Schistosoma mansoni is a parasitic helminth that is vectored through freshwater snails. While the anti-schistosome defense of the South American snail, Biomphalaria glabrata, is well studied, little is known about the immune response of the African snail, Biomphalaria sudanica. We measured expression of five candidate immune genes in B. sudanica 8, 24, and 72 hours post-exposure to S. mansoni using reverse transcription quantitative PCR. Expression patterns of incompatible snails were compared to compatible snails and those sham exposed. We also assessed how diet (lettuce vs. pellet) affected expression of three genes, given prior findings that pellet-fed snails were more susceptible to S. mansoni. Results indicated that incompatible snails constitutively expressed higher levels of superoxide dismutase 1 (SOD1) than compatible snails at multiple time points, and of toll-like receptor (TLR) and granulin (GRN) at a single time point. Parasite-induced expression occurred at 8 hours in SOD1, biomphalysin 2, thioester protein 1 (TEP1), and granulin (GRN); however, for biomphalysin 2 and TEP1, induced expression was only detected for susceptible snails. At 24 hours, biomphalysin 2 expression increased in exposed resistant snails, and at 72 hours, all exposed snails decreased biomphalysin 2 expression compared to controls. Parasite-induced expression of SOD1, biomphalysin 2, TEP1, and GRN supports the hypothesis that these genes play a role in B. sudanica anti-schistosome defense; however, increased expression does not necessarily yield clearance of S. mansoni. SOD1 expression was higher in lettuce-fed snails at 8 and 24 hours, consistent with their greater resistance. Together, these results demonstrate the conserved and unique aspects of the B. sudanica anti-schistosome response.

Gene expression can be quantified using the sensitive technique of quantitative reverse transcription real-time polymerase chain reaction. Inter-sample variances can be minimised through normalisation with an appropriate reference gene. Bemisia tabaci, a significant insect vector of the Begomovirus family, transmits the Tomato Leaf Curl Bangalore Virus, for which there is a dearth of information regarding appropriate reference genes for autophagy. The viral load surpasses the vector’s capacity when autophagy is activated, which is also detrimental to whiteflies, particularly concerning virus translocation. To mitigate this vector using a double-stranded RNA approach, a precise measurement of gene silencing is required. For this investigation, normalisation of housekeeping or internal control genes is necessary. The present work utilised software tools such as geNorm, NormFinder, and BestKeeper to assess the suitability of five reference genes, namely, α-tubulin, β-tubulin, elongation factor, actin, and sucrose synthase, for gene expression studies in viruliferous and non-viruliferous B. tabaci. The analysis of the data showed that β-tubulin, which exhibits more stable expression, is the best-ranked reference gene. Furthermore, the reference genes were verified using the target gene expression of atg3 (an autophagy gene). The current findings enable precise measurement of gene expression in begomovirus-induced autophagy conditions of B. tabaci.

Cathepsin B (CTSB) is a cysteine protease that is widely found in eukaryotes and plays a role in insect growth, development, digestion, metamorphosis, and immunity. In the present study, we examined the role of CTSB in response to environmental stresses in Myzus persicae Sulzer (Hemiptera: Aphididae). Six MpCTSB genes, namely MpCTSB-N, MpCTSB-16D1, MpCTSB-3098, MpCTSB-10270, MpCTSB-mp2, and MpCTSB-16, were identified and cloned from M. persicae. The putative proteins encoded by these genes contained three conserved active site residues, i.e. Cys, His, and Asn. A phylogenetic tree analysis revealed that the six MpCTSB proteins of M. persicae were highly homologous to other Hemipteran insects. Real-time polymerase chain reaction revealed that the MpCTSB genes were expressed at different stages of M. persicae and highly expressed in winged adults or first-instar nymphs. The expression of nearly all MpCTSB genes was significantly upregulated under different environmental stresses (38°C, 4°C, and ultraviolet-B). This study shows that MpCTSB plays an important role in the growth and development of M. persicae and its resistance to environmental stress.

Throughout all the domains of life, and even among the co-existing viruses, RNA molecules play key roles in regulating the rates, duration, and intensity of the expression of genetic information. RNA acts at many different levels in playing these roles. Trans-acting regulatory RNAs can modulate the lifetime and translational efficiency of transcripts with which they pair to achieve speedy and highly specific recognition using only a few components. Cis-acting recognition elements, covalent modifications, and changes to the termini of RNA molecules encode signals that impact transcript lifetime, translation efficiency, and other functional aspects. RNA can provide an allosteric function to signal state changes through the binding of small ligands or interactions with other macromolecules. In either cis or trans, RNA can act in conjunction with multi-enzyme assemblies that function in RNA turnover, processing and surveillance for faulty transcripts. These enzymatic machineries have likely evolved independently in diverse life forms but nonetheless share analogous functional roles, implicating the biological importance of cooperative assemblies to meet the exact demands of RNA metabolism. Underpinning all the RNA-mediated processes are two key aspects: specificity, which avoids misrecognition, and speedy action, which confers timely responses to signals. How these processes work and how aberrant RNA species are recognised and responded to by the degradative machines are intriguing puzzles. We review the biophysical basis for these processes. Kinetics of assembly and multivalency of interacting components provide windows of opportunity for recognition and action that are required for the key regulatory events. The thermodynamic irreversibility of RNA-mediated regulation is one emergent feature of biological systems that may help to account for the apparent specificity and optimal rates.

Juvenile hormone (JH) regulates multiple physiological functions in insects including growth, metamorphosis, and reproduction. Juvenile hormone epoxide hydrolase (JHEH) and juvenile hormone esterase (JHE) are degradative enzymes that metabolise JH, and JH receptor (methoprene-tolerant, Met) functions in the regulation of female reproduction and vitellogenesis. In this study, JH titres in Coccinella septempunctata adult females were determined using ultra high-performance liquid chromatography and tandem mass spectrometry; the JH titres ranged from 0.03 to 0.16 ng g−1 in 5- to 30-day-old female adults. JHEH, JHE, and Met expression were studied in different reproductive stages of C. septempunctata females by quantitative real-time PCR. JHEH transcription levels were highest in 25-day-old female adults and were 1.93-fold higher than expression levels in 5-day-old adults. JHEH and JHE expression levels were inhibited by the addition of JH to the artificial diet. Met expression in C. septempunctata supplied with 3 μl JH in artificial diet was similar to Met transcription in females supplied with an aphid diet, and the results showed that supplementation with 3 μl JH in 582.2 g of artificial diet was the most suitable for reproductive regulation of C. septempunctata. The results of this study provide important insights for the improvement of C. septempunctata artificial diets.

Introduction: Long non-coding RNAs (lncRNAs) are a subset of RNA molecules that have been shown to be involved in gene regulation. A lot of different pathways are involved during gametogenesis and any disturbance to these pathways may have a derogatory impact on producing a haploid gamete and thus a euploid embryo. Steroidogenesis pathway plays a crucial role in gametogenesis. The purpose of this work was to quantify the levels of lnc-CYP11A1-1 and RP11573D15.8 expression levels in aneuploid and euploid embryos. Materials and methods: A total of 20 surplus human embryos, of which 10 euploid and ten aneuploid embryos, were collected from an IVF centre. The expression levels of two lncRNAs, which have been hypothesized to regulate expression of CYP11A1, were evaluated in these embryos. RNA was extracted and used to synthesize cDNA for the experiments. Real-time polymerase chain reaction was performed to evaluate the expression levels of each lncRNA in aneuploid and euploid embryos, respectively. Results and discussion: This study shows that lnc-CYP11A1-1 was more expressed in aneuploid than in euploid embryos. RP11-573D15.8 is expressed more in aneuploid embryos than in euploid ones. The results for RP11-573D15.8 were statistically significant with a p-value of 0.02 (less than the standard threshold of p 0.05), whereas the results for lnc-CYP11A1-1 were not statistically significant with a p-value of 0.07 (greater than the standard threshold of p 0.05). Thus, the result of this study demonstrates that lncRNAs may have a role in gametogenesis and formation of aneuploid gametes.

Modification of mRNA by methylation is involved in post-transcriptional regulation of gene expression by affecting the splicing, transport, stability and translation of mRNA. Methylation of adenosine at N6 (m6A) is one of the most common and important cellular modification occurring in the mRNA of eukaryotes. Evidence that m6A mRNA methylation is involved in regulation of stress response and that its dysregulation may contribute to the pathogenesis of neuropsychiatric disorders is accumulating. We have examined the acute and subchronic (up to 18 days once per day intraperitoneally) effect of the first METTL3/METTL14 activator compound CHMA1004 (methyl-piperazine-2-carboxylate) at two doses (1 and 5 mg/kg) in male and female rats. CHMA1004 had a locomotor activating and anxiolytic-like profile in open field and elevated zero-maze tests. In female rats sucrose consumption and swimming in Porsolt’s test were increased. Nevertheless, CHMA1004 did not exhibit strong psychostimulant-like properties: CHMA1004 had no effect on 50-kHz ultrasonic vocalizations except that it reduced the baseline difference between male and female animals, and acute drug treatment had no effect on extracellular dopamine levels in striatum. Subchronic CHMA1004 altered ex vivo catecholamine levels in several brain regions. RNA sequencing of female rat striata after subchronic CHMA1004 treatment revealed changes in the expression of a number of genes linked to dopamine neuron viability, neurodegeneration, depression, anxiety and stress response. Conclusively, the first-in-class METTL3/METTL14 activator compound CHMA1004 increased locomotor activity and elicited anxiolytic-like effects after systemic administration, demonstrating that pharmacological activation of RNA m6A methylation has potential for neuropsychiatric drug development.

Cervical cancer (CC), one of the most prevalent and detrimental gynaecologic cancers, evolves through genetic and epigenetic alterations resulting in the promotion of oncogenic activity and dysfunction of tumour-suppressing mechanisms. Despite medical advancement, the prognosis for advanced-stage patients remains extremely low due to high recurrence rates and resistance to existing treatments. Thereby, the search for potential prognostic biomarkers is heightened to unravel new modalities of CC pathogenesis and to develop novel anti-cancer therapies. Epitranscriptomic modifications, reversible epigenetic RNA modifications, regulate various biological processes by deciding RNA fate to mediating RNA interactions. This narrative review provides insight into the cellular and molecular roles of endogenous RNA-editing proteins and their associated epitranscriptomic modifications, especially N6-methyladenosine (m6A), 5-methylcytosine (m5C) and N1-methyladenosine (m1A), in governing the development, progression and metastasis of CC. We discussed the in-depth epitranscriptomic mechanisms underlying the regulation of over 50 RNAs responsible for tumorigenesis, proliferation, migration, invasion, survival, autophagy, stemness, epithelial-mesenchymal transition, metabolism (glucose, lipid, glutamate and glutamine), resistance (drug and radiation), angiogenesis and recurrence of CC. Additionally, we provided a concise overview of the therapeutic potential of targeting the altered expression of endogenous RNA-editing proteins and aberrant deposition of RNA modifications on both coding and non-coding RNAs in CC.

Gene expression studies in organisms are often conducted using reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), and the accuracy of RT-qPCR results relies on the stability of reference genes. We examined ten candidate reference genes in Sclerodermus guani, a parasitoid wasp that is a natural enemy of long-horned beetle pests in forestry, including ACT, EF1α, Hsc70, Hsp70, SRSF7, α-tubulin, RPL7A, 18S, 28S, and SOD1, regarding variable biotic and abiotic factors such as body part, life stage, hormone, diet, and temperature. Data were analysed using four dedicated algorithms (ΔCt, BestKeeper, NormFinder, and geNorm) and one comparative tool (RefFinder). Our results showed that the most stable reference genes were RPL7A and EF1α regarding the body part, SRSF7 and Hsc70 regarding the diet, RPL7A and α-tubulin regarding the hormone, SRSF7 and RPL7A regarding the life stage, and SRSF7 and α-tubulin regarding temperature. To ascertain the applicability of specific reference genes, the expression level of the target gene (ACPase) was estimated regarding the body part using the most stable reference genes, RPL7A and EF1α, and the least stable one, SOD1. The highest expression level of ACPase was observed in the abdomen, and the validity of RPL7A and EF1α was confirmed. This study provides, for the first time, an extensive list of reliable reference genes for molecular biology studies in S. guani.

Plant growth requires the integration of internal and external cues, perceived and transduced into a developmental programme of cell division, elongation and wall thickening. Mechanical forces contribute to this regulation, and thigmomorphogenesis typically includes reducing stem height, increasing stem diameter, and a canonical transcriptomic response. We present data on a bZIP transcription factor involved in this process in grasses. Brachypodium distachyon SECONDARY WALL INTERACTING bZIP (SWIZ) protein translocated into the nucleus following mechanostimulation. Classical touch-responsive genes were upregulated in B. distachyon roots following touch, including significant induction of the glycoside hydrolase 17 family, which may be unique to grass thigmomorphogenesis. SWIZ protein binding to an E-box variant in exons and introns was associated with immediate activation followed by repression of gene expression. SWIZ overexpression resulted in plants with reduced stem and root elongation. These data further define plant touch-responsive transcriptomics and physiology, offering insights into grass mechanotranduction dynamics.

Machine learning methods have been used in identifying omics markers for a variety of phenotypes. We aimed to examine whether a supervised machine learning algorithm can improve identification of alcohol-associated transcriptomic markers. In this study, we analysed array-based, whole-blood derived expression data for 17 873 gene transcripts in 5508 Framingham Heart Study participants. By using the Boruta algorithm, a supervised random forest (RF)-based feature selection method, we selected twenty-five alcohol-associated transcripts. In a testing set (30 % of entire study participants), AUC (area under the receiver operating characteristics curve) of these twenty-five transcripts were 0·73, 0·69 and 0·66 for non-drinkers v. moderate drinkers, non-drinkers v. heavy drinkers and moderate drinkers v. heavy drinkers, respectively. The AUC of the selected transcripts by the Boruta method were comparable to those identified using conventional linear regression models, for example, AUC of 1958 transcripts identified by conventional linear regression models (false discovery rate < 0·2) were 0·74, 0·66 and 0·65, respectively. With Bonferroni correction for the twenty-five Boruta method-selected transcripts and three CVD risk factors (i.e. at P < 6·7e-4), we observed thirteen transcripts were associated with obesity, three transcripts with type 2 diabetes and one transcript with hypertension. For example, we observed that alcohol consumption was inversely associated with the expression of DOCK4, IL4R, and SORT1, and DOCK4 and SORT1 were positively associated with obesity, and IL4R was inversely associated with hypertension. In conclusion, using a supervised machine learning method, the RF-based Boruta algorithm, we identified novel alcohol-associated gene transcripts.

Lack of water at limiting levels results in drought stress, which may have an impact on the various stages of a crop's life cycle. Four different genotypes of snapmelon (Cucumis melo L. var. momordica) responded differently to 0, 7 and 21 d of simulated drought stress. Information was collected on a range of morpho-physiological, biochemical and molecular characteristics. Each genotype had longer roots, though BAM-VR-312 had the longest roots overall. As the severity of the drought grew, the net photosynthetic rate (Pn) and stomatal conductance (Gs) dropped. In BAM-VR-312, a smaller decline in relative water content (RWC) was recorded, despite the fact that drought stress caused a significant fall in RWC. BAM-VR-312 had smaller accumulations of electrolyte leakage, hydrogen peroxide, phenol and malondialdehyde, although proline content was greater. A decrease in photosynthetic pigments was noted, though BAM-VR-312 had the least reduction. Antioxidant enzyme activity increased in BAM-VR-312, as evidenced by records of ascorbate peroxidase, catalase, guaiacol peroxidase, glutathione reductase and superoxide dismutase. Similarly, expression level of their respective genes was recorded highest in BAM-VR-312. Overall, the study clearly identified distinct genotype based on morpho-physiological, biochemical and molecular properties under drought stress and revealed that the genotype BAM-VR-312 had more efficient drought tolerance mechanisms than the other genotypes under the drought stress condition.

The gene encoding juvenile hormone response (Krüppel homolog1, Kr-hl) in Coccinella septempunctata was investigated by cloning and analysing expression profiles in different developmental stages and tissues by quantitative real-time polymerase chain reaction (PCR). C. septempunctata Kr-hl (CsKr-hl) encoded a 1338 bp open reading frame (ORF) with a predicted protein product of 445 amino acids; the latter showed high similarity to orthologs in other species and contained eight highly-conserved Zn-finger motifs for DNA-binding. CsKr-hl was expressed in different developmental stages of C. septempunctata. The expression levels of CsKr-hl in eggs, 2nd, 3rd, 4th instar larvae, and pupa were 3.31, 2.30, 7.09, 0.58, and 7.48 times the number of 1st instar larvae, respectively. CsKr-hl expression levels in female adults gradually increased at 25–30 days and were significantly higher than expression at 1–20 days. CsKr-hl expression in 20–30 days-old male adults was significantly higher than males aged 1–15 days. CsKr-hl expression levels in heads of male and female adults were significantly higher than expression levels in the thorax, adipose, and reproductive system. Interestingly, CsKr-hl expression levels in the adipose and reproductive system of female adults were significantly higher than in adult male corresponding organs, which suggest that CsKr-hl plays an important role in regulating reproductive development in C. septempunctata.

This study investigated the effects of Lacticaseibacillus rhamnosus HN001 supplementation on the architecture and gene expression in small intestinal tissues of piglets used as an animal model for infant humans. Twenty-four 10-d-old entire male piglets (4·3 (sd 0·59) kg body weight) were fed an infant formula (IF) (control) or IF supplemented with 1·3 × 105 (low dose) or 7·9 × 106 (high dose) colony-forming units HN001 per ml of reconstituted formula (n 8 piglets/treatment). After 24 d, piglets were euthanised. Samples were collected to analyse the histology and gene expression (RNAseq and qPCR) in the jejunal and ileal tissues, blood cytokine concentrations, and blood and faecal calprotectin concentrations. HN001 consumption altered (false discovery rate < 0·05) gene expression (RNAseq) in jejunal tissues but not in ileal tissues. The number of ileal goblet cells and crypt surface area increased quadratically (P < 0·05) as dietary HN001 levels increased, but no increase was observed in the jejunal tissues. Similarly, blood plasma concentrations of IL-10 and calprotectin increased linearly (P < 0·05) as dietary HN001 levels increased. In conclusion, supplementation of IF with HN001 affected the architecture and gene expression of small intestine tissue, blood cytokine concentration and frequencies, and blood calprotectin concentrations, indicating that HN001 modulated small intestinal tissue maturation and immunity in the piglet model.

Leishmaniasis is a vector-borne parasitic disease caused by Leishmania parasites with a spectrum of clinical manifestations, ranging from skin lesions to severe visceral complications. Treatment of this infection has been extremely challenging with the concurrent emergence of drug resistance. The differential gene expression and the discrepancies in protein functions contribute to the appearance of 2 distinct phenotypes: resistant and sensitive, but the current diagnostic tools fail to differentiate between them. The identification of gene expression patterns and molecular mechanisms coupled with antimony (Sb) resistance can be leveraged to prompt diagnosis and select the most effective treatment methods. The present study attempts to use comparative expression of Sb resistance-associated genes in resistant and sensitive Leishmania, to disclose their relative abundance in clinical or in vitro selected isolates to gain an understanding of the molecular mechanisms of Sb response/resistance. Data suggest that the analysis of resistance gene expression would verify the Sb resistance or susceptibility only to a certain extent; however, none of the individual expression patterns of the studied genes was diagnostic as a biomarker of Sb response of Leishmania. The findings highlighted will be useful in bridging the knowledge gap and discovering innovative diagnostic tools and novel therapeutic targets.

Maintaining genomic stability is crucial for normal development. At earlier stages of preimplantation development, as the embryonic genome activation is not fully completed, the embryos may be more prone to abnormalities. Aneuploidies are one of the most common genetic causes of implantation failure or first-trimester miscarriages. Apoptosis is a crucial mechanism to eliminate damaged or abnormal cells from the organism to enable healthy growth. Therefore, this study aimed to determine the relationship between the expression levels of genes involved in apoptosis in human aneuploid and euploid blastocysts. In total, 32 human embryos obtained from 21 patients were used for this study. Trophectoderm biopsies were performed and next-generation screening was carried out for aneuploidy screening. Total RNA was extracted from each blastocyst separately and cDNA was synthesized. Gene expression levels were evaluated using RT-PCR. The statistical analysis was performed to evaluate the gene expression level variations in the euploid and aneuploid embryos, respectively. The expression level of the BAX gene was significantly different between the aneuploid and euploid samples. BAX expression levels were found to be 1.5-fold lower in aneuploid cells. However, the expression levels of BAK and MAD2L1 genes were similar in each group. This study aimed to investigate the possible role of genes involved in apoptosis and aneuploidy mechanisms. The findings of this investigation revealed that the BAX gene was expressed significantly differently between aneuploid and euploid embryos. Therefore, it is possible that the genes involved in the apoptotic pathway have a role in the aneuploidy mechanism.

The in vitro culture of domestic cat embryos without the zona pellucida affects their implantation capacity. MicroRNAs (miRNAs) have an important role in embryo–maternal communication and implantation. The objective of this study was to evaluate the expression of specific miRNAs in domestic cat blastocysts cultured without the zona pellucida. Two experimental groups were done: (1) domestic cat embryos cultured with the zona pellucida (zona intact control group, ZI); and (2) cultured without the zona pellucida (zona free group, ZF). The cleavage, morula and blastocyst rates were evaluated. The blastocysts and their spent medium were used for miRNA expression analysis using RT-qPCR (miR-21, miR-24, mi25, miR-29, miR-96, miR-98, miR-103, miR-191, miR-196, miR-199, miR-130, miR-155 and miR-302). The pre-mature microRNAs (pre-miRNAs) and miRNAs were evaluated in the blastocysts and only miRNAs were evaluated in the spent medium. No differences were observed in the cleavage, morula and blastocyst rates between the ZF and ZI groups (P > 0.05). For miRNAs analysis, miR-103 and miR-191 had the most stable expression and were selected as internal controls. ZF blastocysts had a higher expression of miR-21, miR-25, miR-29 and miR-199 and a lower expression of miR-96 than their ZI counterparts (P < 0.05). Furthermore, higher levels of miR-21, miR-25 and miR-98 were detected in the spent medium of ZF blastocysts (P < 0.05). In conclusion, in vitro culture of domestic cat embryos without the zona pellucida modifies the expression of miR-21, miR-25, miR-29, miR-199 and miR-96 at the blastocyst stage and the release of miR-21, miR-25 and miR-98.