Response of instream animal communities to a short-term extreme event and to longer-term cumulative impacts in a strategic water resource area,South Africa

Disturbance plays an integral part in generating heterogeneity required for ecosystem persistence, but the increased amplitude and duration of disturbances linked to drivers of global change could result in ecosystem shifts or collapse. Biomonitoring over time provides insights into trajectories of ecosystem change. The responses of two instream animal taxa to two contrasting disturbance events, a major flood event and the long-term cumulative effects of land-use changes, were assessed in 1999–2012 by quantifying variation and change in abundance of functional groups based on flow rate sensitivity, water quality and metrics of ecological condition. All metrics recovered to pre-flood conditions within seven months after the flood event. Similarly, cumulative impacts of land use effected significant decreases in some but not all metrics. Indices that did not change, including SASS total score and ASPT, were the result of insufficient consideration of the decrease in the abundance of sensitive taxa specifically, and the abundance of all taxa in general. The decrease in abundance of sensitive taxa could signal imminent collapse in certain metrics. Evidence is also provided for a shift in the structure of fish assemblages linked to the decrease and loss of taxa sensitive to ecosystem degradation caused by the longer-term impacts of land-use change.     

Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples

Background

DNA methylation plays crucial roles in epigenetic gene regulation in normal development and disease pathogenesis. Efficient and accurate quantification of DNA methylation at single base resolution can greatly advance the knowledge of disease mechanisms and be used to identify potential biomarkers. We developed an improved pipeline based on reduced representation bisulfite sequencing (RRBS) for cost-effective genome-wide quantification of DNA methylation at single base resolution. A selection of two restriction enzymes (Taq^αI and MspI) enables a more unbiased coverage of genomic regions of different CpG densities. We further developed a highly automated software package to analyze bisulfite sequencing results from the Solexa GAIIx system.

Results

With two sequencing lanes, we were able to quantify ~1.8 million individual CpG sites at a minimum sequencing depth of 10. Overall, about 76.7% of CpG islands, 54.9% of CpG island shores and 52.2% of core promoters in the human genome were covered with at least 3 CpG sites per region.

Conclusions

With this new pipeline, it is now possible to perform whole-genome DNA methylation analysis at single base resolution for a large number of samples for understanding how DNA methylation and its changes are involved in development, differentiation, and disease pathogenesis.     

大肠杆菌FC40系统静止期突变中的F因子转移

本研究采用大肠杆菌GM133 rifr细胞和营养收集细胞HB214 strr进行适应性突变实验。在混合30min和2d 后添加链霉素杀死GM133基因型细胞,继续培养5d后,在选择平板上出现了一定数量的lac+strr基因型回复突变菌落。根据这些突变菌落的数量,估计在lac+突变产生之前,GM133和HB214细胞之间的接合频率分别为0.07%和7.47%。在培养了7d的选择平板上添加含链霉素的M9选择培养基,2d 后也观察到大量发生lac+突变但没有形成肉眼可见菌落的营养收集细胞。此外,在lac+突变发生后,也有F因子从GM133细胞转移进入HB214细胞。这些事实表明,在FC40系统的适应性突变实验中发生了真正的F因子转移。 Abstract:The experiment of adaptive mutation was performed by using Escherichia coli GM133 rifr as test cells and HB214 strr as scavenger cells.Transfer frequency between GM133 and HB214 was estimated,based on the number of revertants appeared on the selective plates when GM133 were killed by addition of M9 selective medium containing 100μg/mL of streptomycin at different time.After 30 minutes the cells of GM133 and HB214 were mixed,the estimated transfer frequency was about 0.07%,and two days,7.47%.After selection of 7 days,some HB214 cells with F` factor from GM133 cells and lac+ mutation were observed,but these cells failed to form the colonies which can be seen by the naked-eye.It was demonstrated that actual F` factor transfer events from test cells GM133 to scavenger cells HB214 occurred during the selection.     

Decoupling of light intensity effects on the growth and development of C3 and C4 weed species through sucrose supplementation

Light availability has a profound effect on plant growth and development. One of the ways to study the effects of light intensity on plant growth and development without the confounding problem of photosynthate availability is sucrose injection/supplementation. A greenhouse experiment was conducted to evaluate the effects of light levels (0% and 75% shade) and sucrose injection (distilled water or 150 g sucrose l(-1)) on three weed species: redroot pigweed (Amaranthus retroflexus L., C4), lambsquarters (Chenopodium album L., C3) and velvetleaf (Abutilon theophrasti Medic., C3). The average total sucrose uptake was 7.6 and 5.9 g per plant for 0% and 75% shading, respectively, representing 47% of the average total weed dry weight. Plants injected with sucrose had greater dry weights and shoot-to-root ratios under both light levels. In spite of sucrose supplementation the reduction in dry matter due to shading was greater for roots and reproductive structures than vegetative shoot tissues, indicating light level regulation of morphological changes resulting in changed C allocation that are independent of photosynthate availability. Dry weights of plants injected with sucrose under 75% shading were not different from distilled water-injected unshaded plants. However, both sucrose-injected and control plants, regardless of their photosynthetic pathways, underwent similar changes in allocation of dry matter and morphology due to shading, suggesting that these effects are strictly due to light intensity and not related to photosynthate availability.     

Effects of sequential exposures of sub-lethal doses of amitraz and thiacloprid on learning and memory of honey bee foragers,Apis mellifera

Pollinators, honey bees in particular, are continuously exposed to various mixtures of pesticides, which contribute to their population decline. Both amitraz and thiacloprid have been proven less toxic to honey bees and are frequently applied in- and out-hive, respectively. We examined the sub-lethal effects of amitraz, thiacloprid and their sequential exposure on learning, memory and sugar responsiveness in Apis mellifera using the Proboscis extension response (PER). Sub-lethal doses of amitraz (0.1, 0.2 and 0.4 µg/bee) and thiacloprid (0.05, 0.1 and 0.2 µg/bee) were tested. Sub-lethal effects were observed only at the highest doses of each pesticide treatment; amitraz (0.4 µg/bee) and thiacloprid (0.2 µg/bee) but not in lower doses. In sequential treatment of amitraz and thiacloprid, reduced acquisition and memory retention were significant across all tested doses. The same profile was also obtained on sugar responsiveness of foragers. Our results suggest that the sequential exposure would pose higher risk to honey bee compared to single pesticide exposure by reducing the bees’ appetitive olfactory learning, memory and sugar acuity more than individual pesticide exposures.     

Mitochondrial proteins differential expression during honeybee (Apis mellifera L.) queen and worker larvae caste determination

Despite their similar genetic makeup, honeybee (A. mellifera) queens and workers show alternative morphologies driven by nutritional difference during the larval stage. Although much research have been done to investigate the causes of honeybee caste polymorphism, information at subcellular protein levels is limited. We analyzed queen- and worker-destined larvae mitochondrial proteome at three early developmental stages using combinations of differential centrifugation, two-dimensional electrophoresis, mass spectrometry, bioinformatics, and quantitative real time PCR. In total, 67, 69, and 97 protein spots were reproducibly identified as mitochondrial proteins at 72, 96, and 120 h, respectively. There were significant qualitative and quantitative protein expression differences between the two castes at three developmental stages. In general, the queen-destined larvae up-regulated large proportions of proteins at all of the developmental stages and, in particular, 95% at 72 h. An overwhelming majority of the queen larvae up-regulated proteins were physiometabolic-enriched proteins (metabolism of carbohydrate and energy, amino acid, and fatty acid) and involved in protein folding, and this was further verified by functional enrichment and biological interaction network analyses as a direct link with metabolic rates and cellular responses to hormones. Although wide-ranging mitochondrial proteomes participate to shape the metabolic, physiologic, and anatomic differences between the two castes at 72 h, physiometabolic-enriched proteins were found as the major modulators of the profound marking of this caste differentiation. Owing to nutritional difference, prospective queen larvae showed enhanced growth, and this was manifested through the overexpression of metabolic enzymes. Differently from similar studies targeting the causes of honeybee caste polymorphism, this subcellular level study provides an in-depth insight into mitochondrial proteins-mediated caste polymorphism and greatly improves protein coverage involved during honeybee caste determination. Hence, it is a major step forward in the analysis of the fundamental causes of honeybee caste pathway decision and greatly contributes to the knowledge of honeybee biology. In particular, the consistency between the 22 proteins and mRNA expressions provides us important target genes for the reverse genetic analysis of caste pathway modulation through RNA interference.