mRNA degradation is connected to the translation process up to the degree that 5\'-3\' mRNA degradation follows the last translating ribosome. To study 5\'-3\'co-translational mRNA decay and the associated ribosome dynamics, here we present an improved high-throughput 5\'P degradome RNA sequencing protocol (HT-5Pseq). We exemplify its application in Saccharomyces cerevisiae, but in principle, it could be applied to any other eukaryotic organism. HT-5Pseq is easy, scalable, and uses affordable duplex-specific nuclease-based rRNA depletion. For complete details on the use and execution of this protocol, please refer to Zhang and Pelechano (2021).

Type 2 diabetes mellitus (T2DM) drastically affects the population of Middle East countries with an ever-increasing number of overweight and obese individuals. The precise links between T2DM and gut microbiome composition remain elusive in these populations. Here, we performed 16 S rRNA and ITS2- gene based microbial profiling of 50 stool samples from Emirati adults with or without T2DM. The four major enterotypes initially described in westernized cohorts were retrieved in this Emirati population. T2DM and non-T2DM healthy controls had different microbiome compositions, with an enrichment in Prevotella enterotype in non-T2DM controls whereas T2DM individuals had a higher proportion of the dysbiotic Bacteroides 2 enterotype. No significant differences in microbial diversity were observed in T2DM individuals after controlling for cofounding factors, contrasting with reports from westernized cohorts. Interestingly, fungal diversity was significantly decreased in Bacteroides 2 enterotype. Functional profiling from 16 S rRNA gene data showed marked differences between T2DM and non-T2DM controls, with an enrichment in amino acid degradation and LPS-related modules in T2DM individuals, whereas non-T2DM controls had increased abundance of carbohydrate degradation modules in concordance with enterotype composition. These differences provide an insight into gut microbiome composition in Emirati population and its potential role in the development of diabetes mellitus.

To report the clinical manifestations, ultrastructure and evaluate the efficacy of therapeutic lamellar keratectomy (TLK) and penetrating keratoplasty (PK) for microsporidial stromal keratitis (MSK).
Fourteen MSK cases between 2009 and 2018 were recruited. Each patient\'s clinical presentation, light microscopy, histopathology, PCR and electron microscopy (EM) of corneal samples were reviewed.
The patients were 70.0±4.7 years old (average follow-up, 4.5 years). Time from symptoms to presentation was 10.6±13.0 weeks. The corneal manifestations were highly variable. Corneal scrapings revealed Gram stain positivity in 12 cases (85.7%) and modified Ziehl-Neelsen stain positivity in 9 (64.3%). Histopathology revealed spores in all specimens, while sequencing of small subunit rRNA-based PCR products identified Vittaforma corneae in 82% of patients. EM demonstrated various forms of microsporidial sporoplasm in corneal keratocytes. All patients were treated with topical antimicrobial agents or combined with oral antiparasitic medications for >3 weeks. As all patients were refractory to medical therapy, they ultimately underwent surgical intervention (TLK in 7, PK in 6 and 1 received TLK first, followed by PK). Postoperatively, the infection was resolved in 78.6% of the patients. Nevertheless, a high recurrence rate (21.4%) was noted during 3-year follow-up, with only two patients retained a final visual acuity ≥20/100.
MSK usually presents with a non-specific corneal infiltration refractory to antimicrobial therapy. The diagnosis relies on light microscopic examinations on corneal scrapings and histopathological analyses. Surgical intervention is warranted by limiting the infection; however, it was associated with an overall poor outcome.

Fungal infections, ranging from superficial to life-threatening infections, represent a major public health problem that affects 25% of the worldwide population. In this context, the study of host-pathogen interactions within the host is crucial to advance antifungal therapy. However, since fungal cells are usually outnumbered by host cells, the fungal transcriptome frequently remains uncovered. We compared three different methods to selectively lyse human cells from in vitro mixes, composed of Candida cells and peripheral blood mononuclear cells. In order to prevent transcriptional modification, the mixes were stored in RNAlater. We evaluated the enrichment of fungal cells through cell counting using microscopy and aimed to further enrich fungal nucleic acids by centrifugation and by reducing contaminant nucleic acids from the host. We verified the enrichment of fungal DNA and RNA through qPCR and RT-qPCR respectively and confirmed that the resulting RNA has high integrity scores, suitable for downstream applications. The enrichment method provided here, i.e., lysis with Buffer RLT followed by centrifugation, may contribute to increase the proportion of nucleic acids from fungi in clinical samples, thus promoting more comprehensive analysis of fungal transcriptional profiles. Although we focused on C. albicans, the enrichment may be applicable to other fungal pathogens.

Pathogens and the potential risk they present to public health in recreational waters are of continual public concern. The focus of this study was a year-long sampling campaign to document the presence of Microsporidia and protozoan pathogens in the Bayou Texar waterway in Pensacola, Florida. We used biofilms as sentinel indicators for trapping pathogens in five different locations in Pensacola, Florida. Of the 34 biofilm samples, 16 were positive for pathogens. Of these samples, 13 were positive for Enchephalitozoon spp. (mostly E. cuniculi), 11 were positive for Enterocytozoon bieneusi, and two were positive for Cryptosporidium parvum. The data demonstrate that Microsporidia were easily recovered and primarily present in water during summer months.

In recent years, the opportunistic fungus C.albicans has been linked to ECC.It is important to investigate the relationship between the distribution of C.albicans and early childhood caries (ECC) in 3-5-year-old Uygur and Han children in Kashgar, and the role of C.albicans of distinct genotypes in caries.
Two hundred fifty-six Uygur and 141 Han children were enrolled in the study. The identified C.albicans isolates were genotyped based on 25S rDNA Polymerase Chain Reaction(PCR) amplification, and their acidogenicity, aciduricity, and adhesiveness were examined. Moreover, secreted aspartic protease (Sap) activity and SAP1-5 transcriptional levels were compared in the ECC and caries-free (CF) groups of Uygur children.
C.albicans detection rate was significantly higher in Uygur children than in Han children (44. 5% vs. 31. 2%; χ2= 6.739, P = 0.009);the A genotype was dominant in Uygur and Han children with ECC, the C genotype was dominant in Uygur CF children(P = 0.022). C.albicans acidogenicity and growth were more pronounced in the Uygur ECC group than in CF group, especially at pH 4.0 and 4. 5(pH 4.0, P = 0.012; pH 4. 5, P = 0.029); the average ratios of glass-wall adhesion and the Sap activity was higher in ECC group than in CF group(P < 0.01), and SAP2(P < 0.001) and SAP5(P = 0.001) were expressed more robustly in ECC group.
The strong acidogenicity and aciduricity, Sap activity, and high SAP2 and SAP5 expression might be closely associated with ECC. C.albicans potentially plays a key role in the progression of caries, which most readily affects genotype A carriers and could be attributed to person-to-person environmental variation.

A double-strand break (DSB) is one of the most dangerous DNA lesion, and its repair is crucial for genome stability. Homologous recombination is considered the safest way to repair a DNA DSB and requires an identical or nearly identical DNA template, such as a sister chromatid or a homologous chromosome for accurate repair. Can transcript RNA serve as donor template for DSB repair? Here, we describe an approach that we developed to detect and study DNA repair by transcript RNA. Key features of the method are: (i) use of antisense (noncoding) RNA as template for DSB repair by RNA, (ii) use of intron splicing to distinguish the sequence of the RNA template from that of the DNA that generates the RNA template, and (iii) use of a trans and cis system to study how RNA repairs a DSB in homologous but distant DNA or in its own DNA, respectively. This chapter provides details on how to use a spliced-antisense RNA template to detect and study DSB repair by RNA in trans or cis in yeast cells. Our approach for detection of DSB repair by RNA in cells can be applied to cell types other than yeast, such as bacteria, mammalian cells, or other eukaryotic cells.

Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of second-generation sequencing. Saccharomyces cerevisiae strain CEN.PK113-7D, widely used as a model organism and a cell factory, was selected for this study to demonstrate the superior capability of very long sequence reads for de novo genome assembly. We generated long reads using two common third-generation sequencing technologies (Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)) and used short reads obtained using Illumina sequencing for error correction. Assembly of the reads derived from all three technologies resulted in complete sequences for all 16 yeast chromosomes, as well as the mitochondrial chromosome, in one step. Further, we identified three types of DNA methylation (5mC, 4mC and 6mA). Comparison between the reference strain S288C and strain CEN.PK113-7D identified chromosomal rearrangements against a background of similar gene content between the two strains. We identified full-length transcripts through ONT direct RNA sequencing technology. This allows for the identification of transcriptional landscapes, including untranslated regions (UTRs) (5\' UTR and 3\' UTR) as well as differential gene expression quantification. About 91% of the predicted transcripts could be consistently detected across biological replicates grown either on glucose or ethanol. Direct RNA sequencing identified many polyadenylated non-coding RNAs, rRNAs, telomere-RNA, long non-coding RNA and antisense RNA. This work demonstrates a strategy to obtain complete genome sequences and transcriptional landscapes that can be applied to other eukaryal organisms.

We studied radioprotective effects of a preparation based on yeast RNA and its influence on therapeutic efficiency of ionizing radiation against transplanted tumors. Parenteral administration of yeast RNA preparation to mice in a dose of 10 mg 1 h prior to exposure to ionizing γ-radiation (137Cs) in a lethal dose (LD80/30) increased 30-day survival by 66%; by day 80, 80% of animals survived (vs. 2.5% in the control). Whole-body exposure to ionizing γ-radiation in a dose of 7 Gy significantly increased the mean lifespan of mice with experimental lung metastases or intraperitoneally transplanted leukemia L-1210 by 42 and 20.8%, respectively. RNA preparation injected to the mice with tumors 1 h before irradiation did not affect the therapeutic efficiency of ionizing radiation or significantly potentiated it (in mice with transplanted leukemia L-1210). These results suggest that yeast RNA preparation protects healthy tissues during radiotherapy of malignant tumors.

Microsporida are known as opportunistic unicellular organisms and have recently been reclassified as fungi that have been frequently reported from patients with congenital and acquired immunity failure disorders, worldwide. However, use of immunosuppressive medications in inflammatory bowel disease (IBD) patients significantly decreases overall immunity, and increases their susceptibility to opportunistic infections. Totally, 71 stool samples were collected from IBD patients consisted of 69 ulcerative colitis (UC) patients and two Crohn\'s disease (CD) patients. All patients had taken immunosuppressive and/or immunomodulator drugs for at least 3 weeks. DNA was extracted from all stool samples and Nested PCR was performed using genus-specific primers based on small subunit ribosomal RNA (SSU rRNA) gene. Fisher\'s Exact Test was applied to evaluate statistical association between microsporidia infection and sex, age and types of IBD. Mean of age ± s.d., women and men percentage of the attended patients were 36·17 ± 11·93, 60·6%, and 39·4%, respectively. A 440-bp fragment of SSU rRNA gene attributed to Enterocytozoon bieneusi was amplified from 12·7% of IBD patients. No Encephalitozoon DNA was detected in the samples. No microsporidia-positive sample was found in CD patients. Fisher\'s Exact Test showed that there was no statistically significant correlation between intestinal microsporidiosis and age, sex, and IBD types with P values: 0·389, 1·00, and 1·00, respectively. This study has shown IBD patients undergoing immunosuppressive/immunomodulators medications, which may be susceptible to intestinal microsporida infection. E. bieneusi is the commonest intestinal microsporidan reported from IBD patients.