Acoustic resonances in microfluidic chips: full-image micro-PIV experiments and numerical simulations

We show that full-image micro-PIV analysis in combination with images of transient particle motion is a powerful tool for experimental studies of acoustic radiation forces and acoustic streaming in microfluidic chambers under piezo-actuation in the MHz range. The measured steady-state motion of both large 5 um and small 1 um particles can be understood in terms of the acoustic eigenmodes or standing ultra-sound waves in the given experimental microsystems. This interpretation is supported by numerical solutions of the corresponding acoustic wave equation.Comment: RevTex, 10 pages, 9 eps figures; NOTE first authors changed his name to S. Melker Hagsater in the published versio

Insights on fungal solid-state fermentation for waste valorization : conidia and chitinase production in different reactor configurations

Altres ajuts: Acord transformatiu CRUE-CSICAltres ajuts: Arnau Sala also thanks Universitat Aut'onoma de Barcelona for a predoctoral scholarship.Different reactor configurations are paired with a wide variety of agro-industrial wastes of different biodegradability to produce fungal conidia by solid-state fermentation. This work presents a preliminary comparative study between packed-bed and tray reactor configurations to produce Beauveria bassiana and Trichoderma harzianum conidia using two different substrates in terms of biodegradability: rice husk or beer draff complemented with wood chips. Conidia production, mean temperature and respiration indexes have been analysed in most of the presented reactor configurations. Both strains showed higher conidia production when using beer draff complemented with wood chips as substrate due to the use of a mixture as substrate. When working with beer draff, chitinase analyses obtained similar profiles in both strains but higher overall values using TH. Conidia and chitinase production maximums were not achieved at the same time, having 2-3 days of difference depending on the strain. No significant differences in mean temperature were shown between most of the performed fermentations. As a result of the present work, further scaling of both packed bed and tray configurations using beer draff and wood chips to produce BB or TH conidia would be advisable. More experiments should be performed to optimize both conidia and chitinase productions to enhance the quality of the final product

Thermochromic poly(L-lactic acid) based materials and their printability on different substrates

Portuguese Foundation for Science and Technology (FCT):, Portugal UID/FIS/04650/2020, UID/QUI/00686/2020, NORTE-01-0145-FEDER-000084. Spanish State Research Agency (AEI), Spain and European Regional Development Fund (ERFD): PID2019-106099RB-C43/AEI/10.13039/501100011033. Basque Government Industry Department, Spain, under the ELKARTEK program. This study forms part of the Advanced Materials program and was supported by MCIN, Spain with funding from European Union NextGenerationEU (PRTR-C17.I1) and by the Basque Government under the IKUR program. Publisher Copyright: © 2024 The AuthorsIonic liquids (ILs) have been combined with different polymer matrixes to develop smart and functional materials. Due to their versatility, hybrid materials with specific tailor made properties can be obtained, including printable thermochromic materials, with a strong potential for sensing applications. In this context, the thermochromic IL bis(1-butyl-3-methylimidazolium) tetrachloronickelate ([Bmim]2[NiCl4]) was incorporated into a biopolymer derived matrix, poly(L-lactic acid) (PLLA) in distinct concentrations up to 40% wt. aiming to develop environmentally friendly screen-printable printable thermochromic materials. The addition of IL does not induce changes on the thermal properties of the material. On the other hand, the incorporation of the IL leads to the development of a porous structure in the films, a mechanical plasticizing effect in the polymer matrix, revealed by the decrease of the Young's Modulus from 1110 ± 66 MPa to 572 ± 41 MPa and a increase in the electrical conductivity from 2.89x10-14 S·cm−1 to 2.66x10-8 S·cm−1, for PLLA and the samples with 40 % wt. of IL, respectively. Finally, the thermochromic material was screen-printed on various substrates, including paper, polyethylene terephthalate (PET), textile and wood, opening the way for a wide range of applications.publishersversionpublishe

CDKN2A deletion is a frequent event associated with poor outcome in patients with peripheral T-cell lymphoma not otherwise specified (PTCL-NOS)

Nodal peripheral T-cell lymphoma not otherwise specified (PTCL-NOS) remains a diagnosis encompassing a heterogenous group of PTCL cases not fitting criteria for more homogeneous subtypes. They are characterized by a poor clinical outcome when treated with anthracycline-containing regimens. A better understanding of their biology could improve prognostic stratification and foster the development of novel therapeutic approaches. Recent targeted and whole exome sequencing studies have shown recurrent copy number abnormalities (CNAs) with prognostic significance. Here, investigating 5 formalin-fixed, paraffin embedded cases of PTCL-NOS by whole genome sequencing (WGS), we found a high prevalence of structural variants and complex events, such as chromothripsis likely responsible for the observed CNAs. Among them, CDKN2A and PTEN deletions emerged as the most frequent aberration, as confirmed in a final cohort of 143 patients with nodal PTCL. The incidence of CDKN2A and PTEN deletions among PTCL-NOS was 46% and 26%, respectively. Furthermore, we found that co-occurrence of CDKN2A and PTEN deletions is an event associated with PTCL-NOS with absolute specificity. In contrast, these deletions were rare and never co-occurred in angioimmunoblastic and anaplastic lymphomas. CDKN2A deletion was associated with shorter overall survival in multivariate analysis corrected by age, IPI, transplant eligibility and GATA3 expression (adjusted HR =2.53; 95% CI 1.006-6.3; p=0.048). These data suggest that CDKN2A deletions may be relevant for refining the prognosis of PTCL-NOS and their significance should be evaluated in prospective trials

Heterogeneity of genomic evolution and mutational profiles in multiple myeloma.

Multiple myeloma is an incurable plasma cell malignancy with a complex and incompletely understood molecular pathogenesis. Here we use whole-exome sequencing, copy-number profiling and cytogenetics to analyse 84 myeloma samples. Most cases have a complex subclonal structure and show clusters of subclonal variants, including subclonal driver mutations. Serial sampling reveals diverse patterns of clonal evolution, including linear evolution, differential clonal response and branching evolution. Diverse processes contribute to the mutational repertoire, including kataegis and somatic hypermutation, and their relative contribution changes over time. We find heterogeneity of mutational spectrum across samples, with few recurrent genes. We identify new candidate genes, including truncations of SP140, LTB, ROBO1 and clustered missense mutations in EGR1. The myeloma genome is heterogeneous across the cohort, and exhibits diversity in clonal admixture and in dynamics of evolution, which may impact prognostic stratification, therapeutic approaches and assessment of disease response to treatment

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.

About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 38 histological cancer subtypes within the framework of the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. We identified 19,166 somatically acquired retrotransposition events, which affected 35% of samples and spanned a range of event types. Long interspersed nuclear element (LINE-1; L1 hereafter) insertions emerged as the first most frequent type of somatic structural variation in esophageal adenocarcinoma, and the second most frequent in head-and-neck and colorectal cancers. Aberrant L1 integrations can delete megabase-scale regions of a chromosome, which sometimes leads to the removal of tumor-suppressor genes, and can induce complex translocations and large-scale duplications. Somatic retrotranspositions can also initiate breakage-fusion-bridge cycles, leading to high-level amplification of oncogenes. These observations illuminate a relevant role of L1 retrotransposition in remodeling the cancer genome, with potential implications for the development of human tumors

Genetic Diversity in Wheat: Analysis using Diversity Arrays Technology (DArT) in bread and durum wheats

With increasing demands on the quality and quantity of food required now and in the future, improvements to current agriculture practices are required. Increased food production requires utilisation of more agricultural land, pushing crops into non- traditional areas. The need for advances in agricultural technologies are not only required for current crop varieties, but for new varieties with increased tolerance to environmental stresses. Technological improvement means better crop yields and reduced land, water, fertilizer and pesticide use. Diversity Arrays Technology (DArT) was used to study wheat diversity, specifically to identify polymorphic markers between various wheat cultivars for use in marker- assisted breeding programs. The hybridisation based technology was used to analyse various bread and durum wheat cultivars for increased understanding of genomic diversity. Analysis shows that DArT is able to discriminate between tissue samples from wheat cultivars grown under various environmental stresses with polymorphic markers identified between samples treated with differing salt, light and temperature conditions. Epigenetic diversity was analysed through methylation detection using DArT to identify a list of candidate polymorphic markers. Markers were identified using the methylation sensitive restriction enzyme McrBC to generate control and treated targets. Diversity through cultivar exploration, looking at breeding experiments between cultivars with phenotypic extremes to examine salt tolerance versus in-tolerance using DArT produced a recombinant inbred line genetic linkage map. Bulk segregant analysis was also used to group phenotypic samples. Candidate markers were identified between cultivars that can be used to genotyping tetraploid and hexaploid wheat cultivars for germplasm identification. In addition, the identification of trait-linked molecular markers, such as salt resistance, plant breeders can genotype individual plants and populations of cultivars to determine the most suitable cultivar to plant that best complements to its local environment. This eliminates the need for multiple planting cycles to optimize crop selections, and gives the plant breeder the highest possible chance for crop success (yield, quality, performance and cost)

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 38 histological cancer subtypes within the framework of the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. We identified 19,166 somatically acquired retrotransposition events, which affected 35% of samples and spanned a range of event types. Long interspersed nuclear element (LINE-1; L1 hereafter) insertions emerged as the first most frequent type of somatic structural variation in esophageal adenocarcinoma, and the second most frequent in head-and-neck and colorectal cancers. Aberrant L1 integrations can delete megabase-scale regions of a chromosome, which sometimes leads to the removal of tumor-suppressor genes, and can induce complex translocations and large-scale duplications. Somatic retrotranspositions can also initiate breakage–fusion–bridge cycles, leading to high-level amplification of oncogenes. These observations illuminate a relevant role of L1 retrotransposition in remodeling the cancer genome, with potential implications for the development of human tumors

Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection

Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. We sequenced the genome of R. prolixus, generated assembled sequences covering 95% of the genome ( approximately 702 Mb), including 15,456 putative protein-coding genes, and completed comprehensive genomic analyses of this obligate blood-feeding insect. Although immune-deficiency (IMD)-mediated immune responses were observed, R. prolixus putatively lacks key components of the IMD pathway, suggesting a reorganization of the canonical immune signaling network. Although both Toll and IMD effectors controlled intestinal microbiota, neither affected Trypanosoma cruzi, the causal agent of Chagas disease, implying the existence of evasion or tolerance mechanisms. R. prolixus has experienced an extensive loss of selenoprotein genes, with its repertoire reduced to only two proteins, one of which is a selenocysteine-based glutathione peroxidase, the first found in insects. The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. Comparative protein analyses revealed many lineage-specific expansions and putative gene absences in R. prolixus, including tandem expansions of genes related to chemoreception, feeding, and digestion that possibly contributed to the evolution of a blood-feeding lifestyle. The genome assembly and these associated analyses provide critical information on the physiology and evolution of this important vector species and should be instrumental for the development of innovative disease control methods