Scale morphology of greater lizardfish Saurida tumbil (Bloch, 1795) (Pisces: Synodontidae)

A comparative study comprising scale morphology and squamation of Saurida tumbil was conducted to identify the most useful scale and squamation characters within the different body regions and length groups and to clarify their significance for future systematic studies. The presence of the caudal pores is documented for the first time in teleosts. In addition, the presence of crenae and spines formed by posterior orientation and projection of circuli is recorded for the first time in a member of the Synodontidae. Scales of S. tumbil show some characters that are either never seen or they are exceedingly rare in scales of other teleosts. These are: two types of scalar denticles, denticles in the inter-circular area, and twin or Siamese scales. Several other scale characters have shown a consistent variation in different body regions and in fishes from different length groups. These are: focus position; bilobate rostral field edge; presence of three radii; long, narrow and separated crenae; papillae-form, crowded scalar denticles with posterior directed spines; the number of scale rows between anterior end of the dorsal fin and the lateral line.     

Pollen–plant–climate relationships in sub-Saharan Africa

Aim  To demonstrate that incorporating the bioclimatic range of possible contributor plants leads to improved accuracy in interpreting the palaeoclimatic record of taxonomically complex pollen types.
Location  North Tropical Africa.
Methods  The geographical ranges of selected African plants were extracted from the literature and geo-referenced. These plant ranges were compared with the pollen percentages obtained from a network of surface sediments. Climate-response surfaces were graphed for each pollen taxon and each corresponding plant species.
Results  Several patterns can be identified, including taxa for which the pollen and plant distributions coincide, and others where the range limits diverge. Some pollen types display a reduced climate range compared with that of the corresponding plant species, due to low pollen production and/or dispersal. For other taxa, corresponding to high pollen producers such as pioneer taxa, pollen types display a larger climatic envelope than that of the corresponding plants. The number of species contained in a pollen taxon is an important factor, as the botanical species included in a taxon may have different geographical and climate distributions.
Main conclusions  The comparison between pollen and plant distributions is an essential step towards more precise vegetation and climate reconstructions in Africa, as it identifies taxa that have a high correspondence between pollen and plant distribution patterns. Our method is a useful tool to reassess biome reconstructions in Africa and to characterize accurately the vegetation and climate conditions at a regional scale, from pollen data.     

Serum‐free media for the production of human mesenchymal stromal cells: a review

The regenerative potential of mesenchymal stromal cells (MSC) holds great promise in using them for treatment of a wide range of debilitating diseases. Several types of culture media and systems have been used for large‐scale expansion of MSCs in vitro; however, the majority of them rely heavily on using foetal bovine serum (FBS)‐supplement for optimal cell proliferation. FBS‐based cultures pose the potential threat of spread of transmissible spongiform encephalopathy and bovine spongiform encephalopathy to MSCs and then to their recipients. A recent trend in cell culture is to change from serum‐use to serum‐free media (SFM). In this context, the current review focuses specifically on employment of various SFM for MSCs and discusses existences of various options with which to substitute FBS. In addition, we analyse MSC population growth kinetic patterns using various SFM for large‐scale production of MSCs.     

Three levels of floristical variation in the forests of Chaco,Argentina

Abstract. This paper analyses the floristic variation in the southern segment of the Oriental Chaco, known as the Santa Fe Forest Wedge. Floristical variation in Chaco forests is described at three levels of scale. On the coarsest scale there is a gradient of increasing floristic richness towards the north, related to a geographic temperature gradient. At an intermediate scale different types of forests are arranged according to environmental gradients correlated with topographic elevation. At a fine scale many microsites can be discerned with different micro-environments colonized differentially by species. Microsites arise as the result of site-physiographic history, development of vegetation and the interaction of both and with animals. Several dimensions of regenerationniche variation are distinguished, including canopy and soil characteristics, and propagule dispersal.     

Testing the European stream typology of the Water Framework Directive for macroinvertebrates

In the EU Water Framework Directive (WFD) a typological framework is defined for assessing the ecological quality of water bodies in the future. The conditions in the Directive impose a strong demand for `new' assessment systems. During the AQEM project an assessment system was developed for European streams using macroinvertebrates. The aim of this study was to test if the typology suggested in the WFD is useful for developing an assessment system for macroinvertebrates in streams. In total 889 streams of 29 stream types were sampled in eight countries all over the major geographical gradients in Europe. These stream types fit the WFD typological demands and fit to the major European geographic regions (ecoregions). The sites included gradients from reference conditions (for the definition see Nijboer et al., 2004) to sites with bad ecological quality. Despite standardisation there were large differences between the participating countries concerning the number of taxa, the number of specimens and the taxonomic resolution. The data, including macroinvertebrates and environmental variables were analysed by using Canonical Correspondence Analysis (CCA). The observed macroinvertebrate distribution largely supported the WFD typological criteria. This means that the major macroinvertebrate distribution patterns in European streams follow climatological and geomorphological conditions and are well distinguished in terms of stream types. Furthermore, it was shown that large scale factors affected the macroinvertebrate distribution even on a very fine scale. Most explanatory variables seemed to be scale independent. Even at a fine scale major factors concerning geology, geomorphology and hydrology added to the species occurrences. Within stream types morphology together with physico-chemistry best explained the macroinvertebrates distribution. In conclusion, the WFD typology is useful for an assessment system for streams using macroinvertebrates. The large scale factors were indeed the variables that explained most of the variation in species composition. But as these factors even strongly act at the scale of stream types, a further refinement is most probably necessary to disentangle typological actors from water quality ones.     

Induction of somatic mutations in Ephestia by injections of mustard gas solutions

Summary Experiments were carried out using nitrogen-mustard (HN-2) as mutagenic agent for the induction of somatic mutations in Ephestia.Larvae of the last instar were injected with different concentrations of HN-2. Several mutant scales of the same types as observed after x-ray treatment were scored. The HN-2 induced mutation spectrum differs significantly from the x-ray induced one.Several possible explanations are discussed.     

Distribution of mating type alleles in the wheat pathogen Mycosphaerella graminicola over spatial scales from lesions to continents

A total of 2035 Mycosphaerella graminicola strains collected from 16 geographic locations on four continents were assayed for the mating type locus. RFLP fingerprints were used to identify clones in each population. At the smallest spatial scale analyzed, both mating types were found among fungal strains sampled from different lesions of the same leaf as well as from different pycnidia in the same lesion. At larger spatial scales, the two mating types were found at equal frequencies across spatial scales ranging from several square meters to several thousand square kilometers. Though the absolute frequencies of the two mating types sometimes varied for different sampling units within the same spatial scale in the hierarchy (plots within a field, fields within a country, or different continents of the world), none of the differences were statistically significant from the null hypothesis of equal frequencies for the two mating types. The evolutionary forces likely to maintain the even distribution of the two mating types in this pathogen were discussed.     

Alternative splicing in ascomycetes

Alternative splicing is a complex and regulated process, which results in mRNA with different coding capacities from a single gene. Extend and types of alternative splicing vary greatly among eukaryotes. In this review, I focus on alternative splicing in ascomycetes, which in general have significant lower extend of alternative splicing than mammals. Yeast-like species have low numbers of introns and consequently alternative splicing is lower compared to filamentous fungi. Several examples from single studies as well as from genomic scale analysis are presented, including a survey of alternative splicing in Neurospora crassa. Another focus is regulation by riboswitch RNA and alternative splicing in a heterologous system, along with putative protein factors involved in regulation.     

Plant lectins: the ties that bind in root symbiosis and plant defense

Lectins are a diverse group of carbohydrate-binding proteins that are found within and associated with organisms from all kingdoms of life. Several different classes of plant lectins serve a diverse array of functions. The most prominent of these include participation in plant defense against predators and pathogens and involvement in symbiotic interactions between host plants and symbiotic microbes, including mycorrhizal fungi and nitrogen-fixing rhizobia. Extensive biological, biochemical, and molecular studies have shed light on the functions of plant lectins, and a plethora of uncharacterized lectin genes are being revealed at the genomic scale, suggesting unexplored and novel diversity in plant lectin structure and function. Integration of the results from these different types of research is beginning to yield a more detailed understanding of the function of lectins in symbiosis, defense, and plant biology in general.     

Genetic diversity of Porphyromonas gingivalis isolates recovered from single "refractory" periodontitis sites

Multilocus sequence typing and fimA genotyping were performed on Porphyromonas gingivalis isolates from 15 subjects with "refractory" periodontitis. Several sequence types were detected for most individual pockets. The variation indicated recombination at the recA and pepO genes. The prevalence of fimA genotypes II and IV confirmed their association with periodontitis.     

An analysis of extensible modelling for functional genomics data

Background  

Several data formats have been developed for large scale biological experiments, using a variety of methodologies. Most data formats contain a mechanism for allowing extensions to encode unanticipated data types. Extensions to data formats are important because the experimental methodologies tend to be fairly diverse and rapidly evolving, which hinders the creation of formats that will be stable over time.     

Large Scale Application of Neural Network Based Semantic Role Labeling for Automated Relation Extraction from Biomedical Texts

To reduce the increasing amount of time spent on literature search in the life sciences, several methods for automated knowledge extraction have been developed. Co-occurrence based approaches can deal with large text corpora like MEDLINE in an acceptable time but are not able to extract any specific type of semantic relation. Semantic relation extraction methods based on syntax trees, on the other hand, are computationally expensive and the interpretation of the generated trees is difficult. Several natural language processing (NLP) approaches for the biomedical domain exist focusing specifically on the detection of a limited set of relation types. For systems biology, generic approaches for the detection of a multitude of relation types which in addition are able to process large text corpora are needed but the number of systems meeting both requirements is very limited. We introduce the use of SENNA (“Semantic Extraction using a Neural Network Architecture”), a fast and accurate neural network based Semantic Role Labeling (SRL) program, for the large scale extraction of semantic relations from the biomedical literature. A comparison of processing times of SENNA and other SRL systems or syntactical parsers used in the biomedical domain revealed that SENNA is the fastest Proposition Bank (PropBank) conforming SRL program currently available. 89 million biomedical sentences were tagged with SENNA on a 100 node cluster within three days. The accuracy of the presented relation extraction approach was evaluated on two test sets of annotated sentences resulting in precision/recall values of 0.71/0.43. We show that the accuracy as well as processing speed of the proposed semantic relation extraction approach is sufficient for its large scale application on biomedical text. The proposed approach is highly generalizable regarding the supported relation types and appears to be especially suited for general-purpose, broad-scale text mining systems. The presented approach bridges the gap between fast, cooccurrence-based approaches lacking semantic relations and highly specialized and computationally demanding NLP approaches.     

Moderate disturbances accelerate forest transition dynamics under climate change in the temperate–boreal ecotone of eastern North America

Several temperate tree species are expected to migrate northward and colonize boreal forests in response to climate change. Tree migrations could lead to transitions in forest types, but these could be influenced by several non‐climatic factors, such as disturbances and soil conditions. We analysed over 10,000 forest inventory plots, sampled from 1970 to 2018 in meridional Québec, Canada, to identify what environmental conditions promote or prevent regional‐scale forest transitions. We used a continuous‐time multi‐state Markov model to quantify the probabilities of transitions between forest states (temperate, boreal, mixed, pioneer) as a function of climate (mean temperature and climate moisture index during the growing season), soil conditions (pH and drainage) and disturbances (severity levels of natural disturbances and logging). We further investigate how different disturbance types and severities impact forests' short‐term transient dynamics and long‐term equilibrium using properties of Markov transition matrices. The most common transitions observed during the study period were from mixed to temperate states, as well as from pioneer to boreal forests. In our study, transitions were mainly driven by natural and anthropogenic disturbances and secondarily by climate, whereas soil characteristics exerted relatively minor constraints. While major disturbances only promoted transitions to the pioneer state, moderate disturbances increased the probability of transition from mixed to temperate states. Long‐term projections of our model under the current environmental conditions indicate that moderate disturbances would promote a northward shift of the temperate forest. Moreover, disturbances reduced turnover and convergence time for all transitions, thereby accelerating forest dynamics. Contrary to our expectation, mixed to temperate transitions were not driven by temperate tree recruitment but by mortality and growth. Overall, our results suggest that moderate disturbances could catalyse rapid forest transitions and accelerate broad‐scale biome shifts.     

Ecological Succession,Hydrology and Carbon Acquisition of Biological Soil Crusts Measured at the Micro-Scale

The hydrological characteristics of biological soil crusts (BSCs) are not well understood. In particular the relationship between runoff and BSC surfaces at relatively large (>1 m²) scales is ambiguous. Further, there is a dearth of information on small scale (mm to cm) hydrological characterization of crust types which severely limits any interpretation of trends at larger scales. Site differences and broad classifications of BSCs as one soil surface type rather than into functional form exacerbate the problem. This study examines, for the first time, some hydrological characteristics and related surface variables of a range of crust types at one site and at a small scale (sub mm to mm). X-ray tomography and fine scale hydrological measurements were made on intact BSCs, followed by C and C isotopic analyses. A ‘hump’ shaped relationship was found between the successional stage/sensitivity to physical disturbance classification of BSCs and their hydrophobicity, and a similar but ‘inverse hump’ relationship exists with hydraulic conductivity. Several bivariate relationships were found between hydrological variables. Hydraulic conductivity and hydrophobicity of BSCs were closely related but this association was confounded by crust type. The surface coverage of crust and the microporosity 0.5 mm below the crust surface were closely associated irrespective of crust type. The δ ¹³C signatures of the BSCs were also related to hydraulic conductivity, suggesting that the hydrological characteristics of BSCs alter the chemical processes of their immediate surroundings via the physiological response (C acquisition) of the crust itself. These small scale results illustrate the wide range of hydrological properties associated with BSCs, and suggest associations between the ecological successional stage/functional form of BSCs and their ecohydrological role that needs further examination.     

Modeling grassland aboveground biomass using a pure vegetation index

Remote sensing can be the most effective means of scaling up grassland aboveground biomass (AGB) from the sample scale to the regional scale. Among the remote-sensing approaches, statistical models based on the vegetation index (VI) are frequently used to retrieve grassland AGB because of their simplicity and reliability. However, these types of models have never been comprehensively optimized to overcome VI insensitivity and soil effects. Because grassland AGB is related to grassland type, in our research the integrated orderly classification system for grassland (IOCSG) was used to differentiate grassland types. The study area, located in Inner Mongolia, China, included desert steppe, typical steppe and meadow steppe. A pure VI (PVI) was extracted from the normal VI using spectral mixture analysis (SMA). Using a proportional relationship, PVI models were then constructed based on grassland type. The results demonstrated that the PVI models can have clear advantages over the more commonly used VI models. They simplify the parameterization of VI models and thus enhance models constructed for different regions with different remote sensing data sources. Notably, detailed differentiation of grassland types can improve the accuracy of AGB estimates. The methodology proposed in this study is particularly beneficial for AGB estimates at a national scale, especially for countries such as China with many grassland types.     

Characterization by polymerase chain reaction of ruminant rotaviruses isolated in Italy.

Several group A rotaviruses isolated in Italy from cattle, buffalos and goats were characterized by polymerase chain reaction assay for G- and P-type. G6 and P5 were the types most frequently recovered. The genotypes of buffalo and goat strains were similar to those of cattle isolates.     

Genetics of growth habit and development of new coleus (Solenostemon scutellarioides (L.) Codd) varieties with trailing habit and bright color

A high level of genetic variability for growth habit types is observed in tetraploid, cultivated coleus (Solenostemon scutellarioides (L.) Codd). Very few cultivars with trailing habit exist, and those that are available generally have dark green or purple foliage color. Coleus with trailing growth habit is desirable as it increases its utility for use in hanging baskets, mixed containers, and as ground cover. There is a lack of published information on the genetic mechanism controlling growth habit and the development of new trailing types with orange colors. Two commercial cultivars, "Red Trailing Queen" (RQ) with trailing habit and "Sedona" (S) with upright stature, were selfed and crossed (RQ x S) to produce self and F(1) populations. F(2) populations were produced by selfing plants in the F(1) population. For each population analyzed, growth habit was rated on a visual 1-5 phenotypic scale, where 1 = upright, 2 = semi-upright, 3 = prostrate, 4 = semitrailing, and 5 = trailing. Genotypes were assigned to each phenotype, assuming that upright was dominant to trailing. In this study, growth habit was observed to be controlled by a single gene (U) with additive effects, with upright growth habit designated with a UUUU genotype and trailing growth habit designated with a uuuu genotype. In addition, foliage color was rated on a visual 1-5 phenotypic scale, and purple foliage color was found to be dominant to yellow-orange color. Several new coleus selections with trailing growth habit and orange foliage color were successfully developed.     

New Suppressors of Frameshift Mutations in SALMONELLA TYPHIMURIUM

Several new types of suppressor mutants have been isolated. These were identified among revertants of mutants originally generated by mutagens other than the acridine-derived ICR191. The new suppressors correct mutations other than those with runs of C or G which are recognized by the previously described suppressors. Several frameshift mutations are corrected by more than one suppressor type. Apparently, the DNA base sequence near these mutant sites includes sites of action for several distinct suppressor types.     

基于Ripley L和O-ring函数的森林景观空间分布格局及其关联性

采用空间点格局分析中的Ripley L和O-ring函数,以大兴安岭盘古林场森林资源二类调查数据为例,对比分析2种方法在森林景观类型的空间分布格局及其关联性研究中的差异.结果表明: 2种方法获得的景观空间分布格局在整体趋势上反映一致,都是在中小尺度上呈聚集分布,之后随着尺度的增大主要表现为随机分布特征;景观类型间的关联性存在显著差异,其中,Ripley L函数结果表明,天然落叶松林、天然白桦林分别与针阔混交林在中小尺度上呈负相关,而在更大尺度上整体表现出无关联性或正关联性的趋势,其余景观类型间在所有研究尺度上呈显著负相关; O-ring函数结果则表明,4种森林景观类型两两之间均呈现出相似的关联性变化趋势,即在小尺度上均表现为负相关,在中等尺度上均呈现出不相关性,但在更大尺度上呈正相关趋势;对同一景观类型(或景观类型组),2种方法在不同尺度等级上的空间分布格局及其关联性的判别一致率存在较大差异,其一致性判别率在所有研究尺度上整体呈现出基本不变、先下降后增加和一直下降3种趋势.     

Types of morphogenesis of the dermal skeleton in fossil sharks

Four types of morphogenesis of the dermal skeleton can be distinguished. They differ with regard to scale growth, scale replacement and insertion of new scales during ontogeny. Three of the types occur exclusively in fossil sharks and have been found in only a few articulate specimens. In only one case (Jurassic hybodontids) it is possible to trace the phyletic transition from one type to another. The adaptive significance, both of different types of morphogenesis of the dermal skeleton as well as different types of scale shapes, is discussed.