Presynaptic tubular structures in photoreceptor cells

Summary After the application of fixatives including phosphotungstic acid or a mixture of osmium tetroxide and zinc iodide, complex tubular structures are evident in the presynaptic side of the synapses between photoreceptor and bipolar cells of the rat's retina. In the first case only the limiting membranes are visualized, while in the second only the content of the tubules is stained. These tubules seem to be related, on a morphological ground, with the formation of synaptic vesicles. These tubular structures are not observed when fixation is done with osmium tetroxide or glutaraldehyde-osmium tetroxide.This work has been supported by grants from the Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina, and from National Institutes of Health, U.S.A., (5 RO1 NS 06953-05 NEUA).We want to express our gratitude to Mrs. Haydée Agoff de Zimman and Mr. Alberto Saénz for their skillful technical assistance.     

Evolution vs the number of gene copies per primitive cell

Summary Computer simulations are presented of the rate at which an advantageous mutant would displace the prototype in a replicating system without an accurate segregation mechanism. If the number of gene copies in the system is indefinitely large, Darwinian evolution is essentially stopped because there is no coupling of phenotype with genotype, i.e., there is no growth advantage to the advantageous gene relative to the prototype and therefore no survival of the fittest. The inhibition of evolution due to a number of gene copies<100 would have been not insurmountable. Although the presence of multiple copies would have allowed replacement by an advantageous mutant, it provided a way for the primitive cell to conserve less immediately useful genes that could evolve into different or more effective genes. This possibility was lost as accurate segregation mechanisms evolved and cells with few copies of each gene, such as modern procaryotes, arose.     

Good predictors for the fixation probability on complex networks of multi-player games using territorial interactions

In 2012 Broom and Rychtar developed a new framework to consider the evolution of a population over a non-homogeneous underlying structure, where fitness depends upon multiplayer interactions amongst the individuals within the population played in groups of various sizes (including one). This included the independent model, and as a special case the territorial raider model, which has been considered in a series of subsequent papers. Here individuals are based upon the vertex of a graph but move to interact with their neighbours, sometimes meeting in large groups. The most important single property of such populations is the fixation probability, the probability of a single mutant completely replacing the existing population. In a recent paper we considered the fixation probability for the Birth Death Birth (BDB) dynamics for three games, a Public Goods game, the Hawk–Dove game and for fixed fitnesses for a large number of randomly generated graphs, in particular seeing if important underlying graph properties could be used as predictors. We found two good predictors, temperature and mean group size, but some interesting and unusual features for one type of graph, Barabasi–Albert graphs. In this paper we use a regression analysis to investigate (the usual) three alternative evolutionary dynamics (BDD, DBB, DBD) in addition to the original BDB. In particular, we find that the dynamics split into two pairs, BDB/DBD and BDD/DBB, each of which give essentially the same results and found a good fit to the data using a quadratic regression involving the above two variables. Further we find that temperature is the most important predictor for the Hawk–Dove game, whilst for the Public Goods game the group size also plays a key role, and is more important than the temperature for the BDD/DBB dynamics.     

Two methods for proteomic analysis of formalin‐fixed,paraffin embedded tissue result in differential protein identification,data quality,and cost

Formalin‐fixed paraffin‐embedded (FFPE) tissue is a rich source of clinically relevant material that can yield important translational biomarker discovery using proteomic analysis. Protocols for analyzing FFPE tissue by LC‐MS/MS exist, but standardization of procedures and critical analysis of data quality is limited. This study compared and characterized data obtained from FFPE tissue using two methods: a urea in‐solution digestion method (UISD) versus a commercially available Qproteome FFPE Tissue Kit method (Qkit). Each method was performed independently three times on serial sections of homogenous FFPE tissue to minimize pre‐analytical variations and analyzed with three technical replicates by LC‐MS/MS. Data were evaluated for reproducibility and physiochemical distribution, which highlighted differences in the ability of each method to identify proteins of different molecular weights and isoelectric points. Each method replicate resulted in a significant number of new protein identifications, and both methods identified significantly more proteins using three technical replicates as compared to only two. UISD was cheaper, required less time, and introduced significant protein modifications as compared to the Qkit method, which provided more precise and higher protein yields. These data highlight significant variability among method replicates and type of method used, despite minimizing pre‐analytical variability. Utilization of only one method or too few replicates (both method and technical) may limit the subset of proteomic information obtained.     

Fluorocitrate,an Inhibitor of Glial Metabolism,Inhibits the Up-Regulation of NOS Expression,Activity and NO Production in the Spinal Cord Induced by Formalin Test in Rats

Previous experiments have suggested that nitric oxide plays an important role in nociceptive transmission in the spinal cord. In order to explore the involvement of glia in the NO-mediated nociceptive transmission, the present study was undertaken to investigate the effect of fluorocitrate (FC), an inhibitor of glial metabolism, on NOS expression and activity and NO production in the spinal cord during the process of peripheral inflammatory pain and hyperalgesia induced by formalin test in rats. Sixty adult male Sprague–Dawley rats were randomly assigned into sham, formalin, formalin + normal saline (NS), and formalin + FC groups. The NOS expression, NOS activity and NO production was detected by NADPH-d histochemistry staining, NOS and NO assay kit, respectively. It was found that formalin test significantly up-regulated NOS expression and activity and NO production in the laminae I–II of the dorsal horn and the grey matter around the central canal in the lumbar spinal cord at 1 h after the formalin test. Selective inhibition of glia metabolism with intrathecal administration of FC (1 nmol) significantly inhibited the up-regulation in NOS expression and activity and NO production normally induced by the formalin test, which was represented with decreases in the number and density of the NADPH-d positive cells in the dorsal horn and grey matter around the central canal, and decrease in density of NADPH-d positive neuropil in the dorsal horn in formalin + FC group compared with formalin group. The results suggested that glia may be involved in the NO-mediated nociceptive transmission in the spinal cord. X.-C. Sun, W.-N. Chen and S.-Q. Li contributed equally to this work.     

Chromosome shattering: a mitotic catastrophe due to chromosome condensation failure

Chromosome shattering has been described as a special form of mitotic catastrophe, which occurs in cells with unrepaired DNA damage. The shattered chromosome phenotype was detected after application of a methanol/acetic acid (MAA) fixation protocol routinely used for the preparation of metaphase spreads. The corresponding phenotype in the living cell and the mechanism leading to this mitotic catastrophe have remained speculative so far. In the present study, we used V79 Chinese hamster cells, stably transfected with histone H2BmRFP for live-cell observations, and induced generalized chromosome shattering (GCS) by the synergistic effect of UV irradiation and caffeine posttreatment. We demonstrate that GCS can be derived from abnormal mitotic cells with a parachute-like chromatin configuration (PALCC) consisting of a bulky chromatin mass and extended chromatin fibers that tether centromeres at a remote, yet normally shaped spindle apparatus. This result hints at a chromosome condensation failure, yielding a “shattered” chromosome complement after MAA fixation. Live mitotic cells with PALCCs proceeded to interphase within a period similar to normal mitotic cells but did not divide. Instead they formed cells with highly abnormal nuclear configurations subject to apoptosis after several hours. We propose a factor depletion model where a limited pool of proteins is involved both in DNA repair and chromatin condensation. Chromosome condensation failure occurs when this pool becomes depleted. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. This article has been submitted as a contribution to the festschrift entitled “Uncovering cellular sub-structures by light microscopy” in honour of Professor Cremer’s 65th birthday.     

Continuous Probabilistic Analysis to Evolutionary Game Dynamics in Finite Populations

Evolutionary game dynamics of two strategies in finite population is studied by continuous probabilistic approach. Besides frequency dependent selection, mutation was also included in this study. The equilibrium probability density functions of abundance, expected time to extinction or fixation were derived and their numerical solutions are calculated as illustrations. Meanwhile, individual-based computer simulations are also done. A comparison reveals the consistency between theoretical analysis and simulations.     

Plant cytoplasm preserved by lightning

Usually only an organism with hard parts may be preserved in the fossil record. Cytoplasm, which is a physiologically active part of a plant, is rarely seen in the fossil record. Two Cretaceous plant fossils older than 100 million years with exceptional preservation of cytoplasm are reported here. Some cytoplasm is well preserved with subcellular details while other cytoplasm is highly hydrolyzed in the cortex of the same fossil even though both of preservations may be less than 2 microm away. The unique preservation pattern, sharp contrast of preservation in adjacent cells and the exceptional preservation of cytoplasm in the cortex suggest that lightning should play an important role in the preservation of cytoplasm and that cytoplasmic membranes may be more stable than the cell contents. Interpreting the preservation needs knowledge scattering in several formerly unrelated fields of science, including geophysics, botany, biophysics, cytology and microwave fixation technology. This new interpretation of fossilization will shed new light on preservation of cytoplasm and promote cytoplasm fossils from a position of rarity to a position of common research objects available for biological research. The importance of the identification of cytoplasm in fossil lies not in itself but in how much it influences the future research in paleobotany.     

Root growth and functioning under atmospheric CO2 enrichment

This paper examines the extent to which atmospheric CO₂ enrichment may influence growth of plant roots and function in terms of uptake of water and nutrients, and carbon allocation towards symbionts. It is concluded that changes in dry matter allocation greatly depend on the experimental conditions during the experiment, the growth phase of the plant, and its morphological characteristics. Under non-limiting conditions of water and nutrients for growth, dry matter partitioning to the root is not changed by CO₂ enrichment. The increase in root/shoot ratio, frequently observed under limiting conditions of water and/or nutrients, enables the plant to explore a greater soil volume, and hence acquire more water and nutrients. However, more data on changes in dry matter allocation within the root due to atmospheric CO₂ are needed. It is concluded that nitrogen fixation is favored by CO₂ enrichment since nodule mass is increased, concomitant with an increase in root length. The papers available so far on the influence of CO₂ enrichment on mycorrhizal functioning suggest that carbon allocation to the roots might be increased, but also here more experiments are needed.Abbreviations LAR leaf area ratio - LWR leaf weight ratio - SWR stem weight ratio - RGR relative growth rate - R/S root/shoot - RWR root weight ratio     

Natural abundance of 15N in soils along forest-to-pasture chronosequences in the western Brazilian Amazon Basin

We examined the natural abundance of ¹⁵N in soil profiles along two chronosequences in the western Brazilian Amazon Basin state of Rondônia, to investigate possible mechanisms for changes to soil nitrogen sources and transformations that occur as a result of land use. One chronosequence consisted of forest and 3-, 5- and 20-year-old pasture, the other of forest and 8- and 20-year-old pasture. The ¹⁵N values of surface soil and soil to 1 m depth in the native forest ranged from 9.8 to 13.6 and were higher than reported for temperate forest soils. Fractionation associated with nitrification and denitrification and selective losses of ¹⁵N-depleted nitrate, could potentially result in a strong enrichment of nitrogen in soil organic matter over the time scale of soil development in highly weathered tropical soils. Pasture surface soils were 1–3, depleted in ¹⁵N compared with forest soils. Lower ¹⁵N values in 20-year-old pastures is consistent with greater cumulative inputs of ¹⁵N-depleted atmospheric-derived nitrogen, fixed by free-living bacteria associated with planted pasture grasses in older pastures, or differential plant utilization of soil inorganic N pools with different ¹⁵N values. The pattern of ¹⁵N values following conversion of forest to agricultural use differs from the pattern in the temperate zone, where pasture or cultivated soils are typically more enriched in ¹⁵N than the forest soils from which they were derived.