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Phylogenetic analyses of sequences of the nuc rDNA small subunit (18S), internal transcribed spacer (ITS1-5.8S-ITS2 = ITS), and large subunit (28S) region (= 18S-ITS-28S), as well as sequences of this region concatenated with sequences of the largest subunit of RNA polymerase II (RPB1) gene, proved that the species originally described as Acaulospora polonica (phylum Glomeromycota) represents a new genus and a new family of the ancient order Archaeosporales, here introduced into the Glomeromycota under the names Polonospora and Polonosporaceae, respectively. The phylogenetic analyses and BLASTn queries also indicated that the Polonosporaceae with P. polonica comb. nov. still contains several morphologically undescribed taxa at the ranks of genus and species, which have a worldwide distribution.

Here, we report the first case of Cryptosporidium cf. avium from an inland bearded dragon (Pogona vitticeps) from a wildlife sanctuary in Victoria, Australia. Molecular characterisation was conducted by PCR-coupled sequencing of regions in the small subunit of nuclear RNA (SSU), actin and large subunit of nuclear RNA (LSU) genes. The sequences obtained grouped with those of C. ornithophilus and other C. avium genotypes/variants originating from reptiles or birds. We discuss this case in relation to the current state of knowledge of C. avium of birds and reptiles, considering provenance and environment (agricultural, pet industry, wildlife, zoo or wildlife park) as well as clinical context, and pathological changes associated with cryptosporidiosis in these host animals., Graphical abstract Image 1, Highlights • Characterisation of Cryptosporidium cf. avium from an inland bearded dragon (Pogona vitticeps). • Molecular differentiation of C. cf. avium from other members of the C. avium clade. • Pathogenicity of C. cf. avium seems higher than other members of this clade.

Starch is a major component of wheat (Triticum aestivum L.) endosperm and is an important part of the human diet. The functions of many starch synthesis genes have been elucidated. However, little is known about their regulatory mechanisms in wheat. Here, we identified a novel NAC transcription factor, TaNAC019-A1 (TraesCS3A02G077900), that negatively regulates starch synthesis in wheat and rice (Oryza sativa L.) endosperms. TaNAC019-A1 was highly expressed in the endosperm of developing grains and encoded a nucleus-localized transcriptional repressor. Overexpression of TaNAC019-A1 in rice and wheat led to significantly reduced starch content, kernel weight, and kernel width. The TaNAC019-A1-overexpression wheat lines had smaller A-type starch granules and fewer B-type starch granules than wild-type. Moreover, TaNAC019-A1 could directly bind to the ‘ACGCAG’ motif in the promoter regions of ADP-glucose pyrophosphorylase small subunit 1 (TaAGPS1-A1, TraesCS7A02G287400) and TaAGPS1-B1 (TraesCS7B02G183300) and repress their expression, thereby inhibiting starch synthesis in wheat endosperm. One haplotype of TaNAC019-B1 (TaNAC019-B1-Hap2, TraesCS3B02G092800) was positively associated with thousand-kernel weight and underwent positive selection during the Chinese wheat breeding process. Our data demonstrate that TaNAC019-A1 is a negative regulator of starch synthesis in wheat endosperm and provide novel insight into wheat yield improvement.

Blastocystis is a zoonotic protozoan parasite frequently identified in the intestinal tract of humans and a vast variety of animals, worldwide. Here, we assessed the prevalence of Blastocystis and its subtypes in stool samples of raccoons. Stool samples from 30 raccoons were collected. Total DNA was extracted, and the barcoding region of the small subunit ribosomal rRNA (SSU rRNA) gene was amplified and sequenced. Specific fragment for Blastocystis was successfully amplified in five samples (16.66%). Sequencing analysis revealed ST1, ST2, and ST3 among 1, 2, and 2 Blastocystis-positive samples. Our results documented the presence of Blastocystis subtypes 1-3 in raccoons. Subtype 1 showed higher similarity to the human isolates of Blastocystis. However, it seems that raccoons may emerge as reservoirs for Blastocystis and may be linked to zoonotic transmission of the protist.

Blastocystis has recently been recognized as the most common eukaryotic microbe of the human gut. We investigated the prevalence of Blastocystis and their subtypes in diarrheal and non-diarrheal groups and the associated clinical parameters. A total of 324 stool samples were obtained from 196 diarrheal and 128 non-diarrheal subjects. Blastocystis subtypes were determined by sequencing the small subunit ribosomal DNA (SSU rRNA) gene. Demographic, clinical and laboratory data were collected and analyzed by diarrhea and Blastocystis status. The overall rate of Blastocystis positivity was 9.0% (29/324) but was significantly higher in the non-diarrheal group (18.0% vs. 3.1%, P

In mammalian mitochondria, messenger RNA is processed and matured from large primary transcripts in structures known as RNA granules. The identity of the factors and process transferring the matured mRNA to the mitoribosome for translation is unclear. Nascent mature transcripts are believed to associate initially with the small mitoribosomal subunit prior to recruitment of the large subunit to form the translationally active monosome. When the small subunit fails to assemble, however, the stability of mt‐mRNA is only marginally affected, and under these conditions, the LRPPRC/SLIRP RNA‐binding complex has been implicated in maintaining mt‐mRNA stability. Here, we exploit the activity of a bacterial ribotoxin, VapC20, to show that in the absence of the large mitoribosomal subunit, mt‐mRNA species are selectively lost. Further, if the small subunit is also depleted, the mt‐mRNA levels are recovered. As a consequence of these data, we suggest a natural pathway for loading processed mt‐mRNA onto the mitoribosome., The late stages of the life cycle of mitochondrial messenger RNAs (mt‐mRNAs) are still poorly understood; in particular, protection of mt‐RNAs, their recognition by mitochondrial ribosomes and set‐up of translation. Now, Francesco Bruni and colleagues use the bacterial endoribonuclease VapC20 – inducibly expressed in a cell line – as a novel tool to selectively degrade a part of a large subunit of the mitochondrial ribosome. Using this cellular model, they propose that formation of mRNA‐associated ribosomes is needed for mt‐mRNA stability after transfer from the mt‐mRNA‐stabilising LRPPRC/SLIRP complex. For further information, please also see our Commentary by Borowski and Szczesny: https://febs.onlinelibrary.wiley.com/doi/10.1111/febs.15435.

Although there are molecularly distinct subtypes of prostate cancer, no molecular classification system is used clinically. The ribonucleotide reductase small subunit M2 (RRM2) gene plays an oncogenic role in many cancers. Our previous study elucidated comprehensive molecular mechanisms of RRM2 in prostate cancer (PC). Given the potent functions of RRM2, we set out to determine whether the RRM2 signature can be used to identify aggressive subtypes of PC. We applied gene ontology and pathway analysis in RNA‐seq datasets from PC cells overexpressing RRM2. We refined the RRM2 signature by integrating it with two molecular classification systems (PCS and PAM50 subtypes) that define aggressive PC subtypes (PCS1 and luminal B) and correlated signatures with clinical outcomes in six published cohorts comprising 4000 cases of PC. Increased expression of genes in the RRM2 signature was significantly correlated with recurrence, high Gleason score, and lethality of PC. Patients with high RRM2 levels showed higher PCS1 score, suggesting the aggressive PC feature. Consistently, RRM2‐regulated genes were highly enriched in the PCS1 signature from multiple PC cohorts. A simplified RRM2 signature (12 genes) was identified by intersecting the RRM2 signature, PCS1 signature, and the PAM50 classifier. Intriguingly, inhibition of RRM2 specifically targets PCS1 and luminal B genes. Furthermore, 11 genes in the RRM2 signature were correlated with enzalutamide resistance by using a single‐cell RNA‐seq dataset from PC circulating tumor cells. Finally, high expression of RRM2 was associated with an immunosuppressive tumor‐immune microenvironment in both primary prostate cancer and metastatic prostate cancer using CIBERSORT analysis and LM22, a validated leukocyte gene signature matrix. These data demonstrate that RRM2 is a driver of aggressive prostate cancer subtypes and contributes to immune escape, suggesting that RRM2 inhibition may be of clinical benefit for patients with PC., RRM2 is essential for DNA synthesis and repair. We integrated clinical and experimental datasets to generate RRM2 signatures that not only define subtypes with poor outcomes but also predict enzalutamide resistance. RRM2 overexpression is associated with an immunosuppressive tumor‐immune microenvironment. RRM2 signatures may be novel biomarkers for aggressive prostate cancer subtypes, and targeting RRM2 could be a useful therapeutic strategy.

RNA molecules of all species contain modified nucleotides and particularly m(5)U residues. The vertebrate mitochondrial small subunit rRNA contains m(5)U nucleotide in a unique site. In this work we found an enzyme, TRMT2B, responsible for the formation of this nucleotide and m(5)U residues in a number of mitochondrial tRNA species. Inactivation of the Trmt2B gene leads to a reduction of the activity of respiratory chain complexes I, III and IV, containing the subunits synthesized by the mitochondrial protein synthesis apparatus. Comparative sequence analysis of m(5)U-specific RNA methyltransferases revealed an unusual evolutionary pathway of TRMT2B formation which includes consecutive substrate specificity switches from the large subunit rRNA to tRNA and then to the small subunit rRNA.

Flooding is a significant stress to land plants, depriving them of essential oxygen. Plants have evolved diverse strategies with variable success to survive flooding. Similar strategies have been described in organisms from other kingdoms. Several fungal species can successfully survive a low-oxygen environment by increasing their branched-chain amino acid (BCAA) contents. BCAAs may act as alternative electron acceptors in the respiratory chain under an oxygen-limited environment. The key and first enzyme for BCAA biosynthesis is acetolactate synthase (ALS). We identified two homologous genes encoding the small subunit of ALS in Arabidopsis (Arabidopsis thaliana). We determined that ALS INTERACTING PROTEIN1 (AIP1), which encodes the small subunit of ALS, is strongly expressed in all organs and highly expressed under submergence and low-oxygen stresses. We also showed that the overexpression of AIP1 confers tolerance to low-oxygen stress. These results indicate that ALS may play an essential role under prolonged flooding or oxygen deficiency in Arabidopsis.

Blastocystis sp. is a common pathogen that infects the intestines of humans and animals, causing a threat to public health. However, little information on the prevalence and subtypes of Blastocystis sp. in diarrheic pigs in China is available. Herein, 1254 fecal samples were collected from diarrheic pigs in 37 intensive pig farms in Hunan, Jiangxi, and Fujian provinces in southern China, and the prevalence and subtypes of Blastocystis sp. were investigated. Blastocystis sp. was detected by PCR assay, which amplified the small subunit rRNA (SSU rRNA) gene. Overall prevalence of Blastocystis sp. was 31.4% (394/1254), including 21.5% (66/307), 33.1% (99/299), 58.9% (56/95), and 31.3% (173/553) in suckling piglets, weaned piglets, fattening pigs, and sows, respectively. Moreover, age and region factors were significantly related to prevalence of Blastocystis sp. (p &lt, 0.05). Four Blastocystis sp. subtypes were identified, including ST1, ST3, ST5, and ST14. The preponderant subtype was ST5 (76.9%, 303/394). To our knowledge, ST14 was firstly found in pigs in China. The human-pathogenic subtypes (ST1, ST3, ST5, and ST14) that were observed in this study indicate a potential threat to public health. These findings provided a new sight for studying the genetic structure of Blastocystis sp.

Rabbits are increasingly farmed in Egypt for meat. They are, however, known reservoirs of infectious pathogens. Currently, no information is available on the genetic characteristics of Cryptosporidium spp. in rabbits in Egypt. To understand the prevalence and genetic identity of Cryptosporidium spp. in these animals, 235 fecal samples were collected from rabbits of different ages on nine farms in El-Dakahlia, El-Gharbia, and Damietta Provinces, Egypt during the period from July 2015 to April 2016. PCR-RFLP analysis of the small subunit rRNA gene was used to detect and genotype Cryptosporidium spp. The overall detection rate was 11.9% (28/235). All 28 samples were identified as Cryptosporidium cuniculus. The 16 samples successfully subtyped by the sequence analysis of the partial 60 kDa glycoprotein gene belonged to two subtypes, VbA19 (n = 1) and VbA33 (n = 15). As C. cuniculus is increasingly recognized as a cause of human cryptosporidiosis, Cryptosporidium spp. in rabbits from Egypt have zoonotic potential.

BACKGROUND: The contamination with Entamoeba histolytica, Giardia lamblia, and Salmonella spp. in drinking water is the most prevalent in Indian subcontinent, but often difficult to detect all these pathogens from the drinking water. MATERIALS AND METHODS: A multiplex polymerase chain reaction (mPCR) method was developed to detect contamination of municipality-supplied drinking water with E. histolytica, G. lamblia, and Salmonella spp. The primers were designed to target small subunit of 16S rRNA type gene of E. histolytica and G. lamblia, and invasive A gene of Salmonella typhimurium. The optimized mPCR assay was applied on 158 municipality-supplied drinking water samples collected from Delhi. RESULTS: Out of total 158 water samples, 89 (56.32%) were found positive for the targeted pathogens by mPCR while conventional methods could be detected only in 11 (6.96%) samples. The mPCR assay showed 100% sensitivity and specificity for these pathogens in comparison with culture and microscopic detection. Of the 89 mPCR-positive samples, G. lamblia, E. histolytica, and Salmonella spp. were present in 35 (22.15%), 26 (16.45%), and 28 (17.72%), respectively. Nine (5.69%) samples were positive for both E. histolytica and G. lamblia, 10 (6.32%) were positive for G. lamblia and Salmonella spp., and 8 (5.06%) had Salmonella spp. and E. histolytica. Nonetheless, 3 (1.89%) samples were positive for all three pathogens. CONCLUSIONS: The present assay is an alternative to conventional methods to serve as highly sensitive, specific, and economical means for water quality surveillance to detect the outbreak caused by E. histolytica, G. lamblia, and Salmonella spp. pathogens.

The taxonomy of Hysterothylacium genus remains incomplete and unclear in Turkish waters. In the present study, H. adumcum larvae were morphologically identified from Merlangius merlangus euxinus in the Black Sea, Turkey. The nuclear ribosomal ITS regions (ITS-1, 5.8S subunit, ITS-2) and the small subunit of the mitochondrial ribosomal RNA (rrnS) gene of H. aduncum were amplified and sequenced. The BLAST analysis indicated that present ITS sequences of H. aduncum were identical to that of the reference sequence of H. aduncum (accession no JX413596) recorded previously from the Black Sea, Turkey. The present rrnS gene of H. aduncum from the Black Sea, Turkey (MK886768) showed 97.94 to 99.56% identity with isolates of H. aduncum from the Mediterranean Sea (MF000685-MF000691) and the Chinese waters (MF140344). Moreover, pairwise comparison between the rrnS sequences of the H. aduncum from the Black Sea, Turkey (MK886768) and others H. aduncum isolates from the Mediterranean Sea (MF000685-MF000691), the Chinese waters (MF140344) showed differences ranged from 0.2 and 1.7%. With the present study, H. aduncum from the Black Sea was characterized for the first time by sequencing of the mitochondrial rrnS gene.

Four unarmored heterotrophic dinoflagellates were isolated from the coastal waters of southern Korea. The rDNA sequences of four clonal cultures were determined, and the morphology of one of the four strains was examined using light and scanning and transmission electron microscopy. The large subunit (LSU) and small subunit (SSU) rDNA sequences of each of the strains differed by 0-0.9% from those of the other strains, and the SSU rDNA sequence of the strain differed by 1.8-4.4% from those of other Gyrodinium species, whereas the LSU (D1-D2) rDNA sequence differed by 12.4-22.2%. Furthermore, phylogenetic trees showed that Gyrodinium jinhaense n. sp. formed a distinctive clade among the other Gyrodinium species. Meanwhile, microscopy revealed an elliptical bisected apical structure complex and a cingulum that was displaced by approximately one-quarter of the cell length, which confirmed that the dinoflagellate belonged to the genus Gyrodinium. However, the cell surface was ornamented with 16 longitudinal striations, both on the episome and hyposome, unlike other Gyrodinium species. Furthermore, the cells were observed to have pusule systems and trichocysts but lacked mucocysts. Based on morphology and molecular data, we consider this strain to be a new species in the genus Gyrodinium and thus, propose that it be assigned to the name G. jinhaense n. sp.

The accurate expression of proteins requires the ribosome to efficiently undergo elaborate conformational rearrangements. The most dramatic of these motions is subunit rotation, which is necessary for tRNA molecules to transition between ribosomal binding sites. While rigid-body descriptions provide a qualitative picture of the process, obtaining quantitative mechanistic insights requires one to account for the relationship between molecular flexibility and collective dynamics. Using simulated rotation events, we assess the quality of experimentally-accessible measures for describing the collective displacement of the ~ 4000-residue small subunit. For this, we ask whether each coordinate is able to identify the underlying free-energy barrier and transition state ensemble (TSE). We find that intuitive structurally-motivated coordinates (e.g. rotation angle, inter-protein distances) can distinguish between the endpoints, though they are poor indicators of barrier-crossing events, and they underestimate the free-energy barrier. In contrast, coordinates based on inter-subunit bridges can identify the TSE. We additionally verify that the committor probability for the putative TSE configurations is 0.5, a hallmark feature of any transition state. In terms of structural properties, these calculations implicate a transition state in which flexibility allows for asynchronous rearrangements of the bridges as the ribosome adopts a partially-rotated orientation. These calculations provide a theoretical foundation, upon which experimental techniques may precisely quantify the energy landscape of the ribosome.

Rice is an essential food source for humans. Rice white tip nematode, Aphelenchoides besseyi, is the most important and devastating plant-parasitic nematode of rice. In order to prevent the spread of A. besseyi, a rapid and accurate diagnostic protocol is required for seed certification and quarantine purposes. Here, we developed a qPCR assay based on small subunit ribosomal DNA (SSU rDNA) of A. besseyi and validated it successfully in white tip nematode populations collected from rice-growing fields. Our findings indicate that a dilution series of plasmid DNA of A. besseyi showed a high correlation (R2 = 0.99, efficiency 95%) with Ct values. The different stages of white tip nematode, i.e. egg, juvenile, male and female, were successfully identified using qPCR assay; the single juvenile nematode was also detected without separate DNA isolation. In addition, qPCR assay without the need for a separate nematode extraction step directly identified A. besseyi from infected brown rice, hull and paddy. Since the novel qPCR assay is specific and sensitive for detection of A. besseyi, it could be used for detection and quantification of rice white tip nematode.

Blastocystis genus exist in a wide variety of hosts, including humans, birds, insects, annelids, amphibians, fish, and mammals. PCR-based molecular diagnostic methods have been successfully used to detect Blastocystis spp. in feces, and small subunit ribosomal ribonucleic acid (SSU rRNA) gene-based subtyping is the preferred method for diagnosis. There has been discussion about the subtypes of Blastocystis spp. which has been detected so far. To date, 26 different subtypes have been reported. The aim of this study was to determine the existence and diversity of Blastocystis spp. in cattle. In our study, a total of 80 stool samples were collected from cows and calves at 13 different farms in Burdur and one farm in Aydın. Using molecular method, a total of 9 samples out of 80 samples were found to be positive (11.25%) for Blastocystis. As a result of sequence analysis of Blastocystis positive samples, the subtype 14 was detected on seven samples, while in the other two samples, Blastocystis subtype 10 was identified. The ST10 and ST14 subtypes are commonly reported in animals but not isolated from human. Our analyses showed genetic differences among Blastocystis subtypes. Our study is the first Blastocystis subtyping study from cattle in Turkey.