Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of fishery‐dependent data for the evaluation of depensation: Case study involving the predation of rock lobster (Jasus edwardsii) by octopus (Octopus maorum)

Abstract The relationship between the level of octopus (Octopus maorum) predation and the daily‐average number of lobsters (Jasus edwardsii) per pot was investigated using commercial catch statistics. Octopus predation was found to be inversely correlated with lobster catches, such that, lobsters experienced reduced survival when their daily‐average density in a pot was lower. The reduction in survival at lower densities provides evidence for a depen‐satory mechanism underlying the predator‐prey interaction between pot‐caught octopus and lobster. The effect of lobster density on the feeding response of octopus is unknown so this study could not determine whether depensation was brought about by either predator saturation or predator avoidance tactics used by lobsters. The use of commercial catch statistics to investigate this depensatory effect has disadvantages because the lobster mortality estimates can be biased by the non‐reporting of undersized lobsters caught inside pots, under‐reporting of lobsters killed by octopus, the inability to identify unsuccessful predation attempts made by octopus, and the ability of some lobsters to escape from pots. All the sources of bias would tend to make it difficult to conclusively determine both the absolute proportion of lobsters killed by octopus and the true scale of the depensatory mortality, as the scale of the mortality may be greater than the commercial data suggest. However, the bias will not necessarily reduce our ability to detect the depensatory effect if, as seems likely, the sources of bias are relatively constant across the range of daily‐average catches. Depensation in crustacean stocks affected by pot‐related octopus predation has been rarely studied, and, because depleted stocks lead to fewer lobsters being caught per pot, such depensatory mortality has implications for the population dynamics and management of crustacean stocks.
Characterization of theN-Acetylglucosaminyltransferase Activity Involved in the Biosynthesis of the Staphylococcus epidermidisPolysaccharide Intercellular Adhesin*

The polysaccharide intercellular adhesin (PIA) is an important factor in the colonization of medical devices byStaphylococcus epidermidis. The genes encoding PIA production are organized in the icaADBC(intercellular adhesion) operon. To study the function of the individual genes, we have established anin vitro assay with UDP-N-acetylglucosamine, the substrate for PIA biosynthesis, and analyzed the products by thin-layer chromatography and mass spectrometry. IcaA alone exhibited a low N-acetylglucosaminyltransferase activity and represents the catalytic enzyme. Coexpression of icaA withicaD led to a significant increase in activity. The newly identified icaD gene is located between icaAand icaB and overlaps both genes.N-Acetylglucosamine oligomers produced by IcaAD reached a maximal length of 20 residues. Only when icaA andicaD were expressed together with icaC were oligomer chains that react with PIA-specific antiserum synthesized. IcaA and IcaD are located in the cytoplasmic membrane, and IcaC also has all the structural features of an integral membrane protein. These results indicate a close interaction between IcaA, IcaD, and IcaC. Tunicamycin and bacitracin did not affect the in vitrosynthesis of PIA intermediates or the complete PIA biosynthesisin vivo, suggesting that a undecaprenyl phosphate carrier is not involved. IcaAD represents a novel protein combination among β-glycosyltransferases.
Regulatory T cells have anti-inflammatory effects by diluting TNF

Evaluation of: van Mierlo GJ, Scherer HU, Hameetman M et al.: Cutting edge: TNFR-shedding by CD4+CD25+ regulatory T cells inhibits the induction of inflammatory mediators. J. Immunol. 180(5), 2747–2751 (2008). Regulatory T cells (Tregs) of both human and murine origin were shown to express and shed significant amounts of TNF receptor 2. This is important new information as the shed soluble TNF receptor 2 binds TNF, which may explain the direct anti-inflammatory effects of Tregs. This adds to our current understanding of the various effects that Tregs may exert in order to dampen inflammation and autoimmunity. However, the interplay of these various Treg effects will need to be elucidated, particularly when considering their potential therapeutic use.
A test of recruitment limitation and the potential for artificial enhancement of spiny lobster (Panulirus argus) populations in Florida

Nous avons realise une experience de terrain dans les Cayes de la Floride dans laquelle nous avons manipule la fixation et les abris des langoustines juveniles de l'espece Panulirus argus pour (i) etudier comment ces facteurs influent sur le recrutement local et (ii) evaluer l'efficacite de ces pratiques proposees pour accroitre la population de langoustine. Le nombre de langoustines juveniles de petite taille a augmente de maniere statistiquement significative dans six sites de 0,05 ha ou l'on avait ajoute 12 abris artificiels, mais il est demeure inchange dans trois sites non manipules. Le fait d'ajouter 150 nouveaux pionniers dans trois des sites dans lesquels on avait ajoute des abris n'a pas fait augmenter de maniere mesurable l'abondance des langoustines juveniles au-dela de l'augmentation attribuable a la seule augmentation du nombre d'abris. Les resultats des experiences de marquage-recapture ont confirme que l'augmentation observee du nombre des juveniles de petite taille dans les sites ou l'on avait ajoute des abris n'etait pas attribuable a l'immigration. L'addition de structures artificielles dans les sites d'elevage semble avoir reduit la predation sur les juveniles de petite taille vulnerables et avoir favorise leur implantation locale. Par opposition, les juveniles plus gros et plus mobiles n'etaient pas plus abondants dans les sites ou l'on avait ajoute des abris que dans les sites non manipules. Ces resultats appuient l'hypothese que le recrutement local de P. argus peut etre accru si l'on ajoute aux abris naturels des structures artificielles bien concues, mais les consequences a plus grande echelle de l'accroissement de la population de langoustines sur les communautes naturelles environnantes sont inconnues.
Mitochondrial proline oxidation is affected by hyperosmotic stress in durum wheat seedlings

The important role of plant mitochondria in the adaptation to environmental stresses at subcellular level has recently emerged. In particular, an important mitochondrial mechanism involved in the resistance to environmental stresses is the inhibition of proline oxidation. In order to study this physiological mechanism, we used both washed and purified durum wheat (Triticum durum) mitochondria (DWM) isolated from early seedlings germinated in two different NaCl solutions leading to either moderate or severe damage to growth. To assess the contribution of the osmotic component of stress, a parallel investigation was performed using hyperosmotic mannitol solutions. Comparison of the oxygen uptake rate in the course of proline oxidation, with that of the malate plus glutamate substrate pair and that of succinate showed that an early inhibition of proline oxidation occurs under stress. The drop of the proline-dependent oxygen uptake rate was as a result of a heavy inhibition of proline dehydrogenase (ProDH); on the other hand, malate plus glutamate-dependent and succinate-dependent oxidations were less inhibited, being the maintenance of oxygen uptake rate not dependent on alternative oxidase (AOX) pathway; in fact, DWM-AOX activity did not show any increase under our experimental stress conditions. The selective inhibition of proline oxidation should be considered a mitochondrial adaptation to stress rather than damage to mitochondrial oxidative properties. This result was achieved by means of a novel approach based on the comparison between oxygen uptake rates of washed and purified organelles.
IDENTIFICATION OF ALEXANDRIUM (DINOPHYCEAE) SPECIES USING PCR AND rDNA‐TARGETED PROBES

A PCR (polymerase chain reaction)‐based assay for the detection of Alexandrium species in cultured samples using rDNA‐targeted probes was developed. The internal transcribed spacers 1 and 2 (ITS1 and ITS2) and the 5.8S ribosomal RNA gene (rDNA) from cultured isolates of A. tamarense (Lebour) Taylor, A. catenella (Whedon et Kofoid) Balech, A. fundyense Balech and A. lusitanicum Balech were amplified using PCR and sequenced. Sequence comparisons showed that the 5.8S and ITS1‐ITS2 regions contain sequences specific for the Alexandrium genus, especially at the 3′ end of the 5.8S coding region. PCR primers and a radioactive 32P‐labeled DNA probe were devised for this region. The cross‐reactivity of the PCR primers and probe was tested against cultured isolates of Alexandrium and other dinoflagellates and diatoms. All the Alexandrium isolates screened reacted toward the genus‐specific probe; in contrast, the other groups of microalgae (dinoflagellates and diatoms) did not react with the probe. Furthermore, the PCR amplification technique combined with the use of the rDNA‐target probe allowed us to develop a method for the detection of Alexandrium cells in cultured samples. This PCR method might offer a new approach for the identification and enumeration of the HAB (harmful algal bloom) species present in natural phytoplankton populations.
Expression of vascular endothelial growth factor and its receptors in heart tissue following short-term swimming training

The goal of this study was to investigate the expression of angiogenesis-associated genes in heart tissue in response to short-term exercise. Twenty-six male mice were divided randomly into sedentary and swimming-trained groups. Mice swam without a load for 50 min/day. Swimming training was carried out in six 50-min training sessions over a 9-day period. The mRNA for angiogenesis-related factors, including hypoxia inducible factor-1α (HIF-1α), vascular endothelial growth factor (VEGF), fms-like tyrosine kinase (Flt-1), and kinase insert domain-containing receptor/fetal liver kinase-1 (KDR/Flk-1), was analyzed using real-time reverse transcriptase-polymerase chain reaction (RT-PCR). Also, semi-quantitative RT-PCR was carried out to further determine which of the VEGF isoforms changed in heart tissue. Swimming training significantly increased HIF-1α (1.5-fold), VEGF (2.2-fold), Flt-1 (1.9-fold), and KDR/Flk-1 (2.4-fold) mRNA levels. Also, VEGF188 and VEGF164 mRNA levels were elevated but their relative abundance was the same as in sedentary mice. These results suggest that short-term swimming training stimulates not only the expression of VEGF mRNA, which may be due to increases in VEGF188 and VEGF164 mRNAs, but also Flt-1 and KDR/Flk-1 mRNAs in the heart.
Functional properties of proteins in foods: A survey

Proteins for foods, in addition to providing nutrition, should also possess specific functional properties that facilitate processing and serve as the basis of product performance. Functional properties of proteins for foods connote the physicochemical properties which govern the behavior of protein in foods. This general article collates the published information concerning the major functional properties of food proteins, e.g., solubility, binding properties, surfactant properties, viscogenic texturizing characteristics, etc. The effects of extraction and processing on functional properties and possible correlations between structure and function are discussed, in relation to practical performance in food systems. Modification of proteins to improve functional characteristics is briefly mentioned.
CORRELATIONS BETWEEN THE CHEMICAL STRUCTURE AND THE PHARMACOLOGICAL ACTIONS OF THE STEROIDS1

THE IMPORTANCE OF PHENANTHRENE derivatives in pharmacology and physiology is clearly shown by the fact that so many useful drugs and essential metabolites belong to this group. Morphine, codeine, colchioine, the bile acids, the digitalis aglucons, the toad poisons, many carcinogenic hydrocarbons, the vitamin D group, cholesterol and the steroid hormones all possess the phenanthrene or perhydrophenanthrene nucleus. Up to the present comparatively little attention has been given to the correlations which exist between the chemical structure and the pharmacological actions of the cyclopentano-perhydro-phenanthrene derivatives, and hence it was decided to make a systematic study of this field since an understanding of these correlations is a necessary prerequisite for any planned attempt to synthesize more potent compounds than are now available. Such an investigation was particularly tempting because the very important steroid hormones and their metabolites belong to this group.
Encyclopedia of Life

“Imagine an electronic page for each species of organism on Earth, available everywhere by single access on command. The page contains the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits. The page opens out directly or by linking to other databases, such as ARKive, Ecoport, GenBank and MORPHOBANK. It comprises a summary of everything known about the species’ genome, proteome, geographical distribution, phylogenetic position, habitat, ecological relationships and, not least, its perceived practical importance for humanity.
Movements of Juvenile Common Ravens in an Arid Landscape

Abstract Movement patterns of juvenile birds are poorly understood, yet critically important ecological phenomena, especially for species with a prolonged juvenile period. We evaluated postfledging movements of juvenile common ravens (Corvus corax) in a western Mojave Desert landscape composed of a mosaic of natural and anthropogenic elements. Generally, ravens do not begin breeding until after their fourth year. We marked 2 annual cohorts of juvenile ravens and followed them from dispersal from their natal territory for up to 33 months. Movements of juvenile common ravens were similar for males and females. Conspecifics and confined livestock feeding operations represented important resources for juvenile ravens, and juveniles were rarely located in open desert. However, initial movements from the natal territory to the nearest communal point subsidy rather than the closest anthropogenic resource suggested juvenile dispersal was influenced by the combination of conspecifics and anthropogenic resources, rather than the distribution of those resources. Land managers concerned with growing raven populations should reduce access to concentrated anthropogenic resources such as landfills and dairies, which serve as important resources for juveniles. Because juvenile ravens rarely venture into open desert, reducing their numbers by lethal removal or other means is unlikely to lessen raven predation of desert tortoises (Gopherus agassizii).
Nod factor thin-layer chromatography profiling as a tool to characterize symbiotic specificity of rhizobial strains: application to Sinorhizobium saheli, S. teranga, and Rhizobium sp. strains isolated from Acacia and Sesbania

Rhizobia isolated from Acacia or Sesbania belong to several taxonomic groups, including the newly described species Sinorhizobium sahelì, Sinorhizobium teranga, and the so-called cluster U. A collection of strains belonging to these different groups was analyzed in order to determine whether the host range of a strain could be correlated with various molecular nodulation determinants. Nodulation tests showed that, independently of their taxonomic position, all the strains isolated from the same plant genus exhibited a similar host range, which was different for Sesbania and Acacia isolates. The fact that S. teranga strains nodulate either Acacia or Sesbania led us to subdivide this species into biovars acaciae and sesbaniae. Thin-layer chromatography (TLC) analysis of the Nod factors synthesized by overproducing strains showed that (i) strains isolated from the same plant genus exhibited similar TLC profiles and (ii) profiles of Acacia and Sesbunia symbionts were easily distinguishable, Acacia strains producing, in particular, sulfated molecules. In contrast, no correlation could be established between the host range of a strain and its plasmid content, the nature of the nod gene inducers or the presence of DNA sequences homologous to specific nod genes. We thus propose that Nod factor TLC profiling may be used as an easy and powerful tool for the classification of rhizobial strains on the basis of their symbiotic properties.
Localization and manipulation of small parts using GelSight tactile sensing

Robust manipulation and insertion of small parts can be challenging because of the small tolerances typically involved. The key to robust control of these kinds of manipulation interactions is accurate tracking and control of the parts involved. Typically, this is accomplished using visual servoing or force-based control. However, these approaches have drawbacks. Instead, we propose a new approach that uses tactile sensing to accurately localize the pose of a part grasped in the robot hand. Using a feature-based matching technique in conjunction with a newly developed tactile sensing technology known as GelSight that has much higher resolution than competing methods, we synthesize high-resolution height maps of object surfaces. As a result of these high-resolution tactile maps, we are able to localize small parts held in a robot hand very accurately. We quantify localization accuracy in benchtop experiments and experimentally demonstrate the practicality of the approach in the context of a small parts insertion problem.
Interacting Constraints and the Problem of Similarity in Gastropod Structure and Function*

Abstract. Gastropods have served as research subjects for investigating questions that transcend both the taxon and the field of malacology. A major set of questions arises from repeated patterns in the microstructure, sculptural features, and coiling geometry of gastropod shells. The problem of similarity is one of distinguishing among alternative explanations of repetition and close resemblances. What explains the repetition of structural features? Are features similar as a consequence of shared ancestry (homology) or as a consequence of evolutionary convergence on good functional solutions (analogy)? There is increasing evidence for a third alternative that lies outside the evolutionary sphere, invoking the laws of physics and chemistry, building materials, and the assembly rules that apply strongly to the inorganic calcium carbonate of the gastropod shell. Three concepts are introduced to help organize the analysis of recurring similarities in the shells of marine gastropods. They are (1) remote biomineralization, (2) heterotectonic construction and ontogenetic reorganizations of shell secretion, and (3) structural funicity of the shell. Remote biomineralization produces organized structures without influence of the mantle, extrapallial space, and periostracum. Reticulate meshworks of aragonite on the exterior surfaces of larval shells are an example. Heterotectonic construction recognizes repeated instances of change in coiling geometry of the larval shell (protoconch) and the adult shell (teleoconch). Heterostrophy is an example of heterotectonic construction that is specific to the clade Heterobranchia; but there are many constructional changes that recur in other groups that are not closely-related. Examples include the set of changes that thicken larval shells (imbricate thickening) during the metamorphic reorganization of shell secretion and transition to secretion of new calcium carbonate microstructures. Funicity is a property of shell that results in recurring features that record ontogenetic history and ecological events. Funeous details include growth increments as records of periodic environmental rhythms, isotopic records of climate, and records of interaction with other organisms, including non-lethal damage inflicted by predators and modifications of shells by symbionts. Shells also record details of their post-mortem history, including a rich funeous record in deep time on and in shells in the fossil record.
Seasonal patterns of diet composition, herbage intake and digestibility limit the performance of cattle grazing native pasture in the Falkland Islands

The botanical composition, intake and digestibility of the diet consumed by mature lactating and non-lactating cows grazing a native white grass (Cortaderia pilosa) plant community in the Falkland Islands was measured in four periods between September 1998 and June 1999. Five lactating and five non-lactating cows were used in the summer, autumn and winter; five non-lactating cows were used in the spring. Different cows were used in each period. Plant cuticle patterns in the faeces of cattle were used, in conjunction with the patterns of concentrations of n-alkanes in the faeces, to estimate the botanical composition of the diet and predicted concentrations of C32- and C33-alkanes in the herbage allowed herbage intake and digestibility to be estimated using the n-alkane technique. White grass, sedges and rushes comprised 0·78, 0·64 and 0·63 of the diet in autumn, winter and spring respectively. Fine grasses, smooth-stalked meadow grass (Poa pratensis L.), annual meadow grass (Poa annua L.), bent grass (Agrostis capillaris L.), native fescue (Festuca magellanica Lam.), Yorkshire fog (Holcus lanatus L.), wavy hair grass [Deschampsia flexuosa (L) Trin. ] and early hair grass (Aira praecox L.), were consumed at the expense of sedges and rushes in summer and this coincided with the period of greatest estimated metabolizable energy and crude protein intakes by cows. Lactating cows suffered substantial liveweight loss during autumn and winter and this reflected the low quality of the diet consumed. Phosphorus intakes were insufficient and there was an estimated deficiency of vitamin D in the winter and early spring in cattle that were grazed with the experimental cows. The nutrient restrictions imposed on cattle by the low quality of native pasture during autumn and winter are likely to impair the reproductive potential of breeding females and methods should be investigated to improve the diet consumed by cows during these critical periods if cattle systems are to become sustainable in the Falkland Islands.
CHANGES IN ABSORBANCE SPECTRUM OF THE DIATOM PHAEODACTYLUM TRICORNUTUM UPON MODIFICATION OF PROTEIN STRUCTURE 1, 2

Changes in the absorbance spectrum, of the diatom Phaeodactylum tricornutum which are brought about by heat, urea, stilt, and formaldehyde have been studied. The changes brought about by all agents are similar. Each converts cell suspensions from orange‐brown to yellow‐green. This color change results from an increase in absorbance in the blue and a decrease in absorbance in the green. All agents, except salt, also bring about an increase in absorbance in the red at wavelengths below that of the red peak of chlorophyll, and a decrease in absorbance at longer wavelengths. On heating cells, the absorbance change in the green occurs more rapidly than the changes in the blue and red. The converse is true when cells are treated with 4 M NaCl. Heat or formaldehyde treatments chemically modify chlorophyll pigments which are present in untreated cells. The change in absorbance in the green is probably due to changes in the molecular environment of fucoxanthin which, results from protein modification. The changes in the blue and red are at least partly due to chemical changes in chlorophylls, but may also be due, in part, to protein modification.