Suspension of non-viable fungal spores as a standard for platelet counting.

In the search among biological particles for a standard for counting human platelets, a strain of Absidia corymbifera was found to have spores that resembled platelets. After fixing in formalin and autoclaving the spores had a similar mean cell volume to that of human platelets. A suspension of these killed spores was tested in 100 laboratories and gave consistent results as a standard for human platelet counting. The Absidia corymbifera standard can be used in electronic counting methods but not in sedimentation methods, as the spores will be removed by centrifugation.     

Inhibition of fungal spore germination by gramicidin S and its potential use as a biocontrol against fungal plant pathogens

Gramicidin S, as well as being sporicidal to Bacillus spores, also inhibits germination and emergence of fungal-like spores of Dictyostelium discoideum . The fungal plant pathogen Fusarium nivale is also inhibited and gramicidin S, therefore, is a sporicidal and antifungal antibiotic. Considering these findings the potential use of this antibiotic and its producer organism Bacillus brevis as a biocontrol is discussed.     

Sporoplex: A hypothetical complex of fungal spore with oligonucleotide as a gene delivery vector

Various types of vehicles have been applied for gene delivery, including viral and non-viral vectors. The authors would like to hypothesize that fungal spores also potentially could be used as a gene delivery vehicle, which we call “Sporoplex”.     

Optimal hydration status for cryopreservation of intermediate oily seeds: Citrus as a case study

BACKGROUND AND AIMS: The purpose of this study was to investigate the basis of the optimal hydration status for cryopreservation of intermediate oily seeds using Citrus as a model. METHODS: The relationships between equilibrium relative humidity (RH), seed water content, presence of freezable water as determined by DSC analysis, and germination percentage after immersion in liquid nitrogen (LN) were investigated in Citrus aurantifolia, C. grandis, C. madurensis and C. reticulata. The relationship between the lipid content of seeds and their unfrozen water content was also investigated. KEY RESULTS: Independent of their level of seed desiccation tolerance, the optimal desiccation RH for seed tolerance to LN exposure was 75-80 % in the four species studied. This optimal hydration status always coincided with that at which presence of frozen water could not be detected in seed tissues during the cooling/thawing process. The unfrozen water content of seeds was variable between species and negatively correlated to seed lipid content. Using the present data, those obtained previously in seven coffee species and those reported by other authors for five other species, a significant linear relationship was found between the lipid content and the unfrozen water content of seeds. CONCLUSIONS: This study provides additional evidence that intermediate oily seeds do not withstand the presence of freezable water in their tissues during the cooling/warming process. Moreover, it offers two important applied perspectives: (1) independent of their level of desiccation tolerance, testing germination of seeds of a given oily seed species after equilibration in 75-80 % RH at 25 degrees C and LN exposure, gives a rapid and reliable evaluation of the possibility of cryopreserving whole seeds of this given species; (2) it is now possible to calculate the interval of water contents in which non-orthodox oily seeds of a given species are likely to withstand LN exposure as a function of their lipid content.     

Faecal pellet group counting as a promising method of wild boar population density estimation

The wild boar is a native animal species of the Czech Republic that has significantly increased its population density in recent years. Objective methods of population density estimation are required to inform the intensity of regulation needed for the sustainable management of the wild boar. Population estimation and regulation of the abundance of the wild boar are problematic in comparison to those of other ungulates, and the only widely used method of control is intensive hunting. The purpose of this study was to test if faecal pellet group (FPG) counting was a reliable method of wild boar population censusing in a forest environment. The density of wild boars was evaluated in an area of 22.56 km², circumscribed by both natural and man-made barriers that restrict wild boar migration. As it is essential for proper application of FPG count methods, a separate trial was carried out to determine the daily defecation rate of wild boars. The distribution of faeces in different types of habitat in a forest environment was tested. As the period of faeces accumulation fell within the intensive hunting season, the result is biased by the fact that the calculation includes FPGs produced by animals removed from the population through hunting during winter. The average daily defecation rate of adults and piglets was 4.29 and 5.82, respectively. The corrected (without shot animals) average density of wild boars in the study area estimated by the FPG count at the time of the census was 6.08 individuals (ind.)/km². We have confirmed that an FPG count conducted in winter is applicable for estimation of wild boar abundance on a forested area.     

Flow-cytometric cell counting and DNA estimation for the study of plant cell population dynamics

A one-step procedure is presented for simultaneous measurement of cell number and DNA content in cultured plant cells by flow cytometry. In order to obtain nuclei representative of the growth stadium of the culture and of all phases of the cell cycle, cells were carefully sampled and immediately fixed. Next, nuclei were isolated by enzymatic and mechanical maceration, and stained with a DNA-specific fluorescent dye. In the resultant preparation, cells can be counted at relative ease by means of a fluorescence microscope. However, flow-cytometric counting appeared to be superior to manual counting since the time needed for flow-cytometric counting was one-fourth that for manual counting and the variance between counts of the samples was significantly less. In addition, from the same routine, accurate DNA distributions were obtained as a second important parameter of the population dynamics.     

Diversity, abundance or rare species as a target for the conservation of mammalian carnivores: a case study in Southern Spain

Management goals in protected areas and/or communities usually include diversity as one of the most valuable and confident criteria. Nevertheless, the use of diversity and related indices as a means of evaluating successful management practices could produce conflicting results. Here we report a case study in one of the most important European protected areas. After 6 years of intensive conservation management of the Don~ana National Park, the general abundance and numbers of the target single-species conservation plan (the Iberian lynx) increased, although carnivore community diversity and evenness decreased. This was a result of a disproportionate increase of an oportunistic native species, the red fox. We propose the combined use of diversity, richness and evenness indices when monitoring management practices such as those reported here.     

Estimating abundance for a savanna elephant population using mark–resight methods: a case study for the Tembe Elephant Park, South Africa

Elephants living in dense woodlands are difficult to count. Many elephant populations in Africa occur in such conditions. Estimates of these populations based on total counts, aerial counts and dung counts often lack information on precision and accuracy. We use standard mark–recapture field methods to obtain estimates of population size with associated confidence limits. We apply this approach to a closed elephant population in the Tembe Elephant Park (300 km²), South Africa. A registration count completed in 4 months gives a known population size. We evaluate mark–recapture models against the known population size. Individual identification profiles obtained for elephants during the registration count and mark–recapture events indicate that at least 167 elephants live in the park. We consider this value as an estimate of the minimum number alive. We include 189 sightings of bulls and 37 sightings of breeding herds in the mark–recapture modelling. Of the models we test (Petersen, Schnabel, Schumacher, Jolly–Seber, Bowden's, Poisson and negative binomial), Bowden's gives an estimate closest to the registration count. Assumptions of the model are not violated. For all models except one (negative binomial), our estimates improve with increased sampling intensity. Confidence intervals do not improve with increased effort except for the Schnabel model. Mark–recapture methods should be considered as reliable estimators of population size for elephants occurring in dense woodlands and forests when other methods cannot be relied on.     

川硬皮肿腿蜂携带松墨天牛致病菌的研究

[目的]以生物导弹为理念,应用寄生性昆虫携带病原物双重防治松墨天牛Monochamus alternatus是目前研究的新领域,更是松材线虫病Bursaphelenchus xylophilus防治的新途径.[方法]本文以川硬皮肿腿蜂Scleroderma sichuanensis为载体,通过测定4株松墨天牛致病菌的孢子粉和孢子悬浮剂对其毒力大小和川硬皮肿腿蜂对4株菌的2种剂型的初始携带量及存留量,分析不同菌种与不同剂型对川硬皮肿腿蜂的影响和川硬皮肿腿蜂体表孢子脱落趋势.[结果]川硬皮肿腿蜂雌成蜂携带粉剂孢子的死亡率高于携带悬浮剂的,但川硬皮肿腿蜂对粉剂孢子的携带量却远远高于悬浮剂孢子的携带量.当喷施孢子悬浮剂时,川硬皮肿腿蜂的累计死亡率随浓度增加而增加,同样携带量也随浓度增加而增加;白僵菌对川硬皮肿腿蜂的毒力较绿僵菌高,致死速率也较绿僵菌大,但川硬皮肿腿蜂对白僵菌的携带效果却比绿僵菌的效果好.并且不论剂型和菌种,川硬皮肿腿蜂体表的孢子在第1d后都脱落最为明显,而后均保持较缓慢脱落.[结论]本研究证明川硬皮肿腿蜂携带松墨天牛致病菌的方法是可行的,其中白僵菌孢子粉更适合携带.     

Iron and fungal pathogenesis: a case study with Cryptococcus neoformans

The acquisition of iron from mammalian hosts is an important aspect of infection because microbes must compete with the host for this nutrient and iron perception often regulates virulence factor expression. For example, iron levels are known to influence the elaboration of two major virulence factors, the polysaccharide capsule and melanin, in the pathogenic fungus Cryptococcus neoformans. This pathogen, which causes meningoencephalitis in immunocompromised people, acquires iron through the use of secreted reductants, cell surface reductases, a permease/ferroxidase uptake system and siderophore transporters. In addition, a master regulator, Cir1, integrates iron sensing with the expression of virulence factors, with growth at 37°C and with signalling pathways that also influence virulence. The challenge ahead is to develop mechanistic views of the iron acquisition functions and regulatory schemes that operate when C. neoformans is in host tissue. Achieving these goals may contribute to an understanding of the notable predilection of the fungus for the mammalian central nervous system.     

The measurement of Bacillus mycoides spore adhesion using atomic force microscopy,simple counting methods,and a spinning disk technique

An atomic force microscope has been used to study the adhesion of Bacillus mycoides spores to a hydrophilic glass surface and a hydrophobic-coated glass surface. AFM images of spores attached to the hydrophobic-coated mica surface allowed the measurement of spore dimensions in an aqueous environment without desiccation. The spore exosporium was observed to be flexible and to promote the adhesion of the spore by increasing the area of spore contact with the surface. Results from counting procedures using light microscopy matched the density of spores observed on the hydrophobic-coated glass surface with AFM. However, no spores were observed on the hydrophilic glass surface with AFM, a consequence of the weaker adhesion of the spores at this surface. AFM was also used to quantify directly the interactions of B. mycoides spores at the two surfaces in an aqueous environment. The measurements used "spore probes" constructed by immobilizing a single spore at the apex of a tipless AFM cantilever. The data showed that stretching and sequential bond breaking occurred as the spores were retracted from the hydrophilic glass surface. The greatest spore adhesion was measured at the hydrophobic-coated glass surface. An attractive force on the spores was measured as the spores approached the hydrophobic-coated surface. At the hydrophilic glass surface, only repulsive forces were measured during the approach of the spores. The AFM force measurements were in qualitative agreement with the results of a hydrodynamic shear adhesion assay that used a spinning disk technique. Quantitatively, AFM measurements of adhesive force were up to 4 x 10(3) times larger than the estimates made using the spinning disk data. This is a consequence of the different types of forces applied to the spore in the different adhesion assays. AFM has provided some unique insights into the interactions of spores with surfaces. No other instrument can make such direct measurements for single microbiological cells.     

Conceptual-level workflow modeling of scientific experiments using NMR as a case study

Background  

Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phases, allowing intermediate results to be verified and supporting the proper handling of semantic mismatches and different file formats among the various tools used in the scientific process. Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data. While much research has been conducted on the implementation of scientific workflows, the initial process of actually designing and generating the workflow at the conceptual level has received little consideration.     

Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study

We compare the performances of established means of character selection for discriminant analysis in species distinction with a combination procedure for finding the optimal character combination (minimum classification error, minimum number of required characters), using morphometric data sets from the ant genera Cardiocondyla , Lasius and Tetramorium . The established methods are empirical character selection as well as forward selection, backward elimination and stepwise selection of discriminant analysis. The combination procedure is clearly superior to the established methods of character selection, and is widely applicable.     

The utility of repeated presence data as a surrogate for counts: a case study using butterflies

Abundance data are widely used to monitor long-term population trends for management and conservation of species of interest. Programs that collect count data are often prohibitively expensive and time intensive, limiting the number of species that can be simultaneously monitored. Presence data, on the other hand, can often be collected in less time and for multiple species simultaneously. We investigate the relationship of counts to presence using 49 butterfly species across 4 sites over 9 years, and then compare trends produced from each index. We also employed simulated datasets to test the effect of reduced sampling on the relationship of counts to presence data and to investigate changes in each index’s power to reveal population trends. Presence and counts were highly correlated for most species tested, and population trends based on each index were concordant for most species. The effect of reduced sampling was species-specific, but on a whole, sensitivity of both indices to detect population trends was reduced. Common and rare species, as well as those with a range of life-history and behavioral traits performed equally well. The relationship between presence and count data may break down in cases of very abundant and widespread species with extended flight seasons. Our results suggest that when used cautiously, presence data has the potential to be used as a surrogate for counts. Collection of presence data may be useful for multi-species monitoring or to reduce the duration of monitoring visits without fully sacrificing the ability to infer population trends.     

Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction

MOTIVATION: Feature subset selection is an important preprocessing step for classification. In biology, where structures or processes are described by a large number of features, the elimination of irrelevant and redundant information in a reasonable amount of time has a number of advantages. It enables the classification system to achieve good or even better solutions with a restricted subset of features, allows for a faster classification, and it helps the human expert focus on a relevant subset of features, hence providing useful biological knowledge. RESULTS: We present a heuristic method based on Estimation of Distribution Algorithms to select relevant subsets of features for splice site prediction in Arabidopsis thaliana. We show that this method performs a fast detection of relevant feature subsets using the technique of constrained feature subsets. Compared to the traditional greedy methods the gain in speed can be up to one order of magnitude, with results being comparable or even better than the greedy methods. This makes it a very practical solution for classification tasks that can be solved using a relatively small amount of discriminative features (or feature dependencies), but where the initial set of potential discriminative features is rather large.     

Quantitative estimation of area parameters (with representatives of genus rana as a case study)

A quantitative method of species "point" area analysis is considered that provides the interpolation of species distribution to the whole territory on the basis of its relationships with climatic and relief variables. It is shown that application of standart statistical interpolation techniques is incorrect. The proposed approach is based on interpolation onto the whole territory the species-specific relations with environmental variables detected in single "points". The basic method for the task proves to be the factor analysis. Within the scope of the study, we have considered the methods for quantitative representation of species relationships with climatic and relief variables. The analysis efficiency is demonstrated by an example of three species of brown frogs: Rana temporaria, R. arvalis u R. amurensis.