Miracle-dz/UniFAR-FTUs huggingface dataset:
The recent species of the genus Eburna Lamarck, 1801

The genus Eburna consists o f several very beautiful species with remarkable consistent characters. All spe­ cies are highly glossy and have a very conspicuous false umbilicus or a clearly visible rudimentary false umbili­ cus. Being brigtly coloured, from dark orange to lemon yellow, and with all species occasionally forming white or albino specimens, the group consists of real “collec­ tors items”, well known and sought after by professional as well as amateur malacologists. It is my impression that a lot of confusion exists about the validity of some names, the geographic distribution and the diagnostically im portant morphology. In this paper I discuss the genus as a whole, its place within the subfamily Ancilli­ nae and describe and figure the extant species of the nominal subgenus Eburna s.s. Het geslacht Eburna bestaat uit verschillende mooie soorten met verbazingwekkend constante kenmerken. Alle soorten zijn hoogglanzend en bezitten een opval­ lende schijn-navel of een duidelijk zichtbare rudimentai­ re schijn-navel. Omdat ze fel gekleurd zijn, van donker oranje tot citroengeel en er van alle soorten witte of albino exem plaren bekend zijn, bestaat de groep uit echte “verzam elaars-stukken”, bekend en gew ild bij zowel de beroepsals amateurmalacoloog. De indruk bestaat dat er een hoop verwarring is over de geldigheid van sommige namen, de verspreidingsgebieden en de voor determinatie belangrijke kenmerken. In dit artikel bespreek ik het geslacht in haar geheel, haar plaats in de onderfamilie Ancillinae en beschrijf en beeld de levende soorten van het nominale ondergeslacht Eburna af.
Importance of Mangroves, Seagrass Beds and the Shallow Coral Reef as a Nursery for Important Coral Reef Fishes, Using a Visual Census Technique

Abstract The nursery function of various biotopes for coral reef fishes was investigated on Bonaire, Netherlands Antilles. Length and abundance of 16 commercially important reef fish species were determined by means of visual censuses during the day in six different biotopes: mangrove prop-roots ( Rhizophora mangle ) and seagrass beds ( Thalassia testudinum ) in Lac Bay, and four depth zones on the coral reef (0 to 3 m, 3 to 5 m, 10 to 15 m and 15 to 20 m). The mangroves, seagrass beds and shallow coral reef (0 to 3 m) appeared to be the main nursery biotopes for the juveniles of the selected species. Mutual comparison between biotopes showed that the seagrass beds were the most important nursery biotope for juvenile Haemulon flavolineatum , H. sciurus , Ocyurus chrysurus , Acanthurus chirurgus and Sparisoma viride , the mangroves for juvenile Lutjanus apodus , L. griseus , Sphyraena barracuda and Chaetodon capistratus , and the shallow coral reef for juvenile H. chrysargyreum , L. mahogoni , A. bahianus and Abudefduf saxatilis . Juvenile Acanthurus coeruleus utilized all six biotopes, while juvenile H. carbonarium and Anisotremus surinamensis were not observed in any of the six biotopes. Although fishes showed a clear preference for a specific nursery biotope, most fish species utilized multiple nursery biotopes simultaneously. The almost complete absence of juveniles on the deeper reef zones indicates the high dependence of juveniles on the shallow water biotopes as a nursery. For most fish species an (partial) ontogenetic shift was observed at a particular life stage from their (shallow) nursery biotopes to the (deeper) coral reef. Cluster analyses showed that closely related species within the families Haemulidae, Lutjanidae and Acanthuridae, and the different size classes within species in most cases had a spatial separation in biotope utilization.
The distribution of intertidal macrofauna on the coasts of iceland in relation to temperature

Abstract Records of intertidal macrofauna, mostly collected since 1974, were analysed by the use of a 10×10 km plotting system. Data have been obtained on 208 such squares of the total of378 straddling the intertidal, or 55.0 %. Adequate data were available on 103 species. Nine of 37 obligate intertidal species (24 %) appear to reach distributional limits towards cooler seas going clockwise around Iceland from the south coast. The presence of warm springs in the intertidal extends the range of one species far beyond the main limits. There is no example of obligate intertidal species reaching distributional limits towards warmer seas within Iceland, emphasizing the non-arctic character of the intertidal fauna Of66 species occurring both in the intertidal and subtidal, II (17 %) reach distributional limits towards cooler seas in the intertidal and appear not to penetrate further subtidally, while one species (I %) may show the reverse pattern oflimits towards warmer seas. However, some 34 intertidal-subtida.
Enzymatic synthesis of monoacylglycerol citrate optimized by response surface methodology

The ability of immobilized lipase B from Candida antarctica (Novozym 435) to catalyze the direct esterification of citric acid (CA) and monoglyceride (MG) for citrate esters of monoacylglycerols (CITREM) preparation was investigated. The effects of substrate concentration, molecular-sieve amount, substrate molar ratio, reaction temperature, time, and enzyme load on the conversion of CA in the reaction were investigated. Enzyme screening and the effect of solvent on the esterification were also investigated. RSM was used to optimize the effects of the reaction temperature (45-55 C), the enzyme load (6-10%; relative to the weight of total substrates), and the reaction time (24―48 h) on the conversion of CA. Validation of the RSM model was verified by the good agreement between the experimental and the predicted values of CA conversion. The optimum preparation conditions were as follows: CA concentration 0.12 mol/L, molecular-sieve 120 g/L, molar ratio of MG/CA 2:1, temperature 54.18°C, enzyme load 9.0% (relative to the weight of total substrates), and reaction time 47.5 h. Under the suggested conditions, the conversion of CA was 77.4%. Repeated reaction tests indicated that Novozym 435 could be used eight times under the optimum conditions with 92% of its original catalytic activity still retained.
Diversification of Dombeyoideae (Malvaceae) in the Mascarenes: Old Taxa on Young Islands?

Premise of research. The patterns of diversification of Mascarene taxa remain largely unknown in comparison to other insular systems. Traditional interpretations of insular radiations often assume that endemic taxa radiated after the origin of the insular habitats on which they were established. The Dombeyoideae (Malvaceae) sublineage endemic to Mauritius and Réunion in the Mascarenes is an ideal model to test for the signature of insular diversification. Methodology. We combined molecular sequences for a dense sample of Mascarene dombeyoids together with African, Malagasy, and Asian outgroup species. We estimated divergence times based on two calibration schemes (including or excluding geological calibration). Comparative phylogenetic methods were used to study the diversification rates and the evolution of the floral disparity in the Mascarene clade. Pivotal results. Excluding geological constraints resulted in drastically older age estimates than when we included such calibrations. Diversification patterns suggest a decrease of diversification rates through time. The low morphological disparity indicates an early partitioning of floral characters. Conclusions. The lineage diversification and the morphological disparity are consistent with traditional scenarios of insular radiation. However, the Mascarene clade is older than Réunion and Mauritius, suggesting the onset of radiation before the formation of the archipelago. The diversification might have been driven by geographical opportunity rather than ecological opportunity.
Synthesis of Oligosaccharide Fragments of Mannosylated Lipoarabinomannan Appropriately Functionalized for Neoglycoconjugate Preparation

The synthesis of a panel of oligosaccharides that are fragments of mannosylated lipoarabinomannan from Mycobacterium tuberculosis is reported. The compounds were prepared as their 8‐aminooctyl glycosides to enable their easy incorporation into neoglycoconjugates.
Morfo-anatomia e ontogênese do fruto e da semente de Tipuana tipu (Benth.) O. Kuntze (Fabaceae: Faboideae)

Fruits and seeds of Tipuana tipu were morphologically and anatomically analyzed during development. The origin of the pericarpic wing was elucidated and the hypothesis of the occurrence of polyembriony mentioned in literature was verified. Slides were prepared according to the conventional techniques. The fruit of Tipuana tipu is a typical samara. Its wing originates from the lateral and terminal regions of the ovary and from the lateral of the style. The wing can be already traced in young ovaries of floral buds. Bitegmic ovules develop into testal seeds. The testa is not similar to those seen in typical legume integuments, frequently observed in species with indehiscent fruits. However, the hilum is typical of Faboideae. Seeds are exalbuminous and embryos present cotyledons and embryonic axis well developed. From 100 fruits analyzed mophologically, 61% were one-seeded, 34% two-seeded and only 5% three-seeded. From 144 seeds evaluated, only 2% were polyembryonic, showing two embryos per unit.
Stomatal conductance patterns and environment in high elevation phreatophytes of Wyoming

High-elevation (2305 m) phreatophytes (cottonwood, Populus angustifolia James, and willows, Salix monticola Nutt. and Salix exigua Bebb) in southeastern Wyoming commonly showed a pattern of increasing stomatal conductance (g1) throughout the day, despite minimum leaf water potentials (ψ1) as low as −2.7 MPa. Diurnally, light and leaf temperature were the most important variables influencing g1, but there were also threshold values of ψ1 and leaf-to-air vapor pressure deficit for stomatal closure. Seasonally, maximum daily g1 (gmax) was similar between species, was positively related to minimum air temperature the previous night, and showed a threshold response to soil temperature. Two types of evidence existed for large soil-to-leaf conductances (gs–l) and for liquid water being available to the roots. The first was no change in ψ1 despite increasing transpiration during the afternoon. The second was rapid evening recovery of ψ1 often to values higher than mean soil water potential to 60-cm depth. The com.
Increased dietary phosphorous prevents vertebral deformities in triploid Atlantic salmon (Salmo salar L.)

Triplicate groups of triploid and diploid Atlantic salmon were fed diets with a low (LP, total P: 7.1 g kg−1), medium (MP, total P: 9.4 g kg−1) or high (HP, total P: 16.3 g kg−1) phosphorous (P) level from first feeding (0.18 g) to transfer to sea water (~50 g, duration: 203 days) and subsequently fed a commercial diet in sea water for 426 days (~3 kg). This study examined the short- and long-term effects of dietary P on freshwater performance (mortality, growth), vertebral deformities (radiology), bone cell activity (ALP and TRACP enzyme activity in vertebrae and scales, and fgf23, bgp and igf-I relative gene expression in vertebrae), bone mineralization (ash content) and some parameters related to fish condition (heart and liver size). Irrespective of ploidy, at seawater transfer, fish fed the MP diet had significantly highest length and weight and those fed the LP diet significantly lowest length and weight, while those fed the HP diet had intermediate lengths and weights. Increased dietary phosphorus reduced deformities in both ploidies at seawater transfer; however, triploids fed the LP and MP diets had more deformities than diploids fed the respective diets, while there was no ploidy effect observed for fish fed the HP diet. The vertebral bone ash content at seawater transfer was significantly higher in diploids than in triploids when fed the MP diet only. Alkaline phosphatase (ALP) and tartrate-resistant acid phosphatase (TRACP) enzyme activities and relative gene expression of bone hormones involved in metabolism of plasma phosphate (fgf23) and bone growth (bgp) were not affected by ploidy at seawater transfer, but by dietary P level; LP increased ALP activity and reduced TRACP activity and fgf23 and bgp expression levels in vertebral bone. In scales, LP increased both ALP and TRACP activity. At the termination of the seawater period, the group-wise pattern in occurrence of vertebral deformities was the same as at seawater transfer. The present results on mortality, growth, bone mineralization and development of skeletal deformities all demonstrate that triploids have a higher P requirement than diploids in fresh water. This study shows that an optimalization of P nutrition for triploid Atlantic salmon can improve health and welfare and reduce down-grading of triploid salmon.
Invasion history affects genetic structure in island rat populations

Invasive species usually go through a period of reduced genetic variability due to a bottleneck. The genetic constitution of an invading population should therefore reflect the time since invasion and the number of introduction events. We studied genetic population structure of three rat species occurring sympatrically on the island of Futuna (46 km2), where they were introduced recently (Rattus rattus), 80–170 years ago (R. norvegicus) and about 3000 years ago (R. exulans). From 2007 to 2012, we trapped 3900 rats during a rodent regulation programme over 20 000 trap nights and took 565 rat tissue samples for genetic analyses. By examining genetic variation and spatial distribution of genetic resemblance, we evaluated the consequences of the time after introduction for genetic population structure. Observed heterozygosity, expected heterozygosity, number of alleles and allelic richness generally increased with increasing length of time a species was introduced to the island. The species with longer invasion history had also higher spatial admixture. However, in R. norvegicus, the observed heterozygosity was lower and inbreeding higher than expected by the invasion history. We relate this with the assumption that this species was introduced once or a few times and in low numbers, while R. exulans was intentionally introduced many times by Polynesian navigators and R. rattus had a high chance of being introduced on multiple occasions in recent times.
Databases and computational interaction models of Toll-like receptors

Toll-like receptors (TLRs) recognize pathogen-associated molecular patterns (PAMPs) on invading organisms and are the first line of defense in innate immunity. To date, much has been learned about TLRs and their roles in autoimmune diseases are being unraveled. The autoimmune disease systemic lupus erythematosus (SLE) progresses as a consequence of the inappropriate recognition of self nucleic acids by TLRs. For the development of therapeutic approaches of SLE it is necessary to understand possible negative regulation mechanisms of TLR. Single immunoglobulin interleukin-1 receptor-related molecule (SIGIRR) is the best characterized TLR signaling inhibitor. It can interfere with the receptor complexes and attenuate the recruitment of downstream adaptors to the receptors. So far, the mechanisms of structural interactions between SIGIRR, TLRs and adaptor molecules are unknown. To develop a working hypothesis for these interactions, we constructed three- dimensional models for these single molecules based on computational predictions. Then, models of essential complexes involved in the TLR signaling and the SIGIRR inhibiting processes were yielded through protein-protein docking analysis. With the high-throughput genome sequencing projects, a central repository for the growing amount of TLR sequence information has been created. However, subsequent annotations for these TLR sequences are incomplete. For example, the indicated numbers and positions of leucine-rich repeat (LRR) motifs contained in individual TLR ectodomains are greatly distinct or missing in established databases. In this vein, we have developed a database of TLR structural motifs called TollML (http://tollml.lrz.de). It integrates all TLR protein sequences that have been identified to date. These sequences were semi-automatically partitioned into three levels of structural motif categories. The manual motif identification procedure provided TollML with the most complete and accurate database of LRR motifs compared with other databases that contain TLR data. LRR motifs are present not only in TLRs, but also in many other proteins. To date, more than 6,000 LRR protein sequences and more than 130 crystal structures of them have been determined. This knowledge has increased our ability to use individual LRR structures extracted from the crystal structures as building blocks to model LRR proteins with unknown structures. Because the individual LRR structures are not directly available from any protein structure database, we have developed a conformational LRR database called LRRML (http://lrrml.lrz.de). It collects three- dimensional LRR structures manually identified from all determined crystal structures of LRR-containing proteins and thus provides a source for the structural modeling and analysis of LRR proteins. With the help of TollML and LRRML, we constructed models of the human/mouse TLR5-13 ectodomains and suggested some potential receptor-ligand interaction residues based on these models.
Crustáceos decápodos de las cuencas Copalita, Zimatán y Coyula, en Oaxaca, México

Se estudiaron 13 localidades de las cuencas Copalita, Zimatan y Coyula, Oaxaca. En 4 muestreos se capturaron mas de 3 200 crustaceos decapodos representando 3 familias, 4 generos y 13 especies, y 3 posibles nuevas especies de los generos Atya y Pseudothelphusa. Las especies se analizaron de acuerdo con su abundancia, frecuencia de aparicion y distribucion en las cuencas, y se comparo la composicion de especies y distribucion altitudinal de las localidades. La familia mejor representada fue Palaemonidae con 1 genero y 8 especies, le siguieron Atyidae con 2 generos y 3 especies y Pseudothelphusidae con 1 genero y 3 especies. Potimirim glabra y Atya sp. 1 fueron las especies mas abundantes; A. margaritacea y P. glabra las mas frecuentes, pues se detectaron en 10 de 13 estaciones; Macrobrachium michoacanus se detecto en 9, y M. americanum y M. occidentale en 8 estaciones. Los juveniles de langostino tuvieron una alta frecuencia en 9 de las localidades. La riqueza y el indice de diversidad de especies se incrementaron hacia la porcion baja de los rios; en la porcion alta, los valores fueron bajos y en la media de moderados a altos. Las localidades de muestreo se asociaron en 3 grupos de acuerdo con su altitud.
Genes required for RNA interference

RNA interference (RNAi) is a recently discovered phenomenon in which doublestranded RNA (dsRNA) silences endogenous gene expression in a sequencespecific manner (Fire et al., 1998). Since its discovery, the use of RNAi has become widely employed in many organisms to specifically knock down gene function. RNAi shares a remarkable degree of similarity with silencing phenomena in other organisms (Cogoni et al., 1999a; Sharp, 1999). For instance, RNAi, posttranscriptional gene silencing in plants and cosuppression in fungi can all be activated by the presence of aberrant RNAs (Maine, 2000; Tijsterman et al., 2002a). Additionally, plant, worm, and fly cells or extracts undergoing RNA-mediated interference all contain small dsRNAs, around 25 nucleotides in length, identical to the sequences present in the silenced gene (Baulcombe, 1996; Hammond et al., 2000; Zamore et al., 2000; Catalanotto et al., 2000). The high degree of similarity between these RNA-mediated silencing phenomena supports the notion that they were derived from an ancient and conserved pathway used to regulate gene expression, presumably to eliminate defective RNAs and to defend against viral infections and transposons. (Zamore, 2002). Components of RNAi have also been implicated in developmental processes, suggesting that RNAi may play a broader role in regulating gene expression (Smardon et al., 2000; Knight et al., 2001; et al., Ketting et al., 2001). Although we have learned much about the general mechanisms underlying RNAi, a detailed understanding of how RNAi works remains to be elucidated. In this chapter we will discuss first the biology of RNAi, then the genes required for its function, and we will end with a discussion on recent findings that have implicated chromatin silencing in the mechanism of RNAi.
Analysis of genetic relationships of Central American and Mexican pines using RAPD markers that distinguish species

Phylogenetic relationships were inferred for six Central American and Mexican pine species by analysing RAPD marker differences among pooled DNA samples. This population level pooling strategy discounts low‐frequency allelic variation within taxa, thus obtaining a ‘cumulative genotype’ to compare among taxa. We used the morphologically based taxonomy of pines as the basis for inference concerning molecular marker divergence. Only RAPD polymorphisms that were repeatable and intensely amplified were used. The resulting data set was found to have strong hierarchical structure. Phylogenetic analyses were carried out using both neighbour‐joining and maximum parsimony. The phylogenetic relationships indicated by analysis of the pine RAPD data provide new insights on pine taxonomy. The phylogenetic analyses of the RAPD marker data placed Pinus tecunumanii and P. patula clearly into two different subgroups, strongly supporting the classification of P. tecunumanii as a distinct species, and raise a new set of issues concerning the distinctions between Pinus tecunumanii and P. caribaea. Phylogenetically informative RAPD markers will be useful tools to address ex‐situ conservation issues that involve taxonomic identification and species admixture.
The Effects of Inbreeding on Male Courtship Behaviour and Coloration in Guppies

Despite an extensive literature on inbreeding depression in a variety of traits, relatively little is known about the effects of inbreeding on patterns of sexual behaviour. In this study, we use the guppy Poecilia reticulata to investigate the influence of parental relatedness (full-sib. vs. unrelated matings) on sexual behaviour and colour pattern variation in adult male offspring. Our results revealed that one generation of full-sibling mating resulted in a strong decline in male sexual motivation (courtship intensity and following behaviour) and mating success (number of successful copulations and insemination success ‐ as estimated by the frequency of post-copulatory jerks after mating), but we detected no significant influence of inbreeding on colour pattern variation. Our finding that sexual ornamentation (colour) did not show similar inbreeding depression to courtship behaviour may be due to differences in the genetic basis of these traits. Our findings indicate that courtship can be a sensitive indicator of genetic stress and add to an emerging picture that sexually selected traits can be severely affected by inbreeding depression.
The influence of handling on egg production, egg shell quality and avoidance behaviour of hens

1. Egg production was similar in non‐handled and in regularly handled hens, but was reduced by handling hens unaccustomed to the procedure. 2. Handling reduced avoidance behaviour (”flightiness“) in growers and pullets but its effect declined with age and it had no influence in these hens when mature. 3. Handling affected egg shell quality; it resulted in an increased incidence of cracks and of equatorial bulges. Previous work has suggested that this defect is an indication of stressors applied at a critical period during egg formation. Therefore, handling may be a stressor.