SK channel subtypes enable parallel optimized coding of behaviorally relevant stimulus attributes: A review

Ion channels play essential roles toward determining how neurons respond to sensory input to mediate perception and behavior. Small conductance calcium-activated potassium (SK) channels are found ubiquitously throughout the brain and have been extensively characterized both molecularly and physiologically in terms of structure and function. It is clear that SK channels are key determinants of neural excitability as they mediate important neuronal response properties such as spike frequency adaptation. However, the functional roles of the different known SK channel subtypes are not well understood. Here we review recent evidence from the electrosensory system of weakly electric fish suggesting that the function of different SK channel subtypes is to optimize the processing of independent but behaviorally relevant stimulus attributes. Indeed, natural sensory stimuli frequently consist of a fast time-varying waveform (i.e., the carrier) whose amplitude (i.e., the envelope) varies slowly and independently. We first review evidence showing how somatic SK2 channels mediate tuning and responses to carrier waveforms. We then review evidence showing how dendritic SK1 channels instead determine tuning and optimize responses to envelope waveforms based on their statistics as found in the organism's natural environment in an independent fashion. The high degree of functional homology between SK channels in electric fish and their mammalian orthologs, as well as the many important parallels between the electrosensory system and the mammalian visual, auditory, and vestibular systems, suggest that these functional roles are conserved across systems and species.     

Reindeer habitat use in relation to two small wind farms,during preconstruction,construction, and operation

Worldwide there is a rush toward wind power development and its associated infrastructure. In Fennoscandia, large‐scale wind farms comprising several hundred windmills are currently built in important grazing ranges used for Sámi reindeer husbandry. In this study, reindeer habitat use was assessed using reindeer fecal pellet group counts in relation to two relatively small wind farms, with 8 and 10 turbines, respectively. In 2009, 1,315 15‐m² plots were established and pellet groups were counted and cleaned from the plots. This was repeated once a year in May, during preconstruction, construction, and operation of the wind farms, covering 6 years (2009–2014) of reindeer habitat use in the area. We modeled the presence/absence of any pellets in a plot at both the local (wind farm site) and regional (reindeer calving to autumn range) scale with a hierarchical logistic regression, where spatial correlation was accounted for via random effects, using vegetation type, and the interaction between distance to wind turbine and time period as predictor variables. Our results revealed an absolute reduction in pellet groups by 66% and 86% around each wind farm, respectively, at local scale and by 61% at regional scale during the operation phase compared to the preconstruction phase. At the regional, scale habitat use declined close to the turbines in the same comparison. However, at the local scale, we observed increased habitat use close to the wind turbines at one of the wind farms during the operation phase. This may be explained by continued use of an important migration route close to the wind farm. The reduced use at the regional scale nevertheless suggests that there may be an overall avoidance of both wind farms during operation, but further studies of reindeer movement and behavior are needed to gain a better understanding of the mechanisms behind this suggested avoidance.     

Exploring the linkage between cell culture process parameters and downstream processing utilizing a plackett‐burman design for a model monoclonal antibody

Linkage of upstream cell culture with downstream processing and purification is an aspect of Quality by Design crucial for efficient and consistent production of high quality biopharmaceutical proteins. In a previous Plackett‐Burman screening study of parallel bioreactor cultures we evaluated main effects of 11 process variables, such as agitation, sparge rate, feeding regimens, dissolved oxygen set point, inoculation density, supplement addition, temperature, and pH shifts. In this follow‐up study, we observed linkages between cell culture process parameters and downstream capture chromatography performance and subsequent antibody attributes. In depth analysis of the capture chromatography purification of harvested cell culture fluid yielded significant effects of upstream process parameters on host cell protein abundance and behavior. A variety of methods were used to characterize the antibody both after purification and buffer formulation. This analysis provided insight in to the significant impacts of upstream process parameters on aggregate formation, impurities, and protein structure. This report highlights the utility of linkage studies in identifying how changes in upstream parameters can impact downstream critical quality attributes. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:163–170, 2017     

Application of iterative robust model‐based optimal experimental design for the calibration of biocatalytic models

The aim of model calibration is to estimate unique parameter values from available experimental data, here applied to a biocatalytic process. The traditional approach of first gathering data followed by performing a model calibration is inefficient, since the information gathered during experimentation is not actively used to optimize the experimental design. By applying an iterative robust model‐based optimal experimental design, the limited amount of data collected is used to design additional informative experiments. The algorithm is used here to calibrate the initial reaction rate of an ω‐transaminase catalyzed reaction in a more accurate way. The parameter confidence region estimated from the Fisher Information Matrix is compared with the likelihood confidence region, which is not only more accurate but also a computationally more expensive method. As a result, an important deviation between both approaches is found, confirming that linearization methods should be applied with care for nonlinear models. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1278–1293, 2017     

Comparison of spectroscopy technologies for improved monitoring of cell culture processes in miniature bioreactors

Cell culture process development requires the screening of large numbers of cell lines and process conditions. The development of miniature bioreactor systems has increased the throughput of such studies; however, there are limitations with their use. One important constraint is the limited number of offline samples that can be taken compared to those taken for monitoring cultures in large‐scale bioreactors. The small volume of miniature bioreactor cultures (15 mL) is incompatible with the large sample volume (600 µL) required for bioanalysers routinely used. Spectroscopy technologies may be used to resolve this limitation. The purpose of this study was to compare the use of NIR, Raman, and 2D‐fluorescence to measure multiple analytes simultaneously in volumes suitable for daily monitoring of a miniature bioreactor system. A novel design‐of‐experiment approach is described that utilizes previously analyzed cell culture supernatant to assess metabolite concentrations under various conditions while providing optimal coverage of the desired design space. Multivariate data analysis techniques were used to develop predictive models. Model performance was compared to determine which technology is more suitable for this application. 2D‐fluorescence could more accurately measure ammonium concentration (RMSE_CV 0.031 g L^?1) than Raman and NIR. Raman spectroscopy, however, was more robust at measuring lactate and glucose concentrations (RMSE_CV 1.11 and 0.92 g L^?1, respectively) than the other two techniques. The findings suggest that Raman spectroscopy is more suited for this application than NIR and 2D‐fluorescence. The implementation of Raman spectroscopy increases at‐line measuring capabilities, enabling daily monitoring of key cell culture components within miniature bioreactor cultures. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:337–346, 2017     

原生质体融合构建高效产脂肽工程菌

芽孢杆菌因其可产生多种生理活性物质,在环境污染修复、生物防治、微生物采油等领域具有广阔的应用前景。莫哈韦芽孢杆菌Bacillus mojavensis JF-2和解淀粉芽孢杆菌B. amyloliquefaciens BQ-6是从油田筛选出的产脂肽类表面活性剂菌株, 但在微生物采油实际应用中受到氧气浓度、盐度及pH的限制。原生质体融合是改变微生物代谢功能的一种简便有效的方法,以上述两株芽孢杆菌为对象,利用4因素3水平正交试验来探索菌龄、溶菌酶浓度、酶解温度和酶解时间对原生体制备、再生的影响。此外,对两菌株进行了双亲灭活原生质体融合,通过筛选得到了一株工程菌HY-4,并对其进行了初步的评价。结果表明:菌龄、溶菌酶浓度和酶解时间显著影响芽孢杆菌原生质体制备率及再生率(P<0.05),且在溶菌酶处理前用生理盐水多次洗涤菌体细胞,可提高制备率。两种芽孢杆菌原生质体制备及再生的最优条件均为:菌龄7 h、溶菌酶浓度2.5 mg/ml、酶解时间30 min、酶解温度42 ℃。融合子HY-4的最高耐盐度为15%,可耐50 ℃高温,代谢产脂肽的pH范围为4.0~9.5,且在好氧及厌氧条件下均能够代谢产脂肽,在厌氧条件下生长迅猛(细胞干重>1.6 g/L)。综上所述,融合子HY-4具有较大的应用潜力,该研究为芽孢杆菌的遗传育种打下了方法学基础,并对驱油微生物菌种的选育具有指导意义。     

癌症基因组测序方案制定的研究进展

癌症的基因组测序对于癌症的预防、诊断、预后、治疗以及基础生物学研究都有巨大的潜在的应用价值,正是由于其方向广泛,所以基因组测序的方案制定对于实现特定的研究目标,就显得尤为重要。同时,了解了基因组测序方案制定的规则,也有助于评估如今快速增长的发表文献的正确性和重要性。主要论述高通量测序技术在癌症基因组测序中的实际应用,并讨论癌症基因组测序在方案设计和方法学上如何调整,才能更好地实现特定的研究目的。     

Spatial patterns of Yucatan reef fish communities: Testing models using a multi-scale survey design

Using a hierarchical multi-scale survey design, we examined the spatial patterns of reef fish communities and tested ecological models concerning the relative importance of reef geomorphology and anthropogenic pressure possibly driving community structure. Canonical redundancy analysis was used as a form of multivariate analysis of variance (MANOVA) to asses differences in reef fish community composition at two spatial scales: broad (10⁵ m) and intermediate (10⁴ m). Surveys were conducted on the east coast of the Yucatan Peninsula (Mexican Caribbean fringing reef), including regions and reefs which differed in geomophologic structure and human use. Seven hundred and fourteen line transects were distributed among 13 reef localities belonging to different regions established a priori. Transects covered four types of reef habitat: lagoon, front, slope, and terrace. Tests of significance were based on permutation procedures. Significant differences among regions were found for the lagoon, slope, and terrace fish communities, consistent with the geomorphologic model, but it is only in the reef lagoon that they were consistent with the anthropogenic model, which may indicate an effect of coastal human activities. Significant differences among reefs within regions were observed, which could be associated with local environmental gradients. Canonical nested MANOVA was an appropriate method for testing ecological hypotheses about the functioning of complex biological systems. The use of a surveying strategy that explicitly incorporated the spatial structure represents an important contribution of this paper to coral reef fish ecology.