Algamica: revisions to a key-based computerized counting program for free-living,attached, and benthic algae

A computerized counting program for algae and other microscopic bodies, named Algamica, is presented here. This program is a revised version of the original computer counting program of Hamilton published in 1990. This DOS-based software can enumerate all types of microscopic algae (i.e. phytoplankton, periphyton, diatoms), for which adequate expression of results are provided. Automated calculations of densities, biovolumes, surface areas and carbon biomass are available at the termination of each sample count. A simple counter for other micro-organisms is also available. A comprehensive guide manual file has been added to allow for a friendly first contact with the program and its options. This software conforms to current enumeration methodology. This version is available for PC computers, from website Algamica.ibelgique.com. Minimum required memory is 200 KB.     

Relation of the White Blood Cell Count to Obesity and Insulin Resistance: Effect of Race and Gender

PRATLEY, RICHARD E, CHARLTON WILSON AND CLIFTON BOGARDUS. Relation of the white blood cell count to obesity and insulin resistance: effect of race and gender. Obes Res. Recent reports suggest that the white blood cell (WBC) count is related to plasma insulin concentrations and insulin resistance in healthy individuals. The present study examines whether these relations are independent of obesity and the pattern of body fat distribution and tests whether race and gender affect these relations. WBC counts, insulin responses to a 75 gram oral glucose tolerance test (OGTT) and glucose disposal during a two-step hyperinsulinemic euglycemic clamp were measured in 300 men and women (149 Pima Indians, 100 whites, and 51 blacks) with a wide range of obesity. WBC counts were lower in blacks than Pima Indians or whites and tended to be higher in women than men. The subgroups were comparable in age and body weight, but percent body fat and plasma insulin concentrations were higher and glucose disposal during the glucose clamp was lower in Pima Indians than in blacks or whites. In the group as a whole, the WBC count correlated with obesity (body mass index and percent body fat), the waist to thigh ratio (an index of the pattern of body fat distribution), and plasma insulin concentrations and was negatively related to age and glucose disposal during the clamp. In multiple regression analyses, only age, race and obesity were significantly associated with the WBC count. When the analyses were restricted to Pima men, in whom correlations between the WBC count and the metabolic variables appeared the strongest, the WBC count remained significantly associated with plasma insulin concentrations, but not glucose disposal, after controlling for age and obesity. The results of this study indicate that age, race, and obesity are significantly associated with the WBC count in healthy individuals. Plasma insulin concentrations, but not insulin resistance per se, may also be weakly associated with the WBC count, but this may be population specific.     

Jordan's and other ecogeographical rules, and the vertebral number in fishes

Aim  To explore variation in the number of vertebrae in fishes in the context of Jordan's rule and other ecogeographical rules.
Location  Global.
Methods  The study is based on literature review.
Results  The number of vertebrae varies very widely across the diversity of fishes. Jordan's rule states that vertebral number increases with latitude, and this is widely attributed to ambient temperatures during ontogeny of individual fishes. However, the number of vertebrae may depend on both the ontogenetic environment and inheritance. Diverse other aspects of fish development and ecology are suggested as influencing vertebral number, including fish size, phyletic position, body shape and swimming mode.
Main conclusions  The number of different factors that influence the number of vertebrae in fishes makes for highly complex patterns of variation, and means that unravelling causes is difficult. The question needs to be addressed at the population/species/species group scale; moreover, the lack of discrimination between environmental and inherited causes of variation adds to the complexity.     

Dietary chromium deficiency effect on sperm count and fertility in rats

Male rats raised on a low chromium diet containing less than 100 ppb chromium had decreased sperm counts and decreased fertility at age 8 months compared to the Cr-supplemented controls. Decreased sperm cell production and fertility were not apparent at age 4 months. At age 7–8 months the frequency of conception was 25 percent or less and the sperm count of the low chromium males was approximately 50 percent of that of the Cr-supplemented rats.     

Comparison of removal‐based methods for estimating abundance of five species of prairie songbirds

Estimating species abundance is important for land managers, especially for monitoring conservation efforts. The two main survey methods for estimating avian abundance are point counts and transects. Previous comparisons of these two methods have either been limited to a single species or have not included detection probability. During the 2012 breeding season, we compared and assessed the efficiency (precision for amount of effort) of point count time of detection (PCTD) and dependent double‐observer transect (TRMO) methods based on detection probabilities and abundance estimates of five species of songbirds that use a range of habitats in a prairie system in Montana dominated by sagebrush and grassland vegetation. Our focal species included Vesper Sparrows (Pooecetes gramineus), a generalist species found in both shrub and grassland habitat, shrub‐obligate Brewer's Sparrows (Spizella breweri), and McCown's Longspurs (Rhynchophanes mccownii), Horned Larks (Eremophila alpestris), and Western Meadowlarks (Sturnella neglecta), three species of grassland obligates that prefer different grass heights. Detection probabilities were significantly higher for TRMO surveys, with less variation for all five species and differences most pronounced for Brewer's Sparrows and Horned Larks. PCTD surveys required less field effort (~8–20 fewer people minutes per plot) than TRMO surveys because the TRMO surveys required two people. However, time spent on TRMO surveys provided between 0.38 and 87 times more precision per people minute than PCTD surveys. Our results suggest that TRMO surveys provide a more efficient (measured as time spent per unit of standard error) field‐based technique in sagebrush prairie systems for the species we investigated, resulting in more precise detection and abundance estimates.     

Condition-dependent alteration of cellular immunity by secondary symbionts in the pea aphid,Acyrthosiphon pisum

Endosymbionts can fundamentally alter host physiology. Whether such changes are beneficial or detrimental to one or both partners may depend on the dynamics of the symbiotic relationship. Here we investigate the relationship between facultative symbionts and host immune responses. The pea aphid, Acyrthosiphon pisum, maintains an obligate primary symbiont, but may also harbour one or more facultative, secondary symbionts. Given their more transient nature and relatively recent adoption of a symbiotic lifestyle compared to primary symbionts, secondary symbionts may present a challenge for the host immune system. We assessed the response of several key components of the cellular immune system (phenoloxidase activity, encapsulation, immune cell counts) in the presence of alternative secondary symbionts, investigating the role of host and secondary symbiont genotype in specific responses. There was no effect of secondary symbiont presence on the phenoloxidase response, but we found variation in the encapsulation response and in immune cell counts based largely on the secondary symbiont. Host genotype was less influential in determining immunity outcomes. Our results highlight the importance of secondary symbionts in shaping host immunity. Understanding the complex physiological responses that can be propagated by host-symbiont associations has important consequences for host ecology, including symbiont and pathogen transmission dynamics.     

Diet preferences based on sequence read count: The role of species interaction in tissue bias correction

High-throughput sequencing and metabarcoding techniques provide a unique opportunity to study predator–prey relationships. However, in animal dietary preference studies, how to properly correct tissue bias within the sequence read count and the role of interactions between co-occurring species in metabarcoding mixtures remain largely unknown. In this study, we propose two categories of tissue bias correction indices: sequence read count number per unit tissue (SCN) and its ratio form (SCN ratio). By constructing plant mock communities with different numbers of co-occurring species in metabarcoding mixtures and conducting feeding trails on captive sika deer (Cervus nippon), we demonstrate the features of the SCN and SCN ratio, evaluate their correction effects and assess the role of species interactions during tissue bias correction. Tissue differences between species are defined as the differential ability to generate sequence counts. Our study suggests that pure tissue differences among species without a species interaction is not an optimal correction index for many biomes with limited tissue differences among species. Species interactions in mixtures may amplify tissue differences, which is beneficial for tissue bias correction. However, caution must be taken because varied species interactions among communities may increase the risk of worse correction. Correction effects based on the SCN and SCN ratio are comparable, but the SCN is less influenced by control species than the SCN ratio. Based on our study, several suggestions are provided for future animal diet studies or other high-throughput sequencing studies containing tissue bias.     

Role of TMPRSS6 rs855791 (T > C) polymorphism in reproductive age women with iron deficiency anemia from Lahore,Pakistan

BackgroundIron deficiency anemia (IDA) is the highest nutritional deficiency worldwide. It is a multifactorial disease, with a higher morbidity rate. TMPRSS6 polymorphisms importantly rs855791 is found to play an essential role in iron homeostasis in the human body. The rs855791 (T > C) polymorphism is highly associated with iron levels, and multiple blood parameters, leading to IDA. The role of TMPRSS6 rs855791 polymorphism and the significance of complete blood count (CBC) parameters in the pathogenesis of IDA is not yet studied in the Pakistani population.MethodsWe enrolled 113 cases and 136 controls to conduct a case control study. Complete blood count (CBC) and iron parameters were analyzed for association studies. PCR-RFLP based genotyping was performed.ResultsThe TMPRSS6 rs855791 (T > C) polymorphism is significantly associated with IDA pathogenesis as observed in the codominant model and recessive models (P < 0.05, OR: 1.5 and 95% CI: 0.9, 2.6, P < 0.05, OR: 0.5 and 95% CI: 0.2, 0.9 respectively). Elderly women among cases (30–49 years) were found to be more susceptible to IDA (P < 0.05, AOR: 2.1 and 95% CI: 1.0, 4.2). The most significant parameters associated with IDA were red blood cell count (RBC) and hematocrit (Hct%) (P < 0.05, AOR: 16.5, 95% CI: 7.6, 35.9 and P < 0.05, AOR: 10.1, 95% CI: 2.5, 41.6, respectively).ConclusionTMPRSS6 polymorphism at rs855791 (T > C) is significantly associated with IDA susceptibility in reproductive age women in Pakistan. Age, RBC count and Hct% are found to play an important role in IDA pathogenesis in our study population.     

Principal climatic and edaphic determinants of Culicoides biting midge abundance during the 2007–2008 bluetongue epidemic in the Netherlands,based on OVI light trap data

Palaearctic Culicoides midges (Diptera: Ceratopogonidae) represent a vital link in the northward advance of certain arboviral pathogens of livestock such as that caused by bluetongue virus. The effects of relevant ecological factors on weekly Culicoides vector abundances during the bluetongue virus serotype 8 epidemics in the Netherlands in 2007 and 2008 were quantified within a hurdle modelling framework. The relative role of meteorological parameters showed a broadly consistent association across species, with larger catches linked to temperature‐related variables and lower wind speed. Moreover, vector abundance was found to be influenced by edaphic factors, likely related to species‐specific breeding habitat preferences that differed markedly amongst some species. This is the first study on Culicoides vector species in the Netherlands identified during an entomological surveillance programme, in which an attempt is made to pinpoint the factors that influence midge abundance levels. In addition to providing key inputs into risk‐mitigating tools for midge‐borne pathogens and disease transmission models, the adoption of methods that explicitly address certain features of abundance datasets (frequent zero‐count observations and over‐dispersion) helped enhance the robustness of the ecological analysis.     

Thresholds and Time Lags in Effects of Energy Development on Greater Sage-Grouse Populations

ABSTRACT Rapid expansion of energy development in some portions of the Intermountain West, USA, has prompted concern regarding impacts to declining greater sage-grouse (Centrocercus urophasianus) populations. We used retrospective analyses of public data to explicitly investigate potential thresholds in the relationship between lek attendance by male greater sage-grouse, the presence of oil or gas wells near leks (surface occupancy), and landscape-level density of well pads. We used generalized linear models and generalized estimating equations to analyze data on peak male attendance at 704 leks over 12 years in Wyoming, USA. Within this framework we also tested for time-lag effects between development activity and changes in lek attendance. Surface occupancy of oil or gas wells adjacent to leks was negatively associated with male lek attendance in 5 of 7 study areas. For example, leks that had ≥ 1 oil or gas well within a 0.4-km (0.25-mile) radius encircling the lek had 35–91% fewer attending males than leks with no well within this radius. In 2 of these 5 study areas, negative effects of well surface occupancy were present out to 4.8 km, the largest radius we investigated. Declining lek attendance was also associated with a higher landscape-level density of well pads; lek attendance at well-pad densities of 1.54 well pads/km² (4 well pads/mile²) ranged from 13% to 74% lower than attendance at unimpacted leks (leks with zero well pads within 8.5 km). Lek attendance at a well-pad density of 3.09 well pads/km² (8 well pads/mile²) ranged from 77% to 79% lower than attendance at leks with no well pad within 8.5 km. Further, our analysis of time-lag effects suggested that there is a delay of 2–10 years between activity associated with energy development and its measurable effects on lek attendance. These results offer new information for consideration by land managers on spatial and temporal associations between human activity and lek attendance in sage-grouse, and suggest that regional variation is an important consideration in refining existing management strategies.