Leishmania tarentolae: Utility as an in vitro model for screening of antileishmanial agents

Primary screens for antileishmanial compounds use Leishmania species pathogenic to humans that must be handled under biosafety conditions that cannot be adopted or guaranteed everywhere. Leishmania tarentolae, a parasite isolated from the gecko Tarentolae annularis, has not been considered pathogenic to humans. Promastigotes of L. tarentolae have been previously used as a eukaryotic expression system for the production of recombinant proteins and in the amplification of genes involved in resistance to antileishmanial drugs. To validate the use of this Leishmania species in the screening of antileishmanial drugs, the sensitivity of axenic and intracellular amastigotes of L. tarentolae was compared to the sensitivity showed by Leishmania species causative of human leishmaniasis. The ability of L. tarentolae to grow as axenic amastigotes is first described while its ability to infect several mammalian cells has been confirmed. L. tarentolae amastigotes offer a suitable model for the in vitro screening of compounds for antileishmanial activity.     

Relationship between the culturability of stressed Listeria monocytogenes cells in non-selective and selective culture media and the cellular esterase activity measured by solid phase cytometry

Solid phase cytometry in conjunction with fluorescent probe was applied to rapidly quantify cellular esterase activity of Listeria monocytogenes cells. Viability of cells stressed by several treatments (starvation, NaCl, lactic acid and peracetic acid) was assessed simultaneously by their esterase activity estimated by fluorescence intensity and by their ability to multiply in liquid and solid, non-selective and selective, culture media. It was determined that cell physiological state has a significant impact on the cellular fluorescence intensity which was very dependent on the stress suffered by cells. No general relationship was observed between the bacterial populations observed by cytometry and the populations able to grow on culture media. The link between the cell culturability in non-selective and selective media and the esterase activity was always dependent on the stress suffered. Nevertheless, it was also established that solid phase cytometry is an efficient, sensitive and accurate tool to characterize the ability of non-selective and selective enrichment broths to allow the repair of stressed L. monocytogenes cells by examining the increase in the fraction of the most esterase active cells during the course of resuscitation.     

Conservation ecology of endangered species Paphiopedilum armeniacum (Orchidaceae)

Paphiopedilum armeniacum is an endangered orchid species, endemic to China. During the period of April 2000 to October 2005, 66 observation sites were selected in Luoshapo of Nushan Mountains in Yunnan, China, to carry out the conservation ecological research on P. armeniacum. A total of 443 genets (1302 ramets in total) of P. armeniacum were sampled, their biological characteristics such as reproductive pattern, phenology, and life cycle were observed, and the ecological habits of the species such as the habitat and the structure of communities were studied. Experiments on ex-situ conservation were conducted, and the cloned ramets were replanted to their original habitat after ex-situ reproduction in Shenzhen, Guangdong, China. The relationships between P. armeniacum and climate, vegetation, other environmental factors in the original habitat, and the biological characteristics of asexual offsprings of P. armeniacum, which were replanted to the original habitat after ex-situ cultivation and reproduction, were investigated. The studies show that P. armeniacum in Luoshapo grows very well in secondary shrub boskets or in tussocks on limestone hills. It has both sexual and asexual reproduction. Asexual reproduction serves to complete the sexual reproduction and to extend the lifetime of genets, while it does not reduce sexual reproduction. There are two modes of asexual reproduction-by tillering or by producing rhizomes. The litter of shrub boskets or tussocks provides P. armeniacum with humus, and the rhizome reproduction of P. armeniacum is an adaptation to the litter-covered condition, i.e. to escape from the unfavorable environment. Blooming rate of ramets is 7.39% 1.02%, and fruit set rate from the blooming ramets is 32.23% 12.08%. P. armeniacum is able to invade the moderately destroyed forests and those in early restoring but is unable to grow in large dense forests. P. armeniacum also grows very well in artificial spare woods in Shenzhen and can reproduce many cloned ramets, which can normally bloom and yield fruits after being replanted to the original habitat. The results of this study show that P. armeniacum can be conserved by ex-situ conservation and by replanting the ex-situ reproduced ramets to original habitat. On the basis of the analysis of endangered mechanisms of P. armeniacum, it can be concluded that P. armeniacum has strong capability of both asexual and sexual reproductions, and an emergency mechanism consisted of massive production of rhizomes to cope with damage. Because highly effective pollinating insects that facilitate pollination in P. armeniacum are present in the habitat, flowering ramets produce fruits with large quantity of seeds, many of which in turn grow into new genets that can reproduce many cloned ramets. P. armeniacum makes very effective use of its environment and has distinct characteristics of enduring harsh environmental conditions; therefore, rather than its own inherent biological defects, the main threats facing this species are the destruction of its survival space and the wipe-out collecting of the plants as a result of trading. Based on the analysis mentioned above, certain appropriate strategies have been proposed for the conservation of P. armeniacum.     

Biological treatment of olive mill wastewater by non-conventional yeasts

The ability of lipolytic yeasts to grow on olive mill wastewater (OMW)-based medium and to produce high-value compounds while degrading this waste, was tested. OMW collected from three-phase olive mills from the North region of Portugal were characterized and used. OMW with COD ranging from 100 g L⁻¹ to 200 g L⁻¹ were supplemented with yeast extract and ammonium chloride. Studies of OMW consumption were carried out in batch cultures of Candida rugosa, Candida cylindracea and Yarrowia lipolytica. All strains were able to grow in the OMW-based media, without dilution, to consume reducing sugars and to reduce COD. C. cylindracea was the best strain concerning the lipase production and the reduction of phenolic compounds and COD. For all strains, the phenols degradation was quite difficult, mostly when more easily degradable carbon source is still present in the medium. Among the phenolic compounds tested catechol is the most inhibitory to the cells.     

Embryo structure,seed traits,and productivity of relict vine Aristolochia contorta (Aristolochiaceae)

The herbaceous vine Aristolochia contorta (Aristolochiaceae) is a rare plant with a fragmented area in East Asia. Confocal laser-scanning microscopy and stereomicroscopy were employed to examine the seed and embryo structure. This is the first research on embryo anatomy in Aristolochia. Shape and structure of this embryo may be phylogenetically significant. The seed structure of A. contorta is similar to that of other Aristolochia species. Considerable variation is found for productivity traits; the average seed set is rather low (26.7%). The studied seed and embryo traits of A. contorta are found to be variable, but may be potentially informative at the genus and species level. The restricted productivity and reduced population size threaten the continued survival of A. contorta and, perhaps, the butterfly that depends on it.     

Complete sequencing of Novosphingobium sp. PP1Y reveals a biotechnologically meaningful metabolic pattern

Background

Novosphingobium sp. strain PP1Y is a marine α-proteobacterium adapted to grow at the water/fuel oil interface. It exploits the aromatic fraction of fuel oils as a carbon and energy source. PP1Y is able to grow on a wide range of mono-, poly- and heterocyclic aromatic hydrocarbons. Here, we report the complete functional annotation of the whole Novosphingobium genome.

Results

PP1Y genome analysis and its comparison with other Sphingomonadal genomes has yielded novel insights into the molecular basis of PP1Y’s phenotypic traits, such as its peculiar ability to encapsulate and degrade the aromatic fraction of fuel oils. In particular, we have identified and dissected several highly specialized metabolic pathways involved in: (i) aromatic hydrocarbon degradation; (ii) resistance to toxic compounds; and (iii) the quorum sensing mechanism.

Conclusions

In summary, the unraveling of the entire PP1Y genome sequence has provided important insight into PP1Y metabolism and, most importantly, has opened new perspectives about the possibility of its manipulation for bioremediation purposes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-384) contains supplementary material, which is available to authorized users.     

Structure prediction and evolution of a halo-acid dehalogenase of Burkholderia mallei

Environmental pollutants containing halogenated organic compounds e.g. haloacid, can cause a plethora of health problems. The structural and functional analyses of the gene responsible of their degradation are an important aspect for environmental studies and are important to human well-being. It has been shown that some haloacids are toxic and mutagenic. Microorganisms capable of degrading these haloacids can be found in the natural environment. One of these, a soil-borne Burkholderia mallei posses the ability to grow on monobromoacetate (MBA). This bacterium produces a haloacid dehalogenase that allows the cell to grow on MBA, a highly toxic and mutagenic environmental pollutant. For the structural and functional analysis, a 346 amino acid encoding protein sequence of haloacid dehalogenase is retrieve from NCBI data base. Primary and secondary structure analysis suggested that the high percentage of helices in the structure makes the protein more flexible for folding, which might increase protein interactions. The consensus protein sub-cellular localization predictions suggest that dehalogenase protein is a periplasmic protein 3D2GO server, suggesting that it is mainly employed in metabolic process followed by hydrolase activity and catalytic activity. The tertiary structure of protein was predicted by homology modeling. The result suggests that the protein is an unstable protein which is also an important characteristic of active enzyme enabling them to bind various cofactors and substrate for proper functioning. Validation of 3D structure was done using Ramachandran plot ProsA-web and RMSD score. This predicted information will help in better understanding of mechanism underlying haloacid dehalogenase encoding protein and its evolutionary relationship.     

A comparison of the Caulobacter NA1000 and K31 genomes reveals extensive genome rearrangements and differences in metabolic potential

The genus Caulobacter is found in a variety of habitats and is known for its ability to thrive in low-nutrient conditions. K31 is a novel Caulobacter isolate that has the ability to tolerate copper and chlorophenols, and can grow at 4°C with a doubling time of 40 h. K31 contains a 5.5 Mb chromosome that codes for more than 5500 proteins and two large plasmids (234 and 178 kb) that code for 438 additional proteins. A comparison of the K31 and the Caulobacter crescentus NA1000 genomes revealed extensive rearrangements of gene order, suggesting that the genomes had been randomly scrambled. However, a careful analysis revealed that the distance from the origin of replication was conserved for the majority of the genes and that many of the rearrangements involved inversions that included the origin of replication. On a finer scale, numerous small indels were observed. K31 proteins involved in essential functions shared 80–95% amino acid sequence identity with their C. crescentus homologues, while other homologue pairs tended to have lower levels of identity. In addition, the K31 chromosome contains more than 1600 genes with no homologue in NA1000.     

De novo formation and ultra-structural characterization of a fiber-producing human hair follicle equivalent in vitro

Across many tissues and organs, the ability to create an organoid, the smallest functional unit of an organ, in vitro is the key both to tissue engineering and preclinical testing regimes. The hair follicle is an organoid that has been much studied based on its ability to grow quickly and to regenerate after trauma. But hair follicle formation in vitro has been elusive. Replacing hair lost due to pattern baldness or more severe alopecia, including that induced by chemotherapy, remains a significant unmet medical need.By carefully analyzing and recapitulating the growth conditions of hair follicle formation, we recreated human hair follicles in tissue culture that were capable of producing hair. Our microfollicles contained all relevant cell types and their structure and orientation resembled in some ways excised hair follicle specimens from human skin. This finding offers a new window onto hair follicle development. Having a robust culture system for hair follicles is an important step towards improved hair regeneration as well as to an understanding of how marketed drugs or drug candidates, including cancer chemotherapy, will affect this important organ.     

Siderophore cooperation of the bacterium Pseudomonas fluorescens in soil

While social interactions play an important role for the evolution of bacterial siderophore production in vitro, the extent to which siderophore production is a social trait in natural populations is less clear. Here, we demonstrate that siderophores act as public goods in a natural physical environment of Pseudomonas fluorescens: soil-based compost. We show that monocultures of siderophore producers grow better than non-producers in soil, but non-producers can exploit others'' siderophores, as shown by non-producers'' ability to invade populations of producers when rare. Despite this rare advantage, non-producers were unable to outcompete producers, suggesting that producers and non-producers may stably coexist in soil. Such coexistence is predicted to arise from the spatial structure associated with soil, and this is supported by increased fitness of non-producers when grown in a shaken soil–water mix. Our results suggest that both producers and non-producers should be observed in soil, as has been observed in marine environments and in clinical populations.     

Photoheterotrophic growth of Physcomitrella patens

Physcomitrella patens is a model bryophyte representing an early land plant in the green plant lineage. This organism possesses many advantages as a model organism. Its genome has been sequenced, its predominant life cycle stage is the haploid gametophyte, it is readily transformable and it can integrate transformed DNA into its genome by homologous recombination. One limitation for the use of P. patens in photosynthesis research is its reported inability to grow photoheterotrophically, in the presence of sucrose and the Photosystem II inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea, which prevents linear photosynthetic electron transport. In this communication we describe the facile isolation of a P. patens strain which can grow photoheterotrophically. Additionally, we have examined a number of photosynthetic parameters for this strain grown under photoautotrophic, mixotrophic (in the presence of sucrose) and photoheterotrophic conditions, as well as the 3-(3,4-dichlorophenyl)-1,1-dimethylurea-inhibited state. The ability to grow P. patens photoheterotrophically should significantly facilitate its use in photosynthetic studies.     

不同水稻品种对稻纵卷叶螟生长发育、存活、生殖及飞行能力的影响

系统研究了稻纵卷叶螟在6种不同水稻品种(常规粳稻武育粳3号,杂交粳稻宁粳1号,常规籼稻TN1,杂交籼稻汕优63,超级杂交籼稻两优培九,超级杂交籼粳稻甬优9号)上取食后的发育历期、存活率、卵巢发育进度、繁殖力和飞行能力.结果表明,武育粳3号和宁粳1号能显著延长稻纵卷叶螟未成熟期的发育历期,降低其存活率,延缓卵巢发育进度,降低成虫繁殖率,并提高成虫的飞行能力;不同水稻品种间的影响存在显著差异,其影响从大到小排列为杂交粳稻＞常规粳稻＞常规籼稻＞杂交籼稻＞超级杂交稻.这说明,幼虫期营养对稻纵卷叶螟的生长发育、存活、生殖和飞行能力具有显著影响.     

Asexual propagation in the coral reef macroalga Halimeda (Chlorophyta, Bryopsidales): production, dispersal and attachment of small fragments

Siphonous, green macroalgae of the genus Halimeda are ubiquitous and ecologically important in tropical and subtropical marine environments. It has been hypothesized that the abundance of Halimeda on coral reefs is in part due to the ability of this genus to propagate asexually via vegetative fragmentation. However, vegetative fragmentation has only been documented for H. discoidea in a laboratory setting. To test the hypothesis that vegetative fragmentation contributes to field populations of Halimeda, we examined three aspects of fragmentation by H. tuna (Ellis and Solander) Lamouroux, H. opuntia (Linneaus) Lamouroux and H. goreaui Taylor on Conch Reef in the Florida Keys: (1) short-term (8 days) and long-term (14 weeks) fragment survival and rhizoid production in the laboratory and field (7 and 21 m), (2) size of the fragment pool and (3) influences of herbivory and water motion on production and dispersal of fragments. Although morphologically similar to H. discoidea, only a small percentage of H. tuna fragments survived. Fragments of H. opuntia and H. goreaui were more robust, and survival and rhizoid production were positively correlated with size in short-term trials. In 14-week field trials, one-third or fewer fragments of any species survived at 7 m, potentially because fragments were covered by large amounts of sediment. Survivors included some buried, seemingly dead individuals that turned green when exposed to light, highlighting the remarkable ability of this genus to survive disturbances. There was much less sediment accumulation at 21 m, where more fragments survived. Most (93%) eight-segment fragments of H. opuntia produced attachment rhizoids by the end of the 14-week trial. Overall, a range of 4.7-9.4 fragments of Halimeda m⁻² day⁻¹ were found on Conch Reef; most fragments were generated by H. goreaui. Fish bite marks were evident on 75-85% of the individuals of H. tuna and the number of bites per thallus ranged from 1 to 23. Herbivorous reef fish commonly fed on all three species of Halimeda. Some fish consumed the biomass, while others rejected most bites. For example, 83% of bites were rejected by the blue-striped grunt. Dispersal distances for rejected bites ranged from 0 to 31 m. Water motion was also responsible for fragment dispersal; experimentally produced fragments moved up to 48 cm day⁻¹. Results presented here suggest that asexual propagation of fragments of Halimeda is an important component of the life-history of this genus and vegetative fragmentation contributes to the abundance of this genus on coral reefs.     

A Potent Probiotic Strain from Cheddar Cheese

A lactic acid bacteria Leuconostoc paramesenteroides was isolated and characterized from cheddar cheese and was adapted to grow at low pH (2.0) and high bile salt concentration (2%) by sequential sub-culturing so that it can survive the extreme environmental condition of gut. Cell hydrophobicity assay shows the maximum adherence of the culture to toluene (46.11%). Adhesion ability was confirmed by in vitro assay using rat intestinal epithelial layer. The culture has an antimicrobial activity against food borne pathogens and is vancomycin sensitive. The culture shows a β-galactosidase activity of 3.42 μM/mg protein, which indicates the ability of the culture to hydrolyze lactose for easy absorption. All these properties determine the ability of the culture to be used as a probiotic.     

昆虫蛀蚀对鼠类介导下的锐齿槲栎种子扩散的影响

森林鼠类的种子贮藏行为对植物的扩散和自然更新有着非常重要的影响。然而,鼠类是否具有鉴别虫蛀种子的能力还存在一定的争议。此外,鼠类的鉴别能力是否受到食物丰富度变化的影响也未见相关报道。采用标签标记法,2011年秋季(9—11月,食物丰富季节)和2012年春季(4—6月,食物匮乏季节)分别在秦岭南坡的佛坪国家级自然保护区内,调查了森林鼠类对完好和虫蛀锐齿槲栎(Quercus aliena)种子的选择差异。结果显示:1)在秋季,尽管2种类型种子的存留动态没有显著差异,但是在后期虫蛀种子的存留时间相对更长;而在春季2种类型种子的存留动态则极为显著,几乎所有的完好种子(99%)在释放后的第3天就被鼠类全部扩散,虫蛀种子的存留时间则相对较长。2)在秋季,鼠类更喜好扩散后取食完好种子;而在春季,鼠类则喜好在原地取食绝大部分的种子,并且优先取食完好种子。3)在秋季,鼠类贮藏了更多的完好种子;而在春季,尽管完好种子在释放后第1天便达到贮藏高峰,然而由于后期的大量被捕食,2种类型种子在贮藏动态上没有显示出显著差异。研究结果表明秦岭地区森林鼠类可以准确区分完好与虫蛀种子,但是食物丰富度会影响鼠类对种子的选择策略。在食物丰富的秋季,鼠类更多地选择贮藏完好种子;而在食物相对匮乏的春季,鼠类更倾向于同时取食2种类型种子。森林鼠类通过对2种类型种子的鉴别和选择,影响不同种子的命运,从而可能对种子的扩散和自然更新产生重要影响。     

Acanthamoeba polyphaga is a possible host for Vibrio cholerae in aquatic environments

Acanthamoeba is a genus of free-living amoebae found to be able to host many bacterial species living in the environment. Acanthamoebae and Vibrio cholerae are found in the aquatic environments of cholera endemic areas. Previously it has been shown that V. cholerae O1 and O139 can survive and grow in Acanthamoeba castellanii. The aim of this study was to examine the ability of Acanthamoeba polyphaga to host V. cholerae O1 and O139. The interaction between A. polyphaga and V. cholerae strains was studied by means of viable amoeba cell counts and viable count of the bacteria in the absence and presence of amoebae. The viable count of intracellularly growing bacteria was estimated by utilizing gentamicin assay. Electron microscopy was used to determine the localization of V. cholerae inside A. polyphaga. The results showed that A. polyphaga enhanced growth and survival of V. cholerae, which grew and survived inside the amoeba cells for 2 weeks. The electron microscopy showed that A. polyphaga hosted intracellular V. cholerae localized in the vacuoles of amoeba cell. Neither the presence of V. cholerae together with A. polyphaga nor the intracellular localization of the bacteria inhibited growth and survival of A. polyphaga. The outcome of the interaction between these microorganisms may support strongly the role of A. polyphaga as host for V. cholerae O1 and O139.     

The evolution of growth rates on an expanding range edge

Individuals in the vanguard of a species invasion face altered selective conditions when compared with conspecifics behind the invasion front. Assortment by dispersal ability on the expanding front, for example, drives the evolution of increased dispersal, which, in turn, leads to accelerated rates of invasion. Here I propose an additional evolutionary mechanism to explain accelerating invasions: shifts in population growth rate (r). Because individuals in the vanguard face lower population density than those in established populations, they should (relative to individuals in established populations) experience greater r-selection. To test this possibility, I used the ongoing invasion of cane toads (Bufo marinus) across northern Australia. Life-history theory shows that the most efficient way to increase the rate of population growth is to reproduce earlier. Thus, I predict that toads on the invasion front will exhibit faster individual growth rates (and thus will reach breeding size earlier) than those from older populations. Using a common garden design, I show that this is indeed the case: both tadpoles and juvenile toads from frontal populations grow around 30 per cent faster than those from older, long established populations. These results support theoretical predictions that r increases during range advance and highlight the importance of understanding the evolution of life history during range advance.     

Solar activity affects avian timing of reproduction

Avian timing of reproduction is strongly affected by ambient temperature. Here we show that there is an additional effect of sunspots on laying date, from five long-term population studies of great and blue tits (Parus major and Cyanistes caeruleus), demonstrating for the first time that solar activity not only has an effect on population numbers but that it also affects the timing of animal behaviour. This effect is statistically independent of ambient temperature. In years with few sunspots, birds initiate laying late while they are often early in years with many sunspots. The sunspot effect may be owing to a crucial difference between the method of temperature measurements by meteorological stations (in the shade) and the temperatures experienced by the birds. A better understanding of the impact of all the thermal components of weather on the phenology of ecosystems is essential when predicting their responses to climate change.     

Amplification of Adenine Phosphoribosyltransferase Suppresses the Conditionally Lethal Growth and Virulence Phenotype of Leishmania donovani Mutants Lacking Both Hypoxanthine-guanine and Xanthine Phosphoribosyltransferases

Leishmania donovani cannot synthesize purines de novo and obligatorily scavenge purines from the host. Previously, we described a conditional lethal Δhgprt/Δxprt mutant of L. donovani (Boitz, J. M., and Ullman, B. (2006) J. Biol. Chem. 281, 16084–16089) that establishes that L. donovani salvages purines primarily through hypoxanthine-guanine phosphoribosyltransferase (HGPRT) and xanthine phosphoribosyltransferase (XPRT). Unlike wild type L. donovani, the Δhgprt/Δxprt knock-out cannot grow on 6-oxypurines and displays an absolute requirement for adenine or adenosine and 2′-deoxycoformycin, an inhibitor of parasite adenine aminohydrolase activity. Here, we demonstrate that the ability of Δhgprt/Δxprt parasites to infect mice was profoundly compromised. Surprisingly, mutant parasites that survived the initial passage through mice partially regained their virulence properties, exhibiting a >10-fold increase in parasite burden in a subsequent mouse infection. To dissect the mechanism by which Δhgprt/Δxprt parasites persisted in vivo, suppressor strains that had regained their capacity to grow under restrictive conditions were cloned from cultured Δhgprt/Δxprt parasites. The ability of these suppressor clones to grow in and metabolize 6-oxypurines could be ascribed to a marked amplification and overexpression of the adenine phosphoribosyltransferase (APRT) gene. Moreover, transfection of Δhgprt/Δxprt cells with an APRT episome recapitulated the suppressor phenotype in vitro and enabled growth on 6-oxypurines. Biochemical studies further showed that hypoxanthine, unexpectedly, was an inefficient substrate for APRT, evidence that could account for the ability of the suppressors to metabolize hypoxanthine. Subsequent analysis implied that APRT amplification was also a potential contributory mechanism by which Δhgprt/Δxprt parasites displayed persistence and increased virulence in mice.