An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells.

Tracing the lineage history of cells is key to answering diverse and fundamental questions in biology. Coupling of cell ancestry information with other molecular readouts represents an important goal in the field. Here, we describe the CRISPR array repair lineage tracing (CARLIN) mouse line and corresponding analysis tools that can be used to simultaneously interrogate the lineage and transcriptomic information of single cells in vivo. This model exploits CRISPR technology to generate up to 44,000 transcribed barcodes in an inducible fashion at any point during development or adulthood, is compatible with sequential barcoding, and is fully genetically defined. We have used CARLIN to identify intrinsic biases in the activity of fetal liver hematopoietic stem cell (HSC) clones and to uncover a previously unappreciated clonal bottleneck in the response of HSCs to injury. CARLIN also allows the unbiased identification of transcriptional signatures associated with HSC activity without cell sorting.

Lifelong multilineage contribution by embryonic-born blood progenitors.

Haematopoietic stem cells (HSCs) arise in the embryo from the arterial endothelium through a process known as the endothelial-to-haematopoietic transition (EHT)1-4. This process generates hundreds of blood progenitors, of which a fraction go on to become definitive HSCs. It is generally thought that most adult blood is derived from those HSCs, but to what extent other progenitors contribute to adult haematopoiesis is not known. Here we use in situ barcoding and classical fate mapping to assess the developmental and clonal origins of adult blood in mice. Our analysis uncovers an early wave of progenitor specification-independent of traditional HSCs-that begins soon after EHT. These embryonic multipotent progenitors (eMPPs) predominantly drive haematopoiesis in the young adult, have a decreasing yet lifelong contribution over time and are the predominant source of lymphoid output. Putative eMPPs are specified within intra-arterial haematopoietic clusters and represent one fate of the earliest haematopoietic progenitors. Altogether, our results reveal functional heterogeneity during the definitive wave that leads to distinct sources of adult blood.

Integrating Modular Pipelines with End-to-End Learning: A Hybrid Approach for Robust and Reliable Autonomous Driving Systems.

Autonomous driving navigation relies on diverse approaches, each with advantages and limitations depending on various factors. For HD maps, modular systems excel, while end-to-end methods dominate mapless scenarios. However, few leverage the strengths of both. This paper innovates by proposing a hybrid architecture that seamlessly integrates modular perception and control modules with data-driven path planning. This innovative design leverages the strengths of both approaches, enabling a clear understanding and debugging of individual components while simultaneously harnessing the learning power of end-to-end approaches. Our proposed architecture achieved first and second place in the 2023 CARLA Autonomous Driving Challenge's SENSORS and MAP tracks, respectively. These results demonstrate the architecture's effectiveness in both map-based and mapless navigation. We achieved a driving score of 41.56 and the highest route completion of 86.03 in the MAP track of the CARLA Challenge leaderboard 1, and driving scores of 35.36 and 1.23 in the CARLA Challenge SENSOR track with route completions of 85.01 and 9.55, for, respectively, leaderboard 1 and 2. The results of leaderboard 2 raised the hybrid architecture to the first position, winning the edition of the 2023 CARLA Autonomous Driving Competition.

Variables related to microwave heating-toasting time and water migration assessment with kernel size approaches of specialty maize types.

BACKGROUND: Three main maize types with specialty kernels are used to make ready-to-eat maize by traditional toasting, and microwave toasting may be an innovative application. However, little is known of the toasting process of these Andean maize types. Therefore, the present study aimed to explore the behavior of a broad scope of variables in these maize types. The kernels were packed in sealed paper envelopes and subjected to six microwave heating-toasting times from 0 to 390 s. Subsequently, with actual kernel size approaches, water content (WC), water ratio (WR), and water loss (WL) were analyzed. RESULTS: In addition to WC, WR, and WL, the surface area (S), volume (V), and geometric mean diameter (GMD) behaved like time-related variables with a high correlation depending on the maize types and kernel dimensions. Thus, the WC, WR, and WL third-order polynomial regression curves computed with the spatial (S/V)2 and distance (GMD/2)2 approaches indicated the water variation at each microwave heating-toasting time with a clear difference among maize types a0, a1, and a2. Regarding their exchange profiles without and with the spatial (S/V)2 approach, the maximum rates showed significant differences between maize types and WC and WL. Likewise, the maximum rates displayed significant differences between the spatial (S/V)2 and distance (GMD/2)2 approaches, revealing a notable lack of consistency with the distance (GMD/2)2 approach. CONCLUSION: The kernel size approaches revealed that water migration rates depended on differences in maize types. Such basic information represents the first insight into more physical-based models of water diffusion during raw microwave maize heating-toasting. © 2022 Society of Chemical Industry.

Wine astringency: more than just tannin-protein interactions.

Red wines are characterized by their astringency, a very important sensory attribute that affects the perceived quality of wines. Three mechanisms have been proposed to explain astringency, and two theories describe how these mechanisms work in an integrated manner to produce tactile sensations such as drying, roughening, shrinking and puckering. The factors involved include not only tannins and salivary proteins, but also anthocyanins, grape polysaccharides and mannoproteins, as well as other wine matrix components that modulate their interactions. These multifactorial interactions could be responsible for different sensory responses and therefore need to be further studied. This review presents the latest advances in astringency perception and its possible origins, with special attention on the interactions of components, their impact on oral perception and the development of astringency sub-qualities. Future research efforts should concentrate on understanding the mechanisms involved as well as on the limiting factors related to the conformation and stability of the tannin-salivary protein complexes. © 2021 Society of Chemical Industry.

Nuclear lamina defects cause ATM-dependent NF-κB activation and link accelerated aging to a systemic inflammatory response.

Alterations in the architecture and dynamics of the nuclear lamina have a causal role in normal and accelerated aging through both cell-autonomous and systemic mechanisms. However, the precise nature of the molecular cues involved in this process remains incompletely defined. Here we report that the accumulation of prelamin A isoforms at the nuclear lamina triggers an ATM- and NEMO-dependent signaling pathway that leads to NF-κB activation and secretion of high levels of proinflammatory cytokines in two different mouse models of accelerated aging (Zmpste24(-/-) and Lmna(G609G/G609G) mice). Causal involvement of NF-κB in accelerated aging was demonstrated by the fact that both genetic and pharmacological inhibition of NF-κB signaling prevents age-associated features in these animal models, significantly extending their longevity. Our findings provide in vivo proof of principle for the feasibility of pharmacological modulation of the NF-κB pathway to slow down the progression of physiological and pathological aging.

Loss of MT1-MMP causes cell senescence and nuclear defects which can be reversed by retinoic acid.

MT1-MMP (MMP14) is a collagenolytic enzyme located at the cell surface and implicated in extracellular matrix (ECM) remodeling. Mmp14(-/-) mice present dwarfism, bone abnormalities, and premature death. We demonstrate herein that the loss of MT1-MMP also causes cardiac defects and severe metabolic changes, and alters the cytoskeleton and the nuclear lamina structure. Moreover, the absence of MT1-MMP induces a senescent phenotype characterized by up-regulation of p16(INK4a) and p21(CIP1/WAF) (1), increased activity of senescence-associated ß-galactosidase, generation of a senescence-associated secretory phenotype, and somatotroph axis alterations. Consistent with the role of retinoic acid signaling in nuclear lamina stabilization, treatment of Mmp14(-/-) mice with all-trans retinoic acid reversed the nuclear lamina alterations, partially rescued the cell senescence phenotypes, ameliorated the pathological defects in bone, skin, and heart, and extended their life span. These results demonstrate that nuclear architecture and cell senescence can be modulated by a membrane protease, in a process involving the ECM as a key regulator of nuclear stiffness under cell stress conditions.

Cardiac electrical defects in progeroid mice and Hutchinson-Gilford progeria syndrome patients with nuclear lamina alterations.

Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disease caused by defective prelamin A processing, leading to nuclear lamina alterations, severe cardiovascular pathology, and premature death. Prelamin A alterations also occur in physiological aging. It remains unknown how defective prelamin A processing affects the cardiac rhythm. We show age-dependent cardiac repolarization abnormalities in HGPS patients that are also present in the Zmpste24-/- mouse model of HGPS. Challenge of Zmpste24-/- mice with the ß-adrenergic agonist isoproterenol did not trigger ventricular arrhythmia but caused bradycardia-related premature ventricular complexes and slow-rate polymorphic ventricular rhythms during recovery. Patch-clamping in Zmpste24-/- cardiomyocytes revealed prolonged calcium-transient duration and reduced sarcoplasmic reticulum calcium loading and release, consistent with the absence of isoproterenol-induced ventricular arrhythmia. Zmpste24-/- progeroid mice also developed severe fibrosis-unrelated bradycardia and PQ interval and QRS complex prolongation. These conduction defects were accompanied by overt mislocalization of the gap junction protein connexin43 (Cx43). Remarkably, Cx43 mislocalization was also evident in autopsied left ventricle tissue from HGPS patients, suggesting intercellular connectivity alterations at late stages of the disease. The similarities between HGPS patients and progeroid mice reported here strongly suggest that defective cardiac repolarization and cardiomyocyte connectivity are important abnormalities in the HGPS pathogenesis that increase the risk of arrhythmia and premature death.

Influence of milk pH on the chemical, physical and sensory properties of a milk-based alcoholic beverage.

The research reported in this Research Communication evaluates the effect of milk acidification on the physicochemical and sensory properties of Licor de Oro (or Gold Liqueur; LO), a traditional alcoholic beverage produced in Chiloé island, Chile, which is made by mixing milk acidified with lemon juice and alcohol at a ratio of 1.0:1.0, along with sugar and other spices. The mixture is stored for a couple of weeks and then filtered to obtain a product with a yellowish-transparent appearance, sweetness and acidic taste, milky and alcoholic notes. The lack of information regarding LO processing, mainly in the amount of acid added to the mixture, leads to products of highly variable quality. Thus, the objective of this study was to evaluate the effect of milk acidification on the physicochemical and sensory properties of LO. Raw milk was acidified using citric acid to six different pH values: 6.7 (control), 6.0, 5.3, 4.6, 3.9 and 3.2. These milk treatments were then used to make LO. A decrease of milk pH led to LO with higher levels of sensorial and titratable acidity. LO obtained at pH 6.7 and 6.0 had higher levels of total protein than other treatments, leading to excessive turbidity. In contrast, treatments made at pH ≤5.3 had a typical transparent appearance of LO. These results suggest that a minimum level of milk acidification is required to obtain LO with desired appearance and composition.

Zika Virus Encoding Nonglycosylated Envelope Protein Is Attenuated and Defective in Neuroinvasion.

Zika virus (ZIKV), a mosquito-transmitted flavivirus responsible for sporadic outbreaks of mild and febrile illness in Africa and Asia, reemerged in the last decade causing serious human diseases, including microcephaly, congenital malformations, and Guillain-Barré syndrome. Although genomic and phylogenetic analyses suggest that genetic evolution may have led to the enhanced virulence of ZIKV, experimental evidence supporting the role of specific genetic changes in virulence is currently lacking. One sequence motif, VNDT, containing an N-linked glycosylation site in the envelope (E) protein, is polymorphic; it is absent in many of the African isolates but present in all isolates from the recent outbreaks. In the present study, we investigated the roles of this sequence motif and glycosylation of the E protein in the pathogenicity of ZIKV. We first constructed a stable full-length cDNA clone of ZIKV in a novel linear vector from which infectious virus was recovered. The recombinant ZIKV generated from the infectious clone, which contains the VNDT motif, is highly pathogenic and causes lethality in a mouse model. In contrast, recombinant viruses from which the VNDT motif is deleted or in which the N-linked glycosylation site is mutated by single-amino-acid substitution are highly attenuated and nonlethal. The mutant viruses replicate poorly in the brains of infected mice when inoculated subcutaneously but replicate well following intracranial inoculation. Our findings provide the first evidence that N-linked glycosylation of the E protein is an important determinant of ZIKV virulence and neuroinvasion.IMPORTANCE The recent emergence of Zika virus (ZIKV) in the Americas has caused major worldwide public health concern. The virus appears to have gained significant pathogenicity, causing serious human diseases, including microcephaly and Guillain-Barré syndrome. The factors responsible for the emergence of pathogenic ZIKV are not understood at this time, although genetic changes have been shown to facilitate virus transmission. All isolates from the recent outbreaks contain an N-linked glycosylation site within the viral envelope (E) protein, whereas many isolates of the African lineage virus lack this site. To elucidate the functional significance of glycosylation in ZIKV pathogenicity, recombinant ZIKVs from infectious clones with or without the glycan on the E protein were generated. ZIKVs lacking the glycan were highly attenuated for the ability to cause mortality in a mouse model and were severely compromised for neuroinvasion. Our studies suggest glycosylation of the E protein is an important factor contributing to ZIKV pathogenicity.

MMP-25 Metalloprotease Regulates Innate Immune Response through NF-κB Signaling.

Matrix metalloproteases (MMPs) regulate innate immunity acting over proinflammatory cytokines, chemokines, and other immune-related proteins. MMP-25 (membrane-type 6-MMP) is a membrane-bound enzyme predominantly expressed in leukocytes whose biological function has remained largely unknown. We have generated Mmp25-deficient mice to elucidate the in vivo function of this protease. These mutant mice are viable and fertile and do not show any spontaneous phenotype. However, Mmp25-null mice exhibit a defective innate immune response characterized by low sensitivity to bacterial LPS, hypergammaglobulinemia, and reduced secretion of proinflammatory molecules. Moreover, these immune defects can be tracked to a defective NF-κB activation observed in Mmp25-deficient leukocytes. Globally, our findings provide new mechanistic insights into innate immunity through the activity of MMP-25, suggesting that this proteinase could be a potential therapeutic target for immune-related diseases.

A Synthetic Porcine Reproductive and Respiratory Syndrome Virus Strain Confers Unprecedented Levels of Heterologous Protection.

UNLABELLED: Current vaccines do not provide sufficient levels of protection against divergent porcine reproductive and respiratory syndrome virus (PRRSV) strains circulating in the field, mainly due to the substantial variation of the viral genome. We describe here a novel approach to generate a PRRSV vaccine candidate that could confer unprecedented levels of heterologous protection against divergent PRRSV isolates. By using a set of 59 nonredundant, full-genome sequences of type 2 PRRSVs, a consensus genome (designated PRRSV-CON) was generated by aligning these 59 PRRSV full-genome sequences, followed by selecting the most common nucleotide found at each position of the alignment. Next, the synthetic PRRSV-CON strain was generated through the use of reverse genetics. PRRSV-CON replicates as efficiently as our prototype PRRSV strain FL12, both in vitro and in vivo. Importantly, when inoculated into pigs, PRRSV-CON confers significantly broader levels of heterologous protection than does wild-type PRRSV. Collectively, our data demonstrate that PRRSV-CON can serve as an excellent candidate for the development of a broadly protective PRRSV vaccine. IMPORTANCE: The extraordinary genetic variation of RNA viruses poses a monumental challenge for the development of broadly protective vaccines against these viruses. To minimize the genetic dissimilarity between vaccine immunogens and contemporary circulating viruses, computational strategies have been developed for the generation of artificial immunogen sequences (so-called "centralized" sequences) that have equal genetic distances to the circulating viruses. Thus far, the generation of centralized vaccine immunogens has been carried out at the level of individual viral proteins. We expand this concept to PRRSV, a highly variable RNA virus, by creating a synthetic PRRSV strain based on a centralized PRRSV genome sequence. This study provides the first example of centralizing the whole genome of an RNA virus to improve vaccine coverage. This concept may be significant for the development of vaccines against genetically variable viruses that require active viral replication in order to achieve complete immune protection.

Loss of GLUT4 induces metabolic reprogramming and impairs viability of breast cancer cells.

Metabolic reprogramming strategies focus on the normalization of metabolism of cancer cells and constitute promising targets for cancer treatment. Here, we demonstrate that the glucose transporter 4 (GLUT4) has a prominent role in basal glucose uptake in MCF7 and MDA-MB-231 breast cancer cells. We show that shRNA-mediated down-regulation of GLUT4 diminishes glucose uptake and induces metabolic reprogramming by reallocating metabolic flux to oxidative phosphorylation. This reallocation is reflected on an increased activity of the mitochondrial oxidation of pyruvate and lower lactate release. Altogether, GLUT4 inhibition compromises cell proliferation and critically affects cell viability under hypoxic conditions, providing proof-of-principle for the feasibility of using pharmacological approaches to inhibit GLUT4 in order to induce metabolic reprogramming in vivo in breast cancer models.

Rheological and physical properties of gelatin suspensions containing cellulose nanofibers for potential coatings.

Rheological and physical properties of edible coating formulations containing gelatin, cellulose nanofibers (CNFs), and glycerol are characterized. Measured properties are analyzed in order to optimize edible coating thickness. Results show that coating formulations density increases linearly with gelatin concentration in presence of CNFs. Surface tension decreases with either gelatin or CNF concentration increases. Power law model well described the rheological behavior of edible coating formulations since determination coefficient was high (R(2 )> 0.98) and standard error was low (SE < 0.0052). Formulations showed pseudoplastic (shear-thinning) flow behavior and no time-dependent features were observed. The flow behavior index was not significantly affected by any factor. Consistency coefficient increases with gelatin concentrations but it decreases with glycerol concentrations.

Defective extracellular pyrophosphate metabolism promotes vascular calcification in a mouse model of Hutchinson-Gilford progeria syndrome that is ameliorated on pyrophosphate treatment.

BACKGROUND: Progerin is a mutant form of lamin A responsible for Hutchinson-Gilford progeria syndrome (HGPS), a premature aging disorder characterized by excessive atherosclerosis and vascular calcification that leads to premature death, predominantly of myocardial infarction or stroke. The goal of this study was to investigate mechanisms that cause excessive vascular calcification in HGPS. METHODS AND RESULTS: We performed expression and functional studies in wild-type mice and knock-in Lmna(G609G/+) mice expressing progerin, which mimic the main clinical manifestations of HGPS. Lmna(G609G/+) mice showed excessive aortic calcification, and primary aortic vascular smooth muscle cells from these progeroid animals had an impaired capacity to inhibit vascular calcification. This defect in progerin-expressing vascular smooth muscle cells is associated with increased expression and activity of tissue-nonspecific alkaline phosphatase and mitochondrial dysfunction, which leads to reduced ATP synthesis. Accordingly, Lmna(G609G/+) vascular smooth muscle cells are defective for the production and extracellular accumulation of pyrophosphate, a major inhibitor of vascular calcification. We also found increased alkaline phosphatase activity and reduced ATP and pyrophosphate levels in plasma of Lmna(G609G/+) mice without changes in phosphorus and calcium. Treatment with pyrophosphate inhibited vascular calcification in progeroid mice. CONCLUSIONS: Excessive vascular calcification in Lmna(G609G) mice is caused by reduced extracellular accumulation of pyrophosphate that results from increased tissue-nonspecific alkaline phosphatase activity and diminished ATP availability caused by mitochondrial dysfunction in vascular smooth muscle cells. Excessive calcification is ameliorated on pyrophosphate treatment. These findings reveal a previously undefined pathogenic process in HGPS that may also contribute to vascular calcification in normal aging, because progerin progressively accumulates in the vascular tissue of individuals without HGPS.

Exome sequencing and functional analysis identifies BANF1 mutation as the cause of a hereditary progeroid syndrome.

Accelerated aging syndromes represent a valuable source of information about the molecular mechanisms involved in normal aging. Here, we describe a progeroid syndrome that partially phenocopies Hutchinson-Gilford progeria syndrome (HGPS) but also exhibits distinctive features, including the absence of cardiovascular deficiencies characteristic of HGPS, the lack of mutations in LMNA and ZMPSTE24, and a relatively long lifespan of affected individuals. Exome sequencing and molecular analysis in two unrelated families allowed us to identify a homozygous mutation in BANF1 (c.34G>A [p.Ala12Thr]), encoding barrier-to-autointegration factor 1 (BAF), as the molecular abnormality responsible for this Mendelian disorder. Functional analysis showed that fibroblasts from both patients have a dramatic reduction in BAF protein levels, indicating that the p.Ala12Thr mutation impairs protein stability. Furthermore, progeroid fibroblasts display profound abnormalities in the nuclear lamina, including blebs and abnormal distribution of emerin, an interaction partner of BAF. These nuclear abnormalities are rescued by ectopic expression of wild-type BANF1, providing evidence for the causal role of this mutation. These data demonstrate the utility of exome sequencing for identifying the cause of rare Mendelian disorders and underscore the importance of nuclear envelope alterations in human aging.

Physicochemical Properties of Nanoliposomes Encapsulating Grape Seed Tannins Formed with Ultrasound Cycles.

Grape seeds are an excellent source of flavonoids and tannins with powerful antioxidant properties. However, the astringency of tannins limits their direct incorporation into food. To overcome this challenge, we investigated the encapsulation of grape seed tannins within nanoliposomes formed by ultrasound cycling. We characterized the nanoliposomes' physicochemical properties, including encapsulation efficiency, antioxidant activity, stability, microstructure, and rheological properties. Our findings reveal that the nanoliposomes exhibited excellent stability under refrigerated conditions for up to 90 days with a mean particle size of 228 ± 26 nm, a polydispersity index of 0.598 ± 0.087, and a zeta potential of -41.6 ± 1.30 mV, maintaining a spherical multilamellar microstructure. Moreover, they displayed high antioxidant activity, with encapsulation efficiencies of 79% for epicatechin and 90% for catechin. This innovative approach demonstrates the potential of using ultrasound-assisted nanoliposome encapsulation to directly incorporate grape seed tannins into food matrices, providing a sustainable and efficient method for enhancing their bioavailability and functionality.

Stability and Biaxial Behavior of Fresh Cheese Coated with Nanoliposomes Encapsulating Grape Seed Tannins and Polysaccharides Using Immersion and Spray Methods.

In the food industry context, where fresh cheese stands out as a highly perishable product with a short shelf life, this study aimed to extend its preservation through multi-layer edible coatings. The overall objective was to analyze the biaxial behavior and texture of fresh cheese coated with nanoliposomes encapsulating grape seed tannins (NTs) and polysaccharides (hydroxypropyl methylcellulose; HPMC and kappa carrageenan; KC) using immersion and spray methods, establishing comparisons with uncoated cheeses and commercial samples, including an accelerated shelf-life study. NT, HPMC, and KC were employed as primary components in the multi-layer edible coatings, which were applied through immersion and spray. The results revealed significant improvements, such as a 20% reduction in weight loss and increased stability against oxidation, evidenced by a 30% lower peroxide index than the uncoated samples. These findings underscore the effectiveness of edible coatings in enhancing the quality and extending the shelf life of fresh cheese, highlighting the innovative application of nanoliposomes and polysaccharide blends and the relevance of applying this strategy in the food industry. In conclusion, this study provides a promising perspective for developing dairy products with improved properties, opening opportunities to meet market demands and enhance consumer acceptance.

A conserved splicing mechanism of the LMNA gene controls premature aging.

Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disorder phenotypically characterized by many features of premature aging. Most cases of HGPS are due to a heterozygous silent mutation (c.1824C>T; p.Gly608Gly) that enhances the use of an internal 5' splice site (5'SS) in exon 11 of the LMNA pre-mRNA and leads to the production of a truncated protein (progerin) with a dominant negative effect. Here we show that HGPS mutation changes the accessibility of the 5'SS of LMNA exon 11 which is sequestered in a conserved RNA structure. Our results also reveal a regulatory role of a subset of serine-arginine (SR)-rich proteins, including serine-arginine rich splicing factor 1 (SRSF1) and SRSF6, on utilization of the 5'SS leading to lamin A or progerin production and a modulation of this regulation in the presence of the c.1824C>T mutation is shown directly on HGPS patient cells. Mutant mice carrying the equivalent mutation in the LMNA gene (c.1827C>T) also accumulate progerin and phenocopy the main cellular alterations and clinical defects of HGPS patients. RNAi-induced depletion of SRSF1 in the HGPS-like mouse embryonic fibroblasts (MEFs) allowed progerin reduction and dysmorphic nuclei phenotype correction, whereas SRSF6 depletion aggravated the HGPS-like MEF's phenotype. We demonstrate that changes in the splicing ratio between lamin A and progerin are key factors for lifespan since heterozygous mice harboring the mutation lived longer than homozygous littermates but less than the wild-type. Genetic and biochemical data together favor the view that physiological progerin production is under tight control of a conserved splicing mechanism to avoid precocious aging.