Nested structure acquired through simple evolutionary process

Nested structure, which is non-random, controls cooperation dynamics and biodiversity in plant-animal mutualistic networks. This structural pattern has been explained in a static (non-growth) network models. However, evolutionary processes might also influence the formation of such a structural pattern. We thereby propose an evolving network model for plant-animal interactions and show that non-random patterns such as nested structure and heterogeneous connectivity are both qualitatively and quantitatively predicted through simple evolutionary processes. This finding implies that network models can be simplified by considering evolutionary processes, and also that another explanation exists for the emergence of non-random patterns and might provide more comprehensible insights into the formation of plant-animal mutualistic networks from the evolutionary perspective.     

Embryological ontogeny of aromatase gene expression in Chrysemys picta and Apalone mutica turtles: comparative patterns within and across temperature-dependent and genotypic sex-determining mechanisms

Although the role of aromatase in many estrogen-dependent reproductive and metabolic functions is well documented in vertebrates, its involvement in the ovarian development of species exhibiting temperature-dependent sex determination (TSD) is incompletely understood. This is partly due to the conflicting temporal and spatial pattern of aromatase expression and activity across taxa. To help resolve this ongoing debate, we compared for the first time the embryological ontogeny of aromatase expression in turtles possessing genotypic sex determination (GSD) (Apalone mutica) and TSD (Chrysemys picta) incubated under identical conditions. As anticipated, we found no significant thermal differences in aromatase expression at any stage examined (prior to until the end of the thermosensitive period) in A. mutica. Surprisingly, the same was true for C. picta. When placed in a phylogenetic context, our results suggest that aromatase expression is evolutionarily plastic with respect to sex determination in reptiles, and that differences between reptilian TSD and GSD are not aromatase-driven. Further research across TSD and GSD species is warranted to fully decipher the evolution of functional differences among sex-determining mechanisms.     

Immunohistochemical evidence of cone-based ultraviolet vision in divergent bat species and implications for its evolution

We characterized Fos-like expression patterns in the primary visual cortex (V1) by binocular flicking stimulation with UV light to investigate cone-based UV vision in four bat species representing four lineages: Hipposideros armiger and Scotophilus kuhlii, insectivores using constant frequency (CF) or frequency modulation (FM) echolocation, respectively, and Rousettus leschenaultii and Cynopterus sphinx, cave-roosting and tree-roosting fruit bats, respectively. The optic centre processing the visual image, V1, appears more distinctly immunostaining in S. kuhlii and C. sphinx after 1 h of UV light stimuli while in H. armiger and R. leschenaultii, staining was no more distinct than in corresponding controls. Our immunohistochemical evidence supports differences in the distribution of cone-based UV vision in the order Chiroptera and supports our earlier postulate that due to possible sensory tradeoffs and roosting ecology, defects in the short wavelength opsin genes have resulted in loss of UV vision in CF but not in FM bats. In addition, fruit bats roosting in caves have lost UV vision but not those roosting in trees. Our results thus confirm that bats are a further mammalian taxon that has retained cone-based UV sensitivity in some species.     

Adaptive survival mechanisms and growth limitations of small-stature herb species across a plant diversity gradient

Several biodiversity experiments have shown positive effects of species richness on aboveground biomass production, but highly variable responses of individual species. The well-known fact that the competitive ability of plant species depends on size differences among species, raises the question of effects of community species richness on small-stature subordinate species. We used experimental grasslands differing in species richness (1-60 species) and functional group richness (one to four functional groups) to study biodiversity effects on biomass production and ecophysiological traits of five small-stature herbs (Bellis perennis, Plantago media, Glechoma hederacea, Ranunculus repens and Veronica chamaedrys). We found that ecophysiological adaptations, known as typical shade-tolerance strategies, played an important role with increasing species richness and in relation to a decrease in transmitted light. Specific leaf area and leaf area ratio increased, while area-based leaf nitrogen decreased with increasing community species richness. Community species richness did not affect daily leaf carbohydrate turnover of V. chamaedrys and P. media indicating that these species maintained efficiency of photosynthesis even in low-light environments. This suggests an important possible mechanism of complementarity in such grasslands, whereby smaller species contribute to a better overall efficiency of light use. Nevertheless, these species rarely contributed a large proportion to community biomass production or achieved higher yields in mixtures than expected from monocultures. It seems likely that the allocation to aboveground plant organs to optimise carbon assimilation limited the investment in belowground organs to acquire nutrients and thus hindered these species from increasing their performance in multi-species mixtures.     

Direct anabolic metabolism of three-carbon propionate to a six-carbon metabolite occurs in vivo across tissues and species

Anabolic metabolism of carbon in mammals is mediated via the one- and two-carbon carriers S-adenosyl methionine and acetyl-coenzyme A. In contrast, anabolic metabolism of three-carbon units via propionate has not been shown to extensively occur. Mammals are primarily thought to oxidize the three-carbon short chain fatty acid propionate by shunting propionyl-CoA to succinyl-CoA for entry into the TCA cycle. Here, we found that this may not be absolute as, in mammals, one nonoxidative fate of propionyl-CoA is to condense to two three-carbon units into a six-carbon trans-2-methyl-2-pentenoyl-CoA (2M2PE-CoA). We confirmed this reaction pathway using purified protein extracts provided limited substrates and verified the product via LC-MS using a synthetic standard. In whole-body in vivo stable isotope tracing following infusion of ¹³C-labeled valine at steady state, 2M2PE-CoA was found to form via propionyl-CoA in multiple murine tissues, including heart, kidney, and to a lesser degree, in brown adipose tissue, liver, and tibialis anterior muscle. Using ex vivo isotope tracing, we found that 2M2PE-CoA also formed in human myocardial tissue incubated with propionate to a limited extent. While the complete enzymology of this pathway remains to be elucidated, these results confirm the in vivo existence of at least one anabolic three- to six-carbon reaction conserved in humans and mice that utilizes propionate.     

Mitochondrial DNA and allozymes reveal high dispersal abilities and historical movement across drainage boundaries in two species of freshwater fishes from inland rivers in Queensland, Australia

This study used allozymes and mtDNA variation to test that: 1) populations of two fish species, Nematolosa erebi and Retropinna semoni , in lowland rivers in central Australia were highly connected within drainages, 2) populations in different drainages were highly differentiated and 3) there was evidence of historical connections between two major lowland drainages in inland Australia. Levels of genetic differentiation among populations within drainages were low, but still statistically significant, indicating that populations were not as highly connected as had been predicted. Populations from the Murray–Darling and the Lake Eyre drainages were highly differentiated, indicating no contemporary dispersal across drainage boundaries. Both species showed evidence of historical connections between the two drainage basins, although estimates of the time that these last occurred differed between the two species. Nematolosa erebi populations from the two drainages were estimated to have been separated c . 150 000 years ago, whereas populations of R. semoni , were estimated to have been separated c . 1.5 million years ago.     

BIOMOD – optimizing predictions of species distributions and projecting potential future shifts under global change

A new computation framework (BIOMOD: BIOdiversity MODelling) is presented, which aims to maximize the predictive accuracy of current species distributions and the reliability of future potential distributions using different types of statistical modelling methods. BIOMOD capitalizes on the different techniques used in static modelling to provide spatial predictions. It computes, for each species and in the same package, the four most widely used modelling techniques in species predictions, namely Generalized Linear Models (GLM), Generalized Additive Models (GAM), Classification and Regression Tree analysis (CART) and Artificial Neural Networks (ANN). BIOMOD was applied to 61 species of trees in Europe using climatic quantities as explanatory variables of current distributions. On average, all the different modelling methods yielded very good agreement between observed and predicted distributions. However, the relative performance of different techniques was idiosyncratic across species, suggesting that the most accurate model varies between species. The results of this evaluation also highlight that slight differences between current predictions from different modelling techniques are exacerbated in future projections. Therefore, it is difficult to assess the reliability of alternative projections without validation techniques or expert opinion. It is concluded that rather than using a single modelling technique to predict the distribution of several species, it would be more reliable to use a framework assessing different models for each species and selecting the most accurate one using both evaluation methods and expert knowledge.     

Molecular mechanisms of the polymerization of fibrin and the formation of its three-dimensional network

The results of biochemical, immunochemical, and X-ray studies of the structures of fibrinogen and fibrin molecules were analyzed. The mechanisms of the successive formation of the fibrin three-dimensional network were described: the polymerization of monomeric molecules with the formation of bifilar protofibrils, the lateral association of protofibrils, and the embranchment of the forming fibrils. Data on the electron and confocal microscopy of the polymeric fibrin were considered. The role of the known polymerization centers of fibrin which participated in the formation of protofibrils and their lateral association was discussed. Data on the existence of the previously unknown polymerization centers were given. In particular, the experimental results demonstrated that one of such centers which participated in the formation of protofibrils was located in the Bβ12–46 fragment, and did not require the cleavage of fibrinopeptide B for its functioning. The results of the computer modeling of the spatial structure of the fibrin(ogen) molecule and the intermolecular interactions in the course of the fibrin polymerization were presented. The location of the αC domains in the fibrin(ogen) molecule and their role in the polymerization process were discussed. Information on the structure of the calciumbinding sites of fibrin(ogen) and the functional role of Ca²⁺ in fibrin polymerization was published. The structure of factor XIII(a) and the mechanisms of fibrin stabilization by this factor were briefly described.     

The influence of multiple dispersal mechanisms and landscape structure on population clustering and connectivity in fragmented artesian spring snail populations

Many organisms occupy heterogeneous landscapes that contain both barriers to movement as well as corridors that facilitate dispersal. The extent to which such features determine population connectivity will depend on the mechanisms utilized by organisms to disperse. Here we examined the interaction between landscape structure and dispersal in the endemic aquatic snail, Fonscochlea accepta , in the fragmented artesian spring ecosystem of arid central Australia. We used frequentist and Bayesian analyses of microsatellite data to identify population structure and immigration for 1130 snails sampled from 50 springs across an entire spring complex. We introduce a modified isolation-by-distance analysis to test hypotheses about how populations are clustered and to distinguish the most likely dispersal pathways within and between those clusters. Highly significant differences in F _ST values and significant isolation-by-distance patterns were detected among springs across the entire complex, while Bayesian assignment tests revealed the presence of two hierarchical levels of spring clustering. Clusters were defined by the spatial aggregation of springs, dynamic aquatic habitat connections between springs and the ecology of the snails. Bayesian immigrant identification and our modified isolation-by-distance analysis revealed that dispersal occurs at two geographical scales via two very different mechanisms. Short range dispersal (usually ≤ 300 m) occurs via active movement facilitated by aquatic connections among springs while long-range dispersal (≥ 3 km) is likely facilitated by an animal vector (phoresy). These results underline the importance of both dispersal mode and landscape structure in influencing connectivity rates and patterns among populations.     

Lip anatomy and its implications for the pollination mechanisms of Bulbophyllum species (Orchidaceae)

BACKGROUND AND AIMS: The lip structure of six Brazilian and one Asiatic species of Bulbophyllum with wind-assisted fly pollination (B. involutum, B. ipanemense and B. weddellii) and non-wind-assisted fly pollination (B. epiphytum, B. glutinosum, B. regnellii and B. rothschildianum) was studied to investigate the presence of secretory tissues related to these pollination mechanisms. METHODS: The lip study was carried out through scanning electron microscopy (lip surface) and light microscopy (anatomical features). KEY RESULTS: In most of the species studied, the osmophores (odour glands) were located in the lobes and in the upper surface of the lip callus. Differences in the lip structure were observed between the two groups (the presence of a nectary and the extent of osmophore surface), depending on the mechanism of pollination. Nectaries were found in the cavity callus in B. ipanemense, B. involutum and B. weddellii, even though their pollinators were presumably attracted by the instinct to oviposit. CONCLUSIONS: These findings corroborate the hypothesis that, because pollination in these species is dependent on an unpredictable external factor (wind), nectar is necessary to keep the insect in the flower for a long period. Despite the occurrence of a liquid-like nectar in the flowers of B. epiphytum, B. glutinosum, B. regnelli and B. rothschildianum, no anatomical evidence for nectaries was found in the lips of these species, although a similar structure may occur in another region of the flowers. This observation agrees with the fact that pollination by lip movement in the latter species requires only gravity, with no additional mechanism being needed to keep the flies in the flower.     

Estimating vital statistics and age distributions of measurable soil organic carbon fractions based on their pathway of formation and radiocarbon content

Radiocarbon measurements have been used in combination with "bomb 14C" models to estimate turnover of soil organic carbon fractions. However, the bomb 14C models assume that all SOC fractions are formed directly from external inputs of carbon, which is not always valid because some SOC fractions may receive carbon from other SOC fractions. Due to the continuous inputs of organic carbon, we argue that the most appropriate way to describe the age of SOC is by an age distribution. We developed age distributed models of SOC fractions and derived analytical solutions to them. The models all assume that SOC fraction decay can be described by first-order kinetics, but differ in their assumptions about the pathway of SOC fraction formation. The solutions can be used to estimate age distributions at steady state of different SOC fractions based on their radiocarbon content. These age distributions can be used to calculate the mean age, mean residence time, and other vital statistics of each measurable SOC fraction. Furthermore, if a sequential scheme is used to isolate the SOC fractions, an estimated age distribution of the total SOC can be obtained by adding the contributions of each soil fraction. The age distributions can be very helpful in interpretations of soil organic carbon dynamics in different soils.     

肥胖大鼠模型的建立及其脂代谢相关分子机制研究

目的建立饮食诱导的肥胖(diet-induced obesity,DIO)大鼠模型并初步探讨其发病的分子机制。方法用脂肪含量30%的高脂饲料饲喂雄性SD大鼠25周,观察大鼠体重、Lee’s指数、肝组织病理改变,检测大鼠空腹血糖及空腹血清胰岛素水平,并通过real-time PCR,检测成模大鼠肝脏中乙酰辅酶A羧化酶(ACC)、脂肪酸合酶(FAS)、激素敏感酯酶(HSL)以及固醇调节元件结合蛋白-1c(SREBP-1c)的表达变化。结果高脂饲料饲喂6周后,DIO组大鼠体重、Lee’s指数均显著增加;25周后肝脏脂肪异常蓄积,出现中重度脂肪肝,空腹血糖及胰岛素水平显著升高,出现明显的胰岛素抵抗。肝脏中ACC、FAS和HSL表达显著增加,SREBP-1c表达水平达到正常组的2.56倍,两组间差异极其显著。结论成功建立了DIO大鼠模型,通过检测脂代谢相关基因的表达水平,初步阐释了营养性肥胖的发生与脂代谢变化之间的关系,SREBP-1c,ACC,FAS和HSL参与了DIO的形成,从而初步揭示了脂代谢变化与营养性肥胖的发生的关系。     

Population regulation of territorial species: both site dependence and interference mechanisms matter

Spatial patterns of site occupancy are commonly driven by habitat heterogeneity and are thought to shape population dynamics through a site-dependent regulatory mechanism. When examining this, however, most studies have only focused on a single vital rate (reproduction), and little is known about how space effectively contributes to the regulation of population dynamics. We investigated the underlying mechanisms driving density-dependent processes in vital rates in a Mauritius kestrel population where almost every individual was monitored. Different mechanisms acted on different vital rates, with breeding success regulated by site dependence (differential use of space) and juvenile survival by interference (density-dependent competition for resources). Although territorial species are frequently assumed to be regulated through site dependence, we show that interference was the key regulatory mechanism in this population. Our integrated approach demonstrates that the presence of spatial processes regarding one trait does not mean that they necessarily play an important role in regulating population growth, and demonstrates the complexity of the regulatory process.     

The role of ultraviolet radiation, photosensitizers, reactive oxygen species and ester groups in mechanisms of methane formation from pectin

Ultraviolet (UV) radiation has recently been demonstrated to drive an aerobic production of methane (CH₄) from plant tissues and pectins, as do agents that generate reactive oxygen species (ROS) in vivo independently of UV. As the major building-blocks of pectin do not absorb solar UV found at the earth's surface (i.e. >280 nm), we explored the hypothesis that UV radiation affects pectin indirectly via generation of ROS which themselves release CH₄ from pectin. Decreasing the UV absorbance of commercial pectin by ethanol washing diminished UV-dependent CH₄ production, and this was restored by the addition of the UV photosensitizer tryptophan. Certain ROS scavengers [mannitol, a hydroxyl radical (^•OH) scavenger; 1,4-diazabicyclo[2.2.2] octane; and iodide] strongly inhibited UV-induced CH₄ production from dry pectin. Furthermore, pectin solutions emitted CH₄ in darkness upon the addition of ^•OH, but not superoxide or H₂O₂. Model carbohydrates reacted similarly if they possessed —CH₃ groups [e.g. methyl esters or (more weakly) acetyl esters but not rhamnose]. We conclude that UV evokes CH₄ production from pectic methyl groups by interacting with UV photosensitizers to generate ^•OH. We suggest that diverse processes generating ^•OH could contribute to CH₄ emissions independently of UV irradiation, and that environmental stresses and constitutive physiological processes generating ROS require careful evaluation in studies of CH₄ formation from foliage.     

中枢阿片神经系统对焦虑情绪的调控作用及其机制探讨

吗啡依赖大鼠自发戒断后其主动接触时间和突期舔水次数均显著减少,并可被５－ＨＴ１Ａ受体激动丁螺环酮和色氨酸羟化酸抑制剂对氯苯丙氨酸所对抗。纳曲酮也可使上述两指标降低,并可被吗啡和ＰＣＰＡ所拮抗、被５－羟色氨酸所增强。     

Genomic collinearity and the genetic architecture of floral differences between the homoploid hybrid species Iris nelsonii and one of its progenitors,Iris hexagona

Hybrid speciation represents a relatively rapid form of diversification. Early models of homoploid hybrid speciation suggested that reproductive isolation between the hybrid species and progenitors primarily resulted from karyotypic differences between the species. However, genic incompatibilities and ecological divergence may also be responsible for isolation. Iris nelsonii is an example of a homoploid hybrid species that is likely isolated from its progenitors primarily by strong prezygotic isolation, including habitat divergence, floral isolation and post-pollination prezygotic barriers. Here, we used linkage mapping and quantitative trait locus (QTL) mapping approaches to investigate genomic collinearity and the genetic architecture of floral differences between I. nelsonii and one of its progenitor species I. hexagona. The linkage map produced from this cross is highly collinear with another linkage map produced between I. fulva and I. brevicaulis (the two other species shown to have contributed to the genomic makeup of I. nelsonii), suggesting that karyotypic differences do not contribute substantially to isolation in this homoploid hybrid species. Similar to other studies of the genetic architecture of floral characteristics, at least one QTL was found that explained >20% variance in each color trait, while minor QTLs were detected for each morphological trait. These QTLs will serve as hypotheses for regions under selection by pollinators.     

Confirmation of Escherichia coli and its distinction from Klebsiella species by gas and indole formation at 44 and 44.5 degrees C

AIMS: In the enumeration of coliform bacteria, confirmation of Escherichia coli has been based upon gas and indole production at the elevated incubation temperature. The test for gas production has recently been questioned. The aim of this study was to investigate the impact of gas production test on the reliability of confirmation of E. coli. METHODS AND RESULTS: The impact of several media on growth, gas and/or indole formation was tested at 44 and 44.5 degrees C using 547 environmental isolates. These were mainly E. coli, Klebsiella pneumoniae, K. oxytoca and Enterobacter cloacae strains. Another set of 250 faecal and environmental klebsiellae were tested for their maximum temperature for growth (Tmax) and for gas formation. Escherichia coli and even K. pneumoniae grew well in all the media, but gas production was more dependent on the medium used. Growth of the mainly gas negative Ent. cloacae and K. oxytoca strains was still more sensitive to the medium and incubation conditions. Tryptophan salt broth was the most productive medium for the indole test, followed by lauryl tryptose mannitole and tryptone mannitol ricinoleate broth (TRM). Tmax of K. oxytoca was clearly lower than Tmax of K. pneumoniae but a rather high fraction of its isolates produced indole at 44.5 degrees C. CONCLUSIONS: False-positive E. coli confirmation is possible if gas production is not tested for and the confirmation is based on indole test only. SIGNIFICANCE AND IMPACT OF THE STUDY: Erroneous positive results on routine analysis for E. coli can occur.     

Comparative analyses of complex formation and binding sites between human tumor necrosis factor-alpha and its three antagonists elucidate their different neutralizing mechanisms

Tumor necrosis factor-alpha (TNFα)-blocking therapy, using biologic TNFα antagonists, has been approved for the treatment of several diseases including rheumatoid arthritis, psoriasis and Crohn's disease. There have been few detailed studies of binding characterizations for the complex formation by TNFα and clinically relevant antagonists, particularly Infliximab (Remicade®) and Etanercept (Enbrel®). Here we characterized the binding stoichiometry and size of soluble TNFα–antagonist complexes and identified energetically important binding sites on TNFα for the three antagonists, Etanercept, Infliximab, and the recently developed humanized TNFα neutralizing monoclonal antibody, YHB1411-2. Size-exclusion chromatography and dynamic light scattering analyses revealed that the three antagonists formed distinct thermodynamically stable TNFα–antagonist complexes that exhibited differences in their size and composition. Energetically important binding residues on TNFα were identified for each antagonist by a sequence of experiments that consisted of competition binding assays, fragmentations, loop mutations, and single-point mutations using yeast surface-displayed TNFα, which was further confirmed for solubly purified TNFα mutants by surface plasmon resonance technique. Analyses of the binding geometry based on binding site location, spatial constraints, and valency satisfaction allowed us to interpret the thermodynamically stable complexes as follows: one molecule of Etanercept and one molecule of trimeric TNFα (Etanercept₁––TNFα₁), Infliximab₆–TNFα₃, and YHB1411–2₄-TNFα₂. The distinct features of the soluble antagonist–TNFα complex formation among the antagonists may give further insights into their different neutralizing mechanisms and pharmacokinetic profiles.     

Tetanic contraction induces enhancement of fatigability and sarcomeric damage in atrophic skeletal muscle and its underlying molecular mechanisms

Muscle unloading due to long-term exposure of weightlessness or simulated weightlessness causes atrophy, loss of functional capacity, impaired locomotor coordination, and decreased resistance to fatigue in the antigravity muscles of the lower limbs. Besides reducing astronauts＇ mobility in space and on returning to a gravity environment, the molecular mechanisms for the adaptation of skeletal muscle to unloading also play an important medical role in conditions such as disuse and paralysis. The tail-suspended rat model was used to simulate the effects of weightlessness on skeletal muscles and to induce muscle unloading in the rat hindlimb. Our series studies have shown that the maximum of twitch tension and the twitch duration decreased significantly in the atrophic soleus muscles, the maximal tension of high-frequency tetanic contraction was significantly reduced in 2-week unloaded soleus muscles, however, the fatigability of high- frequency tetanic contraction increased after one week of unloading. The maximal isometric tension of intermittent tetanic contraction at optimal stimulating frequency did not alter in 1- and 2-week unloaded soleus, but significantly decreased in 4-week unloaded soleus. The 1-week unloaded soleus, but not extensor digitorum Iongus （EDL）, was more susceptible to fatigue during intermittent tetanic contraction than the synchronous controls. The changes in K＋ channel characteristics may increase the fatigability during high-frequency tetanic contraction in atrophic soleus muscles. High fatigability of intermittent tetanic contraction may be involved in enhanced activity of sarcoplasmic reticulum Ca2＋-ATPase （SERCA） and switching from slow to fast isoform of myosin heavy chain, tropomyosin, troponin I and T subunit in atrophic soleus muscles. Unloaded soleus muscle also showed a decreased protein level of neuronal nitric oxide synthase （nNOS）, and the reduction in nNOS-derived NO increased frequency of calcium sparks and elevated intracellular resting Ca2＋ concentration （[Ca2＋]i） in unloaded soleus muscles. High [Ca2＋]i activated calpain-1 which induced a higher degradation of desmin. Desmin degradation may loose connections between adjacent myofibrils and further misaligned Z-disc during repeated tetanic contractions. Passive stretch in unloaded muscle could preserve the stability of sarcoplasmic reticulum Ca2＋ release channels by means of keeping nNOS activity, and decrease the enhanced protein level and activity of calpain to control levels in unloaded soleus muscles. Therefore, passive stretch restored normal appearance of Z-disc and resisted in part atrophy of unloaded soleus muscles. The above results indicate that enhanced fatigability of high-frequency tetanic contraction is associated to the alteration in K＋ channel characteristics, and elevated SERCA activity and slow to fast transition of myosin heavy chain （MHC） isoforms increases fatigability of intermittent tetanic contraction in atrophic soleus muscle. The sarcomeric damage induced by tetanic contraction can be retarded by stretch in atrophic soleus muscles.