Abstract
BRCA1-deficient cells have increased IRE1 RNase, which degrades multiple microRNAs. Reconstituting expression of one of these, miR-4638–5p, resulted in synthetic lethality in BRCA1-deficient ...cancer cells. We found that miR-4638-5p represses expression of TATDN2, a poorly characterized member of the TATD nuclease family. We discovered that human TATDN2 has RNA 3′ exonuclease and endonuclease activity on double-stranded hairpin RNA structures. Given the cleavage of hairpin RNA by TATDN2, and that BRCA1-deficient cells have difficulty resolving R-loops, we tested whether TATDN2 could resolve R-loops. Using in vitro biochemical reconstitution assays, we found TATDN2 bound to R-loops and degraded the RNA strand but not DNA of multiple forms of R-loops in vitro in a Mg2+-dependent manner. Mutations in amino acids E593 and E705 predicted by Alphafold-2 to chelate an essential Mg2+ cation completely abrogated this R-loop resolution activity. Depleting TATDN2 increased cellular R-loops, DNA damage and chromosomal instability. Loss of TATDN2 resulted in poor replication fork progression in the presence of increased R-loops. Significantly, we found that TATDN2 is essential for survival of BRCA1-deficient cancer cells, but much less so for cognate BRCA1-repleted cancer cells. Thus, we propose that TATDN2 is a novel target for therapy of BRCA1-deficient cancers.
Graphical Abstract
Graphical Abstract
Background
There is an association between overweight status and life span in kenneled dogs, but a similar association has not been reported for pet dogs.
Objectives
To examine the effects of being ...overweight in middle age on the life span of neutered client‐owned dogs.
Animals
Fifty‐thousand seven‐hundred eighty seven middle‐aged neutered client‐owned dogs attending a network of approximately 900 veterinary hospitals across North America.
Methods
Retrospective case‐control study. For each of 12 breeds, groups of dogs aged between 6.5 and 8.5 years were identified as being in “overweight” or “normal” body condition. Within each breed and sex, differences in life span between dogs in normal body condition and overweight body condition in the 2 groups were then analyzed by Cox proportional hazards models.
Results
For all breeds, instantaneous risk of death for dogs in overweight body condition was greater than those in normal body condition throughout the age range studied, with hazard ratios ranging from 1.35 (99.79% confidence interval CI 1.05‐1.73) for German Shepherd dog to 2.86 (99.79% CI 2.14‐3.83) for Yorkshire Terrier. In all breeds, median life span was shorter in overweight compared with normal weight dogs, with the difference being greatest in Yorkshire Terriers (overweight: 13.7 years, 99.79% CI 13.3‐14.2; normal: 16.2 years, 99.79% CI 15.7‐16.5) and least in German Shepherd dogs (overweight: 12.1 years, 99.79% CI 11.8‐12.4; normal: 12.5 years, 99.79% CI 12.2‐12.9).
Conclusions and Clinical Importance
Veterinary professionals should consider promoting healthy body condition for dogs, particularly from midlife onward.
We sequenced 54 respiratory syncytial virus (RSV) genomes collected during 2021-22 and 2022-23 outbreaks in Washington, USA, to determine the origin of increased RSV cases. Detected RSV strains have ...been spreading for >10 years, suggesting a role for diminished population immunity from low RSV exposure during the COVID-19 pandemic.
Solitary fibrous tumors are an uncommon sarcoma type characterized by NAB2-STAT6 gene fusion. While solitary fibrous tumors metastasize in 5-25% of cases, it has historically been challenging to ...determine which specific tumor and patient characteristics predict aggressive behavior. We previously reported on a novel risk stratification scheme for solitary fibrous tumors incorporating patient age, tumor size, and mitotic activity to predict risk of metastasis. Herein we validate this risk stratification scheme in an independent, lower-risk population of 79 patients with primary non-meningeal solitary fibrous tumors, and propose incorporating tumor necrosis as a fourth variable to further improve the risk score. Fifty-seven percent of cases were considered low risk, 29% intermediate risk, and 14% high risk for metastasis. Of 50 patients with sufficient clinical follow-up data, no metastases developed in the low-risk patients (n=23), while there was a 7% 10-year metastatic risk in the intermediate risk group (n=17), and a 49% 5-year metastatic risk for the high-risk patients (n=10). When tumor necrosis was added as a fourth variable to the model, predictive power was enhanced. Under the revised stratification, the proportion of tumors identified as low risk increased to 66%, with no metastasis at 10 years, intermediate risk cases comprised 24% with 10% risk of metastasis at 10 years, and high risk comprised 10% of cases with 73% risk of metastasis at 5 years. In Kaplan-Meier analysis, this fourth-variable stratification provided significant discrimination between the risk groups (P=0.0005). These findings confirmed the clinical utility of our previously published risk stratification model and support the inclusion of necrosis as a fourth variable in the model.
Although the peptidoglycan cell wall is an essential structural and morphological feature of most bacterial cells, the extracytoplasmic enzymes involved in its synthesis are frequently dispensable ...under standard culture conditions. By modulating a single growth parameter-extracellular pH-we discovered a subset of these so-called 'redundant' enzymes in
are required for maximal fitness across pH environments. Among these pH specialists are the class A penicillin binding proteins PBP1a and PBP1b; defects in these enzymes attenuate growth in alkaline and acidic conditions, respectively. Genetic, biochemical, and cytological studies demonstrate that synthase activity is required for cell wall integrity across a wide pH range and influences pH-dependent changes in resistance to cell wall active antibiotics. Altogether, our findings reveal previously thought to be redundant enzymes are instead specialized for distinct environmental niches. This specialization may ensure robust growth and cell wall integrity in a wide range of conditions.
This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
Microsatellite instability (MSI) and mismatch-repair deficiency (dMMR) in colorectal tumors are used to select treatment for patients. Deep learning can detect MSI and dMMR in tumor samples on ...routine histology slides faster and less expensively than molecular assays. However, clinical application of this technology requires high performance and multisite validation, which have not yet been performed.
We collected H&E-stained slides and findings from molecular analyses for MSI and dMMR from 8836 colorectal tumors (of all stages) included in the MSIDETECT consortium study, from Germany, the Netherlands, the United Kingdom, and the United States. Specimens with dMMR were identified by immunohistochemistry analyses of tissue microarrays for loss of MLH1, MSH2, MSH6, and/or PMS2. Specimens with MSI were identified by genetic analyses. We trained a deep-learning detector to identify samples with MSI from these slides; performance was assessed by cross-validation (N = 6406 specimens) and validated in an external cohort (n = 771 specimens). Prespecified endpoints were area under the receiver operating characteristic (AUROC) curve and area under the precision-recall curve (AUPRC).
The deep-learning detector identified specimens with dMMR or MSI with a mean AUROC curve of 0.92 (lower bound, 0.91; upper bound, 0.93) and an AUPRC of 0.63 (range, 0.59–0.65), or 67% specificity and 95% sensitivity, in the cross-validation development cohort. In the validation cohort, the classifier identified samples with dMMR with an AUROC of 0.95 (range, 0.92–0.96) without image preprocessing and an AUROC of 0.96 (range, 0.93–0.98) after color normalization.
We developed a deep-learning system that detects colorectal cancer specimens with dMMR or MSI using H&E-stained slides; it detected tissues with dMMR with an AUROC of 0.96 in a large, international validation cohort. This system might be used for high-throughput, low-cost evaluation of colorectal tissue specimens.
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Nervous systems contain sensory neurons, local neurons, projection neurons, and motor neurons. To understand how these building blocks form whole circuits, we must distil these broad classes into ...neuronal cell types and describe their network connectivity. Using an electron micrograph dataset for an entire Drosophila melanogaster brain, we reconstruct the first complete inventory of olfactory projections connecting the antennal lobe, the insect analog of the mammalian olfactory bulb, to higher-order brain regions in an adult animal brain. We then connect this inventory to extant data in the literature, providing synaptic-resolution “holotypes” both for heavily investigated and previously unknown cell types. Projection neurons are approximately twice as numerous as reported by light level studies; cell types are stereotyped, but not identical, in cell and synapse numbers between brain hemispheres. The lateral horn, the insect analog of the mammalian cortical amygdala, is the main target for this olfactory information and has been shown to guide innate behavior. Here, we find new connectivity motifs, including axo-axonic connectivity between projection neurons, feedback, and lateral inhibition of these axons by a large population of neurons, and the convergence of different inputs, including non-olfactory inputs and memory-related feedback onto third-order olfactory neurons. These features are less prominent in the mushroom body calyx, the insect analog of the mammalian piriform cortex and a center for associative memory. Our work provides a complete neuroanatomical platform for future studies of the adult Drosophila olfactory system.
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•First complete parts list for second-order neurons of an adult olfactory system•Quantification of left-right stereotypy in cell and synapse number•Axo-axonic connections form hierarchical communities in the lateral horn•Local and memory-related feedback target projection neuron axons
Bates, Schlegel et al. report the first complete part list of second-order neurons in an adult arthropod olfactory system. They show that these neurons are stereotyped across hemispheres and reveal their hierarchical interconnectivity and how they connect to third-order targets and memory-related neurons.
Rictor is a component of the target of rapamycin complex 2 (TORC2). While TORC2 has been implicated in insulin and other growth factor signaling pathways, the key inputs and outputs of this kinase ...complex remain unknown. We identified mutations in the Caenorhabditis elegans homolog of rictor in a forward genetic screen for increased body fat. Despite high body fat, rictor mutants are developmentally delayed, small in body size, lay an attenuated brood, and are short-lived, indicating that Rictor plays a critical role in appropriately partitioning calories between long-term energy stores and vital organismal processes. Rictor is also necessary to maintain normal feeding on nutrient-rich food sources. In contrast to wild-type animals, which grow more rapidly on nutrient-rich bacterial strains, rictor mutants display even slower growth, a further reduced body size, decreased energy expenditure, and a dramatically extended life span, apparently through inappropriate, decreased consumption of nutrient-rich food. Rictor acts directly in the intestine to regulate fat mass and whole-animal growth. Further, the high-fat phenotype of rictor mutants is genetically dependent on akt-1, akt-2, and serum and glucocorticoid-induced kinase-1 (sgk-1). Alternatively, the life span, growth, and reproductive phenotypes of rictor mutants are mediated predominantly by sgk-1. These data indicate that Rictor/TORC2 is a nutrient-sensitive complex with outputs to AKT and SGK to modulate the assessment of food quality and signal to fat metabolism, growth, feeding behavior, reproduction, and life span.
Invasive species are globally on the rise due to human-induced environmental change and are often a source of harm to their new ecosystems. Tracking the spread of invaders is crucial to better manage ...invasive species, and citizen science is often used to collect sighting data. However, this can be unreliable due to the general public's limited expertise for accurate identification and a lack of clear absence data. Here, we introduce a refined method of citizen science by tracking the spread of the invasive lionfish (Pterois miles) in the Mediterranean Sea using dive centers' expertise on local marine wildlife. We contacted 1131 dive centers on the Mediterranean coast via email and received 216 responses reporting whether or not lionfish were present in their area and, if present, the year they were first sighted. Currently, lionfish sightings are observed in the eastern half of the Mediterranean, though the front is continuing to move west with the furthest sighting as far as Corfu, Greece (19.939423°E, 39.428017°N). In 2020, lionfish also expanded their invasive range north on the Turkish Aegean coast to Karaburun (26.520657°E, 38.637033°N), showing that the invasion is ongoing. We found that the invasive range is now exceeding previous invasion models, highlighting the need for additional research on lionfish biology to inform management efforts. Continuous monitoring of invasive fronts based on dive center reports and a better understanding of what makes lionfish so invasive is crucial to creating effective management strategies and mitigating their negative impact on native ecosystems.
•Dive centers offer an refined approach to citizen science for marine invasions.•Robust lionfish establishment in the Mediterranean in 2015.•Invasion continues to spread north and west into Aegean and Ionian Seas.•Lionfish show greater range expansion than predicted by invasion models.•Better tracking and understanding of lionfish can aid in management of species.
The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14
and 18
centuries AD. Here we analyse human remains from ten European archaeological ...sites spanning this period and reconstruct 34 ancient Y. pestis genomes. Our data support an initial entry of the bacterium through eastern Europe, the absence of genetic diversity during the Black Death, and low within-outbreak diversity thereafter. Analysis of post-Black Death genomes shows the diversification of a Y. pestis lineage into multiple genetically distinct clades that may have given rise to more than one disease reservoir in, or close to, Europe. In addition, we show the loss of a genomic region that includes virulence-related genes in strains associated with late stages of the pandemic. The deletion was also identified in genomes connected with the first plague pandemic (541-750 AD), suggesting a comparable evolutionary trajectory of Y. pestis during both events.
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