The production of phytolith‐occluded carbon in China's forests: implications to biogeochemical carbon sequestration

The persistent terrestrial carbon sink regulates long‐term climate change, but its size, location, and mechanisms remain uncertain. One of the most promising terrestrial biogeochemical carbon sequestration mechanisms is the occlusion of carbon within phytoliths, the silicified features that deposit within plant tissues. Using phytolith content–biogenic silica content transfer function obtained from our investigation, in combination with published silica content and aboveground net primary productivity (ANPP) data of leaf litter and herb layer in China's forests, we estimated the production of phytolith‐occluded carbon (PhytOC) in China's forests. The present annual phytolith carbon sink in China's forests is 1.7 ± 0.4 Tg CO₂ yr ^{? 1}, 30% of which is contributed by bamboo because the production flux of PhytOC through tree leaf litter for bamboo is 3–80 times higher than that of other forest types. As a result of national and international bamboo afforestation and reforestation, the potential of phytolith carbon sink for China's forests and world's bamboo can reach 6.8 ± 1.5 and 27.0 ± 6.1 Tg CO₂ yr^?1, respectively. Forest management practices such as bamboo afforestation and reforestation may significantly enhance the long‐term terrestrial carbon sink and contribute to mitigation of global climate warming.     

Large amounts of labile organic carbon in permafrost soils of northern Alaska

Permafrost‐affected soils of the northern circumpolar region represent 50% of the terrestrial soil organic carbon (SOC) reservoir and are most strongly affected by climatic change. There is growing concern that this vast SOC pool could transition from a net C sink to a source. But so far little is known on how the organic matter (OM) in permafrost soils will respond in a warming future, which is governed by OM composition and possible stabilization mechanisms. To investigate if and how SOC in the active layer and adjacent permafrost is protected against degradation, we employed density fractionation to separate differently stabilized SOM fractions. We studied the quantity and quality of OM in different compartments using elemental analysis, ¹³C solid‐phase nuclear magnetic resonance (¹³C‐NMR) spectroscopy, and ¹⁴C analyses. The soil samples were derived from 16 cores from drained thaw lake basins, ranging from 0 to 5500 years of age, representing a unique series of developing Arctic soils over time. The normalized SOC stocks ranged between 35.5 and 86.2 kg SOC m^?3, with the major amount of SOC located in the active layers. The SOC stock is dominated by large amounts of particulate organic matter (POM), whereas mineral‐associated OM especially in older soils is of minor importance on a mass basis. We show that tremendous amounts of over 25 kg OC per square meter are stored as presumably easily degradable OM rich in carbohydrates. Only about 10 kg OC per square meter is present as presumably more stable, mineral‐associated OC. Significant amounts of the easily degradable, carbohydrate‐rich OM are preserved in the yet permanently frozen soil below the permafrost table. Forced by global warming, this vast labile OM pool could soon become available for microbial degradation due to the continuous deepening of the annually thawing active layer.     

Conserved movement of TMS11 between occluded conformations of LacY and XylE of the major facilitator superfamily suggests a similar hinge‐like mechanism

The Δ‐distance maps can detect local remodeling that is difficult to accurately determine using superimpositions. Transmembrane segments (TMSs) 11 in both LacY and XylE of the major facilitator superfamily uniquely contribute the greatest amount of mobile surface area in the outward‐occluded state and undergo analogous movements. The intracellular part of TMS11 moves away from the C‐terminal domain and into the substrate cavity during the conformational change from the outward‐occluded to the inward‐occluded state. A difference was noted between LacY and XylE when they assumed the inward open state after releasing a substrate to the inside in which TMS11 of LacY moved further into the substrate release space, whereas in XylE, TMS11 slightly retracted into the C‐terminal domain. Independent movement of the N‐terminal half of TMS11 suggests that it is flexible in the middle. Repeat‐swapped homology modeling was used to discover that a loop connecting TMSs 10 and 11 in LacY probably moves during the transition between the unavailable outward‐open state and the outward‐occluded state. TMSs 11 and the other elements displaying a notable domain‐independent movement colocalize with the interdomain linker, suggesting that these elements could drive the alternating access movement between the domain halves. Preliminary evidence indicates that analogous movements occur in other members of the major facilitator superfamily. Proteins 2015; 83:735–745. © 2015 Wiley Periodicals, Inc.     

典型黑土区不同生态系统土壤团聚体有机碳分布特征

基于团聚体分组和闭蓄态微团聚体分离技术,利用典型黑土区27年长期定位试验,研究草地生态系统、农田生态系统和裸地生态系统下土壤团聚体及团聚体内部组分中有机碳的分布,以解析不同生态系统下土壤团聚体和有机碳固持间的关系,揭示黑土有机碳的物理稳定性机制。结果显示:与农田相比,草地土壤有机碳含量显著提高7.6%;裸地土壤有机碳含量显著下降14.1%。草地促进了大团聚体(250μm),尤其2000μm团聚体的形成,提高了土壤团聚体的稳定性;裸地则降低了土壤的团聚化程度及稳定性,大团聚体和微团聚体含量下降,粉粘粒含量相应增加。草地大团聚体中有机碳含量显著高于农田,且内部各组分有机碳含量均有显著提高,其中粗颗粒有机质、闭蓄态微团聚体和粉黏粒有机碳含量增幅分别为600%、54%和65%;裸地增加了粉粘粒结合有机碳含量,降低了大团聚体和微团聚体中有机碳含量,且大团聚体和微团聚体内部各组分有机碳含量均有所下降。3种生态系统类型土壤均以总粉粘粒结合有机碳为主,占土壤总有机碳52%—79%,其作为惰性碳库是黑土有机碳的重要组成部分。黑土有机碳的累积或损失主要表现为活性较强的有机碳库-团聚体中颗粒有机质的增加或减少,与农田相比,草地土壤有机碳的累积主要归因于大团聚体中粗颗粒有机质的增加,为总有机碳增量的3倍;裸地土壤有机碳的损失主要归因于微团聚体中总细颗粒有机质的减少,对总有机碳损失的贡献率为60%。     

Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back

Escherichia coli dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate to tetrahydrofolate. During the catalytic cycle, DHFR undergoes conformational transitions between the closed (CS) and occluded (OS) states that, respectively, describe whether the active site is closed or occluded by the Met20 loop. The CS→OS and the reverse transition may be viewed as allosteric transitions. Using a sequence-based approach, we identify a network of residues that represents the allostery wiring diagram. Many of the residues in the allostery wiring diagram, which are dispersed throughout the adenosine-binding domain as well as the loop domain, are not conserved. Several of the residues in the network have been previously shown by NMR experiments, mutational studies, and molecular dynamics simulations to be linked to equilibration conformational fluctuations of DHFR. To further probe the nature of events that occur during conformational fluctuations, we use a self-organized polymer model to monitor the kinetics of the CS→OS and the reverse transitions. During the CS→OS transition, coordinated changes in a number of residues in the loop domain enable the Met20 loop to slide along the α-helix in the adenosine-binding domain. Sliding is triggered by pulling of the Met20 loop by the βG-βH loop and the pushing action of the βG-βH loop. The residues that facilitate the Met20 loop motion are part of the network of residues that transmit allosteric signals during the CS→OS transition. Replacement of M16 and G121, whose C^α atoms are about 4.3 Å in the CS, by a disulfide cross-link impedes that CS→OS transition. The order of events in the OS→CS transition is not the reverse of the forward transition. The contact Glu18-Ser49 in the OS persists until the sliding of the Met20 loop is nearly complete. The ensemble of structures in the transition state in both the allosteric transitions is heterogeneous. The most probable transition-state structure resembles the OS (CS) in the CS→OS (OS→CS) transition, which is in accord with the Hammond postulate. Structures resembling the OS (CS) are present as minor (∼ 1-3%) components in equilibrated CS (OS) structures.     

PCR方法制备地高辛标记DNA探针检测中国对虾非包涵体型杆状病毒

A pair of primers created from information of PmNOBⅢ genome DNA Sal I fragment produced a 355bp band by using Penaeus chinensis non occluded baculovirus (PcNOBV),the WSBV isolate from P.hinensis in mainland China,as the DNA template.The specific PCR product was cloned,sequenced and labeled with digoxigenin (DIG)DNA labeling kit(Boehringer Mannheim).The DIG labeled fragment was tested by dot blot hybridization for sensitivity and specificity with purified PcNOBV nucleocapsid,PcNOBV infected shrimp tissues and healthy shrimp tissues.The detection limit of the DNA probe is 6.8pg of purified PcNOBV DNA.No hybridization signals were observed using DNA from healthy shrimp as template.Healthy P.chinensis,artificially infected P.chinensis and pond reared adult P.chinensis were screened for PcNOBV infection by both PCR and the hybridization assay.The results showed a good relationship between PCR and the hybridization assay.These findings demonstrate that the DIG labeled probe can be used as a sensitive,specific and cost effective reagent for detection of PcNOBV.     

Mycorrhizas and soil structure

In addition to their well-recognized roles in plant nutrition and communities, mycorrhizas can influence the key ecosystem process of soil aggregation. Here we review the contribution of mycorrhizas, mostly focused on arbuscular mycorrhizal fungi (AMF), to soil structure at various hierarchical levels: plant community; individual root; and the soil mycelium. There are a suite of mechanisms by which mycorrhizal fungi can influence soil aggregation at each of these various scales. By extension of these mechanisms to the question of fungal diversity, it is recognized that different species or communities of fungi can promote soil aggregation to different degrees. We argue that soil aggregation should be included in a more complete 'multifunctional' perspective of mycorrhizal ecology, and that in-depth understanding of mycorrhizas/soil process relationships will require analyses emphasizing feedbacks between soil structure and mycorrhizas, rather than a uni-directional approach simply addressing mycorrhizal effects on soils. We finish the discussion by highlighting new tools, developments and foci that will probably be crucial in further understanding mycorrhizal contributions to soil structure.     

Occluded molecular surface: Analysis of protein packing

We describe a novel method to calculate the packing interactions in protein structural models. The method calculates the interatomic occluded surface areas for each atom in the protein model. The identification of, and degree of interaction with, neighboring atoms is accomplished by extending surface normal from a dot surface of each atom to the point of intersection with neighboring atoms. The combined occluded and non-occluded surface areas may be normalized for the amino acid composition of the protein providing a single parameter, the normalized protein surface ratio, which is diagnostic for native-like Structures. Individual residues in the model which are in infrequent occluded surface environments may be identified. The method provides a means to explicitly describe packing densities and packing environments of individual atoms in a protein model. Finally, the method allows estimation of the complementarity between any interacting molecules, for example a ligand binding to a receptor.     

The production of phytoliths in China's grasslands: implications to the biogeochemical sequestration of atmospheric CO2

Among the most promising approaches of long‐term atmospheric CO₂ sequestration is terrestrial biogeochemical carbon sequestration. One of the most promising terrestrial biogeochemical carbon sequestration mechanisms is the occlusion of carbon within phytoliths, the silicified features that deposit within plant tissues. Using phytolith content‐biogenic silica content transfer function obtained from our investigation, in combination with published silica content and above‐ground net primary productivity (ANPP) data of China's grasslands, we estimated the production of phytoliths and phytolith‐occluded carbon (PhytOC) in grasslands. The results show that the average above‐ground phytolith production rates of China's grasslands (10.9 10⁶ t yr^?1 or 1.45% of world grasslands) are much lower than those of other grasslands (e.g. North American nonwoody grasslands) mainly because of much lower ANPP. Assuming a median content of PhytOC of 1.5%, the average above‐ground PhytOC production rates of China's grasslands and world grasslands are estimated to be 0.6 10⁶ t CO₂ yr^?1 and 41.4 10⁶ t CO₂ yr^?1, respectively. The management of grasslands to maximize ANPP has the potential to result in considerable quantities of phytoliths and securely bio‐sequestered carbon.     

Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2

PepT1 and PepT2 are major facilitator superfamily (MFS) transporters that utilize a proton gradient to drive the uptake of di‐ and tri‐peptides in the small intestine and kidney, respectively. They are the major routes by which we absorb dietary nitrogen and many orally administered drugs. Here, we present the crystal structure of PepT_So, a functionally similar prokaryotic homologue of the mammalian peptide transporters from Shewanella oneidensis. This structure, refined using data up to 3.6 Å resolution, reveals a ligand‐bound occluded state for the MFS and provides new insights into a general transport mechanism. We have located the peptide‐binding site in a central hydrophilic cavity, which occludes a bound ligand from both sides of the membrane. Residues thought to be involved in proton coupling have also been identified near the extracellular gate of the cavity. Based on these findings and associated kinetic data, we propose that PepT_So represents a sound model system for understanding mammalian peptide transport as catalysed by PepT1 and PepT2.