Histomorphological changes in murine fibrosarcoma after hypericin-based photodynamic therapy

Histomorphological changes in murine fibrosarcoma after photodynamic therapy (PDT) based on the natural photosensitizer hypericin were evaluated. C3H/DiSn mice were inoculated with fibrosarcoma G5:1:13 cells. When the tumour reached a volume of 40-80 mm(3) the mice were intraperitoneally injected with hypericin, either in a single dose (5 mg/kg; 1 or 6 h before laser irradiation) or two fractionated doses (2.5 mg/kg; 6 and 1 h before irradiation with laser light; 532 nm, 70 mW/cm(2), 168 J/cm(2)). All groups of PDT-treated animals with single and fractionated hypericin dosing presented primary vascular reactions including vascular dilatation, congestion, thrombosis and oedema. Two hours after PDT there were necrotic changes with small, rather focal appearance. One day after therapy the necrotic areas were enhanced, often affecting a complete superficial layer of tumour tissue. Necrotic areas were accompanied with inflammation and haemorrhages.     

Computational modeling reveals key molecular properties and dynamic behavior of disruptor of telomeric silencing 1-like (DOT1L) and partnering complexes involved in leukemogenesis

Disruptor of telomeric silencing 1-like (DOT1L) is the only non-SET domain histone lysine methyltransferase (KMT) and writer of H3K79 methylation on nucleosomes marked by H2B ubiquitination. DOT1L has elicited significant attention because of its interaction or fusion with members of the AF protein family in blood cell biology and leukemogenic transformation. Here, our goal was to extend previous structural information by performing a robust molecular dynamic study of DOT1L and its leukemogenic partners combined with mutational analysis. We show that statically and dynamically, D161, G163, E186, and F223 make frequent time-dependent interactions with SAM, while additional residues T139, K187, and N241 interact with SAM only under dynamics. Dynamics models reveal DOT1L, SAM, and H4 moving as one and show that more than twice the number of DOT1L residues interacts with these partners, relative to the static structure. Mutational analyses indicate that six of these residues are intolerant to substitution. We describe the dynamic behavior of DOT1L interacting with AF10 and AF9. Studies on the dynamics of a heterotrimeric complex of DOT1L1-AF10 illuminated describe coordinated motions that impact the relative position of the DOT1L HMT domain to the nucleosome. The molecular motions of the DOT1L–AF9 complex are less extensive and highly dynamic, resembling a swivel-like mechanics. Through molecular dynamics and mutational analysis, we extend the knowledge previous provided by static measurements. These results are important to consider when describing the biochemical properties of DOT1L, under normal and in disease conditions, as well as for the development of novel therapeutic agents.     

Increase in light interception cost and metabolic mass component of leaves are coupled for efficient resource use in the high altitude vegetation

Global syntheses of leaf trait scaling relationships report an increase in light interception costs or ‘diminishing returns’ with increase in leaf area. However, variation in light interception costs across ecological gradients and plant strategies to cope up with these costs are not adequately understood. We analyzed leaf area (A) – leaf dry mass (M), leaf water mass (W) – M and W – A scaling relationships in plants occurring in a high altitude region of western Himalaya across environmental gradients to understand changes in light interception cost and metabolic mass component. M represents light interception cost, whereas, W is considered as a proxy of metabolic mass component for liquid phase being the ultimate source of metabolic activity. Trait values were measured from 9278 leaves belonging to 136 dominant species occurring at different sites, slope aspects, elevations and habitat types. Overall, light interception cost increased with increasing A (scaling exponent (α) < 1 in A–M relationship) and metabolic mass component increased disproportionately high with increasing M and A. We found significant differences in scaling exponents of leaf trait relationship between sites, elevations, slope aspects and habitat types, indicating that increase in light interception cost was more evident at higher elevations, southern slopes and open habitats. Further, with increase in light interception cost, metabolic mass component also increased (α > 1 in W–M and W–A relationships). The changes in scaling exponents of various leaf trait relationships across ecological gradients indicated that vegetation of different regions have differences in light interception cost and metabolic mass component. Moreover, increasing light interception cost (increase in mechanical and hydraulic tissues) with increasing A and increasing metabolic mass (leaf thickness) with increasing A and M are favored in high altitude vegetation. This could be a key strategy of high altitude plants for efficient resource capture and use in harsh environments.     

CCR5 Is a Therapeutic Target for Recovery after Stroke and Traumatic Brain Injury

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Drainage enhances modern soil carbon contribution but reduces old soil carbon contribution to ecosystem respiration in tundra ecosystems

Warming temperatures are likely to accelerate permafrost thaw in the Arctic, potentially leading to the release of old carbon previously stored in deep frozen soil layers. Deeper thaw depths in combination with geomorphological changes due to the loss of ice structures in permafrost, may modify soil water distribution, creating wetter or drier soil conditions. Previous studies revealed higher ecosystem respiration rates under drier conditions, and this study investigated the cause of the increased ecosystem respiration rates using radiocarbon signatures of respired CO₂ from two drying manipulation experiments: one in moist and the other in wet tundra. We demonstrate that higher contributions of CO₂ from shallow soil layers (0–15 cm; modern soil carbon) drive the increased ecosystem respiration rates, while contributions from deeper soil (below 15 cm from surface and down to the permafrost table; old soil carbon) decreased. These changes can be attributed to more aerobic conditions in shallow soil layers, but also the soil temperature increases in shallow layers but decreases in deep layers, due to the altered thermal properties of organic soils. Decreased abundance of aerenchymatous plant species following drainage in wet tundra reduced old carbon release but increased aboveground plant biomass elevated contributions of autotrophic respiration to ecosystem respiration. The results of this study suggest that drier soils following drainage may accelerate decomposition of modern soil carbon in shallow layers but slow down decomposition of old soil carbon in deep layers, which may offset some of the old soil carbon loss from thawing permafrost.     

Pre-steady-state fluorescence analysis of damaged DNA transfer from human DNA glycosylases to AP endonuclease APE1

Background

DNA glycosylases remove the modified, damaged or mismatched bases from the DNA by hydrolyzing the N-glycosidic bonds. Some enzymes can further catalyze the incision of a resulting abasic (apurinic/apyrimidinic, AP) site through β- or β,δ-elimination mechanisms. In most cases, the incision reaction of the AP-site is catalyzed by special enzymes called AP-endonucleases.

Methods

Here, we report the kinetic analysis of the mechanisms of modified DNA transfer from some DNA glycosylases to the AP endonuclease, APE1. The modified DNA contained the tetrahydrofurane residue (F), the analogue of the AP-site. DNA glycosylases AAG, OGG1, NEIL1, MBD4^cat and UNG from different structural superfamilies were used.

Results

We found that all DNA glycosylases may utilise direct protein–protein interactions in the transient ternary complex for the transfer of the AP-containing DNA strand to APE1.

Conclusions

We hypothesize a fast “flip-flop” exchange mechanism of damaged and undamaged DNA strands within this complex for monofunctional DNA glycosylases like MBD4^cat, AAG and UNG. Bifunctional DNA glycosylase NEIL1 creates tightly specific complex with DNA containing F-site thereby efficiently competing with APE1. Whereas APE1 fast displaces other bifunctional DNA glycosylase OGG1 on F-site thereby induces its shifts to undamaged DNA regions.

General significance

Kinetic analysis of the transfer of DNA between human DNA glycosylases and APE1 allows us to elucidate the critical step in the base excision repair pathway.     

Evidence for key enzymatic controls on metabolism of Arctic river organic matter

Permafrost thaw in the Arctic driven by climate change is mobilizing ancient terrigenous organic carbon (OC) into fluvial networks. Understanding the controls on metabolism of this OC is imperative for assessing its role with respect to climate feedbacks. In this study, we examined the effect of inorganic nutrient supply and dissolved organic matter (DOM) composition on aquatic extracellular enzyme activities (EEAs) in waters draining the Kolyma River Basin (Siberia), including permafrost‐derived OC. Reducing the phenolic content of the DOM pool resulted in dramatic increases in hydrolase EEAs (e.g., phosphatase activity increased >28‐fold) supporting the idea that high concentrations of polyphenolic compounds in DOM (e.g., plant structural tissues) inhibit enzyme synthesis or activity, limiting OC degradation. EEAs were significantly more responsive to inorganic nutrient additions only after phenolic inhibition was experimentally removed. In controlled mixtures of modern OC and thawed permafrost endmember OC sources, respiration rates per unit dissolved OC were 1.3–1.6 times higher in waters containing ancient carbon, suggesting that permafrost‐derived OC was more available for microbial mineralization. In addition, waters containing ancient permafrost‐derived OC supported elevated phosphatase and glucosidase activities. Based on these combined results, we propose that both composition and nutrient availability regulate DOM metabolism in Arctic aquatic ecosystems. Our empirical findings are incorporated into a mechanistic conceptual model highlighting two key enzymatic processes in the mineralization of riverine OM: (i) the role of phenol oxidase activity in reducing inhibitory phenolic compounds and (ii) the role of phosphatase in mobilizing organic P. Permafrost‐derived DOM degradation was less constrained by this initial ‘phenolic‐OM’ inhibition; thus, informing reports of high biological availability of ancient, permafrost‐derived DOM with clear ramifications for its metabolism in fluvial networks and feedbacks to climate.     

Clusterin Is a Potential Lymphotoxin Beta Receptor Target That Is Upregulated and Accumulates in Germinal Centers of Mouse Spleen during Immune Response

Clusterin is a multifunctional protein that participates in tissue remodeling, apoptosis, lipid transport, complement-mediated cell lysis and serves as an extracellular chaperone. The role of clusterin in cancer and neurodegeneration has been extensively studied, however little is known about its functions in the immune system. Using expression profiling we found that clusterin mRNA is considerably down-regulated in mouse spleen stroma upon knock-out of lymphotoxin β receptor which plays pivotal role in secondary lymphoid organ development, maintenance and function. Using immunohistochemistry and western blot we studied clusterin protein level and distribution in mouse spleen and mesenteric lymph nodes in steady state and upon immunization with sheep red blood cells. We showed that clusterin protein, represented mainly by the secreted heterodimeric form, is present in all stromal compartments of secondary lymphoid organs except for marginal reticular cells. Clusterin protein level rose after immunization and accumulated in light zones of germinal centers in spleen - the effect that was not observed in lymph nodes. Regulation of clusterin expression by the lymphotoxin beta signaling pathway and its protein dynamics during immune response suggest a specific role of this enigmatic protein in the immune system that needs further study.     

Sahara: Barrier or corridor? Nonmetric cranial traits and biological affinities of North African late holocene populations

The Garamantes flourished in southwestern Libya, in the core of the Sahara Desert ~3,000 years ago and largely controlled trans-Saharan trade. Their biological affinities to other North African populations, including the Egyptian, Algerian, Tunisian and Sudanese, roughly contemporary to them, are examined by means of cranial nonmetric traits using the Mean Measure of Divergence and Mahalanobis D(2) distance. The aim is to shed light on the extent to which the Sahara Desert inhibited extensive population movements and gene flow. Our results show that the Garamantes possess distant affinities to their neighbors. This relationship may be due to the Central Sahara forming a barrier among groups, despite the archaeological evidence for extended networks of contact. The role of the Sahara as a barrier is further corroborated by the significant correlation between the Mahalanobis D(2) distance and geographic distance between the Garamantes and the other populations under study. In contrast, no clear pattern was observed when all North African populations were examined, indicating that there was no uniform gene flow in the region.