Building a Robust Chromatin Immunoprecipitation Method with Substantially Improved Efficiency

Chromatin immunoprecipitation (ChIP) is the gold-standard method for detection of interactions between proteins and chromatin and is a powerful tool for identification of epigenetic modifications. Although ChIP protocols for plant species have been developed, many specific features of plants, especially woody plants, still hinder the efficiency of immunoprecipitation, resulting in inefficient ChIP enrichment and an active demand for a highly efficient ChIP protocol. In this study, using birch (Betula platyphylla) and Arabidopsis (Arabidopsis thaliana) as the research materials, we identified five factors closely associated with ChIP efficiency, including crosslinking, concentration of chromatin using centrifugal filters, use of a different immunoprecipitation buffer, rescue of DNA with proteinase K, and use of Suc to increase immunoprecipitation efficiency. Optimization of any these factors can significantly improve ChIP efficiency. Considering these factors together, we developed a robust ChIP protocol that achieved a 14-fold improvement in ChIP enrichment for birch and a >6-fold improvement for Arabidopsis compared to the standard ChIP method. As this ChIP method works well in both birch and Arabidopsis, it should also be suitable for other woody and herbaceous species. In addition, this ChIP method enables detection of low-abundance transcription factor-DNA interactions and may extend the application of ChIP in the plant kingdom.

Obesity and Cancer Treatment Outcomes: Interpreting the Complex Evidence

A wealth of epidemiological evidence, combined with plausible biological mechanisms, present a convincing argument for a causal relationship between excess adiposity, commonly approximated as body mass index (BMI, kg/m²), and incident cancer risk. Beyond this relationship, there are a number of challenges posed in the context of interpreting whether being overweight (BMI 25.0-29.9 kg/m²) or obese (BMI ≥ 30.0 kg/m²) adversely influences disease progression, cancer mortality and survival. Elevated BMI (≥ 25.0 kg/m²) may influence treatment selection of, for example, the approach to surgery; the choice of chemotherapy dosing; the inclusion of patients into randomised clinical trials. Furthermore, the technical challenges posed by an elevated BMI may adversely affect surgical outcomes, for example, morbidity (increasing the risk of surgical site infections), reduced lymph node harvest (and subsequent risk of under-staging and under-treatment) and increased risk of margin positivity. Suboptimal chemotherapy dosing, associated with capping chemotherapy in obese patients as an attempt to avoid excess toxicity, might be a driver of poor prognostic outcomes. By contrast, the efficacy of immune checkpoint inhibition may be enhanced in patients who are obese, although in turn, this observation might be due to reverse causality. So, a central research question is whether being overweight or obese adversely affects outcomes either directly through effects of cancer biology or whether adverse outcomes are mediated through indirect pathways. A further dimension to this complex relationship is the obesity paradox, a phenomenon where being overweight or obese is associated with improved survival where the reverse is expected. In this overview, we describe a framework for evaluating methodological problems such as selection bias, confounding and reverse causality, which may contribute to spurious interpretations. Future studies will need to focus on prospective studies with well-considered methodology in order to improve the interpretation of causality.

Correlations of analgesic dosage of morphine with SLC6A4 gene polymorphisms in patients with lung cancer

OBJECTIVE

To investigate the correlations of analgesic dosage of morphine with solute carrier family 6 member 4 (SLC6A4) gene polymorphisms in patients with lung cancer.

PATIENTS AND METHODS

A total of 200 lung cancer patients without cancer pain were selected as painless group, and another 200 lung cancer patients with cancer pain as cancer pain group. Visual Analogue Scale (VAS) was applied to grade the pain, the patients in cancer pain group were treated with morphine, and the dosage of morphine within 24 h was recorded. Then, the genomic deoxyribonucleic acid (DNA) was extracted from the peripheral blood of the research subjects, and the polymorphisms rs1042173 and rs7224199 of SLC6A4 gene were detected.

RESULTS

There was a difference in the genotype distribution of SLC6A4 gene rs7224199 between painless group and cancer pain group (p=0.004), and the frequency of GG genotype was remarkably higher in cancer pain group [75 (0.375)]. The frequency of heterozygous model AC of rs1042173 and recessive model GT + TT of rs7224199 in cancer pain group was evidently lower than that in painless group (p=0.048, p=0.043). Besides, the lung cancer patients in cancer pain group had markedly lower frequency of AG haplotype (p=0.000), but notably higher frequency of AT (p=0.000) and CG (p=0.000) haplotypes of SLC6A4 gene rs1042173 and rs7224199 than those in painless group. No significant differences in genotypes of SLC6A4 gene rs1042173 (p=0.241) and rs7224199 (p=0.316) were detected among the degrees of cancer pain in cancer pain group. The analgesic dosage of morphine for the lung cancer patients was prominently correlated with the genotypes of SLC6A4 gene rs1042173 in cancer pain group. Moreover, in cancer pain group, there were significant differences in the dosage within 24 h (p=0.025), at 24 h after weight correction (p=0.001) and at 24 h after correction of weight and body surface area (p=0.000) among the genotypes, and the morphine dosage for the patients with CC genotype was significantly lower. Furthermore, the morphine dosage within 24 h (p=0.047), at 24 h after weight correction (p=0.042) and at 24 h after correction of weight and body surface area (p=0.031) were distinctly associated with the haplotypes of SLC6A4 gene in cancer pain group, of which the patients with CT haplotype were administered with a remarkably lower morphine dosage.

CONCLUSIONS

The morphine dosage for analgesia has significant correlations with SLC6A4 gene polymorphisms in patients with lung cancer.

Seasonal nitrogen uptake strategies in a temperate desert ecosystem depends on N form and plant species

Symbiotic plants might be able to regulate a limited nitrogen (N) pool, thus avoiding and reducing competition for resources, through the uptake of different chemical N forms. Our aim was to see whether coexisting herbs showed preference for different forms of N in a temperate desert. We conducted a situ experiment using the ¹⁵ N labeling method in the Gurbantunggut Desert of Northwestern China dominated by Erodium oxyrrhynchum, Hyalea pulchella, Nonea caspica and Lactuca undulata during their growing period (April and May). Four desert herb species preferentially relied on ¹⁵ N-NO₃ for their N nutrition. Multi-factor analysis of variance (ANOVA) analysis results showed that species, N forms, months, and soil depths strongly affected N uptake rate. The uptake rate by herbs was higher in May than in April, and higher at 0-5 cm than at 5-15 cm soil layers. Erodium oxyrrhynchum, N. caspica and L. undulata showed different preference on N form over months. Erodium oxyrrhynchum and L. undulata changed their uptake preference from more ¹⁵ N-Glycine in April to more ¹⁵ N-NH4 in May. Although the N uptake rate of four desert herbs varied across different soil depths and months, all species absorbed more inorganic N compared with organic N. The higher preference for ¹⁵ N-NO₃ and ¹⁵ N-NH4 over ¹⁵ N-Gly possibly reflects adaptation to different N forms in temperate desert.

microRNA-331-3p attenuates neuropathic pain following spinal cord injury via targeting RAP1A

Neuropathic pain (NP) after spinal cord injury (SCI) leads to compromised physical and cognitive functions in a majority of patients. Aberrant miRNA expression plays vital roles in the pathogenesis of SCI. This study aims to investigate the effect of miR-331-3p in rats following SCI. Microarray assay was performed in SCI- and sham-operated rats to evaluate the expression of miR-331-3p. Assigned SCI rats were treated with miR-331-3p agomiR alone or miR-331-3p agomiR plus RAP1A-expressing lentivirus or control agomiR. Rat locomotor performance was evaluated by BBB locomotor rating scale. Neuronal tissue damage and apoptosis were detected by histological analyses and Western blot. Inflammation in spinal cord was determined by detection of the expression of inflammatory genes with qRT-PCR, and ELISA. Downstream expression of RAP1A was measured by Western blot. The results showed that SCI induced the downregulation of miR-331-3p in the spinal cord of SCI rats. Overexpression of miR-331-3p improved the locomotor performance, reduced tissue damage, neuronal apoptosis and inflammation in rat SCI model. Rap1a (Ras-related protein Rap-1A) was predicted as a downstream target for miR-331-3p, and upregulation of RAP1A impaired the beneficial effect of miR-331-3p post- SCI, which was shown as worse locomotor activity, more severe tissue damage, as well as promoting apoptosis and inflammation in SCI rats. Furthermore, miR-331-3p reduced the activation of RAP1A downstream genes via inhibiting RAP1A expression. These findings indicate a protective role of miR- 331-3p in the development of SCI via the modulation of RAP1A, and may help to develop novel therapy against SCI-induced complications.

Tobacco control in China and the road to Healthy China 2030

Healthy China 2030 aims to reduce the adult smoking rate from 27.7% in 2015 to 20% by 2030. Achieving this goal requires a review of the tobacco control measures introduced in China to date, the gaps that remain and the opportunities ahead. In 2008, the World Health Organization introduced six measures to reduce demand for tobacco called MPOWER. The progress China has made in implementing these measure varies: 1) monitor tobacco use and prevention policies. The surveillance on tobacco use has been rigorous, but the monitoring and evaluation of tobacco control policies needs to be strengthened; 2) protect people from tobacco use: pushes for national tobacco control legislation have stalled, but 18 subnational legislations have passed; 3) offer help to quit tobacco use. The accessibility and quality of cessation services needs to be improved; 4) warn about the dangers of tobacco. While there are no pictorial health warnings, tobacco control advocates have launched a series of anti-smoking media campaigns to inform the public; 5) enforce bans on tobacco advertising, promotion, and sponsorship. Legal loopholes and poor enforcement remain challenges; 6) raise taxes on tobacco: cigarettes in China are relatively cheap and increasingly affordable, which demonstrates the need for further tobacco tax increases indexed to inflation and income. China maintains a tobacco monopoly that interferes with tobacco control efforts and fails to regulate tobacco products from the public health perspective. Effective MPOWER measures, which depend upon the removal of tobacco industry interference from policymaking, are key to achieving the goal set by Healthy China 2030.

Dietary Inflammatory Index and Leukoaraiosis in Patients with Ischemic Stroke

OBJECTIVES

Diet may change the chronic levels of systemic inflammation, which in turn influence the development of leukoaraiosis (LA). This study aimed to examine the association between dietary inflammatory index (DII) and LA in patients with ischemic stroke.

METHODS

Patients with first-ever ischemic stroke were enrolled from two centers. A semi-quantitative food frequency questionnaire (FFQ) was used to evaluate diet contents. The DII score of each patient was calculated based on the reported diet contents. Presence and degree of LA were evaluated with a magnetic resonance imaging (MRI) scan. LA was graded according to Fazekas scale.

RESULTS

Of the 497 enrolled patients, 337 (67.8%) were detected with LA. Patients with LA had a higher DII score (0.23 vs -0.88, P < 0.001). Logistic regression analysis detected that patients with highest quartile of DII score had an OR of 3.61 (95% CI: 2.05-6.36, P < 0.001) for LA compared with those with lowest quartile of DII. After adjusting for major confounders, the highest DII quartile remained as an independent predictor for LA (OR = 2.66, 95% CI: 1.41-5.00, P = 0.008).

CONCLUSIONS

A pro-inflammatory diet pattern, as indicated by higher DII values, appears to be associated with a higher risk of LA. This result suggested that dietary-mediated inflammation may involved in the pathogenesis of LA, which warrant further study.

Anthropogenic control over wintertime oxidation of atmospheric pollutants

During winter in the mid-latitudes, photochemical oxidation is significantly slower than in summer and the main radical oxidants driving formation of secondary pollutants, such as fine particulate matter and ozone, remain uncertain, owing to a lack of observations in this season. Using airborne observations, we quantify the contribution of various oxidants on a regional basis during winter, enabling improved chemical descriptions of wintertime air pollution transformations. We show that 25-60% of NO_x is converted to N₂O₅ via multiphase reactions between gas-phase nitrogen oxide reservoirs and aerosol particles, with ~93% reacting in the marine boundary layer to form >2.5 ppbv ClNO₂. This results in >70% of the oxidizing capacity of polluted air during winter being controlled, not by typical photochemical reactions, but from these multiphase reactions and emissions of volatile organic compounds, such as HCHO, highlighting the control local anthropogenic emissions have on the oxidizing capacity of the polluted wintertime atmosphere.