NOTES ON THE GENUSUSNEADILL. EX ADANSON

Usnea quercinaBystrek & Górzyńska, based on heterogeneous type material, is lectotypified and becomes a synonym ofU. wirthiiP. Clerc.Usnea wirthiiis new for South America. A distribution map ofU. madeirensisMotyka (Syn.U. silesiacaMotyka) in Europe is given.Usnea hesperinaMotyka (Syn.U. elongataMotyka,U. schadenbergianaGöpp & Stein,U. subgracilisVain.,U. subplicata(Vain.) Motyka) is new for Africa, Asia and South America.Usnea hirta(L.) F. H. Wigg. (Syn.U. corrugataMotyka,U. foveataVain.,U. leprosaMotyka) is new for Africa.Usnea subscabrosaNyl. ex Motyka (Syn.U. santae-annaeMotyka) is new for South America. The holotype ofU. marocanaMotyka (=U. mutabilisStirt.) was found in LBL.     

Osmoregulation by six species of fiddler crabs (Uca) from the Mississippi delta area in the northern Gulf of Mexico

Six species of fiddler crabs (Ocypodidae: Uca) were collected for osmoregulation studies from 25 locations near the delta of the Mississippi River in the northern Gulf of Mexico. Three of the species are classified as members of the Celuca subgenus, Uca spinicarpa, Uca panacea and Uca pugilator, while the remaining three are in the Minuca subgenus, Uca minax, Uca longisignalis and Uca rapax. In the field, U. minax, U. spinicarpa and, occasionally, U. longisignalis are found in freshwater habitats (FW; 0-299 mosM). Two Minuca species, U. longisignalis and U. rapax, are typically collected in brackish water habitats (BW; 300-629 mosM). On the other hand, U. panacea and U. pugilator are most abundant in eurysaline habitats (EH; >630 mosM). In the laboratory, populations of each species were challenged with media ranging from 30 to 3450 mosM (1-110‰). The FW species, U. spinicarpa and U. minax, did not tolerate osmotic concentrations >2100 mosM. The EH species, U. panacea and U. pugilator, however, tolerate concentrations >2800 mosM. The BW species, U. longisignalis and U. rapax, succumb to osmolalities between 2100 and 2800 mosM. Each species keeps its hemolymph concentration fairly constant in 30-1400 mosM solutions. The [ISO], isosmotic medium concentration (in mosM), is calculated for each taxon: U. minax, 659; U. spinicarpa, 682; U. longisignalis, 693; U. rapax, 769; U. pugilator, 816; and U. panacea, 822. In media with >1600 mosM, each species expresses different osmoregulating capabilities. The FW species, U. spinicarpa and U. minax, cannot control hemolymph osmolality above 1500 mosM while the BW-EH species, U. panacea, U. pugilator and U. rapax, regulate hemolymph values in media up to 2300 mosM. Within the FW/BW species U. longisignalis, the ability to osmoregulate corresponds with site of collection. Specimens from FW populations do not regulate as well as those from BW if challenged with hypertonic media. If adapted to a 1800 mosM in the laboratory, survivorship for U. longisignalis shifts to the right and the [ISO] increases to 832 mosM. This suggests that this species adapts to acute hypertonic conditions by tolerating elevated internal osmolality. Generally, these observations extend our knowledge about the physiological capabilities of fiddler crabs from different salinity populations across the northern Gulf of Mexico.     

Vessel length and conductivity of Ulmus branches: ontogenetic changes and relation to resistance to Dutch elm disease

Changes in age of the hydraulic architecture of Ulmus minor and U. minor × U. pumila juvenile wood were studied and related to tolerance to Dutch elm disease (DED). The xylem vessel dimensions and the conductivity to air of 2- to 7-year-old branches were analyzed and quantified. No obvious differences in vessel length distribution and conductivity were found to explain differences in DED tolerance among the U. minor clones, or, at the taxon level, the higher DED tolerance of U. minor × U. pumila. Among the U. minor clones, the more susceptible one had wider vessels and a higher maximum vessel diameter than the more tolerant clone. Relations between vessel lengths, vessel diameters and branch sizes were highly significant, and varied between taxa. The diameter and length of vessels increased with age, and average values stabilized 1–2 years earlier for U. minor than for U. minor × pumila. Mean maximum vessel length was significantly higher in U. minor and increased more with age and maximum vessel diameter than in U. minor × pumila. With each 0.2 m increase in height up the stem, conductivities for U. minor and U. minor × U. pumila decreased by 59 and 50 %, respectively, probably due to shortening of the vessels. The implications of xylem structure for the means of pathogen movement and resistance to DED are discussed.     

Morphological diversity of pedicels in phoretic deutonymphs of Uropodina mites (Acari: Mesostigmata)

The pedicel is a structure that connects the phoretic deutonymph of Uropodina mites with its carrier and enables dispersal. The shapes, lengths and diameters of pedicels formed by Uropoda orbicularis, Trichouropoda ovalis, Uroobovella pulchella and Uroobovella nova were studied by scanning and light microscopy. Pedicels of U. orbicularis and T. ovalis have the shape of a straight stalk. In U. pulchella, the pedicel is extremely short, irregularly shaped and composed of homogeneous material. The longest pedicel is found in U. nova and it may be helically coiled in this species. The length of the pedicel is positively correlated with deutonymph body size between species, but not within species. Pedicels of U. orbicularis and U. pulchella have the largest diameter. The pedicel diameter in U. orbicularis and T. ovalis is inversely proportional to its length, but not in U. nova and U. pulchella. The constituent of pedicel stems in U. pulchella is homogeneous, whereas in U. orbicularis and T. ovalis it contains a bundle of tightly packed fibres. In U. nova coiled pedicels are comprised of two layered materials of different electron density, one of which is electron lucid and located peripherally. Hypotheses on the origin of the pedicel are proposed.     

Diverged subpopulations in tropical Urochloa (Brachiaria) forage species indicate a role for facultative apomixis and varying ploidy in their population structure and evolution

Background Urochloa (syn. Brachiaria) is a genus of tropical grasses sown as forage feedstock, particularly in marginal soils. Here we aimed to clarify the genetic diversity and population structure in Urochloa species to understand better how population evolution relates to ploidy level and occurrence of apomictic reproduction.MethodsWe explored the genetic diversity of 111 accessions from the five Urochloa species used to develop commercial cultivars. These accessions were conserved from wild materials collected at their centre of origin in Africa, and they tentatively represent the complete Urochloa gene pool used in breeding programmes. We used RNA-sequencing to generate 1.1 million single nucleotide polymorphism loci. We employed genetic admixture, principal component and phylogenetic analyses to define subpopulations.ResultsWe observed three highly differentiated subpopulations in U. brizantha, which were unrelated to ploidy: one intermixed with U. decumbens, and two diverged from the former and the other species in the complex. We also observed two subpopulations in U. humidicola, unrelated to ploidy; one subpopulation had fewer accessions but included the only characterized sexual accession in the species. Our results also supported a division of U. decumbens between diploids and polyploids, and no subpopulations within U. ruziziensis and U. maxima.ConclusionsPolyploid U. decumbens are more closely related to polyploid U. brizantha than to diploid U. decumbens, which supports the divergence of both polyploid groups from a common tetraploid ancestor and provides evidence for the hybridization barrier of ploidy. The three differentiated subpopulations of apomictic polyploid U. brizantha accessions constitute diverged ecotypes, which can probably be utilized in hybrid breeding. Subpopulations were not observed in non-apomictic U. ruziziensis. Sexual Urochloa polyploids were not found (U. brizantha, U. decumbens) or were limited to small subpopulations (U. humidicola). The subpopulation structure observed in the Urochloa sexual–apomictic multiploidy complexes supports geographical parthenogenesis, where the polyploid genotypes exploit the evolutionary advantage of apomixis, i.e. uniparental reproduction and clonality, to occupy extensive geographical areas.     

Hybridization and introgression between the exotic Siberian elm, Ulmus pumila, and the native Field elm, U. minor, in Italy

In response to the first Dutch elm disease (DED) pandemic, Siberian elm, Ulmus pumila, was planted to replace the native elm, U. minor, in Italy. The potential for hybridization between these two species is high and repeated hybridization could result in the genetic swamping of the native species and facilitate the evolution of invasiveness in the introduced species. We used genetic markers to examine the extent of hybridization between these two species and to determine the pattern of introgression. We quantified and compared the level of genetic diversity between the hybrids and the two parental species. Hybrids between U. pumila and U. minor were common. The pattern of introgression was not as strongly biased towards U. pumila as was previously observed for hybrids between U. rubra and U. pumila in the United States. The levels of heterozygosity were similar between U. minor and the hybrids and both groups had higher levels of heterozygosity relative to U. pumila. The programs Structure and NewHybrids indicated the presence of first- (F₁) and second- generation (F₂) hybrids and of backcrosses in the hybrid population. The presence of healthy DED resistant U. minor individuals combined with the self-compatibility of U. minor could help explain the presence of F₂ individuals in Italy. The presence of F₂ individuals, where most of the variability present in the hybrids will be released, could facilitate rapid evolution and the potential evolution of invasiveness of U. pumila in Italy.     

The Drosophila U2 snRNP protein U2A' has an essential function that is SNF/U2B" independent

Recruitment of the U2 snRNP to the pre-mRNA is an essential step in spliceosome assembly. Although the protein components of the U2 snRNP have been identified, their individual contributions to function are poorly defined. In vitro studies with the Drosophila and human proteins suggest that two of the U2 snRNP-specific proteins, U2A′ and U2B″, function exclusively as a dimer. In Drosophila the presence of the U2B″ counterpart, Sans-Fille (SNF), in the U2 snRNP is dispensable for viability, suggesting that SNF is not necessary for U2 snRNP function in vivo. With the identification of a single U2A′-like protein in the Drosophila genome, we can now investigate the relationship between SNF and its putative binding partner in vivo. Here we show that Drosophila U2A′ protein interacts with SNF in vivo and, like its human counterpart, is U2 snRNP specific. Unexpectedly, however, we find that loss of function causes lethality, suggesting that U2A′, but not SNF, is critical for U2 snRNP function. Moreover, although we demonstrate that several domains in the SNF protein are important for the interaction with the Drosophila U2A′ protein, including a redundant domain at the normally dispensable C-terminus, we find that U2A′ does not require heterodimer formation for either its vital function or U2 snRNP assembly. Thus together these data demonstrate that in Drosophila U2A′ has an essential function that is unrelated to its role as the partner protein of SNF/U2B″.     

Polymerase chain reaction–hybridization method using urease gene sequences for high-throughput Ureaplasma urealyticum and Ureaplasma parvum detection and differentiation

In this article, we discuss the polymerase chain reaction (PCR)–hybridization assay that we developed for high-throughput simultaneous detection and differentiation of Ureaplasma urealyticum and Ureaplasma parvum using one set of primers and two specific DNA probes based on urease gene nucleotide sequence differences. First, U. urealyticum and U. parvum DNA samples were specifically amplified using one set of biotin-labeled primers. Furthermore, amine-modified DNA probes, which can specifically react with U. urealyticum or U. parvum DNA, were covalently immobilized to a DNA–BIND plate surface. The plate was then incubated with the PCR products to facilitate sequence-specific DNA binding. Horseradish peroxidase–streptavidin conjugation and a colorimetric assay were used. Based on the results, the PCR–hybridization assay we developed can specifically differentiate U. urealyticum and U. parvum with high sensitivity (95%) compared with cultivation (72.5%). Hence, this study demonstrates a new method for high-throughput simultaneous differentiation and detection of U. urealyticum and U. parvum with high sensitivity. Based on these observations, the PCR–hybridization assay developed in this study is ideal for detecting and discriminating U. urealyticum and U. parvum in clinical applications.     

Whole-genome sequencing of a laboratory-evolved yeast strain

Background

Two categories of introns are known, a common U2 type and a rare U12 type. These two types of introns are removed by distinct spliceosomes. The phylogenetic distribution of spliceosomal RNAs that are characteristic of the U12 spliceosome, i.e. the U11, U12, U4atac and U6atac RNAs, suggest that U12 spliceosomes were lost in many phylogenetic groups. We have now examined the distribution of U2 and U12 introns in many of these groups.

Results

U2 and U12 introns were predicted by making use of available EST and genomic sequences. The results show that in species or branches where U12 spliceosomal components are missing, also U12 type of introns are lacking. Examples are the choanoflagellate Monosiga brevicollis, Entamoeba histolytica, green algae, diatoms, and the fungal lineage Basidiomycota. Furthermore, whereas U12 splicing does not occur in Caenorhabditis elegans, U12 introns as well as U12 snRNAs are present in Trichinella spiralis, which is deeply branching in the nematode tree. A comparison of homologous genes in T. spiralis and C. elegans revealed different mechanisms whereby U12 introns were lost.

Conclusions

The phylogenetic distribution of U12 introns and spliceosomal RNAs give further support to an early origin of U12 dependent splicing. In addition, this distribution identifies a large number of instances during eukaryotic evolution where such splicing was lost.     

Seasonal variation of dominant free-floating and attached Ulva species in Rudong coastal area,China

In this paper, species compositions and seasonal variations of attached Ulva species on Porphyra aquaculture rafts and free floating Ulva species at Rudong coastal area, Jiangsu Province of China were investigated during 2010–2011. Based on the sequences analysis of nuclear-encoded ITS (including 5.8S rDNA regions) and 5S rDNA spacer regions, dominant species of both attached and free-floating Ulva samples were identified as Ulva compressa, Ulva linza, Ulva prolifera and Ulva flexuosa. Phylogenetic tree based on sequences of ITS and 5S rDNA spacer regions for attached and free-floating Ulva species was constructed, respectively. Species compositions of the Ulva population attached on aquaculture rafts varied with seasons, and U. prolifera was only found on aquaculture rafts in March 2011 during the 2010–2011 Porphyra yezoensis cultivation season, which had the same sequences of ITS and 5S rDNA spacer regions as that of the dominant species bloomed in the Yellow Sea of China in 2008. Dominant species of the free-floating Ulva population at the early stage of the green tide were U. compressa, U. flexuosa, and U. linza. Free-floating U. prolifera appeared in the middle of May, 2011. ITS sequence similarity rates of U. compressa and U. flexuosa between the attached and free-floating species were 100%. And ITS and 5S rDNA spacer sequences of the attached and the free-floating U. prolifera population also showed no differences. Further study showed that there were two types of free-floating U. prolifera population (Type 5S-A and Type 5S-B) based on 5S rDNA spacer sequences. The present study would provide some useful information for clarifying the outbreak mechanism of green tides occurred in the Yellow Sea, China.     

Synthetic Lethality of Yeast slt Mutations with U2 Small Nuclear RNA Mutations Suggests Functional Interactions between U2 and U5 snRNPs That Are Important for Both Steps of Pre-mRNA Splicing

A genetic screen was devised to identify Saccharomyces cerevisiae splicing factors that are important for the function of the 5′ end of U2 snRNA. Six slt (stands for synthetic lethality with U2) mutants were isolated on the basis of synthetic lethality with a U2 snRNA mutation that perturbs the U2-U6 snRNA helix II interaction. SLT11 encodes a new splicing factor and SLT22 encodes a new RNA-dependent ATPase RNA helicase (D. Xu, S. Nouraini, D. Field, S. J. Tang, and J. D. Friesen, Nature 381:709–713, 1996). The remaining four slt mutations are new alleles of previously identified splicing genes: slt15, previously identified as prp17 (slt15/prp17-100), slt16/smd3-1, slt17/slu7-100, and slt21/prp8-21. slt11-1 and slt22-1 are synthetically lethal with mutations in the 3′ end of U6 snRNA, a region that affects U2-U6 snRNA helix II; however, slt17/slu7-100 and slt21/prp8-21 are not. This difference suggests that the latter two factors are unlikely to be involved in interactions with U2-U6 snRNA helix II but rather are specific to interactions with U2 snRNA. Pairwise synthetic lethality was observed among slt11-1 (which affects the first step of splicing) and several second-step factors, including slt15/prp17-100, slt17/slu7-100, and prp16-1. Mutations in loop 1 of U5 snRNA, a region that is implicated in the alignment of the two exons, are synthetically lethal with slu4/prp17-2 and slu7-1 (D. Frank, B. Patterson, and C. Guthrie, Mol. Cell. Biol. 12:5179–5205, 1992), as well as with slt11-1, slt15/prp17-100, slt17/slu7-100, and slt21/prp8-21. These same U5 snRNA mutations also interact genetically with certain U2 snRNA mutations that lie in the helix I and helix II regions of the U2-U6 snRNA structure. Our results suggest interactions among U2 snRNA, U5 snRNA, and Slt protein factors that may be responsible for coupling and coordination of the two reactions of pre-mRNA splicing.     

Interspecific assistance: fiddler crabs help heterospecific neighbours in territory defence

Theory predicts that territory owners will help established neighbours to repel intruders, when doing so is less costly than renegotiating boundaries with successful usurpers of neighbouring territories. Here, we show for the first time, to our knowledge, cooperative territory defence between heterospecific male neighbours in the fiddler crabs Uca elegans and Uca mjoebergi. We show experimentally that resident U. elegans were equally likely to help a smaller U. mjoebergi or U. elegans neighbour during simulated intrusions by intermediate sized U. elegans males (50% of cases for both). Helping was, however, significantly less likely to occur when the intruder was a U. mjoebergi male (only 15% of cases).     

Hydraulic properties of European elms: xylem safety-efficiency tradeoff and species distribution in the Iberian Peninsula

Key message

Ulmus minor and U. glabra show a trade-off between safety and efficiency in water transport, and U. laevis shows adaptations to waterlogged environments.

Abstract

Three native elm species grow in Europe: Ulmus minor Mill., U. glabra Huds. and U. laevis Pall., and within the Iberian Peninsula their habitats mainly differ in water availability. We evaluated firstly whether vulnerability to xylem embolism caused by water-stress has been a determinant factor affecting their distribution; secondly, if their xylem anatomy differs due to water availability dissimilarities; and thirdly, if these species present a trade-off between water transport safety and efficiency. Plants of the three species were grown in a common-garden in Madrid, Central Spain. The centrifuge method was used for constructing the vulnerability curves, and anatomical measurements were carried out with an optical microscope. We found clear differences in conductivity and cavitation vulnerability between the three species. Although all three elms were highly vulnerable to cavitation, U. minor was significantly more resistant to water stress cavitation. This species reached 50 % loss in conductivity at ?1.1 MPa, compared to U. glabra that did so at ?0.5 MPa, and U. laevis at ?0.4 MPa. Maximum xylem specific conductivity and maximum leaf specific conductivity were two to three times higher in U. glabra when compared to U. minor. A clear trade-off between safety against losses of conductivity and water transport efficiency was observed considering both U. minor and U. glabra samples. Ulmus minor’s hydraulic configuration was better adapted to overcome drought episodes. The expected aridification of the Iberian Peninsula could compromise Ulmus populations due to their high vulnerability to drought stress.     

Javan mongoose or small Indian mongoose–who is where?

The Javan mongoose Urva javanica and the small Indian mongoose Urva auropunctata have been recently shown not to be conspecific. However, the limits of their respective distribution ranges have not been fully defined. In particular, Chinese populations were not attributed to either species using molecular data. Furthermore, the small mongooses found on Hong Kong Island (discovered at the end of the 1980s) were not clearly attributed to U. auropunctata or U. javanica, nor their status (native or introduced) established. The main aims of this study were to: (1) investigate the intraspecific genetic diversity and structure within these two species; and (2) clarify the distribution limits of U. auropunctata and U. javanica, and in particular, to identify Chinese populations, and determine which species occurs on Hong Kong Island (and whether they are native or introduced). The analyses of one nuclear and three mitochondrial genes confirmed the separation of U. javanica and U. auropunctata, and showed that the populations from southern China and Hong Kong Island belong to U. javanica. The intraspecific geographical structure of the two species is clarified, and the taxonomic implications are discussed. In particular, we found a strong divergence of Javan individuals of U. javanica, which should be considered a separate subspecies.