Sequence Alignment/Map format: a comprehensive review of approaches and applications.

The Sequence Alignment/Map (SAM) format file is the text file used to record alignment information. Alignment is the core of sequencing analysis, and downstream tasks accept mapping results for further processing. Given the rapid development of the sequencing industry today, a comprehensive understanding of the SAM format and related tools is necessary to meet the challenges of data processing and analysis. This paper is devoted to retrieving knowledge in the broad field of SAM. First, the format of SAM is introduced to understand the overall process of the sequencing analysis. Then, existing work is systematically classified in accordance with generation, compression and application, and the involved SAM tools are specifically mined. Lastly, a summary and some thoughts on future directions are provided.

Multikingdom characterization of gut microbiota in patients with rheumatoid arthritis and rheumatoid arthritis-associated interstitial lung disease.

Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a serious and common extra-articular disease manifestation. Patients with RA-ILD experience reduced bacterial diversity and gut bacteriome alterations. However, the gut mycobiome and virome in these patients have been largely neglected. In this study, we performed whole-metagenome shotgun sequencing on fecal samples from 30 patients with RA-ILD, and 30 with RA-non-ILD, and 40 matched healthy controls. The gut bacteriome and mycobiome were explored using a reference-based approach, while the gut virome was profiled based on a nonredundant viral operational taxonomic unit (vOTU) catalog. The results revealed significant alterations in the gut microbiomes of both RA-ILD and RA-non-ILD groups compared with healthy controls. These alterations encompassed changes in the relative abundances of 351 bacterial species, 65 fungal species, and 4,367 vOTUs. Bacteria such as Bifidobacterium longum, Dorea formicigenerans, and Collinsella aerofaciens were enriched in both patient groups. Ruminococcus gnavus (RA-ILD), Gemmiger formicilis, and Ruminococcus bromii (RA-non-ILD) were uniquely enriched. Conversely, Faecalibacterium prausnitzii, Bacteroides spp., and Roseburia inulinivorans showed depletion in both patient groups. Mycobiome analysis revealed depletion of certain fungi, including Saccharomyces cerevisiae and Candida albicans, in patients with RA compared with healthy subjects. Notably, gut virome alterations were characterized by an increase in Siphoviridae and a decrease in Myoviridae, Microviridae, and Autographiviridae in both patient groups. Hence, multikingdom gut microbial signatures showed promise as diagnostic indicators for both RA-ILD and RA-non-ILD. Overall, this study provides comprehensive insights into the fecal virome, bacteriome, and mycobiome landscapes of RA-ILD and RA-non-ILD gut microbiota, thereby offering potential biomarkers for further mechanistic and clinical research.

Ultrasensitive Solvatochirochromism of Single Benzene Chromophores.

Solvents influence the structure, aggregation and folding behaviors of solvatochromic compounds. Ultrasensitive solvent mediated chiroptical response is conducive to the fabrication of molecular platform for sensing and recognition, which however, remains great challenges in conceptual or applicable design. Here we report a cysteine-based single benzene chromophore system that shows ultrasensitivity to solvents. Compared to the ratiometrically responsive systems, the chiroptical activities could be triggered or inverted depending on the substituents of chiral entities with an ultralow solvent volume fraction (<1 vol %). One drop of dipolar solvents shall significantly induce the emergence or inversion of chiroptical signals in bulky phases. Based on the experimental and computational studies, the ultrasensitivity is contributed to the intimate interplay between solvents and chiral compounds that anchors the specific chiral conformation. It illustrates that structurally simple organic compounds without aggregation or folding behaviors possess pronounced solvatochiroptical properties, which sheds light on the next-generation of chiroptical sensors and switches.

Identification of a mosaic MTOR variant in purified neuronal DNA in a patient with focal cortical dysplasia using a novel depth electrode harvesting technique.

OBJECTIVE: Recent studies have identified brain somatic variants as a cause of focal epilepsy. These studies relied on resected tissue from epilepsy surgery, which is not available in most patients. The use of trace tissue adherent to depth electrodes used for stereo electroencephalography (EEG) has been proposed as an alternative but is hampered by the low cell quality and contamination by nonbrain cells. Here, we use our improved depth electrode harvesting technique that purifies neuronal nuclei to achieve molecular diagnosis in a patient with focal cortical dysplasia (FCD). METHODS: Depth electrode tips were collected, pooled by brain region and seizure onset zone, and nuclei were isolated and sorted using fluorescence-activated nuclei sorting (FANS). Somatic DNA was amplified from neuronal and astrocyte nuclei using primary template amplification followed by exome sequencing of neuronal DNA from the affected pool, unaffected pool, and saliva. The identified variant was validated using droplet digital polymerase chain reaction (PCR). RESULTS: An 11-year-old male with drug-resistant genetic-structural epilepsy due to left anterior insula FCD had seizures from age 3 years. Stereo EEG confirmed seizure onset in the left anterior insula. The two anterior insula electrodes were combined as the affected pool and three frontal electrodes as the unaffected pool. FANS isolated 140 neuronal nuclei from the affected and 245 neuronal nuclei from the unaffected pool. A novel somatic missense MTOR variant (p.Leu489Met, CADD score 23.7) was identified in the affected neuronal sample. Droplet digital PCR confirmed a mosaic gradient (variant allele frequency = .78% in affected neuronal sample; variant was absent in all other samples). SIGNIFICANCE: Our findings confirm that harvesting neuronal DNA from depth electrodes followed by molecular analysis to identify brain somatic variants is feasible. Our novel method represents a significant improvement compared to the previous method by focusing the analysis on high-quality cells of the cell type of interest.

Cu2O-catalyzed cascade phosphinylation/cyclization of 2'-aminochalcones for the synthesis of hemi-indigo derivatives.

A Cu2O-catalyzed cascade phosphinylation/cyclization reaction of 2'-aminochalcones and diphenylphosphine oxides to produce hemi-indigo derivatives has been developed. This strategy facilitates the sequential formation of a C-P bonds and a C-N bond in a single reaction step. Notably, the approach features one-pot operation, an earth-abundant copper catalyst, readily available starting materials, a broad substrate scope and high compatibility with functional groups, providing 33 compounds in acceptable yields.

HANSynergy: Heterogeneous Graph Attention Network for Drug Synergy Prediction.

Drug synergy therapy is a promising strategy for cancer treatment. However, the extensive variety of available drugs and the time-intensive process of determining effective drug combinations through clinical trials pose significant challenges. It requires a reliable method for the rapid and precise selection of drug synergies. In response, various computational strategies have been developed for predicting drug synergies, yet the exploitation of heterogeneous biological network features remains underexplored. In this study, we construct a heterogeneous graph that encompasses diverse biological entities and interactions, utilizing rich data sets from sources, such as DrugCombDB, PubChem, UniProt, and cancer cell line encyclopedia (CCLE). We initialize node feature representations and introduce a novel virtual node to enhance drug representation. Our proposed method, the heterogeneous graph attention network for drug-drug synergy prediction (HANSynergy), has been experimentally validated to demonstrate that the heterogeneous graph attention network can extract key node features, efficiently harness the diversity of information, and further enhance network functionality through the incorporation of a multihead attention mechanism. In the comparative experiment, the highest accuracy (Acc) and area under the curve (AUC) are 0.877 and 0.947, respectively, in DrugCombDB_early data set, demonstrating the superiority of HANSynergy over the competing methods. Moreover, protein-protein interactions are important in understanding the mechanism of action of drugs. The heterogeneous attention mechanism facilitates protein-protein interaction analysis. By analyzing the changes of attention weight before and after heterogeneous network training, we investigated proteins that may be associated with drug combinations. Additionally, case studies align our findings with existing research, underscoring the potential of HANSynergy in drug synergy prediction. This advancement not only contributes to the burgeoning field of drug synergy prediction but also holds the potential to provide valuable insights and uncover new drug synergies for combating cancer.

Evolutionary Multiobjective Molecule Optimization in an Implicit Chemical Space.

Optimization techniques play a pivotal role in advancing drug development, serving as the foundation of numerous generative methods tailored to efficiently design optimized molecules derived from existing lead compounds. However, existing methods often encounter difficulties in generating diverse, novel, and high-property molecules that simultaneously optimize multiple drug properties. To overcome this bottleneck, we propose a multiobjective molecule optimization framework (MOMO). MOMO employs a specially designed Pareto-based multiproperty evaluation strategy at the molecular sequence level to guide the evolutionary search in an implicit chemical space. A comparative analysis of MOMO with five state-of-the-art methods across two benchmark multiproperty molecule optimization tasks reveals that MOMO markedly outperforms them in terms of diversity, novelty, and optimized properties. The practical applicability of MOMO in drug discovery has also been validated on four challenging tasks in the real-world discovery problem. These results suggest that MOMO can provide a useful tool to facilitate molecule optimization problems with multiple properties.

Enhanced Acetone Sensing Properties Based on Au-Pd Decorated ZnO Nanorod Gas Sensor.

The mature processes of metal oxide semiconductors (MOS) have attracted considerable interest. However, the low sensitivity of metal oxide semiconductor gas sensors is still challenging, and constrains its practical applications. Bimetallic nanoparticles are of interest owing to their excellent catalytic properties. This excellent feature of bimetallic nanoparticles can solve the problems existing in MOS gas sensors, such as the low response, high operating temperature and slow response time. To enhance acetone sensing performance, we successfully synthesized Au-Pd/ZnO nanorods. In this work, we discovered that Au-Pd nanoparticles modified on ZnO nanorods can remarkably enhance sensor response. The Au-Pd/ZnO gas sensor has long-term stability and an excellent response/recovery process. This excellent sensing performance is attributed to the synergistic catalytic effect of bimetallic AuPd nanoparticles. Moreover, the electronic and chemical sensitization of noble metals also makes a great contribution. This work presents a simple method for preparing Au-Pd/ZnO nanorods and provides a new solution for the detection of acetone based on metal oxide semiconductor.

Highly Sensitive and Selective Toluene Gas Sensors Based on ZnO Nanoflowers Decorated with Bimetallic AuPt.

Efficient sensors for toluene detecting are urgently needed to meet people's growing demands for both environment and personal health. Metal oxide semiconductor (MOS)-based sensors have become brilliant candidates for the detection of toluene because of their superior performance over gas sensing. However, gas sensors based on pure MOS have certain limitations in selectivity, operating temperature, and long-term stability, which hinders their further practical applications. Noble metals (including Ag, Au, Pt, Pd, etc.) have the ability to enhance the performance of MOS-based sensors via surface functionalization. Herein, ZnO nanoflowers (ZNFs) modified with bimetallic AuPt are prepared for toluene detection through hydrothermal method. The response of a AuPt@ZNF-based gas sensor can reach 69.7 at 175 °C, which is 30 times, 9 times, and 10 times higher than that of the original ZNFs, Au@ZNFs, and Pt@ZNFs, respectively. Furthermore, the sensor also has a lower optimal operating temperature (175 °C), good stability (94% of previous response after one month), and high selectivity towards toluene, which is the result of the combined influence of the electronic and chemical sensitization of noble metals, as well as the unique synergistic effect of the AuPt alloy. In summary, AuPt@ZNF-based sensors can be further applied in toluene detection in practical applications.

miR-136-5p/FZD4 axis is critical for Wnt signaling-mediated myogenesis and skeletal muscle regeneration.

Skeletal muscle can undergo a regenerative process in response to injury or disease to maintain muscle quality and function. Myogenesis depends on the proliferation and differentiation of myoblasts, and miRNAs can maintain the balance between them by precisely regulating many key factors in the myogenic network. Here, we found that miR-136-5p was significantly upregulated during the proliferation and differentiation of C2C12 cells. We demonstrate that miR-136-5p acts as a myogenic negative regulator during the development of mouse C2C12 myoblasts. In terms of mechanism, miR-136-5p inhibits the formation of ß-catenin/LEF/TCF DNA-binding factor transcriptional regulatory complex by targeting FZD4, a gating protein in the Wnt signaling pathway, thereby enhancing downstream myogenic factors and finally promoting myoblast proliferation and differentiation. In addition, in BaCl2 -induced muscle injury mouse model, miR-136-5p knockdown accelerated the regeneration of skeletal muscle after injury, and further led to the improvement of gastrocnemius muscle mass and muscle fiber diameter, while being suppressed by shFZD4 lentivirus infection. In summary, these results demonstrate the essential role of miR-136-5p/FZD4 axis in skeletal muscle regeneration. Given the conservation of miR-136-5p among species, miR-136-5p may be a new target for treating human skeletal muscle injury and improving the production of animal meat products.

Modulating motor cortical oscillation with coordinated reset multifocal transcranial magnetic stimulation.

According to the theory of coordinated reset (CR) stimulation, multifocal bursts of stimuli delivered in a random order with a specific interval may reduce the resonance power of the oscillatory generator in the epicenter. We develop a noninvasive coordinated multifocal burst stimulation (COMBS) with three repetitive transcranial stimulation machines based on CR theory to modulate the target frequency in the primary motor cortex and to assess its effect on motor cortical excitability in separate experiments. Electroencephalography and electromyography were recorded in 16 healthy participants during a finger-tapping task, both before and after the intervention. The resting oscillatory power at the targeted frequency was not changed by COMBS. α-Band power was increased in both preparation and movement stages and the low ß-band power was increased in the movement stage of the finger tapping task. The extent of low ß-band event-related desynchronization was reduced by COMBS. There were no changes in reaction time, but there was a trend for a reduced error rate after COMBS. In another 14 healthy participants, there were no significant changes in cortical excitability before and after COMBS measured by rest motor threshold, short interval intracortical inhibition, short interval intracortical facilitation, and cortical silent period. The result indicates that COMBS may modify the cortical oscillatory power and its perturbation within specific movement stage.NEW & NOTEWORTHY This is the first study, to our knowledge, to apply coordinated reset (CR) neuromodulation to the motor cortex with three repetitive transcranial magnetic stimulation (rTMS) stimulators to assess its effect on cortical oscillation. The results revealed enhancement of α-band power specifically in preparation and movement stages and low ß-band power in the movement stage of a motor task. It postulated that CR stimulation may modify the motor cortical oscillation in the specific movement stages.

Regulation of alveolar macrophage death in pulmonary fibrosis: a review.

Pulmonary fibrosis (PF) is a disease in which excessive extracellular matrix (ECM) accumulation occurs in pulmonary mesenchyme, which induces the destruction of alveolar structures and poor prognosis. Macrophage death is responsible for ECM accumulation after alveolar epithelial injury in PF. Depending on the local micro-environments, macrophages can be polarized to either classically activated (M1) or alternatively activated (M2) macrophage phenotypes. In general, M1 macrophages can promote inflammation and sterilization, stop the continuous damage process and prevent excessive repair, while M2 macrophages are anti-inflammatory and promote tissue repair, and excessive M2 macrophage activity may inhibit the absorption and degradation of ECM. Emerging evidence has revealed that death forms such as pyroptosis mediated by inflammasome affect polarization direction and ultimately lead to the development of PF. Pharmacological manipulation of macrophages death signals may serve as a logical therapeutic strategy for PF. This review will focus on the current state of knowledge regarding the regulation and underlying mechanisms of macrophages and their mediators in the influence of macrophage death on the development of PF. We expect to provide help in developing effective therapeutic strategies in clinical settings.

Prevalence of diabetic retinopathy in patients with newly diagnosed type 2 diabetes: A systematic review and meta-analysis.

AIMS: Type 2 diabetes mellitus (T2DM) can remain undiagnosed for many years, during which micro- and macro-vascular complications may develop. This study aimed to assess the worldwide prevalence of diabetic retinopathy (DR) in patients with newly diagnosed T2DM. MATERIALS AND METHODS: We systematically searched electronic databases for relevant studies published from inception to 01 January 2022. Selected studies reported the prevalence of DR among patients with newly diagnosed T2DM, specifying the case definition used. Random-effects meta-analysis was used to derive the pooled prevalence. Subgroup and meta-regression analyses were used to investigate variations in the prevalence estimates in terms of available variables. RESULTS: Data from 77 studies including 99,847 patients with newly diagnosed T2DM were included from 26 countries. The pooled prevalence of DR among patients with newly diagnosed T2DM was 13.1% (95% CI, 11.1%-15.1%; I2  = 97.0%). DR was higher in clinic-based samples compared with community-based samples (15.0%, 95% CI = 12.4%-17.8% vs. 11.5%, 95% CI = 8.9%-14.5%; p = 0.05; I2  = 97.0%) and was higher in countries in the WHO African 19.2% (95% CI, 14.6%-24.3%; I2  = 76.0%), South-East Asia 15.4% (95% CI, 10.0%-21.6%; I2  = 79.1%), and European 15.0% (95% CI, 11.2%-19.2%; I2  = 82.0%) regions. A higher proportion of female patients was significantly associated with a lower prevalence of DR in patients with newly diagnosed T2DM. We observed that the prevalence of DR in patients with newly diagnosed T2DM has remained unchanged over time. CONCLUSIONS: Globally, DR is a prevalent complication among patients with newly diagnosed T2DM indicating the importance of establishing effective strategies to promote regular screening for the early diagnosis of T2DM alongside routine ophthalmic assessment at the time of T2DM diagnosis to reduce the burden of vision-threatening retinopathy.

Effects of peripheral blood leukocyte count and tumor necrosis factor-alpha on early death in acute promyelocytic leukemia.

BACKGROUND: Early death remains a major factor in survival in APL. We aimed to analyze the risk factors for differentiation syndrome and early death in acute promyelocytic leukemia (APL). METHODS: The clinical data of APL patients who were newly diagnosed at Mianyang Central Hospital from January 2013 to January 2022 were retrospectively analyzed. RESULTS: Eighty-six newly diagnosed APL patients (37 males and 49 females) were included in this study. The median age was 46 (17-75) years. Sixty-one patients (70.9%) had low/intermediate-risk APL, and 25 patients (29.1%) had high-risk APL. The incidence of differentiation syndrome (DS) was 62.4%. The multivariate analysis showed that a peak white blood cell (WBC) count ≥16 × 10^9/L was an independent risk factor (OR = 11.000, 95% CI: 2.830-42.756, P = 0.001) for DS in all APL patients, while a WBC count ≥10 × 10^9/L on Day 5 was an independent risk factor for DS in low-intermediate risk APL patients (OR = 9.114, 95% CI: 2.384-34.849, P = 0.001). There were 31 patients (36.5%) with mild DS and 22 patients (25.9%) with severe DS. The multivariate analysis showed that WBC count ≥23 × 10^9/L at chemotherapy was an independent risk factor for severe DS (OR = 10.500, 95% CI: 2.344-47.034, P = 0.002). The rate of early death (ED) was 24.4% (21/86). The multivariate analysis showed that male gender (OR = 7.578,95% CI:1.136-50.551, P = 0.036), HGB < 65 g/L (OR = 16.271,95% CI:2.012-131.594, P = 0.009) and WBC count ≥7 × 10^9/L on Day 3(OR = 23.359,95% CI:1.825-298.959, P = 0.015) were independent risk factors for ED. The WBC count at diagnosis, WBC count on Day 3 and WBC count on Day 5 had moderate positive correlations with tumor necrosis factor-α (TNF-α) at diagnosis, and the correlation coefficients were 0.648 (P = 0.012), 0.615 (P = 0.033), and 0.609 (P = 0.035), respectively. The WBC count had no correlation with IL-6. CONCLUSION: During induction treatment, cytotoxic chemotherapy may need to be initiated to reduce the risk of DS for APL patients with a low-intermediate risk WBC count ≥10 × 10^9/L on Day 5 or for all patients with a peak WBC count ≥16 × 10^9/L. Patients with WBC > 7 × 10^9/L on Day 3 have a higher risk of ED. Leukocyte proliferation is associated with TNF-α rather than IL-6, and TNF-α may be a potential biomarker for predicting ED.

A novel PEGylated form of granulocyte colony-stimulating factor, mecapegfilgrastim, for peripheral blood stem cell mobilization in patients with hematologic malignancies.

BACKGROUND: The Pegylated recombinant human granulocyte colony stimulating factor (PEG-rhG-CSF) has longer half-life and is given once only, which is more comfortable for patients. We aimed to evaluate the efficacy of mecapegfilgrastim for hematopoietic stem cell (HSC) mobilization in patients with hematologic malignancies and to explore the potential factors related to HSC mobilization. METHODS: A retrospective analysis was performed on patients who underwent HSC mobilization in the hematology department of Mianyang Central Hospital from April 2016 to November 2022. The number of CD34 + cells collected was compared between the patients receiving mecapegfilgrastim (PEG group) and those receiving recombinant human granulocyte colony-stimulating factor (rhG-CSF group), and the possible factors for mobilization failure were analyzed. RESULTS: The success rates of collecting CD34 + cells in the PEG group and rhG-CSF group were 80.6% and 67.7%, respectively (χ = 1.444, P = 0.229). The median CD34 + cell counts were 3.62 × 10^6/kg and 2.92 × 10^6/kg (P = 0.178), respectively. After combination with plerixafor for mobilization, the median number of CD34 + cells collected in the PEG group and rhG-CSF group were 3.64 × 10^6/kg and 3.92 × 10^6/kg, respectively, with no significant difference (P = 0.754). There was no significant difference in hematopoietic cell recovery or infection between the groups (P > 0.05). Multivariate analysis showed that more than 5 cycles of chemotherapy (OR = 15.897, 95% CI: 1.766-143.127, P = 0.014), a precollection WBC count < 32 × 10^9/L (OR = 14.441, 95% CI: 2.180-95.657, P = 0.006) and a precollection to premobilization lymphocyte ratio < 1.7 (OR = 11.388, 95% CI: 2.129-60.915, P = 0.004) were independent risk factors for HSC mobilization failure. CONCLUSIONS: The HSC mobilization efficacy of mecapegfilgrastim in patients with hematologic malignancies was comparable to that of rhG-CSF, and combination with plerixafor for mobilization was feasible and effective. Patients with more than 5 cycles of chemotherapy before HSC mobilization, a precollection WBC count lower than 32 × 10^9/L, and a precollection lymphocyte count less than 1.7 times the premobilization lymphocyte count have a high probability of HSC mobilization failure.

Genome-wide identification of gap junction (connexins and pannexins) genes in black rockfish (Sebastes schlegelii): Evolution and immune response mechanism following challenge.

Cell-to-cell communication through gap junction channels is very important to coordinate the functions of cells in all multicellular biological tissues. It allows the direct exchange of ions and small molecules (including second messengers, such as Ca2+, IP3, cyclic nucleotides, and oligonucleotides). In this study, a total of 48 members of the gap junction (GJ) protein family were identified from Sebastes schlegelii. In S. schlegelii, GJ proteins were classified into two types, connexin, and pannexin, and then connexins were divided into five subfamilies. The naming of 48 genes was verified through phylogenetic analysis and syntenic analysis. The connexin proteins contained four transmembrane fragments and two extracellular loops, the lengths of the intracellular loop and C-terminal was quite different, and the C-terminal region was highly variable after post-translational modification. PPI analysis showed that GJs interacted with tight junctions, adhesive junctions, and cell adhesions to form a complex network and participated in cell-cell junction organization, ATP binding, ion channel, voltage-gated conduction, wnt signaling pathway, Fc-γ receptor signaling pathway, and DNA replication. In addition, the S. schlegelii GJ protein was highly expressed in intestinal tissues and remarkably regulated after Edwardsiella tarda and Streptococcus iniae infection. The expression of GJs in intestinal cells of S. schlegelii was significantly regulated by LPS and poly (I:C), which was consistent with the results of intestinal tissue stimulation by pathogens. In conclusion, this study can provide valuable information for further research on the function of S. schlegelii GJ proteins.

Curcumin relieves arecoline-induced oral submucous fibrosis via inhibiting the LTBP2/NF-κB axis.

BACKGROUND: Submucosal fibrosis (OSF) of the oral cavity is a chronic scarring disease. Arecoline (Are) is the driving factor for the occurrence and deterioration of OSF. Curcumin plays a vital anti-inflammatory role in Are-induced OSF development. However, its potential pharmacological mechanism needs to be elucidated. METHODS: The relative molecular level was measured via qRT-PCR or Western blot. MTT assay, transwell assay and flow cytometry detected cell proliferation, migration, and apoptosis. The correlation between hypoxia-inducible factor-1α (HIF-1α) and LTBP2 promoter was confirmed through dual-luciferase reporter assay. ELISA was performed to detect inflammatory cytokines levels. RESULTS: Curcumin alleviated Are-induced oral mucosal fibroblast cells fibrosis by reducing oral mucosa fibroblasts viability, promoting cell apoptosis, suppressing cell migration, and down-regulating the levels of fibrosis markers and inflammatory factors. Curcumin relieved Are-induced OSF via inhibiting HIF-1α. Mechanically, HIF-1α bound to the promoter of LTBP2 to transcriptionally activated LTBP2. LTBP2 knockdown relieved Are-induced OSF, and curcumin down-regulated LTBP2 via inhibiting HIF-1α to relieve Are-induced OSF. Moreover, curcumin decreased NF-κB signal associated proteins via inhibiting LTBP2 to relieve Are-induced OSF. CONCLUSION: Curcumin reduced the transcription level of LTBP2 by inhibiting HIF-1α, thereby inactivating NF-κB pathway to alleviate Are-induced OSF.

MYH1F promotes the proliferation and differentiation of chicken skeletal muscle satellite cells into myotubes.

In diploid organisms, interactions between alleles determine phenotypic variation. In previous experiments, only MYH1F was found to show both ASE (spatiotemporal allele-specific expression) and TRD (allelic transmission ratio distortion) characteristics in the pectoral muscle by comparing the genome-wide allele lists of hybrid populations (F1) of meat- and egg- type chickens. In addition, MYH1F is a member of the MYH gene family, which plays an important role in skeletal muscle and non-muscle cells of animals, but the specific expression and function of this gene in chickens are still unknown. Therefore, qRT-PCR was used to detect the expression of MYH1F in different tissues of chicken. Proliferation and differentiation of chicken skeletal muscle satellite cells (SMSCs) have been detected by transfection of MYH1F-specific small interfering RNA (siRNA). The results showed that the expression of MYH1F in chicken skeletal muscle was higher than that in other tissues. Combined with CCK-8 assay, EdU assay, immunofluorescence, and Western blot Assay, it was found that MYH1F knockdown could significantly suppress the proliferation of chicken SMSCs and depress the differentiation and fusion of the cells. These results suggest that MYH1F plays a critical role in myogenesis in poultry, which is of great significance for exploring the regulatory mechanisms of muscle development and improving animal productivity.

miR-138-5p promotes chicken granulosa cell apoptosis via targeting SIRT1.

Granulosa cell (GC) apoptosis is the main trigger of follicular atresia. MicroRNAs (miRNAs) are 18-22 nt RNAs whose function is primarily determined by their extended seed region and are considered to be involved in the biological functions of follicular development, including follicular atresia, folliculogenesis, and oogenesis. MiR-138-5p is known to act on chicken GCs. In this study, we found that miR-138-5p was enriched in reproductive organs, such as the uterus and ovaries. To examine whether miR-138-5p could regulate the biological process of GCs, miR-138-5p was examined by transfection of cells with a mimic or inhibitor of miR-138-5p. Expression levels of caspase-3 and caspase-9 mRNA and protein were markedly increased or decreased after transfection of the mimic or inhibitor, respectively. Furthermore, following miR-138-5p inhibition, SIRT1, one of the target genes of miR-138-5p, was found to increase the mRNA, which is correlated with the increased levels of BCL2 expression, an anti-apoptotic gene in the chicken GCs. These results suggest that miR-138-5p promotes apoptosis in chicken GCs by targeting SIRT1.

Whole transcriptome analysis reveals the key genes and noncoding RNAs related to follicular atresia in broilers.

Broodiness, a maternal behavior, is accompanied by the atresia of follicles and the serious degradation of poultry reproductive performance. The comparison of follicles between brooding and laying hens is usually an ideal model for exploring the regulation mechanism of follicle atresia. In this study, we selected three brooding hens and three laying hens to collect their follicles for whole transcriptome sequencing. The results demonstrated different expression patterns between the follicles of brooding hens and laying hens. In the top 10 differentially expressed genes with the highest expression, MMP10 was relatively low expressed in the follicles of brooding hens, but other nine genes were relatively highly expressed, including LRR1, RACK1, SPECC1L, ABHD2, COL6A3, RPS17, ATRN, BIRC6, PGAM1 and SPECC1L. While miR-21-3p, miR-146a-5p, miR-142-5p and miR-1b-3p were highly expressed in the follicles of brooding hen, miR-106-5p, miR-451, miR-183, miR-7, miR-2188-5p and miR-182-5p were lowly expressed in brooding hen. In addition, we identified 124 lncRNAs specifically expressed in the follicles of brooding hens and 147 lncRNAs specifically expressed in the follicles of laying hens. Our results may provide a theoretical basis for further exploration of the molecular mechanism of broodiness in broilers.