Estimating abundance from detection–nondetection data for randomly distributed or aggregated elusive populations

Estimating abundance is important in many ecological studies in order to understand the spatial and temporal dynamics of a population, which can assist in management and conservation. However, direct estimates of abundance can be difficult and expensive to obtain, particularly for wide-ranging, rare or elusive species. An alternative – estimating from detection-nondetection data – is a challenging but alluring concept to ecologists since the cost and effort of a study can be greatly reduced. This paper describes a method for estimating the abundance of randomly distributed or aggregated populations by using binary data where the probability of detection is less than one. The performances of the models were evaluated by computer simulations comprising 1620 cases. The results show that the accuracy of the abundance estimates increases as the sampling rate, efficiency of survey method, and the number of repeated surveys increase, whereas the accuracy declines as individuals become more aggregated. For a randomly distributed population, using a sampling rate of 0.05 in a survey method with a detection probability of 0.5, and repeating surveys three times provides sufficient accuracy of abundance. For an aggregated population, to achieve reasonably accurate abundance estimates the sampling rate should be doubled and each cell should be repeatedly surveyed on 4 to 6 occasions.     

Morphological phylogeny of alpheid shrimps: parallel preadaptation and the origin of a key morphological innovation, the snapping claw

The Alpheidae-possibly the most diverse family of recent decapod crustaceans-offers attractive opportunities to study the evolution of many intriguing phenomena, including key morphological innovations like spectacular snapping claws, highly specialized body forms, facultative and obligate symbioses with many animal groups, and sophisticated behaviors like eusociality. However, studies of these remarkable adaptations remain hampered by insufficient phylogenetic information. We present the first phylogenetic hypothesis of relationships among 36 extant genera of alpheid shrimps, based on a cladistic analysis of 122 morphological characters from 56 species, and we use this hypothesis to explore evolutionary trends in morphology and species diversity. Our results strongly supported a monophyletic Alpheidae that included two hitherto difficult-to-place genera (Yagerocaris and Pterocaris). Of 35+ nodes among genera, all were supported by at least one morphological character (24 were supported by two or more) and 17 received greater than 50% jackknife support. Unfortunately, many basal nodes were only weakly supported. Six genera appeared nonmonophyletic, including the dominant genus Alpheus (paraphyletic due to inclusion of one clade with three minor genera). Evolutionary trends in alpheid claw form shed some revealing light on how key innovations evolve. First, several functionally significant features of the cheliped (claw bearing leg) evolved independently multiple times, including: asymmetry, folding, inverted orientation, sexual dimorphism, adhesive plaques that enhance claw cocking, and tooth-cavity systems on opposing claw fingers, a preadaptation for snapping. Many conspicuous features of alpheid claw form therefore appear prone to parallel evolution. Second, although tooth-cavity systems evolved multiple times, a functional snapping claw, which likely facilitated an explosive radiation of over 550 species, evolved only once (in Synalpheus + [Alpheus + satellite genera]). Third, adhesive plaques (claw cocking aids) also evolved multiple times, and within snapping alpheids are associated with the most diverse clade (Alpheus + derivative genera). This pattern of parallel preadaptation-multiple independent evolutionary origins of precursors (preadaptations) to what ultimately became a key innovation (adaptation)-suggests alpheid shrimp claws are predisposed to develop features like tooth-cavity and adhesive plaque systems for functional or developmental reasons. Such functional/developmental predisposition may facilitate the origin of key innovations. Finally, moderate orbital hoods-anterior projections of the carapace partly or completely covering the eyes-occur in many higher Alpheidae and likely evolved before snapping claws. They are unique among decapod crustaceans, and their elaboration in snapping alpheids suggests they may protect the eyes from the stress of explosive snaps. Thus one key innovation (orbital hoods) may have facilitated evolution of a second (snapping claws).     

Systemic suppression of cluster-root formation and net P-uptake rates in Grevillea crithmifolia at elevated P supply: a proteacean with resistance for developing symptoms of 'P toxicity'

Grevillea crithmifolia R. Br. is a species of Proteaceae that is resistant to developing P-toxicity symptoms at phosphorus supplies in the root environment that induce P-toxicity symptoms in the closely related Hakea prostrata (Proteaceae). It was discovered previously that development of P-toxicity symptoms in H. prostrata is related to its low capacity to down-regulate net P-uptake rates (i.e. its low plasticity). The plasticity of net P-uptake rates and whole-plant growth responses in G. crithmifolia has now been assessed in two separate experiments: (i) a range of P, from 0 to 200 micromol P d-1, was supplied to whole root systems; (ii) using a split-root design, one root half was supplied with 0, 3, 75, or 225 micromol P d-1, while the other root half invariably received 3 micromol P d-1. Fresh mass was significantly greater in G. crithmifolia plants that had received a greater daily P supply during the pretreatments, but symptoms of P toxicity were never observed. Cluster-root growth decreased from about half the total root fresh mass when the leaf [P] was lowest (c. 0.1 mg P g-1 DM) to complete suppression of cluster-root growth when leaf [P] was 1-2 mg P g-1 DM. Split-root studies revealed that cluster-root initiation and growth, and net P-uptake rates by roots were regulated systemically, possibly by shoot P concentration. It is concluded that, in response to higher P supply, G. crithmifolia does not develop symptoms of P toxicity because of (i) greater plasticity of its net P-uptake capacity, and (ii) its greater plasticity for allocating P to growth and P storage in roots. This ecologically important difference in plasticity is most probably related to a slightly higher nutrient availability in the natural habitat of G. crithmifolia when compared with that of H. prostrata.     

A miniaturized cell-based fluorescence resonance energy transfer assay for insulin-receptor activation

This report describes the development, optimization, and implementation of a miniaturized cell-based assay for the identification of small-molecule insulin mimetics and potentiators. Cell-based assays are attractive formats for compound screening because they present the molecular targets in their cellular environment. A fluorescence resonance energy transfer (FRET) cell-based assay that measures the insulin-dependent colocalization of Akt2 fused with either cyan fluorescent protein or yellow fluorescent protein to the cellular membrane was developed. This ratiometric FRET assay was miniaturized into a robust, yet sensitive 3456-well nanoplate assay with Z' factors of approximately 0.6 despite a very small assay window (less than twofold full activation with insulin). The FRET assay was used for primary screening of a large compound collection for insulin-receptor agonists and potentiators. To prioritize compounds for further development, primary hits were tested in two additional assays, a biochemical time-resolved fluorescence resonance energy transfer assay to measure insulin-receptor phosphorylation and a translocation-based imaging assay. Results from the three assays were combined to yield 11 compounds as potential leads for the development of insulin mimetics or potentiators.     

The role of MAP4K3 in lifespan regulation of Caenorhabditiselegans

The TOR pathway is a kinase signaling pathway that regulates cellular growth and proliferation in response to nutrients and growth factors. TOR signaling is also important in lifespan regulation - when this pathway is inhibited, either naturally, by genetic mutation, or by pharmacological means, lifespan is extended. MAP4K3 is a Ser/Thr kinase that has recently been found to be involved in TOR activation. Unexpectedly, the effect of this protein is not mediated via Rheb, the more widely known TOR activation pathway. Given the role of TOR in growth and lifespan control, we looked at how inhibiting MAP4K3 in Caenorhabditiselegans affects lifespan. We used both feeding RNAi and genetic mutants to look at the effect of MAP4K3 deficiency. Our results show a small but significant increase in mean lifespan in MAP4K3 deficient worms. MAP4K3 thus represents a new target in the TOR pathway that can be targeted for pharmacological intervention to control lifespan.     

Development of a bioprocess to convert PET derived terephthalic acid and biodiesel derived glycerol to medium chain length polyhydroxyalkanoate

Sodium terephthalate (TA) produced from a PET pyrolysis product and waste glycerol (WG) from biodiesel manufacture were supplied to Pseudomonas putida GO16 in a fed-batch bioreactor. Six feeding strategies were employed by altering the sequence of TA and WG feeding. P. putida GO16 reached 8.70 g/l cell dry weight (CDW) and 2.61 g/l PHA in 48 h when grown on TA alone. When TA and WG were supplied in combination, biomass productivity (g/l/h) was increased between 1.3- and 1.7-fold and PHA productivity (g/l/h) was increased 1.8- to 2.2-fold compared to TA supplied alone. The monomer composition of the PHA accumulated from TA or WG was predominantly composed of 3-hydroxydecanoic acid. PHA monomers 3-hydroxytetradeeanoic acid and 3-hydroxytetradecenoic acid were not present in PHA accumulated from TA alone but were present when WG was supplied to the fermentation. When WG was either the sole carbon source or the predominant carbon source supplied to the fermentation the molecular weight of PHA accumulated was lower compared to PHA accumulated when TA was supplied as the sole substrate. Despite similarities in data for the properties of the polymers, PHAs produced with WG present in the PHA accumulation phase were tacky while PHA produced where TA was the sole carbon substrate in the polymer accumulation phase exhibited little or no tackiness at room temperature. The co-feeding of WG to fermentations allows for increased utilisation of TA. The order of feeding of WG and TA has an effect on TA utilisation and polymer properties.     

Use of a blocking primer allows selective amplification of bacterial DNA from microalgae cultures

The production of algae is a crucial component of many aquaculture systems and the role of bacteria in this process is an important although complex one. We report the development of a new blocking primer that allowed PCR amplification of bacterial DNA in the presence of algal chloroplast DNA.     

Serine hydroxymethyltransferase anchors de novo thymidylate synthesis pathway to nuclear lamina for DNA synthesis

The de novo thymidylate biosynthetic pathway in mammalian cells translocates to the nucleus for DNA replication and repair and consists of the enzymes serine hydroxymethyltransferase 1 and 2α (SHMT1 and SHMT2α), thymidylate synthase, and dihydrofolate reductase. In this study, we demonstrate that this pathway forms a multienzyme complex that is associated with the nuclear lamina. SHMT1 or SHMT2α is required for co-localization of dihydrofolate reductase, SHMT, and thymidylate synthase to the nuclear lamina, indicating that SHMT serves as scaffold protein that is essential for complex formation. The metabolic complex is enriched at sites of DNA replication initiation and associated with proliferating cell nuclear antigen and other components of the DNA replication machinery. These data provide a mechanism for previous studies demonstrating that SHMT expression is rate-limiting for de novo thymidylate synthesis and indicate that de novo thymidylate biosynthesis occurs at replication forks.     

Associations between household and neighbourhood socioeconomic status and systolic blood pressure among urban South African adolescents

Factors resulting in high risk for cardiovascular disease have been well studied in high income countries, but have been less well researched in low/middle income countries. This is despite robust theoretical evidence of environmental transitions in such countries which could result in biological adaptations that lead to increased hypertension and cardiovascular disease risk. Data from the South African Birth to Twenty cohort, Bone Health sub-sample (n = 358, 47% female), were used to model associations between household socioeconomic status (SES) in infancy, household/neighbourhood SES at age 16 years, and systolic blood pressure (multivariate linear regression) and risk for systolic pre-hypertension (binary logistic regression). Bivariate analyses revealed household/neighbourhood SES measures that were significantly associated with increased systolic blood pressure. These significant associations included improved household sanitation in infancy/16 years, caregiver owning the house in infancy and being in a higher tertile (higher SES) of indices measuring school problems/environment or neighbourhood services/problems/crime at 16 years of age. Multivariate analyses adjusted for sex, maternal age, birth weight, parity, smoking, term birth, height/body mass index at 16 years. In adjusted analyses, only one SES variable remained significant for females: those in the middle tertile of the crime prevention index had higher systolic blood pressure (β = 3.52, SE = 1.61) compared with the highest tertile (i.e. those with the highest crime prevention). In adjusted analyses, no SES variables were significantly associated with the systolic blood pressure of boys, or with the risk of systolic pre-hypertension in either sex. The lack of association between SES and systolic blood pressure/systolic pre-hypertension at age 16 years is consistent with other studies showing an equalization of adolescent health inequalities. Further testing of the association between SES and systolic blood pressure would be recommended in adulthood to see whether the lack of association persists.