Assembly Pathway and Characterization of the RAG1/2-DNA Paired and Signal-end Complexes

Mammalian immune receptor diversity is established via a unique restricted set of site-specific DNA rearrangements in lymphoid cells, known as V(D)J recombination. The lymphoid-specific RAG1-RAG2 protein complex (RAG1/2) initiates this process by binding to two types of recombination signal sequences (RSS), 12RSS and 23RSS, and cleaving at the boundaries of RSS and V, D, or J gene segments, which are to be assembled into immunoglobulins and T-cell receptors. Here we dissect the ordered assembly of the RAG1/2 heterotetramer with 12RSS and 23RSS DNAs. We find that RAG1/2 binds only a single 12RSS or 23RSS and reserves the second DNA-binding site specifically for the complementary RSS, to form a paired complex that reflects the known 12/23 rule of V(D)J recombination. The assembled RAG1/2 paired complex is active in the presence of Mg²⁺, the physiologically relevant metal ion, in nicking and double-strand cleavage of both RSS DNAs to produce a signal-end complex. We report here the purification and initial crystallization of the RAG1/2 signal-end complex for atomic-resolution structure elucidation. Strict pairing of the 12RSS and 23RSS at the binding step, together with information from the crystal structure of RAG1/2, leads to a molecular explanation of the 12/23 rule.     

Metabolomic analysis identifies altered metabolic pathways in Multiple Sclerosis

Multiple sclerosis (MS) is a chronic, demyelinating disease that affects the central nervous system and is characterized by a complex pathogenesis and difficult management. The identification of new biomarkers would be clinically useful for more accurate diagnoses and disease monitoring. Metabolomics, the identification of small endogenous molecules, offers an instantaneous molecular snapshot of the MS phenotype. Here the metabolomic profiles (utilizing plasma from patients with MS) were characterized with a Gas cromatography-mass spectrometry-based platform followed by a multivariate statistical analysis and comparison with a healthy control (HC) population. The obtained partial least square discriminant analysis (PLS-DA) model identified and validated significant metabolic differences between individuals with MS and HC (R2X = 0.223, R2Y = 0.82, Q2 = 0.562; p < 0.001). Among discriminant metabolites phosphate, fructose, myo-inositol, pyroglutamate, threonate, l-leucine, l-asparagine, l-ornithine, l-glutamine, and l-glutamate were correctly identified, and some resulted as unknown. A receiver operating characteristic (ROC) curve with AUC 0.84 (p = 0.01; CI: 0.75–1) generated with the concentrations of the discriminant metabolites, supported the strength of the model. Pathway analysis indicated asparagine and citrulline biosynthesis as the main canonical pathways involved in MS. Changes in the citrulline biosynthesis pathway suggests the involvement of oxidative stress during neuronal damage. The results confirmed metabolomics as a useful approach to better understand the pathogenesis of MS and to provide new biomarkers for the disease to be used together with clinical data.     

Effects of phosphate-solubilizing bacteria application on soil phosphorus availability in coal mining subsidence area in Shanxi

The effect of phosphate-solubilizing bacteria (PSB) application on phosphorus (P) availability in reclaimed soil in coal mining subsidence region was investigated. Seven treatments were carried out including control, chicken manure (CM), PSB, PSB + tricalcium phosphate (TCP), CM?+?TCP, PSB?+?ground phosphate rock (GPR) and CM?+?GPR. The results showed soil Olsen-P concentration and phosphatase level as well as the yield of pakchoi (Brassica chinensis L.) were significantly higher in PSB application treatments compared to the corresponding CM application treatments. Soil phosphatase, invertase and urease contents were increased most significantly in PSB treatment, 1.18-, 1.31- and 2.32-fold higher than those in the control, respectively. Soil Ca₂-P, Ca₈-P, Fe-P and Al-P concentrations exhibited the greatest increases in PSB?+?TCP treatment, while occluded-P showed minor changes in different treatments. Application of PSB fertilizer reduced the transformation of Olsen-P to Ca₁₀-P, thus increasing P availability in reclaimed soil of coal mining subsidence area.     

Ascorbic acid prolongs the viability and stability of isolated perfused lungs: A mechanistic study using 31P and hyperpolarized 13C nuclear magnetic resonance

Ex vivo lung perfusion (EVLP) has recently shown promise as a means of more accurately gauging the health of lung grafts and improving graft performance post-transplant. However, reperfusion of ischemic lung promotes the depletion of high-energy compounds and a progressive loss of normal mitochondrial function, and it remains unclear how and to what extent the EVLP approach contributes to this metabolic decline. Although ascorbate has been used to mitigate the effects of ischemia–reperfusion injury, the nature of its effects during EVLP are also not clear. To address these uncertainties, this study monitored the energy status of lungs during EVLP and after the administration of ascorbate using ³¹P and hyperpolarized ¹³C NMR (nuclear magnetic resonance). Our experiments demonstrated that the oxidative phosphorylation capacity and pyruvate dehydrogenase flux of lungs decline during ex vivo perfusion. The addition of ascorbate to the perfusate prolonged lung viability by 80% and increased the hyperpolarized ¹³C bicarbonate signal by a factor of 2.7. The effect of ascorbate is apparently due not to its antioxidant quality but rather to its ability to energize cellular respiration given that it increased the lung’s energy charge significantly, whereas other antioxidants (glutathione and α-lipoic acid) did not alter energy metabolism. During ascorbate administration, inhibition of mitochondrial complex I with rotenone depressed energy charge and shifted the metabolic state of the lung toward glycolysis; reenergizing the electron transport chain with TMPD (N,N,N',N'-tetramethyl-p-phenylenediamine) recovered metabolic activity. This indicates that ascorbate slows the decline of the ex vivo perfused lung’s mitochondrial activity through an independent interaction with the electron transport chain complexes.     

Predator and detritivore niche width helps to explain biocomplexity of experimental detritus-based food webs in four aquatic and terrestrial ecosystems

In the study of food webs, the existence and explanation of recurring patterns, such as the scale invariance of linkage density, predator–prey ratios and mean chain length, constitute long-standing issues. Our study focused on litter-associated food webs and explored the influence of detritivore and predator niche width (as δ¹³C range) on web topological structure. To compare patterns within and between aquatic and terrestrial ecosystems and take account of intra-habitat variability, we constructed 42 macroinvertebrate patch-scale webs in four different habitats (lake, lagoon, beech forest and cornfield), using an experimental approach with litterbags. The results suggest that although web differences exist between ecosystems, patterns are more similar within than between aquatic and terrestrial web types. In accordance with optimal foraging theory, we found that the niche width of predators and prey increased with the number of predators and prey taxa as a proportion of total taxa in the community. The tendency was more marked in terrestrial ecosystems and can be explained by a lower per capita food level than in aquatic ecosystems, particularly evident for predators. In accordance with these results, the number of links increased with the number of species but with a significantly sharper regression slope for terrestrial ecosystems. As a consequence, linkage density, which was found to be directly correlated to niche width, increased with the total number of species in terrestrial webs, whereas it did not change significantly in aquatic ones, where connectance scaled negatively with the total number of species. In both types of ecosystem, web robustness to rare species removal increased with connectance and the niche width of predators. In conclusion, although limited to litter-associated macroinvertebrate assemblages, this study highlights structural differences and similarities between aquatic and terrestrial detrital webs, providing field evidence of the central role of niche width in determining the structure of detritus-based food webs and posing foraging optimisation constraints as a general mechanistic explanation of food web complexity differences within and between ecosystem types.     

Phytomass change in natural phytocenosis as an indicator of technogenic pollution of soils with heavy metals

This study considered the possibility of using plant community phytomass for the assessment of soil pollution with heavy metals (HM) from industrial wastes. The three-year-long field experiment was run under the regional natural meadow vegetation; the polymetallic galvanic slime was used as an industrial waste contaminant. It is shown that soil contamination primarily causes decrease of phytomass in the growing phytocenosis. The vegetation experiments determined nonlinear dependence of cultivated and wild plant biomass on the level of soil contamination; it is described by the equations of logistic and Gaussian regression. In the absence of permanent contaminants, the soil is self-cleaned over time. It reproduces phytomass mainly due to the productivity increase of the most pollution-tolerant species in the remaining phytocenosis. This phenomenon is defined as environmental hysteresis. Soil pollution by industrial waste leads to the loss of plant biodiversity. The research shows that the study of the HM impact on ecosystems is expedient given the consideration of the “soil–phytocenosis–pollutant” complex in the “dose–response” aspect. The reaction of phytocenosis on HM showing decline in phytomass leads to serious limitations in the choice of accumulating plants, because the adsorbed HM are rejected through phytomass.     

1 alpha, 25-Dihydroxyvitamin D3 directly induces fusion of alveolar macrophages by a mechanism involving RNA and protein synthesis, but not DNA synthesis

The results of our present study indicate that 1 alpha, 25-dihydroxyvitamin D3[1 alpha, 25(OH)2D3] directly induces fusion of mouse alveolar macrophages without any participation of T-lymphocytes by a mechanism involving RNA and protein synthesis but not DNA synthesis. We have reported that 1 alpha, 25(OH)2D3 induces fusion of alveolar macrophages by a direct mechanism and by a spleen cell-mediated indirect mechanism [(1983) Proc. Natl. Acad. Sci. USA 80, 5583-5587]. Alveolar macrophages pretreated with or without anti-Thy 1.2 antibody and complement fused similarly when they were incubated with 1 alpha, 25(OH)2D3. The vitamin suppressed DNA synthesis, but it significantly enhanced RNA and protein synthesis. The 1 alpha, 25(OH)2D3-induced fusion was blocked by adding actinomycin D or cycloheximide, but not by hydroxyurea.     

The effects of host plant species on adult oviposition and larval performance of the aphid predator Aphidoletes aphidimyza

1. Although preference–performance relationships in insects are typically studied in a bi-trophic context, it is well known that host plants can affect both the preference and performance of natural enemies of herbivorous insects. 2. This study presents evidence from field and laboratory studies that two species of milkweeds, the putatively less defended Asclepias incarnata and the putatively more defended Asclepias syriaca, differentially affect adult oviposition and larval performance in Aphidoletes aphidimyza, an aphid-feeding predatory midge, independent of aphid density. 3. Host plant species affected predatory fly larvae abundance by a factor of 50 in the field and a factor of 8 in the laboratory. Larval and adult emergence rates in our laboratory studies provided strong evidence for reduced performance on A. syriaca. Oviposition in choice and no-choice settings provided some evidence for preference for A. incarnata, and a potentially suppressive effect of A. syriaca. 4. The results provide limited support for the hypothesis that natural selection can lead to positive correlations between adult oviposition preferences and larval performance upon various food sources, even when predatory insects oviposit onto host plants of their herbivorous prey. 5. Preference and performance are not perfectly aligned in this system, however, because ovipositing females do not reject A. syriaca entirely. Potential explanations for mismatches between preference and performance in this system include the neural constraints associated with being a generalist, adaptive time-limited foraging strategies, and unique evolutionary histories of laboratory colonies compared with wild insects.     

Fish and fisheries in hot water: What is happening and how do we adapt?

Rapid climate changes are currently driving substantial reorganizations of marine ecosystems around the world. A key question is how these changes will alter the provision of ecosystem services from the ocean, particularly from fisheries. To answer this question, we need to understand not only the ecological dynamics of marine systems, but also human adaptation and feedbacks between humans and the rest of the natural world. In this review, we outline what we have learned from research primarily in continental shelf ecosystems and fishing communities of North America. Key findings are that marine animals are highly sensitive to warming and are responding quickly to changes in water temperature, and that such changes are often happening faster than similar processes on land. Changes in species distributions and productivity are having substantial impacts on fisheries, including through changing catch compositions and longer distances traveled for fishing trips. Conflicts over access to fisheries have also emerged as species distributions are no longer aligned with regulations or catch allocations. These changes in the coupled natural-human system have reduced the value of ecosystem services from some fisheries and risk doing so even more in the future. Going forward, substantial opportunities for more effective fisheries management and operations, marine conservation, and marine spatial planning are likely possible through greater consideration of climate information over time-scales from years to decades.