Browse Articles

A limitation lifted: A conditional knockdown system reveals essential roles for Polo-like kinase and Aurora kinase 1 in <i>Trypanosoma cruzi</i> cell division

While advances in genome editing technologies have simplified gene disruption in many organisms, the study of essential genes requires development of conditional disruption or knockdown systems that are not available in most organisms. Such is the case for Trypanosoma cruzi , a parasite that causes Chagas disease, a severely neglected tropical disease endemic to Latin America that is often fatal. Our knowledge of the identity of essential genes and their functions in T. cruzi has been severely constrained by historical challenges in very basic genetic manipulation and the absence of RNA interference machinery. Here, we describe the development and use of self-cleaving RNA sequences to conditionally regulate essential gene expression in T. cruzi . Using these tools, we identified essential roles for Polo-like and Aurora kinases in T. cruzi cell division, mirroring their functions in Trypanosoma brucei . Importantly, we demonstrate conditional knockdown of essential genes in intracellular amastigotes, the disease-causing stage of the parasite in its human host. This conditional knockdown system enables the efficient and scalable functional characterization of essential genes in T. cruzi and provides a framework for the development of conditional gene knockdown systems for other nonmodel organisms.

Spatial prediction of dynamic interactions in rats

Animals and humans receive the most critical information from parts of the environment that are immediately inaccessible and highly dynamic. The brain must effectively process potential interactions between elements in such an environment to make appropriate decisions in critical situations. We trained male Long-Evans rats to discriminate static and dynamic spatial stimuli and to generalize novel dynamic spatial stimuli displayed on an inaccessible computer screen. We provide behavioral evidence indicating that rats encode dynamic visuospatial situations by constructing internal static representations that capture meaningful future interactions between objects. These observations support previous findings in humans that such internal static representations can encapsulate relevant spatiotemporal information of dynamic environments. This mechanism would allow animals and humans to process complex time-changing situations neatly.

High precision water quality retrieval in Dianchi Lake using Gaofen 5 data and machine learning methods

Toward equitable major histocompatibility complex binding predictions

Deep learning tools that predict peptide binding by major histocompatibility complex (MHC) proteins play an essential role in developing personalized cancer immunotherapies and vaccines. In order to ensure equitable health outcomes from their application, MHC binding prediction methods must work well across the vast landscape of MHC alleles observed across human populations. Here, we show that there are alarming disparities across individuals in different racial and ethnic groups in how much binding data are associated with their MHC alleles. We introduce a machine learning framework to assess the impact of this data imbalance for predicting binding for any given MHC allele, and apply it to develop a state-of-the-art MHC binding prediction model that additionally provides per-allele performance estimates. We demonstrate that our MHC binding model successfully mitigates much of the data disparities observed across racial groups. To address remaining inequities, we devise an algorithmic strategy for targeted data collection. Our work lays the foundation for further development of equitable MHC binding models for use in personalized immunotherapies.

Identification of suitable qPCR reference genes for the normalization of gene expression in the BL10-mdx and D2-mdx mouse models of Duchenne muscular dystrophy

Duchenne muscular dystrophy (DMD) is an X-linked disorder that is caused by mutations in the DMD gene, leading to progressive muscle wasting and weakness. There is currently no cure for DMD. The BL10-mdx mouse is the most commonly used model in preclinical DMD studies, but it exhibits a mild disease phenotype compared to DMD patients, limiting research translatability. The newer D2-mdx mouse has a more severe phenotype at an early age and may better recapitulate human disease. To compare these mouse models on a transcriptional level with quantitative RT-PCR, stable and reliable reference genes are indispensable. We aimed to evaluate the stability and reliability of a panel of nine candidate reference genes (Actb, Ap3d1, Gapdh, Hmbs, Htatsf1, Pak1ip1, Rpl13a, Sdha and Zfp91) in the gastrocnemius, diaphragm and heart of mice from both strains and their corresponding wild types aged 4 to 52 weeks. Data was analyzed using geNorm, BestKeeper, deltaCt and NormFinder. We found that Htatsf1, Pak1ip1 and Zfp91 are suitable reference genes for normalization of gene expression in dystrophic and healthy mice, regardless of the tissue type or age. In our hands, Actb, Gapdh and Rpl13a were not suitable as reference genes, exhibiting tissue-, age-, or disease specific changes in expression. This study highlights the importance of the selection of suitable reference genes, as their stability can differ between specific experimental setups.

Comprehensive analysis of Metacrinus rotundus full length transcriptome

Tracking proteasome degradation: A cross-organ analysis via intact degradomics mass spectrometry

The proteasome is a multisubunit degradation machinery that is essential for maintaining protein homeostasis by breaking down unnecessary or damaged proteins into peptides. While most of these peptides are further processed into amino acids, a subset evades complete degradation and plays key roles in biological processes such as antigen presentation, signaling, and apoptosis. However, the variability in peptide lengths and the diverse composition of proteasomes make their comprehensive identification and characterization particularly challenging. Here, we present a method that enables real-time identification of generated peptides, as well as uncleaved and partially cleaved protein substrates, revealing the processive nature of protein proteasomal degradation. Our intact degradomics workflow is based on intact mass spectrometry measurements and treats the enzymatically produced peptides as if they were generated within the mass spectrometer, akin to top–down products. We applied this approach to determine the kinetic profile of proteasome degradation and compare the real-time activity of proteasomes isolated from different mouse organs, uncovering distinct functionalities of the complex. Overall, this method offers a valuable tool for studying peptide degradation products across various proteasome configurations, while also enabling the investigation of how interacting proteins, inhibitors, and activators influence proteasome activity. Furthermore, its adaptability makes it applicable to a wide range of other proteolytic complexes, broadening its potential impact in the field.

First validity testing of GluciQuizz, a French self-questionnaire evaluating carb-counting for patients with type 1 diabetes

Objective Carbohydrate intake remains one of the most influential factors affecting post-meal glucose levels in type 1 diabetes (T1D). To individualize and optimize patient education on carbohydrate counting, it is essential to assess their knowledge of carbohydrate counting. For this purpose, we aimed to produce and validate a questionnaire for French-speaking individuals based on the American AdultCarbQuiz questionnaire (43 items). Design The translation and cross-cultural adaptation of the American questionnaire were followed by an analysis conducted by patient and diabetologist expert groups. Participants 190 participants living with T1D, Diabetologist expert group. Main outcome measure(s) Internal consistency and reliability were verified by administering the adapted French version of the questionnaire to 190 participants living with T1D. Analysis Clinical validity was verified by examining the correlation between the questionnaire score and the time in range (TIR) of these participants. Results Translation and back-translation demonstrated good consistency with the original questionnaire. Typical American food items were replaced with foods commonly consumed in France. All items were validated by both patient and diabetologist experts. After analyzing the responses of 190 participant, seven items were considered non-discriminatory and were therefore removed. Internal consistency, assessed by Cronbach’s α, was high, with α =  0.785, 95 CI [0.738–0.826]. Finally, we produced a 36 item French questionnaire named GluciQuizz. TIR correlated with the GluciQuizz score (r =  0.3; p  &lt;  0.0001). Conclusions and implications This study validates a French-language self-administered questionnaire (GluciQuizz), which evaluates different domains of carbohydrate knowledge in a 15-minute quiz for people living with T1D.

Pollen–pistil interactions in divergent wide crosses lead to spatial and temporal pre-fertilization reproductive barrier in flax (Linum usitatissimum L.)

Deep-water corals indicate the Red Sea survived the last glacial lowstand

The Red Sea, a nascent ocean basin connected to the Indian Ocean via a shallow strait, is assumed to have experienced significant environmental changes during the last glacial period due to a sea-level drop likely exceeding 110 m. This study investigates the hypothesis that hydrodynamic restriction led to severe ecological impacts, including basin-wide extinction due to elevated salinity followed by a short time of oxygen depletion. Uranium–Thorium dating of deep-water corals (DWCs) from 26 northern Red Sea sites reveals coral growth during and after the Last Glacial sea-level lowstand, indicating tolerable seawater chemistry. Additional geochemical data show no significant difference in Red Sea chemistry or temperature between the Latest Pleistocene and Holocene. A meta-analysis of 27 deep-sea cores reveals that while planktonic foraminifera experienced local extinction, other microfossil groups seemingly persisted. These findings suggest that the Red Sea survived the last sea-level lowstand, challenging the paradigm of a complete ecological collapse and providing insights into the resilience of marine ecosystems.

Community emergency management policy in China using a policy text tool

Systematically analyzing the current status and problems of the Community Emergency Management Policy (CEMP) system in China and proposing practical suggestions that are conducive to subsequent policy formulation and improvement are important for improving community emergency management capabilities and levels and promoting sustainable community development. Based on the two-dimensional analysis framework of “policy tools–policy objectives”, this paper draws from content analysis and social network analysis, quantitatively analyzing the CEMP texts at the national level from 2004 to 2024. The results show that the CEMP system in China has essentially taken shape, but there are still some problems, such as the uneven use of policy tools, the unbalanced internal structure of policy tools, the large distribution gap of policy objective elements, and the adaptability between policy tools and policy objectives, which needs to be improved. Given these results, we suggest 1) Appropriately increasing the frequency of using demand-type policy tools and effectively optimizing the internal structure of the three main types of policy tools; 2) Comprehensively deepening the reform of CEMP objectives; and 3) Reasonably improving the adaptability between policy tools and objectives.

Short-term overloading exercise attenuates articular chondrocyte features partly via synovium–cartilage interactions mediated by inhibin subunit beta A

OsNLP3 and OsPHR2 orchestrate direct and mycorrhizal pathways for nitrate uptake by regulating NAR2.1–NRT2s complexes in rice

Nitrogen (N) is the most important essential nutrient required by plants. Most land plants have evolved two N uptake pathways, a direct root pathway and a symbiotic pathway, via association with arbuscular mycorrhizal (AM) fungi. However, the interaction between the two pathways is ambiguous. Here, we report that OsNAR2.1–OsNRT2s, the nitrate (NO 3 − ) transporter complexes with crucial roles in direct NO 3 − uptake, are also recruited for symbiotic NO 3 − uptake. OsNAR2.1 and OsNRT2.1/2.2 are coregulated by NIN-like protein 3 (OsNLP3), a key regulator in NO 3 − signaling, and OsPHR2, a major regulator of phosphate starvation responses. More importantly, AM symbiosis induces expression of OsNAR2.1 – OsNRT2s, OsNLP3, and OsSPX4 , encoding an intracellular Pi sensor, in arbuscular-containing cells, but weakens their expression in the epidermis. OsNAR2.1 and OsNLP3 can activate both mycorrhizal NO 3 − uptake and mycorrhization efficiency. Overall, we demonstrate that OsNLP3 and OsPHR2 orchestrate the direct and mycorrhizal NO 3 − uptake pathways by regulating the NAR2.1–NRT2s complexes in rice.

Comparison of leg length discrepancy after total hip arthroplasty: Direct anterior and posterior lateral approach

Background Leg length discrepancy (LLD) after total hip arthroplasty (THA) is a clinical entity that deteriorates clinical outcomes and patients’ satisfaction. Few articles have compared LLD after THA by different surgical approaches. Methods A total of 358 consecutive patients who underwent primary THA between January 2016 and November 2018 were retrospectively reviewed. All 4 surgeons performed THA through both direct anterior approach (DAA) and posterior lateral approach (PLA). The primary outcome measurement was LLD. LLD was measured on post-operative anteroposterior bilateral hip radiograph. The secondary outcomes were acetabular abduction, acetabular anteversion, perceived LLD (pLLD) and HHS at 6 weeks, 1 year and 5 years. Intergroup analyses were performed using the Chi-square test for enumeration data and the independent sample t-test for quantitative data. Results There was no inter-group difference in terms of patients’ demographics. The DAA group had decreased LLD compared to the PLA group (3.0 ± 5.9mm vs. 4.2 ± 4.5mm, p = 0.027). Meanwhile, the DAA group had a smaller acetabular anteversion than the PLA group (12.9 ± 2.9 vs. 18.4 ± 2.9, p &lt; 0.01). At 6-week follow-up, the DAA group had higher HHS (82.2 + 6.2 vs. 80.5 + 6.6, p = 0.015) and less pLLD (P = 0.001) compared to the PLA group. Conclusions DAA results in more accurate leg length equalization, reduced pLLD, and improved short-term outcomes compared with PLA.

Negative pressure wound therapy promotes wound healing by down-regulating miR-155 expression in granulation tissue of diabetic foot ulcers

A long-distance inhibitory system regulates haustoria numbers in parasitic plants

The ability of parasitic plants to withdraw nutrients from their hosts depends on the formation of an infective structure known as the haustorium. How parasites regulate their haustoria numbers is poorly understood, and here, we uncovered that existing haustoria in the facultative parasitic plants Phtheirospermum japonicum and Parentucellia viscosa suppressed the formation of new haustoria located on distant roots. Using Phtheirospermum, we found that this effect depended on the formation of mature haustoria and could be induced through the application of external nutrients. To understand the molecular basis of this root plasticity, we analyzed hormone response and found that existing infections upregulated cytokinin-responsive genes first at the haustoria and then more distantly in Phtheirospermum shoots. We observed that infections increased endogenous cytokinin levels in Phtheirospermum roots and shoots, and this increase appeared relevant since local treatments with exogenous cytokinins blocked the formation of both locally and distantly formed haustoria. In addition, local overexpression of a cytokinin-degrading enzyme in Phtheirospermum prevented this systemic interhaustoria repression and increased haustoria numbers locally. We propose that a long-distance signal produced by haustoria negatively regulates future haustoria, and in Phtheirospermum , such a signaling system is mediated by a local increase in cytokinin to regulate haustoria numbers and balance nutrient acquisition.

Widespread dissemination of Salmonella, Escherichia coli and Campylobacter resistant to medically important antimicrobials in the poultry production continuum in Canada

The Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) monitors Escherichia coli, Salmonella and Campylobacter and their resistance to antimicrobials in broiler chickens at the farm and slaughter plant levels. In response to many years of CIPARS’ observations and farmers’ data, the Chicken Farmers of Canada implemented a strategy to reduce antimicrobial use in 2014. As resistance genes can be transmitted vertically from parents to their offspring, a study was conducted in broiler breeder flocks to assess the frequency of target bacteria, their antimicrobial resistance (AMR) and to obtain a comprehensive picture of AMR in poultry production. Spent breeder flocks slaughtered between 2018 and 2021 were sampled and data from broiler flocks at the farm and slaughter plants were assessed. Salmonella was most frequently detected in farm broiler chickens (46%), while Campylobacter was most frequently detected in broiler breeders (73%). In Campylobacter, high levels (20–24%) of ciprofloxacin resistance were found across the three production stages, and was highest in farm broiler chickens (24%). In E. coli, an indicator organism, low-level ceftriaxone resistance and occasional isolates that were non-susceptible to ciprofloxacin were noted. Using the indicator, fully susceptible E. coli, broiler breeders had the highest frequency (54%) compared to farm (36%) and slaughtered (35%) broiler chickens. In Salmonella broiler breeders had the highest resistance to most antimicrobials tested.Fully susceptible Salmonella was lowest in broiler breeders (16%) compared to farm (42%) and slaughtered (42%) broiler chickens. Salmonella serovars differed between the production stages, but S. Kentucky was the most predominant. Resistance to critically important antimicrobials in human medicine and regional variations in resistance profiles were observed. This study suggests that broiler breeders carry foodborne bacteria resistant to antimicrobials used in human medicine, demonstrating their role in the maintenance of AMR in poultry and the need to adopt a harmonized sector-wide AMU strategy.

Advanced financial security system using smart contract in private ethereum consortium blockchain with hybrid optimization strategy

Options for student loan repayment matter

Document review of the paper-based implementation of the Framework and strategy for disability and rehabilitation in Gauteng, South Africa

Background The prevalence of disability is on the rise globally and in South Africa, with a high number of unmet needs and poor actualisation of the health rights of persons with disabilities. A tool to realise these rights is health policy, such as the framework and strategy for disability and rehabilitation (2015-2022)(FSDR). There are limited data on the implementation outcomes of the FSDR. Objective To review the implementation of the FSDR according to the paper-based provincial reports. Methods The study conducted a document review and utilised a concurrent mixed-method design, combining qualitative and quantitative data extracted from paper-based evaluation templates developed by the South African National Department of Health (NDoH). The qualitative analysis involved thematic coding using the RE-AIM framework to examine the FSDR’s implementation across eight provinces, while quantitative data, such as frequencies and percentages, provided supplementary insights. Results The quantitative results revealed that 87% of the reports from provinces reported physical accessibility to the FSDR, and 62% of provinces received training on the implementation of the FSDR. Only two out of eight provinces have conducted monitoring and evaluation since implementing the FSDR in 2015. Qualitative findings revealed poor reach and adoption of the FSDR owing to a lack of implementation training for end users. The lack of indicators resulted in poor maintenance of the FSDR, as well as the lack of human resources and equipment which resulted in the reduced efficacy of the FSDR. Conclusion The FSDR has not achieved its full level of implementation due to numerous barriers, such as lack of resources, human capacity, and training on implementation.