Wild Genotype Research Articles

Screening the promising wild emmer wheat genotypes containing the Yr15 gene in Türkiye and Syria through molecular markers

Screening the promising wild emmer wheat genotypes containing the Yr15 gene in Türkiye and Syria through molecular markers

Genome-wide characterization and functional analysis of heat shock transcription factors in wild and cultivated rice (Oryza sativa L.)

Due to domestication, the genetic diversity in cultivated rice is lower than that of wild rice species. Recent progress in sequencing the genomes of wild and cultivated rice genus is an important step in identifying their genetic differences associated with abiotic and biotic stresses-resistant ability. Thus, in this study, heat shock transcription factor (Hsf) genes in 6 wild rice accessions, including Oryza barthii, Oryza glumaepatula, Oryza meridionalis, Oryza nivara, Oryza punctate and Oryza rufipogon, and 1 cultivated rice variety Nipponbare were firstly identified, and the evolution of rice Hsf genes were analyzed. Totally, 22, 23, 24, 24, 25, 25 and 25 Hsf genes were identified in the 7 tested rice genomes, Oryza barthii, Oryza glumaepatula, Oryza meridionalis, Oryza nivara, Oryza punctate, Oryza rufipogon and Oryza sativa, respectively. The evolutionary analysis of Hsf genes revealed that Oryza rufipogon was the immediate ancestral progenitor of Oryza sativa. The variation in the number of Hsf genes between wild and cultivated rice genotypes was mainly due to segmental duplication and whole genome duplication (WGD) events, which might contribute to the different stress-tolerant ability between the wild and cultivated rice varieties. Secondly, the function of the Hsf genes in wild and cultivated rice in response to salinity stress was compared. Under salt stress, four Hsf genes, HsfA2b, HsfB4b, HsfB4c and HsfB4d, were exclusively down-regulated in Oryza rufipogon shoots. Whilst, another four Hsf genes, HsfA7a, HsfB2c, HsfC1b and HsfC2b, were up-regulated in the shoots of both the cultivated rice and its ancestral progenitor Oryza rufipogon. Meanwhile, genomic comparison results showed that 1, 1, 5 and 5 nsSNPs were detected in these 4 Hsf genes respectively, which might alter the functions of these genes. RT-qPCR results further confirmed the expression profile of one of these 4 Hsf genes, HsfB2c. The expression pattern of this gene in the cultivated rice variety in response to salt stress was similar with the previously known salt stress-tolerant gene, WRKY28. This indicated that these 4 Hsf genes might be among the conserved genes related to salt stress tolerance in the wild and cultivated rice. In summary, these results provide novel clues to the further functional studies of Hsf genes in rice for breeding programs.

Risk of Cardiovascular Complications Among Type 2 Diabetes Mellitus Patients with GSTP1 Genetic Polymorphism: A Nested Case-Control Study and Docking Studies.

The genetic alteration in the antioxidant gene Glutathione-S-Transferases Pi 1 (GSTP1) namely GSTP1*IIe105Val (rs1695) and GSTP1*Ala114Val (rs1138272) changes the individual susceptibility to cardiovascular disease (CVD) and type 2 diabetes mellitus (T2DM) by altering the substrate binding and catalytic activity. This study aims to investigate the association of GSTP1 rs1695 and rs1138272 polymorphism with CVD development in T2DM patients. Genotyping was performed with 400 study participants-group I: control; group II: T2DM; group III: CVD; and group IV: T2DM/CVD [n = 100 each] by PCR-RFLP. The rs1695 and rs1138272 polymorphism were docked against NPACT and NUBBE database and virtually screened using glide. The study reported that rs1695 polymorphism was associated with T2DM risk under dominant and allelic genetic models [OR = 1.97(1.08-3.59) p = 0.02 and OR = 1.79(1.20-2.66) p = 0.003, respectively]. The val/val genotype, dominant, recessive model, and T allelic genetic model were associated with increased CVD risk [OR = 4.15(1.97-8.73) p = < 0.01; OR = 3.16(1.65-6.04) p = < 0.01; OR = 3.47(1.91-6.31) p = < 0.01; and OR = 2.94(1.95-4.43) p = < 0.01, respectively]. In contrast, rs1695 polymorphism was not associated with CVD development among patients with T2DM. In rs1138272, the wild genotype was only detected and neither heterozygous nor val/val genotype was observed. The docking analysis revealed that the Ile105Val mutation plays a significant role in altering the GSTP1 capacity compared to the Ala115Val mutation. This suggests that the Ile105Val mutation has a greater impact on the protein's structure, function, or susceptibility to diseases compared to the Ala115Val mutation. In summary, genetic alteration in GSTP1 rs1695 potentially contributes to an increased risk of T2DM and CVD.

Transcriptome analysis of Phytophthora cactorum infecting strawberry identified RXLR effectors that induce cell death when transiently expressed in Nicotiana benthamiana

Phytophthora cactorum is a plant pathogenic oomycete that causes crown rot in strawberry leading to significant economic losses every year. To invade the host, P. cactorum secretes an arsenal of effectors that can manipulate host physiology and impair its defense system promoting infection. A transcriptome analysis was conducted on a susceptible wild strawberry genotype (Fragaria vesca) 48 hours post inoculation with P. cactorum to identify effectors expressed during the early infection stage. The analysis revealed 4,668 P. cactorum genes expressed during infection of F. vesca. A total of 539 secreted proteins encoded by transcripts were identified, including 120 carbohydrate-active enzymes, 40 RXLRs, 23 proteolytic enzymes, nine elicitins, seven cysteine rich proteins, seven necrosis inducing proteins and 216 hypothetical proteins with unknown function. Twenty of the 40 RXLR effector candidates were transiently expressed in Nicotiana benthamiana using agroinfiltration and five previously unreported RXLR effector genes (Pc741, Pc8318, Pc10890, Pc20813, and Pc22290) triggered cell death when transiently expressed. The identified cell death inducing RXLR effectors showed 31–66% identity to known RXLR effectors in different Phytophthora species having roles in pathogenicity including both activation and suppression of defense response in the host. Furthermore, homology analysis revealed that these cell death inducing RXLR effectors were highly conserved (82 - 100% identity) across 23 different strains of P. cactorum originating from apple or strawberry.

Application of the Drosophila melanogaster Research Model to Evaluate the Toxicity Levels between Lead and Copper

Applications of the Drosophila melanogaster (D.m.) research model have an important means both for genetic investigations and for the study of metal toxicity, because D.m. has physiological mechanisms comparable to those in human organisms. In this research, the toxic effect of lead (Pb2+) and copper (Cu2+) on four D.m. genotypes—the wild genotype (Oregon-R, used as control) and three mutant genotypes (white, brown, and white-vestigial)—was compared. Five replicates were made to observe the development progress of monitorized genotypes exposed to five different concentrations 0, 0.50, 0.75, 1.00, and 2.00 mM of copper (CuSO4) and lead Pb(C2H3O2)2. Proliferation rates of larvae, pupae, and adults depend on genetic factors, metals used (copper or lead), and their concentrations. The white-vestigial mutant genotype showed the greatest sensitivity at IC50 concentration (inhibition of proliferation of more than 50% compared with the control sample) at doses of 1.00 mM for Cu2+ and 2.00 mM for Pb2+. In contrast, the control genotype (Oregon-R) showed only an inhibition IC50 concentration of 2.00 mM for Cu2+. The white-vestigial mutant genotype showed the greatest sensitivity at IC50 concentration (inhibition of proliferation of more than 50% compared with the control sample) at doses of 1.00 mM for Cu2+ and 2.00 mM for Pb2+. In contrast, the control genotype (Oregon-R) showed an inhibition at the IC50 concentration of 2.00 mM for Cu2+. The results conclude that (i) the dose influences the prolificacy rate in a directly proportional way, (ii) the comparative analyses between Cu2+ and Pb2+ revealed a more acute effect of Cu2+, and (iii) differentiated prolificacy values according to genotypes were recorded. Those reflect the importance of using D.m. as a research model in the comparative studies of the interactions between genetic factors and metal toxicity. Also, this study provides significant information on non-toxic maximum doses for organisms.

Natural selection on feralization genes contributed to the invasive spread of wild pigs throughout the United States.

Despite a long presence in the contiguous United States (US), the distribution of invasive wild pigs (Sus scrofa × domesticus) has expanded rapidly since the 1980s, suggesting a more recent evolutionary shift towards greater invasiveness. Contemporary populations of wild pigs represent exoferal hybrid descendants of domestic pigs and European wild boar, with such hybridization expected to enrich genetic diversity and increase the adaptive potential of populations. Our objective was to characterize how genetic enrichment through hybridization increases the invasiveness of populations by identifying signals of selection and the ancestral origins of selected loci. Our study focused on invasive wild pigs within Great Smoky Mountains National Park, which represents a hybrid population descendent from the admixture of established populations of feral pigs and an introduction of European wild boar to North America. Accordingly, we genotyped 881 wild pigs with multiple high-density single-nucleotide polymorphism (SNP) arrays. We found 233 markers under putative selection spread over 79 regions across 16 out of 18 autosomes, which contained genes involved in traits affecting feralization. Among these, genes were found to be related to skull formation and neurogenesis, with two genes, TYRP1 and TYR, also encoding for crucial melanogenesis enzymes. The most common haplotypes associated with regions under selection for the Great Smoky Mountains population were also common among other populations throughout the region, indicating a key role of putatively selective variants in the fitness of invasive populations. Interestingly, many of these haplotypes were absent among European wild boar reference genotypes, indicating feralization through genetic adaptation.

Sub-microscopic Plasmodium falciparum infections and multiple drug resistant single nucleotide polymorphic alleles in pregnant women from southwestern Nigeria

ObjectivesThe study evaluated sub-microscopic malaria infections in pregnancy using two malaria Rapid Diagnostic Tests (mRDTs), microscopy and RT-PCR and characterized Plasmodium falciparum dihydrofolate reductase (Pfdhfr) and Plasmodium falciparum dihydropteroate synthase (Pfdhps) drug resistant markers in positive samples.MethodsThis was a cross sectional survey of 121 pregnant women. Participants were finger pricked, blood drops were collected for rapid diagnosis with P. falciparum histidine-rich protein 11 rapid diagnostic test kit and the ultra-sensitive Alere Pf malaria RDT, Blood smears for microscopy and dried blood spots on Whatman filter paper for molecular analysis were made. Real time PCR targeting the var acidic terminal sequence (varATS) gene of P. falciparum was carried out on a CFX 96 real time system thermocycler (BioRad) in discriminating malaria infections. For each run, laboratory strain of P. falciparum 3D7 and nuclease free water were used as positive and negative controls respectively. Additionally, High resolution melt analyses was employed for genotyping of the different drug resistance markers.ResultsOut of one hundred and twenty-one pregnant women sampled, the SD Bioline™ Malaria Ag P.f HRP2-based malaria rapid diagnostic test (mRDT) detected eight (0.06%) cases, the ultra-sensitive Alere™ malaria Ag P.f rapid diagnostic test mRDT had similar outcome in the same samples as detected by the HRP2-based mRDT. Microscopy and RT-PCR confirmed four out of the eight infections detected by both rapid diagnostic tests as true positive and RT-PCR further detected three false negative samples by the two mRDTs providing a sub-microscopic malaria prevalence of 3.3%. Single nucleotide polymorphism in Pfdhps gene associated with sulphadoxine resistance revealed the presence of S613 mutant genotypes in three of the seven positive isolates and isolates with mixed wild/mutant genotype at codon A613S. Furthermore, four mixed genotypes at the A581G codon were also recorded while the other Pfdhps codons (A436G, A437G and K540E) showed the presence of wild type alleles. In the Pfdhfr gene, there were mutations in 28.6%, 28.6%, and 85.7% at the I51, R59 and N108 codons respectively. Mixed wild and mutant type genotypes were also observed in 28.6% each of the N51I, and C59R codons. For the Pfcrt, two haplotypes CVMNK and CVIET were observed. The SVMNT was altogether absent. Triple mutant CVIET 1(14.3%) and triple mutant + wild genotype CVIET + CVMNK 1(14.3%) were observed. The Pfmdr1 haplotypes were single mutants YYND 1(14.3%); NFND 1(14.3%) and double mutants YFND 4(57.1%); YYDD 1(14.3%).

Pollen Amount and Viability in Mchare and Selected Wild (AA) Banana (Musa acuminata) Genotypes: Prospects for Breeding

East African diploid cooking bananas, commonly called Mchare, are a staple crop for millions of subsistence farmers in Tanzania, particularly in the Pangani region in northern Tanzania. Several pathogens constrain Mchare production significantly and threaten food security. Sources of resistance to these pathogens have been identified; however, partial male and female sterility impedes successful resistance introgression, complicating the breeding process. Mchare cultivars are also the only known surviving representatives of a diploid banana subgroup that contributed unreduced gametes to many of the most widely grown and successful triploid dessert bananas (‘Cavendish’, ‘Gros-Michel’, ‘Silk’, and ‘Prata’). As such, they represent an essential intermediate step in the conventional improvement of bananas worldwide. We assess the amount and viability of pollen among Mchare and wild genotypes to identify the most fertile Mchare cultivars that can be used in conventional banana improvement. Pollen was collected from 14 banana genotypes for quantification and viability testing over 7 months, and the optimal time for pollen collection was determined to be 0800 HR. Significant variation among banana genotypes in terms of both overall pollen production and percentage of pollen viability was observed. The wild-type bananas ‘Calcutta 4’ [International Musa Germplasm Transit Center (ITC) 0249] and ‘Borneo’ (ITC0253) had the greatest overall pollen production (&gt; 31,000 pollen grains/anther) and viability (∼74%), whereas ‘Ijihu Inkundu’ (ITC1460; Mchare genotype) was the least productive (almost completely sterile), with an average pollen production of a few hundred grains per anther and a viability of 7%. There were significant differences among months in terms of pollen viability, with the greatest average viability observed in May, April, and February (&gt; 51%), and the lowest average pollen viability in July (41%). Significant differences were observed among the Mchare genotypes, with ‘Huti-White’, ‘Huti green bell’ (ITC1559), and ‘Mchare Laini’ consistently producing more substantial amounts of total pollen and an overall more significant proportion of viable pollen. This information is vital to improve Mchare bananas and the global breeding of dessert bananas. The choice of Mchare banana used in improvement programs could affect fertility and the likelihood of breeding success.

Genetic evolution and phylogenetic analysis of porcine epidemic diarrhea virus strains circulating in and outside China with reference to a wild type virulent genotype CHYJ130330 reported from Guangdong Province, China.

During the last decade, porcine epidemic diarrhea virus has detrimental consequences on swine industry, due to severe outbreaks especially in the suckling piglets. In March 2013, an outbreak was reported on a commercial swine farm in Guangdong Province, Southern China. A wild-type PEDV strain named as CHYJ130330 was identified, complete genome was sequenced and deposited in GenBank (accession no. KJ020932). The molecular epidemiological including evolutionary characteristics and pathogenicity assessment were explored during this study with particular interest and focus to develop this candidate strain for new vaccine. The isolates from China pre- and post-2013 shared 96.5-97.2% and 97-99% nt identity respectively with wild-type CHYJ130330 strain which during experimental studies has demonstrated high virulence and 100% mortality in 104 TCID50 group piglets within 5days. The 22 reference strains selected from other parts of the world shared 98-99% identity with our sequence except Chinese (CV777) and S. Korean (vir.DR13, SM98 and atten.DR13) strains sharing 96.8, 97.6, 96.6 and 97.1% identity respectively. The phylogenetic tree revealed most strains reported after 2013 in GII genogroup while the prototype (CV777), S.korean and earlier Chinese (JS2008, 85-7mutant, Atten.vaccine, SD-M, LZC and CH/S) were GI Group. The amino acid sequence of CHYJ130330 E and M protein is highly conserved while ORF3 and N protein having 9 and 17 amino acid substitutions respectively in comparison to CV777 strain. The comparison of full length genome and the structural proteins revealed variations signifying that PEDV variant strains are still the main source of outbreaks in spite of continuous vaccination and also explain the variable trend of large scale outbreaks during this decade as compared to sporadic tendency of disease found before 2010. It is evident from this study that Chinese strains display significant level of mixing with the strains reported from other countries. The strain CHYJ130330 was also adapted successfully to Vero cell line and has shown high virulence in piglets. The information/findings will be helpful to develop a strategy for control of PEDV and have also shown that CHYJ130330 strain has strong virulence and is a more popular clinical strain in recent years, which has the potential to be developed into PEDV vaccine.

Study of the effect of ACYP2 single nucleotide polymorphisms rs843711 and rs843706 in Egyptian patients with hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a multifactorial disease with both genetic and environmental factors contributing to its pathogenesis. ACYP2 is a gene that is related to cell differentiation, apoptosis and prevention of malignant tumors. The ACYP2 gene also affects telomere length. The aim of this study was to evaluate the association between ACYP2 single nucleotide polymorphisms (SNPs) (rs843711), and (rs843706) and incidence of HCC in Egyptian HCC patients. The study included 30 patients with HCC and 30 normal controls. Detection of ACYP2 gene SNPs rs843711, and rs843706 in all study participants was done using real time polymerase chain reaction (RT-PCR). The results showed that all participants including HCC patients and controls carried the heterozygous CA (100%) of the rs843706 SNP (p&gt; 0.05). As for the rs843711, 3.3% of HCC patients had the homozygous TT genotype, 46.7% had the heterozygous CT genotype and 50% had the wild CC genotype, while in the control group, 60% had the heterozygous CT genotype and 40% had the wild CC genotype with no significant difference between both groups (p&gt;0.05). We concluded that there was no association between SNPs ACYP2 rs843706 and rs843711 and occurrence of HCC.

Genetic diversity analysis of banana using SSR markers

Banana, a crucial fruit crop thriving in tropical and sub-tropical regions, facing a notable challenge of elevated sterility across various cultivated banana genotypes. This sterility issue hampers the cultivation of diverse banana varieties. Therefore, a focused endeavour is crucial to thoroughly investigate the richness of diversity within both wild and cultivated banana genotypes, aiming to preserve it for future utilization. In the present study, 21 Musa genotypes were collected from different places of North-Eastern Region, and conserved in the field gene bank at Department of Horticulture, College of Agriculture, Lembucherra, Tripura during 2015-2022. Molecular characterization and DNA fingerprinting of these banana accessions were performed by employing 16 banana SSR markers. The number of alleles per locus ranged from 15 to 24 with an average 20.375. The expected heterozygosity (He) ranged from 0.564-0.967 with a mean of 0.852, and the polymorphic information content (PIC) varies from 0.638–0.945 (mean = 0.859). Genetic diversity analysis showed dissimilar groups, indicating possibility of involvement of different accuminata and balbisiana types in evaluation of banana in NE region. The outcome of the current study will be useful for des igning banana crops against different stresses

Association between vitamin D receptor (APAI rs7975232) genotypes and vitamin D serum levels in Iraqi multiple sclerosis patients

BACKGROUND: Multiple sclerosis (MS) is a long-term condition characterized by chronic inflammation, damage to the myelin sheath, and progressive nerve cell degeneration. It is a heterogeneous and multifactorial disease. The aim of the present investigation was to analyze the connection between variations in the vitamin D receptor gene. (APAI rs7975232) and vitamin D serum levels among MS patients. METHODS: Blood samples were collected from 75 Iraqi patients with MS (33 male, 42 female), and 75 control group volunteers who appeared to be in good health with an age range of 20–50 years. Vitamin D receptor (VDR) gene polymorphism was detected by HRM RT-PCR and vitamin D serum levels were assessed by ELISA. RESULTS: Detection of VDR gene polymorphism in MS patients discovered that the wild genotype was C/C 15 (20%), the heterozygous genotype CA was 27(36%), and the homozygous genotype AA was 33(44%), whilst allele C occurrence was 57(38%) and allele A was 93(62%), compared per control genotype C/C was 40(53.3%), CA genotype was 20(26.6%), AA genotype was 15(20%), C allele frequency was 100(66.6%) and A allele was 50(33.3%) with highly significant difference (P≤0.001). Analysis of vitamin D serum levels showed much higher levels in the control group (43.40±0.85 pg/ml) than in the MS patients group (15.46±0.93 pg/ml; P≤0.001). Result of relationship between Vitamin D serum level with genotype of VDR among individuals with MS was found to be significant decrease (5.3±0.52) at AA genotype of MS patients, followed by (11.79±0.68) in CA genotype and finally (15.52±0.93) in CC genotype, all highly significant (P≤0.01). CONCLUSION: There was a notable correlation observed with VDR (APAI rs7975232) genotypes and Vitamin D serum level in MS Iraqi patients.

Investigation of the morphological, physiological, biochemical, and catabolic characteristics and gene expression under drought stress in tolerant and sensitive genotypes of wild barley [Hordeum vulgare subsp. spontaneum (K. Koch) Asch. & Graebn.

BackgroundBarley (H. vulgare L.) is an important cereal crop cultivated across various climates globally. Barley and its ancestor (H. vulgare subsp. spontaneum) are an economically valuable model for genetic research and improvement. Drought, among various abiotic stresses, is a substantial threat to agriculture due to its unpredictable nature and significant impact on crop yield.ResultsThis study was conducted in both greenhouse and laboratory settings. Prior to the study, wild barley accessions were pre-selected based on their sensitivity or tolerance to drought as determined from fieldwork in the 2020–2021 and 2021–2022 cropping seasons. The effects of three levels of drought stress were evaluated (control, 90–95% field capacity [FC]; mild stress, 50–55% FC; and severe stress, 25–30% FC). Several parameters were assessed, including seedling and root growth, enzymatic activity (CAT, SOD, POD), soluble protein levels, chlorophyll content, carotenoids, abaxial and adaxial stomatal density and dimensions, and relative gene expression of Dhn1, SOD, POD, and CAT. Drought stress significantly increased enzyme activities, especially at 25–30% FC, and more in the tolerant genotype. On the other hand, sensitive genotypes showed a notable increase in stomatal density. Under drought stress, there was a general decline in seedling and root growth, protein content, chlorophyll and carotenoids, and stomatal dimensions. Importantly, gene expression analysis revealed that Dhn1, SOD, POD, and CAT were upregulated under drought, with the highest expression levels observed in the drought-tolerant genotype under severe stress conditions (25–30% FC).ConclusionsOur investigation highlights the distinct morphological, physiological, biochemical, and gene-expression profiles of drought-resistant and drought-sensitive wild barley genotypes under varying degrees of drought.

Abstract 2689: Mass cytometry analysis of CXCR3 expression in tumor-infiltrated myeloid cells as a predictive biomarker For immunotherapy response

Abstract Monocytes have emerged as important regulators of cancer progression. We have recently found that CXCR3+ circulating monocytes in humans are associated with better response to immunotherapy. Here, we aimed to study the functions and heterogeneity of CXCR3+ monocytes in two different triple negative breast cancer (TNBC) tumors in mice, using either AT3 or EO771 tumor cell lines. AT-3 tumors exhibit higher resistance to anti-PD-1 and anti-CTLA-4 therapy in C57BL/6 breast cancer mouse models compared to EO771 tumors. We evaluated 36 surface protein markers on tumor-infiltrated myeloid cells in tumors isolated from each model using CyTOF mass cytometry. Analysis of monocytes, macrophages and dendritic cells in the tumors using unsupervised clustering identified 13 cell subsets. Significant differences were discovered between the two tumor types in frequencies of nine of 13 identified subsets. However, 3 of these subsets displayed relatively high expression of CXCR3 in EO771 tumors when compared to AT-3 tumors. The significant CXCR3 positive subsets were identified as CXCR3+ early macrophages, CXCR3+ Ly6C+CD11blo classical monocytes and Trem2+ CXCR3+ dendritic cells. We observed higher expression of CXCR4, Trem2, and CCR1 in CXCR3+ myeloid cells when compared to their CXCR3− counterparts in both tumor models. To elucidate the role of these CXCR3+ cells, we performed low-input bulk RNA sequencing of CD115+/CD11b+ cells from blood and spleen of EO771 tumor bearing mice with a wild type or CXCR3KO genotype. Ingenuity Pathway Analysis (IPA) of the differentially expressed genes suggests a significant inhibition of the IL-10 signaling pathway of CXCR3KO cells. These differentially expressed markers and genes suggest a functional importance in this subset in migration to the tumor and antigen presentation, both of which are anti-tumoral functions. Ongoing studies are aimed towards understanding the role of CXCR3+ myeloid cells in regulating response to immunotherapies. Citation Format: Gabriel A. Valentin-Guillama, Nandini Chatterjee, Ahmad Alimadadi, Catherine C. Hedrick. Mass cytometry analysis of CXCR3 expression in tumor-infiltrated myeloid cells as a predictive biomarker For immunotherapy response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2689.

The Difference in Shoot Metabolite Profiles of a Wild and a Cultivated Barley Genotype in Response to Four Nitrogen Forms

Plants can utilize different N forms, including organic and inorganic N resources, and show great differences in the utilization efficiency of each N form among species and genotypes within a species. Previously, we found that the Tibetan wild barley genotype (XZ16) was better in the utilization of organic nitrogen in comparison with the cultivated barley genotype (Hua30). In this study, the metabolite profiles of the two barley genotypes were comprehensively compared in their response to four N forms, including nitrate (NO3−), ammonium (NH4+), urea, and glycine. The macro and micro nutrient concentrations in shoots were mostly found to be higher in the nitrate and urea treatments than in ammonium and glycine in both the genotypes. XZ16 had higher concentrations of nutrient ions in the glycine treatment, but Hua30 accumulated more nutrients in the ammonium treatment. Among a total of 163 differentially regulated metabolites, the highest up-regulation and highest down-regulation values were found in XZ16 in the glycine and urea treatments, respectively. Some important metabolites, such as proline, glutamine, serine, asparagine, L-homoserine, aspartic acid, putrescine, ornithine, and 4-aminobutyrate, were up-regulated in the glycine treatment in both the genotypes with a higher fold change in XZ16 than that in Hua30. Similarly, fructose-6-PO4, aconitic acid, and isocitrate were only up-regulated in XZ16 in the glycine treatment. Here, we concluded that the genotype XZ16 exhibited a better response to the glycine treatment, while Hua30 showed a better response to the NH4+ treatment, which is attributed to the better utilization of glycine-N and NH4+-N, respectively.

Early skin inflammatory biomarker is predictive of development and persistence of atopic dermatitis in infants

BackgroundThe STOP AD study, a randomized, open-label trial evaluating the effect of short-term (first four postnatal days to 8 weeks) skin barrier protection using AVEENO® Dermexa Fast & Long-Lasting Balm in infants with a parent with allergic disease, demonstrated decreased cumulative incidence and decreased prevalence of AD at 12 months of age. ObjectiveWe aimed to identify skin biomarkers in the STOP AD study that are associated with risk of development of AD. MethodsSkin swabs were collected from the cheek and antecubital fossa (AF) at baseline, 8 weeks, and 12 months from subsets of study participants from each of the intervention arm (43 of 119) and control arm (43 of 138) and were analyzed for specific cytokines (CCL27, CXCL2, hBD1, IL18, IL8, IL1α, IL1RA, IL1β, S100A8/9, IL36γ) by ELISA. ResultsHigher titers of S100A8/9 at the AF at 8 weeks in infants with filaggrin wild type genotype (FLGwt), but not in those with filaggrin loss-of-function mutations (FLGmut), predicted: 1) Development of AD in the first year of life (p=0.033); 2) Presence of AD at 6 months or 12 months of age (p=0.009 and 0.035, respectively); 3) Persistence of AD between 6 and 12 months of age (p<0.001); 4) Development of AD with the emollient intervention. ConclusionIncreased titers of S100A8/9 from skin swabs of the AF in high-risk infants at 8 weeks with FLGwt was predictive of AD developing in the first year of life and of other AD features. These findings suggest that there are different molecular pathways leading to AD in FLGmut individuals and in FLGwt individuals. Early identification of infants who are likely to develop AD will allow more targeted interventions.

Comparative analysis of 326 chloroplast genomes in Chinese jujube (Ziziphus jujuba): Structural variations, horizontal gene transfer events, and evolutionary patterns impacting its domestication from wild jujube

AbstractJujube (Ziziphus jujuba Mill.), renowned for its nutritional value and health benefits, is believed to have originated in the middle and lower reaches of the Yellow River in China, where it underwent domestication from wild jujube. Nonetheless, the evolutionary trajectory and species differentiation between wild jujube and cultivated jujube still require further elucidation. The chloroplast genome (plastome), characterized by its relatively lower mutation rate compared to the nuclear genome, serves as an excellent model for evolutionary and comparative genomic research. In this study, we analyzed 326 nonredundant plastomes, encompassing 133 jujube cultivars and 193 wild jujube genotypes distributed throughout China. Noteworthy variations in the large single copy region primarily account for the size differences among these plastomes, impacting the evolution from wild jujube to cultivated varieties. Horizontal gene transfer (HGT) unveiled a unique chloroplast‐to‐nucleus transfer event, with transferred fragments predominantly influencing the evolution of the nuclear genome while leaving the plastome relatively unaffected. Population genetics analysis revealed two distinct evolutionary pathways from wild jujube to cultivated jujube: one driven by natural selection with minimal human interference, and the other resulting from human domestication and cultivation. Molecular dating, based on phylogenetic analysis, supported the likelihood that wild jujube and cultivated jujube fall within the same taxonomic category, Z. jujuba. In summary, our study comprehensively examined jujube plastome structures and HGT events, simultaneously contributing novel insights into the intricate processes that govern the evolution and domestication of jujube species.

Introgressed eggplant lines with the wild Solanum incanum evaluated under drought stress conditions1

As access to irrigation water becomes increasingly limited, introgression of relevant genomic regions from drought-tolerant wild genotypes is a promising breeding strategy for crop plants. In this study, nine eggplant (Solanum melongena) introgression lines (ILs) covering altogether 71.6% of the genome of the donor wild relative parent S. incanum were evaluated for drought tolerance under water stress conditions. Plants at the five true leaves stage were irrigated at either 100% (control) or 30% (water stress) field capacity for 14 days, and growth and biochemical traits were measured. Reduced irrigation resulted in decreased growth and increased levels of stress markers such as proline and malondialdehyde. Most ILs had lower growth and biomass production than the cultivated parent under both conditions. However, the wild alleles for two genomic regions related to stem and root dry weight (dwt8 and dwr6%) conferred improved tolerance to water stress. In addition, several S. incanum alleles had a positive effect on important traits that may improve yield under drought conditions, such as leaf water content (lwc12%), water use efficiency (wue1%) and chlorophyll content (chl2 and chl8%). Fine-mapping of the genomic regions for tolerance and reducing linkage drag with regions affecting growth will be crucial for significantly improving eggplant drought tolerance through introgression breeding.

Glutathione S-transferase M1, T1, and P1 polymorphisms and periodontitis in a Caucasian population: a case-control study

BackgroundGlutathione S-transferases (GSTs) play important roles in protecting cells against oxidative stress and toxic chemicals. This study aimed to investigate the distribution of GSTM1, GSTT1, and GSTP1 variants and their roles in periodontitis susceptibility in a Caucasian population.MethodsWe analyzed 406 participants, including 204 healthy controls and 203 periodontitis patients. A multiplex polymerase chain reaction (PCR) approach was used to analyze GSTM1 and GSTT1 loci. GSTP1 variants were detected by PCR-haplotyping method in a subgroup of participants (N = 350). Chi-square or Fisher´s exact tests were used to compare genotypic and allelic differences. The Bonferroni method was applied to correct for multiple comparisons (pcorr).ResultsThe GSTM1 genotype distribution did not differ significantly between controls and periodontitis patients (p = 0.44). Additionally, the wild/null genotypes of GSTT1, Ile105Val and Ala114Val frequencies of GSTP1 were not significantly different between the two groups after correction for multiple comparisons (p = 0.05, p = 0.55, p = 0.02, pcorr>0.05, respectively). The GSTM1 and GSTP1 Ile105Val gene variants were similarly distributed between non-smokers and smokers in both groups (p = 0.38, p = 0.20, and p = 0.14, p = 0.35, respectively). However, the wild genotype of the GSTT1 and Ala114Ala variant of the GSTP1 genes were present more frequently in non-smoking periodontitis patients than in non-smoking controls (p = 0.03, pcorr>0.05, and p = 0.009, pcorr>0.05, respectively) although their frequencies did not differ between smoking periodontitis patients and smoking controls (p = 0.23, p = 0.68, respectively).ConclusionsThis study in a Czech Caucasian population did not confirm a highly significant association between GST gene variants and susceptibility to periodontitis, as previously reported by Arshad and colleagues in Pakistanis. However, a weak relationship between GSTT1 and GSTP1 rs1138272 polymorphisms and periodontitis in non-smokers was observed.

Relationship of calcium-sensing receptor gene polymorphism CASR rs 1042636, CASR rs 1802757, and cinacalcet response among Egyptian hemodialysis patients with secondary hyperparathyroidism

Introduction: Secondary hyperparathyroidism (SHPT) is a common complication associated with morbidity and mortality among hemodialysis (HD) patients. Objectives: The current study aims to evaluate the frequency of CASR gene polymorphism variants related to parathyroid hormone (PTH) regulation (CASR rs1042636 and CASR rs1802757) and to test the hypothesis that single nucleotide polymorphisms (SNPs) in the CASR gene alter the response to cinacalcet among Egyptian HD patients with SHPT. Patients and Methods: A case-control study that included 50 HD patients with intact parathyroid hormone (iPTH) ≥300 pg/mL treated with cinacalcet for a 6-month duration and 40 healthy volunteers as a control group. Eligible patients were recruited from Ain Shams university hospitals. Blood samples were collected from patients and controls to assess allele frequencies of CASR gene polymorphism variants using real-time polymerase chain reaction (PCR), corrected calcium (Ca), phosphorus (P), Ca×P product, iPTH level, and alkaline phosphatase before and after treatment. HD patients were categorized into two groups based on the reduction percentage; responders’ patients (iPTH ≥20%) and non-responders to cinacalcet treatment. Results: Of 50 HD patients, 48 (96%) carried the rs1042636 AA wild gene, while only two (4%) carried the rs1042636 AG mutant gene, 42 (87.5%) carried the rs1802757 CC wild genotype, and 6 (12.5%) carried the CT mutant genotype. The minor alleles T and G were (6.3% and 2%) respectively, with no statistically significant difference between the patient and control groups regarding the CASR genotypes or alleles distribution. There was no significant difference between responders and non-responder’s patient groups regarding CASR genotypes or allele frequencies. Moreover, no significant correlation between CASR genotypes or alleles to delta change of Ca, P, Ca×P product, or PTH was seen. However, CASR rs1802757 CT mutant genotype was associated with a significant reduction in alkaline phosphatase levels after treatment. Conclusion: There is no significant association between the gene polymorphism CASR rs1042636 or CASR rs1802757 and the reduction in PTH levels as a response to cinacalcet treatment among Egyptian HD patients with SHPT.