Optimal selection of 2D reversed-phase–reversed-phase HPLC separation techniques in bottom-up proteomics

Evaluation of: Stephanowitz H, Lange S, Lang D et al. Improved two-dimensional reversed phase–reversed phase LC-MS/MS approach for identification of peptide–protein interactions. J. Proteome Res. 11(2), 1175–1183 (2011).

Recent developments in bottom-up proteomics have supplanted the use of gel-based approaches in favor of multidimensional chromatographic separations of peptide mixtures followed by mass spectrometry analysis. This trend is driven by the desire to eliminate labor-intensive in-gel digestion procedures and increase proteome coverage through better recovery of proteolytic fragments. Introduction of reversed-phase–reversed-phase 2D separation techniques is one of the major improvements that have made this possible. In this article, we review recent developments in 2D HPLC and highlight variations in reversed-phase HPLC separation selectivity that allow for superior peak capacity in peptide fractionation.     

Inhibitory factors affecting the process of enhanced biological phosphorus removal (EBPR) – A mini-review

Enhanced biological phosphorus removal (EBPR) technology has been widely considered as a key strategy in preventing eutrophication and recognized as the advancing front of research in wastewater treatment. The key to keep its high efficiency in biological phosphorus removal is to optimize the operation and management of the system. Previous research in this field has undoubtedly improved understanding of the factors hindered overall efficiency of EBPR. However, it is obvious that much remains to be learnt. This paper attempts to review the fundamental understanding in factors inhibiting the stability and reliability of the EBPR systems in the state-of-the-art research. In view of modeling the EBPR systems, an appropriate extension of the current mechanistic models with these inhibitory factors is recommended in order to better simulate and predict the behavior of full-scale and lab-scale EBPR plants. From the perspectives of the further mechanistic and multi-factors study, the direction of denitrifying dephosphatation and granules/biofilms are also discussed. This comprehensive overview will not only help us to understand the overall mechanism of the EBPR process, but also benefit the researchers and engineers to consider all the possible factors affecting the process in the urban sewage treatment plants.     

Validation of a rodent model of source memory

Source memory represents the origin (source) of information. Recently, we proposed that rats (Rattus norvegicus) remember the source of information. However, an alternative to source memory is the possibility that rats selectively encoded some, but not all, information rather than retrieving an episodic memory. We directly tested this ‘encoding failure’ hypothesis. Here, we show that rats remember the source of information, under conditions that cannot be attributed to encoding failure. Moreover, source memory lasted at least seven days but was no longer present 14 days after studying. Our findings suggest that long-lasting source memory may be modelled in non-humans. Our model should facilitate attempts to elucidate the biological underpinnings of source memory impairments in human memory disorders such as Alzheimer''s disease.     

Persistence of tree cavities used by cavity-nesting vertebrates declines in harvested forests

An abundant supply of cavity-bearing trees is important for maintaining wildlife communities in harvested forests. During harvesting, suitable trees and cavities are directly removed, and the longevity of cavities in retained trees may be reduced by increased exposure to wind and other disturbance factors. We examined patterns of cavity survival in retained trembling aspen (Populus tremuloides) trees in harvested stands compared with those in unharvested mature stands by monitoring the persistence of individual cavities. We followed 930 cavities in 3 harvest treatments for up to 17 years in pre-cut and uncut forest, and up to 13 years post-harvest (reserve patches and dispersed retention), in temperate-mixed forests of interior British Columbia, Canada. Average annual cavity loss rates were 5.6% in pre-cut and uncut forest, 7.2% for cavities in trees retained in reserves, and 8.1% for cavities in retained trees dispersed throughout cuts. Correspondingly, median cavity longevity was 15 years for cavities in pre-cut and uncut forest, 10 years for cavities retained in reserves, and 9 years for those in dispersed retention. Risk of loss increased most for cavities in living trees (factor of 2.17), but we found no detectable difference for cavities in recently dead trees and trees with advanced decay. We suggest retention of a range of aspen size and decay classes to allow for future cavity-tree recruitment in harvested stands. Inclusion of wildlife reserves as part of an overall forest management plan will also help to mitigate the effects of windthrow and maintain long-lived cavity resources required by a large portion of forest wildlife. © 2013 The Wildlife Society     

Effect of nitrogen,phosphorus and potassium on spikelet sterility induced by low temperature at the reproductive stage of rice

Spikelet sterility induced by low temperature at the reproductive stage of rice increased further with the increase of nitrogen supply. Spikelet sterility in Fujisaka-5 did not increase due to low temperature when nitrogen supply was increased from 10 to 40 ppm and at 80 ppm nitrogen supply it was less affected than IR36. Total nitrogen content in the leaves increased with the increase of nitrogen supply and was forced to be associated with the spikelet sterility induced by low temperature. Based on auricle distance between the last two leaves, the most sensitive stage to low temperature damage differed in Fujisaka-5 and IR36. Spikelet sterility induced by low temperature for 10 days was very high in both the varieties and the effect of nitrogen was not clear.The effect of phosphorus on the spikelet sterility induced by low temperature at reproductive stage was not clear except that at the highest phosphorus (P) level (10 ppm) the spikelet sterility increased both in Fujisaka-5 and IR36.Spikelet sterility induced by low temperature at the reproductive stage of rice decreased with the increase of Potassium (K) supply in both Fujisaka-5 and IR36. With an increase of potassium supply, nitrogen (N) content decreased in the leaves and panicles and spikelet sterility induced by low temperature decreased with an increase of the K to N ratio in the leaves and panicles. The results suggest that potassium might play a major role to counteract the low temperature damage at the reproductive stage of rice.     

Rice straw decomposition in rice-field soil

Rice straw, buried in a rice-field during the dry season decomposed at a rate of 0.0075 day-1. Seventy five percent of the biomass, 70 percent carbon, 50 percent nitrogen and 30 percent phosphorus remained after 139 days of decomposition. Rice straw decomposition furnished 33% N and 8% P of the total nitrogen and phosphorus provided by man.     

Response of grazing snails to phosphorus enrichment of modern stromatolitic microbial communities

1. The effects of added phosphorus (P) on the growth, P and RNA : DNA contents, and survivorship of snails grazing on laminated microbial mats (living ‘stromatolites’) were examined in the Rio Mesquites at Cuatro Ciénegas, Mexico (total P, c. 0.60 μmol L^?1) to test the hypothesis that strong P‐limitation of microautotroph growth produces a stoichiometric constraint on herbivores because of mineral P‐limitation. 2. In a 3‐week experiment performed in summer 2001, addition of phosphorus (+15 μmol L^?1) resulted in a strong decline in stromatolite biomass C : P ratio from very high levels (c. 2300 : 1 by atoms) to moderate levels (c. 550 : 1). The endemic hydrobiid snail Mexithauma quadripaludium responded to P‐enrichment with elevated body P content and higher RNA : DNA ratios, especially for small animals likely to be actively growing. This positive response is consistent with the existence of a stoichiometric constraint on snail growth. 3. In a longer experiment (8 weeks) involving a more moderate P enrichment (+5 μmol L^?1) in summer 2002, P enrichment reduced stromatolite C : P ratio from moderate values in control treatments (c. 750) to very low values (<100 : 1). Snails responded to stromatolite P‐enrichment with increased body P content but, in contrast to the first experiment, with lower RNA : DNA ratio, lower growth rates, and higher mortality. 4. These contrasting results suggest that both very high and very low biomass C : P ratios in stromatolites are detrimental to M. quadripaludium performance, leading us to hypothesise that these herbivores live on a ‘stoichiometric knife edge’.     

Assessing Methods for Developing Phosphorus Desorption Isotherms from Soils using Anion Exchange Membranes

Developing desorption isotherms for inorganic phosphorus (P) is a time-consuming and non-standardized procedure. Anion exchange membranes (AEMs) have been successfully used in studies of P desorption kinetics and total membrane-desorbable P, but rarely have they been used for developing P desorption isotherms. Our study had two objectives: (1) to evaluate the suitability of using multiple strips of AEMs (termed the Multiple AEM Method) to develop P desorption isotherms; and (2) to compare the Multiple AEM Method with a sequential-extraction approach using AEMs (termed the Sequential AEM Method) to determine if the manner in which AEMs were used would influence the slope of the desorption isotherm, i.e. the partition coefficient. Both methods yielded well-defined, but numerically different desorption isotherms for all levels of sorbed P. However, estimated K _d values among methods were equivalent in the low and medium levels of P sorbed. The Multiple AEM method was quicker than the Sequential AEM method, but both gave similar K _d values in an agriculturally significant range of soil solution concentrations. These methods should be tested on a range of soil type to determine their suitability in developing P desorption isotherms and to move toward method standardization for desorption isotherms.