dispersal ability and presence of physical barriers. Sloths from the North appear to represent a highly distinct population that we propose may require management as a discrete unit for conservation. We stress the need for additional analyses to better understand the genetic structure and diversity of North andWest regions and suggest that rescue facilities in Costa Rica should consider the genetic background of rehabilitated sloths when planning future reintroductions. Our results also highlight the threat posed by physical isolation due to widespread urbanization and agriculture expansion for a species with a weak dispersal ability.

Genetic and phenotypic differentiation of lumpfish (Cyclopterus lumpus) across the North Atlantic: implications for conservation and aquaculture.

Demand for lumpfish (Cyclopterus lumpus) has increased exponentially over the last decade, both for their roe, which is used as a caviar substitute, and increasingly also as cleaner fish to control sea lice in salmon farming. The species is classified as Near Threatened by the IUCN and there are growing concerns that over-exploitation of wild stocks and translocation of hatchery-reared lumpfish may compromise the genetic diversity of native populations. We carried out a comparative analysis of genetic and phenotypic variation across the species' range to estimate the level of genetic and phenotypic differentiation, and determined patterns of gene flow at spatial scales relevant to management. We found five genetically distinct groups located in the West Atlantic (USA and Canada), Mid Atlantic (Iceland), East Atlantic (Faroe Islands, Ireland, Scotland, Norway and Denmark), English Channel (England) and Baltic Sea (Sweden). Significant phenotypic differences were also found, with Baltic lumpfish growing more slowly, attaining a higher condition factor and maturing at a smaller size than North Atlantic lumpfish. Estimates of effective population size were consistently low across the North East Atlantic (Iceland, Faroe Islands and Norway), the area where most wild lumpfish are fished for their roe, and also for the aquaculture industry. Our study suggests that some lumpfish populations are very small and have low genetic diversity, which makes them particularly vulnerable to over-exploitation and genetic introgression. To protect them we advocate curtailing fishing effort, closing the breeding cycle of the species in captivity to reduce dependence on wild stocks, restricting the translocation of genetically distinct populations, and limiting the risk of farm escapes.

Scanning conformational space with a library of stereo- and regiochemically diverse aminoglycoside derivatives: the discovery of new ligands for RNA hairpin sequences.

A library of stereo- and regiochemically diverse aminoglycoside derivatives was screened at 1 microM using surface plasmon resonance (SPR) against RNA hairpin models of the bacterial A-site, and the HIV viral TAR and RRE sequences. In order to double the stereochemical diversity of the library, the compounds were screened against both enantiomers of each of these sequences. Remarkably, this initial screen suggested that the same four aminoglycoside derivatives bound most tightly to all three of the RNAs, suggesting that these compounds were good RNA binders which, nonetheless, discriminated poorly between the RNA sequences. The interactions between selected isomeric aminoglycoside derivatives and the RNA hairpins were then studied in more detail using an SPR assay. Three isomeric tight-binding aminoglycoside derivatives, which had been identified from the initial screen, were found to bind more tightly to the RNA hairpins (with K(D) values in the range 0.23 to 4.7 microM) than a fourth isomeric derivative (which had K(D) values in the range 6.0 to 30 microM). The magnitude of the tightest RNA-aminoglycoside interactions stemmed, in large part, from remarkably slow dissociation of the aminoglycosides from the RNA targets. The three tight-binding aminoglycoside derivatives were found, however, to discriminate rather poorly between alternative RNA sequences with, at best, around a twenty-fold difference in affinity for alternative RNA hairpin sequences. Within the aminoglycoside derivative library studied, high affinity for an RNA target was not accompanied by good discrimination between alternative RNA sequences.

Redirection of carotenoid metabolism for the efficient production of taxadiene [taxa-4(5),11(12)-diene] in transgenic tomato fruit.

The taxanes are a group of polycyclic diterpenes produced by various species of yew. The potent anticancer drug paclitaxel (marketed as Taxol) is the commercially most important taxane with annual sales in 2000 exceeding 1.6 billion dollars. Paclitaxel is currently obtained either by direct extraction from yew trees or by the extraction of the precursor 10-deactilbaccatin III, which is then converted to paclitaxel by semi-synthesis. Apart from cost, one of the main draw backs to taxol in cancer treatment is the development of resistance by tumours, commonly due to the expression of ABC transporter efflux pumps which remove the drug from the target cell. A number of natural taxanes and semisynthetic derivates, have recently been shown to act as potent inhibitors of ABC transport proteins. These compounds have no effect upon microtubule polymerization (the normal target of paclitaxel), but have the ability to restore drug sensitivity when given in combination with paclitaxel to resistant cell lines. In work to be described elsewhere, we sort to carry out a structure function analysis of the ability of novel oxidised taxanes to act as ABC transporter inhibitors. For this study 100 mg or more of taxadiene [taxa-4(5),11(12)-diene], the first taxane in the paclitaxel pathway, was required as starting material from which to synthesize these compounds. Taxadiene is synthesised directly from geranylgeranyl diphosphate (GGPP), which is found in most plant tissues where it serves as a common precursor for many metabolites. The synthesis and use of GGDP are tightly regulated in most vegetative organs, however, in tomato fruit it is used almost exclusively for the production of coloured carotenoids which accumulate to high levels in the plastid as lycopene crystals. Expressing taxadiene synthase in a yellow-fruited tomato line that lacks the ability to utilise GGPP for carotenoid synthesis allowed GGPP normally utilised for making carotenoids to be re-routed for the production of taxadiene, allowing the facile extraction of 160 mg of highly pure taxadiene from 1 kg of freeze dried fruit.

Synthesis and preliminary anticancer activity studies of C4 and C8-modified derivatives of catechin gallate (CG) and epicatechin gallate (ECG).

We have developed an improved and reliable method for stereoselective functionalization at C4 of naturally occurring (+)-catechin. Our method utilizes DDQ oxidation followed by trapping of the quinonemethide intermediate with allyl alcohol. The quinonemethide intermediate can be regenerated from the allyl ether by exposure to boron trifluoride diethyl etherate. This reactive intermediate can be trapped with a wide range of external nucleophiles. NBS bromination, lithium halogen exchange, and alkylation gave access to C8-allyl derivatives of (+)-catechin, and this allyl group was used in a series of cross-metathesis experiments to prepare novel dimeric catechin-derived products. Gallate ester derivatives of the novel C4- and C8-substituted catechins were prepared, and these materials were screened for potential anticancer activity in a range of human cancer cell lines. From these preliminary cytotoxicity assays (MTT) we found that C8-propyl-catechin gallate was more active (IC50 = 31 microM) than catechin gallate (CG, IC50 = 53 microM) or epicatechin gallate (ECG, IC50 = 76 microM) against the colorectal adenocarcinoma cell line HCT116. Differential sensitivity in pancreas (Pan1), bladder (RT112), stomach (MGLVA1), liver (HepG2), and fibroblasts (46Br.1G1) cell lines was also observed.

Synthesis of a library of stereo- and regiochemically diverse aminoglycoside derivatives.

A library of forty modified aminoglycosides was prepared in which the configuration and regiochemistry of two or three rings was widely varied. The library was based around three core ring systems: the 2-deoxystreptamine ring system found in the natural products, and both enantiomers of (1R*,2R*,4R*,5R*)-2,5-diamino-cyclohexane-1,4-diol and (1R*,3R*,4R*,6R*)-4,6-diaminocyclohexane-1,3-diol. In each case, the core was modified by glycosylation with one or two sugar rings. The absolute configuration of the sugar substituents (d or l), the configuration of the anomeric centres (alpha or beta), and the regiochemical arrangement of the amine(s) were varied.