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NAR Cancer ◽  
2022 ◽  
Vol 4 (1) ◽  
Author(s):  
Laurence Faucher-Giguère ◽  
Audrey Roy ◽  
Gabrielle Deschamps-Francoeur ◽  
Sonia Couture ◽  
Ryan M Nottingham ◽  
...  

ABSTRACT Small nucleolar RNAs (snoRNAs) are an omnipresent class of non-coding RNAs involved in the modification and processing of ribosomal RNA (rRNA). As snoRNAs are required for ribosome production, the increase of which is a hallmark of cancer development, their expression would be expected to increase in proliferating cancer cells. However, assessing the nature and extent of snoRNAs’ contribution to cancer biology has been largely limited by difficulties in detecting highly structured RNA. In this study, we used a dedicated midsize non-coding RNA (mncRNA) sensitive sequencing technique to accurately survey the snoRNA abundance in independently verified high-grade serous ovarian carcinoma (HGSC) and serous borderline tumour (SBT) tissues. The results identified SNORA81, SNORA19 and SNORA56 as an H/ACA snoRNA signature capable of discriminating between independent sets of HGSC, SBT and normal tissues. The expression of the signature SNORA81 correlates with the level of ribosomal RNA (rRNA) modification and its knockdown inhibits 28S rRNA pseudouridylation and accumulation leading to reduced cell proliferation and migration. Together our data indicate that specific subsets of H/ACA snoRNAs may promote tumour aggressiveness by inducing rRNA modification and synthesis.


2022 ◽  
Author(s):  
Olga A. Glazunova ◽  
Konstantin V. Moiseenko ◽  
Natalia V. Shakhova ◽  
Nadezhda V. Psurtseva ◽  
Tatyana V. Fedorova

White-rot fungi isa source of a great variety of oxidative and hydrolytic enzymes suitable for biotechnological applications, e.g. in pulp and paper, textile and food industries, bioethanol production, degradation of recalcitrant environmental pollutants,and others. Steccherinumochraceum is a xylotrophicwhite-rot basidiomycetethat can be found in variousclimatic zones on different woody substrates (mostly well decayed). For this research, seventeenstrains of S. ochraceumwere collected in different regions of Russia from various wood substrates (aspen, alder, oak, hazel, birch and willow). Phylogeneticanalyseswere performedbasedon the nucleotide sequences of ITS1, ITS2, 5.8S rRNA, 28S rRNA, β-tubulin and tef1.Oxidaseandcellulaseactivitieswereassessedbyplate-tests with ABTS and CMC. Forevaluation of biodegradation potential,solid state fermentation on alder and pine sawdust wasperformed. Weightanddensitylossaswellas the C:Nratioweremeasuredafter 90 days of cultivation.All S. ochraceum strains exhibited high oxidative activity towards ABTS, indicating secretion of oxidative enzymes (i.e. laccases and class II peroxidases). Cellulase activity was medium or low for most strains and in some strains – absent. Allstrainswereabletodegradealderandpinesawdust. There was no correlation between the enzymatic activity, biodegradation potential and geographic origin of S. ochraceum strains. However, S. ochraceum strains isolated from the same wood substrates exhibited similar characteristics in most cases. Strain LE-BIN 3398 was the most effective for degrading both alder and pine sawdust and could be regarded as a promising source of oxidative enzymes for biotechnology. Keywords: basidiomycetes, biodegradation, solid state fermentation, oxidase activity, Steccherinumochraceum


2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Xiaoxing Yang ◽  
Guangxiang Tong ◽  
Le Dong ◽  
Ting Yan ◽  
Huan Xu ◽  
...  

AbstractAs a powerful and attractive method for detecting gene expression, qRT-PCR has been broadly used in aquaculture research. Understanding the biology of taimen (Hucho taimen) has drawn increasing interest because of its ecological and economic value. Stable reference genes are required for the reliable quantification of gene expression, but such genes have not yet been optimized for taimen. In this study, the stability levels of 10 commonly used candidate reference genes were evaluated using geNorm, NormFinder, BestKeeper, and RefFinder. The expression levels of the 10 genes were detected using 240 samples from 48 experimental groups consisting of 40 individuals treated under four heat-stress conditions (18, 20, 22, and 24 °C) for 24 h and 26 °C for 4, 24, 48, and 72 h. Six tissues (blood, heart, brain, gill, skin, and liver) were collected from each individual. Ribosomal protein S29 (RPS29) and ribosomal protein L19 (RPL19) were the most stable genes among all of the samples, whereas 28S ribosomal RNA (28S rRNA), attachment region binding protein (ARBP), and 18S ribosomal RNA (18S rRNA) were the least stable. These results were verified by an expression analysis of taimen heat-stress genes (heat shock protein 60, hsp60, and heat shock protein 70, hsp70). In conclusion, RPS29 and RPL19 are the optimal reference genes for qRT-PCR analyses of taimen, irrespective of the tissue and experimental conditions. These results allow the reliable study of gene expression in taimen.


Plant Disease ◽  
2021 ◽  
Author(s):  
José Francisco Díaz-Nájera ◽  
Sergio Ayvar-Serna ◽  
Antonio Mena-Bahena ◽  
Guadalupe Arlene Mora-Romero ◽  
Karla Yeriana Leyva-Madrigal ◽  
...  

Cucurbita argyrosperma, commonly named as winter or cushaw squash, is highly sought for its seeds, which have important uses in culinary arts. During the autumn 2021, powdery mildew-like signs and symptoms were observed on cushaw squash in several commercial fields located in Cocula, Guerrero, Mexico. Signs were initially appeared as whitish powdery patches on both sides of leaves and then covering entire leaves and causing premature senescence. The disease incidence was estimated to be 80% in about 1000 plants in two fields. The mycelium was amphigenous, persistent, white in color, and occurred in dense patches. A voucher specimen was deposited in the Herbarium of the Colegio Superior Agropecuario del Estado de Guerrero under the accession number CSAEG22. For the morphological characterization by light microscopy, fungal structures were mounted in a drop of lactic acid on a glass slide. Microscopic examination showed nipple-shaped hyphal appressoria. Conidiophores (n = 30) were straight, 100 to 190 × 10 to 12 μm and produced 2 to 6 conidia in chains. Foot-cells were cylindrical, 41 to 78 μm long, followed by 1 to 2 shorter cells. Conidia (n = 100) were ellipsoid-ovoid to barrel-shaped, 29.5 to 39.1 × 19.4 to 22.7 μm, and contained conspicuous fibrosin bodies. Germ tubes were produced from a lateral position on conidia. Chasmothecia were not observed during the growing season. The morphological characters were consistent with those of the anamorphic state of Podosphaera xanthii (Braun and Cook 2012). For further confirmation, total DNA was extracted from conidia and mycelia following the CTAB method (Doyle and Doyle 1990), and the internal transcribed spacer (ITS) region and part of the 28S gene were amplified by PCR, and sequenced. The ITS region of rDNA was amplified using the primers ITS5/ITS4 (White et al. 1990). For amplification of the 28S rRNA partial gene, a nested PCR was performed using the primer sets PM3 (Takamatsu and Kano 2001)/TW14 (Mori et al. 2000) and NL1/TW14 (Mori et al. 2000) for the first and second reactions, respectively. Phylogenetic analyses using the Maximum Likelihood method, including ITS and 28S sequences of isolates of Podosphaera spp. were performed and confirmed the results obtained in the morphological analysis. The isolate CSAEG22 grouped in a clade with isolates of Podosphaera xanthii. The ITS and 28S sequences were deposited in GenBank under accession numbers OL423329 and OL423343, respectively. Pathogenicity was confirmed by gently dusting conidia from infected leaves onto ten leaves of healthy C. argyrosperma plants. Five non-inoculated leaves served as controls. The plants were maintained in a greenhouse at 25 to 35 ºC, and relative humidity of 60 to 70%. All inoculated leaves developed similar signs to the original observation after 10 days, whereas control leaves remained symptomless. Microscopic examination of the fungus on inoculated leaves showed that it was morphologically identical to that originally observed on diseased plants, fulfilling Koch’s postulates. Podosphaera xanthii has been previously reported on C. maxima, C. moschata, and C. pepo in Mexico (Yañez-Morales et al. 2009; Farr and Rossman 2021). To our knowledge, this is the first report of P. xanthii causing powdery mildew on C. argyrosperma in Mexico. This pathogen is a serious threat to C. argyrosperma production in Mexico and disease management strategies should be developed.


2021 ◽  
Vol 8 ◽  
Author(s):  
Ondřej Máca ◽  
Marek Kouba ◽  
Erkki Korpimäki ◽  
David González-Solís

Background: Birds act as intermediate or definitive hosts of cyst-forming coccidia parasites of the genus Sarcocystis Lankester, 1882. However, the spectrum of species of Sarcocystis in birds and the role of the latter in the transmission of coccidia are still incomplete for many avian species, including the Tengmalm's owl Aegolius funereus (Linnaeus, 1758). During the research on Tengmalm's owls in Finland, some fledglings were found dead and subsequently parasitologically examined. Therefore, this study is focused on the morphological and molecular description of a Sarcocystis species found in the intestine of the Tengmalm's owl and its possible role as a definitive host.Methods: Eleven fledgling owls in the Kauhava region of west-central Finland were found dead and subsequently were submitted for necropsy and parasitologically examined through the flotation–centrifugation coprological technique for the presence of oocysts/sporocysts of the genus Sarcocystis by light microscopy. Wet mounts were used for the examination of muscle samples (breast, legs, and heart). Polymerase chain reaction (PCR) and nested-PCR were carried out using primers for 18S rRNA, 28S rRNA, ITS1 region, and CO1 genes.Results: All 11 examined owls were parasitized by numerous sporocysts and oocysts in the intestinal mucosa scrapings (prevalence, 100%). Sporulated oocysts and sporocysts measured 16.34–16.96 × 11.47–12.09 μm and 11.85–13.52 × 7.77–9.25 μm, respectively. The skeletal and heart muscles were negative for sarcocysts. Sarcocystis sp. ex Aegolius funereus (hereafter Sarcocystis sp. Af) is closely related to Sarcocystis strixi in the barred owl (Strix varia Barton, 1799) from the USA and Sarcocystis sp. isolate 5 in the European shrew (Sorex araneus Linnaeus, 1758) from the Czech Republic. Phylogenetic analysis allowed determining the relationship of the herein reported Sarcocystis sp. with its congeners.Conclusions: This work provided the first and most comprehensive record on Sarcocystis from owls obtained in Finland, thus highlighting the importance of molecular data in species identification.


Insects ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1125
Author(s):  
Nisha Patwa ◽  
Christopher M. Ranger ◽  
Maximilian Lehenberger ◽  
Peter H. Biedermann ◽  
Michael E. Reding

The fungus-farming ambrosia beetle Xylosandrus germanus (Blandford) uses a pouch-like structure (i.e., mycangium) to transport spores of its nutritional fungal mutualist. Our current study sought to identify reference genes necessary for future transcriptome analyses aimed at characterizing gene expression within the mycangium. Complementary DNA was synthesized using selected tissue types from laboratory-reared and field-collected X. germanus consisting of the whole body, head + thorax, deflated or inflated mycangium + scutellum, inflated mycangium, and thorax + abdomen. Quantitative reverse-transcription PCR reactions were performed using primers for 28S ribosomal RNA (28S rRNA), arginine kinase (AK), carbamoyl-phosphate synthetase 2-aspartate transcarbamylase-dihydroorotase (CAD), mitochondrial cytochrome oxidase 1 (CO1), and elongation factor-1α (EF1α). Reference gene stability was analyzed using GeNorm, NormFinder, BestKeeper, ΔCt, and a comprehensive final ranking by RefFinder. The gene CO1 was identified as the primary reference gene since it was generally ranked in first or second position among the tissue types containing the mycangium. Reference gene AK was identified as a secondary reference gene. In contrast, EF1α was generally ranked in the last or penultimate place. Identification of two stable reference genes will aid in normalizing the expression of target genes for subsequent gene expression studies of X. germanus’ mycangium.


Crustaceana ◽  
2021 ◽  
Vol 94 (11-12) ◽  
pp. 1313-1325
Author(s):  
Elisabeth Mock ◽  
Christoph D. Schubart

Abstract The genus Metopograpsus H. Milne Edwards, 1853 is widespread throughout the Indo-West Pacific and currently consists of seven species that can only be separated by minor morphological differences. Therefore, it represents a good example for the usefulness of genetic analyses for identification and classification. In order to obtain phylogenetic information at both lower and higher evolutionary levels, it is best to use a combination of mitochondrial and nuclear molecular markers. Here we present for the first time a molecular phylogeny based on a relative long fragment of the 28S rRNA nuclear gene for the genus Metopograpsus, after application of newly developed primers. Our data suggest an alternative intrageneric speciation order, with M. thukuhar and M. cannicci holding a basal position and a monophyletic grouping of M. frontalis, M. oceanicus and M. quadridentatus, which differs from prior phylogenetic reconstructions. Previously recognized intraspecific phylogeographic patterns in M. latifrons and M. quadridentatus could not be confirmed, due to limited variability of this conserved nuclear gene and due to an incomplete geographic coverage of the corresponding species. In contrast, the previously indicated phylogenetic subdivision within the formerly widespread species M. thukuhar, which led to the recent description of M. cannicci, is here supported.


RNA ◽  
2021 ◽  
pp. rna.079006.121
Author(s):  
Mario Rivas ◽  
George E Fox

The ribosome is the molecular factory that catalyzes all coded protein synthesis in extant organisms. Eukaryotic ribosomes are typically assembled out of four rRNAs, namely 5S, 5.8S, 18S, and 28S. However, the 28S rRNA of some trypanosomatid organisms has been found to be segmented into six independent rRNAs of different sizes. The two largest segments have multiple sites where they jointly form stems comprised of standard base pairs that can hold them together. However, such regions of interaction are not observed among the four smaller RNAs. Early reports suggested that trypanosomatid segmented ribosome assembly was essentially achieved thanks to their association with rProteins. However, examination of Cryo-EM ribosomal structures from Trypanosoma brucei, Leishmania donovani and Trypanosoma cruzi reveals several long-range nonstandard RNA/RNA interactions. Most of these interactions are clusters of individual hydrogen bonds and so are not readily predictable. However, taken as a whole, they represent significant stabilizing energy that likely facilitates rRNA assembly and the overall stability of the segmented ribosomes. In the context of origin of life studies, the current results provide a better understanding of the true nature of RNA sequence space and what might be possible without an RNA replicase.


2021 ◽  
Vol 8 ◽  
Author(s):  
Anna M. Jażdżewska ◽  
Tammy Horton ◽  
Ed Hendrycks ◽  
Tomasz Mamos ◽  
Amy C. Driskell ◽  
...  

Paralicella tenuipesChevreux, 1908 and Paralicella caperescaShulenberger and Barnard, 1976 are known as widely distributed deep-sea scavenging amphipods. Some recent studies based on genetic data indicated the presence of high intraspecific variation of P. caperesca suggesting it is a species complex. Based on published molecular data from the Pacific and Indian oceans and new material obtained from the North and South Atlantic, we integrated the knowledge on the intraspecific variation and species distribution of the two nominal taxa. The study included analysis of three genes (COI, 16S rRNA, 28S rRNA) and revealed the existence of a single Molecular Operational Taxonomic Unit (MOTU) within P. tenuipes and six different MOTUs forming P. caperesca. The distribution pattern of the recognized lineages varied with three (P. tenuipes, MOTU 1 and MOTU 5 of P. caperesca) being widely distributed. There was evidence of contemporary population connectivity expressed by the share of the same COI haplotypes by individuals from very distant localities. At the same time no signal of recent demographic changes was observed within the studied taxa. The time-calibrated phylogeny suggested the emergence of species to be at the time of Mesozoic/Cenozoic transition that may be associated with global changes of the ocean circulation and deep sea water cooling.


2021 ◽  
Vol 31 (1) ◽  
Author(s):  
Phap Quang Trinh ◽  
Duyen Thi Nguyen ◽  
Linh Thi Mai Le ◽  
Tien Huu Nguyen

Abstract Background Entomopathogenic nematodes (EPNs) are evidently a useful nematode group for the biocontrol of insect pests. It is well known that efficacy of different EPN strains, even belonging to the same species, can be significantly varied in different localities. Therefore, exploring EPNs and testing their efficacy in various ecological regions is of crucial importance to find out more efficient EPN strains. On the other hand, this practice is also needed to enhance the knowledge on diversity and distribution model of EPNs over the world. Results In this study, a species belonging to the genus Steinernema, S. surkhetense, has been characterized for the first time in Vietnam based on morphological and molecular characterizations. Morphological characterizations of infective juveniles, the first and second-generation adults, and molecular characterization of D2-D3 expansion segment of 28S rRNA region were given. Molecular phylogeny of the genus Steinernema was also provided. In addition, the study showed that the lethal efficacy of this local strain to larvae of Galleria mellonella L. was relatively higher than other reported EPN strains in Vietnam. Conclusions The Vietnamese EPN population found in this study was determined to be conspecific with S. surkhetense, revealed its new distribution in Vietnam. Besides, detailed morphological and molecular characterizations of it was provided with small variations compared to other populations in the world, and its relatively high lethal efficacy on larvae of G. mellonella implied that this strain can be potentially a useful strain for biological control of insect pests.


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