Probabilistic settling in the Local Exchange Model of turbulent particle transport

The Local Exchange Model (LEM) is a stochastic diffusion model of particle transport in turbulent flowing water. It was developed mainly for application to particles of near-neutral buoyancy that are strongly influenced by turbulent eddies. Turbulence can rapidly transfer such particles to the bed, where settlement can then occur by, for example, sticking to biofilms (e.g., fine particulate organic matter, or FPOM) or attaching to the substrate behaviorally (e.g., benthic invertebrates). Previous papers on the LEM have addressed the problems of how long (time) and far (distance) a suspended particle will be transported before hitting the bed for the first time. These are the hitting-time and hitting-distance problems, respectively. Hitting distances predicted by the LEM for FPOM in natural streams tend to be much shorter than the distances at which most particles actually settle, suggesting that particles usually do not settle the first time they hit the bed. The present paper extends the LEM so it can address probabilistic settling, where a particle encountering the bed can either remain there for a positive length of time (i.e., settle) or immediately reflect back into the water column, each with positive probability. Previous results for the LEM are generalized by deducing a single set of equations governing the probability distribution and moments of a broad class of quantities that accumulate during particle trajectories terminated by hitting or settling on the bed (e.g., transport time, transport distance, cumulative energy expenditure during transport). Key properties of the settling-time and settling-distance distributions are studied numerically and compared with the observed FPOM settling-distance distribution for a natural stream. Some remaining limitations of the LEM and possible means of overcoming them are discussed.     

Evaluation of alternatives for human lysozyme purification from transgenic rice: impact of phytic acid and buffer

Producing economically competitive recombinant human lysozyme from transgenic rice demands an inexpensive purification process for nonpharmaceutical applications. Human lysozyme is a basic protein, and thus, cation exchange chromatography was the selected method for lysozyme purification. Similar to other protein production systems, the identification of critical impurities in the rice extract was important for the development of an efficient purification process. Previous adsorption data indicated that phytic acid was probably responsible for an unacceptably low cation exchange adsorption capacity. In this study, we confirm that reducing phytic acid concentration improves lysozyme binding capacity and investigate alternative process conditions that reduce phytic acid interference. Compared with the previous best process, the adsorption capacity of human lysozyme was increased from 8.6 to 19.7 mg/mL when rice extract was treated with phytase to degrade phytic acid. Using tris buffer to adjust pH 4.5 extract to pH 6 before adsorption reduced phytic acid interference by minimizing phytic acid-lysozyme interactions, eliminated the need for phytase treatment, and increased the binding capacity to 25 mg/mL. Another method of reducing phytic acid concentration was to extract human lysozyme from rice flour at pH 10 with 50 mM NaCl in 50 mM sodium carbonate buffer. A similar binding capacity (25.5 mg/mL) was achieved from pH 10 extract that was clarified by acidic precipitation and adjusted to pH 6 for adsorption. Lysozyme purities ranged from 95 to 98% for all three processing methods. The tris-mediated purification was the most efficient of the alternatives considered.     

Spatiotemporal variations of CO2 fluxes in a Cynodon-dominated riparian zone of the Three Gorges Reservoir (TGR), China

Aims Riparian ecosystems play an important role in overall ecosystem function, including the global carbon cycle of terrestrial ecosystems, at both landscape and global scales. Yet few studies have reportedin situmeasurements of CO₂in riparian areas where flooding is a unique disturbance to carbon cycling.     

Upper range limit establishment after wildfire of an obligate-seeding montane forest tree fails to keep pace with 20th century warming

Aims How species respond to climate change at local scales will depend on how edaphic and biological characteristics interact with species physiological limits and traits such as dispersal. Obligate seeders, those species that depend on fire for recruitment, have few and episodic opportunities to track a changing climate envelope. In such cases, long-distance seed dispersal will be necessary to take advantage of rare recruitment opportunities. We examine recruitment patterns and seedling growth below, at and above the timberline of an obligate-seeding Australian montane forest tree (Eucalyptus delegatensis) after stand-replacing fire, and place these changes in the context of regional warming.Methods We use two methods to detect whether E. delegatensis can establish and persist above the timberline after stand-replacing wildfire in montane forests in south-east Australia. First, we examine establishment patterns by using belt transects at six sites to quantify how changes in post-fire recruit density with increasing distance above the timberline seven years post-fire. Second, to determine whether dispersal or physiological constraints determine post-fire establishment patterns, we transplanted seedlings and saplings into bare ground above (100 m elevation), at, and below (50 m elevation) timberline 18-months after fire. We monitored seedling growth and survival for one growing season.Important findings There was minimal upslope migration of the species after fire with most saplings observed near seed-bearing timberline trees, with only occasional outpost saplings. Transplanted seedlings and saplings survived equally well across one growing season when planted above existing timberlines, relative to saplings at or below the timberline. Seedling and sapling growth rates also did not differ across these location, although seedlings grew at much faster rates than saplings. These findings suggest that upslope growing season conditions are unlikely to limit initial range expansion of trees after fire. Instead, it is more likely that seed traits governing dispersal modulate responses to environmental gradients, and global change more generally.     

Estuary–ocean connectivity: fast physics,slow biology

Estuaries are connected to both land and ocean so their physical, chemical, and biological dynamics are influenced by climate patterns over watersheds and ocean basins. We explored climate‐driven oceanic variability as a source of estuarine variability by comparing monthly time series of temperature and chlorophyll‐a inside San Francisco Bay with those in adjacent shelf waters of the California Current System (CCS) that are strongly responsive to wind‐driven upwelling. Monthly temperature fluctuations inside and outside the Bay were synchronous, but their correlations weakened with distance from the ocean. These results illustrate how variability of coastal water temperature (and associated properties such as nitrate and oxygen) propagates into estuaries through fast water exchanges that dissipate along the estuary. Unexpectedly, there was no correlation between monthly chlorophyll‐a variability inside and outside the Bay. However, at the annual scale Bay chlorophyll‐a was significantly correlated with the Spring Transition Index (STI) that sets biological production supporting fish recruitment in the CCS. Wind forcing of the CCS shifted in the late 1990s when the STI advanced 40 days. This shift was followed, with lags of 1–3 years, by 3‐ to 19‐fold increased abundances of five ocean‐produced demersal fish and crustaceans and 2.5‐fold increase of summer chlorophyll‐a in the Bay. These changes reflect a slow biological process of estuary–ocean connectivity operating through the immigration of fish and crustaceans that prey on bivalves, reduce their grazing pressure, and allow phytoplankton biomass to build. We identified clear signals of climate‐mediated oceanic variability in this estuary and discovered that the response patterns vary with the process of connectivity and the timescale of ocean variability. This result has important implications for managing nutrient inputs to estuaries connected to upwelling systems, and for assessing their responses to changing patterns of upwelling timing and intensity as the planet continues to warm.     

In situ PEGylation of recombinant hirudin on an anion exchange chromatography column

In this study, an integrated process was developed for successive solid-phase PEGylation of recombinant hirudin variant-2 (HV2) and separation of PEGylated HV2 species on an anion exchange chromatography column (so-called in situ PEGylation). The effects of different PEG sizes, ion exchange resins and reaction conditions on in situ PEGylation were investigated. The results showed that in situ PEGylation efficiently integrates the reaction, separation and purification into a single-unit operation using the same column. In situ PEGylation could improve the selectivity of PEGylation reactions by significantly reducing the formation of multi-PEG-HV2. The pore sizes and internal surface structures of different resins had a significant impact on the yield of mono-PEG-HV2. In contrast to liquid-phase PEGylation, the yield of mono-PEG-HV2 decreased as PEG size increased during the in situ PEGylation process, indicating that in situ PEGylation is a pore diffusion-controlled process. The in vitro and in vivo anticoagulant activities of mono-PEG-HV2 derived from in situ PEGylation were higher than those from liquid-phase PEGylation, indicating that in situ PEGylation could enhance the bioactivity retention of mono-PEG-HV2. The results of this study demonstrated that in situ PEGylation can be used as an effective approach for the development of PEGylated protein drugs.     

Rate heterogeneity across Squamata,misleading ancestral state reconstruction and the importance of proper null model specification

The binary‐state speciation and extinction (BiSSE) model has been used in many instances to identify state‐dependent diversification and reconstruct ancestral states. However, recent studies have shown that the standard procedure of comparing the fit of the BiSSE model to constant‐rate birth–death models often inappropriately favours the BiSSE model when diversification rates vary in a state‐independent fashion. The newly developed HiSSE model enables researchers to identify state‐dependent diversification rates while accounting for state‐independent diversification at the same time. The HiSSE model also allows researchers to test state‐dependent models against appropriate state‐independent null models that have the same number of parameters as the state‐dependent models being tested. We reanalyse two data sets that originally used BiSSE to reconstruct ancestral states within squamate reptiles and reached surprising conclusions regarding the evolution of toepads within Gekkota and viviparity across Squamata. We used this new method to demonstrate that there are many shifts in diversification rates across squamates. We then fit various HiSSE submodels and null models to the state and phylogenetic data and reconstructed states under these models. We found that there is no single, consistent signal for state‐dependent diversification associated with toepads in gekkotans or viviparity across all squamates. Our reconstructions show limited support for the recently proposed hypotheses that toepads evolved multiple times independently in Gekkota and that transitions from viviparity to oviparity are common in Squamata. Our results highlight the importance of considering an adequate pool of models and null models when estimating diversification rate parameters and reconstructing ancestral states.     

The intermediate distance hypothesis of biological invasions

Biological invasions are a worldwide phenomenon, but the global flows between native and alien regions have rarely been investigated in a cross‐taxonomic study. We therefore lack a thorough understanding of the global patterns of alien species spread. Using native and alien ranges of 1380 alien species, we show that the number of alien species follows a hump‐shaped function of geographic distance. We observe distinct variations in the relationship between alien species exchanges and distance among taxonomic groups, which relate to the taxa‐specific dispersal modes and their pathways of introduction. We formulate a simple statistical model, combining trade volume and biogeographic dissimilarity, which reproduces the observed pattern in good agreement with reported data and even captures variations among taxonomic groups. This study demonstrates the universality of the intermediate distance hypothesis of alien species spread across taxonomic groups, which will help to improve the predictability of new alien species arrivals.     

中国北方针叶林生长季碳交换及其调控机制

采用开路式涡动相关法对北方针叶林连续2个生长季节(2007和2008年)的碳交换及其影响因素进行分析.结果表明：北方针叶林生态系统总生产力(GEP)、生态系统呼吸(R_e)和净生态系统碳交换(NEE)在6月下旬到8月中旬的生长旺盛期达到最大值,但各峰值出现的日期并不一致.2007和2008年北方针叶林生长季的日均GEP、日均R_e、日均NEE分别为19.45、15.15、-1.45 g CO₂·m^-2·d^-1和17.67、14.11、-1.37 g CO₂·m^-2·d^-1,2007年碳交换明显大于2008年,这可能是生长季较高的平均温度及光合有效辐射引起(2007年为12.46 ℃和697 μmol·m^-2·s^-1,2008年为11,04 ℃和639 μmol·m^-2·s^-1).北方针叶林的GEP与温度和光合有效辐射具有很好的相关性,其中与气温的相关系数接近0.55(P<0.01);R_e主要受温度调控,相关系数为0.66～0.72(P<0,01);NEE与光合有效辐射相关性最大,相关系数为0.59～0.63 (P<0.01).     

In vitro reconstitution of Sgk3 activation by phosphatidylinositol 3-phosphate

Serum- and glucocorticoid-regulated kinase 3 (Sgk3) is a serine/threonine protein kinase activated by the phospholipid phosphatidylinositol 3-phosphate (PI3P) downstream of growth factor signaling via class I phosphatidylinositol 3-kinase (PI3K) signaling and by class III PI3K/Vps34-mediated PI3P production on endosomes. Upregulation of Sgk3 activity has recently been linked to a number of human cancers; however, the precise mechanism of activation of Sgk3 is unknown. Here, we use a wide range of cell biological, biochemical, and biophysical techniques, including hydrogen–deuterium exchange mass spectrometry, to investigate the mechanism of activation of Sgk3 by PI3P. We show that Sgk3 is regulated by a combination of phosphorylation and allosteric activation. We demonstrate that binding of Sgk3 to PI3P via its regulatory phox homology (PX) domain induces large conformational changes in Sgk3 associated with its activation and that the PI3P-binding pocket of the PX domain of Sgk3 is sequestered in its inactive conformation. Finally, we reconstitute Sgk3 activation via Vps34-mediated PI3P synthesis on phosphatidylinositol liposomes in vitro. In addition to identifying the mechanism of Sgk3 activation by PI3P, our findings open up potential therapeutic avenues in allosteric inhibitor development to target Sgk3 in cancer.