Quantitative study of state 1-state 2 transitions in broken chloroplasts—comparison to in-vivo properties

A detailed quantitative study was conducted on state 1-state 2 transition and its reversal in broken chloroplasts by modulated fluorimetry. The characteristics of the transition obtained supported other previous in-vitro findings. More importantly, a very close quantitative similarity was obtained under suitable conditions to previous in-vivo studies, particularly in approaching a constancy of F_m/F₀ during the transition and the equality of the fractional change of these fluorescence parameters with the calculated light distribution fraction to PS II. This confirms that in broken chloroplasts too, the state transitions involve reciprocal changes in the absorption cross-sections of PS II and PS I.Abbreviations AMP-PNP adenylylimidodiphosphate - LHC II light harvesting chlorophyll a/b-protein complex - MeV methylviologen     

Selective activation of intra-muscular compartments within the trapezius muscle in subjects with Subacromial Impingement Syndrome. A case-control study

Neuromuscular control of the scapular muscles is important in the etiology of shoulder pain. Electromyographical (EMG) biofeedback in healthy people has been shown to support a selective activation of the lower compartment of the trapezius muscle, specifically. The aim of the present paper was to investigate whether patients with Subacromial Impingement Syndrome (SIS) were able to selectively activate the individual compartments within the trapezius muscle, with and without EMG biofeedback to the same extent as healthy controls (No-SIS).Fifteen SIS and 15 No-SIS participated in the study. Sessions with and without visual biofeedback were conducted. Surface EMG was recorded from four compartments of the trapezius muscle. Selective activation was defined as activation above 12% with other muscle parts below 1.5% or activation ratio at or above 95% of the total activation. Without biofeedback significantly fewer SIS subjects than No-SIS achieved selective activation (p = 0.02–0.03).The findings of the study show that without biofeedback No-SIS had a superior scapular muscle control. However, when provided with visual EMG feedback the SIS group performed equally well as the No-SIS group. This indicated that individuals with SIS may benefit from biofeedback training to gain control of the neuromuscular function of the scapular muscle.     

A flexible Bayesian method for detecting allelic imbalance in RNA-seq data

Background

One method of identifying cis regulatory differences is to analyze allele-specific expression (ASE) and identify cases of allelic imbalance (AI). RNA-seq is the most common way to measure ASE and a binomial test is often applied to determine statistical significance of AI. This implicitly assumes that there is no bias in estimation of AI. However, bias has been found to result from multiple factors including: genome ambiguity, reference quality, the mapping algorithm, and biases in the sequencing process. Two alternative approaches have been developed to handle bias: adjusting for bias using a statistical model and filtering regions of the genome suspected of harboring bias. Existing statistical models which account for bias rely on information from DNA controls, which can be cost prohibitive for large intraspecific studies. In contrast, data filtering is inexpensive and straightforward, but necessarily involves sacrificing a portion of the data.

Results

Here we propose a flexible Bayesian model for analysis of AI, which accounts for bias and can be implemented without DNA controls. In lieu of DNA controls, this Poisson-Gamma (PG) model uses an estimate of bias from simulations. The proposed model always has a lower type I error rate compared to the binomial test. Consistent with prior studies, bias dramatically affects the type I error rate. All of the tested models are sensitive to misspecification of bias. The closer the estimate of bias is to the true underlying bias, the lower the type I error rate. Correct estimates of bias result in a level alpha test.

Conclusions

To improve the assessment of AI, some forms of systematic error (e.g., map bias) can be identified using simulation. The resulting estimates of bias can be used to correct for bias in the PG model, without data filtering. Other sources of bias (e.g., unidentified variant calls) can be easily captured by DNA controls, but are missed by common filtering approaches. Consequently, as variant identification improves, the need for DNA controls will be reduced. Filtering does not significantly improve performance and is not recommended, as information is sacrificed without a measurable gain. The PG model developed here performs well when bias is known, or slightly misspecified. The model is flexible and can accommodate differences in experimental design and bias estimation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-920) contains supplementary material, which is available to authorized users.     

不同底物培养的细胞吸附固体基质和有机溶剂的差异

目的:对细菌吸附有机溶剂法进行一定的修改,探索水相溶液pH和电解质浓度对测定细胞疏水性的影响,以及不同底物培养的细胞疏水性的差异性。探索细胞和固体间的静电作用和疏水作用对细菌早期吸附的影响。方法:以9K液体培养基为水相溶液,测定不同pH值和电解质浓度下细胞转移到有机相的吸附率。测定不同底物培养的细胞的Zeta电位以及在石英砂和黄铜矿表面的吸附率。结果:水相溶液pH值的变化并没有引起细胞转移到有机溶液的吸附率的显著变化,而在实验所用的电解质浓度梯度范围内,随着浓度的增加,细胞转移到有机溶剂的吸附率也随之增加,但是以单质硫为底物培养的细胞的吸附率始终大于以Fe2+和黄铜矿为底物培养的细胞。在溶液pH 2.0的条件下,石英砂和黄铜矿带负电,单质硫培养的细胞带正电,而以Fe2+和黄铜矿为底物培养的额细胞带负电。结论:细胞表面疏水性不会受到溶液pH值变化的扰动,但是却会随着电解液浓度的增加而增加,以单质硫为底物培养的细胞的疏水性大于以Fe2+和黄铜矿为底物培养的细胞,不同的细胞表面均含有大量的作为电子供体和电子受体的官能团。不同底物培养的细胞在石英砂和黄铜矿表面的早期吸附受到静电作用和疏水作用力的共同影响。     

龈沟液Chemerin、APN、25(OH)D3与伴2型糖尿病的慢性牙周炎患者牙周指标和Th17/Treg失衡的关系

摘要 目的：探讨龈沟液趋化素（Chemerin）、脂联素（APN）、25-羟维生素D3 [25(OH)D3]与伴2型糖尿病（T2DM）的慢性牙周炎（CP）患者牙周指标和Th17/Treg失衡的关系。方法：选择2021年1月至2022年1月我院口腔科门诊接诊的125例伴T2DM的CP患者,根据CP病情严重程度分为轻度组（42例）、中度组（53例）和重度组（30例）。检测龈沟液中Chemerin、APN、25(OH)D₃水平以及外周血中Th17细胞占比、Treg细胞占比,计算Th17/Treg比值,记录出血指数（SBI）、菌斑指数（PLI）、附着丧失（AL）、牙周袋探诊深度（PD）。分析龈沟液中Chemerin、APN、25(OH)D₃与牙周指标、外周血Th17/Treg的相关性。结果：重度组龈沟液 Chemerin水平和外周血中Th17细胞占比、Th17/Treg比值、PLI、SBI、AL、PD高于中度组和轻度组（P＜0.05）,龈沟液APN、25(OH)D₃水平,外周血Treg细胞占比低于中度组和轻度组（P＜0.05）。龈沟液 Chemerin与PLI、SBI、AL、PD、外周血Th17细胞占比、Th17/Treg比值呈正相关（P＜0.05）,与Treg细胞占比呈负相关（P＜0.05）;龈沟液APN、25(OH)D₃与PLI、SBI、AL、PD、外周血中Th17细胞占比、Th17/Treg比值呈负相关（P＜0.05）,与Treg细胞占比呈正相关（P＜0.05）。结论：伴T2DM 的CP患者龈沟液中Chemerin水平增高,APN、25(OH)D₃水平降低,且与牙周指标和Th17/Treg失衡有关。     

Effects of NaCl salinity on growth, morphology, photosynthesis and proline accumulation of Salvinia natans

The effects of NaCl salinity on growth, morphology and photosynthesis of Salvinia natans (L.) All. were investigated by growing plants in a growth chamber at NaCl concentrations of 0, 50, 100 and 150 mM. The relative growth rates were high (ca. 0.3 d⁻¹) at salinities up to 50 mM and decreased to less than 0.2 d⁻¹ at higher salinities, but plants produced smaller and thicker leaves and had shorter stems and roots, probably imposed by the osmotic stress and lowered turgor pressure restricting cell expansion. Na⁺ concentrations in the plant tissue only increased three-fold, but uptake of K⁺ was reduced, resulting in very high Na⁺/K⁺ ratios at high salinities, indicating that S. natans lacks mechanisms to maintain ionic homeostasis in the cells. The contents of proline in the plant tissue increased at high salinity, but concentrations were very low (<0.1 μmol g⁻¹ FW), indicating a limited capacity of S. natans to synthesize proline as a compatible compound. The potential photochemical efficiency of PSII (F_v/F_m) of S. natans remained unchanged at 50 mM NaCl but was reduced at higher salinities, and the photosynthetic capacity (ETR_max) was significantly reduced at 50 mM NaCl and higher. It is concluded that S. natans is a salt-sensitive species lacking physiological measures to cope with exposure to high NaCl salinity. At low salinities salts are taken up and accumulate in old leaves, and high growth rates are maintained because new leaves are produced at a higher rate than for plants not exposed to salt.     

Responses of the biogas process to pulses of oleate in reactors treating mixtures of cattle and pig manure

The effect of oleate on the anaerobic digestion process was investigated. Two thermophilic continuously stirred tank reactors (CSTR) were fed with mixtures of cattle and pig manure with different total solid (TS) and volatile solid (VS) content. The reactors were subjected to increasing pulses of oleate. Following pulses of 0.5 and 1.0 g oleate/L, the most distinct increase in volatile fatty acid (VFA) concentrations were observed in the reactor with the lowest TS/VS content. This suggests a higher adsorption of oleate on the surfaces of biofibers in the reactor with the highest TS/VS and a less pronounced inhibition of the anaerobic digestion process. On the other hand, addition of 2.0 g oleate/L severely inhibited the process in both reactors, and a significant increase in all VFA concentrations combined with an immediate drop in methane production was noticed. However, 20 days after the reactors had been exposed to oleate both reactors showed a lower VFA concentration along with a higher methane production than before the pulses. This indicates that oleate had a stimulating effect on the overall process. The improved acetogenic and methanogenic activity in the reactors was confirmed in batch activity tests. In addition to this, toxicity tests revealed that the oleate pulses induced an increase in the tolerance level of acetotrophic methanogens towards oleate. When evaluating the usability of different process parameters (i.e., VFA and methane production) as indicators of process recovery, following the inhibition by oleate, propionate was found to be most suitable.     

Salt-Induced Changes in Physio-Biochemical and Antioxidant Defense System in Mustard Genotypes

Salinity stress is a major factor limiting plant growth and productivity of many crops including oilseed. The present study investigated the identification of salt tolerant mustard genotypes and better understanding the mechanism of salinity tolerance. Salt stresses significantly reduced relative water content (RWC), chlorophyll (Chl) content, K⁺ and K⁺ /Na⁺ ratio, photosynthetic rate (P_N), transpiration rate (Tr), stomatal conductance (gs), intercellular CO₂ concentration (Ci) and increased the levels of proline (Pro) and lipid peroxidation (MDA) contents, Na⁺ , superoxide (O₂^•− ) and hydrogen peroxide (H₂O₂) in both tolerant and sensitive mustard genotypes. The tolerant genotypes maintained higher Pro and lower MDA content than the salt sensitive genotypes under stress condition. The activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), glutathione peroxidase (GPX), monodehydroascorbate reductase (MDHAR) and dehydroascorbate reductase (DHAR) were increased with increasing salinity in salt tolerant genotypes, BJ-1603, BARI Sarisha-11 and BARI Sarisha-16, but the activities were unchanged in salt sensitive genotype, BARI Sarisha-14. Besides, the increment of ascorbate peroxidase (APX) activity was higher in salt sensitive genotype as compared to tolerant ones. However, the activities of glutathione reductase (GR) and glutathione S-transferase (GST) were increased sharply at stress conditions in tolerant genotypes as compared to sensitive genotype. Higher accumulation of Pro along with improved physiological and biochemical parameters as well as reduced oxidative damage by up-regulation of antioxidant defense system are the mechanisms of salt tolerance in selected mustard genotypes, BJ-1603 and BARI Sarisha-16.     

老年结直肠癌患者肠道菌群变化与机体免疫炎症营养相关性

目的探讨老年结直肠癌患者肠道菌群变化与机体免疫、炎症、营养指标的相关性,为结直肠癌的防治提供参考。方法纳入2016年1月至2018年6月在我院接受治疗的老年结直肠癌患者30例和同期健康查体的老年人群30例,收集粪便标本,采用FloraCheck~(TM)高通量测序技术对粪便样本中所有细菌的16S rRNA V3-V4区进行DNA测序,序列通过MiSeq 16S宏基因组APP及QIIME软件,分析两组人群间属水平上显著差异性菌群。比较两组人群炎性指标(TNF-α、IL-6、IL-1、IL-12)、营养指标(总蛋白、白蛋白、前白蛋白、转铁蛋白)和免疫指标(CD3~+、CD4~+、CD8~+、NK)的差异。分析老年结直肠癌患者肠道菌群变化与营养、炎症、免疫的内在联系。结果老年结直肠癌组和老年健康组人群免疫指标CD3~+、CD4~+、CD8~+、NK和CD4~+/CD8~+比较差异无统计学意义;炎性指标老年结直肠癌组TNF-α含量较对照组明显增高(t=3.769,P=0.001),两组人群IL-1、IL-6、IL-12比较差异无统计学意义;营养指标老年结直肠癌组白蛋白、前白蛋白较对照组明显下降(t=-4.107,P=0.001;t=-4.366,P=0.001),两组人群总蛋白、转铁蛋白比较差异无统计学意义。老年结直肠癌组肠道差异性菌属变化,包括Eubacterium、Ruminococcaceae_UCG-002、Peptostreptococcus、Porphyromonas和部分炎症指标、营养指标、免疫指标有明显相关性。结论老年结直肠癌患者肠道菌群结构和功能异常,可能是导致患者机体免疫损伤、炎症反应、营养不佳的主要原因之一。有针对性地对肠道菌群结构进行优化,改善肠道菌群对宿主的影响,是一种帮助老年结直肠癌患者促进健康的策略。