Preferential habitats prediction in syngnathids using species distribution models.

Syngnathids are considered as flagship species for marine conservation. Seahorses and pipefish are highly vulnerable to anthropogenic and environmental disturbances, but most species are currently considered Data Deficient by IUCN, requiring more biological and ecological research. Although syngnathids are well known for their unusual breeding biology, some aspects on the ecology of this family have rarely received attention. The knowledge on the factors governing syngnathids distribution is limited to some species and geographical regions. The present study is the first approach to predict syngnathid habitat preference in Spanish coasts, particularly in a marine National Park. In this study, Species Distribution Models (SDMs) were implemented to investigate the preferential habitat and distribution of the pipefish Syngnathus acus in Cíes Archipelago (Atlantic Islands of Galicia National Park, PNIA). Occurrence data of the species obtained from 2016 to 2018 surveys in PNIA were modeled as a function of bathymetric (depth, slope), substrate (sediment texture) and oceanographic (waves exposure) variables, using GAM, Random Forest and Maxent algorithms. From those SDMs, prediction models were built and the ensemble map of predictions was performed. The variables that most determined the distribution of the species were depth and wave exposure. The results of this study provide information on (1) habitat preference in the most dominant species in PNIA, the pipefish S. acus, towards sustainable management of this species in the National Park, and (2) predictive statistical tools for proper spatial conservation plans of this syngnathid species.

Author Correction: Removal of deep-sea sponges by bottom trawling in the Flemish Cap area: conservation, ecology and economic assessment.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Removal of deep-sea sponges by bottom trawling in the Flemish Cap area: conservation, ecology and economic assessment.

Deep-sea sponge grounds are vulnerable marine ecosystems, which through their benthic-pelagic coupling of nutrients, are of functional relevance to the deep-sea realm. The impact of fishing bycatch is here evaluated for the first time at a bathyal, sponge-dominated ecosystem in the high seas managed by the Northwest Atlantic Fisheries Organization. Sponge biomass surfaces created from research survey data using both random forest modeling and a gridded surface revealed 231,140 t of sponges in the area. About 65% of that biomass was protected by current fisheries closures. However, projections of trawling tracks estimated that the sponge biomass within them would be wiped out in just 1 year by the current level of fishing activity if directed on the sponges. Because these sponges filter 56,143 ± 15,047 million litres of seawater daily, consume 63.11 ± 11.83 t of organic carbon through respiration, and affect the turnover of several nitrogen nutrients, their removal would likely affect the delicate ecological equilibrium of the deep-sea benthic ecosystem. We estimated that, on Flemish Cap, the economic value associated with seawater filtration by the sponges is nearly double the market value of the fish catch. Hence, fishery closures are essential to reach sponge conservation goals as economic drivers cannot be relied upon.

Evaluation of the efficacy of Grofactor, a beta-adrenergic agonist based on zilpaterol hydrochloride, using feedlot finishing bulls.

Beta-adrenergic agonists (ß-AA) have been shown to positively impact finishing performance and some carcass traits of feedlot cattle. Our objective was to evaluate the efficacy of a ß-AA on the basis of zilpaterol hydrochloride (Grofactor, Laboratorios Virbac México, Guadalajara, Mexico) on growth and DMI, carcass characteristics, and meat quality of finishing bulls. Forty-five bulls (75% 25% ) initially weighing 448.7 ± 2.58 kg were blocked by BW and randomly assigned to 1 of 3 diets, using pens of 3 animals, in a randomized complete block design: 1) daily feeding without ß-AA in the basal diet (Control), 2) daily feeding with 0.15 mg/kg BW of Grofactor added to the basal diet (ZHG), or 3) daily feeding with 0.15 mg/kg BW of Zilmax (MSD Salud Animal México, Mexico City, Mexico) added to the basal diet (ZHZ). The duration of the feeding period was 30 d with a subsequent 4-d withdrawal period. Compared with Control bulls, the group fed ZHG had a 12% better ( < 0.025) G:F ratio, and their final BW ( 0.094) and ADG ( 0.084) tended to be enhanced. Feedlot performance of ZHG and ZHZ bulls was similar, although the DMI was ∼4% lower ( 0.05) in ZHG bulls vs. the ZHZ and Control groups. The HCW ( 0.001) and dressing percentage ( 0.015) were higher by 20 kg and 3%, respectively, in ZHG bulls vs. Control bulls. The KPH fat was lower ( 0.007) in bulls fed ZHG than in nonsupplemented bulls, but other carcass characteristics were not different in the ZHG and ZHZ bulls, and noncarcass components were not affected by ZHG or ZHZ supplementation. At 48 h postmortem, ZHG bulls had lower ( 0.007) water holding capacity and trended toward ( 0.06) increased chroma and reduced pH ( 0.09) compared to Control bulls. However, compared to ZHZ bulls, ZHG bulls had higher ( 0.02) chroma and a trend ( 0.08) toward increased hue angle. At 14 d postmortem, meat quality variables did not differ between the 3 groups of bulls. Supplementation of ZH Grofactor improved feedlot performance and some carcass characteristics of finishing bulls without affecting meat quality. The effects of Grofactor on feedlot performance, carcass traits, and meat quality were similar to those of Zilmax.

Ancient deep-sea sponge grounds on the Flemish Cap and Grand Bank, northwest Atlantic.

Recent studies on deep-sea sponges have focused on mapping contemporary distributions while little work has been done to map historical distributions; historical distributions can provide valuable information on the time frame over which species have co-evolved and may provide insight into the reasons for their persistence or decline. Members of the sponge family Geodiidae are dominant members of deep-sea sponge assemblages in the northwestern Atlantic. They possess unique spicules called sterrasters, which undergo little transport in sediment and can therefore indicate the Geodiidae sponge historical presence when found in sediment cores. This study focuses on the slopes of Flemish Cap and Grand Bank, important fishing grounds off the coast of Newfoundland, Canada, in international waters. Sediment cores collected in 2009 and 2010 were visually inspected for sponge spicules. Cores containing spicules were sub-sampled and examined under a light microscope for the presence of sterrasters. These cores were also dated using X-radiographs and grouped into five time categories based on known sediment horizons, ranging from 17,000 years BP to the present. Chronological groupings identified Geodiidae sponges in four persistent sponge grounds. The oldest sterrasters were concentrated in the eastern region of the Flemish Cap and on the southeastern slope of the Grand Bank. Opportunistic sampling of a long core in the southeastern region of the Flemish Cap showed the continuous presence of sponge spicules to more than 130 ka BP. Our results indicate that the geodiids underwent a significant range expansion following deglaciation, and support a contemporary distribution that is not shaped by recent fishing activity.

Effects of two beta-adrenergic agonists on finishing performance, carcass characteristics, and meat quality of feedlot steers.

The impact of using 2 beta-adrenergic agonists in feedlot cattle fed finishing diets was evaluated using 54 steers (45 crossbred Charolais and 9 Brangus) initially weighing 424 +/- 26.6 kg in a randomized complete block design with 3 treatments and 6 blocks (i.e., 18 pens with 3 steers per pen). Response variables were feedlot performance, carcass characteristics, and meat quality. Treatments were 1) control (no supplement added); 2) zilpaterol hydrochloride (ZH; 60 mg.steer(-1).d(-1)); and 3) ractopamine hydrochloride (RH; 300 mg.steer(-1).d(-1)). The beta-agonists were added to the diets during the final 33 d of the experiment. The groups of steers fed ZH or RH improved (P < 0.01) ADG by 26 or 24%, respectively, compared with control steers. Steers supplemented with RH consumed less (P = 0.03) DM (8.37 kg) than control steers (8.51 kg), whereas intake was similar (P = 0.37) for ZH and control steers. Addition of either beta-agonist to the diet considerably improved (P < 0.01) the G:F (ZH, 0.253 and RH, 0.248 vs. control, 0.185). Hot carcass weight and carcass yield were enhanced (P < 0.05) with both beta-agonists. The LM area was increased (P = 0.026) by ZH (75.2 cm(2)), but that of RH (72.2 cm(2)) was similar (P = 0.132) to the control steers (66.8 cm(2)). Meat from the ZH- (P = 0.0007) and RH- (P = 0.0267) supplemented steers had greater shear force values than control steers (ZH = 5.11; RH = 4.83; control = 4.39 kg/cm(2)). Variables related to meat color indicated that both beta-agonists led to a similar redness of the LM area related to the control group. In general, feedlot performance was greatly enhanced by beta-adrenergic agonists, and meat tenderness from treated animals was classified as intermediate. Furthermore, meat color was not altered by beta-agonist supplementation.

Domain architecture of a high mobility group A-type bacterial transcriptional factor.

Myxococcus xanthus transcriptional factor CarD participates in carotenogenesis and fruiting body formation. It is the only reported prokaryotic protein having adjacent "AT-hook" DNA-binding and acidic regions characteristic of eukaryotic high mobility group A (HMGA) proteins. The latter are small, unstructured, nonhistone nuclear proteins that function as architectural factors to remodel DNA and chromatin structure and modulate various DNA binding activities. We find CarD to be predominantly dimeric with two stable domains: (a) an N-terminal domain of defined secondary and tertiary structure which is absent in eukaryotic HMGA proteins; (b) a C-terminal domain formed by the acidic and AT-hook segments and lacking defined structure. CarD, like HMGA proteins, binds specifically to the minor-groove of AT-rich DNA present in two appropriately spaced tracts. As in HMGA proteins, casein kinase II can phosphorylate the CarD acidic region, and this dramatically decreases the DNA binding affinity of CarD. The acidic region, in addition to modulating DNA binding, confers structural stability to CarD. We discuss how the structural and functional plasticity arising from domain organization in CarD could be linked to its role as a general transcriptional factor in M. xanthus.

ihfA gene of the bacterium Myxococcus xanthus and its role in activation of carotenoid genes by blue light.

Myxococcus xanthus responds to blue light by producing carotenoids. Several regulatory genes are known that participate in the light action mechanism, which leads to the transcriptional activation of the carotenoid genes. We had already reported the isolation of a carotenoid-less, Tn5-induced strain (MR508), whose mutant site was unlinked to the indicated regulatory genes. Here, we show that OmegaMR508::Tn5 affects all known light-inducible promoters in different ways. It blocks the activation of two of them by light but makes the activity of a third one light independent. The OmegaMR508 locus has been cloned and sequenced. The mutation had occurred at the promoter of a gene we propose is the M. xanthus ortholog of ihfA. This encodes the alpha subunit of the histone-like integration host factor protein. An in-frame deletion within ihfA causes the same effects as the OmegaMR508::Tn5 insertion. Like other IhfA proteins, the deduced amino acid sequence of M. xanthus IhfA shows much similarity to HU, another histone-like protein. Sequence comparison data, however, and the finding that the M. xanthus gene is preceded by gene pheT, as happens in other gram-negative bacteria, strongly argue for the proposed orthology relationship. The M. xanthus ihfA gene shows some unusual features, both from structural and physiological points of view. In particular, the protein is predicted to have a unique, long acidic extension at the carboxyl terminus, and it appears to be necessary for normal cell growth and even vital for a certain wild-type strain of M. xanthus.

The structure of an ECF-sigma-dependent, light-inducible promoter from the bacterium Myxococcus xanthus.

Expression of the Myxococcus xanthus gene crtl is controlled by a light-inducible promoter. The activity of this promoter depends on CarQ, a sigma factor of the extracytoplasmic function (ECF) subfamily. Here, we show thatthe minimum DNA stretch reproducing normal expression of crtl extends from a few bases upstream of the -35 position to a site well downstream of the transcriptional start. The downstream DNA contains an enhancer-like element that remains active when displaced upstream of the promoter. Experimental evidence is provided for the activity of the crtl promoter being critically dependent on a pentanucleotide sequence centred at the -31 position. The similarity of this sequence with the consensus for ECF-sigma-dependent promoters from other bacteria is discussed. The activity of the crtl promoter also depends on certain basepairs at the -10 region. Hence, the operation of ECF-sigma-factors seems to require binding to two different DNA sites, although the -10 sequences of different ECF-sigma-dependent promoters are unrelated to one another, and the ECF-sigma-factors themselves lack the conserved domain known to mediate binding of other sigma-factors to the -10 DNA site.

Prt1, an unusual retrotransposon-like sequence in the fungus Phycomyces blakesleeanus.

This work reports the isolation and structural characterization of Prt1, a 4.7 kb retrotransposon-like sequence from the filamentous fungus Phycomyces blakesleeanus. Two open reading frames are found within Prt1. The first shows no similarity with known genes. The second encodes peptide stretches similar to the reverse transcriptase and RNaseH domains of the Ty3/gypsy family of LTR-retrotransposons. Prt1 lacks long terminal repeats, having instead short (54 bp) terminal inverted repeats. No target site duplication has been found. A single copy of Prt1 was detected in the genome of P. blakesleeanus. Adjacent to this sole copy of Prt1, a cluster of various short sequence repeats, both direct and inverted, is found. These sequences, which are reminiscent of defective, non-retroviral transposable elements, are also represented in other regions of the P. blakesleeanus genome.

High mobility group I(Y)-like DNA-binding domains on a bacterial transcription factor.

The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. However, a single gene, carD, is required for the activation of both light- and starvation-inducible genes. Gene carD has now been sequenced. Its predicted amino acid sequence includes four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA. CarD binds in vitro an A+T-rich element that is required for the proper operation of a carD-dependent promoter in vivo.

A cluster of structural and regulatory genes for light-induced carotenogenesis in Myxococcus xanthus.

In the bacterium Myxococcus xanthus, several genes for carotenoid synthesis lie together at the carA-carB chromosomal locus and are co-ordinately activated by blue light. A 12-kb DNA stretch from wild-type M. xanthus has been sequenced that includes the entire carA-carB gene cluster. According to sequence analysis, the cluster contains 11 different genes. Intergenic distances are very short or nil (implying translational coupling), giving further support to previous evidence indicating that most (or all) of the genes in the cluster form a single operon. At the promoter region, a potential -35 site for the binding of sigma factors is found. However, the -10 region shows little similarity with analogous sites in other bacterial promoters. Five (possibly six) genes in the carA-carB operon code for enzymes acting on early or late steps of the pathway for carotenoid synthesis. Other genes in the operon show no overall similarity with previously known genes. However, peptide stretches in the predicted products of two genes exhibit strong similarity with the DNA binding domain of the MerR family of transcriptional regulators. At least one of the predicted DNA-binding domains is altered in a mutant strain affected in light-regulation of the car genes.

PkpA, a novel Phycomyces blakesleeanus serine/threonine protein kinase.

This work reports the cloning and sequencing of pkpA, a gene of the filamentous fungus Phycomyces blakesleeanus, whose expression seems to be coupled to vegetative growth. This gene encodes a putative serine/threonine-specific protein kinase, whose sequence is related to that of the yeast protein STE20, involved in pheromone-response pathways, and to a number of MAPK kinase proteins. However, detailed analysis of the kinase sequence suggests that PkpA is a novel serine/threonine protein kinase that probably participates as an intermediate in an intracellular system controlling nuclear proliferation in P. blakesleeanus.

A genetic link between light response and multicellular development in the bacterium Myxococcus xanthus.

The Gram-negative bacterium Myxococcus xanthus responds to blue light by producing carotenoid pigments (Car+ phenotype). Genes for carotenoid synthesis lie at two unlinked chromosomal sites, the carC and the carBA operon, but are integrated in a single "light regulon" by the action of common trans-acting regulatory elements. Three known regulatory genes are grouped together at the (light-inducible) carQRS operon. By screening the Car phenotype of a large collection of transposon-induced mutants, we have identified a new car locus that has been named carD (carD1 for the mutant allele). The carD gene product plays a critical role in the light regulon, as it is required for activation of the carQRS and carC promoters by blue light. The carD1 mutant is impaired in the (starvation-induced) developmental process that allows M. xanthus cells both to form multicellular fruiting bodies and to sporulate. Our results indicate that the carD gene product is also required for the expression of a particular set of development-specific genes that are normally activated through the action of intercellular signals.

Isolation of the facA (acetyl-CoA synthetase) gene of Phycomyces blakesleeanus.

A 5.6 kb DNA fragment from the fungus Phycomyces blakesleeanus has been cloned and sequenced. The fragment contains a gene that probably codes for the enzyme acetyl-coenzyme A synthetase (facA). The amino acid sequence deduced for the P. blakesleeanus protein is highly homologous to those of acetyl-coA-synthetases from other organisms. When placed under the control of a constitutive promoter from Aspergillus nidulans, the cloned gene complemented a facA- mutation of this organism. In P. blakesleeanus, the expression of facA is induced by acetate.

Clustering and co-ordinated activation of carotenoid genes in Myxococcus xanthus by blue light.

Blue light activates carotenoid production in the non-photosynthetic, Gram-negative bacterium Myxococcus xanthus. Light is known to stimulate the expression of two unlinked genes for carotenoid synthesis, carB and carC, through a mechanism in which the regulatory genes carA, carQ and carR take part. Genes carQ and carR are linked together at a separate locus, whereas carA is linked to carB. We have introduced Tn5 at various sites between carA and carB. Chemical analyses of the mutant strains demonstrate the presence in this region of a cluster of genes for carotenoid synthesis. Gene expression analysis strongly argues for most (or all) of the genes in the cluster being transcribed from a single, light-inducible promoter under the control of genes carA, carQ and carR.

Growth phase dependence of the activation of a bacterial gene for carotenoid synthesis by blue light.

Myxococcus xanthus responds to blue light by producing carotenoid pigments. A mutation at a gene named carC is known to block the metabolism of phytoene, a carotenoid precursor, and this gene has now been cloned and sequenced. We show here that gene carC, which is homologous to phytoene dehydrogenase genes from other organisms, is tightly regulated by light through a mechanism that operates only when the cells have reached the stationary phase or are starved of a carbon source. A genetic element that mediates the effect of the growth phase has been identified. Gene carC is integrated with another unlinked carotenogenic gene in a single 'light regulon' controlled by common trans-acting genetic elements. A potential -35 site for the binding of sigma factors has been found upstream of the carC transcriptional start. However, the -10 region shows no similarity with analogous sites at promoters of other Gram-negative bacteria.

Accumulation of carotenoids in structural and regulatory mutants of the bacterium Myxococcus xanthus.

Accumulation of carotenoids in Myxococcus xanthus is absolutely dependent on illumination with blue light. We report the analysis of the carotenoids of dark- and light-grown cultures of the wild type and several previously characterized mutants. A carR mutant produces the same carotenoids in the dark as the wild type grown in the light. This agrees with previous evidence indicating that the carR gene codes for a general negative regulator of the system. A cis-dominant mutation in the gene carA causes constitutive expression of the light-inducible gene carB, which is linked to carA. In the dark, the carA mutant produces high levels of phytoene, the first C40 colourless carotenoid precursor; in the light, it produces the same carotenoids as the wild type. Since a mutation in carB blocks accumulation of phytoene, we propose that carB, and probably other linked genes also controlled by carA, code for enzymes involved in the synthesis of phytoene. This is virtually the only carotene accumulated by strains mutated in the gene carC, which is unlinked to the others. Thus carC codes for phytoene dehydrogenase, the enzyme that converts phytoene into coloured carotenoids. The results presented here also provide evidence for control of carotenogenesis by an endproduct that is independent of the blue light effect.

A cytoplasmically inherited mutation in the fungus Phycomyces blakesleeanus.

Fourteen mutants of the fungus Phycomyces blakesleeanus, showing high levels of resistance to copper, were isolated. In all the mutants, copper resistance behaved as a very variable and unstable trait. In the mutant strain MU102, the mutation was demonstrated to be cytoplasmically inherited. In addition, this mutant strain differed from the wild-type in growth, respiration rate, and shape and viability of spores.

Genic and allelic interactions in the carotenogenic response of myxococcus xanthus to blue light.

In the bacterium Myxococcus xanthus, the synthesis of carotenoids requires illumination with blue light. This stimulates transcription of the carB locus, which is positively required for carotenogenesis. Mutations at the carR locus and the only mutation known at carA cause constitutive expression of carB and thus remove the light requirement for carotenoid accumulation (Car(c) phenotype). The carR locus is unlinked, and carA is linked, to carB. We have now identified a novel class of car mutation, closely linked to carR, that block accumulation of carotenoids and transcription of carB, and are epistatic over the Car(c) mutations at carR but not over the Car(c) mutation at carA. We also report here the cloning of a 16-kb DNA fragment that contains the entire carA gene in a shuttle vector for DNA transfer between Escherichia coli and M. xanthus. The study of allelic interactions at this gene strongly indicate that carA is a cis-acting element for the control of carB expression. A regulatory model that satisfies all the indicated data is presented.