Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences

Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. These results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.

RAP80 Phase Separation at DNA Double-Strand Break Promotes BRCA1 Recruitment and Tumor Radio-Resistance

PURPOSE/OBJECTIVE(S)

RAP80 has been characterized as a component of the BRCA1-A complex and is responsible for the recruitment of BRCA1 to DNA double-strand breaks (DSBs). However, we and others found that the recruitment of RAP80 and BRCA1 are not absolutely temporally synchronized, indicating that other mechanisms, apart from physical interaction, may be implicated. Recently, we and other groups have reported that liquid-liquid phase separation (LLPS) is a pivotal mechanism underlying DNA repair factors condensation at DSBs and their function. In this study, we aim to disclose whether RAP80 undergoes LLPS at DSBs and whether it is required for BRCA1 recruitment.

MATERIALS/METHODS

To verify RAP80 is an LLPS protein and its function in DNA damage response (DDR): (1) candidate-mEGFP fusion protein formed condensates in cells and showed fluorescence recovery after photobleaching (FRAP); (2) candidate protein was expressed in Escherichia coli and purified with GST; (3) intrinsically disordered region (IDR) of RAP80 were predicted and tested in cell and in vitro; (4) lentivirus were used to construct RAP80-Knock out (KO) and RAP80 re-expression cell lines; (5) length gradient K63 poly-ubiquitin chains were chemically synthesized and incubated with RAP80 protein in vitro; (6) BRCA1 and RAP80 location were determined through immunofluorescence; (7) RAP80 protein expression in tissue was determined by IHC staining.

RESULTS

Thin layer scanning and 3D reconstruction of the RAP80-mEGFP-expressing cells under a fluorescence microscope showed that RAP80-mEGFP formed spherical condensates with fast FRAP. Observation of purified proteins revealed that GST-RAP80-mEGFP protein formed liquid-like droplets, presenting as a FRAP and the fusion event among adjacent droplets. PEG-8000 and Ficol-400 strengthened the formation of GST-RAP80-mEGFP droplets in vitro. Later, we used a previously developed optoIDR tool to verify that IDR1 (1-254aa) is critical for RAP80 LLPS. To investigate whether the interaction between RAP80 and K63 poly-ubiquitin chains could enhance the condensation of RAP80, we chemically synthesized K63 ubiquitin chains and incubated them with purified GST-RAP80-mCherry proteins. The results showed that supplementation of ubiquitin multipolymer (poly-ubiquitin) significantly induced the LLPS of RAP80, and the ability of RAP80 condensates formation potency was positively correlated with the length of the ubiquitin chain. Consistent with their LLPS capacity, RAP80-WT-mEGFP, RAP80-(IDR1+AIR)-mEGFP groups showed prominent BRCA1 foci, while RAP80-IDR1-mEGFP and RAP80-(SIM+UIM)-mEGFP groups showed delayed BRCA1 recruitment. In rectal cancer tissues, positive staining of the RAP80 protein was mainly observed in the nucleus of cancer cells and high RAP80 expression was correlated with a shorter overall survival time.

CONCLUSION

RAP80 undergoes LLPS to form liquid-like condensates at DSB sites, which is important for BRCA1 recruitment and enhances tumor radio-resistance.

Ubiquitinated H2A.X-Induced RNF168 Condensation Promotes DNA Double-Strand Break Repair and Tumor Radioresistance

PURPOSE/OBJECTIVE(S)

Ubiquitination of histone is an essential process involved in DNA damage response (DSB) serving as scaffolds for DNA repair proteins, but how these factors are recruited so quickly and regulated in a spatiotemporal manner remains poorly understood. Liquid-liquid phase separation (LLPS) has recently emerged as a mechanism for membraneless condensation driven by multivalent interactions. In this study, we aimed to investigate the LLPS potential of RNF168, an E3 ligase essential for DSB repair, and the mechanism underlying its-mediated tumor radio-resistance.

MATERIALS/METHODS

The intrinsic disordered domain (IDR) of RNF168 was determined by the PONDR website. The LLPS properties were validated by droplet formation in vivo and in vitro. RNF168-mEGFP were expressed in Escherichia coli and purified with GST tag. The synthesized K63-linked ubiquitin chains were added to mimic the interactions between RNF168 and radiation-induced ubiquitinated-histone. Effects of RNF168 LLPS on downstream proteins were verified by immunofluorescence.

RESULTS

RNF168-mEGFP recombinant protein formed liquid-like droplets in vivo and co-localized with γ-H2A.X foci after irradiation. The droplet's fluorescence recovered quickly after photobleaching, which could be abolished by 1,6-hexanediol treatment or ATP deprivation. Purified RNF168-mEGFP protein also condensed in vitro, and the size and number of droplets were related to protein concentration, salt concentration, pH, and temperature. Condensation of RNF168 was dependent on the IDR (323-459 amino acid), and more importantly, enhanced by synthesized K63-linked ubiquitin chains. LLPS of RNF168 was required for recruitment of RNF168 to DSB and RNF168-mediated γ-H2A.X ubiquitination. LLPS deficiency of RNF168 resulted in decreased recruitment of 53BP1, BRCA1, and RAP80 proteins, resulting in impaired DSB repair and genomic instability. Notably, higher expression of RNF168 was correlated with a poorer response to neoadjuvant radiochemotherapy in rectal cancer patients. Finally, RNF168 condensate-induced tumor radioresistance was further verified in the xenograft model.

CONCLUSION

RNF168 undergoes LLPS at the DSB site, which is determined by both the IDR domain and the interaction with K63-linked ubiquitin chains. Radiation-induced RNF168 condensation accelerates the accumulation of RNF168 and promotes the recruitment of downstream effectors to DSB, resulting in enhanced DSB repair and tumor radioresistance.

[CIC-rearranged sarcoma: a clinicopathological analysis of four cases]

Objective: To investigate the clinicopathological features and differential diagnosis of CIC-rearranged sarcoma (CRS). Methods: Five CRSs of 4 patients (2 biopsies of pelvic cavity and lung metastasis from case 4) diagnosed in the First Affiliated Hospital of Nanjing Medical University were enrolled from 2019 to 2021. All cases were evaluated by clinical presentation, H&E, immunohistochemical staining and molecular analysis and the related literature was reviewed. Results: There were one male and three females, the age at diagnosis ranged from 18 to 58 (mean 42.5) years. Three cases were from the deep soft tissues of the trunk and one case from the skin of foot. Grossly, the tumor size ranged from 1 to 16 cm. Microscopically, the tumor was arranged in nodules or solid sheets. The tumor cells were typically round or ovoid, with occasional spindled or epithelioid morphology. The nuclei were round to ovoid with vesicular chromatin and prominent nucleoli. Mitotic figures were brisk (>10/10 HPF). Rhabdoid cells were seen in four of five cases. Myxoid change and hemorrhage were observed in all samples and two cases showed geographic necrosis. Immunohistochemically, CD99 was variably positive in all samples, while WT1 and TLE-1 were positive in four of five samples. Molecular analysis showed CIC-rearrangements in all cases. Two patients succumbed within 3 months. One had mediastinal metastasis 9 months after surgery. One underwent adjuvant chemotherapy and remained tumor-free 10 months after diagnosis. Conclusions: CIC-rearranged sarcoma is uncommon and shows aggressive clinical course with dismal prognosis. The morphological and immunohistochemical characteristics can largely overlap with a variety of sarcomas; hence, knowledge of this entity is vital to avoid potential diagnostic pitfalls. Definitive diagnosis requires molecular confirmation of CIC-gene rearrangement.

[Progress in research of determinants of healthy life expectancy]

Objective: To analyze the influencing factors of healthy life expectancy (HLE). Methods: Seven Chinese and English databases were used for the retrieval of related literatures published by May 7, 2022 to identify influencing factors of HLE, including diseases and injuries and their risk factors. Based on the ecological model of health determinants, this study classifies the risk factors of diseases and injuries into five levels: personal characteristics, individual behavior and lifestyle, social network, living and working conditions, and macroscopic socio-economic, cultural and environmental conditions. Contents of research area, HLE indicators, research population, influencing factors, data sources and results were extracted. The frequencies of reported documents of different HLE indicators and influencing factors of different dimensions were visualized by using evidence map, and the empirical studies of four authoritative English medical journals and Chinese core medical journals were further compared and described. Results: A total of 90 studies were selected, in which 26 were conducted in China (28.9%). Fifty-three studies are about diseases and injuries in the first dimension, and all of them have studied non-communicable diseases, accounting for the highest proportion (58.9%). There were 77 studies about the analysis on the determinants of health at five levels by an ecological model, all the studies reported multi-level results. Among them, 53 studies reported personal characteristics (58.9%), 47 studies reported individual behavior and lifestyle (52.2%), 10 studies reported social networks (11.1%), 35 studies reported living and working environment (38.9%), 8 studies reported social economy, culture status and environment condition (8.9%). The literatures about HLE published by 4 authoritative English medical journals and 21 Chinese core medical journals in recent three years were selected. Non-communicable diseases and personal characteristics were the top two most commonly studied factors of HLE, and 11 (52.3%) and 12 (57.1%) studies reported these two kinds of factors respectively. The most important factor contributing to the global disability-adjusted life years of non-communicable diseases was individual behavior and lifestyle, which was the most changeable factor. Conclusions: In recent three years, studies involving influencing factors of HLE were mainly non-communicable diseases and personal characteristics. In the future, individual behavior, lifestyle and working environment should be strengthened.

[Analysis on liver cancer mortality and cause eliminated life expectancy in key areas of 4 provinces, China, 2008-2018]

Objective: To explore the changes of liver cancer mortality and the effect of liver cancer on life expectancy in key areas of four provinces in China from 2008 to 2018 and provide the basis for the evaluation of comprehensive prevention and control of cancer and promotion of the rational allocation of health resources. Methods: Based on the national cause-of-death surveillance in key areas of the 4 provinces from 2008 to 2018, we analyzed the mortality of liver cancer, cause eliminated life expectancy (CELE) and potential gains in life expectancy (PGLEs). Software Joinpoint 4.9.0.0 was used to calculate the average annual percentage change (AAPC). Arriaga's decomposition method was used to estimate the contribution of the changes of liver cancer mortality in each age group to life expectancy. Results: The standardized mortality of liver cancer in key areas of the 4 provinces showed a downward trend from 2008 to 2018 (AAPC=-4.37%, P<0.001). The changes of liver cancer mortality had a positive effect on the increase of life expectancy, with a contribution value of 0.240 years and a contribution degree of 5.62%. The positive effect was greatest in age group 45-49 years (0.041 years, 0.96%), and the negative effect was greatest in age group 50-54 years (-0.015 years, -0.35%). Compared with 2008, the life expectancy increased by 4.27 years (AAPC=0.59%, P<0.001), the liver cancer CELE increased by 4.20 years (AAPC=0.58%, P<0.001), the PGLEs decreased by 0.07 years (AAPC=-0.62%,P<0.001), and life loss rate decreased by 0.13% (AAPC=-1.18%, P=0.001). The liver cancer PGLEs increased in Yongqiao district, Anhui province (0.09 years), and decreased in other districts (counties), with the largest decline was in Fugou county, Henan province (-0.21 years). Conclusions: From 2008 to 2018, the standardized mortality rate of liver cancer in key areas of the 4 provinces decreased gradually, contributing to the growth of life expectancy. The life loss caused by liver cancer decreased gradually, but the PGLEs varied with districts (counties).

[Progress in research on redistribution methods for garbage codes in causes of death data]

The existence of garbage codes in death cause surveillance data sets could influence the accuracy of the death cause statistics, and subsequently affect the precision and effectiveness of public health policy making. International and domestic researchers have studied the characteristics of garbage codes in various death cause data sets from different countries or regions in the world. They proposed several approaches for redistributing garbage codes, such as expert consultancy, fixed proportional reassignment, using the information about death cause chain, building statistical models, and so on. This paper summarizes and compares the principles, applications and limitation of application scenarios of currently common methods for garbage code redistribution in order to provide some references for improving the accuracy and usefulness of the death cause data in China.

[ELF4 promotes proliferation and inhibits apoptosis of human insulinoma cells by activating Akt signaling]

OBJECTIVE

To investigate the effect of overexpression of the oncogenic transcription factor ELF4 on proliferation and apoptosis in human insulinoma cells and explore the underlying mechanism.

METHODS

A human insulinoma BON cell line with stable overexpression of ELF4 (BON-ELF4 cells) was constructed using a recombinant retrovirus vector and the expression of ELF4 protein was verified using Western blotting. MTT assay was used to assess the proliferation of BON-ELF4 cells and BON-Vector cells, and the cell apoptosis induced by treatment with epirubicin (0.1 μmol/L for 24 h) was analyzed by detecting the expressions of cleaved caspase-8, caspase-9, and PARP using Western blotting. Flow cytometry with Annexin VFITC/PI staining was performed to analyze the numbers of apoptotic BON-Vector or BON-ELF4 cells. The expressions of phosphorylated Akt and total Akt in the cells were detected using Western blotting.

RESULTS

BON-ELF4 cell line with stable overexpression of ELF4 was successfully established. ELF4 overexpression significantly promoted the proliferation (P < 0.05) and obviously suppressed epirubicin- induced apoptosis in BON cells, resulting also in significantly reduced expressions of cleaved caspase-8, caspase-9 and PARP (P < 0.05). The results of flow cytometry showed a significantly lower apoptotic rate in BON-ELF4 cells than in BON-Vector cells following epirubicin treatment (6.03% vs 22.90%). The phosphorylation levels of Akt (Thr308 and Ser473) were significantly increased (P < 0.05) while the level of total Akt remained unchanged (P>0.05) in ELF4- overexpressing cells.

CONCLUSION

ELF4 overexpression enhances the proliferation and suppresses apoptosis of insulinomas cells by activating Akt signaling.

Does Tea Drinking Promote Health of Older Adults: Evidence from the China Health and Nutrition Survey

OBJECTIVE

This study selects the health indicators of older adults to analyze the impact of tea drinking on health.

DESIGN

This is a panel data.

SETTING

This study uses data from China Health and Nutrition Survey (CHNS), which covers nine provinces and ten waves, between 1997 and 2015.

PARTICIPANTS

a total of 706 old adults are consistently surveyed in six surveys on issues such as health and nutrition.

MEASUREMENTS

Health of old adults is assessed by self-reported health (SRH), tea drinking is 0-1 dummy variable, and also analyze with the frequency of tea drinking. This study uses ordered probit model to analyze the influence of tea drinking on SRH.

RESULTS

Findings reveal a significant negative correlation between tea drinking and SRH of older adults. It is shows that the significant positive correlation exists between the tea drinking frequency and SRH, but the quadratic term of tea frequency shows the significant negative correlation. It means drinking tea benefits older adults in terms of improved health, but excessive consumption of tea is not healthy for them. The heterogeneity analyses reveal that there are no significant geographic, tea-drinking pattern or gender differences in the conclusion that tea drinking is good for older adults' health.

CONCLUSION

In this study, we find correlation between tea drinking and SRH of older adults, and tea drinking is beneficial toward the improvement of SRH, but drinking tea in excess is not good for older adults' health.

Effects of environmental cleaning bundles on reducing healthcare-associated Clostridioides difficile infection: a systematic review and meta-analysis

Environmental contamination with Clostridioides difficile plays an important role in the transmission of C. difficile infection (CDI) in healthcare and long-term care facilities, which results in prolonged length of stay, higher risk of mortality and increased healthcare costs. Environmental cleaning bundles are introduced to improve environmental cleanliness. This study aimed to evaluate whether environmental cleaning bundles applied in hospital, community and long-term care settings reduce the incidence of healthcare-associated CDI compared with conventional cleaning practices. Relevant databases, websites and trial registration platforms were searched. Two reviewers conducted study screening and selection, data collection, risk of bias assessment and evidence quality assessment independently. Meta-analyses were conducted using Review Manager 5.3. Ten eligible studies [one randomized controlled trial (RCT) and nine non-RCTs] were included. No significant effect of environmental cleaning bundles on the CDI incidence rate was found [risk ratio (RR)=0.96, 95% confidence interval (CI) 0.71-1.29; studies=2; I²=49%; very low quality]. However, the removal of surface markers was improved significantly (RR=1.55, 95% CI 1.30-1.84; studies=3; I²=98%; very low quality), and the percentage of CDI rooms with positive cultures of C. difficile (RR=0.16, 95% CI 0.08-0.31; studies=4; I²=7%; moderate quality) was reduced significantly after the implementation of environmental cleaning bundles. Environmental cleaning bundles may consequently be helpful in improving the thoroughness of cleaning of environmental surfaces in hospital and long-term care settings. More well-conducted RCTs are expected to provide stronger evidence.

[Efficacy and safety of ruxolitinib in the salvage treatment of chronic graft versus-host disease]

Objective: To investigate the efficacy and safety of low-dose Ruxolitinib in the treatment of patients with chronic graft-versus-host disease (cGVHD) and refractory to the first-line and/or second-line drugs after allogeneic hematopoietic stem cell transplantation. Methods: The clinical data was retrospectively analyzed of patients diagnosed with cGVHD in Anhui Provincial Hospital from July 9, 2018 to May 23, 2019. They were refractory to first-line and second-line drugs and were given a low-dose of Ruxolitinib (a dose of 5 mg twice daily if body weight ≥ 25 kg and 2.5 mg twice daily if body weight<25 kg). There was 2.5 mg reduction per week or every two weeks if the condition improved until withdrawal. The efficacy and safety of Ruxolitinib were retrospectively analyzed weekly or biweekly. If the condition improved, the dosage would be reduced by 2.5 mg weekly or biweekly until discontinuance. Results: A total of 47 patients were included in the study,and the median time of taking Ruxolitinib was 55 (21-154) days. The median time of taking effect was 14(7-28) days. The overall response rate was 87.2% (41/47). The complete response rate was 63.8% (30/47) and the partial response rate was 23.4%(11/47). Among them, 13 cases were mild and the overall response rate was 100%(13/13). Twenty one cases were moderate and the overall response rate was 90.5%(19/21). Thirteen cases were severe and the overall response rate was 69.2%(9/13). The highest overall response rate of all organs the was 100% in the gastrointestinal tract (7/7), and it was 95.8%(23/24) for the skin, 83.3%(5/6) for the liver and 76.9%(10/13) for the lung. The highest rate of complete organ response was 95.8% for skin. Eight patients (17%) developed cytopenia, of which 2(4.2%) were with a decrease of 3-4 degree hemoglobin. Recrudescence of cytomegalovirus occurred in 3 patients (6.4%). After withdrawal of Ruxolitinib, 6 patients (12.7%) had recurrence of cGVHD. The median time to relapse was 35.5(7-90) days. All of their conditions were improved after addition of Ruxolitinib. The median time of response was 7(5-14) days. The median follow-up was 208(33-412) days. Three patients(6.4%) died, and all of them died of severe pulmonary infection. Three patients (6.4%) had relapse of primary disease. The 6-month overall survival rate was 95.7%. Conclusion: Low-dose Ruxolitinib has good efficacy and safety in the treatment of cGVHD.

[Effect of KIR/HLA receptor-ligand mode on prognosis of single unrelated cord blood transplantation in patients with hematological malignancies]

目的

探讨自然杀伤细胞免疫球蛋白样受体（KIR）与人类白细胞抗原（HLA）受配体模式对血液病患者单份非血缘脐血移植（sUCBT）预后的影响。

方法

回顾性分析2012年7月至2018年6月270例接受sUCBT的血液病患者。移植前脐血及患者均进行HLA12个位点高分辨配型，选择移植物（脐血）的KIR均同时表达2DL1和2DL2/2DL3抑制性基因，根据患者KIR配体情况分为缺失组（C1/C1或C2/C2）和无缺失组（C1/C2）。

结果

270例血液病患者中男146例（54.1％），女124例（45.9％），中位年龄13（1～62）岁；缺失组174例（64.4％），无缺失组96例（35.6％）。全部患者均采用不含抗胸腺细胞球蛋白（ATG）清髓性预处理方案。缺失组、无缺失组粒细胞植入率均为98.9％（172/174、95/96），中位植入时间分别为16（10～41）d、17（11～33）d（P＝0.705）；血小板植入率分别为88.5％（154/174）、87.5％（84/96），中位植入时间分别为35（11～113）d、38.5（13～96）d（P＝0.317）；缺失组、无缺失组Ⅱ～Ⅳ级急性GVHD发生率分别为38.7％（95％CI 31.4％～45.9％）、50.0％（95％CI 39.6％～59.6％）（P＝0.075），多因素分析显示KIR配体缺失是影响Ⅱ～Ⅳ度急性GVHD发生的独立保护性因素（P＝0.036）。移植后3年累积复发率分别为17.7％（95％CI 11.7％～24.9％）、22.7％（95％CI14.4％～32.2％）（P＝0.288）。中位随访时间742（335～2 512）d，缺失组、无缺失组3年总生存率分别为72.1％（95％CI 64.1％～78.6％）、60.5％（95％CI 47.9％～69.2％）（χ²＝3.629，P＝0.079），3年无病生存率分别为64.9％（95％CI 56.2％～72.3％）、55.4％（95％CI 44.4％～65.0％）（χ²＝3.027，P＝0.082），移植后180 d 非复发死亡率分别为12.1％（95％CI 7.7％～17.4％）、16.7％（95％CI 10.0％～24.8％）（P＝0.328）。

结论

在不含ATG清髓性预处理sUCBT血液病治疗体系中，缺失抑制性KIR配体患者移植后急性GVHD发生率更低。

Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean

Ammonia oxidation to nitrite and its subsequent oxidation to nitrate provides energy to the two populations of nitrifying chemoautotrophs in the energy-starved dark ocean, driving a coupling between reduced inorganic nitrogen (N) pools and production of new organic carbon (C) in the dark ocean. However, the relationship between the flux of new C production and the fluxes of N of the two steps of oxidation remains unclear. Here, we show that, despite orders-of-magnitude difference in cell abundances between ammonia oxidizers and nitrite oxidizers, the two populations sustain similar bulk N-oxidation rates throughout the deep waters with similarly high affinities for ammonia and nitrite under increasing substrate limitation, thus maintaining overall homeostasis in the oceanic nitrification pathway. Our observations confirm the theoretical predictions of a redox-informed ecosystem model. Using balances from this model, we suggest that consistently low ammonia and nitrite concentrations are maintained when the two populations have similarly high substrate affinities and their loss rates are proportional to their maximum growth rates. The stoichiometric relations between the fluxes of C and N indicate a threefold to fourfold higher C-fixation efficiency per mole of N oxidized by ammonia oxidizers compared to nitrite oxidizers due to nearly identical apparent energetic requirements for C fixation of the two populations. We estimate that the rate of chemoautotrophic C fixation amounts to ∼1 × 1013 to ∼2 × 1013 mol of C per year globally through the flux of ∼1 × 1014 to ∼2 × 1014 mol of N per year of the two steps of oxidation throughout the dark ocean.

Diversity and abundance of comammox bacteria in the sediments of an urban lake

AIMS

Although comammox have been discovered in a variety of ecosystems, there are few studies in urban lakes. This paper attempted to confirm whether this ammonia-oxidizing microbe exists in urban lakes and to determine the factors influencing its existence.

METHODS AND RESULTS

This study investigated the diversity and abundance of comammox bacteria in sediments of a typical urban lake in China, and their ecological relationship with other ammonia-oxidizing micro-organisms. The phylogenetic analysis indicated that comammox clade A existed in the sediment of Lake Donghu, and the comammox bacteria co-existed with ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and anaerobic ammonia-oxidizing (anammox) bacteria in the sediment of this lake. The abundances of the ammonia monooxygenase subunit A (amoA) genes for comammox, AOA, AOB and anammox 16S rRNA were 2·43 × 10⁸ , 1·07 × 10⁸ , 3·24 × 10⁷ and 3·21 × 10¹¹ copies per gram dry sediment respectively. Moreover, the amoA gene abundance of comammox was positively correlated with that of AOA and AOB. The redundancy analysis showed that the abundance of the comammox amoA gene was negatively correlated with the concentration of main indicators for nitrogen status in both the sediment and the water column, indicating that eutrophication may inhibit the growth of comammox bacteria.

CONCLUSIONS

Comammox bacteria play an important ecological role in the nitrogen cycle of urban lake sediments.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results indicated comammox bacteria were widespread in urban lakes and eutrophication may inhibit their growth.

[Comparison of umbilical cord blood transplantation and hematopoietic stem cell transplantation from HLA-matched sibling donors in the treatment of myelodysplastic syndrome-EB or acute myeloid leukemia with myelodysplasia-related changes]

目的

比较非血缘脐血干细胞移植（UCBT）与同胞HLA全相合供者造血干细胞移植（MSD-HSCT）治疗骨髓增生异常综合征伴原始细胞增多（MDS-EB）和急性髓系白血病伴骨髓增生异常相关改变（AML-MRC）的临床疗效。

方法

回顾性分析2011年2月至2017年12月接受UCBT/MSD-HSCT的MDS-EB/AML-MRC患者64例，其中MDS-EB 38例，AML-MRC 26例。

结果

①与MSD-HSCT组比较，UCBT组AML-MRC患者比例较高[52.8%（19/36）对25.0%（7/28），P=0.025]，中位年龄较低[13（1.5~52）岁对32（10~57）岁，P=0.001]。②UCBT组与MSD-HSCT组+42 d粒细胞植入率均为100%，中位植入时间分别为17.5（11~31）d、11.5（10~20）d；UCBT组+100 d血小板植入率为91.4%，中位植入时间为40（15~96）d，MSD-HSCT组+100 d血小板植入率为100.0%，中位植入时间为15（11~43）d。③UCBT组和MSD-HSCT组比较，+100 dⅡ~Ⅳ度、Ⅲ/Ⅳ度急性GVHD累积发生率、180 d移植相关死亡率、3年累积复发率、3年总生存率和3年无病生存率差异均无统计学意义（P>0.05）。④UCBT组3年慢性GVHD、重度慢性GVHD的累积发生率均低于MSD-HSCT组[28.3%（95% CI 13.4%~45.3%）对67.9%（95%CI 46.1%~82.4%），P=0.002；10.3%（95%CI 2.5%~24.8%）对50.0%（95%CI 30.0%~67.1%），P<0.001]；UCBT组3年无严重急慢性GVHD及无复发生存（GRFS）率明显高于MSD-HSCT组[55.0%（95%CI 36.0%~70.6%）对28.6%（95%CI 13.5%~45.6%），P=0.038]。

结论

UCBT治疗MDS-EB/AML-MRC患者可获得比MSD-HSCT更好的移植后生存质量。

[Efficacy analysis of unrelated cord blood transplantation in the treatment of refractory and relapsed adult acute leukemia]

目的

探讨非血缘脐血移植（UCBT）挽救治疗难治复发急性白血病（AL）患者的临床疗效和安全性。

方法

回顾性分析2009年11月至2017年5月22例行UCBT挽救治疗的难治复发成人AL患者的临床资料，全部患者采用清髓性预处理方案，均采用环孢素A/短程霉酚酸酯方案预防GVHD。

结果

①22例患者中男9例，女13例，中位年龄23（15~44）岁；中位体重52.5（43~82）kg。所有患者回输脐血有核细胞中位数为3.07（1.71~5.30）×10⁷/kg（受者体重），CD34⁺细胞中位数为1.60（0.63~3.04）×10⁵/kg（受者体重）。②移植后42 d髓系累积植入率为95.5%（95%CI 45.2%~99.7%），中位植入时间为19（13~27）d；移植后120 d血小板累积植入率为81.8%（95%CI 54.2%~93.6%），中位植入时间为42（20~164）d。③Ⅱ~Ⅳ度、Ⅲ~Ⅳ度急性GVHD发生率以及慢性GVHD 2年累积发生率分别为36.4%、13.6%和40.3%。④移植后180 d移植相关死亡率为22.7%；2年累积复发率为18.7%（95%CI 3.6%~42.5%），2年累积无病生存率及累积总生存率分别为53.7%和58.1%。

结论

对于常规化疗无效的难治复发成人AL患者，初步结果显示采用UCBT安全、有效。

Organic matter decomposition sustains sedimentary nitrogen loss in the Pearl River Estuary, China

The Pearl River Estuary (PRE) has long received tremendous amounts of anthropogenic nitrogen, and is facing severe environmental problems. Denitrification and anaerobic ammonium oxidation (anammox) are known to be two major nitrogen removal pathways in estuarine sediments. Through the use of slurry and intact sediment core incubations, we examined the nitrogen removal pathways and quantified the in situ denitrification and anammox with associated gaseous nitrogen production rates. Sedimentary nitrogen removal was predominated by denitrification (93-100%) relative to a minimal contribution (<7%) from anammox. Among the detected environmental factors, salinity, bottom water NO_x^- (nitrate and nitrite) concentration, sedimentary organic matter and dissolved oxygen consumption rates showed good correlations with denitrification and anammox rates. Sedimentary nitrogen loss was mainly supported by endogenic coupled nitrification-denitrification (6.0 ± 1.5 × 10⁶ mol N d^-1), with water-column-delivered NO_x^- (2.1 ± 0.6 × 10⁶ mol N d^-1) as the secondary source. Such results suggested that sedimentary nitrogen removal involved mainly particulate organic form (allochthonous or autochthonous) deposited onto sediments, rather than inorganic forms in overlying water. Meanwhile, total N₂O production from sediments was estimated to be 7.3 ± 2.1 × 10⁴ mol N d^-1, equivalent to ~35% of the daily N₂O emissions in the PRE.

Loss at 16q22.1 identified as a risk factor for intrahepatic recurrence in hepatocellular carcinoma and screening of differentially expressed genes

Copy number alteration (CNA) of chromosome 16, a frequent genetic event in tumors including hepatocellular carcinoma (HCC), has been associated with HCC etiology of hepatitis B virus (HBV) and with clinical outcomes in multiple types of cancer. This study identified CNAs in chromosome 16 in relation to intrahepatic recurrence of HCC in a population with high HBV prevalence, and further screened for differentially expressed genes in recurrence-related CNAs. Array comparative genomic hybridization and expression arrays were used to detect CNAs and gene expression differences, respectively. The associations between CNAs and intrahepatic recurrence were analyzed on 66 patients, follow-up period of 3-73 months. One hundred and nine cases were further evaluated regarding the differentially expressed genes. Losses at 16q and 16p were detected in 62.1% and 51.5% of the 66 cases, respectively. The most recurrent CNAs (with frequency >20%) were losses at 16p13.3-13.2, 16p13.11, 16q11.2-22.1, 16q22.1, 16q22.2-24.2 and 16q24.2. Of the CNAs, 16q22.1 loss was significantly associated with unfavorable intrahepatic recurrence-free survival (P = 0.025). Multivariate Cox analysis identified 16q22.1 loss as an independent risk factor for intrahepatic recurrence (HR = 2.32, 95% CI = 1.26-4.27). A panel of 21 genes, including TRADD, PSMB10, THAP11, CTCF and ESRP2, were significantly downregulated in HCCs with 16q22.1 loss compared to those without the loss. These results suggest that loss at 16q22.1 was associated with increased risk for intrahepatic recurrence of HCC, at least in the HBV-prevalence population. Multiple downregulated genes correlated with the loss were screened.

A novel splice site mutation of the PRKAR1A gene, C.440+5 G>C, in a Chinese family with Carney complex

BACKGROUND

Carney complex (CNC) is an extremely rare, multiple endocrine neoplasia syndrome that occurs in an autosomal dominant manner. Mutations in PRKAR1A have been reported to be a common genetic cause of CNC.

METHODS

In this study, we reported a Chinese pedigree of CNC that manifests mainly as spotty skin pigmentation and primary pigmented nodular adrenocortical disease. Whole blood samples of this pedigree were collected for DNA/RNA analysis. Polymerase chain reaction (PCR) and reverse-transcription polymerase chain reaction analyses were performed to amplify the 11 exons and adjacent introns of PRKAR1A. Direct sequencing was used to detect the mutation, and DNA from 70 Han Chinese people was extracted and sequenced as a control to estimate the frequency of the identified mutation.

RESULTS

Within the pedigree, ten patients with CNC were identified, and a novel heterozygous mutation (c.440+5 G>C in intron 4a) was identified in the PRKAR1A gene. PCR amplification of cDNA from the control subjects and patients was performed. Agarose gel electrophoresis showed only one wild-type band in the cDNA corresponding to the former group, whereas an extra band was present in samples from the latter group corresponding to the skipping of exon 4a; this confirms that the variant affects PRKAR1A splicing.

CONCLUSION

In conclusion, the c.440+5 G>C mutation is a new splice site mutation that has not been reported and has the potential to broaden the mutational spectrum of PRKAR1A that is associated with CNC, which would facilitate genetic diagnosis and counseling for CNC.

[Choice of genetic model on Meta-analysis of genetic association studies: introduction of genetic model-free approach for Bayesian analysis]

Meta-analysis used for genetic association studies became popular among researchers, with the amount of published papers increased rapidly. In this paper, we will focus on the introduction on the selection of genetic models. Traditionally, methods used for Meta-analysis on genetic association studies was to calculate the statistics based on available genetic models which not only increasing the probability of false-positives but also making the interpretation of results more difficult. Hence, a critical step in the Meta-analysis of genetic association studies was to choose the appropriate inheritance model. The aim of this paper was to introduce the theory of Bayesian analysis regarding the genetic model-free approach, in performing the Meta-analysis for studies related to genetic associations.

Osteochondral Interface Stiffening in Mandibular Condylar Osteoarthritis

Osteoarthritis (OA) of the temporomandibular joint (TMJ) is associated with dental biomechanics. A major change during OA progression is the ossification of the osteochondral interface. This study investigated the formation, radiological detectability, and mechanical property of the osteochondral interface at an early stage, the pathogenesis significance of which in OA progression is of clinical interest and remains elusive for the TMJ. Unilateral anterior crossbite (UAC) was performed on 6-wk-old rats as we previously reported. TMJs were harvested at 4, 12, and 20 wk. The progression of TMJ OA was evaluated using a modified Osteoarthritis Research Society International (OARSI) score system. Osteochondral interface was investigated by quantifying the thickness via von Kossa staining of histological slices and in vivo calcium deposition by calcein injection. Tissue ossification was imaged by micro-computed tomography (CT). Mechanical properties were measured at nanoscale using dynamic indentation. Time-dependent TMJ cartilage lesions were elicited by UAC treatment. Geometric change of the condyle head and increased value of the OARSI score were evident in UAC TMJs. At the osteochondral interface, there was not only enhanced deep-zone cartilage calcification but also calcium deposition at the osseous boundary. The thickness, density, and stiffness of the osteochondral interface were all significantly increased. The enhanced ossification of the osteochondral interface is a joint outcome of the aberrant deeper cartilage calcification at the superior region and promoted formation of subchondral cortical bone at the inferior region. The micro-CT detectable ossification from an early stage thus is of diagnostic significance. Although the environment of the cartilage and subchondral bone could be changed due to the stiffness of the interface, whether or not the stiffened interface would accelerate OA progress remains to be confirmed. With that evidence, the osteochondral interface could be a new diagnostic and therapeutic target of the mechanically initiated OA in the TMJ.

Exosomes promote cetuximab resistance via the PTEN/Akt pathway in colon cancer cells

Cetuximab is widely used in patients with metastatic colon cancer expressing wildtype KRAS. However, acquired drug resistance limits its clinical efficacy. Exosomes are nanosized vesicles secreted by various cell types. Tumor cell-derived exosomes participate in many biological processes, including tumor invasion, metastasis, and drug resistance. In this study, exosomes derived from cetuximab-resistant RKO colon cancer cells induced cetuximab resistance in cetuximab-sensitive Caco-2 cells. Meanwhile, exosomes from RKO and Caco-2 cells showed different levels of phosphatase and tensin homolog (PTEN) and phosphor-Akt. Furthermore, reduced PTEN and increased phosphorylated Akt levels were found in Caco-2 cells after exposure to RKO cell-derived exosomes. Moreover, an Akt inhibitor prevented RKO cell-derived exosome-induced drug resistance in Caco-2 cells. These findings provide novel evidence that exosomes derived from cetuximab-resistant cells could induce cetuximab resistance in cetuximab-sensitive cells, by downregulating PTEN and increasing phosphorylated Akt levels.

Matrix replenishing by BMSCs is beneficial for osteoarthritic temporomandibular joint cartilage

OBJECTIVES

The present goal was to explore whether matrix replenishment is the primary requirement for osteoarthritic (OA) cartilage.

METHODS

Cells isolated from the superficial and deep zone cartilage of a pig temporomandibular joint (TMJ) were exposed to fluid flow shear stress (FFSS). Differences in matrix production and cellular differentiation were detected. Unilateral anterior crossbite (UAC) was applied to C57BL/6J female mice. Green fluorescent protein-labeled exogenous bone marrow stromal cells (GFP-BMSCs) were injected weekly into TMJs, starting from 3 weeks of UAC stimulation and continuing for 4-, 8- and 12-weeks. Another GFP-BMSCs injection UAC group stopped receiving injections for 4-weeks after 8-weeks of injections. Assessments were focused on morphological alterations in UAC mouse TMJ cartilage, the expression levels of DAP3, an anoikis marker, CD163, a scavenger receptor family member, and ki67, a proliferation indicator.

RESULTS

FFSS down-regulated type-II collagen expression but stimulated terminal differentiation in cells isolated from deep zone cartilage. It down-regulated aggrecan expression but up-regulated type I collagen in cells isolated from both superficial and deep zones. UAC caused matrix loss and anoikis and enhanced scavenging activity in deep zone chondrocytes without affecting cell proliferation. Superficial fibrillation was obvious in the late stage. Weekly injections of BMSCs largely restored these changes. The implanted BMSCs expressed a high level of CD163 protein but did not show remarkable cell proliferation. Terminating the supply of exogenous BMSCs reversed the restorative effects.

CONCLUSIONS

Scavenging the degraded matrix and replenishing the fibrosis-developmental matrix are the primary requirements for the repair of OA cartilage.

Cord blood NK cells engineered to express IL-15 and a CD19-targeted CAR show long-term persistence and potent antitumor activity

Chimeric antigen receptors (CARs) have been used to redirect the specificity of autologous T cells against leukemia and lymphoma with promising clinical results. Extending this approach to allogeneic T cells is problematic as they carry a significant risk of graft-versus-host disease (GVHD). Natural killer (NK) cells are highly cytotoxic effectors, killing their targets in a non-antigen-specific manner without causing GVHD. Cord blood (CB) offers an attractive, allogeneic, off-the-self source of NK cells for immunotherapy. We transduced CB-derived NK cells with a retroviral vector incorporating the genes for CAR-CD19, IL-15 and inducible caspase-9-based suicide gene (iC9), and demonstrated efficient killing of CD19-expressing cell lines and primary leukemia cells in vitro, with marked prolongation of survival in a xenograft Raji lymphoma murine model. Interleukin-15 (IL-15) production by the transduced CB-NK cells critically improved their function. Moreover, iC9/CAR.19/IL-15 CB-NK cells were readily eliminated upon pharmacologic activation of the iC9 suicide gene. In conclusion, we have developed a novel approach to immunotherapy using engineered CB-derived NK cells, which are easy to produce, exhibit striking efficacy and incorporate safety measures to limit toxicity. This approach should greatly improve the logistics of delivering this therapy to large numbers of patients, a major limitation to current CAR-T-cell therapies.

Aspartate β-hydroxylase disrupts mitochondrial DNA stability and function in hepatocellular carcinoma

The mechanism of aberrant mitochondrial genome and function in hepatocellular carcinoma (HCC) remains largely unknown. Our previous study demonstrated an increased expression of aspartate β-hydroxylase (ASPH) in HCC tissues, which was associated with tumor invasiveness and a worse prognosis. Currently, we unexpectedly observed the presence of ASPH in purified mitochondrial protein fraction. In addition, immunostaining of both exogenously and endogenously expressed ASPH showed a colocalization with mitochondrial biomarkers. This study aimed to investigate whether the mitochondrial ASPH is involved in mitochondrial malfunction in HCC. Our results showed that ASPH overexpression in HCC tissues was correlated with decreased copy numbers of displacement loop (D-loop) and NADH dehydrogenase subunit 1 (ND-1) and enhanced D-loop mutation, suggesting the disrupted mitochondrial DNA (mtDNA) stability. The reduced mtDNA copy numbers were associated with aggressive clinicopathological features of HCC. The loss of mtDNA integrity induced by enforced expression of ASPH was accompanied with mitochondrial dysfunction, which was characterized by the aberrant mitochondrial membrane potential, decreased ATP generation and enhanced reactive oxygen species. In contrast, knocking down ASPH by siRNA in HCC cell lines showed the opposite impact on mtDNA integrity and function. Mass spectrometry and co-immunoprecipitation further identified that ASPH interacted with histone H2A member X (H2AX). ASPH overexpression diminished the interaction between H2AX and mitochondrial transcription factor A (mtTFA), an important DNA-binding protein for mtDNA replication, which then reduced the binding of mtTFA to D-loop region. Collectively, our results demonstrate that ASPH overexpression disrupts the mtDNA integrity through H2AX-mtTFA signal, thereby affecting mitochondrial functions in HCC.

[Review on the evaluation research of the effects of smoke-free legislations on cardiovascular diseases]

A substantial amount of data suggested that exposure to secondhand smoke (SHS) could cause cardiovascular diseases and acute coronary events in nonsmoking adults. In order to protect the public from SHS, more and more countries and regions across the world have enacted and implemented smoke-free legislations. Developed countries, such as USA, Canada, the Great Britain, Ireland, Italy and Spain, have carried out many studies to analyze the effects of smoke-free legislations on the hospital admission, incidence and mortality of cardiovascular diseases with the purpose of confirming the health benefits of the smoking ban and promoting the conduct of the ban. We searched PubMed, EMBASE, Web of Science, Cochrane Library,China National Knowledge Infrastructure(CNKI),WANFANG databaseto summarize the study designs, evaluating indicators, statistical methods and results of these studies to provide reference for evaluating smoke-free legislations in inland cities in China.