Evidence for metabolite composition underlying consumer preference in Sub-Saharan African Musa spp

Breeding programs for disease resistant bananas in Sub-Saharan Africa generated resistant bananas, which did not meet fruit quality characteristics preferred by consumers. The present study aimed to establish chemotypes underlying preferred cooking bananas of Matooke, Mchare and plantain and less preferred Mbidde bananas, used for beer brewing. The metabolite data of Mbidde showed higher levels of metabolites associated with sour, sweet, and astringent taste; as well as different textural properties associated with cell wall composition and lignin content. Significant differences in the majority of specialised and primary metabolites were observed in the pulp of cooking banana groups. Analysis of peel tissue indicated similar metabolic differences in the protective layer surrounding the pulp and suggested a distinct genetic regulation of phenylpropanoid and flavonoid pathways between the genome groups. In summary, the present data can be used to establish metabolic traits associated with consumer preference, which can augment modern breeding programs.

Phase variation modulates the multi-phenotypes displayed by clinical Campylobacter jejuni strains

The high incidence and prevalence of Campylobacter spp. in the food supply chain entail the importance to understand their mechanisms developed to withstand harsh environmental conditions encountered. Different stress conditions and phenotypic approaches were evaluated to study the behaviour of five clinical C. jejuni isolates with different genotypes, including the tolerance to oxygen and the oxidants hydrogen peroxide and cumene hydroperoxide, the motility and the ability to form biofilm on polystyrene and stainless steel at different temperatures and atmospheres. Whole Genome Sequencing was performed to analyse the occurrence of 216 genes involved in these mechanisms plus phase variation. The isolates showed high tolerance to oxygen and peroxide stress with different swimming motility performances and biofilm formation abilities. Aerotolerance was related with a reduced sensitive to peroxide stress and a loss of motility that promotes biofilm formation depending on the material surface. Comparative genomics did not reveal any clear gene pattern, although phase variation occurring during host infection was observed to be crucial for the modulation of the different survival mechanisms adopted by the bacteria. These findings reveal that the bacteria can combine diverse and complex strategies in an efficient manner to survive and persist in the environment.

Phenotypes of Primary Sclerosing Cholangitis and Differential Diagnosis

Primary sclerosing cholangitis is a heterogenous immune-mediated disorder characterized by chronic inflammation and stricturing of the bile ducts. Though the driving pathophysiologic mechanisms remain elusive, there are several observed clinical phenotypes of the disease. The distribution of bile duct involvement, presence of concomitant inflammatory bowel disease, significant infiltration of IgG4-positive plasma cells, and overlapping features with other autoimmune disease has significant implications for prognosis and treatment. As there remains no pathognomonic finding for primary sclerosing cholangitis, a broad differential diagnosis and extensive evaluation of other underlying causes is critical to appropriate management.

Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles

The CRISPR-Cas9 system is a powerful tool for studying gene functions and holds potential for disease treatment. However, precise genome editing requires thorough assessments to minimize unintended on- and off-target effects. Here, we report an unexpected 283-kb deletion on Chromosome 10 (10q23.31) in chronic myelogenous leukemia-derived HAP1 cells, which are frequently used in CRISPR screens. The deleted region encodes regulatory genes, including PAPSS2, ATAD1, KLLN, and PTEN We found that this deletion was not a direct consequence of CRISPR-Cas9 off-targeting but rather occurred frequently during the generation of CRISPR-Cas9-modified cells. The deletion was associated with global changes in histone acetylation and gene expression, affecting fundamental cellular processes such as cell cycle and DNA replication. We detected this deletion in cancer patient genomes. As in HAP1 cells, the deletion contributed to similar gene expression patterns among cancer patients despite interindividual differences. Our findings suggest that the unintended deletion of 10q23.31 can confound CRISPR-Cas9 studies and underscore the importance to assess unintended genomic changes in CRISPR-Cas9-modified cells, which could impact cancer research.

Escitalopram population pharmacokinetics and remedial strategies based on CYP2C19 phenotype

BACKGROUND AND PURPOSE

CYP2C19 is a key factor influencing escitalopram (SCIT) exposure. However, different studies reported various results. This study aims to develop a population pharmacokinetic (popPK) model characterizes the disposition of SCIT in the Chinese population. Based on the popPK model, the study simulates non-adherence scenarios and proposes remedial strategies to facilitate SCIT personalized therapy.

METHODS

Nonlinear mixed-effects modeling using data from two Chinese bioequivalence studies was employed. Monte-Carlo simulation was used to explore non-adherence scenarios and propose remedial strategies based on the proportion of time within the therapeutic window.

RESULTS

Results showed that a one-compartment model with transit absorption and linear elimination described the data well, CYP2C19 phenotypes and weight were identified as significant covariates impacting SCIT exposure. Patients were recommended to take the entire delayed dose immediately if the delay time was no >12 h, followed by the regular regimen at the next scheduled time. When there is one or two doses missed, taking a double dose immediately was recommended to the CYP2C19 intermediate and extensive population, and a 1.5-fold dose was recommended to the CYP2C19 poor metabolizers with the consideration of adverse effects.

LIMITATION

All samples were derived from the homogenized Chinese healthy population for model building, which may pose certain constraints on the ability to identify significant covariates, such as age.

CONCLUSION

The study highlights the importance of considering patient characteristics for personalized medication and offers a unique perspective on utilizing the popPK repository in precision dosing.

Combined deficient response to polysaccharide-based and protein-based vaccines predicts a severe clinical phenotype

OBJECTIVES

Antibody response on polysaccharide- and protein-based vaccines is useful to test B cell functionality. As only few studies have explored the value of studying immune response to both vaccines, we evaluated the clinical value of anti-polysaccharide and anti-protein Luminex-based multiplex assays in context of primary immunodeficiency (PID) diagnosis.

METHODS

A 10-plex Luminex-based assay detecting antibodies to ten pneumococcal polysaccharide (PnPS) serotypes [present in unconjugated Pneumovax, not in 13-valent pneumococcal conjugated vaccine (PCV)] and a 5-plex assay detecting antibodies to five protein antigens (present in DTap/Tdap) were clinically validated in healthy individuals (n=99) and in retrospective (n=399) and prospective (n=108) patient cohorts. Clinical features of individuals with impaired response to PnPS and/or proteins were compared to those with normal response.

RESULTS

Antigen-specific antibody thresholds were determined in healthy individuals. Individuals with impaired anti-PnPS responses and deficient immunoglobulin levels suffered more from autoimmune diseases and had lower B cell levels compared to individuals with impaired anti-PnPS response with normal immunoglobulin levels. Individuals with combined impaired response to PnPS and proteins showed more severe clinical manifestations compared to individuals with isolated impaired response to PnPS or proteins. Eight of the 11 individuals with severely impaired responses to both PnPS and proteins had common variable immunodeficiency. Evaluation of the anti-PnPS response to four serotypes not contained in 20-valent PCV was comparable to evaluation to ten serotypes not contained in 13-valent PCV.

CONCLUSIONS

Multiplexed assessment of anti-PnPS and anti-protein responses combined with immunoglobulin quantification provides useful clinical information to support PID diagnosis.

Multidrug resistance phenotype and its relation to stem cell characteristics in chronic myeloid leukemia

The present work aimed to evaluate the expression profile of genes related to stem cells (SC) characteristics during the acquisition of the multidrug resistance (MDR) phenotype in the chronic myeloid leukemia (CML). For this, the K562 (non MDR) and FEPS (MDR) cell lines were used. K562 cells had resistance induced by exposure to daunorubicin (DNR), and induction was confirmed by flow cytometry with an increase in ABCB1 expression in K562 cells treated at the highest concentration. Real-time PCR gene expression analysis showed a direct relationship in the expression of OCT4 and ABCB1 genes, with an increase in ABCB1 expression after exposure to DNR, followed by an increase in OCT4 gene expression. This direct relationship was confirmed in the MDR FEPS cells that had the ABCB1 gene silenced. For the ALOX5 gene, we observed an inverse relationship with ABCB1, with a decrease in the expression of ALOX5 in the DNR-transformed K562 cells, and an increase in the expression of this gene when ABCB1 was silenced in the FEPS cells. Thus, during the acquisition of the MDR phenotype by the K562 cells, it was possible to observe that there is an increase in the expression of ABCB1, accompanied by the expression of OCT4, while the expression of ALOX5 is decreased.

The effects of different immunocastration protocols on meat quality traits and boar taint compounds in male Bísaro pigs

Immunocastration can be an alternative to surgical castration in Bísaro pigs when there is a need to keep animals on the farm until at least 8 months old. As an autochthonous breed, some particularities must be addressed when doing immunocastration, for which 3 different protocols were tested and two control groups were made with surgically castrated males (SC) and boars (Bo). Two protocols were made in prepubertal pigs, with two (E2) and three inoculations (L3) in the first cycle, and another in adults (A2) with only two inoculations. Physicochemical parameters and boar taint compounds quantification and sensory analysis of the meat from the studied pigs were assessed. Immunocastration provided intermediate values between surgically castrated pigs and entire males, with low levels of boar taint compounds. The L3 group provided closer results to SC, which was also corroborated by the sensory analysis. Although the other two protocols had no significant differences with Bo, there was a positive tendency towards them. As is, the L3 protocol was promising as a good alternative to surgical castration, maintaining the characteristic attributes of the Bísaro pig meat.

Tracking the EMT-like phenotype switching during targeted therapy in melanoma by analyzing extracellular vesicle phenotypes

Melanoma continues to be a leading cause of mortality among skin cancers. Despite advancements in targeted therapy, patients frequently develop resistance, leading to disease progression within a year. This resistance may result from the epithelial-to-mesenchymal transition (EMT)-like phenotype switching of melanoma cells. Tracking EMT-related phenotypic changes on extracellular vesicles (EVs) has potential to inform early about response to targeted therapy and melanoma progression. However, the knowledge on protein biomarkers carried by melanoma EVs involved in the EMT-like process remains unexplored. Herein, we present a biosensor integrating surface-enhanced Raman scattering and alternating current electrohydrodynamics-induced nanomixing enhancement, for sensitive detection of EMT-associated biomarkers on EV surfaces during targeted therapy. This biosensor successfully tracks the EMT-like phenotype switching in melanoma cell lines treated with mitogen-activated protein kinase inhibitor (MAPKi). Longitudinal monitoring of patients who receive MAPKi therapy and develop resistance, our biosensor shows its ability to identify the EMT-like phenotype switching on circulating EVs. This ability potentially can be leveraged to predict the development of resistance to targeted therapy, allowing for timely intervention and personalized treatment strategies.

Depression-like phenotypes in mice with hepatic ischemia/reperfusion injury: A role of gut-microbiota-liver-brain axis via vagus nerve

Depression is a frequent symptom in patients with chronic liver disease; however, the mechanisms underlying this association remain unclear. Dysbiosis of gut microbiota plays a critical role in depression through the gut-brain axis via the vagus nerve. In this study, we investigated whether the gut-microbiota-liver-brain axis plays a role in depression-like phenotypes in mice with hepatic ischemia/reperfusion (HI/R) injury via the vagus nerve. Behavioral tests for depression-like behaviors were performed 7 days after sham or HI/R injury surgery. Mice with HI/R injury exhibited splenomegaly, systemic inflammation, depression-like behaviors, reduced expression of synaptic proteins in the prefrontal cortex (PFC), abnormal composition of gut microbiota, and altered blood metabolites and lipids. Furthermore, there were positive or negative correlations between the relative abundance of microbiome and behavioral data or blood metabolites (or lipids). Moreover, subdiaphragmatic vagotomy significantly blocked these changes in mice with HI/R injury. Notably, depression-like phenotypes in mice with HI/R injury were ameliorated after subsequent single injection of the new antidepressant arketamine. The current findings suggest that HI/R injury induces depression-like phenotypes in mice through the gut-microbiota-liver-brain axis via the subdiaphragmatic vagus nerve. Furthermore, arketamine may have therapeutic potential in the treatment of depression in patients with chronic liver disease.

Tristetraprolin regulates the skeletal phenotype and osteoclastogenic potential through monocytic myeloid-derived suppressor cells

Tristetraprolin (TTP; also known as NUP475, GOS24, or TIS11), encoded by Zfp36, is an RNA-binding protein that regulates target gene expression by promoting mRNA decay and preventing translation. Although previous studies have indicated that TTP deficiency is associated with systemic inflammation and a catabolic-like skeletal phenotype, the mechanistic underpinnings remain unclear. Here, using both TTP-deficient (TTPKO) and myeloid-specific TTPKO (cTTPKO) mice, we reveal that global absence or loss of TTP in the myeloid compartment results in a reduced bone microarchitecture, whereas gain-of-function TTP knock-in (TTPKI) mice exhibit no significant loss of bone microarchitecture. Flow cytometry analysis revealed a significant immunosuppressive immune cell phenotype with increased monocytic myeloid-derived suppressor cells (M-MDSCs) in TTPKO and cTTPKO mice, whereas no significant changes were observed in TTPKI mice. Single-cell transcriptomic analyses of bone marrow myeloid progenitor cell populations indicated a dramatic increase in early MDSC marker genes for both cTTPKO and TTPKO bone marrow populations. Consistent with these phenotypic and transcriptomic data, in vitro osteoclastogenesis analysis of bone marrow M-MDSCs from cTTPKO and TTPKO displayed enhanced osteoclast differentiation and functional capacity. Focused transcriptomic analyses of differentiated M-MDSCs showed increased osteoclast-specific transcription factors and cell fusion gene expression. Finally, functional data showed that M-MDSCs from TTP loss-of-function mice were capable of osteoclastogenesis and bone resorption in a context-dependent manner. Collectively, these findings indicate that TTP plays a central role in regulating osteoclastogenesis through multiple mechanisms, including induction of M-MDSCs that appear to regulate skeletal phenotype.

A combination of proteomics, genetics, and physiology provides insights into the acid-tolerance phenotype of Pseudomonas pergaminensis F77

Acid tolerance is crucial for the effective and persistent mineral weathering by acid-producing bacteria. Here, the molecular basis of the acid tolerance of mineral-weathering Pseudomonas pergaminensis F77 was identified using proteomics analysis of the strain under acid stress. Then, the acid tolerance of strain F77 and its mutants with deletion of the acid tolerance-related genes orf03767, mcp, resR, nueR, yegD, and fxsA, which are involved in the two-component systems, DNA repair, nucleotide binding, and membrane parts, were compared. Finally, the acid tolerance-related physiological mechanisms of strain F77 and its mutants F77ΔnueR and F77ΔresR under acidic conditions were characterized. The significantly upregulated proteins in the acid-adapted and acid-challenged strain F77 included the proteins involved in metabolic pathways associated with ATPase, membrane components, organic acid transmembrane transporters, response to stimulus, nucleotide binding, ABC transporters, and two-component systems. The cell numbers decreased by 24-100% at pH ≤ 4.50, while the membrane fluidity increased by 22-61% at pH ≤ 5.50 for the mutants F77ΔnueR and F77ΔresR, compared with that of strain F77. The intracellular H+-ATPase activities decreased by 29-33% for the mutant F77ΔnueR at pH ≤ 4.50% and 33-79% for the mutant F77ΔresR at all tested pHs (pH ≤ 7.00); meanwhile, the ratios of intracellular NAD+/NADH decreased by 71-91% for the mutant F77ΔresR at all tested pHs (pH ≤ 7.00), compared with that of strain F77. Furthermore, the intracellular putrescine concentrations were reduced by 40-70% for the mutant F77ΔresR at all tested pHs (pH ≤ 7.00) compared with that of strain F77. Our findings suggested that multiple proteins and metabolic pathways were associated with bacterial acid tolerance and revealed that nueR and resR were involved in acid tolerance based on their modulation of multiple acid tolerance-related physiological functions in strain F77.

Performance and robustness analysis reveals phenotypic trade-offs in yeast

To design strains that can function efficiently in complex industrial settings, it is crucial to consider their robustness, that is, the stability of their performance when faced with perturbations. In the present study, we cultivated 24 Saccharomyces cerevisiae strains under conditions that simulated perturbations encountered during lignocellulosic bioethanol production, and assessed the performance and robustness of multiple phenotypes simultaneously. The observed negative correlations confirmed a trade-off between performance and robustness of ethanol yield, biomass yield, and cell dry weight. Conversely, the specific growth rate performance positively correlated with the robustness, presumably because of evolutionary selection for robust, fast-growing cells. The Ethanol Red strain exhibited both high performance and robustness, making it a good candidate for bioproduction in the tested perturbation space. Our results experimentally map the robustness-performance trade-offs, previously demonstrated mainly by single-phenotype and computational studies.

Genetic parameter estimates for sensory and meat quality traits measured at 3 and 29 days of aging of beef from Canadian crossbred cattle

Genetic parameters were estimated for objective and subjective traits assessed after 3 and 29 days aging in meat samples of 1154 commercial beef cattle. Meat attributes [Warner-Bratzler shear force (WBSF), intramuscular fat (IMF), and pH] and sensory traits [flavor intensity (FI), off-flavor (OF), connective tissue (CT), overall tenderness (OT), sustained juiciness (SJ), and overall palatability (OP)] were available. The animal mixed model used included additive genetic and residual effects as random effects, contemporary group as fixed effect and genomic breed composition and slaughter age as covariates. Genetic parameters were estimated using airemlf90 software and single-step genomic BLUP. Heritability estimates for OT (3 and 29 d), OP (3 d) and OF (29 d) were of moderate magnitude ranging from 0.18 ± 0.07 to 0.31 ± 0.07. Heritabilities were negligible or of low magnitude for all other sensory traits with values ranging from 0.03 ± 0.05 to 0.14 ± 0.07. Among objectively measured traits, the estimate of heritability for meat pH was moderate at day 3 (0.20 ± 0.08) and negligible at 29 (0.00 ± 0.05). For IMF and WBSF the heritability estimates were 0.43 ± 0.09 and 0.54 ± 0.09, and 0.22 ± 0.07 and 0.19 ± 0.07 for day 3 and 29, respectively. Genetic correlations between days for each sensory trait tended to be of high and positive magnitude ranging from 0.54 ± 0.60 to 0.99 ± 0.28. Genetic and phenotypic correlations of subjectively assessed traits were consistent in direction and magnitude with WBSF (negative) and IMF (positive) suggesting that genetic selection based on objectively measured traits can be used for meat quality improvement and to increase consumer satisfaction. In addition, selection can be implemented using sensory traits collected after 3 days of aging.

The sacroiliac joint: An original and highly sensitive tool to highlight altered bone phenotype in murine models of skeletal disorders

Bone disorders may affect the skeleton in different ways, some bones being very impaired and others less severely. In translational studies using murine models of human skeletal diseases, the bone phenotype is mainly evaluated at the distal femur or proximal tibia. The sacroiliac joint (SIJ), which connects the spine to the pelvis, is involved in the balanced transfer of mechanical energy from the lumbar spine to the lower extremities. Because of its role in biomechanical stress, the SIJ is a region of particular interest in various bone diseases. Here we aimed to characterize the SIJ in several murine models to develop a highly reliable tool for studying skeletal disorders. We performed a 12-month in vivo micro-computed tomography (micro-CT) follow-up to characterize the SIJ in wild-type (WT) C57BL/J6 mice and compared the bone microarchitecture of the SIJ and the distal femur at 3 months by micro-CT and histology. To test the sensitivity of our methodology, the SIJ and distal femur were evaluated at 3 and 6 months, in 2 murine models of skeletal disorder, X-linked hypophosphatemia (Hyp mice) and HLA-B27 transgenic mice and compared to WT mice. A multimodal analysis was performed, using a combination of microCT and histological analysis. With the Hyp model, the SIJ displayed more bone microarchitecture alterations than the distal femur. Hyp mice showed a significant reduction in trabecular bone at both the distal femur and sacral slope as compared with WT mice, with a significant positive correlation between trabecular bone parameters of the distal femur and sacral side of the SIJ. Furthermore, trabecular bone parameters (Bone Volume/Total Volume (BV/TV), trabecular thickness (Tb.Th), trabecular separation (Tb.Sp), trabecular number (Tb.N), trabecular pattern factor (Tb.Pf)) were significantly increased compared to femoral parameters at the SIJ. The sacral articular cortical bone, which is indicative of osteoarticular lesions, was altered in Hyp mice. Interestingly, in accordance to previous studies, HLA-B27 transgenic mice did not show any osteoarticular lesions as compared with WT mice. Cortical bone parameters (thickness, porosity), as well as scoring performed with double blinding, did not show difference between the 2 genotypes. The characterization and evaluation of the SIJ surface appears very sensitive to emphasize alterations of bone and joint. The SIJ may represent a valuable tool to investigate both bone and local osteoarticular alterations in murine models of skeletal disorders and might be a relevant site for assessing the response to treatment of chronic bone diseases.