Fate of telomere entanglements is dictated by the timing of anaphase midregion nuclear envelope breakdown.

Persisting replication intermediates can confer mitotic catastrophe. Loss of the fission yeast telomere protein Taz1 (ortholog of mammalian TRF1/TRF2) causes telomeric replication fork (RF) stalling and consequently, telomere entanglements that stretch between segregating mitotic chromosomes. At ≤20 °C, these entanglements fail to resolve, resulting in lethality. Rif1, a conserved DNA replication/repair protein, hinders the resolution of telomere entanglements without affecting their formation. At mitosis, local nuclear envelope (NE) breakdown occurs in the cell's midregion. Here we demonstrate that entanglement resolution occurs in the cytoplasm following this NE breakdown. However, in response to taz1Δ telomeric entanglements, Rif1 delays midregion NE breakdown at ≤20 °C, in turn disfavoring entanglement resolution. Moreover, Rif1 overexpression in an otherwise wild-type setting causes cold-specific NE defects and lethality, which are rescued by membrane fluidization. Hence, NE properties confer the cold-specificity of taz1Δ lethality, which stems from postponement of NE breakdown. We propose that such postponement promotes clearance of simple stalled RFs, but resolution of complex entanglements (involving strand invasion between nonsister telomeres) requires rapid exposure to the cytoplasm.

Parallel genetic screens identify nuclear envelope homeostasis as a key determinant of telomere entanglement resolution in fission yeast.

In fission yeast lacking the telomere binding protein, Taz1, replication forks stall at telomeres, triggering deleterious downstream events. Strand invasion from one taz1Δ telomeric stalled fork to another on a separate (non-sister) chromosome leads to telomere entanglements, which are resolved in mitosis at 32°C; however, entanglement resolution fails at ≤20°C, leading to cold-specific lethality. Previously, we found that loss of the mitotic function of Rif1, a conserved DNA replication and repair factor, suppresses cold sensitivity by promoting resolution of entanglements without affecting entanglement formation. To understand the underlying pathways of mitotic entanglement resolution, we performed a series of genomewide synthetic genetic array screens to generate a comprehensive list of genetic interactors of taz1Δ and rif1Δ. We modified a previously described screening method to ensure that the queried cells were kept in log phase growth. In addition to recapitulating previously identified genetic interactions, we find that loss of genes encoding components of the nuclear pore complex (NPC) promotes telomere disentanglement and suppresses taz1Δ cold sensitivity. We attribute this to more rapid anaphase midregion nuclear envelope (NE) breakdown in the absence of these NPC components. Loss of genes involved in lipid metabolism reverses the ability of rif1+ deletion to suppress taz1Δ cold sensitivity, again pinpointing NE modulation. A rif1+ separation-of-function mutant that specifically loses Rif1's mitotic functions yields similar genetic interactions. Genes promoting membrane fluidity were enriched in a parallel taz1+ synthetic lethal screen at permissive temperature, cementing the idea that the cold specificity of taz1Δ lethality stems from altered NE homeostasis.

Initial agronomic benefits of enhanced weathering using basalt: A study of spring oat in a temperate climate.

Addressing soil nutrient degradation and global warming requires novel solutions. Enhanced weathering using crushed basalt rock is a promising dual-action strategy that can enhance soil health and sequester carbon dioxide. This study examines the short-term effects of basalt amendment on spring oat (Avena sativa L.) during the 2022 growing season in NE England. The experimental design consisted of four blocks with control and basalt-amended plots, and two cultivation types within each treatment, laid out in a split plot design. Basalt (18.86 tonnes ha-1) was incorporated into the soil during seeding. Tissue, grain and soil samples were collected for yield, nutrient, and pH analysis. Basalt amendment led to significantly higher yields, averaging 20.5% and 9.3% increases in direct drill and ploughed plots, respectively. Soil pH was significantly higher 256 days after rock application across cultivation types (direct drill: on average 6.47 vs. 6.76 and ploughed: on average 6.69 vs. 6.89, for control and basalt-amended plots, respectively), likely due to rapidly dissolving minerals in the applied basalt, such as calcite. Indications of growing season differences in soil pH are observed through direct measurement of lower manganese and iron uptake in plants grown on basalt-amended soil. Higher grain and tissue potassium, and tissue calcium uptake were observed in basalt-treated crops. Notably, no accumulation of potentially toxic elements (arsenic, cadmium, chromium, nickel) was detected in the grain, indicating that crops grown using this basaltic feedstock are safe for consumption. This study indicates that basalt amendments can improve agronomic performance in sandy clay-loam agricultural soil under temperate climate conditions. These findings offer valuable insights for producers in temperate regions who are considering using such amendments, demonstrating the potential for improved crop yields and environmental benefits while ensuring crop safety.

Genetic counseling and testing for females at elevated risk for breast cancer: Protocol for the randomized controlled trial of the Know Your Risk intervention.

BACKGROUND: Genetic counseling and testing have an important role in the care of patients at elevated risk for breast cancer. However, conventional pre- and post-test genetic counseling is labor and time intensive, less accessible for patients living outside major urban centers, and impractical on a large scale. A patient-driven approach to genetic counseling and testing may increase access, improve patients' experiences, affect efficiency of clinical practice, and help meet workforce demand. The objective of this 2-arm randomized controlled trial is to determine the efficacy of Know Your Risk (KYR), a genetic counseling patient preference intervention. METHODS: Females (n = 1000) at elevated risk (>20% lifetime) for breast cancer will be randomized to the KYR intervention or conventional genetic counseling. The study will provide comprehensive assessment of breast cancer risk by multigene panel testing and validated polygenic risk score. Primary outcome is adherence to National Comprehensive Cancer Network guidelines for a clinical encounter every 6-12 months and an annual mammogram (breast MRI if recommended) determined by medical record review. Secondary outcomes include adherence to other recommended cancer screening tests determined by medical record review and changes in breast cancer knowledge, perception of risk, post-test/counseling distress, and satisfaction with counseling by completion of three surveys during the study. Study aims will be evaluated for non-inferiority of the KYR intervention compared to conventional genetic counseling. CONCLUSION: If efficacious, the KYR intervention has the potential to improve patients' experience and may change how genetic counseling is delivered, inform best practices, and reduce workforce burden. TRIAL REGISTRATION: ClinicalTrials.govNCT05325151.

Outcomes of the "BRCA Quality Improvement Dissemination Program": An initiative to improve patient receipt of cancer genetics services at five health systems.

OBJECTIVE: A quality improvement initiative (QII) was conducted with five community-based health systems' oncology care centers (sites A-E). The QII aimed to increase referrals, genetic counseling (GC), and germline genetic testing (GT) for patients with ovarian cancer (OC) and triple-negative breast cancer (TNBC). METHODS: QII activities occurred at sites over several years, all concluding by December 2020. Medical records of patients with OC and TNBC were reviewed, and rates of referral, GC, and GT of patients diagnosed during the 2 years before the QII were compared to those diagnosed during the QII. Outcomes were analyzed using descriptive statistics, two-sample t-test, chi-squared/Fisher's exact test, and logistic regression. RESULTS: For patients with OC, improvement was observed in the rate of referral (from 70% to 79%), GC (from 44% to 61%), GT (from 54% to 62%) and decreased time from diagnosis to GC and GT. For patients with TNBC, increased rates of referral (from 90% to 92%), GC (from 68% to 72%) and GT (81% to 86%) were observed. Effective interventions streamlined GC scheduling and standardized referral processes. CONCLUSION: A multi-year QII increased patient referral and uptake of recommended genetics services across five unique community-based oncology care settings.

Long-term fertilization and tillage regimes have limited effects on structuring bacterial and denitrifier communities in a sandy loam UK soil.

Denitrification causes loss of available nitrogen from soil systems, thereby reducing crop productivity and increasing reliance on agrochemicals. The dynamics of denitrification and denitrifying communities are thought to be altered by land management practices, which affect the physicochemical properties of the soil. In this study, we look at the effects of long-term tillage and fertilization regimes on arable soils following 16 years of treatment in a factorial field trial. By studying the bacterial community composition based on 16S rRNA amplicons, absolute bacterial abundance and diversity of denitrification functional genes (nirK, nirS and nosZ), under conditions of minimum/conventional tillage and organic/synthetic mineral fertilizer, we tested how specific land management histories affect the diversity and distribution of both bacteria and denitrification genes. Bacterial and denitrifier communities were largely unaffected by land management history and clustered predominantly by spatial location, indicating that the variability in bacterial community composition in these arable soils is governed by innate environmental differences and Euclidean distance rather than agricultural management intervention.

Liver Disease: Evaluation of Patients With Abnormal Liver Test Results.

The prevalence of abnormal liver test results in the general population is estimated to be between 10% and 20%. The terms liver tests or liver chemistries are recommended to describe more accurately the tests used to assess liver health, instead of the term liver function tests. Defining normal ranges for liver transaminase levels can be challenging. Levels are affected by factors such as body mass index and sex. Elevated transaminase levels are associated with increased risks of liver-related and all-cause mortality. Patient with signs or symptoms of liver disease or abnormal liver test results should be evaluated to determine the etiology. For patients with abnormal liver test results, the initial evaluation should include a review of previous laboratory test results, medical and family histories, substance use, and drugs, including over-the-counter drugs and herbal supplements. Physical examination results often are normal but findings may be consistent with acute disease. Tests should include a complete blood cell count; alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, total bilirubin, and albumin levels; prothrombin time; hepatitis B surface antigen; hepatitis B core antibody; hepatitis C antibody; ferritin and iron levels and transferrin saturation; and right upper quadrant abdominal ultrasonography. Additional tests and imaging should be based on patient-specific risk factors and the pattern of abnormal liver test results.

Liver Disease: Nonalcoholic Fatty Liver Disease.

Nonalcoholic fatty liver disease (NAFLD) describes a spectrum of fatty infiltration, inflammation, and fibrosis of the liver caused by metabolic factors. It is projected to become the leading cause of cirrhosis and need for liver transplantation in the United States. Guidelines from the American Association for the Study of Liver Diseases (AASLD) do not recommend routine screening of patients at high risk of NAFLD. European guidelines recommend testing for certain high-risk patients. Hepatic steatosis and nonalcoholic steatohepatitis (NASH) are difficult to diagnose and often go unrecognized until patients have advanced fibrosis or cirrhosis. Noninvasive methods are used to assess fibrosis, such as fibrosis scores and vibration-controlled transient elastography. Liver biopsy remains the reference standard for NASH diagnosis and fibrosis staging. The mainstays of treatment for NAFLD, NASH, and fibrosis are weight loss and a healthy diet. Currently, no drugs have been approved by the Food and Drug Administration (FDA) for management of these conditions. Drugs for diabetes management (eg, glucagon-like peptide 1 receptor agonists, pioglitazone) can be useful in patients with diabetes and NASH. Among patients with NAFLD, cardiovascular disease is a common cause of mortality. Thus, the AASLD guidelines recommend consideration of omega-3 fatty acids for hypertriglyceridemia management in patients with NAFLD, and statins for hyperlipidemia management in most patients with NAFLD and NASH.

Liver Disease: Hepatitis C.

Approximately 4.1 million individuals in the United States have a history of hepatitis C virus (HCV) exposure, including 2.5 million with chronic infection. Screening guidelines recommend one-time, routine, opt out HCV screening for all individuals 18 years or older. Risk-based testing is recommended for specific individuals. Although many patients with chronic hepatitis C may progress to cirrhosis, end-stage liver disease, and hepatocellular carcinoma, early treatment can prevent development of these sequelae. Management of hepatitis C has simplified significantly, and primary care physicians now can monitor and provide treatment for most patients. Adults with chronic hepatitis C who do not have cirrhosis and have not received hepatitis C treatment previously are eligible for primary care-based treatment. These patients should undergo a comprehensive pretreatment evaluation to guide treatment planning. Patients typically are treated with one of two pangenotypic regimens: glecaprevir-pibrentasvir for 8 weeks or sofosbuvir-velpatasvir for 12 weeks. Virologic cure, defined as sustained virologic response (SVR) at 12 weeks after treatment completion, should be confirmed by an undetectable quantitative HCV RNA via polymerase chain reaction test performed 12 weeks or later after treatment completion. Management results in rates of virologic cure of greater than 95% across genotypes. Patients who do not achieve SVR at 12 weeks should be referred to a subspecialist experienced in management of treatment failure.

Liver Disease: Cirrhosis.

Cirrhosis is pathologic scarring of liver tissue that leads to impaired liver function. It can result from any etiology of chronic liver inflammation and causes significant disease burden. Cirrhosis potentially is reversible through management of the cause, such as nonalcoholic fatty liver disease, viral hepatitis, or alcohol use. As liver disease progresses, compensated (ie, asymptomatic) cirrhosis may decompensate, causing ascites, hepatic encephalopathy, or variceal bleeding. Cirrhosis typically is diagnosed with a history, physical examination, and noninvasive testing, which includes laboratory tests, combination scoring indices, and imaging (eg, ultrasonography, transient elastography). Liver biopsy remains the reference standard for diagnosis. It should be used when results of noninvasive evaluation are indeterminate, when the etiology of liver disease remains unknown, or when the result may alter management. Clinicians should counsel patients about alcohol use, obesity management, and prevention of infection. Drugs with potential for hepatotoxicity should be avoided. Clinical assessment with laboratory tests and calculation of the Child-Pugh and Model for End-stage Liver Disease (MELD) scores should occur every 6 months. Clinicians should evaluate for and manage cirrhosis-related complications, including hepatocellular carcinoma, ascites, spontaneous bacterial peritonitis, hepatic encephalopathy, esophageal varices, and other complications. Evaluation for liver transplantation is indicated for patients with a MELD score of 15 or greater, complications of cirrhosis, or hepatocellular carcinoma.

RNAi and Ino80 complex control rate limiting translocation step that moves rDNA to eroding telomeres.

The discovery of HAATIrDNA, a telomerase-negative survival mode in which canonical telomeres are replaced with ribosomal DNA (rDNA) repeats that acquire chromosome end-protection capability, raised crucial questions as to how rDNA tracts 'jump' to eroding chromosome ends. Here, we show that HAATIrDNA formation is initiated and limited by a single translocation that juxtaposes rDNA from Chromosome (Chr) III onto subtelomeric elements (STE) on Chr I or II; this rare reaction requires RNAi and the Ino80 nucleosome remodeling complex (Ino80C), thus defining an unforeseen relationship between these two machineries. The unique STE-rDNA junction created by this initial translocation is efficiently copied to the remaining STE chromosome ends, independently of RNAi or Ino80C. Intriguingly, both RNAi and Ino80C machineries contain a component that plays dual roles in HAATI subtype choice. Dcr1 of the RNAi pathway and Iec1 of Ino80C both promote HAATIrDNA formation as part of their respective canonical machineries, but both also inhibit formation of the exceedingly rare HAATISTE (where STE sequences mobilize throughout the genome and assume chromosome end protection capacity) in non-canonical, pathway-independent manners. This work provides a glimpse into a previously unrecognized crosstalk between RNAi and Ino80C in controlling unusual translocation reactions that establish telomere-free linear chromosome ends.

Combination of arbuscular mycorrhizal fungi and phosphate solubilizing bacteria on growth and production of Helianthus tuberosus under field condition.

In this work, the effects of co-inoculation between an arbuscular mycorrhizal fungus (AMF) and a phosphate solubilizing bacteria (PSB) to promote the growth and production of sunchoke under field condition were investigated during 2016 and 2017. Four treatments were set up as follows: plants without inoculation, with AMF inoculation, with PSB inoculation and with co-inoculation of PSB and AMF. The results showed the presence of PSB and AMF colonization at the harvest stage in both years. This suggested the survival of PSB and successful AMF colonization throughout the experiments. According to correlation analysis, PSB positively affected AMF spore density and colonization rate. Also, both AMF and PSB positively correlated with growth and production of sunchoke. Co-inoculation could enhance various plant parameters. However, better results in 2016 were found in co-inoculation treatment, while AMF inoculation performed the best in 2017. All of these results suggested that our AMF and PSB could effectively promote growth and production of sunchoke under field conditions. Such effects were varied due to different environmental conditions each year. Note that this is the first study showing successful co-inoculation of AMF and PSB for promoting growth and yield of sunchoke in the real cultivation fields.

Centromeres are dismantled by foundational meiotic proteins Spo11 and Rec8.

Meiotic processes are potentially dangerous to genome stability and could be disastrous if activated in proliferative cells. Here we show that two key meiosis-defining proteins, the topoisomerase Spo11 (which forms double-strand breaks) and the meiotic cohesin Rec8, can dismantle centromeres. This dismantlement is normally observable only in mutant cells that lack the telomere bouquet, which provides a nuclear microdomain conducive to centromere reassembly1; however, overexpression of Spo11 or Rec8 leads to levels of centromere dismantlement that cannot be countered by the bouquet. Specific nucleosome remodelling factors mediate centromere dismantlement by Spo11 and Rec8. Ectopic expression of either protein in proliferating cells leads to the loss of mitotic kinetochores in both fission yeast and human cells. Hence, while centromeric chromatin has been characterized as extraordinarily stable, Spo11 and Rec8 challenge this stability and may jeopardize kinetochores in cancers that express meiotic proteins.

Life Science Alliance, from the Academic Editors.

Life Science Alliance is a community-driven journal that brings together research from diverse fields. The journal is first-of-its-kind in uniting not-for-profit publishers and employing the scientific community to change the way authors can publish their work.

Effects of Agronomic Management and Climate on Leaf Phenolic Profiles, Disease Severity, and Grain Yield in Organic and Conventional Wheat Production Systems.

Agricultural intensification over the last 40 years has increased cereal yields, but there is very limited information on the effects of intensification practices (e.g., nondiverse rotations, mineral NPK fertilizer, and pesticides) on crop health and quality. Results from the study reported here suggest that the use of mineral NPK fertilizers reduces phenolic acid and flavonoid concentrations in leaves and increases the susceptibility of wheat to lodging and powdery mildew, when compared to composted FYM inputs. In contrast, the use of herbicides, fungicides, and growth regulators reduces lodging and foliar disease severity but had no effect on phenolic acid and flavonoid concentrations. The use of composted FYM inputs also resulted in a significant grain yield reduction and not substantially reduced the severity of opportunistic pathogens such as Septoria, which remain a major yield limiting factor unless fungicides are used and/or more Septoria resistant varieties become available.

Fission yeast telosomes: non-canonical histone-containing chromatin structures dependent on shelterin and RNA.

Despite the prime importance of telomeres in chromosome stability, significant mysteries surround the architecture of telomeric chromatin. Through micrococcal nuclease mapping, we show that fission yeast chromosome ends are assembled into distinct protected structures ('telosomes') encompassing the telomeric DNA repeats and over half a kilobase of subtelomeric DNA. Telosome formation depends on the conserved telomeric proteins Taz1 and Rap1, and surprisingly, RNA. Although yeast telomeres have long been thought to be free of histones, we show that this is not the case; telomere repeats contain histones. While telomeric histone H3 bears the heterochromatic lys9-methyl mark, we show that this mark is dispensable for telosome formation. Therefore, telomeric chromatin is organized at an architectural level, in which telomere-binding proteins and RNAs impose a unique nucleosome arrangement, and a second level, in which histone modifications are superimposed upon the higher order architecture.

Creation and Implementation of an Environmental Scan to Assess Cancer Genetics Services at Three Oncology Care Settings.

An environmental scan (ES) is an efficient mixed-methods approach to collect and interpret relevant data for strategic planning and project design. To date, the ES has not been used nor evaluated in the clinical cancer genetics setting. We created and implemented an ES to inform the design of a quality improvement (QI) project to increase the rates of adherence to national guidelines for cancer genetic counseling and genetic testing at three unique oncology care settings (OCS). The ES collected qualitative and quantitative data from reviews of internal processes, past QI efforts, the literature, and each OCS. The ES used a data collection form and semi-structured interviews to aid in data collection. The ES was completed within 6 months, and sufficient data were captured to identify opportunities and threats to the QI project's success, as well as potential barriers to, and facilitators of guideline-based cancer genetics services at each OCS. Previously unreported barriers were identified, including inefficient genetic counseling appointment scheduling processes and the inability to track referrals, genetics appointments, and genetic test results within electronic medical record systems. The ES was a valuable process for QI project planning at three OCS and may be used to evaluate genetics services in other settings.

Distinct 'safe zones' at the nuclear envelope ensure robust replication of heterochromatic chromosome regions.

Chromosome replication and transcription occur within a complex nuclear milieu whose functional subdomains are beginning to be mapped out. Here we delineate distinct domains of the fission yeast nuclear envelope (NE), focusing on regions enriched for the inner NE protein, Bqt4, or the lamin interacting domain protein, Lem2. Bqt4 is relatively mobile around the NE and acts in two capacities. First, Bqt4 tethers chromosome termini and the mat locus to the NE specifically while these regions are replicating. This positioning is required for accurate heterochromatin replication. Second, Bqt4 mobilizes a subset of Lem2 molecules around the NE to promote pericentric heterochromatin maintenance. Opposing Bqt4-dependent Lem2 mobility are factors that stabilize Lem2 beneath the centrosome, where Lem2 plays a crucial role in kinetochore maintenance. Our data prompt a model in which Bqt4-rich nuclear subdomains are 'safe zones' in which collisions between transcription and replication are averted and heterochromatin is reassembled faithfully.

RNAi drives nonreciprocal translocations at eroding chromosome ends to establish telomere-free linear chromosomes.

The identification of telomerase-negative HAATI (heterochromatin amplification-mediated and telomerase-independent) cells, in which telomeres are superseded by nontelomeric heterochromatin tracts, challenged the idea that canonical telomeres are essential for chromosome linearity and raised crucial questions as to how such tracts translocate to eroding chromosome ends and confer end protection. Here we show that HAATI arises when telomere loss triggers a newly recognized illegitimate translocation pathway that requires RNAi factors. While RNAi is necessary for the translocation events that mobilize ribosomal DNA (rDNA) tracts to all chromosome ends (forming "HAATIrDNA" chromosomes), it is dispensable for HAATIrDNA maintenance. Surprisingly, Dicer (Dcr1) plays a separate, RNAi-independent role in preventing formation of the rare HAATI subtype in which a different repetitive element (the subtelomeric element) replaces telomeres. Using genetics and fusions between shelterin components and rDNA-binding proteins, we mapped the mechanism by which rDNA loci engage crucial end protection factors-despite the absence of telomere repeats-and secure end protection. Sequence analysis of HAATIrDNA genomes allowed us to propose RNA and DNA polymerase template-switching models for the mechanism of RNAi-triggered rDNA translocations. Collectively, our results reveal unforeseen roles for noncoding RNAs (ncRNAs) in assembling a telomere-free chromosome end protection device.