Modeling for evolving biological networks with scale-free connectivity, hierarchical modularity, and disassortativity

We propose a growing network model that consists of two tunable mechanisms: growth by merging modules which are represented as complete graphs and a fitness-driven preferential attachment. Our model exhibits the three prominent statistical properties are widely shared in real biological networks, for example gene regulatory, protein-protein interaction, and metabolic networks. They retain three power law relationships, such as the power laws of degree distribution, clustering spectrum, and degree-degree correlation corresponding to scale-free connectivity, hierarchical modularity, and disassortativity, respectively. After making comparisons of these properties between model networks and biological networks, we confirmed that our model has inference potential for evolutionary processes of biological networks.     

Invertebrate dispersal and habitat heterogeneity: Expression of biological traits in a seagrass landscape

Seagrass meadows harbour diverse faunal assemblages, but the relative importance of landscapes attributes, settlement processes and biological traits of individual species for recruitment patterns is poorly understood. To quantify the influence of habitat heterogeneity on larval, juvenile and adult post-larval dispersal, invertebrates (> 125 µm) were collected in benthic settlement traps at five occasions (June-August) in three habitats; continuous seagrass, seagrass patches and bare sand. The study was carried out by SCUBA diving in a subtidal (2.5 m depth) seagrass landscape dominated by Zostera marina L. in the Baltic Sea. Traps collected totally > 30 taxa, with non-significant effects of habitat on species richness and total abundance. Total number of invertebrates exhibited strong temporal variability, probably driven by wind-induced bedload and water column transport. Surprisingly, traps located in small (< 12 m²) patches contained on average almost twice as many individuals as traps located in the continuous vegetation. Dominating taxa such as nematodes, copepods, and oligochaetes were found in similar densities across the landscape. In contrast, location within the landscape had strong effects on bivalve settlement and redistribution patterns, resulting in significantly lower densities in continuous vegetation compared to patches and bare sand. A biological trait analysis indicated that semi-mobile taxa with annual protracted direct development, and short-distance dispersal are probably of higher importance for the community assembly process in this environment than long-distance larval dispersal. Results suggest that seagrass landscapes are highly dynamic environments, characterized by time and species-specific effects of landscape attributes on animal dispersal and recruitment. A conceptual model illustrating interactions between settling larvae and landscape heterogeneity is presented.     

一株沙门氏菌裂解性噬菌体的分离鉴定及生物学特性

【目的】从贝类样品中分离到一株沙门氏菌裂解性噬菌体SLMP1,对其进行鉴定及生物学特性分析。【方法】采用双层平板法从贝类样品中分离沙门氏菌噬菌体SLMP1,观察噬菌斑特征,分析SLMP1的宿主范围;利用聚乙二醇8000沉淀浓缩SLMP1颗粒,用氯化铯等密度梯度离心纯化;采用透射电子显微镜观察纯化的SLMP1颗粒;采用酚-氯仿法提取SLMP1核酸,通过核酸酶处理分析核酸类型;分析SLMP1的热稳定性、pH稳定性、最佳感染复数、一步生长曲线及裂菌效果。【结果】SLMP1噬菌斑直径约2–3 mm,圆形透明、边缘清晰;SLMP1能裂解肠沙门氏菌肠亚种和鼠伤寒沙门氏菌;SLMP1头部呈二十面体,直径约62 nm,含非收缩性尾部,尾长约110 nm,属于长尾病毒科;SLMP1核酸为双链DNA;SLMP1在30–60 °C稳定,在pH 4.0–11.0稳定,最佳感染复数为0.001,感染宿主菌潜伏期为10 min、裂解期为120 min、裂解量为51;SLMP1在液体环境中具有良好的裂菌效果。【结论】SLMP1属dsDNA长尾科裂解性噬菌体,具有沙门氏菌生物抑菌剂的应用潜力。     

Design,synthesis and biological activity of a novel ethylenediamine derivatives as H1 receptor antagonists

In this study, a series of novel ethylenediamine compounds were obtained by structural modification of the lead compounds with thonzylamine, and using the principle of modifying by bioisostere formation and modification with alkyl groups. In vitro assay, the biological activities showed that the target compounds have good properties in inhibiting mast cell degranulation and releasing histamine and β-aminohexidase, such as the compounds 5c, 5g, 5k, 5l and 5o, especially of compound 5k to mast cell degranulation is IC₅₀ = 0.0106 ± 0.001 μmol?L^?1, histamine release was IC₅₀ = 0.0192 ± 0.005 μmol?L^?1 and β-hexosaminidase release was IC₅₀ = 0.0455 ± 0.002 μmol?L^?1 in vitro. At the same time, in vivo biological activities assay results showed that have a good Histamie induce bronchospasm effect with relatively long duration and good protective effect in vivo, among which the protective effect of compound 5k was 79.74 ± 0.30%, compounds 5c, 5g, 5k, 5l and 5o could inhibit the capillary permeability of increasing which were caused by histamine.     

FDS,a novel saponin isolated from Felicium decipiens: Lectin interaction and biological complementary activities

Filicium decipiens saponin (FDS) is the first saponin purified from F. decipiens seeds using ion-exchange and gel filtration chromatographies. In the present study, FDS and the aqueous crude extract of F. decipiens seeds were examined for their antifungal properties, hemolytic/cytotoxicity activity. The dried seeds were powdered and homogenized in 10% (w/v) for the preparation of crude extract. Sample obtained from Sephadex-LH-20 demonstrated FDS with a peak at 752.35 g/mol. FDS showed the highest toxicity against Aspergillus flavus, presenting with a low fungicidal concentration at 12.8 μg/mL. Under hemolytic induction, rabbit and cow erythrocytes were more affected by both samples, and the inhibition effect of PpyLL lectin was observed. These characteristics provide fundamental understanding of F. decipiens secondary metabolites, which would benefit future research to prevent dangerous traditional uses and provide agricultural solution.     

The biological standard of living (and its convergence) in Colombia, 1870–2003: A tropical success story

During the 20th century, the evolution of the biological standard of living in Colombia was a tropical success story from the point of view of the secular increase in height as well as the reduction of inequality. During the period 1905-1985 the average height of females and males increased by nearly 9 cm on the basis of 9 million records examined from National Identification Cards. We also study the evolution of height of Colombians on the basis of passport records. The elite group of passport holders was much taller than average, and remained stable for the birth cohorts of 1870-1919. In the early 20th century the height of passport recipients was 168.7 cm (men) and 158 cm (women) compared with 162 cm and 150 cm for heights in the national ID cards. The results also show that Colombians experienced significant regional and intrapersonal convergence in height.     

Genetic analysis of an introduced biological control agent reveals temporal and geographic change,with little evidence of a host mediated shift

The evolution of introduced biological control agents is largely un-explored. Although much is theorized, there is little empirical evidence quantifying the evolutionary dynamics of a biocontrol agent after release into a new environment. In this study we use Diachasmimorpha tryoni, a purposefully introduced biocontrol agent of Ceratitis capitata, to model and quantify spatial, temporal, and host-related evolutionary patterns. This parasitoid has undergone a host shift in its introduced environment, Hawaii, to the gall forming weed biocontrol agent, Eutreta xanthochaeta, an interaction likely mediated by competition for C. capitata with the egg-larval parasitoid Fopius arisanus. To elucidate potential evolutionary patterns we analyzed microsatellites and sequence data extracted from Hawaii and Australian population clusters defined by Structure, in Genepop, Canoco, and IBDWS. Our analysis revealed structuring of Hawaiian D. tryoni populations as defined by significant historic influences related to temporal structure, geographic space, host guild, and augmentative releases. The host-shift parasitoids were not genetically distinct from other Hawaii populations. There were small changes in microsatellite DNA at the population level, but only between Australia and Hawaii populations, not at the host level. These results show that D. tryoni has not undergone host-mediated evolution since introduction to Hawaii, despite the fact that they have expanded their host range in Hawaii to include the gall-forming E. xanthochaeta. To our knowledge this is the first study to quantify genetic differentiation of a biological control agent over geographic space and time using contemporary and museum specimens.     

Synthesis,biological evaluation and molecular modeling of a novel series of fused 1,2,3-triazoles as potential anti-coronavirus agents

Synthesis and biological evaluation of a novel library of fused 1,2,3-triazole derivatives are described. The in-house developed multicomponent reaction based on commercially available starting materials was applied and broad biological screening against various viruses was performed, showing promising antiviral properties for compounds 14d, 14n, 14q, 18f and 18i against human coronavirus 229E. Further in silico studies identified the key molecular interactions between those compounds and the 3-chymotrypsin-like protease, which is essential to the intracellular replication of the virus, supporting the hypothesis that the protease is the target molecule of the potential antiviral derivatives.     

TCDD as a biological response modifier for Mitomycin C: oxygen tension affects enzyme activation, reactive oxygen species and cell death

TCDD was assessed as a biological response modifier for increasing MMC cytotoxicity through aryl hydrocarbon receptor (AhR) activation and increasing levels of bioreductive enzymes. Human MCF-7 cells were exposed to TCDD, MMC and combinations thereof under aerobic or hypoxic conditions. Cytotoxicity, enzyme activities (NQO1, XO, XDH, CYPR, CYP1A, GST and UGT) and intracellular reactive oxygen species (ROS) were subsequently measured. Under aerobic conditions, TCDD alone had no significant toxicity but combinations of TCDD and MMC significantly increased cell death. LD50 values were: MMC alone, 0.89 +/- 0.04 microM; TCDD co-treatment, 0.26 +/- 0.007 microM (P = 0.008 vs. MMC alone) and TCDD pre-treatment, 0.04 +/- 0.01 microM (P = 0.003 vs. MMC alone). Under hypoxia, TCDD itself caused significant cell death, likely due to increased ROS, but no combinations of MMC/TCDD altered the LD50 of MMC. Significant changes in enzyme activities were caused by TCDD under aerobic but not hypoxic conditions while MMC decreased the activity of its activating enzymes regardless of oxygen tension. Greater toxicity of MMC/TCDD combinations in aerobic culture, were most likely mediated by increased levels of bioreductive enzymes caused through AhR activation. Data presented herein also demonstrate that low oxygen tension decreases AhR activation and signaling and increases the inherent toxicity of TCDD.     

Neuronal targeting, internalization, and biological activity of a recombinant atoxic derivative of botulinum neurotoxin A

Non-toxic derivatives of botulinum neurotoxin A (BoNT/A) have potential use as neuron-targeting delivery vehicles, and as reagents to study intracellular trafficking. We have designed and expressed an atoxic derivative of BoNT/A (BoNT/A ad) as a full-length 150 kDa molecule consisting of a 50 kDa light chain (LC) and a 100 kDa heavy chain (HC) joined by a disulfide bond and rendered atoxic through the introduction of metalloprotease-inactivating point mutations in the light chain. Studies in neuronal cultures demonstrated that BoNT/A ad cannot cleave synaptosomal-associated protein 25 (SNAP25), the substrate of wt BoNT/A, and that it effectively competes with wt BoNT/A for binding to endogenous neuronal receptors. In vitro and in vivo studies indicate accumulation of BoNT/A ad at the neuromuscular junction of the mouse diaphragm. Immunoprecipitation studies indicate that the LC of BoNT/A ad forms a complex with SNAP25 present in the neuronal cytosolic fraction, demonstrating that the atoxic LC retains the SNAP25 binding capability of the wt toxin. Toxicity of BoNT/A ad was found to be reduced approximately 100,000-fold relative to wt BoNT/A.     

Some dynamics of spread and infection by aeciospores of Puccinia punctiformis,a biological control pathogen of Cirsium arvense

Systemic disease of Cirsium arvense caused by Puccinia punctiformis depends on teliospores, from telia that are formed from uredinia, on C. arvense leaves. Uredinia result from infection of the leaves by aeciospores which are one main source of dispersal of the fungus. However, factors governing aeciospore spread, germination, infection, and conversion to uredinia and telia have not been extensively investigated. In this study, effective spread of aeciospores from a source area in a field was fitted to an exponential decline model with a predicted maximum distance of spread of 30 m from the source area to observed uredinia on one leaf of one C. arvense shoot. However, the greatest number of shoots bearing leaves with uredinia/telia was observed within 12 m of the source area, and there were no such shoots observed beyond 17 m from the source area. Aeciospore germination under laboratory conditions was low, with a maximum of about 10%. Temperatures between 18 °C and 25 °C were most favorable for germination with maximum germination at 22 °C. Temperature and dew point data collected from the Frederick, MD airport indicated that optimum temperatures for aeciospore germination occurred in late spring from about May 18 to June 20. Dew conditions during this period were favorable for aeciospore germination. A total of 122 lower leaves, 2 per shoot, on 61 C. arvense shoots were individually inoculated in a dew tent in a greenhouse by painting suspensions of aeciospores onto the leaves. Of these inoculated leaves, 47 produced uredinia within an average of 21.2 ± 6.9 days after inoculation. Uredinia were also produced, in the absence of dew, on 17 non-inoculated leaves of 12 shoots. These leaves were up to 4 leaves above leaves on the same shoots that had been individually and separately inoculated. Results of PCR tests for the presence of the fungus in non-inoculated leaves that were not bearing uredinia, showed that 44 leaves above inoculated leaves on 27 shoots were positive for the presence of the fungus. These leaves were up to 5 leaves above inoculated leaves on the same shoot. Uredinia production and positive PCR results on leaves above inoculated leaves on the same shoot indicated that aeciospore infection was weakly systemic. In other tests in which all leaves of plants were spray-inoculated with aeciospores, uredinia were produced by 10 days after inoculation and converted to telia and sole production of teliospores in about 63 days after inoculation. Successful systemic aeciospore infections in late spring would be expected to result in uredinia production in excess of a 1:1 ratio of aeciospore infections to uredinia and ultimately telia production in late summer. In this manner, systemic aeciospore infections would promote increased density of telia that lead to systemic infections of roots in the fall.     

Design,synthesis, nuclear localization,and biological activity of a fluorescent duocarmycin analog,HxTfA

HxTfA 4 is a fluorescent analog of a potent cytotoxic and antimalarial agent, TfA 3, which is currently being investigated for the development of an antimalarial vaccine, PlasProtect®. HxTfA contains a p-anisylbenzimidazole or Hx moiety, which is endowed with a blue emission upon excitation at 318?nm; thus enabling it to be used as a surrogate for probing the cellular fate of TfA using confocal microscopy, and addressing the question of nuclear localization. HxTfA exhibits similar selectivity to TfA for A-tract sequences of DNA, alkylating adenine-N3, albeit at 10-fold higher concentrations. It also possesses in vitro cytotoxicity against A549 human lung carcinoma cells and Plasmodium falciparum. Confocal microscopy studies showed for the first time that HxTfA, and by inference TfA, entered A549 cells and localized in the nucleus to exert its biological activity. At biologically relevant concentrations, HxTfA elicits DNA damage response as evidenced by a marked increase in the levels of γH2AX observed by confocal microscopy and immunoblotting studies, and ultimately induces apoptosis.     

Specific oxygen, ammonia, and nitrate uptake rates of a biological nutrient removal process treating elevated salinity wastewater

Anaerobic/anoxic/aerobic systems inoculated without and with NaCl acclimated cultures, i.e., Models A and B, respectively, were fed with a synthetic wastewater at various salinity levels. After achieving a steady state, the systems were shocked with 70 g/l NaCl for four consecutive days before returning to pre-shock conditions. At the steady-state, the specific oxygen uptake rates (SOURs) increased with an increase of sodium chloride concentration (from 5.40 to 9.72 mg O₂/g mixed liquor suspended solids (MLSS)-h at 0–30 g/l NaCl for Model A and from 6.84 to 17.64 mg O₂/g MLSS-h at 5–30 g/l NaCl for Model B). In contrast, the specific ammonia uptake rate (SAUR) and specific nitrate uptake rate (SNUR) decreased with increasing chloride concentration (from 4.76 to 2.14 mg NH₃–N/g MLSS-h and 2.50 to 1.22 NO3–N/g MLSS-h, for Model A, and from 3.84 to 2.71 mg NH₃–N/g MLSS-hr and 2.54 to 1.82 mg NO₃–N/g MLSS-hr, for Model B). During the shocked period, the SOUR in most scenarios increased whereas the SAUR and SNUR tended to decrease. The impact of the chloride shock on nitrifiers was more obvious than on denitrifiers; however, after a certain recovery period, the activities of both nitrifiers and denitrifiers in terms of SAUR and SNUR were approximately the same as those prior to shock.     

Physical, chemical and microscopic characterization of a new starch from chayote (Sechium edule) tuber and its comparison with potato and maize starches

In this work, the chayote tuber starch (CHS) was isolated and its chemical composition and its physical and microscopic characteristics were determined, and compared with potato (PS) and maize (MS) starches. The starch content in chayote tubers (728 g kg⁻¹ dry weight) was similar to potato tubers (700 g kg⁻¹ dry weight), with a high level of purity (>98%), while its phosphorous content was higher (0.15%) than PS (0.08%) and MS (0.01%). Starch granules were oval, irregular, truncated and rounded with sizes between 7 and 50 μm with smooth surfaces. CHS dispersions (1% and 4%, w/w) showed higher viscosity (75 and 1715 mPa s), than PS (350% and 50% lower) and MS (715% and 600% lower). The gelatinization temperature (65 to 74 °C) was similar in CHS and PS. The pasting properties (RVA) of the starches suggest that CHS showed better characteristics than the commercial potato and maize starches. Therefore, CHS could be used as a thickening agent and a substitute to PS in food dispersions where a high viscosity is needed.     

Release and establishment of a biological control agent, Psyllaephagus pilosus for eucalyptus psyllid (Ctenarytaina eucalypti) in Ireland

An Australian parasitoid wasp, Psyllaephagus pilosus, was collected from a previous release site in France and introduced into a commercial eucalyptus foliage plantation in Co. Kerry in the south west of Ireland to control the eucalyptus (blue gum) psyllid Ctenarytaina eucalypti. The first parasitised psyllid nymphs were observed 26 days after the release was made in late May 1998, and 49 days elapsed before a new generation of adult parasitoids was seen. Visually assessed indices of psyllid parasitism and adult wasp incidence were used to quantify the pattern of adult dispersion and establishment. A second generation of adult wasps emerged in late August, initiating a rapid spread of parasitism throughout the release site during September that culminated in a peak rate of almost 100% parasitism by late October. Subsequently by the end of 1998, an apparently random process of dispersion and successful natural colonisation occurred at eight out of ten monitored plantations at distances up to 70 km from the release point. The first colonisers of the other two sites arrived very late in 1998, and consequently failed to establish viable populations by the following summer. Probably this failure was because the small numbers of colonisers had arrived too late in the growing season to effect population establishment before the onset of winter. Assisted introductions were, therefore, made at these sites in June and August 1999, respectively. Once fully established, the parasitoid had no difficulty in surviving winter conditions at all monitored sites and demonstrated excellent potential as a biological control agent.     

Aquatic biota as potential biological indicators of the contamination,bioaccumulation and health risks caused by organochlorine pesticides in a large,shallow Chinese lake (Lake Chaohu)

Aquatic biota have long been recognized as bioindicators of the contamination caused by hydrophobic organic contaminants (HOCs) in aquatic environments. The primary purpose of the present study is to identify which species of aquatic biota are the most sensitive to organochlorine pesticides (OCPs) in Lake Chaohu and can therefore serve as indicators of the lake's health and assist in the assessment of OCPs risks to human health. OCP levels in eight species of aquatic biota were measured using GC–MS, and the relationships between the biota and OCP levels in the water and suspended solids were studied. DDTs pose potential human health risks and were the predominant OCP components found in the aquatic biota. DDT had the highest mean bioaccumulation factor (BAF) and biota suspended solids accumulation factor (BSSAF) of all of the studied OCP components. The food web magnification factors (FWMF) for p, p′-DDT were greater than 1, implying that biomagnification occurred. This finding indicates that DDTs still pose a serious threat to the ecosystem and human health in Lake Chaohu, even though the agricultural application of DDT powder has been officially banned since 1983. There were significant positive relationships between OCPs levels in Culter erythropterus and those in both water and suspended solids, as well as between OCPs levels in Protosalanx hyalocranius and those in suspended solids. This finding suggests that C. erythropterus and P. hyalocranius are the most sensitive aquatic biota to OCPs and may serve as the most effective bioindicators for monitoring OCP contamination in the water and suspended solids of Lake Chaohu. Megalobrama amblycephala, which contained the highest wet weight mean OCP concentration, is the most sensitive OCP indicator and can be used to assess the human carcinogenic risk of OCPs in Lake Chaohu.     

Formulation of a coupled mechanism between solute diffusion,phosphatase-kinase reactions and membrane potentials for the primary active transport of phosphorylated substrates through biological membranes

Coupled interrelations occurring between a phosphatase/kinase reaction sequence acting in unstirred layers and on both sides of a charged biomembrane pore structure are presented as a plausible kinetic model for the primary active transport of phosphorylated molecules. Simulations conducted at the cell level and with credible numerical values demonstrate that the enzymes positions strongly regulate the membrane permeability for the transported substrate. Depending on both the enzymes positions (more or less far from the membrane) and the membrane charges, the membrane may appear either impervious, either permeable or able to actively transport a phosphorylated substrate. Globally all happens as if, in function of the enzymes positions, a permanent pore may be regulated, changing from a more closed to a more open conformation.     

Prevalence,incidence and molecular characterization of tape worms in Al Taif governorate,KSA and the effectiveness of Spirulina platensis as a biological control in vitro

Cestoda is a class of parasitic worms in the flatworm phylum (Platyhelminthes). Most of the species-and the best-known-are those in the subclass Eucestoda; they are ribbon-like worms as adults, known as tapeworms. The results reported that about 9.94% of selected sheep were infected with tape worms in native breed. Concerning the seasonal incidence of tape worms among sheep, the results revealed that the highest percentage was recorded during winter season (11.3%), while the lowest percentage was recorded during the spring (7.72%). The species of tape worms recorded were Moniezea expansa, Moniezea benedene, Avitellina centripunctata, Thysaniezia giardia and Stilesia hepatic. Molecular characterization of Al Taif Moniezia species cox1 gene records four different species Me Taif1, Me Taif2, Me Taif3 and Me Taif4, that have identity ranged from 90 to 99% to species in Senegal and Ethiopia (Me13, Me14 and Me22). In vitro treatment of Monizia spp. with different concentrations (10, 20, 30 and 50 μglml) of Spirulina platensis extract (Blue-green Algae) affects the morphological architecture of tape worms by using scanning electron microscopy (SEM). The results revealed that Spirulina platensis extract treatment, especially for higher doses 30 and 50 μglml, caused the sucker opening to narrow as a result of scolex swelling more than usual, deformation of the proglottids occurred with circular areas of declare swelling along their margins and microtriches covering the whole tegument appears in several directions. In conclusion, as per of our knowledge it is the first time to record new species of Moniezia species in Al Taif governorate and the anthelmintic potential of Spirulina platensis.