bluuebunny/crossref_metadata_2025 huggingface dataset:
Cooperation With Arbuscular Mycorrhizal Fungi Increases Plant Nutrient Uptake and Improves Defenses Against Insects
Authors: Yu Lu , Zhang Wantong , Geng Yiyi , Liu Kesi , Shao Xinqing
Published: March 2022

Plants have evolved various defense mechanisms to cope with biotic and abiotic stresses. Cooperation with microorganisms, especially arbuscular mycorrhizal fungi (AMF), strengthens the defense capabilities of host plants. To explore the effect of AMF on the growth of Elymus and the defenses against locust feeding, we designed a two-compartment device to connect or cut the mycelia and roots. We used this to investigate communication cues and pathways between donor and receiver plants. We found that AMF significantly increased the nitrogen content and decreased the carbon to nitrogen (C:N) ratio of donor plants and receiver plants and the carbon content of both. After the establishment of the common mycorrhizal network (CMN) with AMF between the two chambers, inoculations of donor plants challenged by locusts caused enhancement in four defense-related enzymes, namely, lipoxygenase, polyphenol oxidase, phenylalanine ammonia lyase, and β-1,3-glucanase, in the receiver plants. The main components of volatile organic compounds emitted by receiver plants were terpenoids. The findings indicated that AMF could not only improve plant growth but also activate the defense response of plants to insect feeding. Four defense enzymes, volatile organic compounds, and carbon and nitrogen content were involved in the defense response, and the mycelial network could act as a conduit to deliver communication signals.
Environmental Seasonality Regulates Community Evenness in Neotropical Bat Communities
Authors: Estrada-Villegas Sergio , Pérez-Torres Jairo , McGill Brian J. , Stevens Richard D.
Published: March 2022

Evenness is a key community property that provides insights into resource acquisition and ecosystem functioning. However, it is unclear how other community properties influence evenness after integrating the effect of environmental gradients. Using 49 neotropical bat communities, we tested the hypothesis that evenness increases in communities that have low species richness and low biomass because the negative effect of richness and biomass on evenness is regulated by environmental seasonality. We selected among path models to determine how temperature seasonality, the most important gradient across study sites, affected richness and biomass as drivers of evenness. Employing three indices of evenness, we found that more seasonal climate reduces species richness, and lower richness increases evenness. Moreover, a decline in biomass with increasing seasonality also increases evenness. A decrease in resource specialization and rarity as sites become more seasonal may explain the negative relationship between seasonality, richness and evenness. Moreover, the negative effect of biomass on richness and evenness may be due to an expansion of niche space and a positive effect of smaller body size on diversification rates, which may allow more species packing and greater richness. We believe our results bring us closer to a unified theory of which factors control evenness in a community.
Impacts of Forest Management on Forest Bird Occurrence Patterns—A Case Study in Central Europe
Authors: Leitão Pedro J. , Toraño Caicoya Astor , Dahlkamp Andreas , Guderjan Laura , Griesser Michael , Haverkamp Paul J. , Nordén Jenni , Snäll Tord , Schröder Boris
Published: March 2022

The global increase in demand for wood products, calls for a more sustainable management of forests to optimize both the production of wood and the conservation of forest biodiversity. In this paper, we evaluate the status and future trends of forest birds in Central European forests, assuming different forest management scenarios that to a varying degree respond to the demand for wood production. To this end, we use niche models (Boosted Regression Trees and Generalized Linear Models) to model the responses of 15 forest bird species to predictors related to forest stand (e.g., stand volume of specific tree species) and landscape structure (e.g., percentage cover), and to climate (bioclimatic variables). We then define five distinct forest management scenarios, ranging from set-aside to productivity-driven scenarios, project them 100 years into the future, and apply our niche models into these scenarios to assess the birds’ responses to different forest management alternatives. Our models show that the species’ responses to management vary reflecting differences in their ecological niches, and consequently, no single management practice can benefit all species if applied across the whole landscape. Thus, we conclude that in order to promote the overall forest bird species richness in the study region, it is necessary to manage the forests in a multi-functional way, e.g., by spatially optimizing the management practices in the landscape.
Population Genomic Sequencing Delineates Global Landscape of Copy Number Variations that Drive Domestication and Breed Formation of in Chicken
Authors: Chen Xia , Bai Xue , Liu Huagui , Zhao Binbin , Yan Zhixun , Hou Yali , Chu Qin
Published: March 2022

Copy number variation (CNV) is an important genetic mechanism that drives evolution and generates new phenotypic variations. To explore the impact of CNV on chicken domestication and breed shaping, the whole-genome CNVs were detected via multiple methods. Using the whole-genome sequencing data from 51 individuals, corresponding to six domestic breeds and wild red jungle fowl (RJF), we determined 19,329 duplications and 98,736 deletions, which covered 11,123 copy number variation regions (CNVRs) and 2,636 protein-coding genes. The principal component analysis (PCA) showed that these individuals could be divided into four populations according to their domestication and selection purpose. Seventy-two highly duplicated CNVRs were detected across all individuals, revealing pivotal roles of nervous system (NRG3,NCAM2), sensory (OR), and follicle development (VTG2) in chicken genome. When contrasting the CNVs of domestic breeds to those of RJFs, 235 CNVRs harboring 255 protein-coding genes, which were predominantly involved in pathways of nervous, immunity, and reproductive system development, were discovered. In breed-specific CNVRs, some valuable genes were identified, includingHOXB7for beard trait in Beijing You chicken;EDN3,SLMO2,TUBB1, andGFPT1for melanin deposition in Silkie chicken; andSORCS2for aggressiveness in Luxi Game fowl. Moreover,CSMD1andNTRK3with high duplications found exclusively in White Leghorn chicken, andPOLR3H,MCM9,DOCK3, andAKR1B1Lfound in Recessive White Rock chicken may contribute to high egg production and fast-growing traits, respectively. The candidate genes of breed characteristics are valuable resources for further studies on phenotypic variation and the artificial breeding of chickens.
Cholesterol-Lowering Phytochemicals: Targeting the Mevalonate Pathway for Anticancer Interventions
Authors: Laka Kagiso , Makgoo Lilian , Mbita Zukile
Published: March 2022

There are a plethora of cancer causes and the road to fully understanding the carcinogenesis process remains a dream that keeps changing. However, a list of role players that are implicated in the carcinogens process is getting lengthier. Cholesterol is known as bad sterol that is heavily linked with cardiovascular diseases; however, it is also comprehensively associated with carcinogenesis. There is an extensive list of strategies that have been used to lower cholesterol; nevertheless, the need to find better and effective strategies remains vastly important. The role played by cholesterol in the induction of the carcinogenesis process has attracted huge interest in recent years. Phytochemicals can be dubbed as magic tramp cards that humans could exploit for lowering cancer-causing cholesterol. Additionally, the mechanisms that are regulated by phytochemicals can be targeted for anticancer drug development. One of the key role players in cancer development and suppression, Tumour Protein 53 (TP53), is crucial in regulating the biogenesis of cholesterol and is targeted by several phytochemicals. This minireview covers the role of p53 in the mevalonate pathway and how bioactive phytochemicals target the mevalonate pathway and promote p53-dependent anticancer activities.
A Novel Pyroptosis-Related Gene Signature for Predicting Prognosis in Kidney Renal Papillary Cell Carcinoma
Authors: Hu Jian , Chen Yajun , Gao Liang , Ge Chengguo , Xie Xiaodu , Lei Pan , Zhang Yuanfeng , Liang Peihe
Published: March 2022

Pyroptosis is defined as an inflammatory form of programmed cell death. Increasing studies have demonstrated that pyroptosis is closely related to tumor development and antitumor process. However, the role of pyroptosis in kidney renal papillary cell carcinoma (KIRP) remains obscure. In this study, we analyzed the expression of 52 pyroptosis-related genes (PRGs) in KIRP, of which 20 differentially expressed PRGs were identified between tumor and normal tissues. Consensus clustering analysis based on these PRGs was used to divided patients into two clusters, from which a significant difference in survival was found (p = 0.0041). The prognostic risk model based on six PRGs (CASP8, CASP9, CHMP2A, GPX4, IL6, and IRF1) was built using univariate Cox regression and LASSO–Cox regression analysis, with good performance in predicting one-, three-, and five-year overall survival. Kaplan–Meier survival analysis showed that the high-risk group had a poor survival outcome (p < 0.001) and risk score was an independent prognostic factor (HR: 2.655, 95% CI 1.192–5.911, p = 0.016). Immune profiling revealed differences in immune cell infiltration between the two groups, and the infiltration of M2 macrophages was significantly upregulated in the tumor immune microenvironment, implying that tumor immunity participated in the KIRP progression. Finally, we identified two hub genes in tumor tissues (IL6 and CASP9), which were validated in vitro. In conclusion, we conducted a comprehensive analysis of PRGs in KIRP and tried to provide a pyroptosis-related signature for predicting the prognosis.
Communicating Endometriosis Pain in France and Australia: An Interview Study
Authors: Ilschner Susanne , Neeman Teresa , Parker Melissa , Phillips Christine
Published: March 2022

Endometriosis is characterized by persistent, fluctuating pain associated with menstruation, a biological function which is socially invisible. The degree and quality of pain cannot easily be measured, observed, or documented. Difficulties in communicating pain pose particular challenges when seeking diagnosis and support from health professionals. In this paper we explore the experiences and characterization of pain by thirteen Australian and thirteen French women with endometriosis. Data were collected through semi-structured interviews using a life-history approach to illness symptoms, diagnosis and treatment. We explore the experiences of women with endometriosis in two phases: from onset of symptoms to seeking advice from a clinician, and from first consulting a clinician to receiving a diagnosis. On average, initial pain symptoms were identified 2.1 years before consulting a health practitioner, after which women reported pain symptoms 8.5 years prior to diagnosis; that is, the time between consulting a clinician and receiving a diagnosis was almost four times the period between experiencing symptoms and consulting a doctor. Pain was often “made real” to doctors by findings consistent with endometriosis on ultrasound and MRI, mostly used in France, or laparoscopy, the predominant diagnostic tool in Australia. No woman described her practitioner using standardized pain assessment tools. Thus, the validation of pain relies largely on disease visibility and the clinician-classified degree of severity rather than self-reported grades of pain or impact on activities of daily living. The invisible and enigmatic pain of this chronic women's disease remains difficult to communicate to doctors, and the recognition of severe pain is often key to timely diagnostic procedures. Clinicians need to be more proactive about severe pain related to menstruation, taking into consideration women's individual circumstances, and maintain a high index of suspicion of underlying endometriosis as a condition characterized primarily by pain.
Microbial Protein Binding to gC1qR Drives PLA2G1B-Induced CD4 T-Cell Anergy
Authors: Pothlichet Julien , Meola Annalisa , Bugault Florence , Jeammet Louise , Savitt Anne G. , Ghebrehiwet Berhane , Touqui Lhousseine , Pouletty Philippe , Fiore Frédéric , Sauvanet Alain , Thèze Jacques
Published: March 2022

The origin of the impaired CD4 T-cell response and immunodeficiency of HIV-infected patients is still only partially understood. We recently demonstrated that PLA2G1B phospholipase synergizes with the HIV gp41 envelope protein in HIV viremic plasma to induce large abnormal membrane microdomains (aMMDs) that trap and inactivate physiological receptors, such as those for IL-7. However, the mechanism of regulation of PLA2G1B activity by the cofactor gp41 is not known. Here, we developed an assay to directly follow PLA2G1B enzymatic activity on CD4 T-cell membranes. We demonstrated that gp41 directly binds to PLA2G1B and increases PLA2G1B enzymatic activity on CD4 membrane. Furthermore, we show that the conserved 3S sequence of gp41, known to bind to the innate sensor gC1qR, increases PLA2G1B activity in a gC1qR-dependent manner using gC1qR KO cells. The critical role of the 3S motif and gC1qR in the inhibition of CD4 T-cell function by the PLA2G1B/cofactor system in HIV-infected patients led us to screen additional microbial proteins for 3S-like motifs and to study other proteins known to bind to the gC1qR to further investigate the role of the PLA2G1B/cofactor system in other infectious diseases and carcinogenesis. We have thus extended the PLA2G1B/cofactor system to HCV and Staphylococcus aureus infections and additional pathologies where microbial proteins with 3S-like motifs also increase PLA2G1B enzymatic activity. Notably, the bacteria Porphyromonas gingivalis, which is associated with pancreatic ductal adenocarcinoma (PDAC), encodes such a cofactor protein and increased PLA2G1B activity in PDAC patient plasma inhibits the CD4 response to IL-7. Our findings identify PLA2G1B/cofactor system as a CD4 T-cell inhibitor. It involves the gC1qR and disease-specific cofactors which are gC1qR-binding proteins that can contain 3S-like motifs. This mechanism involved in HIV-1 immunodeficiency could play a role in pancreatic cancer and several other diseases. These observations suggest that the PLA2G1B/cofactor system is a general CD4 T-cell inhibitor and pave the way for further studies to better understand the role of CD4 T-cell anergy in infectious diseases and tumor escape.
CB2R Activation Regulates TFEB-Mediated Autophagy and Affects Lipid Metabolism and Inflammation of Astrocytes in POCD
Authors: Zhang Lieliang , Wang Xifeng , Yu Wen , Ying Jun , Fang Pu , Zheng Qingcui , Feng Xiaojin , Hu Jialing , Xiao Fan , Chen Shoulin , Wei Gen , Lin Yue , Liu Xing , Yang Danying , Fang Yang , Xu Guohai , Hua Fuzhou
Published: March 2022

Evidence suggests that the accumulation of lipid drots (LDs) accelerates damage to mitochondria and increases the release of inflammatory factors. These have been implicated as a mechanism underlying neurodegenerative diseases or tumors and aging-related diseases such as postoperative cognitive dysfunction (POCD), nevertheless, accumulation of lipid droplets has not been extensively studied in the central nervous system (CNS). Here, we found that after surgery, there was activation of astrocytes and lipid accumulation in the hippocampus. However, cannabinoid receptor type II (CB2R) activation significantly reduced lipid accumulation in astrocytes and change the expression of genes related to lipid metabolism. CB2R reduces the release of the inflammatory factors interleukin-1 beta (IL-1β) and interleukin 6 (IL-6) in peripheral serum and simultaneously improves cognitive ability in mice with POCD. Further research on mechanisms indicates that CB2R activation promotes the nuclear entry of the bHLH-leucine zipper transcription factor, the transcription factor EB (TFEB), and which is a master transcription factor of the autophagy–lysosomal pathway, also reduces TFEB-S211 phosphorylation. When CB2R promotes TFEB into the nucleus, TFEB binds at two sites within promoter region of PGC1α, promoting PGC1α transcription and accelerating downstream lipid metabolism. The aforementioned process leads to autophagy activation and decreases cellular lipid content. This study uncovers a new mechanism allowing CB2R to regulate lipid metabolism and inflammation in POCD.
ACE2 Serum Levels as Predictor of Infectability and Outcome in COVID-19
Authors: Maza María del Carmen , Úbeda María , Delgado Pilar , Horndler Lydia , Llamas Miguel A. , van Santen Hisse M. , Alarcón Balbino , Abia David , García-Bermejo Laura , Serrano-Villar Sergio , Bastolla Ugo , Fresno Manuel
Published: March 2022

Background

COVID‐19 can generate a broad spectrum of severity and symptoms. Many studies analysed the determinants of severity but not among some types of symptoms. More importantly, very few studies analysed patients highly exposed to the virus that nonetheless remain uninfected.

Methods

We analysed serum levels of ACE2, Angiotensin II and anti-Spike antibodies in 2 different cohorts at high risk of viral exposure, highly exposed but uninfected subjects, either high risk health care workers or persons cohabiting with infected close relatives and seropositive patients with symptoms. We tested the ability of the sera of these subjects to neutralize lentivirus pseudotyped with the Spike-protein.

Results

We found that the serum levels of ACE2 are significantly higher in highly exposed but uninfected subjects. Moreover, sera from this seronegative persons can neutralize SARS-CoV-2 infection in cellular assays more strongly that sera from non-exposed negative controls eventhough they do not have anti-CoV-2 IgG antibodies suggesting that high levels of ACE2 in serum may somewhat protect against an active infection without generating a conventional antibody response. Finally, we show that among patients with symptoms, ACE2 levels were significantly higher in infected patients who developed cutaneous as compared with respiratory symptoms and ACE2 was also higher in those with milder symptoms.

Conclusions

These findings suggest that soluble ACE2 could be used as a potential biomarker to predict SARS-CoV-2 infection risk and to discriminate COVID-19 disease subtypes.
Fatty Acid Synthase Is the Key Regulator of Fatty Acid Metabolism and Is Related to Immunotherapy in Bladder Cancer
Authors: Xiong Qiao , Feng Dechao , Wang Ziwei , Ying Yidie , Xu Chuanliang , Wei Qiang , Zeng Shuxiong , Yang Lu
Published: March 2022

Fatty acid metabolism (FAM) genes are potentially useful for predicting prognosis and immunotherapy response in bladder cancer (BC). To examine this, we constructed a prognostic model and identified key FAM genes in BC. Using transcriptional expression profiles and clinical data of BC patients from public datasets and Changhai (CH) hospital, we built and validated a risk-score model based on 13 prognostic FAM genes. Differential gene expression identified fatty acid synthase (FASN) as central to fatty acid metabolism in BC. FASN was differentially expressed between normal and tumor tissue, and was related to survival. In the CH dataset, FASN independently predicted muscle-invasive BC. FASN differential expression was significantly related to immune-cell infiltration and patients with low FASN expression responded better to immune checkpoint inhibitor (ICI) treatment. SREBF1 was predicted as the most significant transcription factor for FASN. Competing endogenous RNA network analysis suggested that lncRNA AC107027.3 may upregulate FASN by competitively binding miR-27A-3p, thereby regulating the immunotherapy response in BC. Dasatinib and temsirolimus are potential FASN-targeting drugs. Our model efficiently predicted prognosis in BC. FASN is central to fatty acid metabolism, and a potential indicator and regulator of ICI treatment.
KIR3DL05 and KIR3DS02 Recognition of a Nonclassical MHC Class I Molecule in the Rhesus Macaque Implicated in Pregnancy Success
Authors: Nicholas Rachel E. , Sandstrom Kjell , Anderson Jennifer L. , Smith Willow R. , Wetzel Molly , Banerjee Priyankana , Janaka Sanath Kumar , Evans David T.
Published: March 2022

Knowledge of the MHC class I ligands of rhesus macaque killer-cell Ig-like receptors (KIRs) is fundamental to understanding the role of natural killer (NK) cells in this species as a nonhuman primate model for infectious diseases, transplantation and reproductive biology. We previously identified Mamu-AG as a ligand for KIR3DL05. Mamu-AG is a nonclassical MHC class I molecule that is expressed at the maternal-fetal interface of the placenta in rhesus macaques similar to HLA-G in humans. Although Mamu-AG and HLA-G share similar molecular features, including limited polymorphism and a short cytoplasmic tail, Mamu-AG is considerably more polymorphic. To determine which allotypes of Mamu-AG serve as ligands for KIR3DL05, we tested reporter cell lines expressing five different alleles of KIR3DL05 (KIR3DL05*001, KIR3DL05*004, KIR3DL05*005, KIR3DL05*008 and KIR3DL05*X) for responses to target cells expressing eight different alleles of Mamu-AG. All five allotypes of KIR3DL05 responded to Mamu-AG2*01:01, two exhibited dominant responses to Mamu-AG1*05:01, and three had low but detectable responses to Mamu-AG3*03:01, -AG3*03:02, -AG3*03:03 and -AG3*03:04. Since KIR3DL05*X is the product of recombination betweenKIR3DL05andKIR3DS02, we also tested an allotype of KIR3DS02 (KIR3DS02*004) and found that this activating KIR also recognizes Mamu-AG2*01:01. Additional analysis of Mamu-AG variants with single amino acid substitutions identified residues in the α1-domain essential for recognition by KIR3DL05. These results reveal variation in KIR3DL05 and KIR3DS02 responses to Mamu-AG and define Mamu-AG polymorphisms that differentially affect KIR recognition.
High-Throughput B Cell Epitope Determination by Next-Generation Sequencing
Authors: Walker Lauren M. , Shiakolas Andrea R. , Venkat Rohit , Liu Zhaojing Ariel , Wall Steven , Raju Nagarajan , Pilewski Kelsey A. , Setliff Ian , Murji Amyn A. , Gillespie Rebecca , Makoah Nigel A. , Kanekiyo Masaru , Connors Mark , Morris Lynn , Georgiev Ivelin S.
Published: March 2022

Development of novel technologies for the discovery of human monoclonal antibodies has proven invaluable in the fight against infectious diseases. Among the diverse antibody repertoires elicited by infection or vaccination, often only rare antibodies targeting specific epitopes of interest are of potential therapeutic value. Current antibody discovery efforts are capable of identifying B cells specific for a given antigen; however, epitope specificity information is usually only obtained after subsequent monoclonal antibody production and characterization. Here we describe LIBRA-seq with epitope mapping, a next-generation sequencing technology that enables residue-level epitope determination for thousands of single B cells simultaneously. By utilizing an antigen panel of point mutants within the HIV-1 Env glycoprotein, we identified and confirmed antibodies targeting multiple sites of vulnerability on Env, including the CD4-binding site and the V3-glycan site. LIBRA-seq with epitope mapping is an efficient tool for high-throughput identification of antibodies against epitopes of interest on a given antigen target.
Update on the Dispersal of Aedes albopictus in Mexico: 1988–2021
Authors: Ortega-Morales Aldo I. , Pérez-Rentería Cresencio , Ordóñez-Álvarez José , Salazar Juan Adrián , Dzul-Manzanilla Felipe , Correa-Morales Fabián , Huerta-Jiménez Herón
Published: March 2022

The Asian tiger mosquito Aedes albopictus (Skuse) is one of the most important mosquito species in public health due to the variety of disease-causing viruses that this species can transmit. In Mexico, Ae. albopictus was reported for the first time in 1990 in the state of Tamaulipas, bordering to the state of Texas (USA). Since then, Ae. albopictus has been reported in 15 Mexican states. Currently, this species is present in all tropical and subtropical regions of the country and its presence is common in the states of the Gulf of Mexico and Chiapas. In the present study, the presence of Ae. albopictus is reported in six additional states: Colima, Guanajuato, Jalisco, Puebla, Oaxaca, and Querétaro. The rapid dispersal of Ae. albopictus in Mexico represents a risk to public health, and the surveillance of this species in regions where it has not yet been reported is essential as part of Mexican entomological surveillance programs.
The Important Marine Mammal Area Network: A Tool for Systematic Spatial Planning in Response to the Marine Mammal Habitat Conservation Crisis
Authors: Tetley Michael J. , Braulik Gill T. , Lanfredi Caterina , Minton Gianna , Panigada Simone , Politi Elena , Zanardelli Margherita , Notarbartolo di Sciara Giuseppe , Hoyt Erich
Published: March 2022

The Important Marine Mammal Areas (IMMAs) initiative was launched by the Marine Mammal Protected Areas Task Force of the International Union for the Conservation of Nature in 2016, as a response to a conservation crisis in the protection of marine mammals and wider global ocean biodiversity. IMMAs identify discrete portions of habitat that are important for one or more marine mammal species, and that have the potential to be delineated and managed for conservation. They are identified by scientific experts during regional workshops, on the basis of satisfying one or more of eight criteria that capture critical aspects of marine mammal biology, ecology and population structure. Candidate IMMAs undergo independent scientific review prior to being accepted, and then are publicly available via a searchable and downloadable database and a dedicated online e-Atlas. Between 2016 and 2021, eight expert workshops - engaging more than 300 experts - have resulted in the identification of 173 IMMAs located in 90 countries or territories, across a third of the globe. IMMAs identified to date provide important habitats for 58 of the 131 recognized marine mammal species. Around two-thirds of all IMMAs (65%) were identified on the basis of important habitat for a marine mammal species that is threatened on the IUCN Red List. Approximately 61% of IMMA surface areas occur within Exclusive Economic Zone waters, while 39% fall within areas beyond national jurisdiction. The Task Force undertook implementation planning exercises for IMMAs in Palau (Micronesia), the Andaman Islands (India) and the Bazaruto Archipelago and Inhambane Bay (Mozambique), engaging with a range of stakeholders including government and management bodies. IMMAs are increasingly being utilized in environmental impact assessments, marine planning exercises and in international, national and supra-regional conservation, policy and management initiatives, including the Convention on Migratory Species and Convention on Biological Diversity, as well as the design and management of Marine Protected Areas (MPAs) and the extension of MPA networks. The Task Force is working toward completing a global network of IMMAs that will contribute the scientific information needed to fulfill the current collective goal of protecting 30% of the ocean by 2030.
Genetic Evaluation of Growth and Survival-Related Traits in Yesso Scallop Patinopecten yessoensis in Sea-Based Culture System
Authors: Wu Fucun , Liu Chao , Zhang Jibiao , Zhang Guofan
Published: March 2022

Worldwide, the bivalve aquaculture industry has realized or recognized the potential gains from selective breeding programs using phenotypic and pedigree data. Yesso scallop Patinopecten yessoensis are among the most important commercial shellfish in China. A family-based breeding program to investigate the genetic variations for growth and survival-related traits at suspended and bottom environments of sea-based culture systems was reported in this study. We proposed and conducted a novel phenotyping technique to longitudinally evaluate the shell heights in the yesso scallop. At harvest after rearing for 20 months, the individual shell heights at 6, 10, 16, and 20 months were simultaneously obtained by the growth rings in the outer shells of the animals. Meanwhile, the body weight (BW) of the survived individuals at harvest was also recorded. Variance components and genetic parameters for growth and survival-related traits were estimated using an animal and threshold model, respectively. In the suspended environment, the heritability estimates for BW and shell heights at specific ages ranged from moderate to high (0.328–0.853). The estimated correlations between shell heights at contiguous ages were consistently high, ranging from 0.890 to 0.958 but decreased with increasing intervals between ages (0.496–0.828). The estimated correlations between shell heights at contiguous ages and BW at harvest were similar, ranging from 0.535 to 0.983. The heritability estimates for individual survival at harvest were at a low level of 0.128 by the probit-threshold model. While at the bottom environment, estimates of heritability for growth and survival-related traits were similar but slightly lower than those at the suspended environment. Furthermore, the genetic correlation for BW between the two environments was very small, which probably indicates genotype-by-environment interaction effects for growth in the yesso scallop. The study can provide prior information, which might develop a new idea for selection in this species. The results are discussed concerning selection work with yesso scallop, and solutions for accurate estimation of genetic parameters and increasing genetic gain are also outlined.
Effective Diagnosis of Prostate Cancer Based on mRNAs From Urinary Exosomes
Authors: Gan Jiahua , Zeng Xing , Wang Xiong , Wu Ya , Lei Ping , Wang Zhihua , Yang Chunguang , Hu Zhiquan
Published: March 2022

Background

Novel non-invasive biomarkers are urgently required to improve the diagnostic sensitivity and specificity of prostate cancer (PCa). Therefore, the diagnostic value of following candidate genes (ERG, PCA3, ARV7, PSMA, CK19, and EpCAM) were estimated by testing mRNAs from urinary exosomes of patients with primary PCa.

Methods

Exosomes were obtained using size-exclusion chromatography (SEC), out of which RNAs were extracted, then analyzed by quantitative reverse transcription-polymerase chain reaction according to manufacturer’s protocol.

Results

The expression of urinary exosomal ERG, PCA3, PSMA, CK19, and EpCAM were significantly increased in patients with PCa compared with healthy males. In addition, the levels of urinary exosomal ERG, ARV7, and PSMA were intimately correlated with the Gleason score in PCa patients (P < 0.05). The receiver operating characteristic curves (ROCs) showed that urinary exosomal ERG, PCA3, PSMA, CK19, and EpCAM were able to distinguish patients with PCa from healthy individuals with the area under the curve (AUC) of 0.782, 0.783, 0.772, 0.731, and 0.739, respectively. Urinary exosomal PCA3 and PSMA distinguished PCa patients from healthy individuals with an AUC of 0.870. Combination of urinary exosomal PCA3, PSMA with serum PSA and PI-RADS achieved higher AUC compared with PSA alone (0.914 and 0.846, respectively). Kaplan-Meier curves demonstrated that PCA3, ARV7, and EpCAM were associated in androgen-deprivation therapy (ADT) failure time which is defined as from the initiation of ADT in hormone-sensitive stage to the development of castration-resistant prostate cancer.

Conclusion

These findings suggested that mRNAs from urinary exosomes have the potential in serving as novel and non-invasive indicators for PCa diagnosis and prediction.
Patient-Reported Symptoms and Sequelae 12 Months After COVID-19 in Hospitalized Adults: A Multicenter Long-Term Follow-Up Study
Authors: Comelli Agnese , Viero Giulia , Bettini Greta , Nobili Alessandro , Tettamanti Mauro , Galbussera Alessia Antonella , Muscatello Antonio , Mantero Marco , Canetta Ciro , Martinelli Boneschi Filippo , Arighi Andrea , Brambilla Paolo , Vecchi Maurizio , Lampertico Pietro , Bonfanti Paolo , Contoli Marco , Blasi Francesco , Gori Andrea , Bandera Alessandra
Published: March 2022

Objective

Our knowledge on the long-term consequences of COVID-19 is still scarce despite the clinical relevance of persisting syndrome. The aim of this study was to analyze patient-reported outcomes, including assessment by specific questionnaires of health impairment and symptoms.

Methods

This is a prospective, observational and multicenter cohort study coordinated by Fondazione IRCSS Ca' Granda Ospedale Maggiore Policlinico di Milano and Istituto di Ricerche Farmacologiche Mario Negri IRCCS including eight hospitals located in North and Central Italy. A telephone interview to assess rehospitalization, access to health care resources, general health status subjective evaluation, and symptoms was performed at 12 months after the discharge in patients admitted to hospital because of COVID-19 from February 2020 to the end of May 2020.

Results

Among the 776 patients discharged alive, 44 (5.7%) died, 456 subjects (58.8%) completed the questionnaire and 276 (35.6%) were not reachable or refused to join the telephone interview. The mean age of the study population was 59.4 years (SD 14.1), 69.8% of individuals needed oxygen support during hospitalization and 10.4% were admitted to ICU. Overall, 91.7% of participants reported at least one symptom/sequela at 12 months. Exertional dyspnea (71.7%), fatigue (54.6%), and gastrointestinal symptoms (32.8%) were the most reported ones. Health issues after discharge including hospitalization or access to emergency room were described by 19.4% of subjects. Female and presence of comorbidities were independent predictors of whealth impairment and presence of ≥2 symptoms/sequelae after 12 months from hospitalization for COVID-19.

Conclusions

Patient-reported symptoms and sequelae, principally dyspnea and fatigue, are found in most individuals even 12 months from COVID-19 hospitalization. Long-term follow-up based on patient-centered outcome can contribute to plan tailored interventions.
Subretinal Therapy: Technological Solutions to Surgical and Immunological Challenges
Authors: Ladha Reza , Caspers Laure E. , Willermain François , de Smet Marc D.
Published: March 2022

Recent advances in ocular gene and cellular therapy rely on precisely controlled subretinal delivery. Due to its inherent limitations, manual delivery can lead to iatrogenic damage to the retina, the retinal pigment epithelium, favor reflux into the vitreous cavity. In addition, it suffers from lack of standardization, variability in delivery and the need to maintain proficiency. With or without surgical damage, an eye challenged with an exogenous viral vector or transplanted cells will illicit an immune response. Understanding how such a response manifests itself and to what extent immune privilege protects the eye from a reaction can help in anticipating short- and long-term consequences. Avoidance of spillover from areas of immune privilege to areas which either lack or have less protection should be part of any mitigation strategy. In that regard, robotic technology can provide reproducible, standardized delivery which is not dependent on speed of injection. The advantages of microprecision medical robotic technology for precise targeted deliveries are discussed.
Biological Soil Crusts as Ecosystem Engineers in Antarctic Ecosystem
Authors: Barrera Andrea , Acuña-Rodríguez Ian S. , Ballesteros Gabriel I. , Atala Cristian , Molina-Montenegro Marco A.
Published: March 2022

Biological soil crusts (BSC) are considered as pivotal ecological elements among different ecosystems of the world. The effects of these BSC at the micro-site scale have been related to the development of diverse plant species that, otherwise, might be strongly limited by the harsh abiotic conditions found in environments with low water availability. Here, we describe for the first time the bacterial composition of BSCs found in the proximities of Admiralty Bay (Maritime Antarctica) through 16S metabarcoding. In addition, we evaluated their effect on soils (nutrient levels, enzymatic activity, and water retention), and on the fitness and performance of Colobanthus quitensis, one of the two native Antarctic vascular plants. This was achieved by comparing the photochemical performance, foliar nutrient, biomass, and reproductive investment between C. quitensis plants growing with or without the influence of BSC. Our results revealed a high diversity of prokaryotes present in these soil communities, although we found differences in terms of their abundances. We also found that the presence of BSCs is linked to a significant increase in soils’ water retention, nutrient levels, and enzymatic activity when comparing with control soils (without BSCs). In the case of C. quitensis, we found that measured ecophysiological performance parameters were significantly higher on plants growing in association with BSCs. Taken together, our results suggest that BSCs in Antarctic soils are playing a key role in various biochemical processes involved in soil development, while also having a positive effect on the accompanying vascular flora. Therefore, BSCs would be effectively acting as ecosystem engineers for the terrestrial Antarctic ecosystem.
Molecular Characteristic, Antibiotic Resistance, and Detection of Highly Immunoreactive Proteins of Group B Streptococcus Strains Isolated From Urinary Tract Infections in Polish Adults
Authors: Dobrut Anna , Ochońska Dorota , Brzozowska Ewa , Górska Sabina , Kaszuba-Zwoinska Jolanta , Gołda-Cępa Monika , Gamian Andrzej , Brzychczy-Wloch Monika
Published: March 2022

Group B streptococcus (GBS) is one of the uropathogens that causes urinary tract infections (UTIs). The aims of this article were molecular characterization, an analysis of antimicrobial susceptibility profiles, adherence to bladder endothelial cells, and the detection of immunoreactive proteins of 94 clinical strains of GBS isolated from adult Polish patients with UTI. Antibiotic susceptibilities were determined by disk diffusion. Serotyping and Alp family genes detection were studied using multiplex PCR. Genetic profiles were determined by pulsed-field gel electrophoresis. The adherence ability of the studied strains was estimated by incubation on human bladder microvascular endothelial cell line. Immunoreactive proteins were studied by immunoblotting. Antibiotic susceptibility investigation revealed that 22% of GBS strains were resistant to erythromycin, whereas 18% demonstrated resistance to clindamycin. cMLSB was present in 76% of the resistant strains, M phenotype was detected in 14%, whereas iMLSB was present for 10%. The most common serotype was serotype III (31%), followed by serotype V (27%), and serotype Ia (17%). The genes that dominated among other Alp genes were: epsilon (29%), alp2 (27%), and rib (23%). The most common co-occurring serotypes and Alp genes were: Ia and epsilon, III and rib, III and alp2, V and alp2, and V and alp3 (p < 0.001). The PFGE method showed high clonality for serotype V and cMLSB (p < 001). The PFGE method showed high clonality for serotype V. Furthermore, this serotype was significantly associated with the cMLSB phenotype (p < 0.001). The most common immunoreactive proteins demonstrated masses of 50 kDa and 45–47 kDa. Although examined GBS isolates showed high genetic diversity, immunoreactive proteins were common for most of the studied GBS isolates, which may indicate their conservation, and allows to consider them as potential immunodiagnostic markers. Although the examined GBS isolates showed high genetic diversity, immunoreactive proteins were shared by most of the studied GBS isolates. It may indicate their conservation, thus allowing to consider them as potential immunodiagnostic markers.
Picophytoplankton in the West Pacific Ocean: A Snapshot
Authors: Wang Feng , Wei Yuqiu , Zhang Guicheng , Zhang Linlin , Sun Jun
Published: March 2022

Marine picophytoplankton have crucial ecological value and make an important contribution to marine primary productivity. While biomass of phytoplankton in general is projected to decline as a result of global warming, picophytoplankton will likely dominate in the future oceans due to their growth advantages in an oligotrophic environment. To better understand the biography of picophytoplankton, we undertook a comprehensive study of the distribution patterns of picophytoplankton, carbon biomass, and Chl a concentrations, etc. based on large-scale sampling in the tropical Western Pacific Ocean. In terms of cellular abundance, Prochlorococcus was the most abundant group (averaging [1.03 ± 0.40] × 104 cells/mL), followed by Synechococcus (averaging [1.31 ± 1.22] × 103 cells/mL) and then picoeucaryote (averaging [4.83 ± 2.84] × 102 cells/mL). The picophytoplankton size-fractionated chlorophyll a (Pico-Chl a) accounted for about 30% of the total Chl a, with Prochlorococcus and picoeukaryotes contributing 41 and 35%, respectively, of the Pico-Chl a-normalized carbon biomass, indicating the ecological importance of picophytoplankton as the primary producers. In terms of biogeographic distribution, the picophytoplankton communities exhibited contrasting patterns. The surface distribution of Prochlorococcus and Synechococcus was concentrated in the low latitude of the 142°E section, while picoeucaryote was more abundant near the 130°E and equator sections. Synechococcus was higher in the shallow layer at 25 m, and it was extremely tolerant of high-light irradiation, while Prochlorococcus and picoeucaryote were distributed in the deep Chlorophyll maximum layer (DCM) (about 100 m). From the carbon-to-Chlorophyll a ratios, which was derived from Prochlorococcus and picoeucaryote population groups, we found that the ratio varied widely, from 0.19 to 75.56, and was highest at the depth of 200 m. Of these, Prochlorococcus had an important contribution. The correlation analysis of environmental factors showed that Prochlorococcus, Synechococcus, and picoeucaryote were negatively correlated with nutrient concentration. We concluded that Prochlorococcus group was dominant in the WPO, both in abundance and biomass, and the various abiotic factors such as temperature, salinity, and nutrient concentrations were closely correlated with the spatial variation in the picophytoplankton community. These findings aid our understanding of how contrasting environmental conditions influence picophytoplankton community and the importance of picophytoplankton in contributing the carbon pool in the oligotrophic ocean.
Heterogeneity of Starved Yeast Cells in IF1 Levels Suggests the Role of This Protein in vivo
Authors: Galkina Kseniia V. , Zubareva Valeria M. , Kashko Nataliia D. , Lapashina Anna S. , Markova Olga V. , Feniouk Boris A. , Knorre Dmitry A.
Published: March 2022

In mitochondria, a small protein IF1 suppresses the hydrolytic activity of ATP synthase and presumably prevents excessive ATP hydrolysis under conditions of energy deprivation. In yeast Saccharomyces cerevisiae, IF1 homologs are encoded by two paralogous genes: INH1 and STF1. INH1 expression is known to aggravate the deleterious effects of mitochondrial DNA (mtDNA) depletion. Surprisingly, no beneficial effects of INH1 and STF1 were documented for yeast so far, and the functions of INH1 and STF1 in wild type cells are unclear. Here, we put forward a hypothesis that INH1 and STF1 bring advantage during the fast start of proliferation after reentry into exponential growth from post-diauxic or stationary phases. We found that yeast cells increase the concentration of both proteins in the post-diauxic phase. Post-diauxic phase yeast cells formed two subpopulations distinct in Inh1p and Stf1p concentrations. Upon exit from the post-diauxic phase cells with high level of Inh1-GFP started growing earlier than cells devoid of Inh1-GFP. However, double deletion of INH1 and STF1 did not increase the lag period necessary for stationary phase yeast cells to start growing after reinoculation into the fresh medium. These results point to a redundancy of the mechanisms preventing uncontrolled ATP hydrolysis during energy deprivation.
Soil Aggregation Shaped the Distribution and Interaction of Bacterial-Fungal Community Based on a 38-Year Fertilization Experiment in China
Authors: Chen Jie , Song Dali , Liu Donghai , Sun Jingwen , Wang Xiubin , Zhou Wei , Liang Guoqing
Published: March 2022

Soil aggregates provide different ecological niches for microorganisms, and in turn, the microbial interactions affect soil aggregation process. The response of the microbial community in bulk soil to different fertilization regimes has been well studied; however, the co-occurrence patterns of bacteria and fungi in different aggregates under various fertilization regimes remain unclear. Based on the long-term field experiment, we found that fertilization regimes contributed more to fungal than to bacterial community composition. Long-term fertilization decreased microbial interactions in large macroaggregates (LM), macroaggregates (MA) and silt and clay (SC) fractions, but increased in microaggregates (MI). The application of manure with inorganic fertilizers (NPKM) significantly increased the intensive cooperation between bacteria and fungi in LM and MA. Microbial communities in LM and MA were well separated and showed strong competition against microbes in MI and SC; hence, we concluded that the microbial habitat could be divided into two groups, large fractions (LM and MA) and small fractions (MI and SC). The bacterial genera Anaerolinea, Nocardioides, Ohtaekwangia, Geoalkalibacter, Lysobacter, Pedomicrobium, and Flavisolibacter were keystone taxa in inorganic fertilization, and Roseiflexus, Nitrospira, and Blastocatella were keystone taxa in NPKM, which were all sensitive to soil aggregation. In this study, we demonstrated that the NPKM decreased the microbial interactions within and between kingdoms in LM, MA, and SC, but enhanced nutrient availability and microbial interactions in MI, leading to the formation of biofilms and the strengthening of stress tolerance, which finally stimulated the formation and stabilization of soil aggregates. Thus, this study revealed how soil microbial competition or cooperation responded to different fertilization regimes at aggregate scales, and provided evidence for the stimulation of soil stability.