Species distributions: virtual or real – the case of Arbaciella elegans (Echinoidea: Arbaciidae)

The distribution of species is expressed by their occurrence in local faunal lists often compiled by non‐taxonomists. In the case of rare or cryptic species, this can pose a severe limitation on the validity and thus the application of the resulting biodiversity data. Here, we show an example of a shallow‐water echinoid to illustrate problematic distribution data based on misidentification. This species, Arbaciella elegans, was established on the basis of Central African material and later reported from various places in the Mediterranean and the Northern Atlantic. Morphological comparison with the type material casts considerable doubt on the validity of these records. Genetical characterization of material from the Azores clearly shows that the dark Arbaciella phenotype reported to the Mediterranean and north‐east Atlantic in fact represents juveniles of another species, namely Arbacia lixula.     

Exploring the carbohydrate‐binding ability of Canavalia bonariensis lectin in inflammation models

Lectins are a group of proteins of non‐immune origin recognized for their ability to bind reversibly to carbohydrates. Researchers have been intrigued by oligosaccharides and glycoconjugates for their involvement as mediators of complex cellular events and then many biotechnological applications of lectins are based on glycocode decoding and their activities. Here, we report a structural and biological study of a ConA‐like mannose/glucose‐specific lectin from Canavalia bonariensis seeds, CaBo. More specifically, we evaluate the binding of CaBo with α‐methyl‐D‐mannoside (MMA) and mannose‐1,3‐α‐D‐mannose (M13) and the resultant in vivo effects on a rat model of acute inflammation. A virtual screening was also carried out to cover a larger number of possible bindings of CaBo. In silico analysis demonstrated the stability of CaBo interaction with mannose‐type ligands, and the lectin was able to induce acute inflammation in rats with the participation of the carbohydrate recognition domain (CRD) and histamine release. These results confirm the ability of CaBo to interact with hybrid and high‐mannose N‐glycans, supporting the hypothesis that CaBo's biological activity occurs primarily through its interaction with cell surface glycosylated receptors.     

Purification,Chemical, and Immunochemical Properties of a New Lectin from Mimosoideae (Parkia Discolor)

ABSTRACT

A glucose/mannose-binding lectin was isolated from seeds of Parkia discolor (Mimosoideae) using affinity chromatography on Sephadex G-100 gel. The protein presented a unique component in SDS-PAGE corresponding to a molecular mass of 58,000 Da, which is very similar to that of a closely related lectin from Parkia platycephala. Among the simple sugars tested, mannose was the best inhibitor, but biantennary glycans, containing the trimannoside core, present in N-glycoproteins, also seem to be powerful inhibitors of the haemagglutinating activity induced by the purified lectin. The protein was characterised by high content of glycine and proline and absence of cysteine. Rabbit antibodies, anti-P. platycephala seed lectin, recognised the P.discolor lectin. However, no cross-reaction was observed when a set of other legume lectins from sub-family Papilionoideae and others from families Moraceae and Euphorbiaceae were assayed with the Parkia lectins. This suggests that Parkia lectins comprise a new group of legume lectins exhibiting distinct characteristics.     

Sexual differences in reproductive phenology and their consequences for the demography of Baccharis dracunculifolia (Asteraceae), a dioecious tropical shrub

Patterns of phenological variation and reproductive investment were studied in the dioecious shrub Baccharis dracunculifolia DC (Asteraceae), and possible consequences on survivorship were evaluated. The sex ratio was determined in a natural field population (n = 921) of B. dracunculifolia in Belo Horizonte, Brazil. Fifty-two males and 56 females were sampled at random from this population. During the reproductive season of 1999, inflorescence production, shoot growth and mortality, and xylem water potential were recorded for each individual. The population sex ratio was male-biased (1.27 : 1, P < 0.05), and was associated with a higher mortality of female shoots (38.4 vs. 23.1 %, P < 0.05), and individuals (17.8 vs. 11.5 %, P < 0.1), despite lower water stress in female plants. Flowering phenology also differed between the sexes, with males producing more inflorescences, and earlier, than females. Owing to fruit maturation, the number of inflorescences supported by females was higher than that supported by males later in the reproductive season. This occurred during the dry season, and drought stress may have been responsible for the greater female mortality. Thus, the male-biased sex ratio in this population of B. dracunculifolia is probably due to different reproductive functions of males and females. Intersexual differences in reproductive phenology had consequences for plant demography.     

BiC2PAM: constraint-guided biclustering for biological data analysis with domain knowledge

Background

Biclustering has been largely used in biological data analysis, enabling the discovery of putative functional modules from omic and network data. Despite the recognized importance of incorporating domain knowledge to guide biclustering and guarantee a focus on relevant and non-trivial biclusters, this possibility has not yet been comprehensively addressed. This results from the fact that the majority of existing algorithms are only able to deliver sub-optimal solutions with restrictive assumptions on the structure, coherency and quality of biclustering solutions, thus preventing the up-front satisfaction of knowledge-driven constraints. Interestingly, in recent years, a clearer understanding of the synergies between pattern mining and biclustering gave rise to a new class of algorithms, termed as pattern-based biclustering algorithms. These algorithms, able to efficiently discover flexible biclustering solutions with optimality guarantees, are thus positioned as good candidates for knowledge incorporation. In this context, this work aims to bridge the current lack of solid views on the use of background knowledge to guide (pattern-based) biclustering tasks.

Methods

This work extends (pattern-based) biclustering algorithms to guarantee the satisfiability of constraints derived from background knowledge and to effectively explore efficiency gains from their incorporation. In this context, we first show the relevance of constraints with succinct, (anti-)monotone and convertible properties for the analysis of expression data and biological networks. We further show how pattern-based biclustering algorithms can be adapted to effectively prune of the search space in the presence of such constraints, as well as be guided in the presence of biological annotations. Relying on these contributions, we propose BiClustering with Constraints using PAttern Mining (BiC2PAM), an extension of BicPAM and BicNET biclustering algorithms.

Results

Experimental results on biological data demonstrate the importance of incorporating knowledge within biclustering to foster efficiency and enable the discovery of non-trivial biclusters with heightened biological relevance.

Conclusions

This work provides the first comprehensive view and sound algorithm for biclustering biological data with constraints derived from user expectations, knowledge repositories and/or literature.

     

Is filament clipping an effective tool for tissue sampling in <Emphasis Type="Italic">Hippocampus guttulatus</Emphasis>?

Examining genetic diversity, population structure, and geographic distribution has become an important part in the conservation strategies of endangered populations. However, these studies rely on tissue samples collection for DNA analysis which may be problematic for species with a sensitive conservation status. Partial fin-clipping has been employed for tissue collection, due to the increased popularity of DNA-based analysis for ecological and fisheries studies, however, fin clipping can potentially affect behavior, swimming performance, predator avoidance and the ability to find and capture prey. This study aimed to test the effects of filament clipping using captive breed seahorses (Hippocampus guttulatus) as an alternative tool for tissue sample. Clipped filaments regrew on average 0.05?±?0.02 mm/day for 3 months and no mortality or disease was observed during the experiment. Filaments provided enough tissue for DNA analysis. This study provided valuable information regarding a new sampling technique that does not impair the seahorse locomotion. This methodology may be used in population’s genetic studies of other species that have skin filaments as a morphological trait.     

Molecular comparisons of native range collections of Gadirtha fusca,a potential biological control agent of Chinese tallowtree

Chinese tallowtree, Triadica sebifera (L.) Small (Euphorbiaceae), is one of the worst invasive weeds of the southeastern USA impacting coastal wetlands, forests, and natural areas. A proposed biological control candidate, the defoliating moth Gadirtha fusca Pogue (Lepidoptera: Nolidae) shows high specificity for the target weed Chinese tallowtree. A total of 13 field sites were sampled in the native range of this herbivore species. To determine if all individuals were the same taxon, molecular DNA analyses were conducted of these collections. These included collections from 2012, 2015 and 2016, from three regions and two adult color morphs. Molecular COI analysis was performed on thirty colonized individuals from these collections. The results of this analysis arranged all taxa into a single clade with average genetic divergence values of 0.3%. Comparison of these G. fusca sequences and those from other Gadirtha spp. all had divergence values that were equal to or exceeded 5%. These results indicate that all the G. fusca collections were a single species and they were distinct from other known members of this genus.     

Partition of malathion in synthetic and native membranes

Partition coefficients of [14C]malathion in model and native membranes are affected by temperature, cholesterol content, and lipid chain length. Partition in egg phosphatidylcholine bilayers decreases linearly with temperature, over a range (10-40 degrees C) at which the lipid is in the liquid-crystalline state. Addition of 50 mol% cholesterol severely decreases partition and practically abolishes the temperature dependence. First-order phase transitions of dimyristoyl-, dipalmitoyl- and distearoylphosphatidylcholines (DMPC, DPPC and DSPC) are accompanied by a sharp increase in malathion partition. Apparently, the insecticide is easily accommodated in bilayers of short-aliphatic-chain lipids, since the partitions were 225, 135 and 48 in DMPC, DPPC and DSPC, respectively, at temperatures 10 Cdeg below the midpoint of their transitions. Partition values in native membranes decrease sequentially as follows: sarcoplasmic reticulum, mitochondria, brain microsomes, myelin and erythrocytes. This dependence parallels the relative content of cholesterol and is similar in liposomes of total extracted lipids, although the absolute partitions showed decreased values.     

Nerve growth factor restores mRNA levels and the expression of neuropeptides in the suprachiasmatic nucleus of rats submitted to chronic ethanol treatment and withdrawal

Brain Cell Biology - Chronic ethanol treatment and withdrawal from alcohol decrease the synthesis and expression of neuropeptides in the hypothalamic suprachiasmatic nucleus. Given the existing...     

Corticosterone replacement restores normal morphological features to the hippocampal dendrites, axons and synapses of adrenalectomized rats

A thorough evaluation of hippocampal dendrites, axons and synaptic contacts has not been undertaken following prolonged periods of absence of corticosteroids despite the marked granule cell loss which occurs in the dentate gyrus of adrenalectomized rats. Thus, we have applied morphometric techniques to analyse the dendrites of granule and pyramidal cells, the mossy fiber system, and the number and morphology of synapses between the mossy fibers and the excrescences of CA3 pyramidal cells in rats submitted to different periods of adrenalectomy. In addition, to search for the presence of neuritic reorganisation in the hippocampal formation once normal corticosteroid levels were re-established, we incorporated in this study a group of rats replaced with corticosterone one month after adrenalectomy. The results obtained in adrenalectomized rats showed a striking impoverishment of the dendrites of surviving granule cells, subtle alterations in the apical dendritic arborization of CA3 pyramidal cells and no changes in the apical dendrites of CA1 pyramidal cells. In addition, in adrenalectomized rats there was a progressive reduction in the total number of synapses established between mossy fibers and CA3 pyramids, as a consequence of a reduction in the volume of the suprapyramidal part of the mossy fiber system, and profound changes in the morphology of mossy fiber terminals and CA3 dendritic excrescences. A remarkable reorganisation of neurites was found to occur following the administration of low doses of corticosterone, completely reversing the adrenalectomy-induced synaptic loss and partially restoring the morphology of hippocampal axons and dendrites. These plastic mechanisms provide a sound structural basis for the reversibility of cognitive deficits observed after corticosterone administration to adrenalectomized rats.