Bias in the Logarithm of Microbial Density Estimates from Serial Dilutions

The bias in the most-probable-number (MPN) estimate of microbial densities derived from serial dilutions might be less important than it has appeared to be. For many purposes, bias in the logarithm of the MPN is more important than bias in the MPN, and the bias in the logarithm is much less. The lesser bias has been reduced by using the theorems of Salama, Koch, and Tolley. Formulas and tables are provided.     

The influence of temperature and nitrate on vegetative growth and nitrogen accumulation by nodulated soybeans

Summary Inoculated soybeans [Glycine max (L.) Merrill] were grown in controlled environments to evaluate the relationship between temperature and applied NO₃−N on growth rates, N accumulation, and acetylene reduction activity during the vegetative growth stage. Soybeans were grown at day/night temperatures of 22/18 and 26/22°C in sand culture with daily applications of 21.4 mM (high) and 2.1 mM (low) NO₃−N in a complete nutrient solution for durations of 14, 21, and 42 days after emergence and with an N-free solution. Dry matter and N accumulation were greater at 26/22 than 22/18°C. In general, both increased as the level and duration of applied NO₃−N was increased. These increases were attributable to an abbreviation in the interval between emergence and onset of rapid growth. The presence and assimilation of NO₃−N, even at the high level, did not inhibit development of functional nodules. Neither mass nor acetylene reduction activity of nodules was reduced by high NO₃−N; however, the root mass was increased by NO₃−N more than the nodule mass. There was an interaction between temperature and NO₃−N on specific nodule activity as measured by acetylene reduction. The specific nodule activity was unaffected by NO₃−N at 22/18°C, but at 26/22°C the specific activity was lower in the absence of NO₃−N than when NO₃−N was present. Apparently, rapid early growth at 26/22°C depleted cotyledonary reserves of N before nodules became active and, thereafter, the plants were unable to develop adequate leaf area to support nodule development and functioning. This result has implications in N fertilization of late-planted soybeans. Paper number 6637 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, North Carolina, 27650. The research was supported in part by a grant from the North Carolina Soybean Producers Association and by USDA-SEA-CR grant 701-15-26.     

Ex Situ Normothermic Machine Perfusion of Donor Livers

In contrast to conventional static cold preservation (0-4 °C), ex situ machine perfusion may provide better preservation of donor livers. Continuous perfusion of organs provides the opportunity to improve organ quality and allows ex situ viability assessment of donor livers prior to transplantation. This video article provides a step by step protocol for ex situ normothermic machine perfusion (37 °C) of human donor livers using a device that provides a pressure and temperature controlled pulsatile perfusion of the hepatic artery and continuous perfusion of the portal vein. The perfusion fluid is oxygenated by two hollow fiber membrane oxygenators and the temperature can be regulated between 10 °C and 37 °C. During perfusion, the metabolic activity of the liver as well as the degree of injury can be assessed by biochemical analysis of samples taken from the perfusion fluid. Machine perfusion is a very promising tool to increase the number of livers that are suitable for transplantation.     

Generation of a neutral FST baseline for testing local adaptation on gill raker number within and between European whitefish ecotypes in the Baltic Sea basin

Divergent selection at ecologically important traits is thought to be a major factor driving phenotypic differentiation between populations. To elucidate the role of different evolutionary processes shaping the variation in gill raker number of European whitefish (Coregonus lavaretus sensu lato) in the Baltic Sea basin, we assessed the relationships between genetic and phenotypic variation among and within three whitefish ecotypes (sea spawners, river spawners and lake spawners). To generate expected neutral distribution of F_ST and to evaluate whether highly variable microsatellite loci resulted in deflated F_ST estimates compared to less variable markers, we performed population genetic simulations under finite island and hierarchical island models. The genetic divergence observed among (F_CT = 0.010) and within (F_ST = 0.014–0.041) ecotypes was rather low. The divergence in gill raker number, however, was substantially higher between sea and river spawners compared to observed microsatellite data and simulated neutral baseline (P_CT > F_CT). This suggests that the differences in gill raker number between sea and river spawners are likely driven by divergent natural selection. We also found strong support for divergent selection on gill raker number among different populations of sea spawners (P_ST > F_ST), most likely caused by highly variable habitat use and diverse diet. The putative role of divergent selection within lake spawners initially inferred from empirical microsatellite data was not supported by simulated F_ST distributions. This work provides a first formal test of divergent selection on gill raker number in Baltic whitefish, and demonstrates the usefulness of population genetic simulations to generate informative neutral baselines for P_ST–F_ST analyses helping to disentangle the effects of stochastic evolutionary processes from natural selection.     

A modified multiplex ligation-dependent probe amplification method for the detection of 22q11.2 copy number variations in patients with congenital heart disease

Background

Copy number variations (CNVs) of chromosomal region 22q11.2 are associated with a subset of patients with congenital heart disease (CHD). Accurate and efficient detection of CNV is important for genetic analysis of CHD. The aim of the study was to introduce a novel approach named CNVplex®, a high-throughput analysis technique designed for efficient detection of chromosomal CNVs, and to explore the prevalence of sub-chromosomal imbalances in 22q11.2 loci in patients with CHD from a single institute.

Results

We developed a novel technique, CNVplex®, for high-throughput detection of sub-chromosomal copy number aberrations. Modified from the multiplex ligation-dependent probe amplification (MLPA) method, it introduced a lengthening ligation system and four universal primer sets, which simplified the synthesis of probes and significantly improved the flexibility of the experiment. We used 110 samples, which were extensively characterized with chromosomal microarray analysis and MLPA, to validate the performance of the newly developed method. Furthermore, CNVplex® was used to screen for sub-chromosomal imbalances in 22q11.2 loci in 818 CHD patients consecutively enrolled from Shanghai Children’s Medical Center. In the methodology development phase, CNVplex® detected all copy number aberrations that were previously identified with both chromosomal microarray analysis and MLPA, demonstrating 100% sensitivity and specificity. In the validation phase, 22q11.2 deletion and 22q11.2 duplication were detected in 39 and 1 of 818 patients with CHD by CNVplex®, respectively. Our data demonstrated that the frequency of 22q11.2 deletion varied among sub-groups of CHD patients. Notably, 22q11.2 deletion was more commonly observed in cases with conotruncal defect (CTD) than in cases with non-CTD (P < 0.001). With higher resolution and more probes against selected chromosomal loci, CNVplex® also identified several individuals with small CNVs and alterations in other chromosomes.

Conclusions

CNVplex® is sensitive and specific in its detection of CNVs, and it is an alternative to MLPA for batch screening of pathogenetic CNVs in known genomic loci.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1590-5) contains supplementary material, which is available to authorized users.     

Effective number of breeders provides a link between interannual variation in stream flow and individual reproductive contribution in a stream salmonid

The effective number of breeders that give rise to a cohort (N_b) is a promising metric for genetic monitoring of species with overlapping generations; however, more work is needed to understand factors that contribute to variation in this measure in natural populations. We tested hypotheses related to interannual variation in N_b in two long‐term studies of brook trout populations. We found no supporting evidence for our initial hypothesis that reflects (defined as the number of adults in a population at the time of reproduction). was stable relative to and did not follow trends in abundance (one stream negative, the other positive). We used stream flow estimates to test the alternative hypothesis that environmental factors constrain N_b. We observed an intermediate optimum autumn stream flow for both (R² = 0.73, P = 0.02) and full‐sibling family evenness (R² = 0.77, P = 0.01) in one population and a negative correlation between autumn stream flow and full‐sib family evenness in the other population (r = ?0.95, P = 0.02). Evidence for greater reproductive skew at the lowest and highest autumn flow was consistent with suboptimal conditions at flow extremes. A series of additional tests provided no supporting evidence for a related hypothesis that density‐dependent reproductive success was responsible for the lack of relationship between N_b and N_C (so‐called genetic compensation). This work provides evidence that N_b is a useful metric of population‐specific individual reproductive contribution for genetic monitoring across populations and the link we provide between stream flow and N_b could be used to help predict population resilience to environmental change.     

Sequence‐tagged high‐density genetic maps of Zoysia japonica provide insights into genome evolution in Chloridoideae

Zoysiagrass (Zoysia spp.), belonging to the genus Zoysia in the subfamily Chloridoideae, is widely used in domestic lawns, sports fields and as forage. We constructed high‐density genetic maps of Zoysia japonica using a restriction site‐associated DNA sequencing (RAD‐Seq) approach and an F₁ mapping population derived from a cross between ‘Carrizo’ and ‘El Toro’. Two linkage maps were constructed, one for each of the parents. A map consisting of 2408 RAD markers distributed on 21 linkage groups was constructed for ‘Carrizo’. Another map with 1230 RAD markers mapped on 20 linkage groups was constructed for ‘El Toro’. The average distance between adjacent markers of the two maps was at 0.56 and 1.4 cM, respectively. Comparative genomics analysis was carried out among zoysiagrass, rice and sorghum genomes and a highly conserved collinearity in the gene order was observed among the three genomes. Chromosome collinearity was disrupted at centromeric regions for each chromosome pair between zoysiagrass and sorghum genomes. However, no obvious synteny gaps were observed across the centromeric regions between zoysiagrass and rice genomes. Two homologous chromosomes for each of the 10 sorghum chromosomes were found in the zoysiagrass genome, indicating an allotetraploid origin for zoysiagrass. The reduction of the basic chromosome number from 12 to 10 in chloridoids and panicoids took place via independent single‐step nested chromosome fusion events after the two subfamilies diverged from a common ancestor. The genetic maps will assist in genome sequence assembly, targeted gene isolation and comparative genomic analyses among grasses.     

水稻土泥浆体系中多氯联苯的微生物厌氧脱氯

考察了厌氧水稻土泥浆体系中高氯代多氯联苯混合物Aroclor1260的脱氯过程,并对体系中的微生物群落结构变化进行分析.结果表明： Aroclor1260可在厌氧水稻土泥浆体系中发生脱氯,经过128 d,总消减率达到55.5%,在泥浆体系中引入驯化的脱氯富集培养体反而使脱氯效果下降,消减率为46.9%.Aroclor1260的主要脱氯过程发生在五、六、七氯联苯,其中七氯联苯脱氯过程最显著,五氯联苯作为脱氯产物有一定累积.有机物厌氧发酵产生的H₂会被脱氯过程所消耗,从而将体系中的氢分压维持在较低水平,抑制产甲烷过程而保证脱氯过程的持续进行.不同条件和培养方式驯化得到的微生物群落结构差异较大,富集培养体引入可能导致其与原体系中脱氯相关菌群竞争,从而改变体系原有菌群结构,这可能是导致其脱氯效率下降的原因.     

The northward shifting neophyte Tragopogon dubius is just as effective in forming mycorrhizal associations as the native T. pratensis

Background: As a consequence of climate warming, many organisms are shifting their range towards higher latitudes and altitudes. As not all do so at the same speed, this may disrupt biotic interaction. Release from natural enemies through range expansion can result in invasiveness, whereas loss of mutualists can reduce plant vigour and fitness. One of the most important groups of plant symbiotic mutualists is the arbuscular mycorrhizal fungi (AMF).

Aims: We used greenhouse experiments to test whether Tragopogon dubius, a species that has recently expanded its range northward and colonised the Netherlands, is able to associate with the same AMF as the native congener T. pratensis.

Methods: In soils collected from four locations in the new range of T. dubius we compared the density of infective AMF propagules associating with both plant species, as well as AMF colonisation of the roots. The AMF community structure in the roots of these species was also analysed using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE).

Results: Tragopogon dubius and T. pratensis did not differ in any of these characteristics.

Conclusions: We therefore conclude that the range-shifting T. dubius is as effective in the formation of mycorrhiza as the native congener.