Expansion Segments Research Articles

G-Quadruplexes in Human Ribosomal RNA

rRNA is the single most abundant polymer in most cells. Mammalian rRNAs are nearly twice as large as those of prokaryotes. Differences in rRNA size are due to expansion segments, which contain extended tentacles in metazoans. Here we show that the terminus of an rRNA tentacle of Homo sapiens contains 10 tandem G-tracts that form highly stable G-quadruplexes in vitro. We characterized rRNA of the H. sapiens large ribosomal subunit by computation, circular dichroism, UV melting, fluorescent probes, nuclease accessibility, electrophoretic mobility shifts, and blotting. We investigated Expansion Segment 7 (ES7), oligomers derived from ES7, intact 28S rRNA, 80S ribosomes, and polysomes. We used mass spectrometry to identify proteins that bind to rRNA G-quadruplexes in cell lysates. These proteins include helicases (DDX3, CNBP, DDX21, DDX17) and heterogeneous nuclear ribonucleoproteins. Finally, by multiple sequence alignments, we observe that G-quadruplex-forming sequences are a general feature of LSU rRNA of Chordata but not, as far as we can tell, of other species. Chordata ribosomes present polymorphic tentacles with the potential to switch between inter- and intramolecular G-quadruplexes. To our knowledge, G-quadruplexes have not been reported previously in ribosomes.

Description of Basiria khouzestanensis n. sp. (Nematoda: Tylenchidae) from Iran and its phylogenetic relationships with other species in the family.

Basiria khouzestanensis n. sp., recovered from the rhizosphere of orange in Khouzestan Province, south-western Iran, is described and illustrated based on morphological, morphometric and molecular data. The new species is characterized by having short body length (430-635 µm), lateral fields composed of four incisures, with non areolated bands, cephalic region smooth and continuous with body contour, stylet 9-12.5 µm long, basal bulb short and pyriform to slightly cylindrical, V = 63.3 (58-65.5), spermatheca non-offset, tail elongate-conoid, tail tip with various shapes and males with 16.5 (15-18) μm long spicules. Morphologically, the new species is similar to five known species of the genus: B. babhi, B. brevia, B. graminophila, B. lauta and B. shahidi. Morphological comparisons with these species are discussed. The sequence of the D2-D3 expansion segments of 28S rDNA gene for the new species was also used for molecular phylogenetic analysis. The phylogenetic relationships of the new species in relation to representatives of the family Tylenchidae, obtained from Bayesian inference (BI) analysis of the D2-D3 sequences, are presented and discussed. The new species clusters in a subclade containing three unidentified species of the genus Basiria from Iran with high support.

Survey of slug-parasitic nematodes in East and West Flanders, Belgium and description of Angiostoma gandavensis n. sp. (Nematoda: Angiostomidae) from arionid slugs.

A survey for slug-associated nematodes in five locations of East and West Flanders in Belgium revealed the presence of one new and six known slug-parasitic nematodes, Agfa flexilis (Dujardin, 1845), Alloionema appendiculatum (Schneider, 1859), Angiostoma dentiferum (Mengert, 1953), Angiostoma limacis (Dujardin, 1845), Angiostoma norvegicum (Ross et al., 2017) and Phasmarhabditis hermaphrodita (Schneider, 1859). Angiostoma norvegicum and P. hermaphrodita are recorded for the first time in Belgium. The six known species are documented by light microscopy (LM) microphotographs and informative DNA sequences. Angiostoma gandavensis n. sp. (Angiostomatidae), discovered from arionid slugs, is described based on light microscopy, scanning electron microscopy (SEM) and molecular data. Based on analyses of D2D3 expansion segment of 28S and 18S rDNA sequences, this new species is found to be related to A. limacis, A. norvegicum, A. margaretae (Ross et al., 2011) and A. milacis (Ivanova and Wilson, 2009). The new species can be distinguished from these others based on morphological characters such as the distinctive mucronate structures at the tail tip of both sexes, presence of lateral ala, reflexed female ovaries and the number and arrangement pattern of male genital papillae.

Research on Automatic Tracking of Bacteria Movement Based on Embedded Systems

The traditional culture and monitoring of bacteria is a very complicated task. There are some drawbacks to this task, such as time-consuming, high repeatability requirement, poor observation and even demand forthe extreme environment. However, the automatic tracking could help us avoid these problems. Through image enhancement, expansion, corrosion, binarization, and threshold segmentation of the image obtained by the automated platform, the growth of bacteria in the culture medium was recorded and analyzed in real time. The simulation results showthat the device could continuously record the growth of bacteria for twenty hours accurately, which is more precisethan manual operation. The automation device can improve the effectiveness and uniformity of biological experiments, and significantly reduce the time and economic costs.

Description of Discocriconemella sinensis n. sp. (Nematoda: Criconematidae) from the rhizosphere of Camellia sinensis in China

Summary Discocriconemella sinensis n. sp. isolated in Hangzhou, Zhejiang, China, from the rhizosphere of Camellia sinenis is described. The new species was characterised morphologically and molecularly. Important morphological details were elucidated by SEM photographs. The new species is characterised by an uninterrupted rounded cephalic disc, en face showing a rectangular labial plate with slit-like oral apertures, labial plate surrounded by slightly elevated projections resembling rudimentary lobes, R = 66 (64-69), Rex = 21 (17-24), stylet 74 (67-81) μm long, excretory pore located at the base of the pharyngeal bulb, vulva open, tail short and conoid with a lobed terminus. The species belongs to the group 1 lip pattern. Morphologically, it is most similar to D. discolabia, D. mauritiensis, D. mineira and D. perseae. This is the first new Discocriconemella species described from China. Phylogenetic analyses based on analysis of the D2-D3 expansion segments of the 28S rRNA, ITS rRNA, partial 18S rRNA, and COI gene revealed that the new species formed a separate clade from other criconematid species, thereby supporting its status as a new species of the genus. The new species showed close relationships with Criconemoides informis.

First report of Longidorus mindanaoensis Coomans, De Ley, Jimenez and De Ley, 2012 (Nematoda: Longidoridae) From a Mangrove Forest in Vietnam.

Longidorus mindanaoensis was recovered from a mangrove forest in Vietnam. The recovered population is in general morphological agreement with the type population, and the characters of pharyngeal bulb, i.e. the same unique pattern of pharyngeal glands nuclei as well as the lip region morphology, amphidial fovea shape and size and position of vulva corroborated its identity. Molecular studies of the recovered population using D2–D3 expansion segments of large subunit ribosomal DNA (LSU rDNA D2–D3) revealed the D2–D3 sequence of recovered population is 99.6% similar to the sequence of the type population. A new morphometric range for body size was recorded for the species based upon present Vietnamese population, and present study emphasized the diversity of Longidorus spp. in Vietnam could be higher than previously assumed.

Phylogenetic relationships of Cacopaurus pestis Thorne, 1943 within representatives of the Tylenchulidae Skarbilovich, 1947 as inferred from ITS and D2-D3 expansion segments of 28S-rRNA sequences

Summary The Persian sessile nematode (Cacopaurus pestis) and pin nematodes (Paratylenchus spp.) are sedentary ectoparasitic nematodes associated with many plant species worldwide. In this study, we provide morphological and molecular characterisation of seven populations of C. pestis and eight species of Paratylenchus recovered from north-western Iran. A total of 26 new sequences of D2-D3 expansion segments of 28S rRNA and ITS rRNA were obtained and used to reconstruct phylogenetic trees. Results of phylogenetic analyses revealed that the subfamilies of Tylenchulidae form well-separated clades, but that the genera Cacopaurus and Paratylenchus (= Gracilacus) in the subfamily Paratylenchinae are clustered in one clade. It appears that the previously used character of “stylet length greater than 40 μm” is not homologous and evolved more than once within the Paratylenchinae.

New observations on Miculenchus Andrássy, 1959 (Nematoda: Tylenchidae) with descriptions of two new and one known species from Iran

Summary During nematological surveys in grasslands and natural forests of north and north-western Iran, three species of Miculenchus, including two new and one known species, were recovered and characterised based upon morphological and molecular approaches. Miculenchus brevisalvus n. sp., the first new species, is mainly characterised by its short females 334-388 μm long and with a short 6.0-7.5 μm long stylet, pyriform to pyriform-elongate pharyngeal bulb, 4-8 μm long post-uterine sac (PUS), offset rounded spermatheca filled with small spheroid sperm, elongate conoid tail 62-83 μm long with a sharp tip, and males with simple cloacal lips. Miculenchus muscus n. sp., the second new species, is characterised by a combination of the following features: body 401-467 μm long, well-developed protuberant labial plate at the anterior end under light microscopy, stylet 7-9 μm long, pyriform pharyngeal bulb, PUS 4-9 μm long, gradually narrowing conical tail 62-74 μm long with a finely pointed or sharp end and bearing several fine bristles at tip, and a male with projecting cloacal lips. Both newly described species were morphologically compared with four currently known species of the genus, viz., M. elegans, M. salmae, M. salvus, and M. tesselatus. Miculenchus salmae was also recovered and reported from Iran for the first time. It is mainly characterised by lacking a PUS and the characteristic vagina shape. Miculenchus muscus n. sp. and M. salmae were both characterised using scanning electron microscopic images, yielding new morphological observations for the genus. All three species are studied for their molecular phylogenetic characters using sequences of near-full length fragments of the small subunit ribosomal RNA gene (SSU rDNA) and the D2-D3 expansion segments of the large subunit ribosomal RNA gene (LSU rDNA D2-D3). In both SSU and LSU phylogenies, all currently sequenced species of Miculenchus formed a monophyletic group with maximal clade support in both Bayesian inference and maximum likelihood analysis.

Molecular and morphological characterization of Paurodontella composticola n. sp. (Nematoda: Hexatylina, Sphaerulariidae) from Iran.

A new species of the genus Paurodontella, P. composticola n. sp., collected from Nazar Abad City, Alborz Province, Iran, is described and illustrated. The new species has a body length of 803–1053 μm (females n = 10) and 620 and 739 μm (males n = 2). The cuticle is weakly annulated with four lateral lines. Cephalic region is annulated and continuous with body contour. The stylet is 8.0 to 9.0 μm long with asymmetrical knobs. Esophageal basal bulb is present with a small posterior extension projecting into the intestine. Excretory pore is situated at the level of esophageal basal bulb region. Post-uterine sac is 5 to 8 μm long and uterus is without diverticulum. Tails of both sexes are similar, short and sub-cylindrical. Males have 24 to 25 μm long bursa leptoderan and spicules 24 or 25 µm long. A non-branching oviduct is present to form a uterine diverticulum; the new species is closely related to five known species of the genus, namely P. asymmetrica, P. balochistanica, P. densa, P. iranica and P. niger. It most closely resembles P. iranica, but differs from it morphologically by a shorter stem-like extension projecting into lumen of intestine and male with sub-cylindrical tail vs conoid. In addition to morphological comparisons, the molecular phylogenetic analyses based on 733 bp of the partial sequence of 28S D2/D3 expansion segments of the large subunit rDNA gene (LSU) revealed this as a new species.

Description of Hirschmanniella dicksoni n. sp. (Nematoda: Pratylenchidae) from rhizosphere soil of limpograss from Florida, USA

Abstract Hirschmanniella dicksoni n. sp. isolated from the rhizosphere soil of limpograss is described and illustrated based on morphology and molecular characters. The new species is characterized by its body length, 1,582 to 1,929 µm, hemispherical lip region with 6 to 7 annules, stylet length 19 to 21 µm, irregularly areolated lateral fields, oval spermatheca filled with rounded sperm, intestine not overlapping the rectum, and tail length 103 to 149 µm, usually with ventral projection with subterminal notch. Males are similar to the females except for their shorter body length and presence of secondary sexual characteristics, with spicules length 19 to 30 µm. The new species is closely related with H. mucronata, H. belli, and H. oryzae. Compared with these three species, the new species has a relatively longer tail and a terminus shape tail with a ventral projection with a subterminal notch. Other morphological and morphometric characteristics that separate these species are as follows: lip region, number of lip annuli, and spicules length. Molecular sequence analysis using the D2–D3 expansion segments of 28S and the ITS rRNA sequences showed that the new species is genetically distinct. D2–D3 sequence of H. dicksoni n. sp. showed 99 and 95% sequence homology with an undescribed species of Hirschmanniella isolated from the Colorado River in Yuma, Arizona, and H. oryzae, respectively. ITS sequence of the new species also showed 88% sequence homology with H. oryzae. The phylogenetic analysis of D2–D3 and ITS region grouped H. dicksoni n. sp., as sister species, with H. oryzae.

Morphological and Molecular Characterization of Coslenchus paramaritus n. sp. and C. cancellatus (Cobb, 1925) Siddiqi, 1978 (Nematoda: Tylenchidae) from Iran.

Coslenchus paramaritus n. sp. and C. cancellatus were identified based on morphological, morphometric, and molecular characteristics. The new species, C. paramaritus n. sp., is characterized by its cuticle with 18 longitudinal ridges excluding lateral lines, wide cuticular annuli (2.6–3.0 µm), a long tail (94–128 µm), the presence of males and the absence of sexual dimorphism in head shape. Molecular phylogenetic studies of the new species using D2–D3 expansion segments of 28S rRNA revealed that the new species formed a sister clade with three unknown populations of Coslenchus in Bayesian inference (BI) phylogeny, while C. cancellatus formed a sister clade with other Coslenchus species including C. oligogyrus, C. franklinae, C. costatus, C. turkeyensis and three unknown populations. C. cancellatus is recovered from Iran for the first time.

Morphological and molecular characterisation of Chitwoodius coffeae sp. n. (Dorylaimida: Tylencholaimidae) from Vietnam, with a revised taxonomy of the genus

Summary Chitwoodius coffeae sp. n. is described, including SEM observations and molecular (D2-D3 expansion segment of the rDNA 28S) analysis, from a coffee plantation in the Central Highlands of Vietnam. The new species is characterised by its 1.69-2.01 mm long body in females and 1.29-1.51 mm in males, lip region offset by deep constriction and 15-17 μm broad, odontostyle 27-30 μm long, neck 340-473 μm long, pharyngeal expansion occupying 52-54% of total neck length, uterus a simple tube-like structure 68-106 μm long, vulva longitudinal (V = 54-59), tail short and rounded conoid (20-28 μm, c = 54-88, c′ = 0.6-0.8) with a nearly terminal projection of inner cuticle layer, spicules 60-64 μm long, and 7-10 spaced ventromedian supplements without hiatus. SEM pictures, available for the first time for a representative of the genus, show a hexagonal (nearly hexastellate) oral field divided into six sectors by the existence of six deep incisures. Molecular analyses, also presented for the first time for a representative of the genus, results in a narrow evolutionary relationship among Chitwoodius and Tylencholaimus, and supports the monophyly of the Tylencholaimidae. This is the first record of Chitwoodius in Asian Far East territories. Chitwoodius ahmadi sp. n. is proposed for a misattributed population of C. seshadrii.

Integrative taxonomy of Xiphinema histriae and Xiphinema lapidosum from Spain.

Three populations of Xiphinema non-americanum group species were detected in agricultural and natural ecosystems, during routine surveys for plant-parasitic nematodes in Spain. Based on morphological and molecular analyses, the species were identified as Xiphinema histriae and Xiphinema lapidosum, being this the first record and molecular characterization of both species in Spain. The morphometrics and morphology of the Spanish populations agree with those of the original description and paratype specimens and the present study provided a first description of the second to fourth juvenile stages of both species. A detailed study on the morphology in the Spanish populations of X. histriae, as well as in paratypes, showed a pseudo-Z-organ with weakly muscularized wall and containing numerous small dense granular bodies, which was different to the original description by Lamberti et al. (1993). This new finding suggests that X. histriae must be considered a member of the morphospecies Group 5 of X. non-americanum. Phylogenetic analysis based on D2 to D3 expansion segments of 28S gene, ITS1 and partial CoxI gene indicated that X. histriae and X. lapidosum are phylogenetically related with other Xiphinema non-americanum group spp. reported from Spain. Considering the pathological and economic importance of this group of nematodes, the combination of morphological characters, measurements, and molecular analysis is crucial for accurate identification of these species.

Ficophagus curtipes n. sp. (Nematoda: Aphelenchoididae), an associate of Ficus curtipes in China

Summary A new nematode species was recovered from the syconia of Ficus curtipes from Xishuangbanna Tropical Botanical Garden, Yunnan, China. It is described herein as Ficophagus curtipes n. sp. and is differentiated from all currently described species in the genus by the possession of a spicule with a ventrally recurved tip (terminal barb). It is further characterised by possessing a short post-uterine sac, an ovoid spermatheca, presence of crustaformeria, excretory pore located near the head, amoeboid sperm, three pairs of subventral papillae on the male tail, rounded male tail tip without mucron, rose-thorn-shaped spicules without cucullus and absence of gubernaculum (= apophysis). Ficophagus curtipes n. sp. was differentiated from other sequenced species by the partial small subunit rRNA gene and D2-D3 expansion segments of the large subunit rRNA gene. Phylogenetic analyses suggested that F. curtipes n. sp. has a closer relationship with F. benjamina and F. microcarpus in the same highly supported monophyletic clade than to the other sequenced Ficophagus and Schistonchus s.l. species.

On the synonymy of Trophotylenchulus asoensis and T. okamotoi with T. arenarius, and intra-generic structure of Paratylenchus (Nematoda: Tylenchulidae)

Abstract Two populations of the genus Trophotylenchulus and 10 species of the genus Paratylenchus from Iran were characterized based on morphometric, morphological and molecular characters. Our observations on the two populations of Trophotylenchulus from Iran revealed that T. asoensis and T. okamotoi have been distinguished from T. arenarius, on the basis of the features which cannot be longer considered as stable diagnostic characters. One of the populations shows a mixed combination of the characters of T. arenarius and T. asoensis; it has morphometrics more similar to T. arenarius but shows affinities with T. asoensis in the tail terminus shape of females and second-stage juveniles (J2) and in having a reduced stylet in males. The other population fit well with T. okamotoi; it has females with generally bluntly rounded tails typical for T. okamotoi, but sometimes with finely rounded tail termini, like those of T. arenarius or T. asoensis. The sequences of D2–D3 expansion segments of 28 S rRNA gene for the two populations are identical with each other, but only 4 bp (0.67%) difference with T. arenarius sequence deposited in the GenBank. Considering no stable difference allow separating species, synonymy of T. asoensis and T. okamotoi with T. arenarius, which has already been proposed, is supported and confirmed here. All studied Paratylenchus species with stylets longer than 40 µm, except P. straeleni, formed a basal cluster to Cacopaurus pestis and species of Paratylenchus bearing stylets shorter than 40 µm; thus, validity of Gracilacus cannot be rejected using our data sets. However, the synonymy of Paratylenchoides was supported by the positioning of P. sheri within representatives of Paratylenchus in the inferred phylogenetic tree.

Paratylenchus jasmineae sp. n. (Nematoda: Paratylenchinae) from rhizosphere of Jasminum sambac in India

Summary A new species of pin nematode, Paratylenchus jasmineae sp. n., was isolated and described from the rhizosphere of jasmine in India. The new species can be diagnosed by having a relatively larger body length of 248-355 μm, stylet length of 24.6-28.5 μm, lateral field with four lateral lines, the presence of small post-vulval uterine sac and absence of advulval flaps in the females. Additional morphological characters included continuous lip region with small projected submedian lobes, large and oblong-shaped spermatheca, the presence of prevulval swelling, and arcuate conoid tail with finely rounded terminus. Molecular characterisation of the species was carried out based on internal transcribed spacer sequence (ITS rRNA) and D2-D3 expansion segment of 28S rRNA subunit. Phylogenetic analyses based on ITS and D2-D3 molecular markers resulted in clear separation of P. jasmineae sp. n. from other Paratylenchus species.

Ficophagus auriculatae n. sp. (Nematoda: Aphelenchoididae), an associate of the Ficus auriculata-complex in China

Summary A new nematode species was recovered from the syconia of Ficus auriculata-complex, including F. auriculata, F. oligodon and F. hainanensis, from Xishuangbanna Tropical Botanical Garden, China. It is described herein as Ficophagus auriculatae n. sp. and is characterised by possessing the combined characters of a short post-uterine sac, excretory pore located between the metacorpus and the stylet basal knobs, testis multi-reflexed, amoeboid sperm, three pairs of subventral papillae on male tail, rounded male tail tip without mucron, absence of gubernaculum (= apophysis) and sickle-shaped spicules with terminal cucullus. Ficophagus auriculatae n. sp. was differentiated from other sequenced species by the partial small subunit rRNA gene and D2-D3 expansion segments of the large subunit rRNA gene. Phylogenetic analysis with the above-mentioned sequences suggested that F. auriculatae n. sp. has a closer relationship with F. fleckeri in the same highly supported monophyletic clade than with the other sequenced Ficophagus and Schistonchus sensu lato species.

Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation.

The majority of eukaryotic proteins are N-terminally α-acetylated by N-terminal acetyltransferases (NATs). Acetylation usually occurs co-translationally and defects have severe consequences. Nevertheless, it is unclear how these enzymes act in concert with the translating ribosome. Here, we report the structure of a native ribosome-NatA complex from Saccharomyces cerevisiae. NatA (comprising Naa10, Naa15 and Naa50) displays a unique mode of ribosome interaction by contacting eukaryotic-specific ribosomal RNA expansion segments in three out of four binding patches. Thereby, NatA is dynamically positioned directly underneath the ribosomal exit tunnel to facilitate modification of the emerging nascent peptide chain. Methionine amino peptidases, but not chaperones or signal recognition particle, would be able to bind concomitantly. This work assigns a function to the hitherto enigmatic ribosomal RNA expansion segments and provides mechanistic insights into co-translational protein maturation by N-terminal acetylation.

MORPHOLOGICAL AND MOLECULAR CHARACTERISATION OF ECUMENICUS MONOHYSTERA (NEMATODA DORYLAIMIDA QUDSIANEMATIDAE) AND ITS PHYLOGENETIC RELATIONS FROM IRAN

Ecumenicus monohysterawas collected from the rhizosphere of faba bean (Vicia fabaL.) fields in Khuzestanprovince, south-western Iran. Morphological and morphometric data are provided for this species. Additionally,sequence of the D2-D3 expansion segments of 28S rRNA gene for this species wasalso used for molecularphylogenetic analysis. The phylogenetic relationships of E. monohysterain relation to representatives of the orderDorylaimida, obtained from Bayesian inference (BI) analysis of the D2-D3 sequences, are presented and discussed.

Morphological and molecular characterization of two new species of the genus Aporcelinus Andrássy, 2009 (Nematoda, Dorylaimida, Aporcelaimidae) from the USA, with new insights on the phylogeny of the genus.

Two new species of the genus Aporcelinus from the USA are described and illustrated. Aporcelinus floridensis sp. n. is characterized by its 1.12-1.52 mm long body, lip region offset by marked constriction and 14.5-17.0 μm broad with perioral liplets, odontostyle 16.5-20.0 μm at its ventral side and 1.1-1.2 times the lip region diameter, neck 316-395 μm long, pharyngeal expansion occupying 43-48% of total neck length, uterus simple and 33-56 μm long or 0.8-1.2 times the corresponding body diameter, V = 48-54, female tail conical (36-49 μm long, c = 27-41, c' = 1.2-2.0) with finely rounded terminus and no hyaline portion, and male absent. Aporcelinus paolae sp. n. is characterized by its 1.29-1.80 mm long body, lip region offset by marked constriction and 14-16 μm broad, odontostyle 15-17 μm at its ventral side and 1.0-1.1 times the lip region diameter, neck 314-397 μm long, pharyngeal expansion occupying 43-53% of total neck length, uterus tripartite and 128-164 μm long or 2.6-3.6 times the corresponding body diameter, V = 53-57, female tail conical (30-39 μm long, c = 40-51, c' = 1.1-1.3) with finely rounded terminus and variably re-curved dorsad, male tail conical (27-36 μm, c = 39-59, c' = 0.9-1.2), ventrally straight and dorsally convex, spicules 48-54 μm long, and 7-9 irregularly spaced ventromedian supplements lacking hiatus. The analyses of the D2-D3 expansion segments of 28S rRNA (LSU) gene sequences of the two new species confirmed the monophyly of the genus, based upon currently available data, showing a close relationship between the genera Aporcelinus and Makatinus, and justified the placement of Aporcelaimellus, Makatinus and Aporcelinus under the subfamily Aporcelaimellinae.