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2022 ◽  
Vol 36 (2) ◽  
Author(s):  
Sanuja Fernando ◽  
Thalia Salagaras ◽  
Nisha Schwarz ◽  
Lauren Sandeman ◽  
Joanne T. M. Tan ◽  
...  

2022 ◽  
Author(s):  
Yu Sun ◽  
Jun Zhao

Abstract Background: Cancer is the leading cause of death in the world. The mechanism is not fully elucidated and the therapeutic effect is also unsatisfactory. In our study, we aim to find new target gene in pan-cancer.Methods: Differentially expressed genes (DEGs) was screened out in various types of cancers from GEO database. The expression of DEG (TCEAL2) in tumor cell lines, normal tissues and tumor tissues was calculated. Then the clinical characteristics, DNA methylation, tumor infiltration and gene enrichment of TCEAL2 was studied. Results: TCEAL2 expressions were down-regulated in most cancers. Its expression and methylation were positively or negatively associated with prognosis in different cancers. The tumor infiltration results revealed that TCEAL2 was significantly related with many immune cells especially NK cells and immune-related genes in majority cancers. Furthermore, tau protein and tubulin binding were involved in the molecular function mechanisms of TCEAL2. Conclusion: TCEAL2 may be a novel prognostic marker in different cancers and may affect tumor through immune infiltration.


2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Yongkang Yang ◽  
Haiquan Lu ◽  
Chelsey Chen ◽  
Yajing Lyu ◽  
Robert N. Cole ◽  
...  

AbstractHypoxia-inducible factor-1 (HIF-1) is a transcription factor that acts as a regulator of oxygen (O2) homeostasis in metazoan species by binding to hypoxia response elements (HREs) and activating the transcription of hundreds of genes in response to reduced O2 availability. RNA polymerase II (Pol II) initiates transcription of many HIF target genes under non-hypoxic conditions but pauses after approximately 30–60 nucleotides and requires HIF-1 binding for release. Here we report that in hypoxic breast cancer cells, HIF-1 recruits TRIM28 and DNA-dependent protein kinase (DNA-PK) to HREs to release paused Pol II. We show that HIF-1α and TRIM28 assemble the catalytically-active DNA-PK heterotrimer, which phosphorylates TRIM28 at serine-824, enabling recruitment of CDK9, which phosphorylates serine-2 of the Pol II large subunit C-terminal domain as well as the negative elongation factor to release paused Pol II, thereby stimulating productive transcriptional elongation. Our studies reveal a molecular mechanism by which HIF-1 stimulates gene transcription and reveal that the anticancer effects of drugs targeting DNA-PK in breast cancer may be due in part to their inhibition of HIF-dependent transcription.


Plant Disease ◽  
2022 ◽  
Author(s):  
Liu Yang ◽  
Tian Yuan ◽  
Xia Zhao ◽  
Yue Liang ◽  
UWAREMWE CONSTANTINE ◽  
...  

Root rot is a serious disease in plantations of A. sinensis, severely affecting yield and quality and threatening sustainable production. Fusarium isolates (n=32) were obtained from field samples of root rot tissue, leaves and infected soil. Isolates were identified by comparing the sequences of their internal transcribed spacer (ITS) region and translation elongation factor 1-ɑ (TEF-1ɑ) to sequences of known species in the NCBI-database. These Fusarium isolates include F. tricinctum (43.75%), F. equiseti (31.25%), F. solani (9.37%), F. oxysporum (6.25%), F. acuminatum (6.25%), and F. incarnatum (3.12%). For pathogenicity testing under greenhouse conditions, seven isolates were selected based on a phylogenetic analysis, including four strains of F. tricinctum and one strain each of F. solani, F. oxysporum, and F. acuminatum. The seven isolates were all pathogenic but differed in their ability to infect: the four F. tricinctum strains were capable pathogens causing root rot in A. sinensis at 100% incidence and the highly aggressive. Furthermore, the symptoms of root rot induced by those seven isolates were consistent with typical root rot cases in the field, but their disease severity varied. Observed histopathological preparations of F. tricinctum-infected seedlings and tissue-slides results showed this fungal species can penetrate epidermal cells and colonize the cortical cells where it induces necrosis and severe plasmolysis. Plate confrontation experiments showed that isolated rhizosphere bacteria inhibited the Fusarium pathogens that cause root rot in A. sinensis. Our results provide timely information for informing the use of biocontrol agents for suppression of root rot disease.


Plant Disease ◽  
2022 ◽  
Author(s):  
Martina Sanna ◽  
Massimo Pugliese ◽  
Maria Lodovica GULLINO ◽  
Monica Mezzalama

Maize (Zea mays L.) is a cereal crop of great economic importance in Italy; production is currently of 60,602,320 t, covering 588,597 ha (ISTAT 2021). Trichoderma species are widespread filamentous fungi in soil, well known and studied as biological control agents (Vinale et al., 2008). Seeds of a yellow grain hybrid (class FAO 700, 132 days) were collected in September 2020 from an experimental field located in Carmagnola (TO, Italy: GPS: 44°53'11.0"N 7°40'60.0"E) and tested with blotter test (Warham et al., 1996) to assess their phytosanitary condition. Over the 400 seeds tested, more than 50% showed rotting and development of green mycelium typical of the genus Trichoderma. Due to the high and unexpected percentage of decaying kernels, ten colonies were identified by morphological and molecular methods. Single conidia colonies of one Trichoderma (T5.1) strain were cultured on Potato Dextrose Agar (PDA) for pathogenicity tests, and on PDA and Synthetic Nutrient-Poor Agar (SNA) for morphological and molecular identification. The colonies grown on PDA and SNA showed green, abundant, cottony, and radiating aerial mycelium, and yellow pigmentation on the reverse. Colony radius after 72 h at 30°C was of 60-65 mm on PDA and of 50-55 mm on SNA. The isolates produced one cell conidia 2.8 - 3.8 µm long and 2.1 - 3.6 µm wide (n=50) on SNA. Conidiophores and phialides were lageniform to ampulliform and measured 4.5 – 9.7 µm long and 1.6 – 3.6 µm wide (n=50); the base measure 1.5 – 2.9 µm wide and the supporting cell 1.4 – 2.8 µm wide (n=50). The identity of one single-conidia strain was confirmed by sequence comparison of the internal transcribed spacer (ITS), the translation elongation factor-1α (tef-1α), and RNA polymerase II subunit (rpb2) gene fragments (Oskiera et al., 2015). BLASTn searches of GenBank using ITS (OL691534) the partial tef-1α (OL743117) and rpb2 (OL743116) sequences of the representative isolate T5.1, revealed 100% identity for rpb2 to T. afroharzianum TRS835 (KP009149) and 100% identity for tef-1α to T. afroharzianum Z19 (KR911897). Pathogenicity tests were carried out by suspending conidia from a 14-days old culture on PDA in sterile H2O to 1×106 CFU/ml. Twenty-five seeds were sown in pots filled with a steamed mix of white peat and perlite, 80:20 v/v, and maintained at 23°C under a seasonal day/night light cycle. Twenty primary ears were inoculated, by injection into the silk channel, with 1 ml of a conidial suspension of strain T5.1 seven days after silk channel emergence (BBCH 65) (Pfordt et al., 2020). Ears were removed four weeks after inoculation and disease severity, reaching up to 75% of the kernels of the twenty cobs, was assessed visually according to the EPPO guidelines (EPPO, 2015). Five control cobs, inoculated with 1 ml of sterile distilled water were healthy. T. afroharzianum was reisolated from kernels showing a green mold developing on their surface and identified by resequencing of tef-1α gene. T. afroharzianum has been already reported on maize in Germany and France as causal agent of ear rot of maize (Pfordt et al. 2020). Although several species of Trichoderma are known to be beneficial microorganisms, our results support other findings that report Trichoderma spp. causing ear rot on maize in tropical and subtropical areas of the world (Munkvold and White, 2016). The potential production of mycotoxins and the losses that can be caused by the pathogen during post-harvest need to be explored. To our knowledge this is the first report of T. afroharzianum as a pathogen of maize in Italy.


2022 ◽  
Vol 2022 ◽  
pp. 1-19
Author(s):  
Sarfraz Ahmed ◽  
Muhammad Ibrahim ◽  
Chanin Nantasenamat ◽  
Muhammad Farrukh Nisar ◽  
Aijaz Ahmad Malik ◽  
...  

DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.


2022 ◽  
Vol 12 ◽  
Author(s):  
Haiyan Fu ◽  
Tubiao Huang ◽  
Cheng Yin ◽  
Zhenhua Xu ◽  
Chao Li ◽  
...  

Bradysia odoriphaga (Diptera: Sciaridae) is the most serious root maggot pest which causes substantial damage to the Chinese chive. Organophosphate (OP) and neonicotinoid insecticides are widely used chemical pesticides and play important roles in controlling B. odoriphaga. However, a strong selection pressure following repeated pesticide applications has led to the development of resistant populations of this insect. To understand the insecticide resistance mechanism in B. odoriphaga, gene expression analysis might be required. Appropriate reference gene selection is a critical prerequisite for gene expression studies, as the expression stability of reference genes can be affected by experimental conditions, resulting in biased or erroneous results. The present study shows the expression profile of nine commonly used reference genes [elongation factor 1α (EF-1α), actin2 (ACT), elongation factor 2α (EF-2α), glucose-6-phosphate dehydrogenase (G6PDH), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ribosomal protein L10 (RPL10), ribosomal protein S3 (RPS3), ubiquitin-conjugating enzyme (UBC), and α-tubulin (TUB)] was systematically analyzed under insecticide stress. Moreover, we also evaluated their expression stability in other experimental conditions, including developmental stages, sexes, and tissues. Five programs (NormFinder, geNorm, BestKeeper, RefFinder, and ΔCt) were used to validate the suitability of candidate reference genes. The results revealed that the most appropriate sets of reference genes were RPL10 and ACT across phoxim; ACT and TUB across chlorpyrifos and chlorfluazuron; EF1α and TUB across imidacloprid; EF1α and EF2α across developmental stages; RPL10 and TUB across larvae; EF1α and ACT across tissues, and ACT and G6PDH across sex. These results will facilitate the standardization of RT-qPCR and contribute to further research on B. odoriphaga gene function under insecticides stress.


2022 ◽  
Vol 10 (2) ◽  
pp. 01-06
Author(s):  
Frank Mayer

Bacteria possess an EF-Tu-based cytoskeleton.This article presents a short review. A number of questions which are not discussed in the former publications can be asked, such as: all bacteria possess a ribosomal protein synthesis system and, hence, also EF-Tu. EF-Tu is produced in an amount that is higher than the need for a function as translation elogation factor in ribsomal protein synthesis. This article tries to answer the question regarding the surplus of EF-Tu: formation of a "cell-wide web" by self-assembly as a feafure that stabilizes cell integrity. An additional question can be asked: what is the origin of this bacterial cytoskeleton? This article contains a speculation on this topic. A third question regards the'ntteructjon of ribosomes in the process of protemsynthesis: does the EF-Tu protein move to the ribosome, or does the ribosome move to the EF-Tu intergated in a fibril of the bacterial cytoskeleton? The former publication depicts electron micrographs which show colocalizatton of botth entities. EF-Tu is an example for aprotein with two independent functions: participation in the ribosomal protein synthesis as a kanslation elongation factor, and component of a bacterial cytoskeleton. This situation can open up a discussion ofthe sequence of events and states of early cells during evolution.


2022 ◽  
Vol 8 (1) ◽  
pp. 70
Author(s):  
Vanice Rodrigues Poester ◽  
Rossana Patricia Basso ◽  
David A. Stevens ◽  
Lívia Silveira Munhoz ◽  
Vanessa Brito de Souza Rabello ◽  
...  

We describe the successful treatment of a series of 30 zoonotic sporotrichosis cases from southern Brazil. Sporothrix brasiliensis was the species genotypically identified in all 25 confirmed cases. Five other cases were classified as probable, without laboratory confirmation, but with clinical and epidemiological data of cat-transmitted sporotrichosis. Two isolates were sequenced by translation elongation factor-1 alpha (EF1α) loci in order to compare their sequences, and both of them showed distinct genotypes from S. brasiliensis strains from other Brazilian states. Itraconazole (ITZ) or potassium iodide (KI) were the first choice treatment in 28 and 2 cases, respectively. Microdilution assay showed a wild-type profile of S. brasiliensis isolates to ITZ. However, a lack of clinical response occurred in 42% of cases, especially those treated with ITZ 100 mg/day, and treatment needed modifications, by either increased doses or antifungal combinations. Clinical cure required a mean of 187 days of treatment, which was dependent on the clinical form of the disease and age of patients. Therapy, including dosages and durations, for cutaneous forms of sporotrichosis requires re-evaluation, since cases caused by S. brasiliensis may influence treatment efficacy.


Phytotaxa ◽  
2022 ◽  
Vol 530 (2) ◽  
pp. 177-188
Author(s):  
LI-RONG LIU ◽  
GENG-SHEN WANG ◽  
LIU-KUN JIA ◽  
JU-QING KANG ◽  
ZHU-LIANG YANG ◽  
...  

Types and recently collected samples of two Paxillus species namely P. rhytidophyllus and P. yunnanensis, originally described from southwestern China, were critically restudied based on morphology and molecular phylogenetic data of DNA sequences from the large subunit of the nuclear ribosomal RNA (nrLSU), the nuclear ribosomal internal transcribed spacer (ITS), and the translation elongation factor 1-α (tef1-α). The results showed that these two species belong to Boletinellus and Tricholomopsis, respectively. Thus, two new combinations, Boletinellus rhytidophyllus and Tricholomopsis yunnanensis are proposed. Boletinellus rhytidophyllus is characterized by a deeply decurrent and shallow hymenophore which is poroid-lamellate to alveolate, slightly thick-walled (0.6–1 μm) basidiospores, occasionally 2- to 4-spored basidia, rare or infrequent hymenial cystidia, and a trichodermal pileipellis. Tricholomopsis yunnanensis is characterized by a convex pileus densely covered by red-violet to red-brown fibrillose squamules, a yellowish stipe sparsely covered with red to red-brown fibrillose squamules, subglobose to broadly ellipsoid basidiospores, prominent large cheilocystidia measuring 60–195 × 11–39 μm, and a palisadic pileipellis. New descriptions and line drawings of these two species and their comparisons with allied taxa are presented.


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