bluuebunny/crossref_metadata_2025 huggingface dataset:
Programmed Cell Death Tunes Tumor Immunity
Authors: Liu Jing , Hong Minjing , Li Yijia , Chen Dan , Wu Yangzhe , Hu Yi
Published: March 2022

The demise of cells in various ways enables the body to clear unwanted cells. Studies over the years revealed distinctive molecular mechanisms and functional consequences of several key cell death pathways. Currently, the most intensively investigated programmed cell death (PCD) includes apoptosis, necroptosis, pyroptosis, ferroptosis, PANoptosis, and autophagy, which has been discovered to play crucial roles in modulating the immunosuppressive tumor microenvironment (TME) and determining clinical outcomes of the cancer therapeutic approaches. PCD can play dual roles, either pro-tumor or anti-tumor, partly depending on the intracellular contents released during the process. PCD also regulates the enrichment of effector or regulatory immune cells, thus participating in fine-tuning the anti-tumor immunity in the TME. In this review, we focused primarily on apoptosis, necroptosis, pyroptosis, ferroptosis, PANoptosis, and autophagy, discussed the released molecular messengers participating in regulating their intricate crosstalk with the immune response in the TME, and explored the immunological consequence of PCD and its implications in future cancer therapy developments.
Breast Density and Estradiol Are Major Determinants for Soluble TNF-TNF-R Proteins in vivo in Human Breast Tissue
Authors: Ekstrand Jimmy , Zemmler Maja , Abrahamsson Annelie , Lundberg Peter , Forsgren Mikael , Dabrosin Charlotta
Published: March 2022

High mammographic density and exposure to sex steroids are independent risk factors for breast cancer by yet unknown mechanisms. Inflammation is one hallmark of cancer and the tumor necrosis factor family of proteins (TNFSFs) and receptors (TNFRSFs) are key determinants of tissue inflammation. The relationship between TNFSFs/TNFRSFs and breast tissue density or local breast estradiol levels is unknown. We investigated whether TNFSFs and soluble TNFRSFs (sTNFRSFs) are dysregulated in vivo in human breast cancer and dense breast tissue of postmenopausal women. We explored TNFSF/TNFRSF correlations with breast density and estradiol, both locally in the breast and in abdominal subcutaneous (s.c.) fat as a measure of systemic effects. Microdialysis was used for local sampling of in vivo proteins and estradiol in a total of 73 women; 12 with breast cancer, 42 healthy postmenopausal women with different breast densities, and 19 healthy premenopausal women. Breast density was determined as lean tissue fraction (LTF) using magnetic resonance imaging. Microdialysis was also performed in estrogen receptor (ER) positive breast cancer in mice treated with the pure anti-estrogen fulvestrant and tumor tissue was subjected to immunohistochemistry. 23 members of the TNFSF/sTNFRSF families were quantified using proximity extension assay.Our data revealed upregulation of TNFSF10, 13 and 13B, TNFRSF6, 6B, 9, 11A, 11B, 13B, 14, and 19, and TNFR-1 and -2 in ER+ breast cancer in women. In dense breast tissue TNFSF10, 13, and 14, TNFRSF3, 6, 9, 10B, 13B, 14, 19, and TNFR-1 and -2 were upregulated. Certain TNFSFs/TNFRSFs were increased in premenopausal breasts relative to postmenopausal breasts. Furthermore, estradiol correlated with most of the TNFSF/sTNFRSF members, though LTF only correlated with some of the proteins. Several of these associations were breast tissue-specific, as very few correlated with estradiol in abdominal s.c. fat. Estrogen dependent regulations of TNFSF2 (TNF-α) and TNF-R2 were corroborated in ER+ breast cancer in mice. Taken together, our data indicate TNFSFs/sTNFRSFs may represent potential targetable pathways for treatment of breast cancer patients and in prevention of breast cancer development in women with dense breasts.
Comprehensive Analysis of Nasal Polyps Reveals a More Pronounced Type 2 Transcriptomic Profile of Epithelial Cells and Mast Cells in Aspirin-Exacerbated Respiratory Disease
Authors: Bangert Christine , Villazala-Merino Sergio , Fahrenberger Martin , Krausgruber Thomas , Bauer Wolfgang M. , Stanek Victoria , Campion Nicholas James , Bartosik Tina , Quint Tamara , Regelsberger Guenther , Niederberger-Leppin Verena , Bock Christoph , Schneider Sven , Eckl-Dorna Julia
Published: March 2022

Chronic rhinosinusitis with nasal polyps is affecting up to 3% of Western populations. About 10% of patients with nasal polyps also suffer from asthma and intolerance to aspirin, a syndrome called aspirin-exacerbated respiratory disease. Although eosinophilic inflammation is predominant in polyps of both diseases, phenotypic differences in the tissue-derived microenvironment, elucidating disease-specific characteristics, have not yet been identified. We sought to obtain detailed information about phenotypic and transcriptional differences in epithelial and immune cells in polyps of aspirin-tolerant and intolerant patients. Cytokine profiles in nasal secretions and serum of patients suffering from aspirin-exacerbated respiratory disease (n = 10) or chronic rhinosinusitis with nasal polyps (n = 9) were assessed using a multiplex mesoscale discovery assay. After enrichment for immune cell subsets by flow cytometry, we performed transcriptomic profiling by employing single-cell RNA sequencing. Aspirin-intolerant patients displayed significantly elevated IL-5 and CCL17 levels in nasal secretions corresponding to a more pronounced eosinophilic type 2 inflammation. Transcriptomic profiling revealed that epithelial and mast cells not only complement one another in terms of gene expression associated with the 15-lipoxygenase pathway but also show a clear type 2-associated inflammatory phenotype as identified by the upregulation ofPOSTN,CCL26, andIL13in patients with aspirin-exacerbated respiratory disease. Interestingly, we also observed cellular stress responses indicated by an increase ofMTRNR2L12,MTRNR2L8, andNEAT1across all immune cell subsets in this disease entity. In conclusion, our findings support the hypothesis that epithelial and mast cells act in concert as potential drivers of the pathogenesis of the aspirin-exacerbated respiratory disease.
Glycoconjugate Nanoparticle-Based Systems in Cancer Immunotherapy: Novel Designs and Recent Updates
Authors: Barchi Joseph J.
Published: March 2022

For many years, cell-surface glycans (in particular, Tumor-Associated Carbohydrate Antigens, TACAs) have been the target of both passive and active anticancer immunotherapeutic design. Recent advances in immunotherapy as a treatment for a variety of malignancies has revolutionized anti-tumor treatment regimens. Checkpoint inhibitors, Chimeric Antigen Receptor T-cells, Oncolytic virus therapy, monoclonal antibodies and vaccines have been developed and many approvals have led to remarkable outcomes in a subset of patients. However, many of these therapies are very selective for specific patient populations and hence the search for improved therapeutics and refinement of techniques for delivery are ongoing and fervent research areas. Most of these agents are directed at protein/peptide epitopes, but glycans–based targets are gaining in popularity, and a handful of approved immunotherapies owe their activity to oligosaccharide targets. In addition, nanotechnology and nanoparticle-derived systems can help improve the delivery of these agents to specific organs and cell types based on tumor-selective approaches. This review will first outline some of the historical beginnings of this research area and subsequently concentrate on the last 5 years of work. Based on the progress in therapeutic design, predictions can be made as to what the future holds for increasing the percentage of positive patient outcomes for optimized systems.
Clinical and Genetic Features of Chinese Adult Patients With Chronic Non-Bacterial Osteomyelitis: A Single Center Report
Authors: Zhao Mengzhu , Wu Di , Yu Keyi , Shen Min
Published: March 2022

Objectives

Chronic non-bacterial osteomyelitis (CNO) is a rare polygenic autoinflammatory bone disease. We aimed to characterize the clinical manifestations and gene variants of Chinese adult patients with CNO.

Methods

By reviewing data of all CNO patients being diagnosed and followed up at the Center for Adult Autoinflammation Diseases, Department of Rheumatology, Peking Union Medical College Hospital, clinical and genetic features of these patients were evaluated and concluded.

Results

The median age of disease onset was 19 (6-64) years old, and adult-onset was observed in 6 (60%) patients. The mean time of diagnosis delay was 92 ± 78 months. The common symptoms were bone pain (10, 100%), fever (9, 90%), and arthritis (6, 60%). In total, there were 54 skeletal lesions, and each patient had no less than 2 lesions. The most frequently affected sites included lower limbs (20.5%), mandible, vertebrae and pelvis (17.5%, separately). Variants of 4 genes were detected in our study including COL1A1, PSTPIP1, LRP5 and CLCN7. In seven patients who were treated with combination therapy containing tumor necrosis factor (TNF) α inhibitors, five (55.6%) had a complete response and 2 (44.4%) had a partial response.

Conclusion

This is the first and largest case series of CNO in the Chinese adult patients. Four novel genetic mutations potentially associated with CNO were identified. Notably, CNO should be considered in the differential diagnosis of adult patients with long disease course and recurrent multifocal osteomyelitis of unknown cause, and these patients might benefit from combination therapy containing TNFα inhibitors.
Natural Killer Cells Infiltration in the Joints Exacerbates Collagen-Induced Arthritis
Authors: Wu Lisheng , Wang Ran , Zhou Yi , Zhao Di , Chen Feilong , Wu Xianghui , Chen Xiaoguang , Chen Shixian , Li Juan , Zhu Junqing
Published: March 2022

Introduction

The role of natural killer (NK) cells in rheumatoid arthritis remains controversial. We aimed to assess the role of NK cells in the pathogenesis of rheumatoid arthritis.

Materials and Methods

The percentage of NK cells in the peripheral blood, spleen, lymph nodes and inflamed paws from collagen-induced arthritis mice were examined through the disease progression. Correlation between the proportion of NK cells and subsets with arthritis score, histopathological changes, and bone destruction were evaluated. Adoptive cell transfer was performed to determine the effect of NKp46+NK cells on arthritis development, and the role of receptor NKp46 was explored with NKp46 knockout mice.

Results

The percentage of NK cells in peripheral blood decreased at the late stage of the disease and negatively correlated with arthritis score. NK cells increased in the inflamed paws during arthritis development and were positively associated with arthritis score, histopathological change, and bone destruction. Adoptive transfer of NKp46+NK cells before disease onset resulted in increased NK cells infiltration in the joints, higher incidence of arthritis, more severe clinical symptoms, and more pronounced joint inflammation and bone damage. NKp46 deficiency had no significant influence on the incidence and severity of arthritis in collagen-induced arthritis mice.

Conclusions

NK cell infiltration in the joints positively correlates with arthritis progression, inflammation, and bone destruction. The pathogenic role of NK cells in rheumatoid arthritis may be independent of the receptor NKp46.
Variation of Immune Cell Responses in Humans Reveals Sex-Specific Coordinated Signaling Across Cell Types
Authors: Fragiadakis Gabriela K. , Bjornson-Hooper Zachary B. , Madhireddy Deepthi , Sachs Karen , Chen Han , McIlwain David R. , Spitzer Matthew H. , Bendall Sean C. , Nolan Garry P.
Published: March 2022

Assessing the health and competence of the immune system is central to evaluating vaccination responses, autoimmune conditions, cancer prognosis, and treatment. With an increasing number of studies examining immune dysregulation, there is a growing need for a curated reference of variation in immune parameters in healthy individuals. We used mass cytometry (CyTOF) to profile blood from 86 humans in response to 15 ex vivo immune stimuli. We present reference ranges for cell-specific immune markers and highlight differences that appear across sex and age. We identified modules of immune features that suggest there exists an underlying structure to the immune system based on signaling pathway responses across cell types. We observed increased MAPK signaling in inflammatory pathways in innate immune cells and greater overall coordination of immune cell responses in females. In contrast, males exhibited stronger pSTAT1 and pTBK1 responses. These reference data are publicly available as a resource for immune profiling studies.
Diagnosis and Treatment of a Patient With Severe Combined Immunodeficiency Due to a Novel Homozygous Mutation in the IL-7Rα Chain
Authors: Mansour Rana , Bsat Yasmin El , Fadel Anthony , El-Orfali Youmna , Noun Dolly , Tarek Nidale , Kabbara Nabil , Abboud Miguel , Massaad Michel J.
Published: March 2022

The interleukin-7 receptor (IL-7R) is expressed on lymphoid cells and plays an important role in the development, homeostasis, survival, and proliferation of T cells. Bi-allelic mutations in the IL-7Rα chain abolish T cell development and function resulting in severe combined immunodeficiency disease. In this manuscript, we investigate a 1 year-old patient born to consanguineous parents, who suffered from autoimmune hemolytic anemia since birth associated with recurrent severe infections. Flow cytometric analysis of the patient’s peripheral blood demonstrated elevated numbers of B and NK cells, decreased numbers of T cells, defective thymic output, a predominance of memory T cells, and absent T cell proliferation. Next Generation Sequencing identified a novel homozygous pathogenic mutation in IL7RA (c.379G>A) that resulted in aberrant IL7RA RNA splicing and absent IL-7Rα expression. The patient was successfully transplanted using her HLA-matched relative as donor. One year after transplant, the patient is clinically stable with normal reconstitution of donor T cells that express IL-7Rα, a significant increase in the percentages of recent thymic emigrant and peripheral T cells, normalization of naïve and memory T cells, and restoration of her T cell’s proliferative response. Therefore, using genetic and functional approaches, we identified a novel deleterious mutation in IL-7Rα that results in T-B+NK+ phenotype, and report successful hematopoietic stem cell transplantation of the patient. This represents the first bedside-to-bench-and-back case entirely performed on a patient with severe combined immunodeficiency at the American University of Beirut Medical Center.
A Risk Model Developed Based on Necroptosis Predicts Overall Survival for Hepatocellular Carcinoma and Identification of Possible Therapeutic Drugs
Authors: Li Zedong , Fang Jianyu , Chen Sheng , Liu Hao , Zhou Jun , Huang Jiangsheng , Liu Sushun , Peng Yu
Published: March 2022

Background

Necroptosis is a form of regulatory cell death (RCD) that attracts and activates immune cells, resulting in pro-tumor or anti-tumor effects. The purpose of this study was to investigate genes associated with necroptosis, to construct a risk score for predicting overall survival in patients with hepatocellular carcinoma, and to find potentially effective drugs.

Methods

The three algorithms ssGSEA, EPIC, and ESTIMATE were used to quantify the immune cell infiltration of the samples, differentially expressed genes (DEGs) analysis, and weighted gene co-expression network analysis were used to screen necroptosis related genes. Variables were screened according to random survival forest analysis, and combinations with significant p-values and a low number of genes were defined as prognostic signatures by using log-rank test after gene combination. Based on the sensitivity data of PRISM and CTRP2.0 datasets, we predicted the potential therapeutic agents for high-NRS patients.

Results

Seven genes such as TOP2A were used to define necroptosis-related risk score (NRS). The prognostic value of risk score was further validated, where high NRS was identified as a poor prognostic factor and tended to have higher grades of histologic grade, pathologic stage, T stage, BCLC, CLIP, and higher AFP. Higher NRS was also negatively correlated with the abundance of DCs, Neutrophils, Th17 cells, Macrophages, Endothelial, and positively correlated with Th2 cells. Necroptosis is often accompanied by the release of multiple cytokines, and we found that some cytokines were significantly correlated with both NRS and immune cells, suggesting that necroptosis may affect the infiltration of immune cells through cytokines. In addition, we found that TP53 mutations were more common in samples with high NRS, and these mutations may be associated with changes in NRS. Patients with high NRS may be more sensitive to gemcitabine, and gemcitabine may be an effective drug to improve the prognosis of patients with high NRS, which may play a role by inhibiting the expression of TOP2A.

Conclusions

We constructed a necroptosis-related scoring model to predict OS in HCC patients, and NRS was associated with immune response, TP53 mutation, and poor clinical classification in HCC patients. In addition, gemcitabine may be an effective drug for high-NRS patients.
Tracing Seal Predation Back to the Source Colony of Their Penguin Prey: A Trace Element and Stable Isotope Analysis
Authors: Reinhold Sarah-Lena , Goldsworthy Simon D. , Arnould John P.Y. , Gillanders Bronwyn M. , Connell Sean D. , McIntosh Rebecca R.
Published: March 2022

Marine predators recovering from historic, commercial, over-harvesting can create conservation challenges when they prey on vulnerable species. Pinniped predation of seabirds presents one such challenge and identifying the source colonies experiencing seal predation are needed to inform conservation management and decision planning. Here, we present a novel application of stable isotope and trace element techniques to identify the source colony of little penguins (Eudyptula minor) predated by long-nosed fur seals (Arctocephalus forsteri). We created baseline biochemical ‘feather-prints’ from feathers for six major breeding colonies across south-east Australia to compare with feathers from predated penguins recovered from seal scats. Feeding trials of captive seals confirmed that digestion of penguin feathers did not compromise stable isotope (δ13C and δ15N) or trace element (Al, Ti, Sr and Mg) signatures. The resulting biochemical ‘feather-prints’ were found to be robust in being correctly classified to local sites (78%) and broader regions (85%). The distinguishing ‘feather-prints’ appeared to be driven by industrial inputs from land, colony-specific foraging patterns and potentially proximity to oceanographic systems (i.e. upwelling). Here, we show that 46-70% of predated feathers were assigned to ‘local’ penguin colonies. We consider that the regional penguin abundances and the proximity of their colonies to seal sites, as well as demographic-specific foraging patterns may shape their contribution to seal diet at local, regional and inter-regional scales. This diagnostic tool is powerful, having broad applications identifying seabird colonies at greatest risk to pinniped predation and informing targeted, site-specific, conservation effort.
Recent Trends in Live Feeds for Marine Larviculture: A Mini Review
Authors: Pan Yen-Ju , Dahms Hans-Uwe , Hwang Jiang-Shiou , Souissi Sami
Published: March 2022

In marine larviculture, farmed larvae mainly rely on the alimentation of a group of small-sized phytoplankton and zooplankton referred to as live feed. Under the diversifying demands of human consumption and ornamental aquarium industry, new species of live feed and their innovative production methods are essential focuses for sustainable larviculture of many emerging fish and invertebrate species. The selection of proper live feed for larval feeding is based on several parameters, such as size, morphology, nutritional value, stock density, and growth rate. This review aims to highlight the biological characteristics, production approach, common larviculture applications as well as recent innovations in the aquaculture technology of live feed organisms (microalgae, ciliated protists, rotifer, Artemia, copepod, and others).
Spin Properties and Metal-Semiconductor Transition of Nitrogen-Containing Zigzag Graphyne Nanoribbon Caused by Magnetic Atom Doping
Authors: Min Zi-Cong , Peng Xiao-Fang , Tan Shi-Hua
Published: March 2022

In this study, the density function theory (DFT) was used to study the influence of the magnetic atoms (Fe, Co, Ni) doping on the electrical properties of nitrogen-containing zigzag graphyne-like nanoribbon (N-ZGyNR). The results show that, by doping different atoms into the natural “holes” of N-ZGyNR, the changes in the structure, magnetic moment distribution and electrical properties of N-ZGyNR are different. Due to the incomplete saturation of the edge C atoms, the initial N-ZGyNR presents metallicity and spin degeneracy. The doping of Fe atoms will cause the C-C bond in N-ZGyNR to be completely broken, resulting in structural distortion, and about 0.8e- will transfer from Fe to N-ZGyNR. Compared with Fe doping, Co/Ni doping has a smaller effect on the N-ZGyNR and will not cause structural distortion, but will redistribute the spin charge in N-ZGyNR, thereby forming a band gap of 60 meV near the Fermi level to realize the transition of metal-semiconductor. The above results show that the electrical properties of N-ZGyNR can be controlled by magnetic atom doping, and the metal-semiconductor transition can be realized by Co/Ni doping, which provides a new alternative for spintronic devices.
Shedding of SARS-CoV-2 for 85 Days in COVID-19 Patients With Type 2 Diabetes Mellitus and Lung Metastasis: A Case Report
Authors: Wu Xiaoheng , Shen Min , Quan Hui , Zhang Xianqin , Xu Fengcheng , Li Juan , He Miao , Pan Dongmei , Cao Ling , Yue Changwu , Liu Tianhu , Jia Xu
Published: March 2022

Background

COVID-19 (coronavirus disease 2019) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seriously endangers people's lives. The variation in SARS-CoV-2 makes the research and development of vaccines and specific drugs particularly important. However, the prevention and diagnosis of COVID-19 cannot be underestimated in the control of the epidemic.

Case Presentation

We introduced a 65-year-old female patient who was diagnosed with COVID-19. The SARS-CoV-2 nucleic acid test result of this patient was positive again during treatment. It took 85 days from the first symptom to the final cure. According to the known reports, she is currently the patient with the longest virus shedding in Sichuan Province, China. Due to the patient's special condition, she was treated in four hospitals before and after, and she was diagnosed with type 2 diabetes mellitus (T2DM) and right lung metastatic adenocarcinoma. We fully introduced the patient's epidemiological history, diagnosis, testing, and treatment process. The patient was finally discharged from the hospital under the treatment of antiviral, hypoglycaemic, anti-anxiety, and a combination of Chinese and Western medicine.

Conclusions

The epidemic is still rampant, and we should not relax our efforts in the prevention and control of viruses. For the elderly, especially those who are suffering from complications or vulnerable to diseases, it is recommended to extend the observation time. Additionally, medical workers should pay attention to the mental state of patients.
Polyphasic Identification and Genomic Insights of Leptothermofonsia sichuanensis gen. sp. nov., a Novel Thermophilic Cyanobacteria Within Leptolyngbyaceae
Authors: Tang Jie , Shah Mahfuzur R. , Yao Dan , Jiang Ying , Du Lianming , Zhao Kelei , Li Liheng , Li Meijin , Waleron Michal M. , Waleron Malgorzata , Waleron Krzysztof , Daroch Maurycy
Published: March 2022

Thermal environments are an important reservoir of thermophiles with significant ecological and biotechnological potentials. However, thermophilic isolates remain largely unrecovered from their habitats and are rarely systematically identified. In this study, we characterized using polyphasic approaches a thermophilic strain, PKUAC-SCTAE412 (E412 hereafter), recovered from Lotus Lake hot spring based in Ganzi prefecture, China. The results of 16S rRNA/16S-23S ITS phylogenies, secondary structure, and morphology comparison strongly supported that strain E412 represent a novel genus within Leptolyngbyaceae. This delineation was further confirmed by genome-based analyses [phylogenomic inference, average nucleotide/amino-acid identity, and the percentages of conserved proteins (POCP)]. Based on the botanical code, the isolate is herein delineated asLeptothermofonsia sichuanensisgen. sp. nov, a genus adjacent to recently delineatedKovacikiaandStenomitos. In addition, we successfully obtained the first complete genome of this new genus. Genomic analysis revealed its adaptations to the adverse hot spring environment and extensive molecular components related to mobile genetic elements, photosynthesis, and nitrogen metabolism. Moreover, the strain was capable of modifying the composition of its light-harvesting apparatus depending on the wavelength and photoperiod, showing chromatic adaptation capacity characteristic for T1 and T2 pigmentation types. Other physiological studies showed the strain’s ability to utilize sodium bicarbonate and various sulfur compounds. The strain was also shown to be diazotrophic. Interestingly, 24.6% of annotated protein-coding genes in the E412 genome were identified as putatively acquired, hypothesizing that a large number of genes acquired through HGT might contribute to the genome expansion and habitat adaptation of those thermophilic strains. Most the HGT candidates (69.4%) were categorized as metabolic functions as suggested by the KEGG analysis. Overall, the complete genome of strain E412 provides the first insight into the genomic feature of the genusLeptothermofonsiaand lays the foundation for future global ecogenomic and geogenomic studies.
To the Gut Microbiome and Beyond: The Brain-First or Body-First Hypothesis in Parkinson’s Disease
Authors: Nuzum Nathan D. , Loughman Amy , Szymlek-Gay Ewa A. , Teo Wei-Peng , Hendy Ashlee M. , Macpherson Helen
Published: March 2022

There is continued debate regarding Parkinson’s disease etiology and whether it originates in the brain or begins in the gut. Recently, evidence has been provided for both, with Parkinson’s disease onset presenting as either a “body-first” or “brain-first” progression. Most research indicates those with Parkinson’s disease have an altered gut microbiome compared to controls. However, some studies do not report gut microbiome differences, potentially due to the brain or body-first progression type. Based on the etiology of each proposed progression, individuals with the body-first progression may exhibit altered gut microbiomes, i.e., where short-chain fatty acid producing bacteria are reduced, while the brain-first progression may not. Future microbiome research should consider this hypothesis and investigate whether gut microbiome differences exist between each type of progression. This may further elucidate the impact of the gut microbiome in Parkinson’s disease and show how it may not be homogenous across individuals with Parkinson’s disease.
The Cropping Obstacle of Garlic Was Associated With Changes in Soil Physicochemical Properties, Enzymatic Activities and Bacterial and Fungal Communities
Authors: Yu Jinyang , Liu Yihao , Wang Zuyu , Huang Xiaohui , Chai Dan , Gu Yunfu , Zhao Ke , Yu Xiumei , Shuai Zhengbin , Liu Hanjun , Zhang Xiaoping , Penttinen Petri , Chen Qiang
Published: March 2022

Aims

In garlic cultivation, long-time monoculture has resulted in continuous-cropping obstacles. However, the cause has not been studied to date.

Methods

We analyzed soils from garlic fields in Pengzhou, China, to determine continuous-cropping obstacle related changes in soil physicochemical properties and enzyme activities, and in the diversity and composition of bacterial and fungal communities. Furthermore, we examined the relationships between soil properties and the bacterial and fungal communities.

Results

The soil pH and the soil catalase, urease, invertase, and polyphenol oxidase activities were lower in the cropping obstacle soil than in the healthy control soil. The richness and diversity of the bacteria were lower in the cropping obstacle soil than in the control. The bacterial and fungal communities in the cropping obstacle soil were clearly different from those in the control soil. The differences in bacterial communities between the cropping obstacle soil and the control soil were associated with differences in pH and available potassium content. The taxa with higher relative abundances in the cropping obstacle soils included potential plant pathogens and the taxa with lower relative abundances included potential plant growth promoters.

Conclusion

The enrichment of plant pathogens and the depletion of plant growth promoting fungi may have contributed to the poor growth of garlic in the cropping obstacle soil. The enzyme activity and microbial community differences were associated with acidification that was likely an important factor in the deterioration of the soil ecological environment and the garlic cropping obstacle. The results provide information to guide agricultural practices in cultivating garlic.
Response of Fungal Sub-Communities in a Maize-Wheat Rotation Field Subjected to Long-Term Conservation Tillage Management
Authors: Zhang Cunzhi , Liu Hao , Liu Senlin , Hussain Sarfraz , Zhang Liting , Yu Xiaowei , Cao Kaixun , Xin Xiuli , Cao Hui , Zhu Anning
Published: March 2022

Conservation tillage is an advanced agricultural technology that seeks to minimize soil disturbance by reducing, or even eliminating tillage. Straw or stubble mulching in conservation tillage systems help to increase crop yield, maintain biodiversity and increase levels of exogenous nutrients, all of which may influence the structure of fungal communities in the soil. Currently, however, the assembly processes and co-occurrence patterns of fungal sub-communities remain unknown. In this paper, we investigated the effects of no-tillage and straw mulching on the composition, assembly process, and co-occurrence patterns of soil fungal sub-communities in a long-term experimental plot (15 years). The results revealed that combine straw mulching with no-tillage significantly increased the richness of fungi but not their diversity. Differential abundance analysis and principal component analysis (PCA) indicated that tillage management had a greater effect on the fungal communities of abundant and intermediate taxa than on the rare taxa. Available phosphorus (AP) and total nitrogen (TN) were the major determinants of fungal sub-communities in NT treatment. The abundant fungal sub-communities were assembled by deterministic processes under medium strength selection, while strong conservation tillage strength shifts the abundant sub-community assembly process from deterministic to stochastic. Overall, the investigation of the ecological network indicated that no-tillage and straw mulching practices decreased the complexity of the abundant and intermediate fungal networks, while not significantly influencing rare fungal networks. These findings refine our knowledge of the response of fungal sub-communities to conservation tillage management techniques and provide new insights into understanding fungal sub-community assembly.
Isolation of Anaerobic Bromate-Reducing Bacteria Using Different Carbon Sources and Transcriptomic Insights From Klebsiella variicola Glu3
Authors: Wang Dan , Wang Yicheng , Lv Xinyue , Cai Xunchao , Iqbal Waheed , Yang Bo , Zhou Dan , Rensing Christopher , Mao Yanping
Published: March 2022

Bromate, a possible human carcinogen, can be reduced to innocuous bromide by microorganisms. To characterize bromate reducers, microbes were enriched anaerobically from activated sludge by using bromate as the sole electron acceptor and different carbon sources as the electron donor. Bacteria that showed significant bromate-reducing activity but not coupled to cell growth were isolated. Two whole genomes of the isolates, namely, Raoultella electrica Lac1 and Klebsiella variicola Glu3, were reconstructed by Illumina and Nanopore sequencing. Transcriptomic analysis suggested that neither the respiratory nitrate reductase, the selenate reductase, nor the dimethylsulfoxide reductase was involved in the bromate reduction process, and strain K. variicola Glu3 reduced bromate via a yet undiscovered enzymatic mechanism. The results provide novel phylogenetic insights into bromate-reducing microorganisms and clues in putative genes encoding enzymes related to bromate reduction.
A Detoxification-Free Process for Enhanced Ethanol Production From Corn Fiber Under Semi-Simultaneous Saccharification and Fermentation
Authors: Guo Yingjie , Huang Jiamin , Xu Nuo , Jia Hexue , Li Xuezhi , Zhao Jian , Qu Yinbo
Published: March 2022

Corn fiber, a by-product from the corn-processing industry, is an attractive feedstock for cellulosic ethanol because of its rich carbohydrate content (mainly residual starch, cellulose, and hemicellulose), abundant reserves, easy collection, and almost no transportation cost. However, the complex structure and components of corn fiber, especially hemicellulose, make it difficult to be effectively hydrolyzed into fermentable sugars through enzymatic hydrolysis. This study developed a simple and easy industrialized process without detoxification treatment for high-yield ethanol produced from corn fiber. Corn fiber was pretreated by dilute acid under the conditions optimized by Box-Behnken design (0.5% H2SO4 at 105°C for 43 min), and 81.8% of total sugars, including glucose, xylose, and arabinose, could be recovered, then the mixture (solid and hydrolysates) was directly used for semi-simultaneous saccharification and fermentation without detoxification, and ethanol yield reached about 81% of the theoretical yield.
In-Depth Characterization of Plant Growth Promotion Potentials of Selected Alkanes-Degrading Plant Growth-Promoting Bacterial Isolates
Authors: Alotaibi Fahad , St-Arnaud Marc , Hijri Mohamed
Published: March 2022

The use of plant growth-promoting rhizobacteria (PGPR) as a bioremediation enhancer in plant-assisted phytoremediation requires several steps, consisting of the screening, selection, and characterization of isolates. A subset of 50 bacterial isolates representing a wide phylogenetic range were selected from 438 morphologically different bacteria that were originally isolated from a petroleum hydrocarbon (PHC)-polluted site of a former petrochemical plant. Selected candidate bacteria were screened using six conventional plant growth-promoting (PGP) traits, complemented with the genetic characterization of genes involved in alkane degradation, as well as other pertinent functions. Finally, the bacterial isolates were subjected to plant growth promotion tests using a gnotobiotic approach under normal and stressed conditions. Our results indicated that 35 bacterial isolates (70%) possessed at least four PGP traits. Twenty-nine isolates (58%) were able to utilize n-hexadecane as a sole carbon source, whereas 43 isolates (86%) were able to utilize diesel as the sole carbon source. The presence of catabolic genes related to hydrocarbon degradation was assessed using endpoint PCR, with the alkane monooxygenase (alkB) gene found in 34 isolates, the cytochrome P450 hydroxylase (CYP153) gene found in 24 isolates, and the naphthalene dioxygenase (nah1) gene found to be present in 33 isolates. Thirty-six strains (72%) promoted canola root elongation in the growth pouch assay. After several rounds of screening, seven bacterial candidates (individually or combined in a consortium) were tested for canola root and shoot growth promotion in substrates amended by different concentrations of n-hexadecane (0%, 1%, 2%, and 3%) under gnotobiotic conditions. Our results showed that Nocardia sp. (WB46), Pseudomonas plecoglossicida (ET27), Stenotrophomonas pavanii (EB31), and Gordonia amicalis (WT12) significantly increased the root length of canola grown in 3% n-hexadecane compared with the control treatment, whereas Nocardia sp. (WB46) and Bacillus megaterium (WT10) significantly increased shoot length compared to control treatment at the same concentration of n-hexadecane. The consortium had a significant enhancement effect on root length compared to all isolates inoculated individually or to the control. This study demonstrates that the combination of PGPR traits and the PHC degradation potential of bacteria can result in an enhanced beneficial effect in phytoremediation management, which could lead to the development of innovative bacterial inoculants for plants to remediate PHC-contaminated soils.
Mutation in the RNA-Dependent RNA Polymerase of a Symbiotic Virus Is Associated With the Adaptability of the Viral Host
Authors: Lu Hong , Li Jing , Yang Pengcheng , Jiang Fei , Liu Hongran , Cui Feng
Published: March 2022

Host adaptation has the potential to cause rapid genetic variation in symbiotic microorganisms in insects. How mutations in symbiotic viruses favor viral fitness in hosts and even influence host adaptability to new environments remains elusive. Here, we explored the role of genetic divergence at one site of a symbiotic virus, Acyrthosiphon pisum virus (APV), in the host aphid’s adaptation to unfavorable plants. Based on the transcriptomes of the pea aphid Vicia faba colony and Vicia villosa colony, 46 single nucleotide polymorphism (SNP) sites were found in the APV genomes from the two aphid colonies. One SNP at site 5,990, G5990A, located at the RNA-dependent RNA polymerase (RdRp) domain, demonstrated a predominance from G to A when the host aphids were shifted from V. faba to the low-fitness plants V. villosa or Medicago sativa. This SNP resulted in a substitution from serine (S) to asparagine (N) at site 196 in RdRp. Although S196N was predicted to be located at a random coil far away from conserved functional motifs, the polymerase activity of the N196 type of RdRp was increased by 44.5% compared to that of the S196 type. The promoted enzymatic activity of RdRp was associated with a higher replication level of APV, which was beneficial for aphids as APV suppressed plant’s resistance reactions toward aphids. The findings showed a novel case in which mutations selected in a symbiotic virus may confer a favor on the host as the host adapts to new environmental conditions.
Inactivation of Fluorescent Lipid Bilayers by Irradiation With 300 keV Electrons Using Liquid Cell Transmission Electron Microscopy
Authors: Moser Trevor , Evans James E.
Published: March 2022

Liquid cell transmission electron microscopy allows for imaging of samples in a fully hydrated state at high resolution and has the potential for visualizing static or dynamic biological structures. However, the ionizing nature of the electron beam makes it difficult to discern real physiological dynamics from radiation induced artifacts within liquid cell samples. Electron flux thresholds for achieving high resolution structures from biological samples frozen in ice have been described extensively by the cryo-electron microscopy field, while electron flux thresholds which do not result in a functional change for biological samples within the hydrated environment of a transmission electron microscope liquid cell is less clear. Establishing these functional thresholds for biologically relevant samples is important for accurate interpretation of results from liquid cell experiments. Here we demonstrate the electron damage threshold of fluorescently tagged lipid bilayers by quantifying the change in fluorescence before and after electron exposure. We observe the reduction of fluorescent signal in bilayers by 25% after only 0.0005 e−/Å2 and a reduction of over 90% after 0.01 e−/Å2. These results indicate that the loss of function occurs at irradiation thresholds far below a typical single high resolution (scanning) transmission electron microscopy image and orders of magnitude below fluxes used for preserving structural features with cryo-electron microscopy.
Compound Motor Action Potentials During a Modest Nerve Crush
Authors: Hamad Mohammed Nazmy , Boroda Nickolas , Echenique Diego Barragan , Dieter Raymond A. , Amirouche Farid M. L. , Gonzalez Mark H. , Kerns James M.
Published: March 2022

Nerve crush injury results in axonotmesis, characterized by disruption of axons and their myelin sheaths with relative sparing of the nerve’s connective tissue. Despite the widespread use of crush injury models, no standardized method for producing these lesions has been established. We characterize a crush model in which a narrow forceps is used to induce a modest and controlled compressive injury. The instantaneous compound motor action potential (CMAP) is monitored in situ and in real-time, allowing the characterization of neuromuscular response during and after injury. The tibial nerves of 11 anesthetized rats were surgically isolated. After the placement of electrodes, CMAPs were elicited and registered using a modular-data-acquisition system. Dumont-#5 micro-forceps were instrumented with a force transducer allowing force measurement via a digital sensor. Baseline CMAPs were recorded prior to crush and continued for the duration of the experiment. Nerve crushing commenced by gradually increasing the force applied to the forceps. At a target decrease in CMAP amplitude of 70%–90%, crushing was halted. CMAPs were continually recorded for 5–20 min after the termination of the crushing event. Nerves were then fixed for histological assessment. The following post-crush mean values from 19 trials were reported: peak CMAP amplitude decreased by 81.6% from baseline, duration of crush was 17 sec, rate of applied force was 0.03 N/sec, and maximal applied force was 0.5 N. A variety of agonal phenomena were evident post-lesion. Following the initial decrease in CMAP, 8 of 19 trials demonstrated a partial and transient recovery, followed by a further decline. Thirteen trials exhibited a CMAP amplitude near zero at the end of the recording. Twelve trials demonstrated a superimposed EMG background response during and after the crush event, with disappearance occurring within 4–8 min. Qualitative histology assessment at the lesion site demonstrated a correspondence between CMAP response and partial sparing of nerve fibers. By using a targeted decline in CMAP amplitude as the endpoint, researchers may be able to produce controlled, brief, and reproducible crush injuries. This model can also be used to test interventions aimed at enhancing subsequent regeneration and behavioral recovery.
A New Functional Magnetic Resonance Imaging Localizer for Preoperative Language Mapping Using a Sentence Completion Task: Validity, Choice of Baseline Condition, and Test–Retest Reliability
Authors: Elin Kirill , Malyutina Svetlana , Bronov Oleg , Stupina Ekaterina , Marinets Aleksei , Zhuravleva Anna , Dragoy Olga
Published: March 2022

To avoid post-neurosurgical language deficits, intraoperative mapping of the language function in the brain can be complemented with preoperative mapping with functional magnetic resonance imaging (fMRI). The validity of an fMRI “language localizer” paradigm crucially depends on the choice of an optimal language task and baseline condition. This study presents a new fMRI “language localizer” in Russian using overt sentence completion, a task that comprehensively engages the language function by involving both production and comprehension at the word and sentence level. The paradigm was validated in 18 neurologically healthy volunteers who participated in two scanning sessions, for estimating test–retest reliability. For the first time, two baseline conditions for the sentence completion task were compared. At the group level, the paradigm significantly activated both anterior and posterior language-related regions. Individual-level analysis showed that activation was elicited most consistently in the inferior frontal regions, followed by posterior temporal regions and the angular gyrus. Test–retest reliability of activation location, as measured by Dice coefficients, was moderate and thus comparable to previous studies. Test–retest reliability was higher in the frontal than temporo-parietal region and with the most liberal statistical thresholding compared to two more conservative thresholding methods. Lateralization indices were expectedly left-hemispheric, with greater lateralization in the frontal than temporo-parietal region, and showed moderate test-retest reliability. Finally, the pseudoword baseline elicited more extensive and more reliable activation, although the syllable baseline appears more feasible for future clinical use. Overall, the study demonstrated the validity and reliability of the sentence completion task for mapping the language function in the brain. The paradigm needs further validation in a clinical sample of neurosurgical patients. Additionally, the study contributes to general evidence on test–retest reliability of fMRI.
The Effects of Intermittent Trunk Flexion With and Without Support on Sitting Balance in Young Adults
Authors: Voglar Matej , Kozinc Žiga , Kingma Idsart , van Dieën Jaap H. , Šarabon Nejc
Published: March 2022

Prolonged trunk flexion is known to affect passive and active stabilization of the trunk. Previous studies have evaluated changes in spinal range of motion, muscle activity and reflex behavior induced by prolonged trunk flexion, whereas the effect on sitting postural control is vastly underexplored. In this study, we compared the effects of supported and unsupported intermittent trunk flexion on center of pressure (CoP) motion during sitting on an unstable seat. Participants (n = 21; 11 males, 23.2 ± 2.0 years; 10 females, age 24.3 ± 4.0) were exposed to 1-h intermittent (60-s sets with 30 s of rest) trunk flexion (80% of the maximal range of motion) and CoP root mean square distance, velocity and frequency before and after the exposure were assessed. Contrary to our hypothesis, there were no main effects of exposure (pre. vs. post flexion protocol; p = 0.128–0.709), no main effects of condition (supported vs. unsupported; p = 0.134–0.931), and no interaction between exposure and condition (p = 0.163–0.912). Our results indicate that prolonged intermittent flexion does not induce any changes in CoP motion during a seated balance task, regardless of the presence of a trunk support during prolonged intermittent flexion. This suggests a successful compensation of decreased passive stiffness by increased reflex activity.
Excessive Inorganic Phosphate Burden Perturbed Intracellular Signaling: Quantitative Proteomics and Phosphoproteomics Analyses
Authors: Hetz Rebecca , Beeler Erik , Janoczkin Alexis , Kiers Spencer , Li Ling , Willard Belinda B. , Razzaque Mohammed S. , He Ping
Published: March 2022

Inorganic phosphate (Pi) is an essential nutrient for the human body which exerts adverse health effects in excess and deficit. High Pi-mediated cytotoxicity has been shown to induce systemic organ damage, though the underlying molecular mechanisms are poorly understood. In this study, we employed proteomics and phosphoproteomics to analyze Pi-mediated changes in protein abundance and phosphorylation. Bioinformatic analyses and literature review revealed that the altered proteins and phosphorylation were enriched in signaling pathways and diverse biological processes. Western blot analysis confirms the extensive change in protein level and phosphorylation in key effectors that modulate pre-mRNA alternative splicing. Global proteome and phospho-profiling provide a bird-eye view of excessive Pi-rewired cell signaling networks, which deepens our understanding of the molecular mechanisms of phosphate toxicity.