Journal: Non-coding RNA Research

Article Title: The pachytene-specific lncRNA 1700008K24Rik is essential for mouse spermatogenesis and functions as a conserved piRNA precursor

doi: 10.1016/j.ncrna.2026.04.001

Figure Lengend Snippet: lncRNA TDRG1 acts as a piRNA precursor to generate piRNAs A. RT‒qPCR analysis of TDRG1 overexpression in GC-2 spd(ts) cells. Gapdh was used as the internal reference; empty vector transfection as the control (Ctrl). The relative expression was calculated relative to the expression level of Gapdh . Relative expression was normalized to Gapdh , and calculated versus shCtrl. Data are shown as mean ± SD; n = 3. Statistical significance was determined by unpaired t -test (∗∗∗ P < 0.001). B. Expression levels of TDRG1 -related piRNAs after TDRG1 overexpression in GC-2 spd(ts), detected by RT‒qPCR. U6 snRNA was used as the internal reference; empty vector transfection as the control (Ctrl). Three piRNAs (piR-128687, piR-115293 and piR-103374) with no sequences overlap to 1700008K24Rik were used as negative controls. Relative expression was normalized to U6 , and calculated versus shCtrl. Data are shown as mean ± SD; n = 3. Statistical significance was determined by unpaired t -test (∗ P < 0.05, ∗∗ P < 0.01, ∗∗∗ P < 0.001, NS: no significant difference).

Article Snippet: Reverse transcription of mRNAs or lncRNAs was performed using a reverse transcription kit (HiScript® II 1st Strand cDNA Synthesis Kit (+gDNA wiper), Vazyme, Cat# R212-01), while reverse transcription of piRNAs was carried out using a piRNA reverse transcription kit (miRNA First Strand cDNA Synthesis Kit (Tailing Reaction), Sangon Biotech, Cat# B532451). qPCR was performed via qPCR reagent (AceQ qPCR SYBR Green Master Mix, Vazyme, Cat# Q111-02) on a qPCR detection system (Bio-Rad) using the specific primers listed in in the “Multimedia component 3” file. mRNA or lncRNA expression was calculated, referring to that of the gene Gapdh , while piRNA expression was calculated, referring to that of the gene U6 .

Techniques: Over Expression, Plasmid Preparation, Transfection, Control, Expressing

Journal: Non-coding RNA Research

Article Title: The pachytene-specific lncRNA 1700008K24Rik is essential for mouse spermatogenesis and functions as a conserved piRNA precursor

doi: 10.1016/j.ncrna.2026.04.001

Figure Lengend Snippet: RNA-seq analysis of 1700008K24Rik -overexpressing GC-2 spd(ts) cells A . Volcano plot displaying differentially expressed genes (DEGs) in GC-2 spd(ts) cells overexpressing 1700008K24Rik versus control, based on RNA-seq data. The x-axis shows log 2 (fold change) the y-axis shows -log 10 ( P value). Red, green, and gray dots indicate up-regulated, down-regulated and non-DEGs, respectively. B-C . Gene Ontology (GO) enrichment analysis of up-regulated (B) and down-regulated (C) genes after 1700008K24Rik overexpression in GC-2 spd(ts) cells. Selected biological processes that were potentially involved are listed on the right. D . KEGG pathway enrichment analysis of down-regulated genes after 1700008K24Rik overexpression in GC-2 spd(ts) cells. Related pathways that were potentially involved are listed on the right. E-F . RT‒qPCR validation of RNA-seq results for up-regulated (E) and down-regulated (F) genes following 1700008K24Rik overexpression in GC-2 spd(ts) cells. Gapdh was used as the internal control; empty vector transfectionas the experimental control (Ctrl). Relative expression was calculated versus Ctrl. Data are presented as the mean ± SD; n = 3. Statistical significance was determined by unpaired t- test (∗ P < 0.05, ∗∗ P < 0.01, NS: not significant). G . Predicted targets of the 1700008K24Rik-related piRNAs among the differentially expressed genes, analyzed using miRanda algorithm. Shown are eight spermatogenesis-related genes harboring potential piRNA targeting sites.

Article Snippet: Reverse transcription of mRNAs or lncRNAs was performed using a reverse transcription kit (HiScript® II 1st Strand cDNA Synthesis Kit (+gDNA wiper), Vazyme, Cat# R212-01), while reverse transcription of piRNAs was carried out using a piRNA reverse transcription kit (miRNA First Strand cDNA Synthesis Kit (Tailing Reaction), Sangon Biotech, Cat# B532451). qPCR was performed via qPCR reagent (AceQ qPCR SYBR Green Master Mix, Vazyme, Cat# Q111-02) on a qPCR detection system (Bio-Rad) using the specific primers listed in in the “Multimedia component 3” file. mRNA or lncRNA expression was calculated, referring to that of the gene Gapdh , while piRNA expression was calculated, referring to that of the gene U6 .

Techniques: RNA Sequencing, Control, Over Expression, Biomarker Discovery, Plasmid Preparation, Expressing

Journal: Non-coding RNA Research

Article Title: The pachytene-specific lncRNA 1700008K24Rik is essential for mouse spermatogenesis and functions as a conserved piRNA precursor

doi: 10.1016/j.ncrna.2026.04.001

Figure Lengend Snippet: Knockdown of 1700008K24Rik impairs mouse spermatogenesis. A . Visualization of AAV9 virus delivery into mouse seminiferous tubules, with trypan blue indicating successful injection. B . RT‒qPCR analysis of 1700008K24Rik knockdown efficiency in mouse testes. Three-week-old mice were injected with AAV9-shRNA-GFP (shRNA) and analyzed after one month. The contralateral testis injected nontargeted shRNA (shCtrl) served as the control. Gapdh was used as the internal reference. Relative expression was calculated versus Ctrl. Data are presented as the mean ± SD; n = 3. Statistical significance was determined by unpaired t- test (∗∗ P < 0.01, NS: not significant). C . Representative images of testis size AAV9-shRNA-GFP (shRNA) and AAV9-shCtrl-GFP (shCtrl) injected mice. Viruses were delivered at 3 weeks of age; tissues were collected one month post-injection. n = 3. D . Testis weight quantification of shRNA and shCtrl groups. Relative testis weight was normalized to shCtrl. Data are shown as mean ± SD; n = 3. Statistical significance was determined by unpaired t -test (∗∗∗ P < 0.001), n = 3. E . H&E staining of paraffin-embedded testis sections from shRNA and shCtrl groups. Scale bars: 100 μm (overview) and 20 μm (magnified). F . Seminiferous epithelium thickness measurement in shRNA and shCtrl groups. Thickness was assessed from five H&E-stained sections per testis. Data are shown as mean ± SD; n = 3. Statistical significance was determined by unpaired t -test (∗ P < 0.05, ∗∗ P < 0.01). G . Epididymal sperm counts in shRNA and shCtrl groups. Relative sperm count was calculated versus shCtrl. Data are shown as mean ± SD; n = 3. Statistical significance was determined by unpaired t -test (∗∗ P < 0.01), n = 3. H . Expression levels of 1700008K24Rik -related piRNAs in shRNA or shCtrl testes, detected by RT‒qPCR. Three piRNAs (piR-128687, piR-115293 and piR-103374) with no sequence overlap to 1700008K24Rik were used as negative controls. Relative expression was calculated versus Ctrl. Data are presented as the mean ± SD; n = 3. Statistical significance was determined by unpaired t- test (∗ P < 0.05, ∗∗ P < 0.01, ∗∗∗ P < 0.001, NS: not significant).

Article Snippet: Reverse transcription of mRNAs or lncRNAs was performed using a reverse transcription kit (HiScript® II 1st Strand cDNA Synthesis Kit (+gDNA wiper), Vazyme, Cat# R212-01), while reverse transcription of piRNAs was carried out using a piRNA reverse transcription kit (miRNA First Strand cDNA Synthesis Kit (Tailing Reaction), Sangon Biotech, Cat# B532451). qPCR was performed via qPCR reagent (AceQ qPCR SYBR Green Master Mix, Vazyme, Cat# Q111-02) on a qPCR detection system (Bio-Rad) using the specific primers listed in in the “Multimedia component 3” file. mRNA or lncRNA expression was calculated, referring to that of the gene Gapdh , while piRNA expression was calculated, referring to that of the gene U6 .

Techniques: Knockdown, Virus, Injection, shRNA, Control, Expressing, Staining, Sequencing

Journal: Synthetic and Systems Biotechnology

Article Title: Metabolic reprogramming of abscisic acid-producing strain Botrytis cinerea TB-31 toward terpenoid biosynthesis using a CRISPR/Cas9 ribonucleoprotein system

doi: 10.1016/j.synbio.2025.12.002

Figure Lengend Snippet: Transcriptomic analysis of B. cinerea strains TB-31, △ bcaba3 , and △ bcaba1234 . (A)∼(B) Regression analysis between transcriptomic data (RNA-seq) and RT‒qPCR validation. △ bcaba3 vs. TB-31: R 2 = 0.94, P < 0.001 (A); △ bcaba1234 vs. TB-31: R 2 = 0.97, P < 0.001 (B). (C) Heatmap of the relative transcriptional levels of the genes in the MVA pathway in △ bcaba1234 compared with those in TB-31. Gene transcription levels were normalized using Z score transformation, calculated as (X-mean)/SD, to represent the number of standard deviations above or below the mean transcription level. Upregulated genes are highlighted in red, while downregulated genes are shown in blue. The data are derived from three independent biological replicates. (D) Heatmap of the relative transcriptional levels of DEGs involved in other secondary metabolism pathways in △ bcaba1234 compared with those in TB-31. (E) Heatmap of the relative transcriptional levels of genes involved in intracellular primary metabolic pathways in the △ bcaba1234 strain compared with those in the TB-31 strain. Metabolic pathways are marked with gray boxes. PPP: pentose phosphate pathway; TCA: tricarboxylic acid cycle; GYC: glyoxylate cycle.

Article Snippet: The sgRNAs were transcribed using the T7 High Yield RNA Transcription Kit (Nanjing Vazyme Biotech Co., Ltd., Nanjing, China), and then purified using the RNA Clean & Concentrator Kit (Zymo Research Corp., Irvine, California, USA).

Techniques: RNA Sequencing, Biomarker Discovery, Transformation Assay, Derivative Assay

Journal: Animal Nutrition

Article Title: Nutritional programming through early exposure to soybean meal: Effects on growth performance, intestinal health, metabolism, and microbiota of juvenile largemouth bass ( Micropterus salmoides )

doi: 10.1016/j.aninu.2025.11.005

Figure Lengend Snippet: The expression of immune defense-related genes in largemouth bass fry fed soybean meal. Immune effector factors (A); immune tolerance-related transcription factors (B, C, and D); and immune signal transduction factors (E and F). There were significant differences indicated by different letters on bars ( P < 0.05), n = 6. FM1: fish meal-based diet for Phase 1; SBM1: 15% soybean meal diet for Phase 1.

Article Snippet: RNA samples with a concentration greater than 100 ng/μL and an OD 260 /OD 280 ratio between 1.8 and 2.2 were considered to have acceptable integrity. cDNA synthesis was performed using a reverse transcription kit (PC7002, Aidlab Bio Inc., Beijing, China).

Techniques: Expressing, Transduction

Journal: Animal Nutrition

Article Title: Nutritional programming through early exposure to soybean meal: Effects on growth performance, intestinal health, metabolism, and microbiota of juvenile largemouth bass ( Micropterus salmoides )

doi: 10.1016/j.aninu.2025.11.005

Figure Lengend Snippet: The expression of immune defense-related genes in largemouth bass fed soybean meal was mean ± SEM ( n = 4). Immune effector factors (A); immune tolerance-related transcription factors (B, C, and D); and immune signal transduction factors (E and F). Significant differences were observed between different letters on bars ( P < 0.05). F1F2: fish meal-based diet for Phase 1 (FM1) followed by fish meal-based diet for Phase 2 (FM2; F1S2: FM1 followed by 25% soybean meal diet for Phase 2 (SBM2); S1F2: 15% soybean meal diet for Phase 1 (SBM1) followed by FM2; S1S2: SBM1 followed by SBM2.

Article Snippet: RNA samples with a concentration greater than 100 ng/μL and an OD 260 /OD 280 ratio between 1.8 and 2.2 were considered to have acceptable integrity. cDNA synthesis was performed using a reverse transcription kit (PC7002, Aidlab Bio Inc., Beijing, China).

Techniques: Expressing, Transduction

Journal: bioRxiv

Article Title: CXCR6⁺ natural killer cell immunotherapy preserves CD4⁺ T helper cells in humanized mice

doi: 10.64898/2026.05.28.728486

Figure Lengend Snippet: A) Expansion kinetics of sorted CXCR6⁻ and CXCR6⁺ NK cells from independent peripheral blood NK-cell donors during 15 days of ex vivo culture with CXCL16-expressing feeder cells, irradiated allogeneic PBMC feeders, and cytokine supplementation. B) Representative post-expansion flow cytometry plots showing maintenance of CXCR6-defined NK-cell phenotypes following expansion. C) Representative intracellular HIV-Gag flow cytometry plots from the indicated culture conditions. Activated primary CD4⁺ T cells from a single peripheral blood donor were infected with HIV-1 Q23.17 at an MOI of 0.01 and cultured alone or co-cultured for 3 days with day 14-expanded CXCR6⁺ or CXCR6⁻ NK cells at a 1:1 effector-to-target ratio. HIV infection was quantified by intracellular HIV-Gag staining and flow cytometry. D) Quantification of HIV suppression assay results. CXCR6⁺ and CXCR6⁻ NK cells were tested using NK cells from five independent genetically unrelated donors, with the same HIV-infected CD4⁺ T-cell target donor used across all NK donor and subset conditions. For each NK donor and condition, the CD4 + T cell-frequency was determined by flow cytometry, triplicate technical wells per donor were averaged before statistical analysis, and the five NK donors were analyzed as biological replicates. Donor-level paired comparisons were analyzed using two-sided paired tests with Holm correction for multiple comparisons. CXCR6⁺ NK cells significantly reduced the frequency of HIV-Gag⁺ CD4⁺ T cells compared with HIV-only cultures, p = 0.000064. CXCR6⁻ NK cells also significantly reduced HIV-Gag⁺ CD4⁺ T cells compared with HIV-only cultures, p = 0.004059. CXCR6⁺ NK cells suppressed HIV significantly more effectively than paired CXCR6⁻ NK cells, p = 0.009637. Data are presented as mean ± SD, with each color representing an independent NK-cell donor. **p < 0.01, ****p < 0.0001.

Article Snippet: RPMI 8866 cells were transduced with lentiviral particles (pLenti C mGFP, Origene) carrying CXCL16 transcript variant 1 (TV1, NM_022059) or variant 2 (TV2, NM_001100812).

Techniques: Ex Vivo, Expressing, Irradiation, Flow Cytometry, Infection, Cell Culture, Staining, HIV Inhibition Assay