bluuebunny/crossref_metadata_2025 huggingface dataset:
Case Report: Hemophagocytic Lymphocytosis in a Patient With Glutaric Aciduria Type IIC
Authors: Huang Lingtong , Wu Wei , Zhu Yijing , Yu Huili , Tang Lingling , Fang Xueling
Published: January 2022

Hemophagocytic lymphocytosis (HLH) is a rare disease caused by inborn errors of immunity (IEI), secondary to infection, lymphoma or autoimmune disorders, but we often overlook the fact that HLH can be secondary to inborn errors of metabolism (IEM). Here, we describe a patient who was diagnosed with glutaric aciduria type IIC complicated by features suggestive of possible HLH. The diagnosis of glutaric aciduria type IIC, a IEM, was confirmed by whole exome sequencing. The patient was treated with coenzyme Q10 and riboflavin which effectively improved her liver function. During treatment, the patient developed severe anemia and thrombocytopenia. Persistent fever, splenomegaly, cytopenias, increased ferritin, hypertriglyceridemia, hypofibrinogenemia, and hemophagocytosis in the bone marrow pointed to the diagnosis of HLH; however, the patient eventually died of gastrointestinal bleeding. After other potential causes were ruled out, the patient was diagnosed with glutaric aciduria type IIC complicated by features suggestive of possible HLH. When cytopenias occurs in IEM patients, HLH is a possible complication that cannot be ignored. This case suggests a possible relationship between IEM and risk for immune dysregulation.
IL-17 Aggravates Pseudomonas aeruginosa Airway Infection in Acute Exacerbations of Chronic Obstructive Pulmonary Disease
Authors: Ding Fengming , Han Lei , Fu Qiang , Fan Xinxin , Tang Rong , Lv Chengjian , Xue Yishu , Tian Xue , Zhang Min
Published: January 2022

Pseudomonas aeruginosa airway infection increases risks of exacerbations and mortality in chronic obstructive pulmonary disease (COPD). We aimed to elucidate the role of IL-17 in the pathogenesis. We examined the expression and influences of IL-23/IL-17A in patients with stable COPD (n = 33) or acute COPD exacerbations with P. aeruginosa infection (n = 34). A mouse model of COPD (C57BL/6) was used to investigate the role of IL-17A in host inflammatory responses against P. aeruginosa infection through the application of IL-17A–neutralizing antibody or recombinant IL-17A. We found that P. aeruginosa infection increased IL-23/17A signaling in lungs of both COPD patients and COPD mouse models. When COPD mouse models were treated with neutralizing antibody targeting IL-17A, P. aeruginosa induced a significantly less polymorphonuclear leukocyte infiltration and less bacterial burden in their lungs compared to those of untreated counterparts. The lung function was also improved by neutralizing antibody. Furthermore, IL-17A-signaling blockade significantly reduced the expression of pro-inflammatory cytokine IL-1β, IL-18, TNF-α, CXCL1, CXCL15 and MMP-9, and increased the expression of anti-inflammatory cytokine IL-10 and IL-1Ra. The application of mouse recombinant IL-17A exacerbated P. aeruginosa-mediated inflammatory responses and pulmonary dysfunction in COPD mouse models. A cytokine protein array revealed that the expression of retinol binding protein 4 (RBP4) was down-regulated by IL-17A, and exogenous RBP4-recombinant protein resulted in a decrease in the severity of P. aeruginosa-induced airway dysfunction. Concurrent application of IL-17A-neutralizing antibody and ciprofloxacin attenuated airway inflammation and ventilation after inoculation of P. aeruginosa in COPD mouse models. Our results revealed that IL-17 plays a detrimental role in the pathogenesis of P. aeruginosa airway infection during acute exacerbations of COPD. Targeting IL-17A is a potential therapeutic strategy in controlling the outcomes of P. aeruginosa infection in COPD patients.
The cGAS-STING Pathway in Bacterial Infection and Bacterial Immunity
Authors: Liu Nanxin , Pang Xiaoxiao , Zhang Hua , Ji Ping
Published: January 2022

Cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) (cGAMP) synthase (cGAS), along with the adaptor stimulator of interferon genes (STING), are crucial components of the innate immune system, and their study has become a research hotspot in recent years. Many biochemical and structural studies that have collectively elucidated the mechanism of activation of the cGAS-STING pathway with atomic resolution have provided insights into the roles of the cGAS-STING pathway in innate immunity and clues to the origin and evolution of the modern cGAS-STING signaling pathway. The cGAS-STING pathway has been identified to protect the host against viral infection. After detecting viral dsDNA, cGAS synthesizes a second messenger to activate STING, eliciting antiviral immune responses by promoting the expression of interferons (IFNs) and hundreds of IFN-stimulated genes (ISGs). Recently, the cGAS-STING pathway has also been found to be involved in response to bacterial infections, including bacterial pneumonia, melioidosis, tuberculosis, and sepsis. However, compared with its functions in viral infection, the cGAS-STING signaling pathway in bacterial infection is more complex and diverse since the protective and detrimental effects of type I IFN (IFN-I) on the host depend on the bacterial species and infection mode. Besides, STING activation can also affect infection prognosis through other mechanisms in different bacterial infections, independent of the IFN-I response. Interestingly, the core protein components of the mammalian cGAS-STING signaling pathway have been found in the bacterial defense system, suggesting that this widespread signaling pathway may have originated in bacteria. Here, we review recent findings related to the structures of major molecules involved in the cGAS-STING pathway and the effects of the cGAS-STING pathway in various bacterial infections and bacterial immunity, which may pave the way for the development of new antibacterial drugs that specifically kill bacteria without harmful effects on the host.
DNA Damage Repair in Brain Tumor Immunotherapy
Authors: Zhao Shihong , Xu Boya , Ma Wenbin , Chen Hao , Jiang Chuanlu , Cai Jinquan , Meng Xiangqi
Published: January 2022

With the gradual understanding of tumor development, many tumor therapies have been invented and applied in clinical work, and immunotherapy has been widely concerned as an emerging hot topic in the last decade. It is worth noting that immunotherapy is nowadays applied under too harsh conditions, and many tumors are defined as “cold tumors” that are not sensitive to immunotherapy, and brain tumors are typical of them. However, there is much evidence that suggests a link between DNA damage repair mechanisms and immunotherapy. This may be a breakthrough for the application of immunotherapy in brain tumors. Therefore, in this review, first, we will describe the common pathways of DNA damage repair. Second, we will focus on immunotherapy and analyze the mechanisms of DNA damage repair involved in the immune process. Third, we will review biomarkers that have been or may be used to evaluate immunotherapy for brain tumors, such as TAMs, RPA, and other molecules that may provide a precursor assessment for the rational implementation of immunotherapy for brain tumors. Finally, we will discuss the rational combination of immunotherapy with other therapeutic approaches that have an impact on the DNA damage repair process in order to open new pathways for the application of immunotherapy in brain tumors, to maximize the effect of immunotherapy on DNA damage repair mechanisms, and to provide ideas and guidance for immunotherapy in brain tumors.
Temporal Distribution of Arsenic and Metals in Soil From King George Island, Antarctica
Authors: Trevizani Tailisi H. , Montone Rosalinda C. , Figueira Rubens C. L.
Published: January 2022

The polar regions are vulnerable to impacts caused by local and global pollution. The Antarctic continent has been considered an environment that has remained little affected by human activities. Direct exposure to contaminants may occur in areas continuously occupied by research stations for several decades. Admiralty Bay on the southeast coast of King George Island, has potential for being affected by human activities due research stations operating in the area, including the Brazilian Commandant Ferraz Antarctic Station (CFAS). The levels of metals and arsenic were determined in soils collected near CFAS (points 5, 6, 7, and 9), Base G and at two points distant from the CFAS: Refuge II and Hennequin. Samples were collected after the fire in CFAS occurred in February 2012, up to December 2018 to assess the environmental impacts in the area. Al and As were related with Base G. Refuge II and Hennequin can be considered as control points for this region. As a consequence of the accident, the increased levels for Cd, Cu, Pb, and Zn, especially at point 9 (inside the CFAS) and in the soil surrounding the CFAS in 2013. The results from 2016 to 2018 demonstrated a reduction in levels of all studied metals near CFAS, which may be related to the leaching of metals into Admiralty Bay; it is thus, being important the continue monitoring soil, sediments, and Antarctic biota.
Influence of Functional Group Modification on the Toxicity of Nanoplastics
Authors: Zhang Haihong , Cheng Haodong , Wang Yudi , Duan Zhenghua , Cui Wenjie , Shi Yansong , Qin Li
Published: January 2022

Nanoplastics (NPs) are ubiquitous in harvested organisms at various trophic levels, and more concerns on their diverse responses and wide species-dependent sensitivity are continuously increasing. However, systematic study on the toxic effects of NPs with different functional group modifications is still limited. In this review, we gathered and analyzed the toxic effects of NPs with different functional groups on microorganisms, plants, animals, and mammalian/human cells in vitro. The corresponding toxic mechanisms were also described. In general, most up-to-date relevant studies focus on amino (−NH2) or carboxyl (−COOH)-modified polystyrene (PS) NPs, while research on other materials and functional groups is lacking. Positively charged PS-NH2 NPs induced stronger toxicity than negatively charged PS-COOH. Plausible toxicity mechanisms mainly include membrane interaction and disruption, reactive oxygen species generation, and protein corona and eco-corona formations, and they were influenced by surface charges of NPs. The effects of NPs in the long-term exposure and in the real environment world also warrant further study.
Plastic After an Extreme Storm: The Typhoon-Induced Response of Micro- and Mesoplastics in Coastal Waters
Authors: Nakajima Ryota , Miyama Toru , Kitahashi Tomo , Isobe Noriyuki , Nagano Yuriko , Ikuta Tetsuro , Oguri Kazumasa , Tsuchiya Masashi , Yoshida Takao , Aoki Kunihiro , Maeda Yosaku , Kawamura Kiichiro , Suzukawa Maki , Yamauchi Takuya , Ritchie Heather , Fujikura Katsunori , Yabuki Akinori
Published: January 2022

Extreme storms, such as tropical cyclones, are responsible for a significant portion of the plastic debris transported from land to sea yet little is known about the storm response of microplastics and other debris in offshore and open waters. To investigate this, we conducted floating plastic surveys in the center of Sagami Bay, Japan approximately 30 km from the coastline, before and after the passage of a typhoon. The concentrations (number of particles/km2) of micro- and mesoplastics were two orders of magnitude higher 1-day after the typhoon than the values recorded pre-typhoon and the mass (g/km2) of plastic particles (sum of micro- and mesoplastics) increased 1,300 times immediately after the storm. However, the remarkably high abundance of micro- and mesoplastics found at 1-day after the typhoon returned to the pre-typhoon levels in just 2 days. Model simulations also suggested that during an extreme storm a significant amount of micro- and mesoplastics can be rapidly swept away from coastal to open waters over a short period of time. To better estimate the annual load of plastics from land to sea it is important to consider the increase in leakages of plastic debris into the ocean associated with extreme storm events.
Small Blubber Samples (50 mg) Sufficient for Analyses of 10 Stress and Reproductive Steroid Hormones in Gray and Fin Whales via Liquid Chromatography Mass Spectrometry
Authors: Wittmaack Christiana , Urbán Ramírez Jorge , Bernot-Simon Daniela , Martínez-Aguilar Sergio , Subbiah Seenivasan , Surles James G. , Looney Mary , Kumar Naveen , Halaska Barbie , Duignan Pádraig J. , Knauss Madelyn , Burns Kristen , Godard-Codding Céline A. J.
Published: January 2022

Information on stress, reproductive fitness, and health is difficult to obtain in wild cetaceans but critical for conservation and management. The goal of this study was to develop a methodology requiring minimal blubber mass for analysis of reproductive and stress steroid hormones and, hence, suitable for cetacean biopsies. Blubber biopsies and samples were collected from free-ranging and stranded gray and fin whales. Steroid hormones were extracted from blubber samples as small as 50 mg using liquid-liquid extraction methodology developed to handle the high fat content of blubber. Samples were analyzed via liquid chromatography with tandem mass spectrometry for 10 hormones: aldosterone, androstenedione, cortisol, cortisone, corticosterone, 17β-estradiol, estrone, 17α-hydroxyprogesterone, progesterone, and testosterone. As part of the optimization, homogenization via bead beating and blade dispersion were compared, and the former found superior. To investigate optimal yet minimal tissue mass required, hormone panels were compared among paired 50, 150, and 400 mg samples, the latter two being commonly reported masses for hormone blubber analysis. Results indicated that 50 mg of blubber was suitable and sometimes superior. Additionally, significant differences in precision values were observed between species, possibly stemming from differences in blubber composition, and relevant to homogenization technique selection and calibration methods that use blubber matrix matches obtained from a species other than the study species. Based on recovery and precision values, our methodology was accurate and precise in the measurement of spiked known quantities for all 10 hormones, confirming the methodology capabilities in 50 mg blubber mass in both species. Altogether, and in our specific sample sets, all endogenous hormones, except corticosterone, were identified above the detection limit in 50 mg gray whale blubber samples while all endogenous hormones, except aldosterone, cortisone, estrone, and progesterone, were detected in 50 mg fin whale blubber samples. We present a robust methodology for the analysis of multiple reproductive and stress steroid hormones in minimal masses of cetacean blubber compatible with small biopsies. Finally, we identified statistically significant differences in corticosteroid concentrations between stranded and free ranging animals.
Origin of Local Structures of U-Co Melts: A First-Principles Study
Authors: Zhang Huanqing , Sun Honggang , Li Qiutong , Wang Li
Published: January 2022

The local structures of U-Co melts have been studied by first-principle calculations. Two sub-peaks are observed in the first peaks of U-U pair distribution functions. The Voronoi polyhedral analyses also show two separate core-shell U-U distances. Therefore, the calculated results propose that U atoms will play dual roles, “chemical” and “topological”, in the local structures of U-Co melts. In addition, the chemical effect of U atoms will be strengthened when containing more U atoms. The interaction of Co and U atoms is slightly affected by the compositions. The Co-centered clusters are mostly prism-like or antiprism-like polyhedral, which can be predicted by the solute-solvent model. The distribution of the coordinated numbers of Co atoms is much narrower than that of U atoms, showing relatively stable Co-centered clusters. The chemical and topological roles of U atoms are intuitively observed in the electron density of U-Co melts, which presents both metallic and covalent bonding characteristics for U-U bonds. In the end, we conclude that the partial localization of U 5f-electron is responsible for the dual roles of U atoms. The present results provide a theoretical understanding of the origin of the local structures of U-Co melts.
Experimental and Modeling Study of Wall Film Effect on Combustion Characteristics of Premixed Flame in a Constant Volume Combustion Bomb
Authors: Bai Shijie , Zhang Hongsheng , Li Chang , Wu Chaohui , Liang Xingyu , Wang Kun
Published: January 2022

The primary objective of the present study was to investigate the impact of wall film on the combustion characteristics of premixed flames in internal combustion engines through the joint experimental and numerical techniques. The interaction between the premixed methane-air flame and n-dodecane film attached to the wall of a constant volume combustion bomb was experimentally examined. The flame propagation processes, as well as pressure evolution were quantitatively characterized. Then, computational fluid dynamic (CFD) simulation was performed incorporating the combustion chemistry model. To enable efficient simulation of the chemically reacting flow in engine chambers, a simplified modeling approach based on a two-step reaction scheme was developed. A compact reaction model for the selected model fuel n-dodecane was constructed and reduced to include 35 chemical species and 180 reactions. The flame propagation process of the premixed flame and its interaction with dry and wet walls was studied. The results showed that the propagation of the premixed flame could be divided into four stages, and the existence of the slit structure increased the instability of the flame structure in the near-wall region. The wall film tended to promote emissions, producing more unburned hydrocarbons, soot precursors and aldehydes.
Case Report: Effectiveness of Targeted Treatment in a Patient With Pancreatic Cancer Harboring PALB2 Germline Mutation and KRAS Somatic Mutation
Authors: Wu Wei , Liu Yu , Jin Yuzhi , Liu Lulu , Guo Yixuan , Xu Mian , Hao Qing , Li Dazhi , Fang Weijia , Zhang Aibin , Zhao Peng
Published: January 2022

Pancreatic cancer is one of the most leading causes of cancer death worldwide. The rapid development of next-generation sequencing (NGS) and precision medicine promote us to seek potential targets for the treatment of pancreatic cancer. Here, we report a female pancreatic cancer patient who underwent radical surgical excision after neoadjuvant chemotherapy. After the surgery, the patient underwent gemcitabine + S-1 therapy, capecitabine + albumin paclitaxel therapy and irinotecan therapy successively, however, MRI review revealed tumor progression. The surgical tissue sample was subjected to next-generation sequencing (NGS), and PALB2 germline mutation and KRAS somatic mutation were identified. The patient then received olaparib (a PARP inhibitor) + irinotecan and the disease stabilized for one year. Due to the increased CA19-9, treatment of the patient with a combination of trametinib (a MEK inhibitor) and hydroxychloroquine resulted in stable disease (SD) with a significant decrease of CA19-9. This case demonstrated that the NGS may be a reliable method for finding potential therapeutic targets for pancreatic cancer.
Characteristics of Silicone Oil Emulsification After Vitrectomy for Rhegmatogenous Retinal Detachment: An Ultrasound Biomicroscopy Study
Authors: Zhao Hongmei , Yu Jian , Zong Yuan , Jiang Chunhui , Zhu Haohao , Xu Gezhi
Published: January 2022

Purpose: To investigate the characteristics of silicone oil (SO) emulsification after vitrectomy for rhegmatogenous retinal detachment (RRD) and possible correlations with clinical factors.

Methods: Patients who underwent primary pars plana vitrectomy with SO injection for RRD followed by SO removal at the Eye and ENT Hospital of Fudan University between January 2016 and January 2020 were included. Ultrasound biomicroscopy (UBM) images of the anterior segment were taken before SO removal. Eight signs of SO emulsification in the UBM images were graded as 1 (present) or 0 (not present) and the grades for all signs in each eye were summed. Correlations between SO emulsification grade and clinical factors were determined.

Results: A total of 118 patients (118 eyes) were enrolled in this study. Emulsified SO particles were found in all 118 eyes (100%). The eight signs were more frequently detected in the superior part of the eye. The mean total SO emulsification grade was 19.99 ± 12.98 (range: 1–36). Younger age and male (both P < 0.05) were associated with higher total SO emulsification grade. Patients with intraocular pressure (IOP) > 21 mmHg or the use of antiglaucoma medications at the time of SO removal had a higher total SO emulsification grade, were younger, and were more frequently male (all P < 0.05) than patients without ocular hypertension.

Conclusions: UBM could play an important role in the diagnosis and grading of SO emulsification. Younger patients and males are more prone to SO emulsification, which may lead to elevated IOP.
Deep Learning in Prostate Cancer Diagnosis Using Multiparametric Magnetic Resonance Imaging With Whole-Mount Histopathology Referenced Delineations
Authors: Li Danyan , Han Xiaowei , Gao Jie , Zhang Qing , Yang Haibo , Liao Shu , Guo Hongqian , Zhang Bing
Published: January 2022

Background: Multiparametric magnetic resonance imaging (mpMRI) plays an important role in the diagnosis of prostate cancer (PCa) in the current clinical setting. However, the performance of mpMRI usually varies based on the experience of the radiologists at different levels; thus, the demand for MRI interpretation warrants further analysis. In this study, we developed a deep learning (DL) model to improve PCa diagnostic ability using mpMRI and whole-mount histopathology data.

Methods: A total of 739 patients, including 466 with PCa and 273 without PCa, were enrolled from January 2017 to December 2019. The mpMRI (T2 weighted imaging, diffusion weighted imaging, and apparent diffusion coefficient sequences) data were randomly divided into training (n = 659) and validation datasets (n = 80). According to the whole-mount histopathology, a DL model, including independent segmentation and classification networks, was developed to extract the gland and PCa area for PCa diagnosis. The area under the curve (AUC) were used to evaluate the performance of the prostate classification networks. The proposed DL model was subsequently used in clinical practice (independent test dataset; n = 200), and the PCa detective/diagnostic performance between the DL model and different level radiologists was evaluated based on the sensitivity, specificity, precision, and accuracy.

Results: The AUC of the prostate classification network was 0.871 in the validation dataset, and it reached 0.797 using the DL model in the test dataset. Furthermore, the sensitivity, specificity, precision, and accuracy of the DL model for diagnosing PCa in the test dataset were 0.710, 0.690, 0.696, and 0.700, respectively. For the junior radiologist without and with DL model assistance, these values were 0.590, 0.700, 0.663, and 0.645 versus 0.790, 0.720, 0.738, and 0.755, respectively. For the senior radiologist, the values were 0.690, 0.770, 0.750, and 0.730 vs. 0.810, 0.840, 0.835, and 0.825, respectively. The diagnosis made with DL model assistance for radiologists were significantly higher than those without assistance (P < 0.05).

Conclusion: The diagnostic performance of DL model is higher than that of junior radiologists and can improve PCa diagnostic accuracy in both junior and senior radiologists.
Association of Gender, Diagnosis, and Obesity With Retention Rate of Secukinumab in Spondyloarthropathies: Results Form a Multicenter Real-World Study
Authors: García-Dorta Alicia , León-Suarez Paola , Peña Sonia , Hernández-Díaz Marta , Rodríguez-Lozano Carlos , González-Dávila Enrique , Hernández-Hernández María Vanesa , Díaz-González Federico
Published: January 2022

Background: Secukinumab has been shown effective for psoriatic arthritis (PsA) and axial spondylarthritis (AxSpA) in randomized trials. The aim of this study was to analyze baseline patient and disease characteristics associated with a better retention rate of secukinumab under real-world conditions.

Patients and Methods: Real-life, prospective multicenter observational study involving 138 patients, 61 PsA and 77 AxSpA, who were analyzed at baseline, 6, 12 months and subsequently every year after starting secukinumab regardless of the line of treatment. Demographics and disease characteristics, measures of activity, secukinumab use, and adverse events were collected. Drug survival was analyzed using Kaplan-Meier curves and factors associated with discontinuation were evaluated using Cox regression. The machine-learning J48 decision tree classifier was also applied.

Results: During the 1st year of treatment, 75% of patients persisted with secukinumab, but accrued 71% (n = 32) in total losses (n = 45). The backward stepwise (Wald) method selected diagnosis, obesity, and gender as relevant variables, the latter when analyzing the interactions. At 1 year of follow-up, the Cox model showed the best retention rate in the groups of AxSpa women (95%, 95% CI 93–97%) and PsA men (89%, 95% CI 84–93%), with the worst retention in PsA women (66%, 95% CI 54–79%). The J48 predicted secukinumab retention with an accuracy of 77.2%. No unexpected safety issues were observed.

Conclusions: Secukinumab shows the best retention rate at 1 year of treatment in AxSpA women and in PsA men, independently of factors such as the time of disease evolution, the line of treatment or the initial dose of the drug.
Construction of Aerobic/Anaerobic-Substrate-Induced Gene Expression Procedure for Exploration of Metagenomes From Subseafloor Sediments
Authors: Wakamatsu Taisuke , Mizobuchi Saki , Mori Fumiaki , Futagami Taiki , Terada Takeshi , Morono Yuki
Published: January 2022

Substrate-induced gene expression (SIGEX) is a high-throughput promoter-trap method. It is a function-based metagenomic screening tool that relies on transcriptional activation of a reporter gene green fluorescence protein (gfp) by a metagenomic DNA library upon induction with a substrate. However, its use is limited because of the relatively small size of metagenomic DNA libraries and incompatibility with screening metagenomes from anaerobic environments. In this study, these limitations of SIGEX were addressed by fine-tuning metagenome DNA library construction protocol and by using Evoglow, a green fluorescent protein that forms a chromophore even under anaerobic conditions. Two metagenomic libraries were constructed for subseafloor sediments offshore Shimokita Peninsula (Pacific Ocean) and offshore Joetsu (Japan Sea). The library construction protocol was improved by (a) eliminating short DNA fragments, (b) applying topoisomerase-based high-efficiency ligation, (c) optimizing insert DNA concentration, and (d) column-based DNA enrichment. This led to a successful construction of metagenome DNA libraries of approximately 6 Gbp for both samples. SIGEX screening using five aromatic compounds (benzoate, 3-chlorobenzoate, 3-hydroxybenzoate, phenol, and 2,4-dichlorophenol) under aerobic and anaerobic conditions revealed significant differences in the inducible clone ratios under these conditions. 3-Chlorobenzoate and 2,4-dichlorophenol led to a higher induction ratio than that for the other non-chlorinated aromatic compounds under both aerobic and anaerobic conditions. After the further screening of induced clones, a clone induced by 3-chlorobenzoate only under anaerobic conditions was isolated and characterized. The clone harbors a DNA insert that encodes putative open reading frames of unknown function. Previous aerobic SIGEX attempts succeeded in the isolation of gene fragments from anaerobes. This study demonstrated that some gene fragments require a strict in vivo reducing environment to function and may be potentially missed when screened by aerobic induction. The newly developed anaerobic SIGEX scheme will facilitate functional exploration of metagenomes from the anaerobic biosphere.
Occurrence, Distribution, and Genetic Diversity of Alfalfa (Medicago sativa L.) Viruses in Four Major Alfalfa-Producing Provinces of China
Authors: Guo Zhipeng , Zhang Tingting , Chen Zhao , Niu Junpeng , Cui Xuewen , Mao Yue , Hassan Mahmood Ul , Kareem Hafiz Abdul , Xu Nan , Sui Xin , Gao Shuanghong , Roy Momi , Cui Jian , Wang Quanzhen
Published: January 2022

Alfalfa (Medicago sativa L.) is one of the most widely cultivated forage crops in the world. China is the second largest producer of alfalfa in terms of the planting area worldwide, with Gansu, Henan, Inner Mongolia, and Shaanxi provinces being the production hubs. Alfalfa viruses have been reported on a small-scale survey in some of these areas, but they have not been well characterized. In the present study, seven viruses were detected in 12 fields of 10 cities/counties of the four abovementioned provinces by high-throughput sequencing and assembly of small RNA. Their incidence, distribution, and genetic diversity were analyzed by enzyme-linked immunosorbent assay, polymerase chain reaction (PCR)/reverse transcription-PCR and clone sequencing. The results showed that alfalfa mosaic virus (AMV), pea streak virus (PeSV), lucerne transient streak virus (LTSV), alfalfa dwarf virus (ADV), Medicago sativa alphapartitivirus 1 (MsAPV1), MsAPV2, and alfalfa leaf curl virus (ALCV) were the main viruses infecting alfalfa in four examined provinces. AMV and MsAPV1 had the highest incidences in all 4 provinces. SDT analysis of the 7 viruses isolated in China revealed a highly conserved among AMV, LTSV, ADV, MsAPV1, MsAPV2, and ALCV, but the sequence was a high variation between China isolates to abroad isolates in PeSV, ADV, and ALCV. To our knowledge, this is the first report of ADV in Inner Mongolia and Gansu, ALCV in Inner Mongolia, MsAPV1 and MsAPV2 in all 4 provinces, and PeSV and LTSV in China. These findings provide a basis for future research on the genetic evolution of alfalfa viruses in China and on strategies to prevent diseases in alfalfa caused by these viruses.
Comparison of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates From Rooks (Corvus frugilegus) and Contemporary Human-Derived Strains: A One Health Perspective
Authors: Nagy Bálint József , Balázs Bence , Benmazouz Isma , Gyüre Péter , Kövér László , Kaszab Eszter , Bali Krisztina , Lovas-Kiss Ádám , Damjanova Ivelina , Majoros László , Tóth Ákos , Bányai Krisztián , Kardos Gábor
Published: January 2022

During winter, a large number of rooks gather and defecate at the park of a university clinic. We investigated the prevalence of extended-spectrum beta-lactamase (ESBL)–producing Escherichia coli in these birds and compared recovered isolates with contemporary human isolates. In 2016, fecal samples were collected from 112 trap-captured rooks and investigated for presence of ESBL producers using eosin methylene blue agar supplemented by 2 mg/L cefotaxime; 2,455 contemporary human fecal samples of patients of the clinics sent for routine culturing were tested similarly. In addition, 42 ESBL-producing E. coli isolates collected during the same period from inpatients were also studied. ESBL genes were sought for by PCR and were characterized by sequencing; E. coli ST131 clones were identified. Epidemiological relatedness was determined by pulsed-field gel electrophoresis and confirmed using whole genome sequencing in selected cases. Thirty-seven (33%) of sampled rooks and 42 (1.7%) of human stools yielded ESBL-producing E coli. Dominant genes were blaCTX–M–55 and blaCTX–M–27 in corvid, blaCTX–M–15 and blaCTX–M–27 in human isolates. ST162 was common among rooks. Two rook-derived E. coli belonged to ST131 C1-M27, which was also predominant (10/42) among human fecal and (15/42) human clinical isolates. Another potential link between rooks and humans was a single ST744 rook isolate grouped with one human fecal and three clinical isolates. Despite possible contact, genotypes shared between rooks and humans were rare. Thus, rooks are important as long-distance vectors and reservoirs of ESBL-producing E. coli rather than direct sources of infections to humans in our setting.
Low-Cost Clamp-On Photometers (ClampOD) and Tube Photometers (TubeOD) for Online Cell Density Determination
Authors: Deutzmann Jörg S. , Callander Grace , Gu Wenyu , Müller Albert L. , McCully Alexandra L. , Ahn Jenna Kim , Kracke Frauke , Spormann Alfred M.
Published: January 2022

Optical density (OD) measurement is the gold standard to estimate microbial cell density in aqueous systems. Recording microbial growth curves is essential to assess substrate utilization, gauge sensitivity to inhibitors or toxins, or determine the perfect sampling point. Manual sampling for cuvette-photometer-based measurements can cause disturbances and impact growth, especially for strictly anaerobic or thermophilic microbes. For slow growing microbes, manual sampling can cause data gaps that complicate analysis. Online OD measurement systems provide a solution, but are often expensive and ill-suited for applications such as monitoring microbial growth in custom or larger anaerobic vessels. Furthermore, growth measurements of thermophilic cultures are limited by the heat sensitivity of complex electronics. Here, we present two simple, low-cost, self-assembled photometers—a “TubeOD” for online measurement of anaerobic and thermophilic cultures in Hungate tubes and a “ClampOD” that can be attached to virtually any transparent growth vessel. Both OD-meters can be calibrated in minutes. We detail the manufacturing and calibration procedure and demonstrate continuous acquisition of high quality cell density data of a variety of microbes, including strict anaerobes, a thermophile, and gas-utilizing strains in various glassware. When calibrated and operated within their detection limits (ca. 0.3–90% of the photosensor voltage range), these self-build OD-meters can be used for continuous measurement of microbial growth in a variety of applications, thereby, simplifying and enhancing everyday lab operations.
Differential Synergistic Interactions Among Four Different Wheat-Infecting Viruses
Authors: Tatineni Satyanarayana , Alexander Jeff , Qu Feng
Published: January 2022

Field-grown wheat (Triticum aestivum L.) plants can be co-infected by multiple viruses, including wheat streak mosaic virus (WSMV), Triticum mosaic virus (TriMV), brome mosaic virus (BMV), and barley stripe mosaic virus (BSMV). These viruses belong to four different genera in three different families and are, hence, genetically divergent. However, the impact of potential co-infections with two, three, or all four of them on the viruses themselves, as well as the wheat host, has yet to be examined. This study examined bi-, tri-, and quadripartite interactions among these viruses in wheat for disease development and accumulation of viral genomic RNAs, in comparison with single virus infections. Co-infection of wheat by BMV and BSMV resulted in BMV-like symptoms with a drastic reduction in BSMV genomic RNA copies and coat protein accumulation, suggesting an antagonism-like effect exerted by BMV toward BSMV. However, co-infection of either BMV or BSMV with WSMV or TriMV led to more severe disease than singly infected wheat, but with a decrease or no significant change in titers of interacting viruses in the presence of BMV or BSMV, respectively. These results were in stark contrast with exacerbated disease phenotype accompanied with enhanced virus titers caused by WSMV and TriMV co-infection. Co-infection of wheat by WSMV, TriMV, and BMV or BSMV resulted in enhanced synergistic disease accompanied by increased accumulation of TriMV and BMV but not WSMV or BSMV. Quadripartite interactions in co-infected wheat by all four viruses resulted in very severe disease synergism, leading to the death of the most infected plants, but paradoxically, a drastic reduction in BSMV titer. Our results indicate that interactions among different viruses infecting the same plant host are more complex than previously thought, do not always entail increases in virus titers, and likely involve multiple mechanisms. These findings lay the foundation for additional mechanistic dissections of synergistic interactions among unrelated plant viruses.
Decreased CDKL2 Expression in Clear Cell Renal Cell Carcinoma Predicts Worse Overall Survival
Authors: Chen Zhan , Lv Yan , He Lu , Wu Shunli , Wu Zhuang
Published: January 2022

Background: Clear cell renal cell carcinoma (ccRCC) is the most frequent and lethal type of kidney cancer. Although differential expression of cyclin-dependent kinase-like 2 (CDKL2) has been reported to be associated with tumor progression in other cancers, its prognostic value, and potential mechanism in patients with ccRCC still remain unknown.

Methods: Gene expression analysis was conducted using The Cancer Genome Atlas (TCGA), Gene Expression Omnibus, and International Cancer Genome Consortium databases. Further, clinicopathologic analysis; Kaplan–Meier survival analysis; weighted gene co-expression network analysis; gene set enrichment analysis; gene ontology enrichment; methylation; and immune infiltration analyses were performed using TCGA-kidney renal clear cell carcinoma profiles. CDKL2 translational levels were analyzed using The Human Protein Atlas database.

Results:CDKL2 expression was decreased in ccRCC samples retrieved from the four databases. Gender, survival status, histologic grade, clinical stage, TNM classification, and tumor status were closely related to CDKL2 expression. In addition, CDKL2 downregulation was an independent prognostic factor for poor prognosis in multivariate analysis. Enrichment analyses using multiple tests revealed that CDKL2 is not just closely related to immune response but this association is highly correlated as well. Further, we found that CDKL2 expression was significantly correlated with the infiltration levels of T cell CD4 memory resting; monocytes; macrophages M0, M1, and M2; dendritic cells resting; mast cells resting; plasma cells; T cell CD8; and T cell regulatory.

Conclusion: This is the first report to study the expression of CDKL2 in ccRCC, wherein we suggest that decreased CDKL2 expression is closely correlated with poor prognosis in ccRCC. We consider that CDKL2 is a novel and potential prognostic biomarker associated with immune infiltrates in ccRCC.
A Liquid State Perspective on Dynamics of Chromatin Compartments
Authors: Laghmach Rabia , Di Pierro Michele , Potoyan Davit
Published: January 2022

The interior of the eukaryotic cell nucleus has a crowded and heterogeneous environment packed with chromatin polymers, regulatory proteins, and RNA molecules. Chromatin polymer, assisted by epigenetic modifications, protein and RNA binders, forms multi-scale compartments which help regulate genes in response to cellular signals. Furthermore, chromatin compartments are dynamic and tend to evolve in size and composition in ways that are not fully understood. The latest super-resolution imaging experiments have revealed a much more dynamic and stochastic nature of chromatin compartments than was appreciated before. An emerging mechanism explaining chromatin compartmentalization dynamics is the phase separation of protein and nucleic acids into membraneless liquid condensates. Consequently, concepts and ideas from soft matter and polymer systems have been rapidly entering the lexicon of cell biology. In this respect, the role of computational models is crucial for establishing a rigorous and quantitative foundation for the new concepts and disentangling the complex interplay of forces that contribute to the emergent patterns of chromatin dynamics and organization. Several multi-scale models have emerged to address various aspects of chromatin dynamics, ranging from equilibrium polymer simulations, hybrid non-equilibrium simulations coupling protein binding and chromatin folding, and mesoscopic field-theoretic models. Here, we review these emerging theoretical paradigms and computational models with a particular focus on chromatin’s phase separation and liquid-like properties as a basis for nuclear organization and dynamics.
Impaired Glymphatic Function and Pulsation Alterations in a Mouse Model of Vascular Cognitive Impairment
Authors: Li Mosi , Kitamura Akihiro , Beverley Joshua , Koudelka Juraj , Duncombe Jessica , Lennen Ross , Jansen Maurits A. , Marshall Ian , Platt Bettina , Wiegand Ulrich K. , Carare Roxana O. , Kalaria Rajesh N. , Iliff Jeffrey J. , Horsburgh Karen
Published: January 2022

Large vessel disease and carotid stenosis are key mechanisms contributing to vascular cognitive impairment (VCI) and dementia. Our previous work, and that of others, using rodent models, demonstrated that bilateral common carotid stenosis (BCAS) leads to cognitive impairment via gradual deterioration of the neuro-glial-vascular unit and accumulation of amyloid-β (Aβ) protein. Since brain-wide drainage pathways (glymphatic) for waste clearance, including Aβ removal, have been implicated in the pathophysiology of VCI via glial mechanisms, we hypothesized that glymphatic function would be impaired in a BCAS model and exacerbated in the presence of Aβ. Male wild-type and Tg-SwDI (model of microvascular amyloid) mice were subjected to BCAS or sham surgery which led to a reduction in cerebral perfusion and impaired spatial learning acquisition and cognitive flexibility. After 3 months survival, glymphatic function was evaluated by cerebrospinal fluid (CSF) fluorescent tracer influx. We demonstrated that BCAS caused a marked regional reduction of CSF tracer influx in the dorsolateral cortex and CA1-DG molecular layer. In parallel to these changes increased reactive astrogliosis was observed post-BCAS. To further investigate the mechanisms that may lead to these changes, we measured the pulsation of cortical vessels. BCAS impaired vascular pulsation in pial arteries in WT and Tg-SwDI mice. Our findings show that BCAS influences VCI and that this is paralleled by impaired glymphatic drainage and reduced vascular pulsation. We propose that these additional targets need to be considered when treating VCI.
Preservation of Retinal Function Through Synaptic Stabilization in Alzheimer's Disease Model Mouse Retina by Lycium Barbarum Extracts
Authors: Liu Jinfeng , Baum Larry , Yu Shasha , Lin Youhong , Xiong Guoying , Chang Raymond Chuen-Chung , So Kwok Fai , Chiu Kin
Published: January 2022

In Alzheimer's disease (AD), amyloid β deposition-induced hippocampal synaptic dysfunction generally begins prior to neuronal degeneration and memory impairment. Lycium barbarum extracts (LBE) have been demonstrated to be neuroprotective in various animal models of neurodegeneration. In this study, we aimed to investigate the effects of LBE on the synapse loss in AD through the avenue of the retina in a triple transgenic mouse model of AD (3xTg-AD). We fed 3xTg-AD mice with low (200 mg/kg) or high (2 g/kg) dose hydrophilic LBE daily for 2 months from the starting age of 4- or 6-month-old. For those started at 6 month age, at 1 month (though not 2 months) after starting treatment, mice given high dose LBE showed a significant increase of a wave and b wave in scotopic ERG. After 2 months of treatment with high dose LBE, calpain-2, calpain-5, and the oxidative RNA marker 8-OHG were downregulated, and presynaptic densities in the inner plexiform layer but not the outer plexiform layer of the retina were significantly increased, suggesting the presynaptic structure of retina was preserved. Our results indicate that LBE feeding may preserve synapse stability in the retina of 3xTg-AD mice, probably by decreasing both oxidative stress and intracellular calcium influx. Thus, LBE might have potential as a neuroprotectant for AD through synapse preservation.
Monthly At-Home Computerized Cognitive Testing to Detect Diminished Practice Effects in Preclinical Alzheimer's Disease
Authors: Jutten Roos J. , Rentz Dorene M. , Fu Jessie F. , Mayblyum Danielle V. , Amariglio Rebecca E. , Buckley Rachel F. , Properzi Michael J. , Maruff Paul , Stark Craig E. , Yassa Michael A. , Johnson Keith A. , Sperling Reisa A. , Papp Kathryn V.
Published: January 2022

Introduction: We investigated whether monthly assessments of a computerized cognitive composite (C3) could aid in the detection of differences in practice effects (PE) in clinically unimpaired (CU) older adults, and whether diminished PE were associated with Alzheimer's disease (AD) biomarkers and annual cognitive decline.

Materials and Methods:N = 114 CU participants (age 77.6 ± 5.0, 61% female, MMSE 29 ± 1.2) from the Harvard Aging Brain Study completed the self-administered C3 monthly, at-home, on an iPad for one year. At baseline, participants underwent in-clinic Preclinical Alzheimer's Cognitive Composite-5 (PACC5) testing, and a subsample (n = 72, age = 77.8 ± 4.9, 59% female, MMSE 29 ± 1.3) had 1-year follow-up in-clinic PACC5 testing available. Participants had undergone PIB-PET imaging (0.99 ± 1.6 years before at-home baseline) and Flortaucipir PET imaging (n = 105, 0.62 ± 1.1 years before at-home baseline). Linear mixed models were used to investigate change over months on the C3 adjusting for age, sex, and years of education, and to extract individual covariate-adjusted slopes over the first 3 months. We investigated the association of 3-month C3 slopes with global amyloid burden and tau deposition in eight predefined regions of interest, and conducted Receiver Operating Characteristic analyses to examine how accurately 3-month C3 slopes could identify individuals that showed >0.10 SD annual decline on the PACC-5.

Results: Overall, individuals improved on all C3 measures over 12 months (β = 0.23, 95% CI [0.21–0.25], p < 0.001), but improvement over the first 3 months was greatest (β = 0.68, 95% CI [0.59–0.77], p < 0.001), suggesting stronger PE over initial repeated exposures. However, lower PE over 3 months were associated with more global amyloid burden (r = −0.20, 95% CI [−0.38 – −0.01], p = 0.049) and tau deposition in the entorhinal cortex (r = −0.38, 95% CI [−0.54 – −0.19], p < 0.001) and inferior-temporal lobe (r = −0.23, 95% CI [−0.41 – −0.02], p = 0.03). 3-month C3 slopes exhibited good discriminative ability to identify PACC-5 decliners (AUC 0.91, 95% CI [0.84–0.98]), which was better than baseline C3 (p < 0.001) and baseline PACC-5 scores (p = 0.02).

Conclusion: While PE are commonly observed among CU adults, diminished PE over monthly cognitive testing are associated with greater AD biomarker burden and cognitive decline. Our findings imply that unsupervised computerized testing using monthly retest paradigms can provide rapid detection of diminished PE indicative of future cognitive decline in preclinical AD.