Construction of castor functional markers fingerprint and analysis of genetic diversity

In order to provide a molecular basis for selecting good hybrid combinations for the identification of castor bean germplasm resources, fingerprint and genetic diversity analysis of 52 castor bean materials from 12 regions in 5 countries were constructed by using the Functinal Markers (FMs) associated with fatty acid metabolism-related genes. A total of 72 alleles were amplified by 29 pairs of FMs with an average of 2.483 per marker and the polymorphic information content was 0.103–0.695. Shannon’s information index (I), observed heterozygosity (Ho) and expected heterozygosity (He) were 0.699, 0.188 and 0.436 respectively. The clustering results indicated that the castor germplasm could be divided into two groups with the genetic similarity coefficient of 0.59. The genetic similarity of 12 regions ranged from 0.518 to 0.917 and the genetic distance was between 0.087 and 0.658. A total of 5 pairs of core primers were screened to construct a digital fingerprint of different castor germplasm resources, which could distinguish all 52 germplasms. This study provides a scientific basis for screening high-quality castor germplasm resources and broadening the genetic basis of castor breeding at the molecular level.     

Development of polymorphic SSR markers and their applicability in genetic diversity evaluation in <i>Euptelea pleiosperma</i>

Euptelea pleiosperma is a characteristic species of East Asian flora with both ornamental and scientific values. Based on the reduced-representation sequencing (RRS) technology of RAD-Seq, this study conducted high-throughput Illumina paired-end sequencing to find SSR marker information in the genome of E. pleiosperma, and to screen and verify polymorphism of SSR markers. We obtained 5.5G of high-quality data using RAD-Seq. The total number of contigs of the RAD tags was 299,376, with the maximum contig length of 2,062 bp and the average length of 445 bp. From these sequences, we identified 20,718 SSR loci, with a distribution density of one SSR per 6.45 kb (1/6.45 kb). Among all SSRs, dinucleotides (52.00%) were the most detected SSRs, followed by mononucleotides (21.63%). AG/CT was the dominant motif in the SSR loci, accounting for 34.8%. Primers were successfully designed for 14,593 loci, and 100 pairs of these primers were randomly selected for chemical synthesis and validated by SSR-PCR amplification in 20 individuals of E. pleiosperma. Seventy-nine primers were able to amplify the target bands. Cervus 3.0 software was used to analyze the selected 20 SSR loci with good polymorphism. For the 20 SSR markers, the number of alleles ranged from 4 to 9, and the observed heterozygosity and expected heterozygosity were from 0.35 to 0.75 and 0.541 to 0.875, respectively. The information content of polymorphic loci ranged from 0.463 to 0.848, with an average value of 0.638. Among them, there were 18 highly polymorphic loci, and 20 SSR loci did not deviate from the HardyWeinberg equilibrium. Furthermore, the 20 pairs of SSR primers were used to conduct PCoA analysis based on Nei’s genetic distance of 51 individuals from three populations. The results showed that these SSR markers could distinguish genetic differences based on different geographical locations.     

Phytohormonal and metabolism analysis of <i>Brassica rapa</i> L. ssp. <i>pekinensis</i> with different resistance during <i>Plasmodiophora brassicae</i> infection

Clubroot of Chinese cabbage (Brassica rapa L. ssp. pekinensis), caused by the obligate parasite Plasmodiophora brassicae, accounts for serious yield losses. The aim of our study was to explore the phytohormone levels and metabolome changes in the roots of resistant and susceptible B. rapa genotypes at a late stage of infection, i.e., 28 days post-infection. Both genotypes showed decreased auxin levels after P. brassicae infection except for indole-3-acetic acid. Overall, the susceptible genotype had higher auxin and cytokinin levels after infection, with the exception of trans-zeatin and 3- indolebutyric acid as compared to the resistant genotype. Jasmonic acid levels declined after infection regardless of the genotype. Resistance against clubroot was evident with the increased levels of salicylic acid in the resistant genotype. The susceptible genotype had a higher number of differentially accumulated metabolites (DAMs) (262) than the resistant genotype (238) after infection. Interestingly, 132 DAMs were commonly detected in both genotypes when infected with the pathogen, belonging to metabolite classes such as phenolic acids, amino acids, and derivatives, glucosinolates, organic acids, flavonoids, nucleotides and derivatives, and fatty acids. The differential metabolite analysis revealed that metabolites related to amino acid biosynthesis, fatty acid biosynthesis and elongation, glutathione metabolism, and glucosinolate metabolism were highly accumulated in the resistant genotype, suggesting their essential roles in resistance against P. brassicae infection.     

Biosynthesis of raw starch degrading β-cyclodextrin glycosyltransferase by immobilized cells of <i>Bacillus licheniformis</i> using potato wastewater

The study was sought to enhance the synthesis of thermal stable β-cyclodextrin glycosyltransferase (β-CGTase) using potato wastewater as a low-cost medium and assess the degree to which it is efficient for industrial production of β-cyclodextrin (β-CD) from raw potato starch. Thermophilic bacteria producing β-CGTase was isolated from Saudi Arabia and the promising strain was identified as Bacillus licheniformis using phylogenetic analysis of the 16S rRNA gene. Alginate-encapsulated cultures exhibited twice-fold of β-CGTase production more than free cells. Scanning electron microscopy (SEM) of polymeric capsules indicated the potential for a longer shelf-life, which promotes the restoration of activity in bacterial cells across semi-continuous fermentation of β-CGTase production for 252 h. The optimal conditions for β-CGTase synthesis using potato wastewater medium were at 36 h, pH of 8.0, and 50°C with 0.4% potato starch and 0.6% yeast extract as carbon and nitrogen sources, respectively. The purified enzyme showed a specific activity of 63.90 U/mg with a molecular weight of ∼84.6 kDa as determined by SDS-PAGE analysis. The high enzyme activity was observed up to 60°C, and complete stability was achieved at 75°C. High levels of activity and stability were shown at pH 8.0, and the pH range from 7.0–10.0, respectively. The enzyme has an appreciable affinity for raw potato starch with a Km of 5.7 × 10⁻⁶ M and a Vmax of 87.71 µmoL/mL/min. β-CD production was effective against 25 U/g of raw potato starch. The outcomes demonstrated its feasibility to develop a fermentation process by integrating the cost-effective production of β-CGTase having distinctive properties for β-CD production with ecofriendly utilization of potato wastewater.     

Polymorphic information and genetic diversity in <i>Brassica</i> species revealed by RAPD markers

Randomly amplified polymorphic DNA (RAPD) is a tremendously convenient approach used to discriminate between Brassica species owing to its accuracy and speed. RAPD primers generate adequate genetic information that can be used in the primer-marker system. In this work, twenty RAPD-PCR based markers were executed to generate polymorphic data, like polymorphic information content (PIC), mean resolving power (MRP), resolving power (RP), effective multiplex ratio (EMR), and marker index (MI) for the first time and genetic distance among and between six Brassica species were calculated. Our results indicated that 20 primers produced a total of 231 scored band and generated 87% polymorphic bands. Average PIC, MRP, RP, MI, and EMR values were 0.088, 0.65, 6.7, 0.78, and 8.9, respectively. PIC showed an overall negative correlation with MRP, RP, MI, and EMR, whereas MRP, RP, and EMR, were positively correlated with each other. Genetic identities ranged from 41.99% (between Brassica napus and Brassica oleracea) to 68.83% (between Brassica campestris and Brassica oleracea). Dendrogram results showed no clustering between species except between Brassica campestris and Brassica nigra. Nevertheless, these results will be helpful to acquire useful information about the markers and their use to determine the genomic structures of Brassica species. Further, based on genetic distance and polymorphic information, new hybrids can be developed for effective oilseed production.     

Organogenesis and plant regeneration of <i>Arachis villosa</i> Benth. (Leguminosae) through leaf culture

With the aim of developing an efficient plant regeneration protocol, leaflet explants of three accessions of Arachis villosa Benth. (S2866, S2867 and L97) were cultured on basic Murashige and Skoog medium supplemented with different combinations of plant growth regulators: α-naphthalenacetic acid, indole-3-butyric acid, 6-benzylaminopurine, kinetin and thidiazuron. The accession L97 was the only one able to differentiate buds through indirect organogenesis. The most suitable combination for bud regeneration was the basic medium added with 13.62 μM thidiazuron and 4.44 μM 6-benzylaminopurine. These results show the important role of the genotype in morphogenetic responses and the organogenetic effect of thidiazuron in Arachis villosa accession L97. A thidiazuron lacking media (only 0.54 μM α-naphthalenacetic acid, 13.95 μM kinetin and 13.32 μM 6-benzylaminopurine were added) promoted the elongation of the regenerated buds. Adventitious rooting was achieved 90 days after the isolated shoots were transferred to a rooting medium containing 0.54 μM α-naphthalenacetic acid.     

Co-ordinated combination of Embden-Meyerhof-Parnas pathway and pentose phosphate pathway in <i>Escherichia coli</i> to promote L-tryptophan production

In this study, phosphoenolpyruvate and erythrose-4-phosphate are efficiently supplied by collaborative design of Embden-Meyerhof-Parnas (EMP) pathway and pentose phosphate (PP) pathway in Escherichia coli, thus increasing the L-tryptophan production. Firstly, the effects of disrupting EMP pathway on L-tryptophan production were studied, and the results indicated that the strain with deletion of phosphofructokinase A (i.e., E. coli JW-5 ΔpfkA) produced 23.4 ± 2.1 g/L of L-tryptophan production. However, deletion of phosphofructokinase A and glucosephosphate isomerase is not conducive to glucose consumption and cell growth, especially deletion of glucosephosphate isomerase. Next, the carbon flux in PP pathway was enhanced by introduction of the desensitized glucose-6-phosphate dehydrogenase (zwf) and 6-phosphogluconate dehydrogenase (gnd) and thus increasing the L-tryptophan production (i.e., 26.5 ± 3.2 g/L vs. 21.7 ± 1.3 g/L) without obviously changing the cell growth (i.e., 0.41 h⁻¹ vs. 0.44 h⁻¹) as compared with the original strain JW-5. Finally, the effects of co-modifying EMP pathway and PP pathway on L-tryptophan production were investigated. It was found that the strain with deletion of phosphofructokinase A as well as introduction of the desensitized zwf and gnd (i.e., E. coli JW-5 zwf243 gnd361 ΔpfkA) produced 31.9 ± 2.7 g/L of L-tryptophan, which was 47.0% higher than that of strain JW-5. In addition, the glucose consumption rate of strain JW-5 zwf243 gnd361 ΔpfkA was obviously increased despite of the bad cell growth as compared with strain JW-5. The results of this study have important reference value for the following application of metabolic engineering to improve aromatic amino acids producing strains.     

Screening and evaluation of chilli (<i>Capsicum annuum</i> L.) genotypes for waterlogging tolerance at seedling stage

Waterlogging is an illustrious abiotic stress and the constrictions it enforces on plant roots have negative effects on growth and development. This study was undertaken to investigate waterlogging stress tolerant potential in chilli (Capsicum annum L.) genotypes through evaluating morphological, physiological, biochemical and anatomical parameters. Thirty-five days old seedlings of 10 chilli genotypes were exposed to waterlogging stress maintaining water height 3–5 cm over the soil surface artificially for three days. This duration (36–38 DAE) was termed as waterlogging period, and subsequent withdrawal of waterlogging condition (39–45 DAE) was regarded as a recovery phase. Based on their survival performance, two tolerant genotypes viz., SRC-517 and BARI morich-2 and two susceptible genotypes viz., AHM-206 and RI-1(6) were selected for studying stress tolerance mechanism. Under waterlogging, however, both genotypes (tolerant and susceptible) exhibited reduced root shoot length, dry weight ratio, petiole weight and leaf area, and noticeable reduction regarding these parameters was observed in susceptible genotypes. Moreover, tolerant genotypes displayed a higher recovery than susceptible genotypes after removal of waterlogging stress. Lower reduction of leaf area and photosynthetic pigments as well as higher reduction of relative water content (RWC) were noticed in susceptible genotypes. Higher accumulation of proline and total antioxidant capacity (TAC) during waterlogging condition in tolerant genotypes suggested lower oxidative damage. Although both genotypes lost total soluble sugar (TSS) relative to control at waterlogging stress, better performance was recorded in tolerant genotypes. During the period after the removal of extra water, a similar genotypic response in terms of TSS gain was seen. Undoubtedly, under flooding conditions, the development of aerenchyma cells in tolerant genotypes is a means of tolerance mechanism for long-term survival. Thus, the morpho-physiological and biochemical changes help to understand the tolerance mechanism in chilli under waterlogging stress.     

Expression analysis of <i>OsSERK</i>, <i>OsLEC1</i> and <i>OsWOX4</i> genes in rice (<i>Oryza</i> sativa L.) callus during somatic embryo development

Somatic embryogenesis is an asexual reproduction process that occurs in many plant species, including rice. This process contains several totipotency markers such as Somatic Embryogenesis Receptor-like Kinase (SERK), Leafy Cotyledon1 (LEC1) and WUSCHEL-Related Homeobox4 (WOX4) and also a helpful model for embryo development and clones and transformations. Here, we report the gene expression during somatic embryo development correlates with regeneration frequency in 14 Javanica rice (pigmented and non-pigmented) using modifified N6 media supplemented with Kinetin (2.0 mg/L) and NAA (1.0 mg/L). Although there have been advances in understanding the genetic basis of somatic embryogenesis in other varieties, rice is still unexplored, especially during somatic embryo development. Moreover, for the formation of callus induction from immature embryos, 2,4-D (2.0 mg/L, 3.0 mg/L) was used. This study analysed the gene expression of OsSERK, OsWOX4 and OsLEC1 genes through RT-PCR analysis. Higher expression of the OsLEC1 gene indicates that their function may correlate in the in vitro with the high response of rice after transfer to regeneration media. This study found that rice varieties of pigmented rice (MS Pendek and Gogoniti II) and non-pigmented rice (Pandan Ungu) showed high regeneration frequency, showing higher OsLEC1 expression than other varieties because OsLEC1 promotes the maturation of somatic embryos in plant regeneration on day 14. However, the contrast with Genjah nganjuk may be effective because of other regulatory genes. RT-PCR analysis showed OsSERK had less expression level than OsLEC1 and OsWOX4 in the varieties, which correlate with the percentage of plant regeneration, but not for Gogoniti II. In conclusion, the higher percentage of plant regeneration correlates with the higher expression level of OsLEC1 at day 14 of media regeneration of rice.     

<i>Agrobacterium rhizogenes</i> vs auxinic induction for <i>in vitro</i> rhizogenesis of <i>Prosopis chilensis</i> and <i>Nothofagus alpina</i>

The induction and improvement of in vitro rhizogenesis of microshoots of Prosopis chilensis (Mol.) Stuntz and Nothofagus alpina (Poep. et Endl. Oerst.) were compared using Agrobacterium rhizogenes (Ar) versus indole-3-butyric acid (IBA) in the culture media. Microshoots of P. chilensis (1-2 cm length), coming from in vitro grown seedlings, were cultivated in a modified Broadleaved Tree Medium (BTMm) containing half salt concentration of macronutrients and 0.05 mg.L^-1 benzilaminopurine (BAP). After 30 days, microshoots with 2-4 leaves were selected and cultured in BTMm-agar in presence or abscense of Ar and in combination with IBA. For N. alpina, the apical shoots with the first 2 true leaves, from 5 weeks old seedlings, were cultured in the abovementioned medium, but with 0.15 mg.L^-1 of BAP. After 2 months, microshoots with 2-3 leaves were selected and cultured in BTMm-agar, supplemented with 5 mg.L^-1 IBA or in liquid BTMm on perlite and, in the presence or absence of A. rhizogenes (Ar) and in combination with 3 mg.L^-1 IBA. Rooting in P. chilensis reached 100.0% when Ar infection was produced in the presence of IBA, increasing both, the number and dry weight of roots. In N. alpina, 90.0% of rooting efficiency was obtained when Ar infection was produced in liquid culture and in the absence of auxin.     

Morphological study of the spermatogenesis in the teleost <i>Piaractus mesopotamicus</i>

The spermatogenesis of Piaractus mesopotamicus was investigated under light and transmission electron microscopy. The specimens were captured from their natural environment (Rio Miranda and Rio Aquidauana, Pantanal Matogrossense, Brazil) during April and September. The results were compared with the spermatogenic data of specimens under captivity condition. In both conditions, P. mesopotamicus presented the typical spermatogenesis pattern of the teleost fishes, showing no significative differences. The spermatozoon was classified as type I, which has a globular head without acrosome, a short middle piece and a long tail constituted only by the flagellum. This type of spermatozoon is considered the basic type in fishes.     

Storage lipids and proteins of <i>Euterpe edulis</i> seeds

Comparative studies on fatty acid and protein composition of the endosperm and embryo of palmito (Euterpe edulis Martius) were conducted using gas-liquid chromatography and sodium dodecyl sulfate–polyacrylamide gel electrophoresis. On a dry weight basis, the embryo contained extremely lower amounts of lipids and proteins than did the endosperm, which was associated with the scarce lipid and protein bodies previously reported in axis and cotyledon. The fatty acid composition also exhibited differences between both tissues: (I) the fatty acid diversity was greater in embryo than in endosperm; (II) embryo and endosperm contained predominantly linoleic, palmitic, oleic and stearic acids even though the relative values were different for each tissue. As compared to other palm species, the higher fatty acid unsaturation in Euterpe edulis seed could be involved in the previously reported short longevity and recalcitrant behavior during storage. Proteins of both tissues were heterogeneous in molecular mass. Some proteins were tissue-specific, but other were common, among them a highly glycosylated protein which migrated at about 55 kDa. We hypothesize that the latter, also reported in all previously studied palm species, is one of the proteins characterizing the Arecaceae family.     

Association between preterm birth risk and polymorphism and expression of the DNA repair genes <i>OGG1</i> and <i>APE1</i> in Saudi women

Genomic instability and mutations caused by increases in oxidative stress during pregnancy can damage the fetoplacental unit and can upshot preterm birth. Oxidative damage to DNA may possibly be involved in etiology of preterm birth (PTB) which can be repaired by DNA repair gene. In the present study, we assessed the association of base excision repair gene family by analyzing the association of single nucleotide polymorphisms and genes expression in 8-oxoguanine glycosylase-1 (OGG1) and apurinic-apyrimidinic endonuclease 1 (APE1) genes with risk of preterm birth in Saudi women. We analyzed genotypes of four single nucleotide polymorphisms (SNPs) (rs1052133, rs293795, rs2072668 and rs2075747) in OGG1 gene and three SNPs (rs1130409, rs3136814, and rs3136817) in APE1 gene using TaqMan Genotyping assay kits in 50 pairs of preterm cases and individually matched controls. Also, gene expression level was explored by RT-PCR in 10 pairs of preterm placental tissues and individually matched normal placental tissues. Two OGG1 SNP, rs1052133 (OR=0.497; c2=1.11; p=0.292) and rs2072668 (OR=0.408; c2=1.90; p=0.167) and one APE1 SNP rs3136817 (OR=0.458; c2=0.40; p=0.527) showed nonsignificant protective effect against PTB development. The expression of both genes under study was found lower in the PTB patients. Genotype and allele frequencies of both gene SNPs did not show any association with the risk of preterm delivery in Saudi women (P˃0.05). However, synthesis and release of OGG1 and APE1 proteins decreased in preterm placental tissues compared to term delivery reflects the probability of being one of the mechanisms leading to preterm birth.     

Salinity induced anatomical and morphological changes in <i>Chloris gayana</i> Kunth roots

Chloris gayana Kunth is a grass species valuable as forage which was introduced into Argentina to be used as pasture in saline soils of subtropical and warm-temperate zones, given its good adaptability to drought, salinity and mild freezing. However, its tolerance varies according to the cultivar. In tetraploid cultivars, important reductions in yield have been observed. Here, a study of the variations produced on the root and stem system by salinity at different NaCl concentrations (0, 150 y 250 mM) was performed in the Boma cultivar, with the aim of determining the anatomical and morphological alterations produced by the salt excess. Plants cultivated with the highest level of salinity showed, in the whole, significant differences in the measured variables. A diminution in absolute values of the variables and a major reduction in vascular tissue dimensions were observed, which suggests that the lack of tolerance to salt stress could be related to a deficient adaptation to absorb and transport water and nutrients from the roots.     

Identification of <i>PtGai</i> (a DELLA protein) in trifoliate orange and expression patterns in response to drought stress

Gibberellins (GAs) are an important hormone in regulating plant growth and development, and DELLA protein is an essential negative regulator of GA signal transduction. The aim of the study was to clone a GA-inhibiting protein DELLA from trifoliate orange (Poncirus trifoliata L. Raf.) and to analyze the bioinformations and expression patterns of the protein gene in tissues and in response to drought stress. A DELLA protein was isolated from trifoliate orange and named as PtGai (Genebank number: MZ170959). The PtGai protein had 1731 bp open reading frames, along with 576 amino acid codes, and also grouped with sweet orange (XM_006430552.4). The PtGai protein sequence was 65% homology with the sequences of DELLA proteins in other plant families. PtGai protein existed in the nucleus based on the prediction of subcellular localization. PtGai protein could be expressed in roots, stems, and leaves, along with the highest expression in stems. PtGai was upregulated by drought stress in leaves and roots, along with the decrease of root total GA concentration and the inhibition of shoot and root biomass production. It indicated the characteristics of PtGai protein and the roles of PtGai in GA synthesis and plant growth.     

Targeting the “undruggable” cancer driver genes: <i>Ras</i>, <i>myc</i>, and <i>tp53</i>

The term “undruggable” is to describe molecules that are not targetable or at least hard to target pharmacologically. Unfortunately, some targets with potent oncogenic activity fall into this category, and currently little is known about how to solve this problem, which largely hampered drug research on human cancers. Ras, as one of the most common oncogenes, was previously considered “undruggable”, but in recent years, a few small molecules like Sotorasib (AMG-510) have emerged and proved their targeted anti-cancer effects. Further, myc, as one of the most studied oncogenes, and tp53, being the most common tumor suppressor genes, are both considered “undruggable”. Many attempts have been made to target these “undruggable” targets, but little progress has been made yet. This article summarizes the current progress of direct and indirect targeting approaches for ras, myc, two oncogenes, and tp53, a tumor suppressor gene. These are potential therapeutic targets but are considered “undruggable”. We conclude with some emerging research approaches like proteolysis targeting chimeras (PROTACs), cancer vaccines, and artificial intelligence (AI)-based drug discovery, which might provide new cues for cancer intervention. Therefore, this review sets out to clarify the current status of targeted anti-cancer drug research, and the insights gained from this review may be of assistance to learn from experience and find new ideas in developing new chemicals that directly target such “undruggable” molecules.     

Isolation and molecular characterization of a <i>cax</i> gene from <i>Capsella bursa-pastoris</i>

A new cation exchangers (CAXs) gene was cloned and characterized from Capsella bursapastoris by rapid amplification of cDNA ends (RACE). The full-length cDNA sequence of cax from C. bursa-pastoris (designated as Cbcax51) was 1754 bp containing a 1398 bp open reading frame encoding a polypeptide of 466 amino-acid residues with a calculated molecular mass of 50.5 kDa and an isoelectric point of 5.69. The predicted CbCAX51 contained an IMP dehydrogenase/GMP reductase domain, two Na⁺/Ca²⁺ exchanger protein domains. Comparative and bioinformatics analyses revealed that CbCAX51 showed extensive homology with CAX from other plant species. The expression analysis by different treatments indicated that Cbcax51 could be activated by cold triggering and was related to the cold acclimation process, but its expression is regulated negatively by drought and not affected by ABA or salt.