Dose-dependent effects of histone methyltransferase NSD2 on site-specific double-strand break repair.

Histone modifications are catalyzed and recognized by specific proteins to regulate dynamic DNA metabolism processes. NSD2 is a histone H3 lysine 36 (H3K36)-specific methyltransferase that is associated with both various transcription regulators and DNA repair factors. Specifically, it has been implicated in the repair of DNA double-strand breaks (DSBs); however, the role of NSD2 during DSB repair remains enigmatic. Here, we show that NSD2 does not accumulate at DSB sites and that it is not further mobilized by DSB formation. Using three different DSB repair reporter systems, which contained the endonuclease site in the active thymidine kinase gene (TK) locus, we demonstrated separate dose-dependent effects of NSD2 on homologous recombination (HR), canonical-non-homologous end joining (c-NHEJ), and non-canonical-NHEJ (non-c-NHEJ). Endogenous NSD2 has a role in repressing non-c-NHEJ, without affecting DSB repair efficiency by HR or total NHEJ. Furthermore, overexpression of NSD2 promotes c-NHEJ repair and suppresses HR repair. Therefore, we propose that NSD2 has functions in chromatin integrity at the active regions during DSB repair.

Clinical outcomes of multidrug-resistant tracheobronchial tuberculosis receiving anti-tuberculosis regimens containing bedaquiline or delamanid.

The treatment of multidrug-resistant tracheobronchial tuberculosis poses challenges, and research investigating the efficacy of bedaquiline or delamanid as treatment for this condition is limited. This retrospective cohort study was conducted from 2017 to 2021. The study extracted data of patients with multidrug-resistant tracheobronchial tuberculosis from medical records and followed up on prognoses. Participants were divided into three groups: the bedaquiline, delamanid, and control group. Clinical outcomes and the risk factors associated with early culture conversion were analyzed. This study included 101 patients, with 32, 25, and 44 patients in the bedaquiline, delamanid, and control groups respectively. The differences in the treatment success rates among the three groups did not show statistical significance. Both the bedaquiline and delamanid groups had significantly higher culture conversion rates compared to the control after 2 or 6 months of treatment, with significantly shorter median times to culture conversion (bedaquiline group: 2 weeks, delamanid group: 2 weeks, control group: 12 weeks, P < 0.001). Treatment with bedaquiline or delamanid were identified as independent predictors of culture conversion at 2 months (bedaquiline group: aOR = 13.417, 95% CI 4.067-44.260, delamanid group: aOR = 9.333, 95% CI 2.498-34.878) or 6 months (bedaquiline group: aOR = 13.333, 95% CI 3.379-52.610, delamanid group: aOR = 5.000, 95% CI 1.357-18.426) of treatment through multivariable logistic regression analyses. The delamanid group showed better improvement in lumen stenosis compared to bedaquiline. Regimens containing bedaquiline or delamanid may accelerate the culture conversion during the early treatment phase in multidrug-resistant tracheobronchial tuberculosis, and delamanid appears to have the potential to effectively improve airway stenosis.

AMMI an GGE biplot analysis of grain yield for drought-tolerant maize hybrid selection in Inner Mongolia.

Due to the ongoing global warming, maize production worldwide is expected to be heavily inflicted by droughts. The grain yield of maize hybrids is an important factor in evaluating their suitability and stability. In this study, we utilized the AMMI model and GGE biplot to analyze grain yield of 20 hybrids from the three tested environments in Inner Mongolia in 2018 and 2019, aiming at selecting drought-tolerant maize hybrids. AMMI variance analysis revealed highly significant difference on main effects for genotype, environment, and their interaction. Furthermore, G11 (DK159) and G15 (JKY3308) exhibited favorable productivity and stability across all three test environments. Moreover, G10 (LH1) emerged as the most stable hybrid according to the AMMI analysis and the GGE biplot. Bayannur demonstrated the highest identification ability among the three tested sites. Our study provides accurate identification for drought-resilient maize hybrids in different rain-fed regions. These findings can contribute to the selection of appropriate hybrids that exhibit productivity, stability, and adaptability in drought-prone conditions.

Effects of straw return with potassium fertilizer on the stem lodging resistance, grain quality and yield of spring maize (Zea mays L.).

This experiment aimed to study the effects of straw return combined with potassium fertilizer on stem lodging resistance, grain quality, and yield of spring maize. The objective was to provide a scientific basis for the rational utilization of Inner Mongolia spring maize straw and potassium fertilizer resources. The test material used was 'Xianyu 335', and the study was conducted in three ecological regions from east to west of Inner Mongolia (Tumochuan Plain Irrigation Area, Hetao Plain Irrigation Area, and Lingnan Warm Dry Zone). A split-plot design was employed, with the straw return method as the main plot and potassium fertilizer dosage as the secondary plot. We determined the stem resistance index, grain quality, and yield. The results showed that both straw return and potassium application improved stem lodging resistance, grain quality, and maize yield. Combining straw return with the reasonable application of potassium fertilizer enhanced the effectiveness of potassium fertilizer, increased lodging resistance, maize yield, and improved grain quality and yield stability. Under the straw return treatment, with potassium application compared to no potassium application, significant increases were observed in maize plant height, stem diameter, dry weight of stems, stem compressive strength, stem bending strength, grain protein content, yield, straw potassium accumulation content, and soil available potassium content. These increases were up to 30.79 cm, 2.63 mm, 15.40 g, 74.93 N/mm2, 99.65 N/mm2, 13.68%, 3142.43 kg/hm2, 57.97 kg/hm2, and 19.80 mg/kg, respectively. Therefore, the interaction of straw return and potassium fertilizer was found to be the most effective measure for maintaining high-yield and stress-resistant cultivation, improving grain quality, and optimizing the management of straw and potassium fertilizer resources. This approach is suitable for promotion and application in the spring maize growing areas of Inner Mongolia.

Differences in epidemiological and clinical features between adult and pediatric tracheobronchial tuberculosis patients in Southwest China.

Background: Tracheobronchial tuberculosis (TBTB) is a common form of extrapulmonary tuberculosis that affects the tracheobronchial tree. However, the mechanism has not been fully elucidated. Comparisons of clinical characteristics in various age groups can aid in the understanding of TBTB. Methods: This retrospective study was conducted at the Public Health Clinical Center of Chengdu between July 2017 and December 2021, including adults and children with TBTB. Clinical data were extracted from medical records. T/T' test, Mann-Whitney U test, Chi-square test, or Fisher's exact test were used in this study. Results: This study enrolled 347 patients with TBTB (175 adults and 172 children). Adult females were more susceptible to TBTB, whereas gender-based differences were not observed in children. Children had a higher occurrence of irritant dry cough and fever, and acute hematogenous disseminated PTB, and specific types of EPTB, but a shorter interval before diagnosis, and lower diagnostic yields compared to adults (P < 0.05). Adults presented more extensive lung lesions and cavitations as compared to children. Granulation hyperplasia and lymph fistula were more frequently observed in children, as well as airway stenosis, but less severe. Conclusions: The study revealed important variations exist in multiple respects between adults and children with TBTB.

Klotho protects chromosomal DNA from radiation-induced damage.

Klotho is an anti-aging, single-pass transmembrane protein found mainly in the kidney. Although aging is likely to be associated with DNA damage, the involvement of Klotho in protecting cells from DNA damage is still unclear. In this study, we examined DNA damage in human kidney cells and mouse kidney tissue after ionizing radiation (IR). The depletion and overexpression of Klotho in human kidney cells reduced and increased the cell survival rates after IR, respectively. The formation of γ-H2AX foci, representing DNA damage, was significantly elevated immediately after IR in cells with Klotho depletion and decreased in cells overexpressing Klotho. These results were confirmed in mouse renal tissues after IR. Quantification of DNA damage by a comet assay revealed that the Klotho knockdown significantly increased the amount of DNA damage immediately after IR, suggesting that Klotho protects chromosomal DNA from the induction of damage, rather than facilitating DNA repair. Consistent with this notion, Klotho was detected in both the nucleus and cytoplasm. In the nucleus, Klotho may serve to protect chromosomal DNA from damage, leading to its anti-aging effects.

Comprehensive application of bio-char and nitrogen fertilizer in dry-land maize cultivation.

Drought stress and the scarcity of nitrogen fertilizer are two of the important abiotic factors affecting maize growth. Bio-char can enhance the maize yield. Therefore, two field experiments were carried out in the 2 years (2019-2020) to study the effects of nitrogen fertilizer at three levels and four levels of bio-char on endogenous protective enzymes, dry matter accumulation, and yield of the maize 'Xianyu 335' under two different irrigation methods. A split-plot system in three replications was established to conduct the field trials. Two irrigation methods (Regular irrigation and Irregular irrigation) were in the main plots, three nitrogen fertilization levels (0, 150, 300 kg h-1 m2) were in sub-plots, and four bio-char levels (0, 8, 16, 24 t h-1 m-2) were in the sub-sub plots. Each sub-plot consisted of 9 rows with 5 m length and 0.6 m width, and each sub-plot area was 30 m2 in the 2 years. The results indicated that the irrigation methods, the nitrogen, and bio-char supply significantly affected the maize endogenous protective enzymes, dry matter accumulation, and yield in the 2 years. Under the same irrigation method, nitrogen fertilizer and bio-char significantly improved the endogenous protective enzyme activity, dry matter accumulation, and yield of maize compared to the treatment without nitrogen fertilizer and bio-char. The above characteristics improved with increased bio-char supply and nitrogen fertilization at 150 kg h-1 m-2. The treatment of C24N150 recorded the highest values for the parameters of maize endogenous protective enzymes activity, dry matter accumulation, and yield under different irrigation methods during the two harvest seasons.

Potentials of straw return and potassium supply on maize (Zea mays L.) photosynthesis, dry matter accumulation and yield.

Maize (Zea mays L.) is considered one of the most important grains in the world. Straw return has the effect of reducing soil bulk density and increasing soil porosity. Straw returning and potassium fertilizer can supplement soil potassium content. The improvement of soil structure and the optimization of soil nutrient levels provide a good environment for high yield and high efficiency of maize. Therefore, three field experiments were carried out over a three-year period (2018-2020) to study the effects of straw returning on photosynthesis, dry matter accumulation and yield of maize 'Xianyu 335' under two different fertilization methods and four potassium application levels. The results showed that straw returning and potassium application had significant effects on the above indicators. The above indicators were significantly improved by deep tillage straw returning compared with no tillage straw returning. Increasing potassium supply can promote the effect of straw returning. The photosynthesis, dry matter accumulation and yield parameters of maize treated with straw returning and deep tillage combined with 60 kg/hm2 potassium fertilizer (SFK60) reached the highest in the three harvest seasons. The corn planting profit of SFK45 treatment is the highest, which is $1868.92 per ha. Therefore, SFK45 is an effective way to ensure stable and high yield of corn and maximize farmers' income.

Evaluating Individual Radiosensitivity for the Prediction of Acute Toxicities of Chemoradiotherapy in Esophageal Cancer Patients.

In this work, individual radiosensitivity was evaluated using DNA damage response and chromosomal aberrations (CAs) in peripheral blood lymphocytes (PBLs) for the prediction of acute toxicities of chemoradiotherapy (CRT) in esophageal cancer patients. Eighteen patients with esophageal cancer were enrolled in this prospective study. Prescribed doses were 60 Gy in 11 patients and 50 Gy in seven patients. Patients received 2 Gy radiotherapy five days a week. PBLs were obtained during treatment just before and 15 min after 2 Gy radiation therapy on the days when the cumulative dose reached 2, 20, 40 Gy and 50 or 60 Gy. PBLs were also obtained four weeks and six months after radiotherapy in all and 13 patients, respectively. Dicentric and ring chromosomes in PBLs were counted to evaluate the number of CAs. Gamma-H2AX foci per cell were scored to assess DNA double-strand breaks. We analyzed the association between these factors and adverse events. The number of γ-H2AX foci before radiotherapy showed no significant increase during CRT, while their increment was significantly reduced with the accumulation of radiation dose. The mean number of CAs increased during CRT up to 1.04 per metaphase, and gradually decreased to approximately 60% six months after CRT. Five patients showed grade 3 toxicities during or after CRT (overreactors: OR), while 13 had grade 2 or less toxicities (non-overreactors: NOR). The number of CAs was significantly higher in the OR group than in the NOR group at a cumulative dose of 20 Gy (mean value: 0.63 vs. 0.34, P = 0.02), 40 Gy (mean value: 0.90 vs. 0.52, P = 0.04), and the final day of radiotherapy (mean value: 1.49 vs. 0.84, P = 0.005). These findings suggest that number of CAs could be an index for predicting acute toxicities of CRT for esophageal cancer.

Physiological Basis of Heterosis for Nitrogen Use Efficiency of Maize.

Efficient use of nitrogen inputs for concurrent improvements in grain yield and nitrogen use efficiency (NUE) has been recognized as a viable strategy for sustainable agriculture development. Yet, there is little research on the possible physiological basis of maize hybrid heterosis for NUE and measurable traits that are corresponding to the NUE heterosis. A field study was conducted for two years to evaluate the heterosis for NUE and determine the relationship between NUE and its physiological components. Two commercial hybrids, 'Xianyu335' and 'Zhengdan958', and their parental inbred lines, were grown at 0 (0 N) and 150 kg N ha-1 (150 N), in a randomized complete block design with four replications each year. Compared to their parental lines, both hybrids displayed a significant heterosis, up to 466%, for NUE. N internal efficiency (NIE) accounted for 52% of the variation in heterosis for NUE, while there was generally negligible heterosis for nitrogen recovery efficiency (NRE). Heterosis for NIE and thereby for NUE in maize was ascribed to (i) an earlier establishment of pre-anthesis source for N accumulation, which phenotypically exhibited as a faster leaf appearance rate with higher maximum LAI and photosynthetic nitrogen use efficiency; (ii) a larger amount of N being remobilized from the vegetative tissues, especially from leaves, during the grain filling. Phenotypically, there was notably a rapid reduction in post-anthesis specific weights of leaf and stalk, but with maintained functionally stay-green ear leaves; and (iii) a higher productive efficiency per unit grain N, which was characterized by a reduced grain N concentration and enhanced sink strength.

[A rapid method based on advanced polymer chromatography for analyzing the products of the acid-catalyzed depolymerization of lignosulfonate].

In this study, a fast and efficient method for the separation and analysis of the products in the acid-catalyzed depolymerization of commercially available sodium lignosulfonate has been developed. The depolymerized lignosulfonate products were well separated and characterized by advanced polymer chromatography (APC) employing four ACQUITY APC XT columns in series and a ultraviolet detector. The developed method enabled the detection of relative-low-molecular-mass lignin degradation products with peak molecular weights (Mp) of 720, 490, and 260 Da, and an extremely low polydispersity index (PDI) of 1, indicating almost complete conversion of lignosulfonate to smaller molecules. The effects of reaction temperature, time, and catalyst/lignin ratio on the reaction products were systematically investigated. High yields of depolymerization (>80%) could be obtained under the mild acid-catalyzed conditions at 130℃ for 60 min using a catalyst/lignin ratio of 2.334:1. Preliminary studies also indicated that the mild acid-catalytic mechanism is unaffected by the reaction time, temperature, or catalyst concentration, thus suggesting the specificity of the catalytic procedure employed.

Matrin3 promotes homologous recombinational repair by regulation of RAD51.

Matrin3 is a highly conserved inner nuclear matrix protein involved in multiple stages of RNA metabolism. Although Matrin3 may also play a role in DNA repair, its precise roles have remained unclear. In this study, we showed that the depletion of Matrin3 led to decreased homologous recombination (HR) efficiency and increased radiation sensitivity of cells. Matrin3-depleted cells showed impaired DNA damage-dependent focus formation of RAD51, a key protein in HR. These findings suggest that Matrin3 promotes HR by regulating RAD51.

Chromosomal Abnormalities in Human Lymphocytes after Computed Tomography Scan Procedure.

The incidence of chromosomal abnormalities and cancer risk correlates well with the radiation dose after exposure to moderate- to high-dose ionizing radiation. However, the biological effects and health risks at less than 100 mGy, e.g., from computed tomography (CT) have not been ascertained. To investigate the biological effects of low-dose exposure from a CT procedure, we examined chromosomal aberrations, dicentric and ring chromosomes (dic+ring), in peripheral blood lymphocytes (PBLs), using FISH assays with telomere and centromere PNA probes. In 60 non-cancer patients exposed to CT scans, the numbers of dicentric and ring chromosomes were significantly increased with individual variation. The individual variations in the increment of dicentric and ring chromosomes after CT procedures were confirmed using PNA-FISH analysis of PBLs from 15 healthy volunteers after in vitro low-dose exposure using a 137Cs radiation device. These findings strongly suggest that appropriate medical use of low-dose radiation should consider individual differences in radiation sensitivity.

Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome.

Mutations of the Glu76 residue of canonical histone H2B are frequently found in cancer cells. However, it is quite mysterious how a single amino acid substitution in one of the multiple H2B genes affects cell fate. Here we found that the H2B E76K mutation, in which Glu76 is replaced by Lys (E76K), distorted the interface between H2B and H4 in the nucleosome, as revealed by the crystal structure and induced nucleosome instability in vivo and in vitro. Exogenous production of the H2B E76K mutant robustly enhanced the colony formation ability of the expressing cells, indicating that the H2B E76K mutant has the potential to promote oncogenic transformation in the presence of wild-type H2B. We found that other cancer-associated mutations of histones, H3.1 E97K and H2A.Z.1 R80C, also induced nucleosome instability. Interestingly, like the H2B E76K mutant, the H3.1 E97K mutant was minimally incorporated into chromatin in cells, but it enhanced the colony formation ability. In contrast, the H2A.Z.1 R80C mutant was incorporated into chromatin in cells, and had minor effects on the colony formation ability of the cells. These characteristics of histones with cancer-associated mutations may provide important information toward understanding how the mutations promote cancer progression.

Distinct roles of ATM and ATR in the regulation of ARP8 phosphorylation to prevent chromosome translocations.

Chromosomal translocations are hallmarks of various types of cancers and leukemias. However, the molecular mechanisms of chromosome translocations remain largely unknown. The ataxia-telangiectasia mutated (ATM) protein, a DNA damage signaling regulator, facilitates DNA repair to prevent chromosome abnormalities. Previously, we showed that ATM deficiency led to the 11q23 chromosome translocation, the most frequent chromosome abnormalities in secondary leukemia. Here, we show that ARP8, a subunit of the INO80 chromatin remodeling complex, is phosphorylated after etoposide treatment. The etoposide-induced phosphorylation of ARP8 is regulated by ATM and ATR, and attenuates its interaction with INO80. The ATM-regulated phosphorylation of ARP8 reduces the excessive loading of INO80 and RAD51 onto the breakpoint cluster region. These findings suggest that the phosphorylation of ARP8, regulated by ATM, plays an important role in maintaining the fidelity of DNA repair to prevent the etoposide-induced 11q23 abnormalities.

SUMO modification system facilitates the exchange of histone variant H2A.Z-2 at DNA damage sites.

Histone exchange and histone post-translational modifications play important roles in the regulation of DNA metabolism, by re-organizing the chromatin configuration. We previously demonstrated that the histone variant H2A.Z-2 is rapidly exchanged at damaged sites after DNA double strand break induction in human cells. In yeast, the small ubiquitin-like modifier (SUMO) modification of H2A.Z is involved in the DNA damage response. However, whether the SUMO modification regulates the exchange of human H2A.Z-2 at DNA damage sites remains unclear. Here, we show that H2A.Z-2 is SUMOylated in a damage-dependent manner, and the SUMOylation of H2A.Z-2 is suppressed by the depletion of the SUMO E3 ligase, PIAS4. Moreover, PIAS4 depletion represses the incorporation and eviction of H2A.Z-2 at damaged sites. These findings demonstrate that the PIAS4-mediated SUMOylation regulates the exchange of H2A.Z-2 at DNA damage sites.

Relaxed Chromatin Formation and Weak Suppression of Homologous Pairing by the Testis-Specific Linker Histone H1T.

Linker histones bind to nucleosomes and compact polynucleosomes into a higher-order chromatin configuration. Somatic and germ cell-specific linker histone subtypes have been identified and may have distinct functions. In this study, we reconstituted polynucleosomes containing human histones H1.2 and H1T, as representative somatic and germ cell-specific linker histones, respectively, and found that H1T forms less compacted chromatin, as compared to H1.2. An in vitro homologous pairing assay revealed that H1T weakly inhibited RAD51/RAD54-mediated homologous pairing in chromatin, although the somatic H1 subtypes, H1.0, H1.1, H1.2, H1.3, H1.4, and H1.5, substantially suppressed it. An in vivo recombination assay revealed that H1T overproduction minimally affected the recombination frequency, but significant suppression was observed when H1.2 was overproduced in human cells. These results suggested that the testis-specific linker histone, H1T, possesses a specific function to produce the chromatin architecture required for proper chromosome regulation, such as homologous recombination.

Enhanced gefitinib-induced repression of the epidermal growth factor receptor pathway by ataxia telangiectasia-mutated kinase inhibition in non-small-cell lung cancer cells.

The epidermal growth factor receptor (EGFR) tyrosine kinase signaling pathways regulate cellular activities. The EGFR tyrosine kinase inhibitors (EGFR-TKIs) repress the EGFR pathway constitutively activated by somatic EGFR gene mutations and have drastically improved the prognosis of non-small-cell lung cancer (NSCLC) patients. However, some problems, including resistance, remain to be solved. Recently, combination therapy with EGFR-TKIs and cytotoxic agents has been shown to improve the prognosis of NSCLC patients. To enhance the anticancer effects of EGFR-TKIs, we examined the cross-talk of the EGFR pathways with ataxia telangiectasia-mutated (ATM) signaling pathways. ATM is a key protein kinase in the DNA damage response and is known to phosphorylate Akt, an EGFR downstream factor. We found that the combination of an ATM inhibitor, KU55933, and an EGFR-TKI, gefitinib, resulted in synergistic cell growth inhibition and induction of apoptosis in NSCLC cell lines carrying the sensitive EGFR mutation. We also found that KU55933 enhanced the gefitinib-dependent repression of the phosphorylation of EGFR and/or its downstream factors. ATM inhibition may facilitate the gefitinib-dependent repression of the phosphorylation of EGFR and/or its downstream factors, to exert anticancer effects against NSCLC cells with the sensitive EGFR mutation.

hCAS/CSE1L regulates RAD51 distribution and focus formation for homologous recombinational repair.

Homologous recombinational repair (HR) is one of the major repair systems for DNA double-strand breaks. RAD51 is a key molecule in HR, and the RAD51 concentration in the cell nucleus increases after DNA damage induction. However, the mechanism that regulates the intracellular distribution of RAD51 is still unclear. Here, we show that hCAS/CSE1L associates with RAD51 in human cells. We found that hCAS/CSE1L negatively regulates the nuclear protein level of RAD51 under normal conditions. hCAS/CSE1L is also required to repress the DNA damage-induced focus formation of RAD51. Moreover, we show that hCAS/CSE1L plays roles in the regulation of the HR activity and in chromosome stability. These findings suggest that hCAS/CSE1L is responsible for controlling the HR activity by directly interacting with RAD51.

Regulation of homologous recombinational repair by lamin B1 in radiation-induced DNA damage.

DNA double-strand breaks (DSBs) are the major lethal lesion induced by ionizing radiation (IR). RAD51-dependent homologous recombination (HR) is one of the most important pathways in DSB repair and genome integrity maintenance. However, the mechanism of HR regulation by RAD51 remains unclear. To understand the mechanism of RAD51-dependent HR, we searched for interacting partners of RAD51 by a proteomics analysis and identified lamin B1 in human cells. Lamins are nuclear lamina proteins that play important roles in the structural organization of the nucleus and the regulation of chromosome functions. Immunoblotting analyses revealed that siRNA-mediated lamin B1 depletion repressed the DNA damage-dependent increase of RAD51 after IR. The repression was abolished by the proteasome inhibitor MG132, suggesting that lamin B1 stabilizes RAD51 by preventing proteasome-mediated degradation in cells with IR-induced DNA damage. We also showed that lamin B1 depletion repressed RAD51 focus formation and decreased the survival rates after IR. On the basis of these results, we propose that lamin B1 promotes DSB repair and cell survival by maintaining the RAD51 protein levels for HR upon DSB induction after IR.