Mechanisms of Classification of Visual Objects in Children with Different Styles of Cognitive Activity

A sample of seven-year-old children was divided into reflective and impulsive groups using the matching familiar figures test (MFFT). Event-related potentials of different regions of the cerebral cortex were studied in children from these groups performing classification of visual-object shapes on the basis of only one discriminative feature or with the use of additional information. Comparison of the success of visual-stimulus identification in reflective and impulsive children under the conditions of alternative choice (MFFT) and classification according to a specified discriminative feature demonstrates differences in the mechanisms of both selection and analysis of the sensory characters of the stimulus. When the shape of a visual object is classified according to the discriminative feature, the initial stages of analysis in impulsive children are accompanied by the emergence of wave N80 in the left hemisphere, which may reflect the higher rate of detection of the discriminative feature by these children. Impulsive children are also characterized by an earlier development and a higher amplitude of component P300 compared to reflective children. In the latter, waves N250 and N350, indicating continuing information processing, are superposed on this positive component. If the picture presented to children contains an element consistent with the discriminative feature, the N350 amplitude in the right temporo-parieto-occipital region and the negative shift corresponding to the N350 wave in the left temporo-parieto-occipital region are increased in reflective and impulsive children, respectively. Additional information increased wave N400 in the left frontal region.     

Erythematous Oral Candidiasis in Patients with Controlled Type II Diabetes Mellitus and Complete Dentures

Diabetes mellitus (DM) is a systemic condition characterized by a deficient sugar metabolism, which affects the immune system and favors the development of yeasts. The aim of the present study was to perform biochemical, morphological, exoenzyme analyses of Candida species and the molecular identification (DNA) of C. albicans in patients with type II diabetes mellitus. The exoenzyme quantification was compared to non-diabetic patients as controls. Two hundred and seventy-four patients who make use of complete dentures were evaluated, 28 of whom had diabetes and erythematous oral candidiasis. Other thirty patients presented the same clinical feature but without diabetes. Samples were isolated for biochemical identification (auxonogram), morphological identification (production of germ tubes) and PCR molecular identification (DNA). The capability of the Candida samples in producing phospholipases and proteinases was also determined. The diabetic patients had a greater diversity of Candida species (Fischer’s exact test, P = 0.04). The production of proteinases by C. albicans in patients with diabetes was greater than in the control group (unpaired “t” test P < 0.003). However, there was no difference between groups for phospholipase production (unpaired “t” test P > 0.05). It was concluded that patients with controlled DM exhibited systemic conditions predisposing C. albicans proteinase increased production.     

Characterization of wine Lactobacillus plantarum by PCR-DGGE and RAPD-PCR analysis and identification of Lactobacillus plantarum strains able to degrade arginine

Summary Screening of strains isolated from red wine undergoing malolactic fermentation allowed the identification of lactic acid bacteria able to degrade arginine. A denaturing gradient gel electrophoresis approach, using the rpoB gene as the molecular target, was developed in order to characterize the isolated strains. Several strains were identified as Lactobacillus plantarum and were typed by RAPD-PCR with several randomly designed primers. Almost all of the␣L. plantarum strains identified were able to produce citrulline and ammonia, suggesting that the ability of␣L.␣plantarum to degrade arginine is a common feature in wine. During the characterization of the newly identified L.␣plantarum strains, the presence of genes coding for the arginine deiminase (ADI) pathway was observed in the strains able to produce citrulline, while the lack of this genes was observed in strain unable to produce citrulline. These results suggest that the degradation of arginine in L. plantarum is probably strain-dependent.     

Forensic species identification of large macaws using DNA barcodes and microsatellite profiles

Using mitochondrial and nuclear markers species identification was conducted in the case of seized feathers. Earlier, we had sequenced cytochrome c oxidase subunit I (COI) both from 10 seized specimens and 43 validation specimens from captive macaws belonging to 4 Ara species (A. macao, A. chloropterus, A. ararauna, and A. ambiguus) and identified 19 haplotypes based on COI sequences. Species-level identification using Barcode of Life Data Systems showed that seized feathers shared the highest similarity with scarlet macaws (A. macao), and this result was supported by the tree-base identification with high bootstrap values. Moreover, microsatellite profiles in AgGT17 locus showed that patterns of allelic distribution in the seized feathers were apparently distinct from those of red-and-green macaw (A. chloropterus), but were overlapped with those of A. macao, suggesting that all of seized feathers were derived from several individuals of A. macao. We also determined the parentage of hybrid macaws by the combination of COI barcodes and microsatellite profiles. The technique presented here will contribute to forensic identification and future conservation of large macaws that have been lost due to deforestation.     

六种沉香属植物叶片解剖结构研究

为比较沉香属不同种植物间的叶片形态解剖特征,将不同来源的六种沉香属植物在海南省兴隆南药园种植,运用石蜡切片法和撕片法对其成熟叶片的解剖特征进行观察,并对叶片的上下表皮,叶脉和叶横切面等12项数量性状进行统计分析。结果表明:六种沉香属植物叶片解剖结构基本一致,均为典型的异面叶,由表皮、叶肉和叶脉组成,表现出典型的旱生形态特点。表皮细胞单层,气孔微下陷,仅分布在下表皮,上下表皮上零星分布着表皮毛。叶肉组织发达,栅栏组织由1~2层排列紧密地圆柱状细胞组成,其间分布着大量的长方晶体,海绵组织内有一层排列较整齐,染色较深的异细胞组成的下皮层。主脉维管束双韧型,呈圆环状,内含大量异细胞。方差分析表明,除栅海比外,叶片厚度、叶脉条数、主脉厚度等其余11项数量指标在六种植物间差异均达到显著水平。聚类分析将这六种植物聚成3类,Aquilaria sinensis(白木香),A.crassna和A.banaensis聚为一类,A.baillonii和A.malaccensis聚为一类;A.yunnanensis(云南沉香)单独为一类。该研究结果为沉香属植物的物种鉴定提供了解剖学依据,同时对沉香属植物合理开发利用具有重要意义。     

k-gram方法识别microRNA前体

MicroRNAs (miRNAs) 是动植物中较短的参与调控基因表达的功能性非编码RNA序列. 第一个miRNA是通过实验手段发现的，然而通过实验手段识别miRNA在技术上仍然具有很大的挑战性和不完整性. 因此，miRNA基因识别需要寻求计算方法来弥补实验方法的不足. 提出了一个全新的miRNA前体的识别方法. 在构造识别模型中，把初级序列和序列二级结构相结合，采用k-gram方法把序列信息映射到高维特征空间中，然后通过特征选取方法提取特征，并用这些特征为miRNA前体的识别构造了基于SVM的识别模型. 同时，采用隐马尔可夫模型(HMM)的学习方法进行了比较. 实验结果表明，该方法是有效的，可以达到较高的敏感性和特异性.     

A New Filter Based Cultivation Approach for Improving Aspergillus Identification using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS)

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) is widely used in clinical laboratories for routine identification of bacteria and yeasts. However, methodological difficulties are still apparent when applied to filamentous fungi. The liquid cultivation method recommended by Bruker Daltonics GmbH for identification of filamentous fungi by MALDI-TOF MS is labour intensive and time-consuming. In this study, growth of Aspergillus species on different (porous) surfaces was investigated with the aim to develop a more reliable, quicker and less laborious identification method using MALDI-TOF MS. Mycelial growth without sporulation mimicking liquid cultivation and reliable MALDI-TOF MS spectra were obtained when A. fumigatus strains were grown on and in between a polycarbonate membrane filter on Sabouraud dextrose agar. A database of in-house reference spectra was created by growing Aspergillus reference strains (mainly focusing on sections Fumigati and Flavi) under these selected conditions. A test set of 50 molecularly identified strains grown under different conditions was used to select the best growth condition for identification and to perform an initial validation of the in-house database. Based on these results, the cultivation method on top of a polycarbonate filter proved to be most successful for species identification. This method was therefore selected for the identification of two sets of clinical isolates that mainly consisted of Aspergilli (100 strains originating from Indonesia, 70 isolates from Qatar). The results showed that this cultivation method is reliable for identification of clinically relevant Aspergillus species, with 67% and 76% correct identification of strains from Indonesia and Qatar, respectively. In conclusion, cultivation of Aspergilli on top of a polycarbonate filter showed improved results compared to the liquid cultivation protocol recommended by Bruker in terms of percentage of correct identification, ease of MSP creation, time consumption, cost and labour intensity. This method can be reliably applied for identification of clinically important Aspergilli and has potential for identification of other filamentous fungi.

     

Identification of specific proteins from seed embryos by two-dimensional gel electrophoresis for the discrimination between indica and japonica rice

Summary Proteins extracted from seed embryos of 29 different cultivated rice (Oryza sativa L.) and one wild rice (O. rufipogon Griff.) were compared by two-dimensional gel electrophoresis analysis. Among more than 300 protein spots on the gel we found some interesting variations in ten spots which were individually designated as proteins A-J. Protein E was observed in all indica cultivars but was not found in those of the subspecies japonica. In contrast, protein F was only detected in japonica cultivars. Protein A existed in all japonica cultivars but, with the exception of IR-36, could not be found in other indica cultivars. Therefore, proteins A, E and F can be used as markers for the identification of indica and japonica. Some so-called Javanica cultivars showed the characteristics of japonica subspecies with regard to proteins A and F, while one other cultivar of Javanica expressed a type intermediate between indica and japonica interms of proteins A and E. One feature discriminating between Javanica and japonica cultivars was found in the D, G, and J proteins which were expressed strongly in Javanica cultivars but were scarcely expressed in those of japonica. Expression of subspecies-specific proteins E and F in f₁ hybrids was also investigated.     

Chediak–Higashi Syndrome: A Rare Disorder of Lysosomes and Lysosome Related Organelles

Chediak–Higashi Syndrome (CHS) is a rare autosomal recessive disorder characterized by severe immunologic defects including recurrent bacterial infections, impaired chemotaxis and abnormal natural killer (NK) cell function. Patients with this syndrome exhibit other symptoms such as an associated lymphoproliferative syndrome, bleeding tendencies, partial albinism and peripheral neuropathies. The classic diagnostic feature of CHS is the presence of huge lysosomes and cytoplasmic granules within cells. Similar defects are found in other mammals, the most well studied being the beige mouse and Aleutian mink. A positional cloning approach resulted in the identification of the Beige gene on chromosome 13 in mice and the CHS1/LYST gene on chromosome 1 in humans. The protein encoded by this gene is 3801 amino acids and is highly conserved throughout evolution. The identification of CHS1/Beige has defined a family of genes containing a common BEACH motif. The function of these proteins in vesicular trafficking remains unknown.     

Population dynamics of bacteria associated with different strains of the pine wood nematode Bursaphelenchus xylophilus after inoculation in maritime pine (Pinus pinaster)

For a long time it was thought that Bursaphelenchus xylophilus was the only agent of the pine wilt disease. Recently, it was discovered that there are bacteria associated with the nematodes that contribute to the pathogenesis of this disease, mainly through the release of toxins that promote the death of the pines. Among the species most commonly found, are bacteria belonging to the Bacillus, Pantoea, Pseudomonas and Xanthomonas genera.The main objective of this work was to study the effect of inoculation of maritime pine (Pinus pinaster) with four different nematode isolates, in the bacterial population of nematodes and trees, at different stages of disease progression. The monitoring of progression of disease symptoms was also recorded. Also, the identification of bacteria isolated from the xylem of trees and the surface of nematodes was performed by classical identification methods, by the API20E identification system and by sequencing of bacterial DNA.The results showed that for the symptoms progression, the most striking difference was observed for the pines inoculated with the avirulent isolate, C14-5, which led to a slower and less severe aggravation of symptoms than in pines inoculated with the virulent isolates. In general, it was found that bacterial population, inside the tree, increased with disease progression. A superior bacterial quantity was isolated from pines inoculated with the nematode isolates HF and 20, and, comparatively, few bacteria were isolated from pines inoculated with the avirulent isolate. The identification system API20E was insufficient in the identification of bacterial species; Enterobacter cloacae species was identified in 79% of the isolated bacterial colonies and seven of these colonies could not be identified by this method. Molecular identification methods, through bacterial DNA sequencing, allowed a more reliable identification: eleven different bacterial species within the Bacillus, Citrobacter, Enterobacter, Escherichia, Klebsiella, Paenibacillus, Pantoea and Terribacillus genera were identified. General bacterial diversity increased with the progression of the disease. Bacillus spp. were predominant at the earlier stage of disease progression and Klebsiella oxytoca at the later stages. Furthermore, bacterial species isolated from the surface of nematodes were similar to those isolated from the xylem of pines.In the present work new bacterial species were identified which have never been reported before in this type of study and may be associated with their geographical origin (Portugal). P. pinaster, the pine species used in this study, was different from those commonly grown in Japan and China. Furthermore, it was the first time that bacteria were isolated and identified from an avirulent pine wood nematode isolate.     

A simple medium for isolation and identification of Candida albicans directly from clinical specimens

A simple and specific medium consisting of chitosan, trypticase, Tween-80 and agar is devised to isolate the organisms directly from the clinical specimens and to produce germ tubes and chlamydospores for rapid differentiation and identification of Candida albicans from other closely related Candida species. By manipulating the incubating conditions, the specific phase of the organism can be produced in liquid or on solid medium at different time intervals to study the physiology of the organism.Many methods and media have been proposed in the past for identification of Candida albicans and to differentiate this from the closely related species of Candida (5–8, 15). Taschdjian, Burchall&Kozinn (15) showed that C. albicans produces germ tube within an hour or two when it is grown in human or animal serum or serum substitutes. The specificity of this germ tube test was later confirmed by various workers by using different media (3–5). The distinctive feature that differentiates C. albicans from other species is the production of chlamydospores (14). However, in all these studies three types of media were required to isolate the organisms from clinical specimens and to produce germ tubes and chlamydospores for identification. Recently studies have shown that a single medium can be employed to produce both structural components of the organism from the primary isolation medium but the preparation of the medium is more exhaustive (1) and time consuming (13) than the medium to be described here. The present investigation was therefore undertaken to develop a simple and specific medium to isolate the organism directly from the clinical specimens and to produce various morphological phases of Candida albicans to differentiate from other closely related Candida species for clinical diagnosis and to provide a medium to study the physiology and metabolism of the organism under in vitro conditions.Supported in part by Grant CA 20917, National Cancer Institute, National Institutes of Health and ALSAC.     

Verification of an Edwardsiella ictaluri‐specific diagnostic PCR

Aims: To verify the specificity of a PCR assay for the identification and diagnosis of Edwardsiella ictaluri. Methods and Results: An Edwardsiella ictaluri‐specific PCR assay was developed utilizing two features of the ribosomal DNA gene clusters. The first feature is the presence of two ribosomal gene clusters located in tandem to one another (the inter‐ribosomal spacer, IRS). This characteristic is present in the Edwardsiella genus but absent in the other sequenced members of the Enterobacteriaceae. The second feature is the presence of an intervening sequence (IVS) in the 23S rRNA gene of Edw. ictaluri. To verify the specificity of this assay, we tested genomic DNA from a variety of bacterial species. The IVS/IRS PCR assay results in an c. 2000‐bp product from all Edw. ictaluri isolates tested, but not from any other species including Edwardsiella tarda. Conclusions: The IVS/IRS PCR assay is highly specific for Edw. ictaluri and useful as a tool for identifying this pathogen. Significance and Impact of the Study: This research verifies the specificity of PCR‐based assay for Edw. Ictaluri, and we describe this assay as a highly versatile diagnostic tool for its identification.     

Simple technique for distinguishing Yellow‐bellied Flycatchers from Cordilleran and Pacific‐slope flycatchers

Flycatchers of the genus Empidonax are readily misidentified in the field, in the hand, and even in museum collections. We describe a novel plumage feature that can be used to distinguish Yellow‐bellied Flycatchers (E. flaviventris) from the two species that comprise the Western Flycatcher complex, Cordilleran Flycatchers (E. occidentalis) and Pacific‐slope Flycatchers (E. difficilis). The length of the buffy fringing on the anterior edge of each secondary feather, visible on the folded wing, is significantly shorter in Yellow‐bellied Flycatchers than in Western flycatchers, with minimal overlap. A definitive identification can be made using a simple formula that includes measurements of wing chord and the length of the buffy fringing along the outer edge of the first secondary (S1). This method provides definitive in‐hand identification, and the difference in length of the buffy fringing on the secondaries is also a useful field mark for visual identification. Testing our method with 113 museum specimens that had been identified a priori based on locality, we correctly identified 112 specimens. The exception was a specimen from Illinois that had been assumed to be a Yellow‐bellied Flycatcher. However, based on our formula, it was a Western flycatcher and analysis of its mtDNA sequence confirmed this result, proving the utility of our method.     

Development of a method based on surface enhanced laser desorption and ionization time of flight mass spectrometry for rapid identification of <Emphasis Type="Italic">Klebsiella pneumoniae</Emphasis>

A method based on surface enhanced laser desorption and ionization time of flight mass spectrometry (SELDI-TOF MS) was developed for the rapid identification of Klebsiella pneumoniae by directly applying bacterial colonies without further protein extraction. A total of 40 K. pneumoniae and 114 other related microorganisms isolated clinically were analyzed by SELDI-TOF MS. An identification model for K. pneumoniae was established by artificial neural networks (ANNs) with classification accuracy of 100%. The model was blindly tested with 43 K. pneumoniae and 53 control bacteria again. The results showed that the model was successful with accuracy of 96.9%, sensitivity of 100% and specificity of 943%. This strategy is potential for rapid identification of K. pneumoniae.     

Comparative Cytogenetics Among Allopatric Populations of the Fish, Hoplias Malabaricus. Cytotypes with 2n = 42 Chromosomes

The available chromosomal data on Hoplias malabaricus make possible the identification of three major karyotypic forms in this fish group, all of them bearing 2n = 42 chromosomes, and named as Cytotypes A, B and E in previous studies. While Cytotype A and B share a general macrokaryotypic feature, Cytotype E is well differentiated concerning the morphology and size of some chromosome pairs. On the other hand, Cytotype B presents an exclusive XX/XY sex chromosome system. Six allopatric populations, belonging to Cytotype A, were subjected to cytogenetic analysis in the present study. Despite their basic karyotypic similarity, some differences in the chromosome formulae, as well as in the heterochromatin and Ag-NORs locations, were observed among populations indicating that they no more correspond to a unit, at least in the cytogenetical level. This revised version was published online in July 2006 with corrections to the Cover Date.     

Sequence analysis of mitochondrial 16S ribosomal RNA gene fragment from seven mosquito species

Mosquitoes are vectors for the transmission of many human pathogens that include viruses, nematodes and protozoa. For the understanding of their vectorial capacity, identification of disease carrying and refractory strains is essential. Recently, molecular taxonomic techniques have been utilized for this purpose. Sequence analysis of the mitochondrial 16S rRNA gene has been used for molecular taxonomy in many insects. In this paper, we have analysed a 450 bp hypervariable region of the mitochondrial 16S rRNA gene in three major genera of mosquitoes,Aedes, Anopheles andCulex. The sequence was found to be unusually A + T rich and in substitutions the rate of transversions was higher than the transition rate. A phylogenetic tree was constructed with these sequences. An interesting feature of the sequences was a stretch of Ts that distinguished betweenAedes andCulex on the one hand, andAnopheles on the other. This is the first report of mitochondrial rRNA sequences from these medically important genera of mosquitoes.     

Occurrence of Apristurus species in the Galicia Bank Seamount (NE Atlantic)

The aim of this study was to identify some of the Apristurus species by combining morphometric and genetic tools. Several specimens of the genus Apristurus were caught on the Galicia Bank Seamount (NE Atlantic), between 1460 and 1809 m depths, during a multidisciplinary survey carried out in 2011 within the framework of the INDEMARES Project. Morphometric and genetic analyses were conducted to aid the identification of the specimens collected. A total of 20 specimens were identified, of which 18 corresponded to Apristurus aphyodes (Nakaya and Stehmann, 1998 ), one to A. profundorum (Goode and Bean, 1896 ) and one to A. melanoasper Iglesias, Nakaya & Stehmann, 2004 . Genetic results based on the mtDNA COI sequences (682–690 bp fragment of the COI gene) support the identification of A. profundorum and A. melanoasper, with a bootstrap of 99 and 96%, respectively. The identification of A. aphyodes was also performed using a 499 bp fragment of the 16S mitochondrial gene. These are the first records of the Apristurus species from Galician waters, which extends their known area of distribution and provides more information on different biological and ecological aspects of this complex taxonomic group.     

Is fungal species richness and composition related to the occurrence of the old‐growth associated wood‐decaying Amylocystis lapponica?

Amylocystis lapponica (Romell) Singer is a widely distributed wood‐decaying polypore fungus found throughout the Northern Hemisphere. Despite its huge distribution range it occurs rather patchily and seems narrowly associated with old‐growth forest stands. Notably, it has been used as an ‘indicator species’, believed to reflect the long‐term presence of dead wood, naturalness of forest stands, and indirectly, species richness and possibly composition. In this study we focused on the last issue – whether or not there is a link between the occurrence of A. lapponica and the species richness and composition of other wood‐decaying fungi. Selecting log characteristics and microclimate as similar as possible, we compared 12 logs with and 12 logs without visible fruit bodies of A. lapponica to examine: 1) if visible fruit bodies corresponded with molecular identification of the mycelia, 2) if fungal species richness and composition of the substrate were related to A. lapponica occurrence, and 3) if A. lapponica was restricted to certain parts of the log. Fungal species were recorded by inspecting visible fruit bodies and by culture isolation and ITS sequencing from wood disc samples. Laboratory and field identification of A. lapponica had 71% correspondence, and mycelia were identified in two logs without visible fruit bodies. Twice as many fungal species were detected using ITS sequencing compared to fruit body identification. Total species richness was similar between the two log categories, but number of species per log was slightly higher in A. lapponica logs. Antrodia serialis (Fr.) Donk, and possibly also Fomitopsis pinicola (Sw.:Fr.) P. Karst. and Phellinus nigrolimitatus (Romell) Bourdot & Galzin, occurred more frequently in A. lapponica logs. Mycelia of A. lapponica were restricted to less decayed parts of the wood in the centre of the middle part of the logs.