Colony stimulating factor-1 receptor drives glomerular parietal epithelial cell activation in focal segmental glomerulosclerosis.

Parietal epithelial cells (PECs) are kidney progenitor cells with similarities to a bone marrow stem cell niche. In focal segmental glomerulosclerosis (FSGS) PECs become activated and contribute to extracellular matrix deposition. Colony stimulating factor-1 (CSF-1), a hematopoietic growth factor, acts via its specific receptor, CSF-1R, and has been implicated in several glomerular diseases, although its role on PEC activation is unknown. Here, we found that CSF-1R was upregulated in PECs and podocytes in biopsies from patients with FSGS. Through in vitro studies, PECs were found to constitutively express CSF-1R. Incubation with CSF-1 induced CSF-1R upregulation and significant transcriptional regulation of genes involved in pathways associated with PEC activation. Specifically, CSF-1/CSF-1R activated the ERK1/2 signaling pathway and upregulated CD44 in PECs, while both ERK and CSF-1R inhibitors reduced CD44 expression. Functional studies showed that CSF-1 induced PEC proliferation and migration, while reducing the differentiation of PECs into podocytes. These results were validated in the Adriamycin-induced FSGS experimental mouse model. Importantly, treatment with either the CSF-1R-specific inhibitor GW2580 or Ki20227 provided a robust therapeutic effect. Thus, we provide evidence of the role of the CSF-1/CSF-1R pathway in PEC activation in FSGS, paving the way for future clinical studies investigating the therapeutic effect of CSF-1R inhibitors on patients with FSGS.

Domestication signatures in the non-conventional yeast Lachancea cidri.

Evaluating domestication signatures beyond model organisms is essential for a thorough understanding of the genotype-phenotype relationship in wild and human-related environments. Structural variations (SVs) can significantly impact phenotypes playing an important role in the physiological adaptation of species to different niches, including during domestication. A detailed characterization of the fitness consequences of these genomic rearrangements, however, is still limited in non-model systems, largely due to the paucity of direct comparisons between domesticated and wild isolates. Here, we used a combination of sequencing strategies to explore major genomic rearrangements in a Lachancea cidri yeast strain isolated from cider (CBS2950) and compared them to those in eight wild isolates from primary forests. Genomic analysis revealed dozens of SVs, including a large reciprocal translocation (~16 kb and 500 kb) present in the cider strain, but absent from all wild strains. Interestingly, the number of SVs was higher relative to single-nucleotide polymorphisms in the cider strain, suggesting a significant role in the strain's phenotypic variation. The set of SVs identified directly impacts dozens of genes and likely underpins the greater fermentation performance in the L. cidri CBS2950. In addition, the large reciprocal translocation affects a proline permease (PUT4) regulatory region, resulting in higher PUT4 transcript levels, which agrees with higher ethanol tolerance, improved cell growth when using proline, and higher amino acid consumption during fermentation. These results suggest that SVs are responsible for the rapid physiological adaptation of yeast to a human-related environment and demonstrate the key contribution of SVs in adaptive fermentative traits in non-model species.IMPORTANCEThe exploration of domestication signatures associated with human-related environments has predominantly focused on studies conducted on model organisms, such as Saccharomyces cerevisiae, overlooking the potential for comparisons across other non-Saccharomyces species. In our research, employing a combination of long- and short-read data, we found domestication signatures in Lachancea cidri, a non-model species recently isolated from fermentative environments in cider in France. The significance of our study lies in the identification of large array of major genomic rearrangements in a cider strain compared to wild isolates, which underly several fermentative traits. These domestication signatures result from structural variants, which are likely responsible for the phenotypic differences between strains, providing a rapid path of adaptation to human-related environments.

A special drop: Characterising yeast isolates associated with fermented beverages produced by Australia's indigenous peoples.

Way-a-linah, an alcoholic beverage produced from the fermented sap of Eucalyptus gunnii, and tuba, a fermented drink made from the syrup of Cocos nucifera fructifying bud, are two of several fermented beverages produced by Australian Aboriginal and Torres Strait people. Here we describe the characterisation of yeast isolates from samples associated with the fermentation of way-a-linah and tuba. Microbial isolates were obtained from two different geographical locations in Australia - the Central Plateau in Tasmania, and Erub Island in the Torres Strait. While Hanseniaspora species and Lachancea cidri were the most abundant species in Tasmania, Candida species were the most abundant in Erub Island. Isolates were screened for tolerance to stress conditions found during the production of fermented beverages and for enzyme activities relevant to the appearance, aroma and flavour of these beverages. Based on screening results, eight isolates were evaluated for their volatile profile during the fermentation of wort, apple juice and grape juice. Diverse volatile profiles were observed for beers, ciders and wines fermented with different isolates. These findings reveal the potential of these isolates to produce fermented beverages with unique aroma and flavour profiles and highlight the vast microbial diversity associated with fermented beverages produced by Australia's Indigenous peoples.

Late Pleistocene-dated divergence between South Hemisphere populations of the non-conventional yeast L. cidri.

Most organisms belonging to the Saccharomycotina subphylum have high genetic diversity and a vast repertoire of metabolisms and lifestyles. Lachancea cidri is an ideal yeast model for exploring the interplay between genetics, ecological function and evolution. Lachancea cidri diverged from the Saccharomyces lineage before the whole-genome duplication and is distributed across the South Hemisphere, displaying an important ecological success. We applied phylogenomics to investigate the genetic variation of L. cidri isolates obtained from Australia and South America. Our approach revealed the presence of two main lineages according to their geographic distribution (Aus and SoAm). Estimation of the divergence time suggests that SoAm and Aus lineages diverged near the last glacial maximum event during the Pleistocene (64-8 KYA). Interestingly, we found that the French reference strain is closely related to the Australian strains, with a recent divergence (405-51 YA), likely associated to human movements. Additionally, we identified different lineages within the South American population, revealing that Patagonia contains a similar genetic diversity comparable to that of other lineages in S. cerevisiae. These findings support the idea of a Pleistocene-dated divergence between South Hemisphere lineages, where the Nothofagus and Araucaria ecological niches likely favoured the extensive distribution of L. cidri in Patagonia.

Molecular approaches improving our understanding of Brettanomyces physiology.

Brettanomyces species, and particularly B. bruxellensis as the most studied representative, are strongly linked to industrial fermentation processes. This association is considered either positive or undesirable depending on the industry. While in some brewing applications and in kombucha production Brettanomyces yeasts contribute to the flavour and aroma profile of these beverages, in winemaking and bioethanol production Brettanomyces is considered a spoilage or contaminant microorganism. Nevertheless, understanding Brettanomyces biology and metabolism in detail will benefit all industries. This review discusses recent molecular biology tools including genomics, transcriptomics, and genetic engineering techniques that can improve our understanding of Brettanomyces physiology and how these approaches can be used to make the industrial potential of this species a reality.

In vivo CD40 Silencing by siRNA Infusion in Rodents and Evaluation by Kidney Immunostaining.

The co-stimulatory molecule CD40 and its ligand CD40L play a key role in the regulation of immunological processes and are involved in the pathophysiology of autoimmune and inflammatory diseases. Inhibition of the CD40-CD40L axis is a promising therapy, and a number of strategies and techniques have been designed to hinder its functionality. Our group has broad experience in silencing CD40 using RNAi technology, and here we summarize protocols for the systemic administration of a specific anti-CD40 siRNA in different rodents models, in addition to the subsequent quantification of CD40 expression in murine kidneys by immunostaining. The use of RNAi technology with specific siRNAs to silence genes is becoming an essential method to investigate gene functions and is rapidly emerging as a therapeutic tool. Graphic abstract: CD40 siRNA mechanism.

Adaptive evolution of sulfite tolerance in Brettanomyces bruxellensis.

Brettanomyces bruxellensis is considered one of the most problematic microbes associated with wine production. Sulfur dioxide is commonly used to inhibit the growth of B. bruxellensis and limit the potential wine spoilage. Brettanomyces bruxellensis wine isolates can grow at higher concentrations of this preservative than isolates from other sources. Thus, it has been suggested that the use of sulfite may have selected for B. bruxellensis strains better adapted to survive in the winemaking environment. We utilized laboratory adaptive evolution to determine the potential for this to occur. Three B. bruxellensis strains, representative of known genetic variation within the species, were subjected to increasing sublethal sulfur dioxide concentrations. Individual clones isolated from evolved populations displayed enhanced sulfite tolerance, ranging from 1.6 to 2.5 times higher than the corresponding parental strains. Whole-genome sequencing of sulfite-tolerant clones derived from two of the parental strains revealed structural variations affecting 270 genes. The region containing the sulfite efflux pump encoding gene, SSU1, showed clear copy number variants in all sequenced clones. Regardless of parental strain genetic background, SSU1 copy number changes were reproducibly associated with one SSU1 haplotype. This work clearly demonstrates adaptive evolution of B. bruxellensis when exposed to sublethal sulfites and suggests that, similar to Saccharomyces cerevisiae wine yeast, the mechanism responsible involves the gene SSU1.

Imaging Manifestations of Genitourinary Tuberculosis.

The genitourinary region is one of the most common sites of extrapulmonary tuberculosis (TB) involvement. The imaging features of genitourinary TB are protean and can mimic other entities, including malignancy, and pose a diagnostic dilemma. Hematogenous seeding and lymphatic spread of mycobacteria from pulmonary, tonsillar, and nodal TB are implicated in the pathogenesis of genitourinary TB. In addition, contiguous extension from the urinary tract and sexual transmission are described as sources of genital TB. Genitourinary TB can be indolent and results in nonspecific signs and symptoms; thus, imaging has a vital role in the working diagnosis for these cases. Classic uroradiologic signs of genitourinary TB are primarily described from the era of intravenous urography and conventional radiography. Now, CT, CT urography, MRI, and US are used in the diagnosis and management. Familiarity with the imaging features of genitourinary TB may help guide the diagnosis and, in turn, lead to timely management. US has a vital role in the evaluation of scrotal and female genital TB. MRI offers superior soft-tissue contrast resolution and excellent depiction of anatomic detail. The various imaging manifestations of genitourinary TB are highlighted. ©RSNA, 2021.

RSNA-STR-ACR Consensus Statement for COVID-19 CT Patterns: Interreader Agreement in 240 Consecutive Patients and Association With RT-PCR Status.

PURPOSE: The aim of this study was to study interreader agreement of the RSNA-STR-ACR (Radiological Society of North America/Society of Thoracic Radiology/American College of Radiology) consensus statement on reporting chest computed tomography (CT) findings related to COVID-19 on a sample of consecutive patients confirmed with reverse transcriptase-polymerase chain reaction (RT-PCR) for severe acute respiratory syndrome coronavirus 2. MATERIALS AND METHODS: This institutional review board-approved retrospective study included 240 cases with a mean age of 47.6 ± 15.9 years, ranging from 20 to 90 years, who had a chest CT and RT-PCR performed. Computed tomography images were independently analyzed by 2 thoracic radiologists to identify patterns defined by the RSNA-STR-ACR consensus statement, and concordance was determined with weighted κ tests. Also, CT findings and CT severity scores were tabulated and compared. RESULTS: Of the 240 cases, 118 had findings on CT. The most frequent on the RT-PCR-positive group were areas of ground-glass opacities (80.5%), crazy-paving pattern (32.2%), and rounded pseudonodular ground-glass opacities (22.9%). Regarding the CT patterns, the most frequent in the RT-PCR-positive group was typical in 75.9%, followed by negative in 17.1%. The interreader agreement was 0.90 (95% confidence interval, 0.80-0.96) in this group. The CT severity score had a mean difference of -0.07 (95% confidence interval, -0.48 to 0.34) among the readers, showing no significant differences regarding visual estimation. CONCLUSIONS: The RSNA-STR-ACR consensus statement on reporting chest CT patterns for COVID-19 presents a high interreader agreement, with the typical pattern being more frequently associated with RT-PCR-positive examinations.

COVID-19: Abdominal and Pelvic Imaging Findings: A Primer for Radiologists.

ABSTRACT: The COVID-19 pandemic presents an ongoing global health threat. The SARS-CoV-2 is known to cause substantial pulmonary disease, and most of the current radiological publications are dedicated to describing and characterizing these findings. However, studies regarding imaging findings in the abdomen and pelvis of infected patients are still very limited. The aim of this review is to discuss the most frequent abdominal manifestations based on the current literature and representative images from our local experience.

Acute Pancreatitis Imaging in MDCT: State of the Art of Usual and Unusual Local Complications. 2012 Atlanta Classification Revisited.

Acute pancreatitis is an inflammatory disease in which most common etiologies are biliary lithiasis and alcoholism. Acute pancreatitis can be classified into 2 groups according to its morphologic features: interstitial edematous pancreatitis and necrotizing acute pancreatitis. The prognosis of this group of diseases and its complications varies significantly and contrast-enhanced computed tomography is the imaging study of choice for the diagnosis and detection of complications. . In this review, we aim to summarize the changes introduced in the revised Atlanta classification and describe other usual and unusual local complications of acute pancreatitis that are not analyzed in that classification. We will also describe early detection signs and provide an accurate interpretation of complications on contrast-enhanced computed tomography that will lead to prompt management decisions which can reduce the morbidity and mortality of these patients.

Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii.

Over the course of human history and in most societies, fermented beverages have had a unique economic and cultural importance. Before the arrival of the first Europeans in Australia, Aboriginal people reportedly produced several fermented drinks including mangaitch from flowering cones of Banksia and way-a-linah from Eucalyptus tree sap. In the case of more familiar fermented beverages, numerous microorganisms, including fungi, yeast and bacteria, present on the surface of fruits and grains are responsible for the conversion of the sugars in these materials into ethanol. Here we describe native microbial communities associated with the spontaneous fermentation of sap from the cider gum Eucalyptus gunnii, a Eucalyptus tree native to the remote Central Plateau of Tasmania. Amplicon-based phylotyping showed numerous microbial species in cider gum samples, with fungal species differing greatly to those associated with winemaking. Phylotyping also revealed several fungal sequences which do not match known fungal genomes suggesting novel yeast species. These findings highlight the vast microbial diversity associated with the Australian Eucalyptus gunnii and the native alcoholic beverage way-a-linah.

Targeted gene deletion in Brettanomyces bruxellensis with an expression-free CRISPR-Cas9 system.

The ability to genetically manipulate microorganisms has been essential for understanding their biology and metabolism. Targeted genome editing relies on highly efficient homologous recombination, and while this is readily observed in the yeast Saccharomyces cerevisiae, most non-conventional yeast species do not display this trait and remain recalcitrant to targeted editing methods. CRISPR-based editing can bypass the requirement for high levels of native homologous recombination, enabling targeted modification to be more broadly implemented. While genetic transformation has been reported previously in Brettanomyces bruxellensis, a yeast with broad biotechnological potential and responsible for significant economic losses during the production of fermented beverages, targeted editing approaches have not been reported. Here, we describe the use of an expression-free CRISPR-Cas9 system, in combination with gene transformation cassettes tailored for B. bruxellensis, to provide the means for targeted gene deletion in this species. Deletion efficiency was shown to be dependent on homologous flanking DNA length, with higher targeting efficiencies observed with cassettes containing longer flanking regions. In a diploid strain, it was not possible to delete multiple alleles in one step, with heterozygous deletants only obtained when using DNA cassettes with long flanking regions. However, stepwise transformations (using two different marker genes) were successfully used to delete both wild-type alleles. Thus, the approach reported here will be crucial to understand the complex physiology of B. bruxellensis. Key points • The use of CRISPR-Cas9 enables targeted gene deletion in Brettanomyces bruxellensis. • Homozygous diploid deletions are possible with step-wise transformations. • Deletion of SSU1 confirmed the role of this gene in sulphite tolerance.

Identification of flocculant wine yeast strains with improved filtration-related phenotypes through application of high-throughput sedimentation rate assays.

In most yeast-driven biotechnological applications, biomass is separated from the aqueous phase after fermentation or production has finished. During winemaking, yeasts are removed after fermentation by racking, filtration, or centrifugation, which add costs to the overall process and may reduce product yield. Theoretically, clarification and filtration can be aided through use of yeast strains that form flocs due to cell-cell binding, a process known as flocculation. However, because early flocculation can cause stuck/sluggish fermentations, this phenotype is not common amongst commercially available wine yeasts. In this study we sought to identify wine strains that exhibit late-fermentation flocculant behaviour using two complementary approaches; a high-throughput sedimentation rate assay of individual strains and a competitive sedimentation assay using a barcoded yeast collection. Amongst 103 wine strains, several exhibited strong sedimentation at the end of the wine fermentation process under various environmental conditions. Two of these strains, AWRI1688 and AWRI1759, were further characterised during red winemaking trials. Shiraz wines produced with both strains displayed improved filtration-related properties. AWRI1759 produced wines with greater filterability, whereas AWRI1688 enabled the recovery of larger wine volumes after racking. Thus, this study demonstrates the effective use of sedimentation screening assays to identify wine yeasts with practical winemaking applications.

Estudio imagenológico del síndrome aórtico agudo / Imaging approach to acute aortic syndrome

Acute aortic syndromes include a spectrum of life-threatening aortic conditions. A review of the diagnostic aspects of the acute aortic syndrome was made, from the perspective of the imaging techniques available for this purpose. The advantages and disadvantages of each technique and its diagnostic performance were evaluated. Emphasis was placed on the relevance of clinical information as a fundamental tool for suspecting this syndrome and appropriately choosing the imaging technique. Our main objective is to provide information about the diagnosis of this condition, especially in the context of emergency services.

Volatile profile of reduced alcohol wines fermented with selected non-Saccharomyces yeasts under different aeration conditions.

Over the last decades there has been an increase in ethanol concentration in wine. High ethanol concentration may impact negatively wine flavor and can be associated with harmful effects on human health. In this study, we investigated a microbiological approach to reduce wine ethanol concentration, using three non-Saccharomyces yeast strains (Metschnikowia pulcherrima, Torulaspora delbrueckii and Zygosaccharomyces bailii) in sequential fermentations with S. cerevisiae under different aeration conditions. At the same time, we evaluated the volatile profile of the resulting reduced alcohol Chardonnay wines. Results showed that the non-Saccharomyces yeasts tested were able to reduce wine ethanol concentration when oxygen was provided. Compared to S. cerevisiae wines, ethanol reduction was 1.6% v/v, 0.9% v/v and 1.0% v/v for M. pulcherrima, T. delbrueckii and Z. bailii sequential fermentations, respectively. Under the conditions evaluated here, aeration did not affect acetic acid production for any of the non-Saccharomyces strains tested. Although aeration affected wine volatile profiles, this was depended on yeast strain. Thus, wines produced with M. pulcherrima under aeration of 0.05 volume of air per volume of culture per minute (VVM) showed excessive ethyl acetate content, while Z. bailli wines produced with 0.05 VVM aeration had increased concentrations of higher alcohols and volatile acids. Increased concentrations of these compounds over their sensory thresholds, are likely to impact negatively on wine sensory profile. Contrarily, all three non-Saccharomyces strains under 0.025 VVM aeration conditions produced wines with reduced ethanol concentration and acceptable chemical volatile profiles.

Competition experiments between Brettanomyces bruxellensis strains reveal specific adaptation to sulfur dioxide and complex interactions at intraspecies level.

Recent studies have suggested a strong niche adaptation for Brettanomyces bruxellensis strains according to human-related fermentation environments, including beer, wine and bioethanol. This is further supported by a correlation between B. bruxellensis genetic grouping and tolerance to SO2, the main antimicrobial used in wine. The allotriploid AWRI1499-like cluster, in particular, shows high SO2 tolerance suggesting that the genetic configuration observed for these strains may confer a selective advantage in winemaking conditions. To test this hypothesis, we evaluated the relative selective advantage of representatives of the three main B. bruxellensis genetic groups in presence of SO2. As a proof-of-concept and using recently developed transformation cassettes, we compared strains under different SO2 concentrations using pairwise competitive fitness experiments. Our results showed that AWRI1499 is specifically adapted to environments with high SO2 concentrations compared to other B. bruxellensis wine strains, indicating a potential correlation between allotriploidisation origin and environmental adaptation in this species. Additionally, our findings suggest different types of competition between strains, such as coexistence and exclusion, revealing new insights on B. bruxellensis interactions at intraspecies level.