The use and misuse of regression models in landscape genetic analyses

The field of landscape genetics has been rapidly evolving, adopting and adapting analytical frameworks to address research questions. Current studies are increasingly using regression‐based frameworks to infer the individual contributions of landscape and habitat variables on genetic differentiation. This paper outlines appropriate and inappropriate uses of multiple regression for these purposes, and demonstrates through simulation the limitations of different analytical frameworks for making correct inference. Of particular concern are recent studies seeking to explain genetic differences by fitting regression models with effective distance variables calculated independently on separate landscape resistance surfaces. When moving across the landscape, organisms cannot respond independently and uniquely to habitat and landscape features. Analyses seeking to understand how landscape features affect gene flow should model a single conductance or resistance surface as a parameterized function of relevant spatial covariates, and estimate the values of these parameters by linking a single set of resistance distances to observed genetic dissimilarity via a loss function. While this loss function may involve a regression‐like step, the associated nuisance parameters are not interpretable in terms of organismal movement and should not be conflated with what is actually of interest: the mapping between spatial covariates and conductance/resistance. The growth and evolution of landscape genetics as a field has been rapid and exciting. It is the goal of this paper to highlight past missteps and demonstrate limitations of current approaches to ensure that future use of regression models will appropriately consider the process being modeled, which will provide clarity to model interpretation.     

Duration of Maternal Antibodies against Canine Distemper Virus and Hendra Virus in Pteropid Bats

Old World frugivorous bats have been identified as natural hosts for emerging zoonotic viruses of significant public health concern, including henipaviruses (Nipah and Hendra virus), Ebola virus, and Marburg virus. Epidemiological studies of these viruses in bats often utilize serology to describe viral dynamics, with particular attention paid to juveniles, whose birth increases the overall susceptibility of the population to a viral outbreak once maternal immunity wanes. However, little is understood about bat immunology, including the duration of maternal antibodies in neonates. Understanding duration of maternally derived immunity is critical for characterizing viral dynamics in bat populations, which may help assess the risk of spillover to humans. We conducted two separate studies of pregnant Pteropus bat species and their offspring to measure the half-life and duration of antibodies to 1) canine distemper virus antigen in vaccinated captive Pteropus hypomelanus; and 2) Hendra virus in wild-caught, naturally infected Pteropus alecto. Both of these pteropid bat species are known reservoirs for henipaviruses. We found that in both species, antibodies were transferred from dam to pup. In P. hypomelanus pups, titers against CDV waned over a mean period of 228.6 days (95% CI: 185.4–271.8) and had a mean terminal phase half-life of 96.0 days (CI 95%: 30.7–299.7). In P. alecto pups, antibodies waned over 255.13 days (95% CI: 221.0–289.3) and had a mean terminal phase half-life of 52.24 days (CI 95%: 33.76–80.83). Each species showed a duration of transferred maternal immunity of between 7.5 and 8.5 months, which was longer than has been previously estimated. These data will allow for more accurate interpretation of age-related Henipavirus serological data collected from wild pteropid bats.     

Cauli: A Mouse Strain with an Ift140 Mutation That Results in a Skeletal Ciliopathy Modelling Jeune Syndrome

Cilia are architecturally complex organelles that protrude from the cell membrane and have signalling, sensory and motility functions that are central to normal tissue development and homeostasis. There are two broad categories of cilia; motile and non-motile, or primary, cilia. The central role of primary cilia in health and disease has become prominent in the past decade with the recognition of a number of human syndromes that result from defects in the formation or function of primary cilia. This rapidly growing class of conditions, now known as ciliopathies, impact the development of a diverse range of tissues including the neural axis, craniofacial structures, skeleton, kidneys, eyes and lungs. The broad impact of cilia dysfunction on development reflects the pivotal position of the primary cilia within a signalling nexus involving a growing number of growth factor systems including Hedgehog, Pdgf, Fgf, Hippo, Notch and both canonical Wnt and planar cell polarity. We have identified a novel ENU mutant allele of Ift140, which causes a mid-gestation embryonic lethal phenotype in homozygous mutant mice. Mutant embryos exhibit a range of phenotypes including exencephaly and spina bifida, craniofacial dysmorphism, digit anomalies, cardiac anomalies and somite patterning defects. A number of these phenotypes can be attributed to alterations in Hedgehog signalling, although additional signalling systems are also likely to be involved. We also report the identification of a homozygous recessive mutation in IFT140 in a Jeune syndrome patient. This ENU-induced Jeune syndrome model will be useful in delineating the origins of dysmorphology in human ciliopathies.     

Response of benthic macroinvertebrates to whole-lake, non-native fish treatments in mid-elevation lakes of the Trinity Alps, California

Introduced fish reduce the abundance and diversity of native aquatic fauna, but the effect can be reduced in complex habitats. We manipulated fish populations in forested mountain lakes to determine whether or not fish affected benthic macroinvertebrate composition across lakes with differing habitat complexity. We compared abundance, biomass, body-length, and community structure of benthic macroinvertebrates from 16 lakes with three treatments (fish stocked, suspended stocking, fish removed) and unstocked fishless “controls”. Over 4 years, we assessed the relative importance of fish and environmental variables influencing the composition of benthic macroinvertebrates. Control lakes had the greatest overall abundance of macroinvertebrates when chironomid midges were excluded. Abundances of insects in the clinger/swimmer functional group and caddisflies were greatest in the control lakes but were primarily influenced by habitat variables including the availability of aquatic vegetation and wood. Total biomass and mean body length of macroinvertebrates were not affected by treatment. Taxon richness of macroinvertebrates was about 40% greater in the control lakes compared to the treatment lakes but did not differ among treatments. Our results suggest that fish reduce susceptible macroinvertebrate richness and abundances, but that changes associated with alterations of fish composition are confounded by other factors in complex lake habitats.     

Treating hop plants with (Z)-jasmone increases colonization by Phorodon humuli (Hemiptera: Aphididae) spring migrants

Hop plants were sprayed with (Z)-jasmone, at a rate of 50 g ha(-1), during the spring migration of the damson-hop aphid Phorodon humuli (Schrank) in 2002 and 2003. Numbers of P. humuli spring migrants colonizing hop plants, Humulus lupulus L., 2-6 and 7-11 days after applying this treatment were assessed in both years. During the first five-day period, significantly more spring migrants were found on hop plants treated with (Z)-jasmone, in comparison with control plants, in 2002. By contrast, no significant difference was evident in the second five-day period. Although the migration in 2003 was much lighter than in 2002, greater numbers of migrants were again removed from treated plants. Indeed, more spring migrants were removed from plants sprayed with (Z)-jasmone in this year during both five-day periods (11 and 44%, respectively) compared with the 23% greater numbers removed in the first five-day period in 2002. Therefore, unlike some other species of aphid, where numbers were consistently lower on plots sprayed with (Z)-jasmone, spraying the secondary host of P. humuli with this compound appears to increase colonization by spring migrants.     

The bone marrow plasma cell labeling index by flow cytometry

The bone marrow plasma cell labeling index is the most important prognostic indicator for patients with multiple myeloma. Traditionally, this test has been performed as a two color immunofluorescent microscope technique which is time consuming and requires a degree of subjectivity in its interpretation. We have assessed various adaptations of this method to flow cytometry. A bromodeoxyuridine method has been compared with a propidium iodide DNA method to detect cells in S phase and CD38-FITC has been compared with CD38-FITC + CD138-FITC and CD38-biotin + streptavidin FITC to identify plasma cells. The mean channel fluorescent intensity of the plasma cell peaks for each of these markers was 12. 7, 17.4 and 35.3 respectively demonstrating the superiority of CD38-biotin + streptavidin FITC. Analysis after propidium iodide staining provided a good correlation with the slide technique (r = 0. 71; P < 0.0001) but the bromodeoxyuridine method did not correlate with the slide method (r = 0.09; P = NS). The labeling index values obtained from either of the flow methods were greater than the microscopic method. Thus a labeling index of >4% will replace the traditional >1% threshold for identifying patients with a significantly increased labeling index. The advantages of the new method are that it takes less time to perform, is more objective and provides additional data on ploidy and cell cycle status.     

Prostaglandin F2alpha-induced estrus in ewes exhibiting estrous cycles of different duration

Effects of prostaglandin F(2alpha) (PGF(2alpha)), administered during the mid-luteal phase of the estrous cycle, were examined in ewes exhibiting estrous cycles classified as short (< or =16.5 days, short-cycle ewes, n = 10) or long (> or =18 days, long-cycle ewes, n = 9) based on the durations of two estrous cycles (cycles -2 and -1) before treatment. The ewes received (i.m.) 20mg of PGF(2alpha) on day 10 of the third estrous cycle (cycle 0) followed, 36 h later, by 25 microg of gonadotropin releasing hormone (GnRH) to time the events of ovulation. Duration of subsequent estrous cycles +1 and +2 were recorded, and then the ewes were treated with the same combination of PGF(2alpha) and GnRH beginning on day 10 of estrous cycle +3. Ovaries were recovered 6h after GnRH administration to assess development of pre-ovulatory follicles. The proportion of ewes that exhibited estrus after PGF(2alpha) and GnRH treatment on cycle 0 was not different (P > 0.05) between short- and long-cycle ewes. Onset of estrus occurred sooner (P < 0.05) after PGF(2alpha) injection in short-cycle ewes than in long-cycle ewes (1.9 +/- 0.1 days and 2.3 +/- 0.1 days, duration of cycle 0 was 11.9 and 12.3 days, respectively). Duration of estrous cycle +1 was 1.2 days longer (P < 0.01) than cycle -1 in short-cycle ewes. However, duration of estrous cycle +1 did not change (P > 0.05) after PGF(2alpha) and GnRH administration in ewes having long cycles. Pre-ovulatory follicles did not differ (P > 0.05) in numbers, diameter, layers of granulosa cells nor concentrations of progesterone and estradiol-17beta in follicular fluid between short- and long-cycle ewes after PGF(2alpha) and GnRH treatment. In conclusion, ewes having short or long estrous cycles responded differently to PGF(2alpha) and GnRH treatment with respect to the interval to onset of estrus and duration of the subsequent estrous cycle.     

Latrunculin B or ATP depletion induces cofilin-dependent translocation of actin into nuclei of mast cells

Increasing cellular G-actin, using latrunculin B, in either intact or permeabilized rat peritoneal mast cells, caused translocation of both actin and an actin regulatory protein, cofilin, into the nuclei. The effect was not associated with an increase in the proportion of apoptotic cells. The major part of the nuclear actin was not stained by rhodamine-phalloidin but could be visualized with an actin antibody, indicating its monomeric or a conformationally distinct state, e.g. cofilin-decorated filaments. Introduction of anti-cofilin into permeabilized cells inhibited nuclear actin accumulation, implying that an active, cofilin-dependent, import exists in this system. Nuclear actin was localized outside the ethidium bromide-stained region, in the extrachromosomal nuclear domain. In permeabilized cells, the appearance of nuclear actin and cofilin was not significantly affected by increasing [Ca(2+)] and/or adding guanosine 5'-O-(3-thiotriphosphate), but was greatly promoted when ATP was withdrawn. Similarly, ATP depletion in intact cells also induced nuclear actin accumulation. In contrast to the effects of latrunculin B, ATP depletion was associated with an increase in cortical F-actin. Our results suggest that the presence of actin in the nucleus may be required for certain stress-induced responses and that cofilin is essential for the nuclear import of actin.     

New synthesis of (+/-)-alpha-CMBHC and its confirmation as a metabolite of alpha-tocopherol (vitamin E)

There is currently interest in the metabolism of the various compounds which make up the vitamin E family, especially with regards to the possible use of vitamin E metabolites as markers of oxidative stress and adequate vitamin E supply. A number of vitamin E metabolites have been described to date and we have recently developed a method to extract and quantitate a range of vitamin E metabolites in human urine. During the development of this method a new metabolite of alpha-tocopherol was identified, which we tentatively characterised as 5-(6-hydroxy-2,5,7,8-tetramethyl-chroman-2-yl)-2-methyl-pentanoic acid (alpha-CMBHC).(1) Here we describe the synthesis of alpha-CMBHC as a standard and confirm that it is a metabolite of alpha-tocopherol.