Search Results (42)

The standard immunosuppressive treatments in heart transplantation are calcineurin inhibitors, corticosteroids, and antimetabolite agents or inhibitors of the mammalian target of rapamycin. Pharmacogenetic studies show the impact on clinical course of genetic variability in genes that encode transporters, metabolizers, or molecular targets of immunosuppressants. The aim of this systematic review is to elucidate the role that pharmacogenetics of immunosuppressant drugs plays in clinical outcomes upon heart transplantation. PubMed, EMBASE, the Cochrane Central Register, and the Database of Abstracts of Reviews of Effects were searched without restrictions. The 64 studies analyzed followed these criteria: (1) were based on clinical data on heart transplantation patients; (2) analyzed the associations between polymorphisms and clinical response; (3) analyzed the impact of polymorphisms on immunosuppressant safety. CYP3A4/5 variants were associated with higher doses of tacrolimus, whereas POR*28 variants with lower doses—ABCB1, ABCC2, SLCO1B1, and SLC13A1—contribute to interindividual variability in drug absorption, distribution, and toxicity. An ABCC2 polymorphism (rs717620) was related to higher risk of graft rejection in pediatrics. Variations in HLA-G, TNF-α and TGF-β genes influence transplant rejection risk and immune response. Implementing pharmacogenetic screening of polymorphisms could enhance therapeutic outcomes by improving drug efficacy, reducing toxicity, and ultimately increasing heart graft survival rates. Strong evidence supports genotyping for CYP3A5 and TPMT, but further research is required for transporter genes and cytokine polymorphisms. Full article

Background: Neisseria meningitidis (N. meningitidis) is a leading cause of acute meningitis and is classified into 13 serogroups, six of which are predominantly associated with invasive meningococcal disease. This study aimed to investigate the genotype, subgenotype, and antigenic profiles of N. meningitidis serogroup B strains isolated in Vietnam. Methods: Genotyping was performed on 106 N. meningitidis strains isolated from clinical samples from Vietnamese patients and nasopharyngeal swabs of healthy adolescents between 2019 and 2024. The genetic profiles, including the porA, porB, fetA, fHbp, abcZ, adk, aroE, fumC, gdh, pdhC, and pgm genes, were analyzed using Sanger sequencing and bioinformatic methods. Results: We found that 84.9% of the strains carried VR3 families 36 or 35-1, with VR1, VR2, and VR3 families 22-25, 14, and 36 being the most prevalent. Among the 106 serogroup B isolates, 20 variants of the porB allele 3 were identified, with porB 3-1212 being the most frequent (30.2%). Dominant PorB variable loops included L1.6, L4.5, L5.7, L6.6, and L7.13. fHbp variant group 2 was predominant (104/106 strains), and 12 FetA allele variants were identified, with F1-7 being the most common (47.2%). Three clonal complexes were identified, and clonal complex ST-32 was the most predominant. Fifty-five strains (51.9%) belonged to sequence types that have not yet been assigned to any clonal complexes, and 15 strains (14.1%) with allelic profiles were not assigned to STs. The 3-253 and 3-1212 alleles of porB, the F1-7 variant of FetA, the ST-44 and ST-1576 sequence types, and the ST-41/44 complex were observed more frequently in patients compared to asymptomatic carriers, suggesting their association with more virulence. Conclusions: This study showed a high genetic and antigenic diversity of N. meningitidis serogroup B isolates in Vietnam, with VR3 family 36 most common and porB 3-1212 as the predominant allele. fHbp variant group 2 and FetA allele F1-7 were most frequent. ST-32 was the dominant clonal complex, though many strains remained unassigned, highlighting the need for ongoing molecular surveillance. Full article

Campylobacter spp. are the causative agents of campylobacteriosis, a major foodborne illness globally, with millions of cases reported annually. These pathogens pose significant risks to both human and animal health. Conventional culture-based diagnostic methods are labor-intensive and time-consuming, underscoring the need for more efficient molecular detection strategies. This study employed a pangenomic analysis to identify novel gene-specific markers for pathogenic Campylobacter species and subspecies, laying the groundwork for their application in diverse diagnostic assays. A curated dataset of 105 high-quality genomes, representing 33 species and 9 subspecies, was analyzed using the Roary ILP Bacterial Annotation Pipeline. The results revealed substantial genomic diversity within the genus, with core gene counts varying across different nucleotide identity thresholds. Ribosomal genes such as rpsL, rpsJ, rpsS, rpmA, rpsK, rpsU, rpsG, rpmH, and rpsZ were consistently identified in the core genome, whereas accessory genes exhibited marked variability. This study uncovered novel and highly specific genetic markers for various Campylobacter species, including petB, clpX, and carB for C. coli; hypothetical proteins for C. jejuni and C. fetus; porA2 for C. lari; and mdtJ for C. upsaliensis. These markers demonstrated a specificity of at least 90% with minimal cross-reactivity with non-target organisms. The findings underscore the genomic heterogeneity within Campylobacter and provide essential genetic targets for the enhanced molecular detection of its pathogenic species, subspecies, and biovars. Full article

The availability of yeast surface display nanobody (Nb) libraries offers a convenient way to acquire antigen-specific nanobodies that may be useful for protein structure–function studies and/or therapeutic applications, complementary to the conventional method of acquiring nanobodies through immunization in camelids. In this study, we developed a general approach to select nanobodies for cytochrome P450 enzymes from a highly diverse yeast display library. We tested our method on three P450 enzymes including CYP102A1, neuronal nitric oxide synthase (nNOS), and the complex of CYP2B4:POR, using a novel streamlined approach where biotinylated P450s were bound to fluorescent-labeled streptavidin for Nb screening. The Nb–antigen binders were selectively enriched using magnetic-activated cell sorting (MACS) and fluorescence-activated cell sorting (FACS). After two rounds of MACS, the population of positive binders was enriched by >5-fold compared to the naïve library. The subsequent FACS selection, with a gating of 0.1%, identified 634, 270, and 215 positive binders for CYP102A1, nNOS, and CYP2B4:POR, respectively. The positive binders for CYP102A1 were further triaged based on EC₅₀ determined at various antigen concentrations. DNA sequencing of the top 30 binders of CYP102A1 resulted in 26 unique clones, 8 of which were selected for over-expression and characterization. They were found to inhibit CYP102A1-catalyzed oxidation of omeprazole with IC₅₀ values in the range of 0.16–2.8 µM. These results validate our approach and may be applied to other protein targets for the effective selection of specific nanobodies. Full article

Chlamydia trachomatis (Ct) is the most common cause of bacterial sexually transmitted infections (STIs) worldwide. Ct infections are often asymptomatic in women, leading to severe reproductive tract sequelae. Development of a vaccine against Chlamydia is crucial. The Chlamydia major outer membrane protein (MOMP) is a prime vaccine antigen candidate, and it can elicit both neutralizing antibodies and protective CD4+ T cell responses. We have previously designed chimeric antigens composed of immunogenic variable regions (VDs) and conserved regions (CDs) of MOMP from Chlamydia muridarum (Cm) expressed into a carrier protein (PorB), and we have shown that these were protective in a mouse model of Cm respiratory infection. Here, we generated corresponding constructs based on MOMP from Ct serovar F. Preliminary structure analysis of the three antigens, PorB/VD1-3, PorB/VD1-4 and PorB/VD1-2-4, showed that they retained structure features consistent with those of PorB. The antigens induced robust humoral and cellular responses in mice with different genetic backgrounds. The antibodies were cross-reactive against Ct, but only anti-PorB/VD1-4 and anti-PorB/VD1-2-4 IgG antibodies were neutralizing, likely due to the antigen specificity. The cellular responses included proliferation in vitro and production of IFN-γ by splenocytes following Ct re-stimulation. Our results support further investigation of the PorB/VD antigens as potential protective candidates for a Chlamydia subunit vaccine. Full article

The eradication of Helicobacter pylori is a valid strategy for preventing gastric cancer; however, the therapeutic failure of first-line treatments in Colombia is associated with high resistance to metronidazole and amoxicillin. This study explored alternative antibiotics and analyzed point mutations in resistance genes to furazolidone and rifampicin in order to include them in rescue therapy regimens. A total of 239 complete genomes of Helicobacter pylori Colombian strains were compared to that of the ATCC 26695 strain to identify mutations in the rpoB and porD genes for rifampicin and furazolidinone resistance, respectively. While rifampicin resistance mutations were not found, only 0.84% of the isolates showed the porD gene, suggesting that Helicobacter pylori is sensitive to these antibiotics. A phylogenomic analysis of Helicobacter pylori revealed an independent lineage in Colombia (hspColombia). The absence of point mutations in the rpoB gene, together with the scarce mutations identified in the porD gene of Helicobacter pylori, suggest that the hspColombia isolates are sensitive to rifampicin and furazolidone, which could be key to including these antibiotics in the rescue therapies against Helicobacter pylori. Full article

The GLK gene family plays a crucial role in the regulation of chloroplast development and participates in chlorophyll synthesis. However, the precise mechanism by which GLK contributes to citrus’s chlorophyll synthesis remains elusive. The GLK gene family causes variations in the photosynthetic capacity and chlorophyll synthesis of different citrus varieties. In this study, we identified tissue-specific members and the key CcGLKs involved in chlorophyll synthesis. A total of thirty CcGLK transcription factors (TFs) were discovered in the citrus genome, distributed across all nine chromosomes. The low occurrence of gene tandem duplication events and intronic variability suggests that intronic variation may be the primary mode of evolution for CcGLK TFs. Tissue-specific expression patterns were observed for various GLK family members; for instance, CcGLK12 and CcGLK15 were specifically expressed in the skin, while CcGLK30 was specific to the ovary, and CcGLK10, CcGLK6, CcGLK21, CcGLK2, CcGLK18, CcGLK9, CcGLK28, and CcGLK8 were specifically expressed in the leaves. CcGLK4, CcGLK5, CcGLK11, CcGLK23, CcGLKl7, CcGLK26, and CcGLK20 may participate in the regulation of the ALA, prochlorophylate, protoporphyrin IX, Mg-protoporphyrin IX, Chl b, T-Chl, MG-ProtoIX ME, and POR contents in citrus. Full article

The therapeutic management of Crohn’s disease (CD), a chronic relapsing–remitting inflammatory bowel disease (IBD), is highly challenging. Surgical resection is sometimes a necessary procedure even though it is often associated with postoperative recurrences (PORs). Tofacitinib, an orally active small molecule Janus kinase inhibitor, is an anti-inflammatory drug meant to limit PORs in CD. Whereas bidirectional interactions between the gut microbiota and the relevant IBD drug are crucial, little is known about the impact of tofacitinib on the gut microbiota. The HLA-B27 transgenic rat is a good preclinical model used in IBD research, including for PORs after ileocecal resection (ICR). In the present study, we used shotgun metagenomics to first delineate the baseline composition and determinants of the fecal microbiome of HLA-B27 rats and then to evaluate the distinct impact of either tofacitinib treatment, ileocecal resection or the cumulative effect of both interventions on the gut microbiota in these HLA-B27 rats. The results confirmed that the microbiome of the HLA-B27 rats was fairly different from their wild-type littermates. We demonstrated here that oral treatment with tofacitinib does not affect the gut microbial composition of HLA-B27 rats. Of note, we showed that ICR induced an intense loss of bacterial diversity together with dramatic changes in taxa relative abundances. However, the oral treatment with tofacitinib neither modified the alpha-diversity nor exacerbated significant modifications in bacterial taxa induced by ICR. Collectively, these preclinical data are rather favorable for the use of tofacitinib in combination with ICR to address Crohn’s disease management when considering microbiota. Full article

The Direction of Arrival (DOA) estimation of coherent signals in co-prime arrays has become a popular research topic. However, traditional spatial smoothing and subspace algorithms fail to perform well under low signal-to-noise ratio (SNR) and small snapshots. To address this issue, we have introduced an Enhanced Spatial Smoothing (ESS) algorithm that utilizes a space-time correlation matrix for de-noising and decoherence. Finally, an Estimating Signal Parameter via Rotational Invariance Techniques (ESPRIT) algorithm is used for DOA estimation. In comparison to other decoherence methods, when the SNR is −8 dB and the number of snapshots is 150, the mean square error (MSE) of the proposed algorithm approaches the Cramér–Rao bound (CRB), the probability of resolution (PoR) can reach over 88%, and, when the angular resolution is greater than $4°$, the estimation accuracy can reach over 90%. Full article

Chlorophyll is an indispensable photoreceptor in plant photosynthesis. Its anabolic imbalance is detrimental to individual growth and development. As an essential epigenetic modification, DNA methylation can induce phenotypic variations, such as leaf color transformation, by regulating gene expression. Albino line XN1376B is a natural mutation of winter wheat cultivar XN1376; however, the regulatory mechanism of its albinism is still unclear. In this study, we found that low temperatures induced albinism in XN1376B. The number of chloroplasts decreased as the phenomenon of bleaching intensified and the fence tissue and sponge tissue slowly dissolved. We identified six distinct TaPOR (protochlorophyllide oxidoreductase) genes in the wheat genome, and TaPOR2D was deemed to be related to the phenomenon of albinism based on the expression in different color leaves (green leaves, white leaves and returned green leaves) and the analysis of promoters’ cis-acting elements. TaPOR2D was localized to chloroplasts. TaPOR2D overexpression (TaPOR2D-OE) enhanced the chlorophyll significantly in Arabidopsis, especially at two weeks; the amount of chlorophyll was 6.46 mg/L higher than in WT. The methylation rate of the TaPOR2D promoter in low-temperature albino leaves is as high as 93%, whereas there was no methylation in green leaves. Correspondingly, three DNA methyltransferase genes (TaMET1, TaDRM and TaCMT) were up-regulated in white leaves. Our study clarified that the expression of TaPOR2D is associated with its promoter methylation at a low temperature; it affects the level of chlorophyll accumulation, which probably causes the abnormal development of plant chloroplasts in albino wheat XN1376B. The results provide a theoretical basis for in-depth analysis of the regulation of development of plant chloroplasts and color variation in wheat XN1376B leaves. Full article

Cadmium (Cd) is a pervasive, toxic environmental pollutant that preferentially accumulates in the tubular epithelium of the kidney. Current evidence suggests that the cumulative burden of Cd here leads to the progressive loss of the glomerular filtration rate (GFR). In this study, we have quantified changes in estimated GFR (eGFR) and albumin excretion (E_alb) according to the levels of blood Cd ([Cd]_b) and excretion of Cd (E_Cd) after adjustment for confounders. E_Cd and E_alb were normalized to creatinine clearance (C_cr) as E_Cd/C_cr and E_alb/C_cr. Among 482 residents of Cd-polluted and non-polluted regions of Thailand, 8.1% had low eGFR and 16.9% had albuminuria (E_alb/C_cr) × 100 ≥ 20 mg/L filtrate. In the low Cd burden group, (E_Cd/C_cr) × 100 < 1.44 µg/L filtrate, eGFR did not correlate with E_Cd/C_cr (β = 0.007) while an inverse association with E_Cd/C_cr was found in the medium (β = −0.230) and high burden groups (β = −0.349). Prevalence odds ratios (POR) for low eGFR were increased in the medium (POR 8.26) and high Cd burden groups (POR 3.64). Also, eGFR explained a significant proportion of E_alb/C_cr variation among those with middle (η² 0.093) and high [Cd]_b tertiles (η² 0.132) but did not with low tertiles (η² 0.001). With an adjustment of eGFR, age and BMI, the POR values for albuminuria were increased in the middle (POR 2.36) and high [Cd]_b tertiles (POR 2.74) and those with diabetes (POR 6.02) and hypertension (2.05). These data indicate that (E_Cd/C_cr) × 100 of 1.44 µg/L filtrate (0.01–0.02 µg/g creatinine) may serve as a Cd threshold level based on which protective exposure guidelines should be formulated. Full article

Salt stress disrupts cellular ion homeostasis and adversely impacts plant growth and productivity. We examined the regulatory mechanisms of porphyrin biosynthesis, photoprotection, and antioxidant properties in salt-stressed rice seedlings. In response to 150 mM NaCl, the rice seedlings exhibited dehydration, reduced relative water content, and increased levels of conductivity, malondialdehyde, and H₂O₂. The expression levels of the salt-stress-responsive genes NHX1, SOS1, and MYB drastically increased after NaCl treatment. The seedlings grown under NaCl stress displayed declines in F_v/F_m, Φ_PSII, rETR_max, and photochemical quenching but increases in nonphotochemical quenching (NPQ) and the expression of genes involved in zeaxanthin formation, BCH, and VDE. Under salt stress conditions, levels of chlorophyll precursors significantly decreased compared to controls, matching the downregulation of CHLD, CHLH, CHLI, and PORB. By contrast, NaCl treatment led to increased heme content at 24 h of treatment and significant upregulations of FC2, HO1, and HO2 compared to controls. Salt-stressed seedlings also increased their expression of CATs (catalases) and APXs (ascorbate peroxidases) as well as the activities of superoxide dismutase, CAT, APX, and peroxidase. Our results indicate that chlorophyll and heme biosynthesis involve the protective strategies for salt stress alleviation through photoprotection by the scavenging of chlorophyll precursors and NPQ as well as activating antioxidant enzymes. Full article

Tacrolimus (TAC) is a narrow-therapeutic-range immunosuppressant drug used after organ transplantation. A therapeutic failure is possible if drug levels are not within the therapeutic range after the first year of treatment. Pharmacogenetic variants and drug–drug interactions (DDIs) are involved. We describe a patient case of a young man (16 years old) with a renal transplant receiving therapy including TAC, mycophenolic acid (MFA), prednisone and omeprazole for prophylaxis of gastric and duodenal ulceration. The patient showed great fluctuation in TAC blood concentration/oral dose ratio, as well as pharmacotherapy adverse effects (AEs) and frequent diarrhea episodes. Additionally, decreased kidney function was found. A pharmacotherapeutic follow-up, including pharmacogenetic analysis, was carried out. The selection of the genes studied was based on the previous literature (CYP3A5, CYP3A4, POR, ABCB1, PXR and CYP2C19). A drug interaction with omeprazole was reported and the nephrologist switched to rabeprazole. A lower TAC concentration/dose ratio was achieved, and the patient’s condition improved. In addition, the TTT haplotype of ATP Binding Cassette Subfamily B member 1 (ABCB1) and Pregnane X Receptor (PXR) gene variants seemed to affect TAC pharmacotherapy in the studied patient and could explain the occurrence of long-term adverse effects post-transplantation. These findings suggest that polymorphic variants and co-treatments must be considered in order to achieve the effectiveness of the immunosuppressive therapy with TAC, especially when polymedicated patients are involved. Moreover, pharmacogenetics could influence the drug concentration at the cellular level, both in lymphocyte and in renal tissue, and should be explored in future studies. Full article

The physiological state of overwintering tea leaves is crucial for the growth and quality formation of spring tea shoots. Low temperatures in winter can easily cause damage to overwintering tea plants, leading to leaf chlorosis and abnormal physiological functions. Many pieces of research have shown that shading could promote chlorophyll (Chl) accumulation in tea leaves, but the impact on overwintering tea plants is not yet known. In this study, different shading rates (no-shading, S0%; 30% shading, S30%; 75% shading, S75%) were used to treat overwintering tea plants, which explored the effect of shading on the color and physiological functions of tea leaves. The results showed that Chl, carotenoid, and soluble sugar (SS) contents were S75% > S30% > S0%, and the net photosynthetic rate (Pn) was S75% > S30% > S0%. Transcriptome analysis showed that the genes involved in chlorophyll and carotenoid metabolism (such as protochlorophyllide reductase POR and zeaxanthin epoxidase ZEP) and photosynthesis (such as photosystem II P680 reaction center D2 protein PsbA and photosystem II CP47 chlorophyll apoprotein PsbB) were significantly up-regulated under shading. In addition, many differentially expressed genes (DEGs) were enriched in “starch and sucrose metabolism (ko00500)” and “anthocyanin biosynthesis (ko00942)” pathways. In summary, this study provided a theoretical basis and technical support for maintaining green leaves and normal physiological functions of overwintering tea plants. Full article

Radish (Raphanus sativus) plants exhibit varied root colors due to the accumulation of chlorophylls and anthocyanins compounds that are beneficial for both human health and visual quality. The mechanisms of chlorophyll biosynthesis have been extensively studied in foliar tissues but remain largely unknown in other tissues. In this study, we examined the role of NADPH:protochlorophyllide oxidoreductases (PORs), which are key enzymes in chlorophyll biosynthesis, in radish roots. The transcript level of RsPORB was abundantly expressed in green roots and positively correlated with chlorophyll content in radish roots. Sequences of the RsPORB coding region were identical between white (948) and green (847) radish breeding lines. Additionally, virus-induced gene silencing assay with RsPORB exhibited reduced chlorophyll contents, verifying that RsPORB is a functional enzyme for chlorophyll biosynthesis. Sequence comparison of RsPORB promoters from white and green radishes showed several insertions and deletions (InDels) and single-nucleotide polymorphisms. Promoter activation assays using radish root protoplasts verified that InDels of the RsPORB promoter contribute to its expression level. These results suggested that RsPORB is one of the key genes underlying chlorophyll biosynthesis and green coloration in non-foliar tissues, such as roots. Full article