snpR: User friendly population genomics for SNP data sets with categorical metadata

The analysis of genomic data can be an intimidating process, particularly for researchers who are not experienced programmers. Commonly used analyses are spread across many programs, each requiring their own specific input formats, and so data must often be repeatedly reorganized and transformed into new formats. Analyses often require splitting data according to metadata variables such as population or family, which can be challenging to manage in large data sets. Here, we introduce snpR, a user-friendly data analysis package in R for processing SNP genomic data. snpR is designed to automate data subsetting and analyses across categorical metadata while also streamlining repeated analyses by integrating approaches contained in many different packages in a single ecosystem. snpR facilitates iterative and efficient analyses centred on a single R object for an entire analysis pipeline.     

A differential proteomics study of cerebrospinal fluid from individuals with Niemann-Pick disease,Type C1

Niemann-Pick, type C1 (NPC1) is a fatal, neurodegenerative disease, which belongs to the family of lysosomal diseases. In NPC1, endo/lysosomal accumulation of unesterified cholesterol and sphingolipids arise from improper intracellular trafficking resulting in multi-organ dysfunction. With the proximity between the brain and cerebrospinal fluid (CSF), performing differential proteomics provides a means to shed light to changes occurring in the brain. In this study, CSF samples obtained from NPC1 individuals and unaffected controls were used for protein biomarker identification. A subset of these individuals with NPC1 are being treated with miglustat, a glycosphingolipid synthesis inhibitor. Of the 300 identified proteins, 71 proteins were altered in individuals with NPC1 compared to controls including cathepsin D, and members of the complement family. Included are a report of 10 potential markers for monitoring therapeutic treatment. We observed that pro-neuropeptide Y (NPY) was significantly increased in NPC1 individuals relative to healthy controls; however, individuals treated with miglustat displayed levels comparable to healthy controls. In further investigation, NPY levels in a NPC1 mouse model corroborated our findings. We posit that NPY could be a potential therapeutic target for NPC1 due to its multiple roles in the central nervous system such as attenuating neuroinflammation and reducing excitotoxicity.     

Differences in Body Image and Depression Among Obese Women With and Without Binge Eating Disorder

Obese individuals with binge eating disorder (BED) differ from obese non-binge eating (NBE) individuals in a number of clinically relevant ways. This study examined attitudinal responses to various measures of body image in women seeking obesity treatment, by comparing NBE participants (n=80) to those with BED (n=48). It was hypothesized that women with BED would demonstrate greater attitudinal disturbance of body image compared to NBE individuals. It was further hypothesized that significant differences between groups would remain after statistically controlling for degree of depression. Consistent with the primary hypothesis, BED participants reported significantly increased attitudinal disturbance in body dissatisfaction and size perception compared to NBE participants. Although shared variance was observed between measures of depression and body image on some items, several aspects of increased body image disturbance remained after statistically controlling for depression. Treatment implications and recommendations for future research are discussed.     

SOURCES OF INORGANIC CARBON FOR PHOTOSYNTHESIS BY THREE SPECIES OF MARINE DIATOM1

The utilization of inorganic carbon by three species of marine diatom, Skeletonema costatum (Grev.) Cleve. Ditylum brightwellii (West) Grun., and Chaetoceros calcitrans Paulsen was investigated using an inorganic carbon isotopic disequilibnum technique and inorganic carbon dose-response curves. Stable carbon isotope data of the diatoms are also presented. Observed rates of photosynthetic oxygen evolution were greater than could be accounted for by the theoretical rate of CO₂ supply from the uncatalyzed dehydration of HCO₃^? in the external medium, suggesting use of HCO₃^? as an inorganic carbon source. Data from the isotopic disequilibrium experiment demonstrate the use of both HCO₃^? and CO₂ for photosynthesis. Carbon isotope discrimination values support the use of HCO₃^? by the diatoms.     

The embryology and relationships ofPenaeaceae (Myrtales)

Two species ofPenaeaceae (Penaea mucronata andSaltera sarcocolla), a unique South African family ofMyrtales, were investigated embryologically.Penaeaceae clearly agrees with otherMyrtales in its basic embryological characteristics, and further is characterized by its highly specialized features: ephemeral endothecium, 16-nucleatePenaea-type embryo sac, and unique ovular form. A wider range of affinities of families includingPenaeaceae, Oliniaceae, Rhynchocalycaceae, Alzateaceae, andCrypteroniaceae sensu stricto, as well as a possible common divergence from an ancestral line leading toLythraceae and/orMelastomataceae, are discussed on embryological and other grounds.     

A new human T-cell differentiation antigen: Unexpected expression on chronic lymphocytic leukemia cells

Monoclonal antibody 10.2 reacts with a monomorphic antigen expressed on the surface of virtually all thymocytes, as well as thymus-dependent lymphocytes in the peripheral blood and bone marrow. In contrast, antibody 10.2 did not react with normal peripheral blood B cells, monocytes, or the non-T-cell fraction of bone marrow. This complement fixing IgG2a antibody also reacted with extablished leukemic T-cell lines, but not with cell lines of either normal or malignant B-cell origin. Similarly, when tested against acute leukemia blasts, the 10.2 antibody reacted with those from patients with T-cell acute leukemia, but not with those from patients with acute null cell or non-lymphocytic leukemia. An unexpected exception to this pattern was the reaction of 10.2 antibody with leukemic cells from patients with B-cell type chronic lymphocytic leukemia. Immune precipitates formed with 10.2 antibody and detergent lysates of radiolabeled T-cells contained three polypeptides with molecular weights of 65 000, 55 000, and 50000 daltons. It has not been determined whether all three of these polypeptides contain the 10.2 antigenic determinant, or whether these proteins represent a multimeric antigen complex.PJM is a Junior Faculty Clinical Fellow of the American Cancer Society.     

The acquisition of inorganic carbon by four red macroalgae

Photosynthesis was studied in four species of red marine macroalgae: Palmaria palmata, Laurencia pinnatifida, Lomentaria articulata and Delesseria sanguinea. The rate of O₂ evolution for submersed photosynthesis was measured as a function of incident photon flux density at normal pH and inorganic carbon concentration (pH 8.0, 2 mol m^–3), and as a function of inorganic carbon concentration at pH 8.0 at saturating and at limiting photon flux density. The rate of CO₂ uptake was measured for emersed photosynthesis as a function of CO₂ partial pressure at saturating photon flux density. Previous pH-drift results suggest that Palmaria and Laurencia are able to use HCO _inf3 ^sup– as well as CO₂ whereas Lomentaria and Delesseria are restricted to CO₂. None of the algae are saturated by 2 mol m^–3 inorganic carbon at high light (400 mol m^–2 s^–1) but are saturated at low light (35 mol m^–2 s^–1). The inorganic C concentration at which half the light-saturated rate of O₂ evolution is achieved is higher for Palmaria and Laurencia (1.51 and 1.85 mol m^–3) than for Lomentaria and Delesseria (0.772 and 0.841 mol m^–3). The lower values for the latter two species could reflect their putative restriction to CO₂. If expressed in terms of CO₂, the half-saturation values yield 7.2 and 7.8 mmol m^–3 respectively, which are very similar to values obtained previously during pH-drift experiments but at lower concentrations of HCO _inf3 ^sup– , consistent with restriction to CO₂. The photosynthetic conductance (m s^–1), calculated from the initial slope for photosynthesis at low concentrations of inorganic carbon, correlates with the suggested ability to extract inorganic carbon based on pH-drift results. Calculations made assuming that CO₂ is the only species diffusing across the boundary layer are consistent with boundary layer thicknesses of 20 and 19 m for Lomentaria and Delesseria respectively, which is feasible given the rapid water movement in the experiments. For Laurencia however, an unreasonably small boundary layer thickness of 6 m is necessary to explain the flux, which indicates co-diffusion by HCO _inf3 ^sup– . In the apparent absence of external carbonic anhydrase, direct uptake of HCO _inf3 ^sup– , rather than external conversion to CO₂ is indicated in this species. In air, the CO₂ concentration at which photosynthesis is half-maximal increases in the same order as the ability to raise pH in drift experiments. At 21 kPa the CO₂ compensation partial pressures for Palmaria and Laurencia at 0.56 and 1.3 Pa are low enough to suggest a carbon-concentrating mechanism is operating, while those of Lomentaria at 1.8 Pa and particularly that of Delesseria at 4.5 Pa could be explained without a carbon-concentrating mechanism. The algae tested (all except Delesseria) showed more O₂ evolution than could be accounted for with a photosynthetic quotient of 1.0 and uncatalysed conversion of HCO _inf3 ^sup– to CO₂ outside the cell in high light at pH 8.0 when high algal fresh weight per unit medium was used. These results are concordant with other data suggesting use of HCO _inf3 ^sup– by Palmaria and Laurencia, but discordant with the rest of the available information in indicating use of HCO _inf3 ^sup– by Lomentaria. The reason for this is unclear. The lightsaturated rate of O₂ evolution on an algal area basis and the photon flux density needed to saturate photosynthesis were related partly to the habitat from which the seaweeds were collected, but more strongly to the ability to use HCO _inf3 ^sup– . Values for the two users of HCO _inf3 ^sup– , Palmaria (population used was intertidal; also occurs subtidally) and Laurencia (intertidal/shaded intertidal), were greater than for Lomentaria (shaded intertidal), which was greater than Delesseria (subtidal), both of which are believed to be restricted to CO₂. In accordance with earlier ¹³C data and, for Delesseria, estimates of the achieved growth rates in situ, carbon is likely to be saturating and use of HCO _inf3 ^sup– is unlikely to occur in the normal low-light habitats of Lomentaria and Delesseria. Analysis of N-use efficiencies show that they are closer to the low-CO₂-affinity Laminariales than the high-CO₂-affinity Fucaceae.     

Discrimination between12C and13C by marine plants

Summary The natural abundance¹³C/¹²C ratios (as δ¹³C) of organic matter of marine macroalgae from Fife and Angus (East Scotland) were measured for comparison with the species' ability to use CO₂ and HCO ₃ ^- for photosynthesis, as deduced from previously published pH-drift measurements. There was a clear difference in δ¹³C values for species able or unable to use HCO ₃ ^- . Six species of Chlorophyta, 12 species of Phaeophyta and 8 species of Rhodophyta that the pH-drift data suggested could use HCO ₃ ^- had δ¹³C values in the range -8.81‰ to -22.55‰. A further 6 species of Rhodophyta which the pH-drift data suggested could only use CO₂ had δ¹³C values in the range -29.90‰ to-34.51‰. One of these six species (Lomentaria articulata) is intertidal; the other five are subtidal and so have no access to atmospheric CO₂ to complicate the analysis. For these species, calculations based on the measured δ¹³C of the algae, the δ¹³C of CO₂ in seawater, and the known¹³C/¹²C discrimination of CO₂ diffusion and RUBISCO carboxylation suggest that only 15–21% of the limitation to photosynthesisin situ results from CO₂ diffusion from the bulk medium to the plastids; the remaining 79–85% is associated with carboxylation reactions (and, via feedback effects, down-stream processes). This analysis has been extended for one of these five species,Delesseria sanguinea, by incorporating data onin situ specific growth rates, respiratory rates measured in the laboratory, and applying Fick's law of diffusion to calculate a boundary layer thickness of 17–24 μm. This value is reasonable for aDelesseria sanguinea frondin situ. For HCO ₃ ^- -using marine macroalgae the range of δ¹³C values measured can be accommodated by a CO₂ efflux from algal cells which range from 0.306 of the gross HCO ₃ ^- influx forEnteromorpha intestinalis (δ¹³C=-8.81‰) in a rockpool to 0.787 forChondrus crispus (δ¹³C=-22.55‰). The relatively high computed CO₂ efflux for those HCO ₃ ^- -users with the more negative δ¹³C values implies a relatively high photon cost of C assimilation; the observed photon costs can be accommodated by assuming coupled, energy-independent inorganic carbon influx and efflux. The observed δ¹³C values are also interpreted in terms of water movement regimes and obtaining CO₂ from the atmosphere. Published δ¹³C values for freshwater macrophytes were compared with the ability of the species to use CO₂ and HCO ₃ ^- and again there was an apparent separation in δ¹³C values for these two groups. δ¹³C values obtained for marine macroalgae for which no pH-drift data are available permit predictions, as yet untested, as to whether they use predominantly CO₂ or HCO ₃ ^-     

Chromosome numbers in some North American species of the genus Cirsium. III. Western United States,Mexico, and Guatemala

New data are presented on chromosome numbers for 36 species, two varieties, and two hybrids ofCirsium (Compositae). These include first reports forC. rhothophilum (2n = 34),C. andrewsii (2n = 32),C. crassicaule (2n = 32),C. quercetorum (2n= 32, 112),C. pascuarense (2n= 32),C. douglasii var.canescens (2n = 30, 34),C. hydrophilum (2n = 32),C. neomexicanum (2n = 30),C. cymosum (2n = 30, 34),C. acantholepis (2n= 34),C. radians (2n = 34), C.grahami (2n = 32),C. nigriceps (2n = 36),C. andersonii (2n= 32, 64),C. anartiolepis (2n = 34), andC. subcoriaceum (2n= 34). The published data on chromosome numbers of Eurasian and AmericanCirsium are summarized. In Eurasia, speciation has taken place primarily at the diploid level but is occasionally reinforced by polyploidy. The ancestral base number of 17 has been preserved in almost all species, and there is little evidence that reduction in chromosome number has played a significant role in speciation. In America speciation has proceeded exclusively at the diploid level, but the ancestral genome of 17 chromosomes has been retained in only about half of the species examined. In the remaining species, restructuring of the genome has occurred resulting in a reduction in number from 17 to 9 in extreme cases. Polyploidy, when seen, is of no significance. It is suggested that all species with greatly reduced numbers may represent products of a single reduction series.