Integrated mRNA-miRNA transcriptome profiling of blood immune responses potentially related to pulmonary fibrosis in forest musk deer.

Background: Forest musk deer (FMD, ) is a critically endangered species world-widely, the death of which can be caused by pulmonary disease in the farm. Pulmonary fibrosis (PF) was a huge threat to the health and survival of captive FMD. MicroRNAs (miRNAs) and messenger RNAs (mRNAs) have been involved in the regulation of immune genes and disease development.

Nanosponge for Iron Chelation and Efflux: A Ferroptosis-Inhibiting Approach for Myocardial Infarction Therapy.

Myocardial infarction (MI), a consequence of coronary artery occlusion, triggers the degradation of ferritin, resulting in elevated levels of free iron in the heart and thereby inducing ferroptosis. Targeting myocardial ferroptosis through the chelation of excess iron has therapeutic potential for MI treatment. However, iron chelation in post ischemic injury areas using conventional iron-specific chelators is hindered by ineffective myocardial intracellular chelation, rapid clearance, and high systemic toxicity.

Detecting rare thalassemia in children with anemia using third-generation sequencing.

Background: In China, conventional genetic testing methods can only detect common thalassemia variants. Accurate detection of rare thalassemia is crucial for clinical diagnosis, especially for children that need long-term blood transfusion. This study aims to explore the application value of third-generation sequencing (TGS) in the diagnosis of rare thalassemia in children with anemia.

slORFfinder: a tool to detect open reading frames resulting from trans-splicing of spliced leader sequences.

Trans-splicing of a spliced leader (SL) to the 5' ends of mRNAs is used to produce mature mRNAs in several phyla of great importance to human health and the marine ecosystem. One of the consequences of the addition of SL sequences is the change or disruption of the open reading frames (ORFs) in the recipient transcripts. Given that most SL sequences have one or more of the trinucleotide NUG, including AUG in flatworms, trans-splicing of SL sequences can potentially supply a start codon to create new ORFs, which we refer to as slORFs, in the recipient mRNAs.

Comparison of the Distribution and Changes in the Antibiotic Resistance of Clinical Bacterial Isolates from the Lower Respiratory Tract of Children in Shenzhen Before the Epidemic, During the Epidemic, and During the Period of Normalized Prevention and Control of COVID-19.

Introduction: This study aimed to understand the impact of the coronavirus disease 2019 (COVID-19) epidemic on the distribution and antibiotic resistance of pathogenic bacteria isolated from the lower respiratory tract of children in our hospital.

Methods: Antimicrobial susceptibility tests were performed on bacteria isolated clinically from the lower respiratory tracts of children in our hospital from 2018 to 2021 by the Kirby-Bauer method and automated systems.

Results: From 2018 to 2021, the top three lower respiratory tract clinical isolates in our hospital were Streptococcus pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae.

Hypertension Promotes the Proliferation and Migration of ccRCC Cells by Downregulation of TIMP3 in Tumor Endothelial Cells through the miR-21-5p/TGFBR2/P38/EGR1 Axis.

Unlabelled: Recent studies have demonstrated that hypertension correlates with tumorigenesis and prognosis of clear-cell renal cell carcinoma (ccRCC); however, the underlying molecular mechanisms remain unclear. By analyzing bulk and single-cell RNA sequencing data and experimental examining of surgical excised ccRCC samples, we found that tissue inhibitors of metalloproteinases 3 (TIMP3), a pivotal paracrine factor in suppressing tumor progression, was significantly reduced in the tumor endothelial cells of patients with hypertensive ccRCC. Besides, in tumor xenograft of NCG mouse model, compared with saline normotensive group the expression of TIMP3 was significantly decreased in the angiotensin II-induced hypertension group.

Nanomaterials-Mediated Therapeutics and Diagnosis Strategies for Myocardial Infarction.

The alarming mortality and morbidity rate of myocardial infarction (MI) is becoming an important impetus in the development of early diagnosis and appropriate therapeutic approaches, which are critical for saving patients' lives and improving post-infarction prognosis. Despite several advances that have been made in the treatment of MI, current strategies are still far from satisfactory. Nanomaterials devote considerable contribution to tackling the drawbacks of conventional therapy of MI by improving the homeostasis in the cardiac microenvironment via targeting, immune modulation, and repairment.

YTHDF2 is a Potential Biomarker and Associated with Immune Infiltration in Kidney Renal Clear Cell Carcinoma.

Clear cell renal cell carcinoma (ccRCC or KIRC) has a high mortality rate globally. It is necessary to identify biomarkers and investigate the mechanisms those biomarkers are associated with, to improve the prognosis of patients with KIRC. N6-Methyladenosine (m6A) affects the fate of modified RNA molecules and is involved in tumor progression.

De novo transcriptome assemblies of Epicauta tibialis provide insights into the sexual dimorphism in the production of cantharidin.

Blister beetles have medicinal uses for their defensive secretion cantharidin, which has curative effects on many cancers and other diseases. It was demonstrated that sexual dimorphism exists in the production of cantharidin between male and female adults. This study performed a de novo assembly of Epicauta tibialis transcriptomes and analyzed the differentially expressed genes (DEGs) between male and female adults to help to find genes and pathways associated with cantharidin biosynthesis.

Patient-derived organoids of bladder cancer recapitulate antigen expression profiles and serve as a personal evaluation model for CAR-T cells .

Objectives: Recent advances in patient-derived cancer organoids have opened a new avenue for personalised medicine. We aimed to establish an technological platform to evaluate chimeric antigen receptor (CAR)-T cell-mediated cytotoxicity against bladder cancer.

Methods: Patient-derived bladder cancer organoids (BCOs) were derived using classic medium containing R-spondin 1 and noggin.

Organoid Cultures Derived From Patients With Papillary Thyroid Cancer.

Context: Papillary thyroid cancer (PTC) has been one of the most frequent endocrine malignancies around the world. Although most PTC patients have a favorable prognosis, a subgroup of patients die, especially when disease recurrence occurs. There is a pressing need for clinically relevant preclinical thyroid cancer models for personalized therapy because of the lack of in vitro models that faithfully represent the biology of the parental tumors.

Patient-derived organoid (PDO) platforms to facilitate clinical decision making.

Based on recent advances in organoid research as well as the need to find more accurate models for drug screening in cancer research, patient-derived organoids have emerged as an effective in vitro model system to study cancer. Showing numerous advantages over 2D cell lines, 3D cell lines, and primary cell culture, organoids have been applied in drug screening to demonstrate the correlation between genetic mutations and sensitivity to targeted therapy. Organoids have also been used in co-clinical trials to compare drug responses in organoids to clinical responses in the corresponding patients.

A CRISPR-Cas12a-based specific enhancer for more sensitive detection of SARS-CoV-2 infection.

Background: Real-time reverse transcription-PCR (rRT-PCR) has been the most effective and widely implemented diagnostic technology since the beginning of the COVID-19 pandemic. However, fuzzy rRT-PCR readouts with high Ct values are frequently encountered, resulting in uncertainty in diagnosis.

Methods: A Specific Enhancer for PCR-amplified Nucleic Acid (SENA) was developed based on the Cas12a trans-cleavage activity, which is specifically triggered by the rRT-PCR amplicons of the SARS-CoV-2 Orf1ab (O) and N fragments.

Human Lung Adenocarcinoma-Derived Organoid Models for Drug Screening.

Lung cancer is an extremely heterogeneous disease, and its treatment remains one of the most challenging tasks in medicine. Few existing laboratory lung cancer models can faithfully recapitulate the diversity of the disease and predict therapy response. Here, we establish 12 patient-derived organoids from the most common lung cancer subtype, lung adenocarcinoma (LADC).

Comparative Transcriptomics Reveals the Expression Differences Between Four Developmental Stages of American Cockroach ().

The globally distributed American cockroach () is considered a pest, but it has been widely used in traditional Chinese medicine. In the past, the American cockroach's genome and transcriptomes were sequenced, but the differential expression transcripts between developmental stages were unavailable. We performed the assembly and analysis of American cockroach transcriptomes from four developmental stages.

Isolation and strategies of novel tetranucleotide microsatellites with polymorphisms from different chromosomes of the rhesus monkey (Macaca mulatta).

A total of 45 tetranucleotide chromosome-specific microsatellite markers with polymorphism were developed successfully based on three reference rhesus monkey genomes and on In-silico PCR prescreening. The polymorphic information content (PIC) values of 45 polymorphic microsatellite loci ranged from 0.487 to 0.

TesG is a type I secretion effector of Pseudomonas aeruginosa that suppresses the host immune response during chronic infection.

Pseudomonas aeruginosa is a versatile Gram-negative pathogen with intricate intracellular regulatory networks that enable it to adapt to and flourish in a variety of biotic and abiotic habitats. However, the mechanism permitting the persistent survival of P. aeruginosa within host tissues and causing chronic symptoms still remains largely elusive.

The first draft genome of Lophophorus: A step forward for Phasianidae genomic diversity and conservation.

The monal genus (Lophophorus) is a branch of Phasianidae and its species inhabit the high-altitude mountains of the Qinghai-Tibet Plateau. The Chinese monal, L. lhuysii, is a threatened endemic bird of China that possesses high-altitude adaptability, diversity of plumage color and potentially low reproductive life history.

The draft genome sequence of forest musk deer (Moschus berezovskii).

Background: The forest musk deer, Moschus berezovskii, is one of seven musk deer (Moschus spp.) and is distributed in Southwest China. Akin to other musk deer, the forest musk deer has been traditionally and is currently hunted for its musk (i.

Genome-wide mining of perfect microsatellites and tetranucleotide orthologous microsatellites estimates in six primate species.

Advancement in genome sequencing and in silico mining tools have provided new opportunities for comparative primate genomics of microsatellites. The SSRs (simple sequence repeats) numbers were not correlated with the genome size (Pearson, r=0.310, p=0.

Generation and characterization of the blood transcriptome of Macaca thibetana and comparative analysis with M. mulatta.

Transcriptome profiles provide a large transcript sequence data set for genomic study, particularly in organisms that have no accurate genome data published. The Tibetan macaque (Macaca thibetana) is commonly considered to be an endemic species to China and an important animal in biomedical research in the present day. In the present study, we report the de novo assembly and characterization of the blood transcriptome of the Tibetan macaque from three individuals, and we also sequenced the blood transcriptome of the rhesus macaque (Macaca mulatta) for comparison.

Comparative transcriptome analysis of Trueperella pyogenes reveals a novel antimicrobial strategy.

Trueperella pyogenes is a prevalent opportunistic bacterium that normally causes diverse suppurative lesions, endometritis and pneumonia in various economically important animals. Although the genomic information of this species has been announced, little is known about its functional profiles. In this study, by performing a comparative transcriptome analysis between the highly and moderately virulent T.

Identification of Triplophysa species from the Qinghai-Tibetan Plateau (QTP) and its adjacent regions through DNA barcodes.

The genus Triplophysa is the largest and most difficult to identity morphologically fish group of superfamily Cobitoidea with 140 currently valid species, and is mainly distributed in the Qinghai-Tibetan Plateau (QTP) and adjacent regions. Most species within this genus possess highly similar morphological characteristics for adaption to the highland environment and are very difficult to be identified only based on morphology. The traditional species identification, mainly based on external morphological diagnostic characters, leads to inconsistent results in many cases.

Nutrient reduction induced stringent responses promote bacterial quorum-sensing divergence for population fitness.

Bacteria use a cell-cell communication system termed quorum-sensing (QS) to adjust population size by coordinating the costly but beneficial cooperative behaviors. It has long been suggested that bacterial social conflict for expensive extracellular products may drive QS divergence and cause the "tragedy of the commons". However, the underlying molecular mechanism of social divergence and its evolutionary consequences for the bacterial ecology still remain largely unknown.

Distinct patterns of simple sequence repeats and GC distribution in intragenic and intergenic regions of primate genomes.

As the first systematic examination of simple sequence repeats (SSRs) and guanine-cytosine (GC) distribution in intragenic and intergenic regions of ten primates, our study showed that SSRs and GC displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation. Our results suggest that the majority of SSRs are distributed in non-coding regions, such as the introns, TEs, and intergenic regions. In these primates, trinucleotide perfect (P) SSRs were the most abundant repeats type in the 5'UTRs and CDSs, whereas, mononucleotide P-SSRs were the most in the intron, 3'UTRs, TEs, and intergenic regions.