FuzzyID2: A software package for large data set species identification via barcoding and metabarcoding using hidden Markov models and fuzzy set methods

Species identification through DNA barcoding or metabarcoding has become a key approach for biodiversity evaluation and ecological studies. However, the rapid accumulation of barcoding data has created some difficulties: for instance, global enquiries to a large reference library can take a very long time. We here devise a two‐step searching strategy to speed identification procedures of such queries. This firstly uses a Hidden Markov Model (HMM) algorithm to narrow the searching scope to genus level and then determines the corresponding species using minimum genetic distance. Moreover, using a fuzzy membership function, our approach also estimates the credibility of assignment results for each query. To perform this task, we developed a new software pipeline, FuzzyID2, using Python and C++. Performance of the new method was assessed using eight empirical data sets ranging from 70 to 234,535 barcodes. Five data sets (four animal, one plant) deployed the conventional barcode approach, one used metabarcodes, and two were eDNA‐based. The results showed mean accuracies of generic and species identification of 98.60% (with a minimum of 95.00% and a maximum of 100.00%) and 94.17% (with a range of 84.40%–100.00%), respectively. Tests with simulated NGS sequences based on realistic eDNA and metabarcode data demonstrated that FuzzyID2 achieved a significantly higher identification success rate than the commonly used Blast method, and the TIPP method tends to find many fewer species than either FuzztID2 or Blast. Furthermore, data sets with tens of thousands of barcodes need only a few seconds for each query assignment using FuzzyID2. Our approach provides an efficient and accurate species identification protocol for biodiversity‐related projects with large DNA sequence data sets.     

Experimental stress during molt suggests the evolution of condition‐dependent and condition‐independent ornaments in the king penguin

Sexual selection and social selection are two important theories proposed for explaining the evolution of colorful ornamental traits in animals. Understanding signal honesty requires studying how environmental and physiological factors during development influence the showy nature of sexual and social ornaments. We experimentally manipulated physiological stress and immunity status during the molt in adult king penguins (Aptenodytes patagonicus), and studied the consequences of our treatments on colourful ornaments (yellow‐orange and UV beak spots and yellow‐orange auricular feather patches) known to be used in sexual and social contexts in this species. Whereas some ornamental features showed strong condition‐dependence (yellow auricular feather chroma, yellow and UV chroma of the beak), others were condition‐independent and remained highly correlated before and after the molt (auricular patch size and beak UV hue). Our study provides a rare examination of the links between ornament determinism and selection processes in the wild. We highlight the coexistence of ornaments costly to produce that may be honest signals used in mate choice, and ornaments for which honesty may be enforced by social mediation or rely on genetic constraints.     

Effects of serotonin on the cardio-circulatory system of the European eel (Anguilla anguilla) in vivo

The effects of serotonin on continuously recorded cardiac parameters (heart rate, cardiac output, cardiac stroke volume), ventral and dorsal aortic blood pressures, branchial and systemic vascular resistances were investigated in the European eel in vivo. Intravenous administration of serotonin (30 g · kg^–1) caused a marked bradycardia (45%) and a simultaneous decrease in cardiac output (50%), ventral (35%) and dorsal (50%) aortic blood pressures. Branchial resistance was markedly increased (60%) and systemic resistance decreased (30%). Cardiac stroke volume remained unchanged. The effects of serotonin on cardiac mained unchanged. The effects of serotonin on cardiac parameters were suppressed either by methysergide or a bilateral section of the cardiac vagus. Bradycardia could then be regarded as the consequence of a vagal mechanism triggered by serotonin action on central methysergide-sensitive serotonergic receptors. No inotropic effect of serotonin was observed. This lack of myocardiac contractility modification is discussed. The serotonin-mediated branchial vasoconstriction was attenuated by vagotomy, whereas the residual increase in branchial resistance (40%) was suppressed by methysergide. The serotonin-mediated branchial vasoconstriction could be the consequence of both a passive mechanism (compliance) caused by the decrease in cardiac output and an active mechanism involving methysergide-sensitive serotonergic receptors of the branchial vasculature. A possible involvement of this vasomotor effect in gill oxygen uptake is discussed. The serotonin-induced systemic vasodilation was insensitive either to cardiac vagotomy or to 5-HT_1/2, 5-HT₃ and 5-HT₄ receptor antagonists, suggesting the involvement of a local mechanism which remains to be assessed.Abbreviations CSV cardiac stroke volume - DAP dorsal aortic pressure - HR heart rate - QC cardiac output - VAP ventral aortic pressure - VR _b branchial vascular resistance - VR _s systemic vascular resistance - VR _t total vascular resistance - 5-HT 5-Hydroxytryptamine serotonin - RBI Research Biochemical Incorporated, metoclopramide HCl     

Control of threonine pathway in E. coli. application to biotechnologies

Threonine is an essential amino acid for mammals and birds and an adequate supply is necessary for growth and maintenance. Its production has become the aim of metabolic bioengineering and genetic manipulations. We propose in this paper a rational approach for increasing threonine production in anE. coli strain based on metabolic control theory. We have derived a way to measure the control coefficients of threonine pathwayin vivo. The method consists in modelling the results of presteady-state experiments. Thein vivo concentrations and activities of the enzymes can then be measured and introduced into the model, so that thein vivo steady-state of the pathway can be evaluated. With such a model it is possible to calculate the theoretical values of the control coefficients of the threonine synthesis fluxin vivo.     

Ethanol fermentation using a glucose negative mutant ofZymomonas mobilis

Summary The fermentation of an equimolar mixture of glucose and fructose into ethanol and sorbitol by a glucose negative mutant ofZymomonas mobilis was monitored. The results were analyzed using a recently described method based on polynomial fitting and calculation of intantaneous and overall parameters. These parameters described well the physiology of this mixed-substrate mixed-product fermentation. Growth of the mutant was greatly inhibited on this medium. Fructose was quantitatively converted into sorbitol while glucose was oxidized into gluconic acid .This latter product was utilized as substrate for cell growth and ethanol production.Nomenclature X biomass concentration, g/l - S total sugar concentration, g/l - Glu glucose concentration, g/l - Fru fructose concentration, g/l - Sor sorbitol concentration, g/l - P ethanol concentration, g/l - t fermentation time, h - specific growth rate, h^-1 - q_s specific sugar uptake rate, g/g.h - q_G specific glucose uptake rate, g/g.h - q_F specific fructose uptake rate, g/g.h - q_P specific ethanol productivity, g/g.h - q_Sor specific sorbitol productivity, g/g.h - Y_X/S biomass yield on total sugar, g/g - Y_P/S ethanol yield on total sugar, g/g - Y_Sor/S sorbitol yield on total sugar, g/g - y_Sor/f sorbitol yield on fructose, g/g - Y_P/G ethanol yield on glucose, g/g     

Molecular cloning and characterization of the extracellular sucrase gene (sacC) of Zymomonas mobilis

The Zymomonas mobilis gene sacC that encodes the extracellular sucrase (protein B46) was cloned and expressed in Escherichia coli. the gene was found to be present downstream to the already described levansucrase gene sacB in the cloned chromosomal fragment of Z. mobilis. The expression product was different from SacB and exhibited sucrase but not levansucrase activity; therefore, SacC behaves like a true sucrase. Expression of sacC in E. coli JM109 and XL1 was very low; overexpression was observed in E. coli BL21 after induction of the T7 polymerase expression system with IPTG. Subcellular fractionation of the E. coli clone carrying plasmid pLSS2811 showed that more than 70% of the sucrase activity could be detected in the cytoplasmic fraction, suggesting that the enzyme was soluble and not secreted in E. coli. The nucleotide sequence analysis of sacC revealed an open reading frame 1239 bp long coding for a 413 amino acid protein with a molecular mass of 46 kDa. The first 30 deduced amino acids from this ORF were identical with those from the N-terminal sequence of the extracellular sucrase (protein B46) purified from Z. mobilis ZM4. No leader peptide sequence could be identified in the sacC gene. The amino acid sequence of SacC showed very little similarity to those of other known sucrases, but was very similar to the levansucrases of Z. mobilis (61.5%), Erwinia amylovora (40.2%) and Bacillus subtilis (25.6%).     

Distribution of catch-relaxing peptide (CARP)-like immunoreactive neurons in the central and peripheral nervous system of Helix pomatia

Immunocytochemistry was performed on the nervous system of Helix by the use of an antibody raised against a myotropic neuropeptide, the catch-relaxing peptide (CARP), isolated from Mytilus edulis. In each ganglion of the central nervous system of Helix pomatia, numerous CARP-immunoreactive cell bodies and a dense immunoreactive fiber system could be observed with a dominancy in the cerebral and pedal ganglia. The majority of the immunoreactive neurons are unipolar, although multipolar neurons also occur. In the neuropil areas, CARP-immunoreactive fibers show extensive arborization, which may indicate a central role of CARP. CARP-immunoreactive elements could be observed in each investigated peripheral nerve and peripheral areas, namely in the intestine, heart, aorta, buccal mass, lips, and foot. However, CARP-immunoreactive cell bodies could only be demonstrated in the intestine and the foot musculature. Thin varicose CARP-immunoreactive fibers were observed over both muscle and gland cells in the different peripheral organs, suggesting a peripheral role of CARP. In vivo CARP injection into the body cavity (10^-3, 10^-4, 10^-5 M) altered the general behavioral state of the animals and induced the relaxation of the musculature of the whole body wall indicating that CARP has a significant role in the regulation of muscle contraction.     

The occurrence of phenylpropanoid glycosides in Italian Orobanche spp.

The occurrence of phenylpropanoid glycosides in a number of Orobanche spp. collected in Italy is shown and chemosystematic implications are discussed.