Late Quaternary eolian sand depositional record for southwestern Kansas: Landscape sensitivity to droughts

Eolian deposits and landforms are ubiquitous in western Kansas, particularly south of the Arkansas River with the presence of a stabilized dune field. Stratigraphic studies and associated optical dating reveal a complex depositional history for this dune field spanning the late Quaternary. The oldest eolian deposits from ca. 16 to 12 ka completely or partially bury high terraces with ages of ca. 16 and 33 ka. It is unknown whether these eolian deposits reflect regional aridity and/or a change in sediment availability with the transition of the Arkansas River from a single channel to a braided system. There is pervasive evidence for episodic eolian erosion and deposition ca. 9.8 to 6.3 ka, generally coincident with loess deposition on upland surfaces [Olson, C.G., Nettleton, W.D., Porter, D.A., Brasher, B.R., 1997. Middle Holocene aeolian activity on the High Plains of west-central Kansas. Holocene, 7(3): 255–261], and thus it is inferred to reflect regional aridity. Sites within the dune field show a sequence of eolian sands and weak buried soils, reflecting either dune migration or sand sheet accretion at ca. 1490, 430, 380–320, 180, and 70 yr ago, which correspond well with continental-scale droughts in the tree-ring record. Eolian sand in the Arkansas River dune field may be derived principally with variability in fluvial activity and in climate during the late Pleistocene to the middle Holocene, with substantial reactivation of eolian systems during decadal-scale drought variability in the past 2000 yr.     

Optimal taxonomic groups for biodiversity assessment: a meta‐analytic approach

A fundamental decision in biodiversity assessment is the selection of one or more study taxa, a choice that is often made using qualitative criteria such as historical precedent, ease of detection, or available technical or taxonomic expertise. A more robust approach would involve selecting taxa based on the a priori expectation that they will provide the best possible information on unmeasured groups, but data to inform such hypotheses are often lacking. Using a global meta‐analysis, we quantified the proportion of variability that each of 12 taxonomic groups (at the Order level or above) explained in the richness or composition of other taxa. We then applied optimization to matrices of pairwise congruency to identify the best set of complementary surrogate groups. We found that no single taxon was an optimal surrogate for both the richness and composition of unmeasured taxa if we used simple methods to aggregate congruence data between studies. In contrast, statistical methods that accounted for well‐known drivers of cross‐taxon congruence (spatial extent, grain size, and latitude) lead to the prioritization of similar surrogates for both species richness and composition. Advanced statistical methods were also more effective at describing known ecological relationships between taxa than simple methods, and show that congruence is typically highest between taxonomically and functionally dissimilar taxa. Birds and vascular plants were most frequently selected by our algorithm as surrogates for other taxonomic groups, but the extent to which any one taxon was the ‘optimal’ choice of surrogate for other biodiversity was highly context‐dependent. In the absence of other information – such as in data‐poor areas of the globe, and under limited budgets for monitoring or assessment – ecologists can use our results to assess which taxa are most likely to reflect the distribution of the richness or composition of ‘total’ biodiversity.     

Digit ratios by computer-assisted analysis confirm lack of anatomical evidence of prenatal androgen exposure in clinical phenotypes of polycystic ovary syndrome

Background  

We recently showed that women with four clinical phenotypes of polycystic ovary syndrome (PCOS) do not demonstrate anatomical evidence of elevated prenatal androgen exposure as judged by a lower ratio of the index (2D) to ring (4D) finger. However, those findings conflicted with a previous study where women with PCOS had lower right hand 2D:4D compared to healthy female controls. Both these studies used Vernier calipers to measure finger lengths - a method recently shown to be less reliable at obtaining finger length measurements than computer-assisted analysis.     

Comparison of high throughput screening technologies for luminescence cell-based reporter screens

As higher density formats become more and more common in HTS labs, the expectations for maintaining faster, lower cost screens puts great pressure on traditional 96-well screens. In some cases higher density formats are not compatible with the assay. This seems especially true in cell-based assays. In our case, the nature of the cells' response forced us to remain in 96-well plates. In this paper, we describe the development of a luminescence reporter assay and its performance in two detection modes, flash and glow. The advantages in cost and throughput for each technique are explored, along with automation considerations. An additional new technology, the use of pins for low-volume transfers, is also briefly described because of its dramatic effect on our screen's throughput. However, it will be more thoroughly presented in a future publication. Comparing the technologies available for HTS aids in designing automated systems that meet the unique needs of each assay.     

建立正常人肺血管容量的无创精确测量方法的初步报告*

目的: 由于传统呼吸调控环路忽略了对血液循环的决定性作用,肺（静脉）血管容量相关研究甚少,亟需建立肺血管容量测量方法。方法: 选择正常志愿者完成CT全肺扫描,图像数据经过计算机软件分析处理,从肺尖到肺底以40~50层进行肺野手工切划,相邻层间由计算机自动模拟连接,在去除干扰后进行全肺血管（≥0.6 mm）高精度三维立体成像技术处理,进而计算全肺和肺血管容积。结果: 12例正常志愿者从肺尖到肺底CT扫描图片层数为530±98（431~841）张。全肺和肺血管的总容积是3705±857（2398~5383）ml ,肺血管血液总的容积是125±32（94~201）ml。按肺静脉系统血管容量约为全肺血管血液容量一半计算,应该是63±16（47~100）ml。结论: 肺CT扫描数据分析三维立体成像建立肺血管容量无创测量方法精确可行。     

Contribution of phenazine antibiotic biosynthesis to the ecological competence of fluorescent pseudomonads in soil habitats.

Phenazine antibiotics produced by Pseudomonas fluorescens 2-79 and Pseudomonas aureofaciens 30-84, previously shown to be the principal factors enabling these bacteria to suppress take-all of wheat caused by Gaeumannomyces graminis var. tritici, also contribute to the ecological competence of these strains in soil and in the rhizosphere of wheat. Strains 2-79 and 30-84, their Tn5 mutants defective in phenazine production (Phz-), or the mutant strains genetically restored for phenazine production (Phz+) were introduced into Thatuna silt loam (TSL) or TSL amended with G. graminis var. tritici. Soils were planted with three or five successive 20-day plant-harvest cycles of wheat. Population sizes of Phz- derivatives declined more rapidly than did population sizes of the corresponding parental or restored Phz+ strains. Antibiotic biosynthesis was particularly critical to survival of these strains during the fourth and fifth cycles of wheat in the presence of G. graminis var. tritici and during all five cycles of wheat in the absence of take-all. In pasteurized TSL, a Phz- derivative of strain 30-84 colonized the rhizosphere of wheat to the same extent that the parental strain did. The results indicate that production of phenazine antibiotics by strains 2-79 and 30-84 can contribute to the ecological competence of these strains and that the reduced survival of the Phz- strains is due to a diminished ability to compete with the resident microflora.     

Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq)

Degraded DNA from suboptimal field sampling is common in molecular ecology. However, its impact on techniques that use restriction site associated next‐generation DNA sequencing (RADSeq, GBS) is unknown. We experimentally examined the effects of in situDNA degradation on data generation for a modified double‐digest RADSeq approach (3RAD). We generated libraries using genomic DNA serially extracted from the muscle tissue of 8 individual lake whitefish (Coregonus clupeaformis) following 0‐, 12‐, 48‐ and 96‐h incubation at room temperature posteuthanasia. This treatment of the tissue resulted in input DNA that ranged in quality from nearly intact to highly sheared. All samples were sequenced as a multiplexed pool on an Illumina MiSeq. Libraries created from low to moderately degraded DNA (12–48 h) performed well. In contrast, the number of RADtags per individual, number of variable sites, and percentage of identical RADtags retained were all dramatically reduced when libraries were made using highly degraded DNA (96‐h group). This reduction in performance was largely due to a significant and unexpected loss of raw reads as a result of poor quality scores. Our findings remained consistent after changes in restriction enzymes, modified fold coverage values (2‐ to 16‐fold), and additional read‐length trimming. We conclude that starting DNA quality is an important consideration for RADSeq; however, the approach remains robust until genomic DNA is extensively degraded.     

A phototrophic gliding filamentous bacterium of hot springs,Chloroflexus aurantiacus,gen. and sp. nov.

Chloroflexus aurantiacus, gen. and sp. n., is a filamentous phototrophic bacterium of hot springs. On an agar surface, holotype strain J-10-fl glides at 0.01–0.04 μm/sec. The filaments are 0.6–0.7 μm in width and indeterminate in length. Pigments include bacteriochlorophyll c and bacteriochlorophyll a (identified by spectrophotometry) in addition to β and γ-carotene and glycosides of the latter. Chlorobium vesicles are present. Photoheterotrophic growth occurs under anaerobic conditions. Aerobic chemoheterotrophic growth also occurs in darkness or light. Bacteriochlorophyll syntheses cease under aerobic conditions but some types of carotenoids continue to be made. The filament coloration is orange under all except anaerobic conditions in low light intensity where it is dull green. The pH optimum is near 8, the temperature optimum between 52° and 60°C. The DNA base composition for strain J-10-fl is 54.9 ± 1.0 moles % guanine + cytosine. Chloroflexus is unique in that there have been no previous reports of filamentous or gliding phototrophic bacteria. The combinations of bacteriochlorophylls a and c and the presence of chlorobium vesicles in a photoheterotroph and in an organism capable of aerobic growth are also unique. This metabolically versatile organism extends the taxonomic and phylogenetic limits of the “green line” of phototrophic bacteria.