Development and application of oligonucleotide-based chromosome painting for chromosome 4D of Triticum aestivum L

Chromosome painting is a useful technique for distinguishing specific chromosomes (fragments), elucidating the genetic relationships of different genomes or chromosomes, and identifying chromosomal rearrangements. The development of chromosome- or genome-specific probes is fundamental for chromosome painting. The possibility for developing such probes specifically painting homoeologous chromosomes in allopolyploid species has been questioned since that chromosomes belonging to the same homoeologous group share highly conserved sequences. In the present study, we attempted to construct a wheat chromosome 4D-specific oligo probe library by selecting 4D-specific sequences in reference genome of common wheat cv. Chinese Spring (CS, 2n = 6x = 42, AABBDD). The synthesized library contains 27,392 oligos. Oligo painting using the probe library confirmed its specificity, shown by that only chromosome 4D could be painted in three wheat genotypes and CS nulli-tetrasomic line N4AT4D. Oligo painting was successfully used to define the 4D breakpoints in CS deletion lines involving 4D and two wheat-Haynaldia villosa 4D-4V translocation lines. Thirteen wheat relatives and a Triticum durum-H. villosa amphiploid were used for oligo painting. Except the 4D in two Aegilops tauschii accessions, the 4M in Ae. comosa and 4U in Ae. umbellulata could be painted. In tetraploid Ae. ventricosa, both 4D and 4M could be painted; however, the signal intensity of 4M was less compared with 4D. No painted chromosome was observed for the other alien species. This indicated that the relationship among D/M/U was closer than that among D/A/B as well as D with genomes H/R/S^s/S^c/Y/P/N/J. Our successful development of 4D-specific oligo probe library may serve as a model for developing oligo probes specific for other homoeologous chromosomes.

MicroRNA-370-3p inhibits cell proliferation and induces chronic myelogenous leukaemia cell apoptosis by suppressing PDLIM1/Wnt/β-catenin signaling

Growing evidence has suggested that microRNA-370-3p (miR-370-3p) is downregulated and acts as a suppressor in several cancers. However, the role of miR-370-3p in chronic myeloid leukemia (CML) remains unknown. Here, the expression level and molecular mechanism of miR-370-3p in CML were investigated. Firstly, the expression of miR-370-3p has markedly decreased in the peripheral blood mononuclear cells (PBMCs) of patients with CML and in cell lines. Moreover, miR-370-3p in CML cells upregulated and downregulated proliferation and apoptosis, respectively. Notably, miR-370-3p directly targeted the 3'-untranslated region of PDZ and LIM domain protein 1 (PDLIM1). A negative correlation was observed between the levels of miR-370-3p and PDLIM1 in the PBMCs of patients with CML and healthy volunteers. PDLIM1 was shown to have an oncogenic role in CML cells by promoting proliferation and suppressing apoptosis. Finally, the miR-370-3p-PDLIM1-Wnt/β-catenin signaling axis was indicated to play an important role in CML progression.

A Linear Regression Predictor for Identifying N6-Methyladenosine Sites Using Frequent Gapped K-mer Pattern

N6-methyladenosine (m⁶A) is one of the most common and abundant modifications in RNA, which is related to many biological processes in humans. Abnormal RNA modifications are often associated with a series of diseases, including tumors, neurogenic diseases, and embryonic retardation. Therefore, identifying m⁶A sites is of paramount importance in the post-genomic age. Although many lab-based methods have been proposed to annotate m⁶A sites, they are time consuming and cost ineffective. In view of the drawbacks of the intrinsic methods in RNA sequence recognition, computational methods are suggested as a supplement to identify m⁶A sites. In this study, we develop a novel feature extraction algorithm based on the frequent gapped k-mer pattern (FGKP) and apply the linear regression to construct the prediction model. The new predictor is used to identify m⁶A sites in the Saccharomyces cerevisiae database. It has been shown by the 10-fold cross-validation that the performance is better than that of recent methods. Comparative results indicate that our model has great potential to become a useful and effective tool for genome analysis and gain more insights for locating m⁶A sites.

A C-type lectin with a single carbohydrate-recognition domain involved in the innate immune response of Tribolium castaneum

C-type lectins are one of the pattern-recognition proteins involved in innate immunity in invertebrates. Although there are 16 C-type lectin genes that have been identified in the genome of Tribolium castaneum, their functions and mechanisms in innate immunity remain unknown. Here, we identified one C-type lectin orthologue, TcCTL6 (TC003708), by sequencing random clones from the cDNA library of the coleopteran beetle, T. castaneum. TcCTL6 contains a 654 bp open reading frame encoding a protein of 217 amino acids that includes a single carbohydrate-recognition domain. The expression of TcCTL6 was significantly induced by Escherichia coli, Staphylococcus aureus and stimulation with carbohydrates, including lipopolysaccharide and peptidoglycan. A binding assay suggested that the recombinant TcCTL6 not only bound to lipopolysaccharide and peptidoglycan but also bound to Gram-positive (S. aureus, Bacillus subtilis and Bacillus thuringiensis) and Gram-negative bacteria (E. coli and Pseudomonas aeruginosa) in the presence of calcium ions. Furthermore, when TcCTL6 was knocked down by RNA interference, four antimicrobial peptides (attacin1, attacin2, coleoptericin1 and coleoptericin2) were significantly decreased. These results demonstrate that TcCTL6 plays a vital role in the immune response towards pathogen infection by influencing the expression of antimicrobial peptides and the agglutination of bacteria in the presence of calcium ions in T. castaneum.

FoxP3 in Treg cell biology: a molecular and structural perspective

Regulatory T cells (T_regs) are specialized in immune suppression and play a dominant role in peripheral immune tolerance. T_reg cell lineage development and function maintenance is determined by the forkhead box protein 3 (FoxP3) transcriptional factor, whose activity is fine‐tuned by its post‐translational modifications (PTMs) and interaction partners. In this review, we summarize current studies in the crystal structures, the PTMs and interaction partners of FoxP3 protein, and discuss how these insights may provide a roadmap for new approaches to modulate T_reg suppression, and new therapies to enhance immune tolerance in autoimmune diseases.

MiR-223 regulates CDDP resistance in pancreatic cancer via targeting FoxO3a

OBJECTIVE

FoxO3a is a well-defined tumor suppressor gene in the forkhead transcription factor O subfamily (FoxO), and its reduction is related to the occurrence of various tumors. It was found that miR-223 expression is abnormally elevated in pancreatic cancer tissues. Bioinformatics analysis revealed a targeted complementary binding relationship between miR-223 and FoxO3a. This study explored whether miR-155 regulates the expression of FoxO3a and affects the proliferation, apoptosis, and cisplatin (CDDP) resistance of oral cancer cells.

MATERIALS AND METHODS

Dual-Luciferase reporter gene assay validated the targeted relationship between miR-223 and FoxO3a. The CDDP-resistant pancreatic cancer cell line BXPC3/CDDP was established, and the expressions of miR-223 and FoxO3a were compared. BXPC3/CDDP cells were divided into miR-NC group and miR-223 inhibitor group. QRT-PCR was adopted to test miR-223 and FoxO3a mRNA expressions. Western blot was performed to determine FoxO3a protein expression. Cell apoptosis was detected by flow cytometry and cell proliferation was detected by EdU staining.

RESULTS

There was a targeted regulatory relationship between miR-223 and FoxO3a mRNA. The expression of miR-223 was significantly higher, while the expression of FoxO3a mRNA and protein was significantly lower in BXPC3/CDDP cells than that in BXPC3 cells. Cell Counting Kit-8 (CCK-8) experiments showed that the same concentration of CDDP exhibited significantly lower proliferation inhibition in BXPC3/CDDP cells than BXPC3 cells. Compared with miR-NC group, transfection of miR-223 inhibitor significantly increased the expression of FoxO3a in BXPC3/CDDP cells, which significantly attenuated cell proliferation and enhanced apoptosis in CDDP-treated cells.

CONCLUSIONS

Increased expression of miR-233 was associated with CDDP resistance in pancreatic cancer cells. Inhibition of miR-223 expression upregulated FoxO3a expression, restrained pancreatic cancer cell proliferation, promoted cell apoptosis, and enhanced CDDP sensitivity in pancreatic cancer cells.

Hot topic: Automated assessment of reticulo-ruminal motility in dairy cows using 3-dimensional vision

Reticulo-ruminal motility is a well-established indicator of gastrointestinal health in dairy cows. The currently available methods for assessing motility are labor-intensive, costly, and impractical to use regularly for all cows on a farm. We hypothesized that the reticulo-ruminal motility of dairy cows could be assessed automatically and remotely using a low-cost 3-dimensional (3D) camera. In this study, a 3D vision system was constructed and mounted on the frame of an automatic milking robot to capture the left paralumbar fossa of 20 primiparous cows. For each cow, the system recorded 3D images at 30 frames per second during milking. Each image was automatically processed to locate the left paralumbar fossa region and quantify its average concavity. Then, the average concavity values from all images of 1 cow during 1 milking process were chronologically assembled to form an undulation signal. By applying fast Fourier transformation to the signal, we identified cyclic oscillations that occurred in the same frequency range as reticulo-ruminal contractions. To validate the oscillation identification, 2 trained assessors visually identified reticulo-ruminal contractions from the same 3D image recordings on screen. The matching sensitivity between the automatically identified oscillations and the manually identified reticulo-ruminal contractions was 0.97. This 3D vision system can automate the assessment of reticulo-ruminal motility in dairy cows. It is noninvasive and can be implemented on farms without distressing the cows. It is a promising tool for farmers, giving them regular information about the gastrointestinal health of individual cows and helping them in daily farm management.

Latrophilin mediates insecticides susceptibility and fecundity through two carboxylesterases, esterase4 and esterase6, in Tribolium castaneum

Latrophilin (LPH) is known as an adhesion G-protein-coupled receptor which involved in multiple physiological processes in organisms. Previous studies showed that lph not only involved the susceptibility to anticholinesterase insecticides but also affected fecundity in Tribolium castaneum. However, its regulatory mechanisms in these biological processes are still not clear. Here, we identified two potential downstream carboxylesterase (cce) genes of Tclph, esterase4 and esterase6, and further characterized their interactions with Tclph. After treatment of T. castaneum larvae with carbofuran or dichlorvos insecticides, the transcript levels of Tcest4 and Tcest6 were significantly induced from 12 to 72 h. RNAi against Tcest4 or Tcest6 led to the higher mortality compared with the controls after the insecticides treatment, suggesting that these two genes play a vital role in detoxification of insecticides in T. castaneum. Furthermore, with insecticides exposure to Tclph knockdown beetles, the expression of Tcest4 was upregulated but Tcest6 was downregulated, indicating that beetles existed a compensatory response against the insecticides. Additionally, RNAi of Tcest6 resulted in 43% reductions in female egg laying and completely inhibited egg hatching, which showed the similar phenotype as that of Tclph knockdown. These results indicated that Tclph affected fecundity by positively regulating Tcest6 expression. Our findings will provide a new insight into the molecular mechanisms of Tclph involved in physiological functions in T. castaneum.

[Study on insecticide resistance of Culex pipiens pallens in southwest region of Shandong Province]

OBJECTIVE

To explore the sensitivity of Culex pipiens pallens to common chemical insecticides in the southwestern region of Shandong Province, so as to provide a theoretical basis for the development of reasonable and effective mosquito control measures.

METHODS

The resistance of Cx. pipiens pallens larvae to 5 chemical insecticides, such as cypermethrin, deltamethrin, DDVP, propoxur, and acetofenate were tested by using the WHO biological test method in 2018, and the co-toxicity coefficients after compounding the above-mentioned insecticides were tested by using a drug compounding method.

RESULTS

The resistance indexes of Cx. pipiens pallens to cypermethrin, deltamethrin, DDVP, propoxur, and acetofenate in 3 cities were 144.43-557.54, 118.17-445.33, 6.44-19.00, 2.37-8.10, and 0.88-2.98, respectively, and expect the difference between the DDVP resistances of Cx. pipiens pallens in Jining City and Heze City was not statistically significant (P > 0.05), all the other differences were statistically significant (all P < 0.05). The synergistic coefficients of cypermethrin + DDVP, cypermethrin + propoxur, DDVP + acetofenate, and propoxur + acetofenate were 199.58 - 456.95, 190.56 - 292.37, 123.32 - 319.24, and 192.31 - 367.32, respectively. The lower synergism was observed by using the mixture of DDVP + propoxur (synergistic coefficient: 99.87-108.36) .

CONCLUSIONS

After decades of chemical control, Cx. pipiens pallens in the southwestern region of Shandong Province has produced different degrees of resistance to common chemical insecticides. Therefore, comprehensive control measures should be taken to control mosquito breeding and prevent the development of insecticide resistance.

Multiple functions of miR-8-3p in the development and metamorphosis of the red flour beetle, Tribolium castaneum

The microRNA miR-8-3p is conserved among insects and closely involved in development and immunity, but its functions in vivo are unexplored in the red flour beetle, Tribolium castaneum. Here, we show that miR-8-3p was highly expressed in late larva and early adult stages, as determined by quantitative real-time PCR. It was enriched in the fat body and cuticle in late larval tissues and abundant in the head and cuticle in early adult tissues, indicating this microRNA plays important roles during T. castaneum development. Specific inhibition of miR-8-3p in late larvae led to metamorphosis defects in the development of wings, eyes, legs and embryo. Moreover, a series of genes related to organism development were identified as miR-8-3p targets by computational prediction and microRNA-messenger RNA interaction validation, including Wingless, Eyg, Fpps and Sema-1a. These genes were critical for the regulation of the larva-to-adult transition. Eyg, as a functional target of miR-8-3p, participates in eye development, which was further confirmed by luciferase assay and loss-of-function analyses. In brief, miR-8-3p is broadly involved in the development of wings, eyes and legs through its target genes and has extensive regulatory roles during T. castaneum development.

Automated body condition scoring of dairy cows using 3-dimensional feature extraction from multiple body regions

Machine vision technology has been used in automated body condition score (BCS) classification of dairy cows. The current vision-based classifications use information acquired from a limited number of body regions of the cow. Our study aimed to improve automated BCS classification by including multiple body condition-related features extracted from 3 viewpoints in 8 body regions. The data set of this study included 44 lactating cows with their BCS evenly distributed over the scale of BCS from 1.5 to 4.5 units. The body images of these cows were recorded over 2 consecutive days using 3-dimensional cameras positioned to view the cow from the top, right side, and rear. Each image was automatically processed to identify anatomical landmarks on the body surface. Around these anatomical landmarks, the bony prominences and body surface depressions were quantified to describe 8 body condition-related features. A manual BCS of each cow was independently assigned by 2 trained assessors using the same predefined protocol. With the extracted features as inputs and manual BCS as the reference, we built a nearest-neighbor classification model to classify BCS and obtained an overall classification sensitivity of 0.72 using a 10-fold cross-validation. We conclude that the sensitivity of automated BCS classification has been improved by expanding the selection of body condition-related features extracted from multiple body regions.

Insecticidal activities and mechanism of extracts from neem leaves against Oxya chinensis

ABSTRACT In this study, neem leaves were successively extracted with petroleum ether, 95% ethanol and water and the insecticidal activities of these extracts against Oxya chinensis larvae were measured. The results showed that 95% ethanol extract gave the highest extraction yield and insecticidal activity, and it was further extracted with five different solvents. The petroleum ether extract from the 95% ethanol extract possessed the highest insecticidal activity with median lethal concentration values ranging from 14.93 to 55.66mg/mL. The gas chromatography-mass spectrometer analysis showed that the petroleum ether extract mainly composed of alkanes, olefin, esters and amide. The pathological examination revealed that the prominent lesions, including reduced regenerative cells in midgut and swelled and degenerated cylindrical cells, were observed in the 5th instar Oxya chinensis after treatment. The ultrastructural features showed that the cylindrical cells, microvilli and mitochondria were seriously damaged. These results suggested that the petroleum ether extract from neem leaves had potent insecticidal activity and could be a candidate insecticide.