Sampling procedures and species estimation: testing the effectiveness of herbarium data against vegetation sampling in an oceanic island

Questions: What is the relationship between species assemblages in herbarium collections and species abundances in the field, and how trustworthy are herbarium data in vegetation science? Location: Guadalupe Island, Baja California, Mexico. Methods: We compared species‐abundance distribution and evenness in 110 vegetation plots in Guadalupe Island against data from four herbaria. We tested whether the relative frequencies derived from herbarium specimens differed significantly from species frequencies in the field. We compared the rarefaction curves for both field and herbarium data sets, and tested whether taxonomic collectors accumulated new species at a higher rate than that observed in ecological plot sampling. Results: At any given sampling effort, the total number of observed species was higher in herbarium data. The relative abundance of common species in the field was higher, and the evenness of the distribution was lower, than in herbarium data. There was no significant correlation between species abundances in the field and in the herbaria. By selectively targeting rare species, collectors accumulate previously unseen species much faster than through ecological sampling. Conclusions: Because collectors aim for the rarer species and avoid the more common ones, the relative abundance of species in herbarium collections cannot be interpreted as a predictor of their true abundance in the field. Any statistical procedure that requires the sample to be representative of the true abundance distribution is likely to show errors when applied to herbarium data. However, because collectors actively search for rare species their rate of species accumulation is higher and their floristic lists are more complete than those obtained through ecological field sampling.     

分形理论及其在土壤空间变异研究中的应用

土壤具有不同程度的空间变异性,土壤空间变异研究对于土壤管理有重要意义.本文简要综述了分形理论及其在土壤空间变异研究中的应用,重点讨论了利用矩方法计算土壤属性分形维,多重分形分析土壤空间变异性及基于多重分形谱参数的土壤属性尺度转换.早期研究验证了分形理论在分析土壤空间变异中的有效性和应用潜力,国内外近期研究则报道了利用分形及多重分形理论分析土壤空间变异的最新进展.分形理论可以成为量化土壤属性空间变异性及尺度转换的重要工具.     

Exponential decay characteristics of the stochastic integer multiple neural firing patterns

Integer multiple neural firing patterns exhibit multi-peaks in inter-spike interval (ISI) histogram (ISIH) and exponential decay in amplitude of peaks, which results from their stochastic mechanisms. But in previous experimental observation that the decay in ISIH frequently shows obvious bias from exponential law. This paper studied three typical cases of the decay, by transforming ISI series of the firing to discrete binary chain and calculating the probabilities or frequencies of symbols over the whole chain. The first case is the exponential decay without bias. An example of this case was discovered on hippocampal CA1 pyramidal neuron stimulated by external signal. Probability calculation shows that this decay without bias results from a stochastic renewal process, in which the successive spikes are independent. The second case is the exponential decay with a higher first peak, while the third case is that with a lower first peak. An example of the second case was discovered in experiment on a neural pacemaker. Simulation and calculation of the second and third cases indicate that the dependency in successive spikes of the firing leads to the bias seen in decay of ISIH peaks. The quantitative expression of the decay slope of three cases of firing patterns, as well as the excitatory effect in the second case of firing pattern and the inhibitory effect in the third case of firing pattern are identified. The results clearly reveal the mechanism of the exponential decay in ISIH peaks of a number of important neural firing patterns and provide new understanding for typical bias from the exponential decay law.     

Know when to run,know when to hide: can behavioral differences explain the divergent invasion success of two sympatric lizards?

Invasive species represent a select subset of organisms that have successfully transitioned through each stage of the introduction process (transportation, establishment, and spread). Although there is a growing realization that behavior plays a critical role in invasion success, few studies have focused on the initial stages of introduction. We examined whether differences in the grouping tendencies and exploratory behavior of two sympatric lizard species could contribute to their divergent invasion success. While the nondirected activity of the two species did not differ, the invasive delicate skink (Lampropholis delicata) was found to be more exploratory than the congeneric noninvasive garden skink (L. guichenoti), which enabled it to more effectively locate novel environments and basking site resources. The delicate skink also exhibited a greater tendency to hide, which may act to enhance its probability of ensnarement in freight and cargo and decrease its likelihood of detection during transit. The grouping tendencies of the two species did not differ. Together, our results suggest that while the two species have an equivalent "opportunity" for unintentional human-assisted transportation, several pre-existing behavioral traits may enhance the success of the delicate skink in negotiating the initial stages of the introduction process, and subsequent post-establishment spread.     

Process development and cGMP manufacturing of a recombinant ricin vaccine: An effective and stable recombinant ricin a‐chain vaccine—RVEc™

Ricin is a potent toxin and a potential bioterrorism weapon with no specific countermeasures or vaccines available. The holotoxin is composed of two polypeptide chains linked by a single disulfide bond: the A‐chain (RTA), which is an N‐glycosidase enzyme, and the B‐chain (RTB), a lectin polypeptide that binds galactosyl moieties on the surface of the mammalian target cells. Previously (McHugh et al.), a recombinant truncated form of RTA (rRTA1‐33/44‐198 protein, herein denoted RVEa?) expressed in Escherichia coli using a codon‐optimized gene was shown to be non‐toxic, stable, and protective against a ricin challenge in mice. Here, we describe the process development and scale‐up at the 12 L fermentation scale, and the current Good Manufacturing Practice (cGMP)‐compliant production of RVEc? at the 40 L scale. The average yield of the final purified bulk RVEc? is approximately 16 g/kg of wet cell weight or 1.2 g/L of fermentation broth. The RVEc? was >99% pure by three HPLC methods and SDS‐PAGE. The intact mass and peptide mapping analysis of RVEc? confirmed the identity of the product and is consistent with the absence of posttranslational modifications. Potency assays demonstrated that RVEc? was immunoprotective against lethal ricin challenge and elicited neutralizing anti‐ricin antibodies in 95–100% of the vaccinated mice. Published 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011.     

Process and economic evaluation for monoclonal antibody purification using a membrane-only process

In recent years, the market for therapeutic monoclonal antibodies (mAb) has grown exponentially, and with this there has been a desire to reduce the costs associated with production and purification of these high-value biological products. A typical mAb purification process involves three adsorption/chromatography steps [protein A, ion exchange (IEX), and hydrophobic interaction (HIC)], along with ultrafiltration, nanofiltration, and microfiltration. With the development of membrane adsorption/chromatography as a viable alternative to traditional pack bed systems, the opportunity exists to complete the entire downstream purification process using only membrane operations. In this study, the process simulation tool SuperPro Designer was used to evaluate the application of recently developed ultra-high capacity electrospun nanofibrous adsorption membranes as a replacement for conventional chromatographic media in the downstream mAb production process. The simulation showed that nanofibrous adsorption membranes in place of the three packed bed chromatography steps reduced the required volume of protein A, IEX, and HIC adsorptive medium by 25, 80, and 80%, respectively. In addition, the membrane-only process reduced the downstream processing time by 50%, decreased the number of labor hours associated with the purification steps by 40%, generated 40% less aqueous waste, and reduced the overall downstream process operating expenses per unit product by 23%. There were also significant savings in facility construction costs and the price of fixed equipment required for separations. With these savings not only is the membrane-only process economically competitive with the traditional packed bed operations, but it offers the possibility of moving toward more disposable process.     

Effect of needle geometry on flow rate and cell damage in the dispensing-based biofabrication process

Biodispensing techniques have been widely applied in biofabrication processes to deliver cell suspensions and biomaterials to create cell-seeded constructs. Under identical operating conditions,two types of dispensing needles—tapered and cylindrical—can result in different flow rates of material and different cell damage percent induced by the mechanical forces. In this work, mathematical models of both flow rate and cell damage percent in biodispensing systems using tapered and cylindrical needles, respectively, were developed, and experiments were carried out to verify the effectiveness of the developed models. Both simulations and experiments show tapered needles produce much higher flow rates under the same pressure conditions than cylindrical needles. Use of a lower pressure in a tapered needle can therefore achieve the same flow rate as that in a cylindrical needle. At equivalent flow rates, cell damage in a tapered needle is lower than that in a cylindrical one. Both Schwann cells and 3T3 fibroblasts, which have been widely used in tissue engineering, were used to validate the cell damage models. Application of the developed models to specify the influence of process parameters, including needle geometry and air pressure, on the flow rate and cell damage percent represents a significant advance for biofabrication processes.The models can be used to optimize process parameters to preserve cell viability and achieve the desired cell distribution in dispensing-based biofabrication.     

Chemo-enzymatic epoxidation-process options for improving biocatalytic productivity

The reactor choice is crucial when designing a process where inactivation of the biocatalyst is a problem. The main bottleneck for the chemo-enzymatic epoxidation has been found to be enzyme inactivation by the hydrogen peroxide, H(2) O(2) , substrate. In the work reported here, the effect of reaction parameters on the reaction performance have been investigated and used to establish suitable operating strategies to minimize the inactivation of the enzyme, using rapeseed methyl ester (RME) as a substrate in a solvent-free system. The use of a controlled fed-batch reactor for maintaining H(2) O(2) concentration at 1.5 M resulted in increased productivity, up to 76 grams of product per gram of biocatalyst with higher retention of enzyme activity. Further investigation included a multistage design that separated the enzymatic reaction and the saturation of the RME substrate with H(2) O(2) into different vessels. This setup showed that the reaction rate as well as enzyme inactivation is strongly dependent on the H(2) O(2) concentration. A 20-fold improvement in enzymatic efficiency is required for reaching an economically feasible process. This will require a combination of enzyme modification and careful process design.     

Polymer peel‐off mask for high‐resolution surface derivatization,neuron placement and guidance

We present a dry lift‐off method using a chemically resistant spin‐on plastic, polyimide, to pattern surfaces with high accuracy and resolution. Using well‐known lithographic and reactive ion etching techniques, the spin‐on polymer is patterned over a silicon dioxide surface. The plastic efficiently adheres to the silicon dioxide surface during the chemical modification and is readily lifted‐off following the derivatization process, permitting highly reliable surface derivatization. The verticality of the reactive ion etch enables sub‐micrometer features to be patterned, down to 0.8 µm. The technique is used to pattern neurons on silicon dioxide surfaces: efficient neuron placement over a 4 mm area is shown for patterns larger than 50 µm while process guidance is shown for 10 µm patterns. Biotechnol. Bioeng. 2013; 110: 2236–2241. © 2013 Wiley Periodicals, Inc.