Impact of thermosonication on kiwi juice quality

Traditional heat treatments such as pasteurization are usually used in fruit juice preservation. However, due to undesirable quality changes, industries seek other processing technologies that can retain the fruit juices' quality. This study aims to develop a high quality and safe-to-drink kiwi (Actinidia deliciosa cv. Hayward) juice throughout the application of thermosonication treatments (TS). Listeria innocua (a surrogate of the pathogenic L. monocytogenes) was used as a safety indicator. pH, SSC, colour, cloud value, total phenolics, total chlorophylls, and minerals were evaluated as quality parameters. TS was carried out with an ultrasound homogenizer at a constant frequency of 20 kHz, 80% amplitude and discontinued pulsation (10s on, 5s off). The juice samples were submitted to TS at 45, 50 and 55°C for 15, 10 and 3 minutes, respectively. Thermal treatments (HT) were performed at the same temperatures for 60, 25 and 10 minutes. Juices' quality and safety were evaluated before and after treatments. All the treatments fulfil the FDA recommendation of 5-log microbial reduction. Most of the quality parameters were retained after both processes. These results proved that a mild heat process could be applied to fruit juices, allowing the obtention of a safe and improved final product's quality.info:eu-repo/semantics/publishedVersio

Application of ultrasound treatments in the processing and production of high-quality and safe-to-drink kiwi juice

This study explores the potential of thermosonication as an alternative to traditional heat treatments, such as pasteurization, in the processing of fruit juices. Conventional methods often lead to undesirable quality changes in fruit juices, whereas thermosonication offers promising results regarding microbial inactivation and quality preservation. This work focused on the inactivation kinetics of Listeria innocua 2030c, a surrogate for pathogenic L. monocytogenes, in kiwifruit juice using thermosonication at 45 °C, 50 °C, and 55 °C. These treatments were compared with equivalent heat treatments. Quality attributes of the juice were also evaluated to assess process efficiency. Survival data of L. innocua were fitted with the Weibull model, estimating first decimal reduction times (δ) and shape parameters (n). The results reveal temperature and process dependencies on δ, while n remains mostly temperature and treatment independent. Thermosonication outperforms heat treatment, achieving higher L. innocua reductions while retaining quality attributes like pH, soluble solid content, and total phenolics and chlorophylls. Thermosonication at 55 °C stands out, providing a 6.2-log-cycle reduction in just 3 min with superior quality retention. These findings highlight the synergistic effect of temperature and ultrasound, making mild heat processes feasible while enhancing product quality. Thermosonication, particularly at 55 °C, emerges as an effective alternative to traditional thermal treatments for fruit juices, offering improved microbial safety without compromising product quality.info:eu-repo/semantics/publishedVersio

Impact of thermosonication on kiwi juice quality

Traditional heat treatments such as pasteurization are usually used in fruit juice preservation. However, due to undesirable quality changes, industries seek other processing technologies that can retain the fruit juices' quality. This study aims to develop a high quality and safe-to-drink kiwi (Actinidia deliciosa cv. Hayward) juice throughout the application of thermosonication treatments (TS). Listeria innocua (a surrogate of the pathogenic L. monocytogenes) was used as a safety indicator. pH, SSC, colour, cloud value, total phenolics, total chlorophylls, and minerals were evaluated as quality parameters. TS was carried out with an ultrasound homogenizer at a constant frequency of 20 kHz, 80% amplitude and discontinued pulsation (10s on, 5s off). The juice samples were submitted to TS at 45, 50 and 55°C for 15, 10 and 3 minutes, respectively. Thermal treatments (HT) were performed at the same temperatures for 60, 25 and 10 minutes. Juices' quality and safety were evaluated before and after treatments. All the treatments fulfil the FDA recommendation of 5-log microbial reduction. Most of the quality parameters were retained after both processes. These results proved that a mild heat process could be applied to fruit juices, allowing the obtention of a safe and improved final product's quality.info:eu-repo/semantics/publishedVersio

Limited Lifespan of Fragile Regions in Mammalian Evolution

An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of fragile regions in mammalian genomes, the most comprehensive phylogenomic study of mammals (Ma et al. (2006) Genome Research 16, 1557-1565) raised some doubts about their existence. We demonstrate that fragile regions are subject to a "birth and death" process, implying that fragility has limited evolutionary lifespan. This finding implies that fragile regions migrate to different locations in different mammals, explaining why there exist only a few chromosomal breakpoints shared between different lineages. The birth and death of fragile regions phenomenon reinforces the hypothesis that rearrangements are promoted by matching segmental duplications and suggests putative locations of the currently active fragile regions in the human genome

GKAP Acts as a Genetic Modulator of NMDAR Signaling to Govern Invasive Tumor Growth.

Genetic linkage analysis previously suggested that GKAP, a scaffold protein of the N-methyl-D-aspartate receptor (NMDAR), was a potential modifier of invasion in a mouse model of pancreatic neuroendocrine tumor (PanNET). Here, we establish that GKAP governs invasive growth and treatment response to NMDAR inhibitors of PanNET via its pivotal role in regulating NMDAR pathway activity. Combining genetic knockdown of GKAP and pharmacological inhibition of NMDAR, we implicate as downstream effectors FMRP and HSF1, which along with GKAP demonstrably support invasiveness of PanNET and pancreatic ductal adenocarcinoma cancer cells. Furthermore, we distilled genome-wide expression profiles orchestrated by the NMDAR-GKAP signaling axis, identifying transcriptome signatures in tumors with low/inhibited NMDAR activity that significantly associate with favorable patient prognosis in several cancer types

Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma

Genetically engineered mouse models (GEMMs) of cancer are increasingly being used to assess putative driver mutations identified by large-scale sequencing of human cancer genomes. To accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole-exome sequencing of tumors from three GEMMs of lung adenocarcinoma driven by mutant epidermal growth factor receptor (EGFR), mutant Kirsten rat sarcoma viral oncogene homolog (Kras), or overexpression of MYC proto-oncogene. Tumors from EGFR- and Kras-driven models exhibited, respectively, 0.02 and 0.07 nonsynonymous mutations per megabase, a dramatically lower average mutational frequency than observed in human lung adenocarcinomas. Tumors from models driven by strong cancer drivers (mutant EGFR and Kras) harbored few mutations in known cancer genes, whereas tumors driven by MYC, a weaker initiating oncogene in the murine lung, acquired recurrent clonal oncogenic Kras mutations. In addition, although EGFR- and Kras-driven models both exhibited recurrent whole-chromosome DNA copy number alterations, the specific chromosomes altered by gain or loss were different in each model. These data demonstrate that GEMM tumors exhibit relatively simple somatic genotypes compared with human cancers of a similar type, making these autochthonous model systems useful for additive engineering approaches to assess the potential of novel mutations on tumorigenesis, cancer progression, and drug sensitivity

PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes

Developmental and lineage plasticity have been observed in numerous malignancies and have been correlated with tumor progression and drug resistance. However, little is known about the molecular mechanisms that enable such plasticity to occur. Here, we describe the function of the plant homeodomain finger protein 6 (PHF6) in leukemia and define its role in regulating chromatin accessibility to lineage-specific transcription factors. We show that loss of Phf6 in B-cell leukemia results in systematic changes in gene expression via alteration of the chromatin landscape at the transcriptional start sites of B-cell- and T-cell-specific factors. Additionally, Phf6KO cells show significant down-regulation of genes involved in the development and function of normal B cells, show up-regulation of genes involved in T-cell signaling, and give rise to mixed-lineage lymphoma in vivo. Engagement of divergent transcriptional programs results in phenotypic plasticity that leads to altered disease presentation in vivo, tolerance of aberrant oncogenic signaling, and differential sensitivity to frontline and targeted therapies. These findings suggest that active maintenance of a precise chromatin landscape is essential for sustaining proper leukemia cell identity and that loss of a single factor (PHF6) can cause focal changes in chromatin accessibility and nucleosome positioning that render cells susceptible to lineage transition.National Cancer Institute ; F31-CA183405 - National Institutes of Health ; 1122374 - National Science Foundation ; Ludwig Center for Molecular Oncology at Massachusetts Institute of Technology ; Koch Institute ; Dana-Farber/Harvard Cancer Center ; P30-CA14051 - Koch Institute ; NCI ; NIH ; National Science Foundatio

A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes

The reconstruction of ancestral genome architectures and gene orders from homologies between extant species is a long-standing problem, considered by both cytogeneticists and bioinformaticians. A comparison of the two approaches was recently investigated and discussed in a series of papers, sometimes with diverging points of view regarding the performance of these two approaches. We describe a general methodological framework for reconstructing ancestral genome segments from conserved syntenies in extant genomes. We show that this problem, from a computational point of view, is naturally related to physical mapping of chromosomes and benefits from using combinatorial tools developed in this scope. We develop this framework into a new reconstruction method considering conserved gene clusters with similar gene content, mimicking principles used in most cytogenetic studies, although on a different kind of data. We implement and apply it to datasets of mammalian genomes. We perform intensive theoretical and experimental comparisons with other bioinformatics methods for ancestral genome segments reconstruction. We show that the method that we propose is stable and reliable: it gives convergent results using several kinds of data at different levels of resolution, and all predicted ancestral regions are well supported. The results come eventually very close to cytogenetics studies. It suggests that the comparison of methods for ancestral genome reconstruction should include the algorithmic aspects of the methods as well as the disciplinary differences in data aquisition

Arm-specific dynamics of chromosome evolution in malaria mosquitoes

<p>Abstract</p> <p>Background</p> <p>The malaria mosquito species of subgenus <it>Cellia </it>have rich inversion polymorphisms that correlate with environmental variables. Polymorphic inversions tend to cluster on the chromosomal arms 2R and 2L but not on X, 3R and 3L in <it>Anopheles gambiae </it>and homologous arms in other species. However, it is unknown whether polymorphic inversions on homologous chromosomal arms of distantly related species from subgenus <it>Cellia </it>nonrandomly share similar sets of genes. It is also unclear if the evolutionary breakage of inversion-poor chromosomal arms is under constraints.</p> <p>Results</p> <p>To gain a better understanding of the arm-specific differences in the rates of genome rearrangements, we compared gene orders and established syntenic relationships among <it>Anopheles gambiae, Anopheles funestus</it>, and <it>Anopheles stephensi</it>. We provided evidence that polymorphic inversions on the 2R arms in these three species nonrandomly captured similar sets of genes. This nonrandom distribution of genes was not only a result of preservation of ancestral gene order but also an outcome of extensive reshuffling of gene orders that created new combinations of homologous genes within independently originated polymorphic inversions. The statistical analysis of distribution of conserved gene orders demonstrated that the autosomal arms differ in their tolerance to generating evolutionary breakpoints. The fastest evolving 2R autosomal arm was enriched with gene blocks conserved between only a pair of species. In contrast, all identified syntenic blocks were preserved on the slowly evolving 3R arm of <it>An. gambiae </it>and on the homologous arms of <it>An. funestus </it>and <it>An. stephensi</it>.</p> <p>Conclusions</p> <p>Our results suggest that natural selection favors specific gene combinations within polymorphic inversions when distant species are exposed to similar environmental pressures. This knowledge could be useful for the discovery of genes responsible for an association of inversion polymorphisms with phenotypic variations in multiple species. Our data support the chromosomal arm specificity in rates of gene order disruption during mosquito evolution. We conclude that the distribution of breakpoint regions is evolutionary conserved on slowly evolving arms and tends to be lineage-specific on rapidly evolving arms.</p