AT-specific DNA visualization revisits the directionality of bacteriophage λ DNA ejection.

In this study, we specifically visualized DNA molecules at their AT base pairs after in vitro phage ejection. Our AT-specific visualization revealed that either end of the DNA molecule could be ejected first with a nearly 50% probability. This observation challenges the generally accepted theory of Last In First Out (LIFO), which states that the end of the phage λ DNA that enters the capsid last during phage packaging is the first to be ejected, and that both ends of the DNA are unable to move within the extremely condensed phage capsid. To support our observations, we conducted computer simulations that revealed that both ends of the DNA molecule are randomized, resulting in the observed near 50% probability. Additionally, we found that the length of the ejected DNA by LIFO was consistently longer than that by First In First Out (FIFO) during in vitro phage ejection. Our simulations attributed this difference in length to the stiffness difference of the remaining DNA within the phage capsid. In conclusion, this study demonstrates that a DNA molecule within an extremely dense phage capsid exhibits a degree of mobility, allowing it to switch ends during ejection.

Multi-hazard assessment for flood and Landslide risk in Kalimantan and Sumatra: Implications for Nusantara, Indonesia's new capital.

Situated within the Ring of Fire and characterized by a tropical climate and high seismic activity, Indonesia is uniquely vulnerable to natural disasters such as floods and landslides. These events pose significant threats to both the population and infrastructure. This study predicts areas exposed to flood and landslide risk by considering various environmental factors related to climate, topography, and land use. The predictive performance of three machine learning models-naïve Bayes, k-nearest neighbors, and random forest (RF)-was evaluated by comparing the AUC, RMSE, and R2 values of each model. Ultimately, the RF model, which demonstrated the highest accuracy, was used to prioritize disaster impact factors and generate hazard maps. The results identified the interaction of rainfall, land use, and slope aspect as the most critical determinants of hazard occurrence. The predicted hazard maps revealed that approximately 26.7 % of the study area was vulnerable to either floods or landslides, with 16.8 % of the area experiencing both. The new capital of Nusantara showed a relatively higher multi-hazard risk than did the overall study area and protected zones, with 22.1 % of the hazard area vulnerable to both flooding and landslides. In single hazard zones, areas classified as at risk for floods had a higher mean probability of experiencing both hazards (43 %), as compared to areas classified as at risk for landslides (22 %). As a result, urban planners and relevant stakeholders can now utilize the hazard maps developed in this study to prioritize infrastructure reinforcement and disaster risk areas, integrating land use planning with risk assessment to mitigate the impact of disasters. By employing these strategies, Indonesia and other countries facing similar challenges can now enhance their disaster preparedness and response capabilities in new capital regions and other areas, ultimately planning for more sustainable urban development.

Scanning Electron Microscopy Imaging of Large DNA Molecules Using a Metal-Free Electro-Stain Composed of DNA-Binding Proteins and Synthetic Polymers.

This paper presents the first scanning electron microscopy (SEM)-based DNA imaging in biological samples. This novel approach incorporates a metal-free electro-stain reagent, formulated by combining DNA-binding proteins and synthetic polymers to enhance the visibility of 2-nm-thick DNA under SEM. Notably, DNA molecules stain with proteins and polymers appear as dark lines under SEM. The resulting DNA images exhibit a thickness of 15.0±4.0 nm. As SEM is the primary platform, it integrates seamlessly with various chemically functionalized large surfaces with the aid of microfluidic devices. The approach allows high-resolution imaging of various DNA structures including linear, circular, single-stranded DNA and RNA, originating from nuclear and mitochondrial genomes. Furthermore, quantum dots are successfully visualized as bright labels that are sequence-specifically incorporated into DNA molecules, which highlights the potential for SEM-based optical DNA mapping. In conclusion, DNA imaging using SEM with the novel electro-stain offers electron microscopic resolution with the ease of optical microscopy.

Multi-hazard exposure mapping under climate crisis using random forest algorithm for the Kalimantan Islands, Indonesia.

Numerous natural disasters that threaten people's lives and property occur in Indonesia. Climate change-induced temperature increases are expected to affect the frequency of natural hazards in the future and pose more risks. This study examines the consequences of droughts and forest fires on the Indonesian island of Kalimantan. We first create maps showing the eleven contributing factors that have the greatest impact on forest fires and droughts related to the climate, topography, anthropogenic, and vegetation. Next, we used RF to create single and multi-risk maps for forest fires and droughts in Kalimantan Island. Finally, using the Coupled Model Intercomparison Project (CMIP6) integrated evaluation model, a future climate scenario was applied to predict multiple risk maps for RCP-SSP2-4.5 and RCP-SSP5-8.5 in 2040-2059 and 2080-2099. The probability of a 22.6% drought and a 21.7% forest fire were anticipated to have an influence on the study's findings, and 2.6% of the sites looked at were predicted to be affected by both hazards. Both RCP-SSP2-4.5 and RCP-SSP5-8.5 have an increase in these hazards projected for them. Researchers and stakeholders may use these findings to assess risks under various mitigation strategies and estimate the spatial behavior of such forest fire and drought occurrences.

The effect of gemigliptin treatment on immune parameters including regulatory T cells in patients with type 2 diabetes and moderate to very severe chronic renal impairment.

It is crucial to understand the impact of DPP-4 inhibitors on the immune system, particularly T cell differentiation, maturation, and proliferation, in patients with type 2 diabetes and CKD. This prospective observational study aimed to investigate the distribution of immune cells (particularly regulatory T cells), following the administration of gemigliptin, a DPP-4 inhibitor, in patients with type 2 diabetes mellitus and chronic kidney disease. We enrolled 28 patients with type 2 diabetes, aged 20 to 69, who had been taking a daily dose of 50mg gemigliptin for <3 months and had chronic kidney disease stages 3, 4, or 5, including that undergoing dialysis. T regulatory cells were defined as CD4 + CD25 high CD127 low/- FoxP3 + phenotype, and flow cytometry was used to examine the distribution of T regulatory cells. In the patient group, blood samples were collected at baseline, as well as at 3 and 6 months after initiating medication. Of the 28 patients, 17 (60.7%) were male and the mean age was 61.82 ±â€…8.03 years. Serum Cr ≥ 1.5 mg/dL was 16 (57%), and Cr < 1.5 mg/dL was 12 (43%). The number of CD4(+)/CD25(+) cells did not significantly increase or decrease in baseline, 3 months, and 6 months time changes, and the number of CD127(-/FoxP3(+) cells did not change significantly. Treatment with gemigliptin for 3 and 6 months did not significantly alter the number, percentage, or ratio of circulating Treg cells in patients with type 2 diabetes and CKD. Therefore, the administration of gemigliptin may help maintain regulatory T cells or have no significant impact.

Lack of Efficacy and Safety of Eculizumab for Treatment of Antibody-Mediated Rejection Following Renal Transplantation.

BACKGROUND: We evaluated the efficacy and safety of eculizumab in comparison with plasmapheresis and intravenous immunoglobulin therapy in renal transplant recipients diagnosed with antibody-mediated rejection (AMR). METHODS: This was a multicenter, open-label, prospective, randomized analysis. The patients were randomized by therapy type (eg, eculizumab infusions or standard of care [SOC]: plasmapheresis/intravenous immunoglobulin). The patients (ie, eculizumab arm: 7 patients, SOC arm: 4 patients) were evaluated for the continued presence of donor-specific antibodies (DSAs) and C4d (staining on biopsy), as well as histologic evidence, using repeat renal biopsy after treatment. RESULTS: The allograft biopsies revealed that eculizumab did not prevent the progression to transplant glomerulopathy. Only 2 patients in the SOC arm experienced rejection reversal, and no graft losses occurred in either group. After AMR treatment, the DSA titers generally decreased compared to titers taken at the time of AMR diagnosis. There were no serious adverse effects in the eculizumab arm. CONCLUSIONS: Eculizumab alone cannot treat AMR effectively and does not prevent acute AMR from progressing to chronic AMR or transplant glomerulopathy. However, it should be considered as a potential alternative therapy because it may be associated with decreased DSA levels.