bluuebunny/crossref_metadata_2025 huggingface dataset:
Variation in resource use between adult and juvenile Semipalmated Sandpipers (Calidris pusilla) and use of physiological indicators for movement decisions highlights the importance of small staging sites during southbound migration in Atlantic Canada
Authors: Linhart Rebeca C. , Hamilton Diana J. , Paquet Julie , Bellefontaine Sara C. , Davis Siena , Doiron Parker B. , Gratto-Trevor Cheri L.
Published: December 2022

Semipalmated Sandpipers (Calidris pusilla) are Arctic-breeding shorebirds that use staging sites in Atlantic Canada during their annual migration to South America. The Bay of Fundy has long been recognized as a critical staging site for migrating Semipalmated Sandpipers and supports a large prey base. The diet of adult sandpipers in the Bay is flexible but the diet of juveniles, which arrive later, is not well documented. Comparatively little is known about the prey base and how it is utilized by sandpipers at sites in Atlantic Canada outside the Bay. Plasma metabolite measures can provide useful insight to assess habitat quality for sandpipers and have not yet been measured in Semipalmated Sandpipers in Atlantic Canada. To address these knowledge gaps we sampled shorebird habitat to estimate invertebrate availability in the Bay of Fundy and the Northumberland Strait. Concurrently, we collected blood samples from adult and juvenile sandpipers for analysis of plasma metabolite levels and isotopic estimates of dietary niche in both regions. We found that sites on the Northumberland Strait hosted a more diverse and variable prey base than sites within the Bay of Fundy, and that sandpipers were selective when foraging there, appearing to prefer bivalves. Juveniles may occupy a broader dietary niche than adults along the Northumberland Strait, though appear to gain weight as efficiently. Sandpipers sampled along the Northumberland Strait had higher plasma triglyceride concentrations than those within the Bay of Fundy, which may suggest differences in fattening rate or dietary fat intake. Sandpipers that had lower triglyceride concentrations on the Northumberland Strait were more likely to move into the Bay of Fundy, while sandpipers with high triglyceride values tended to remain on the Strait. These data suggest that sandpipers made movement decisions within the region depending on their physiological state. Our results suggest adult and juvenile Semipalmated Sandpipers successfully use a variety of staging habitats in Atlantic Canada. This is an encouraging finding for sandpiper conservation in the region, but also indicates that maintaining access to a broad variety of staging habitats is critical, supporting calls for stronger conservation measures throughout the region.
Warming and phosphorus enrichment alter the size structure and body stoichiometry of aquatic gastropods
Authors: Wang Tao , Zhang Peiyu , Zhang Huan , Wang Huan , Su Xiyang , Zhang Min , Xu Jun
Published: December 2022

Aquatic gastropods are important integral components of the macroinvertebrate community in freshwater ecosystems and play critical roles in freshwater ecosystems by contributing to biodiversity, nutrient cycling, and water quality. However, the variation of aquatic gastropods’ community structure under the combined effects of warming and nutrient enrichment remains largely unknown. To investigate this question, we performed an outdoor mesocosm experiment examining the interaction of warming (a 4.5 °C increase in mean temperature above ambient conditions) and nutrient enrichment (phosphorus addition) on the aquatic gastropods’ community and dominant population (Bellamya aeruginosa). We analyzed the changes in community dynamics (abundance and biomass), size structure, and stoichiometric traits (only B. aeruginosa). Results showed that phosphorus enrichment alone had a positive effect on the total abundance and biomass of gastropods, as well as the abundance and biomass of B. aeruginosa. Warming alone only produced a positive effect on total abundance. However, the combined effects of warming and phosphorus enrichment negatively affected the biomass and abundance of the whole gastropod community and the dominant gastropod population. The body mass of B. aeruginosa increased because of warming, whereas the body mass of the gastropod community negatively responded to warming. Phosphorus enrichment alone had no remarkable effects on body mass. The combined effects of warming and phosphorus enrichment negatively affected the whole community’s body mass but had no substantial effect on the body mass of B. aeruginosa. For body stoichiometric traits, warming or phosphorus enrichment alone produced positive effects on the nitrogen and phosphorus contents of B. aeruginosa. The combined effects caused adverse effects on the contents of the two elements. The effect of warming alone only decreased the ratio of nitrogen to phosphorus. Results suggested that the response levels in size structure between the gastropod community and the dominant population differed remarkably. Composition species shift was the main cause of the decrease in aquatic gastropods’ community size structure. The shift in species composition at the whole gastropod community level caused by warming and phosphorus enrichment may result in more complex and unpredicted consequences through cascade effects on the structure and function of freshwater ecosystems.
Dendritic cell-natural killer cell cross-talk modulates T cell activation in response to influenza A viral infection
Authors: Harvey Abigail G. , Graves Athens M. , Uppalapati Chandana K. , Matthews Saoirse M. , Rosenberg Stephanie , Parent Emma G. , Fagerlie Madison H. , Guinan Jack , Lopez Brina S. , Kronstad Lisa M.
Published: December 2022

Influenza viruses lead to substantial morbidity and mortality including ~3-5 million cases of severe illness and ~290,000-650,000 deaths annually. One of the major hurdles regarding influenza vaccine efficacy is generating a durable, robust cellular immune response. Appropriate stimulation of the innate immune system is key to generating cellular immunity. Cross-talk between innate dendritic cells (DC) and natural killer (NK) cells plays a key role in activating virus-specific T cells, yet the mechanisms used by influenza A viruses (IAV) to govern this process remain incompletely understood. Here, we used anex vivoautologous human primary immune cell culture system to evaluate the impact of DC-NK cell cross-talk and subsequent naïve T cell activation at steady-state and after exposure to genetically distinct IAV strains–A/California/07/2009 (H1N1) and A/Victoria/361/2011 (H3N2). Using flow cytometry, we found that exposure of DCs to IAV in co-culture with NK cells led to a decreased frequency of CD83+and CD86+cells on DCs and an increased frequency of HLA-DR+on both DCs and NK cells. We then assessed the outcome of DC-NK cell cross-talk on T cell activation. At steady-state, DC-NK cell cross-talk increased pan T cell CD69 and CD25 expression while exposure to either IAV strain reduced pan T cell CD25 expression and suppressed CD4+and CD8+T cell IFN-γ and TNF production, following chemical stimulation with PMA/Ionomycin. Moreover, exposure to A/Victoria/361/2011 elicited lower IFN-γ production by CD4+and CD8+T cells compared with A/California/07/2009. Overall, our results indicate a role for DC-NK cell cross-talk in T cell priming in the context of influenza infection, informing the immunological mechanisms that could be manipulated for the next generation of influenza vaccines or immunotherapeutics.
Systemic complications of rheumatoid arthritis: Focus on pathogenesis and treatment
Authors: Wu Di , Luo Yehao , Li Tong , Zhao Xinyi , Lv Ting , Fang Gang , Ou Peiqi , Li Hongyi , Luo Xiaofan , Huang An , Pang Yuzhou
Published: December 2022

As a systemic autoimmune disease, rheumatoid arthritis (RA) usually causes damage not only to joints, but also to other tissues and organs including the heart, kidneys, lungs, digestive system, eyes, skin, and nervous system. Excessive complications are closely related to the prognosis of RA patients and even lead to increased mortality. This article summarizes the serious complications of RA, focusing on its incidence, pathogenesis, clinical features, and treatment methods, aiming to provide a reference for clinicians to better manage the complications of RA.
AbAgIntPre: A deep learning method for predicting antibody-antigen interactions based on sequence information
Authors: Huang Yan , Zhang Ziding , Zhou Yuan
Published: December 2022

Introduction

Antibody-mediated immunity is an essential part of the immune system in vertebrates. The ability to specifically bind to antigens allows antibodies to be widely used in the therapy of cancers and other critical diseases. A key step in antibody therapeutics is the experimental identification of antibody-antigen interactions, which is generally time-consuming, costly, and laborious. Although some computational methods have been proposed to screen potential antibodies, the dependence on 3D structures still limits the application of these methods.

Methods

Here, we developed a deep learning-assisted prediction method (i.e., AbAgIntPre) for fast identification of antibody-antigen interactions that only relies on amino acid sequences. A Siamese-like convolutional neural network architecture was established with the amino acid composition encoding scheme for both antigens and antibodies.

Results and Discussion

The generic model of AbAgIntPre achieved satisfactory performance with the Area Under Curve (AUC) of 0.82 on a high-quality generic independent test dataset. Besides, this approach also showed competitive performance on the more specific SARS-CoV dataset. We expect that AbAgIntPre can serve as an important complement to traditional experimental methods for antibody screening and effectively reduce the workload of antibody design. The web server of AbAgIntPre is freely available at http://www.zzdlab.com/AbAgIntPre.
Monoclonal antibodies constructed from COVID-19 convalescent memory B cells exhibit potent binding activity to MERS-CoV spike S2 subunit and other human coronaviruses
Authors: Peng Yuan , Liu Yongcheng , Hu Yabin , Chang Fangfang , Wu Qian , Yang Jing , Chen Jun , Teng Shishan , Zhang Jian , He Rongzhang , Wei Youchuan , Bostina Mihnea , Luo Tingrong , Liu Wenpei , Qu Xiaowang , Li Yi-Ping
Published: December 2022

Introduction

The Middle East respiratory syndrome coronavirus (MERS-CoV) and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are two highly contagious coronaviruses causing MERS and COVID-19, respectively, without an effective antiviral drug and a long-lasting vaccine. Approaches for diagnosis, therapeutics, prevention, etc., particularly for SARS-CoV-2 that is continually spreading and evolving, are urgently needed. Our previous study discovered that >60% of sera from convalescent COVID-19 individuals, but <8% from general population, showed binding activity against the MERS-CoV spike protein, indicating that SARS-CoV-2 infection boosted antibodies cross-reactive with MERS-CoV.

Methods

To generate antibodies specific to both SARS-CoV-2 and MERS-CoV, here we screened 60 COVID-19 convalescent sera against MERS-CoV spike extracellular domain and S1 and S2 subunits. We constructed and characterized monoclonal antibodies (mAbs) from COVID-19 convalescent memory B cells and examined their binding and neutralizing activities against human coronaviruses.

Results and Discussion

Of 60 convalescent serum samples, 34 showed binding activity against MERS-CoV S2, with endpoint titers positively correlated with the titers to SARS-CoV-2 S2. By sorting single memory B cells from COVID-19 convalescents, we constructed 38 mAbs and found that 11 mAbs showed binding activity with MERS-CoV S2, of which 9 mAbs showed potent cross-reactivity with all or a proportion of spike proteins of alphacoronaviruses (229E and NL63) and betacoronaviruses (SARS-CoV-1, SARS-CoV-2, OC43, and HKU1). Moreover, 5 mAbs also showed weak neutralization efficiency against MERS-CoV spike pseudovirus. Epitope analysis revealed that 3 and 8 mAbs bound to linear and conformational epitopes in MERS-CoV S2, respectively. In summary, we have constructed a panel of antibodies with broad-spectrum reactivity against all seven human coronaviruses, thus facilitating the development of diagnosis methods and vaccine design for multiple coronaviruses.
Advances in pathogenesis and nanoparticles (NPs)-mediated treatment of psoriasis
Authors: Shen Qian , Liu Rong , Tan Shiyu , Xu Xiaoding , Fang Junyue , Li Rong
Published: December 2022

Psoriasis is a chronic papulosquamous skin disease with an autoimmune pathogenic traits and strong genetic predisposition. In the past few decades, with the rapid development of molecular biology and cell biology, the inherent pathogenesis of psoriasis has been gradually elucidated, in which cytokine inflammatory loops, cell signaling pathways, and epigenetic factors such as miRNAs have been demonstrated to play important roles in regulating the development and progression of psoriasis. More importantly, understanding the pathogenesis of psoriasis has promoted the development of effective treatment for psoriasis. In this review, we systemically summarized the molecular mechanisms regulating the development and progression psoriasis, introduced various therapeutics used for clinical psoriasis therapy, and highlighted the recent advances in nanoparticles (NPs)-mediated drug delivery for psoriasis treatment.
Manipulating T-cell metabolism to enhance immunotherapy in solid tumor
Authors: Chen Chen , Wang Zehua , Ding Yi , Qin Yanru
Published: December 2022

Cellular metabolism is not only essential for tumor cells to sustain their rapid growth and proliferation, but also crucial to maintain T cell fitness and robust immunity. Dysregulated metabolism has been recognized as a hallmark of cancer, which provides survival advantages for tumor cells under stress conditions. Also, emerging evidence suggests that metabolic reprogramming impacts the activation, differentiation, function, and exhaustion of T cells. Normal stimulation of resting T cells promotes the conversion of catabolic and oxidative metabolism to aerobic glycolysis in effector T cells, and subsequently back to oxidative metabolism in memory T cells. These metabolic transitions profoundly affect the trajectories of T-cell differentiation and fate. However, these metabolic events of T cells could be dysregulated by their interplays with tumor or the tumor microenvironment (TME). Importantly, metabolic competition in the tumor ecosystem is a new mechanism resulting in strong suppression of effector T cells. It is appreciated that targeting metabolic reprogramming is a promising way to disrupt the hypermetabolic state of tumor cells and enhance the capacity of immune cells to obtain nutrients. Furthermore, immunotherapies, such as immune checkpoint inhibitor (ICI), adoptive cell therapy (ACT), and oncolytic virus (OV) therapy, have significantly refashioned the clinical management of solid tumors, they are not sufficiently effective for all patients. Understanding how immunotherapy affects T cell metabolism provides a bright avenue to better modulate T cell anti-tumor response. In this review, we provide an overview of the cellular metabolism of tumor and T cells, provide evidence on their dynamic interaction, highlight how metabolic reprogramming of tumor and T cells regulate the anti-tumor responses, describe T cell metabolic patterns in the context of ICI, ACT, and OV, and propose hypothetical combination strategies to favor potent T cell functionality.
Variations in dynamic tumor-associated antigen-specific T cell responses correlate with HCC recurrence after thermal ablation
Authors: Zang Chaoran , Zhao Yan , Liu Guihai , Li Kang , Qin Ling , Zhang Yuewei , Sun Jianping , Wang Qi , Ma Liang , Zhao Peng , Sun Yu , Guo Dandan , Yuan Chunwang , Dong Tao , Zhang Yonghong
Published: December 2022

Background

Ablative therapy is a recommended treatment for hepatocellular carcinoma (HCC) not only for its effective eradication of tumors, but also for its induction of host immunity. However, the high 5-year recurrence rate after ablation underlines the poor understanding of the antitumor immunity response. Here, we investigated the effects of thermal ablation on antitumor immunity.

Methods

We analyzed the dynamics of tumor-associated antigen (TAA)-specific immune responses and changes in peripheral blood mononuclear cell phenotype in patients with HCC before and after tumor ablation. We used the IFN-γ ELISPOT assay and immunophenotyping by flow cytometry to evaluate the effects of ablation on host immunity. The correlation between the T cell response and disease outcome was explored to uncover the efficacy of the immune response in inhibiting HCC recurrence.

Results

Different TAA-specific T cell responses were identified among patients before and after ablation. One week after ablation, there was an improved immune state, with a switch from the dominance of an AFP-specific T cell response to that of a SMNMS-specific T cell response, which was correlated with better survival. Furthermore, an improvement in immune status was accompanied by a lower level of PD1+ and Tim3+ T cells in CD8+ T cells. Although this functional state was not durable, there was a higher degree of AFP-specific T cell responses at 4-weeks post-ablation. Furthermore, T cells presented a more exhausted phenotype at 4-weeks post-ablation than at the 1-week timepoint.

Conclusions

Ablation elicits a transient antitumor immune response in patients with HCC by changing the profile of the T cell response and the expression of immune checkpoint molecules, which correlated with longer recurrence-free survival of patients with HCC.
Modulation of the symbionts light environment in hospite in scleractinian corals
Authors: Galindo-Martínez Claudia Tatiana , Chaparro Arelys , Enríquez Susana , Iglesias-Prieto Roberto
Published: December 2022

The upregulation of animal chromoproteins (CPs) during thermal stress produces “colorful” bleached corals that facilitate coral recovery after bleaching. In situ measurements indicate that animal CPs present in coral tissues reduce the elevated internal light environment of the remaining symbionts in bleached or low-pigmented stressed corals. However, there is still a lack of understanding regarding the extent to which animal CPs contribute to modifying the internal light environment of the symbionts in hospite. In this study, we evaluate the effect of three animal CPs on the optical properties of the coral tissue and their internal light environment using a numerical model. The model allows estimations of the absorbance spectra of corals as a function of changes in symbiont and animal pigmentation, as well as descriptions of the light environment in hospite of the symbionts. These descriptions were derived from the quantification of the contribution of each pigment component to light absorption, together with the contribution of the coral skeleton’s reflectance. Simulations indicate that animal CPs upregulation modifies the spectral distribution and the intensity of the internal light field. Animal CPs can reduce up to 11% of the light intensity in hospite when present individually, and up to 24% when present in combination. Such reduction may play a critical role in preventing the full development of the bleached phenotype when irradiance rises to excessive levels at low coral pigmentation, facilitating coral recovery and symbiont tissue re-colonization after bleaching. Accordingly, coral’s CPs components need to also be considered when selecting coral species for future restoration efforts.
Advancing best practices for assessing trends of ocean acidification time series
Authors: Sutton Adrienne J. , Battisti Roman , Carter Brendan , Evans Wiley , Newton Jan , Alin Simone , Bates Nicholas R. , Cai Wei-Jun , Currie Kim , Feely Richard A. , Sabine Christopher , Tanhua Toste , Tilbrook Bronte , Wanninkhof Rik
Published: December 2022

Assessing the status of ocean acidification across ocean and coastal waters requires standardized procedures at all levels of data collection, dissemination, and analysis. Standardized procedures for assuring quality and accessibility of ocean carbonate chemistry data are largely established, but a common set of best practices for ocean acidification trend analysis is needed to enable global time series comparisons, establish accurate records of change, and communicate the current status of ocean acidification within and outside the scientific community. Here we expand upon several published trend analysis techniques and package them into a set of best practices for assessing trends of ocean acidification time series. These best practices are best suited for time series capable of characterizing seasonal variability, typically those with sub-seasonal (ideally monthly or more frequent) data collection. Given ocean carbonate chemistry time series tend to be sparse and discontinuous, additional research is necessary to further advance these best practices to better address uncharacterized variability that can result from data discontinuities. This package of best practices and the associated open-source software for computing and reporting trends is aimed at helping expand the community of practice in ocean acidification trend analysis. A broad community of practice testing these and new techniques across different data sets will result in improvements and expansion of these best practices in the future.
The rule of law for marine environmental governance in maritime transport: China’s experience
Authors: Xing Houqun , Cao Xingguo , Su Zixiu
Published: December 2022

Maritime transport is a major source of pollution of marine environment, which is the essential object in a series of international maritime legislations and various countries’ domestic laws. Focused on protecting the marine environment, China has spent over 40 years developing the rule of law for marine environmental governance in maritime transport, including efforts made in legislation, law enforcement, and the judiciary. In this article, we attempt to examine China’s experience and practice in the marine environment, explain the logic and consideration in relevant practices, and summarize China’s paradigm for the rule of law for such governance. China has sought to resolve two major issues: the relationship between domestic and international law and the balance of interests between flag, coastal, and port states, offering a vivid model of marine environmental governance on which other countries can base their own legal systems. The findings reveal that with following and enforcing the international law of the sea, now China’s domestic laws have form lawful authority on binding foreign vessels. China is continually strengthening the construction of its legislative system to harmonize inconsistencies and keep pace with international marine environmental law. To eliminate administrative inefficiency resulting from cumbersome procedures, China has reformed its maritime enforcement system by consolidating multiple administrations. China’s independent maritime judicial system is meeting the demand to develop environmental specialization, enabling further exploitation of its profession in solving maritime environment cases and implementing environmental legislation.
Survival prediction using the Freiburg index of post-TIPS survival (FIPS) in critically ill patients with acute- on chronic liver failure: A retrospective observational study
Authors: Luxenburger Hendrik , Schmidt Katharina , Biever Paul , Supady Alexander , Sekandarzad Asieb , Roehlen Natascha , Reincke Marlene , Neumann-Haefelin Christoph , Schultheiss Michael , Wengenmayer Tobias , Thimme Robert , Bettinger Dominik
Published: December 2022

Background and aim

Liver cirrhosis in patients treated in the intensive care unit (ICU) is associated with high mortality. Well established scores are useful to allow for assessment of prognosis and support ICU treatment guidance. However, currently used scoring systems often do not reflect the complexity of critically ill patients. Therefore, we tested the newly developed Freiburg index-of post-TIPS survival (FIPS) score in order to assess its potential role for prognostication of cirrhotic patients in the ICU.

Methods

A total of 310 patients with liver cirrhosis treated in the ICU between 2010 and 2021 were enrolled in this retrospective observational study. Prognostic factors for mortality and 28-day mortality were assessed. Moreover, using c indices the prognostic discrimination of different prognostic scores was analyzed.

Results

The FIPS score allowed to discriminate patients with high ICU mortality and within 28-days after ICU treatment (ICU mortality: 42.2 vs. 59.9%, p = 0.008 and 28-day mortality: 43.3 vs. 74.1%, p < 0.001). However, the FIPS score in its current composition showed no superior prognostic discrimination compared to other established scores. Multivariable analyses identified the FIPS score (HR 1.25 [1.04–1.49], p = 0.015) and lactate at admission (HR 1.07 [1.04–1.09], p < 0.001) as significant predictors of ICU mortality. Lactate at admission substantially improved patient risk stratification within each FIPS risk groups.

Conclusion

Similar to other commonly used scores, the FIPS score in its current composition does not allow a sufficiently reliable prognostication of critically ill patients treated in the ICU. However, adding lactate as additional factor to the FIPS score may improve its prognostic ability.
Biofilm and pathogenic factor analysis of Gardnerella vaginalis associated with bacterial vaginosis in Northeast China
Authors: Ma Xiaolu , Wang Xiaoxi , Ye Shengna , Liu Jinnan , Yuan Hong , Wang Nan
Published: December 2022

Introduction

Gardnerella vaginalis is a major pathogen responsible for bacterial vaginosis (BV). However, the recurrence of infection and the antibiotic resistance of biofilms remain significant challenges for the treatment of BV. In this study, we aimed to analyze the pathogenic factors and drug sensitivity associated with the clinical treatment of BV in Northeast China.

Methods

Subgroups were identified by clade-specific polymerase chain reaction (PCR). Biofilm formation was measured by crystal violet staining, confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM). The inhibition and eradication of biofilm formation were measured by XTT and broth recovery-based methods.

Results

Of the 24 samples of G. vaginalis, 11 samples and American Type Culture Collection (ATCC) 14018 formed biofilms; the remainder did not. The positive rates of detection for the sialidase A and vly genes in the 24 G. vaginalis samples were 100% and 79.2%, respectively. Moreover, 21 samples (87.5%) showed resistance to metronidazole and 16 (66.7%) presented with sensitivity towards clindamycin. The biofilm MIC80 (BMIC80) of metronidazole for ATCC14018 was 16 μg/ml while that of clindamycin was 0.125 μg/ml. The minimum biofilm eradication concentration (MBEC) of metronidazole was > 256 μg/ml while that of clindamycin was > 2 μg/ml.

Discussion

Our results revealed that G. vaginalis is more resistant to metronidazole than clindamycin and neither metronidazole nor clindamycin are able to effectively eradicate vaginal biofilms. Thus, the role of antibiotics and biofilms in BV requires further investigation.
Characteristics of intestinal microbiota in C57BL/6 mice with non-alcoholic fatty liver induced by high-fat diet
Authors: Yan Guangwen , Li Shuaibing , Wen Yuhang , Luo Yadan , Huang Jingrong , Chen Baoting , Lv Shuya , Chen Lang , He Lvqin , He Manli , Yang Qian , Yu Zehui , Xiao Wudian , Tang Yong , Li Weiyao , Han Jianhong , Zhao Fangfang , Yu Shumin , Kong Fang , Abbasi Benazir , Yin Hongmei , Gu Congwei
Published: December 2022

Introduction

As a representation of the gut microbiota, fecal and cecal samples are most often used in human and animal studies, including in non-alcoholic fatty liver disease (NAFLD) research. However, due to the regional structure and function of intestinal microbiota, whether it is representative to use cecal or fecal contents to study intestinal microbiota in the study of NAFLD remains to be shown.

Methods

The NAFLD mouse model was established by high-fat diet induction, and the contents of the jejunum, ileum, cecum, and colon (formed fecal balls) were collected for 16S rRNA gene analysis.

Results

Compared with normal mice, the diversity and the relative abundance of major bacteria and functional genes of the ileum, cecum and colon were significantly changed, but not in the jejunum. In NAFLD mice, the variation characteristics of microbiota in the cecum and colon (feces) were similar. However, the variation characteristics of intestinal microbiota in the ileum and large intestine segments (cecum and colon) were quite different.

Discussion

Therefore, the study results of cecal and colonic (fecal) microbiota cannot completely represent the results of jejunal and ileal microbiota.
Soil bacterial community changes along elevation gradients in karst graben basin of Yunnan-Kweichow Plateau
Authors: Li Qiang , Qiu Jiangmei , Liang Yueming , Lan Gaoyong
Published: December 2022

Elevation gradients could provide natural experiments to examine geomorphological influences on biota ecology and evolution, however little is known about microbial community structures with soil depths along altitudinal gradients in karst graben basin of Yunnan-Kweichow Plateau. Here, bulk soil in A layer (0 ~ 10 cm) and B layer (10 ~ 20 cm) from two transect Mounts were analyzed by using high-throughput sequencing coupled with physicochemical analysis. It was found that the top five phyla in A layer were Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia, and the top five phyla in B layer were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi in a near-neutral environment. Edaphic parameters were different in two layers along altitudinal gradients. Besides that, soil microbial community compositions varied along altitudinal gradient, and soil organic carbon (SOC) and total nitrogen (TN) increased monotonically with increasing elevation. It was further observed that Shannon indexes with increasing altitudes in two transect Mounts decreased monotonically with significant difference (p = 0.001), however beta diversity followed U-trend with significant difference (p = 0.001). The low proportions of unique operational taxonomic units (OTUs) appeared at high altitude areas which impact the widely accepted elevation Rapoport’s rules. The dominant Bradyrhizobium (alphaproteobacterial OTU 1) identified at high altitudes in two layers constitutes the important group of free-living diazotrophs and could bring fixed N into soils, which simultaneously enhances SOC and TN accumulation at high altitudes (p < 0.01). Due to different responses of bacterial community to environmental changes varying with soil depths, altitudinal gradients exerted negative effects on soil bacterial communities via soil physical properties and positive effects on soil bacterial diversities via soil chemical properties in A layer, however the results in B layer were opposite. Overall, our study is the first attempt to bring a deeper understanding of soil microbial structure patterns along altitudinal gradients at karst graben basin areas.
RNA-Seq-based transcriptome analysis of methicillin-resistant Staphylococcus aureus growth inhibition by propionate
Authors: Im Jintaek , Lee Dongwook , Park Ok-Jin , Natarajan Sathishkumar , Park Junhyung , Yun Cheol-Heui , Han Seung Hyun
Published: December 2022

Staphylococcus aureus is a pathogen that causes a variety of infectious diseases such as pneumonia, endocarditis, and septic shock. Methicillin-resistant S. aureus (MRSA) evades virtually all available treatments, creating the need for an alternative control strategy. Although we previously demonstrated the inhibitory effect of sodium propionate (NaP) on MRSA, the regulatory mechanism of this effect remains unclear. In this study, we investigated the regulatory mechanism responsible for the inhibitory effect of NaP on MRSA using RNA-Seq analysis. Total RNAs were isolated from non-treated and 50 mM NaP-treated S. aureus USA300 for 3 h and transcriptional profiling was conducted by RNA-Seq analysis. A total of 171 differentially expressed genes (DEGs) with log2 fold change ≥2 and p < 0.05 was identified in the NaP treatment group compared with the control group. Among the 171 genes, 131 were up-regulated and 40 were down-regulated. Upon gene ontology (GO) annotation analysis, total 26 specific GO terms in “Biological process,” “Molecular function,” and “Cellular component” were identified in MRSA treated with NaP for 3 h. “Purine metabolism”; “riboflavin metabolism”; and “glycine, serine, and threonine metabolism” were identified as major altered metabolic pathways among the eight significantly enriched KEGG pathways in MRSA treated with NaP. Furthermore, the MRSA strains deficient in purF, ilvA, ribE, or ribA, which were the up-regulated DEGs in the metabolic pathways, were more susceptible to NaP than wild-type MRSA. Collectively, these results demonstrate that NaP attenuates MRSA growth by altering its metabolic pathways, suggesting that NaP can be used as a potential bacteriostatic agent for prevention of MRSA infection.
Characterization of integrative and conjugative elements carrying antibiotic resistance genes of Streptococcus suis isolated in China
Authors: Wang Jianping , Qi Kexin , Bai Xuemei , Wu Zongfu , Kang Weiming , Liang Pujun , Zheng Han , Xu Jianguo
Published: December 2022

Streptococcus suis, an emerging zoonotic pathogen, is important reservoirs of antibiotic resistance genes that play critical roles in the horizontal transfer of corresponding resistances. In the present study, 656 antibiotic resistance (AR) genes were detected in 154 of 155 genomes of S. suis strains isolated from the nasopharynx of slaughtered pigs and the lungs of diseased pigs in China. The AR genes were clustered into 11 categories, consisting of tetracycline, macrolides, lincosamide, streptogramin, aminoglycoside, trimethoprim, amphenicols, nucleoside, quinupristin/dalfopristin, glycopeptide, and oxazolidinones resistance genes. In order to investigate the transmission patterns of the AR genes, AR genes-associated the mobile genetic elements (MGEs) were extracted and investigated. Twenty ICEs, one defective ICE, one tandem ICE, and ten prophages were found, which mainly carried tetracycline, macrolides/lincosamides/streptogramin (MLS), and aminoglycosides resistance genes. Three types of DNA cargo with AR genes were integrated into specific sites of ICEs: integrative mobilizable elements (IMEs), cis-IMEs (CIMEs), and transposon Tn916. Obvious differences in AR gene categories were found among the three cargo types. IMEs mainly harbored tetracycline and MLS resistance genes. CIMEs mainly carried aminoglycoside resistance genes, while transposon Tn916 carried only the tet (M) gene. Nearly all AR genes in ICEs were carried by IMEs and CIMEs. IMEs were prevalent and were also detected in additional 29 S. suis genomes. The horizontal transfer of IMEs and CIMEs may play critical role in ICE evolution and AR gene transmission in the S. suis population. Our findings provide novel insights into the transmission patterns of AR genes and the evolutionary mechanisms of ICEs in S. suis.
Effects of different microbial agents on bedding treatment of ectopic fermentation of buffalo manure
Authors: Niu Kaifeng , Chao Chen , Zhang Xinxin , An Zhigao , Zhou Jiayan , Yang Liguo
Published: December 2022

Introduction

The rapid development of the farming industry has increased the amount of manure produced by livestock and poultry, causing increasingly prominent environmental pollution problems. In recent years, due to the increase in conventional bedding material costs, an increasing number of farmers choose to use harmless recycled manure as bedding. Manure bedding treatment of farms can not only solve the problem of manure pollution, but also resource utilization of manure and cost savings.

Methods

This study compared the effects of five microbial agents (Microbial agents A, B, C, E, F) on buffalo manure bedding treatment by testing the temperature, moisture content, pH, microbial bacteria distribution of buffalo manure ectopic fermentation, and screened the lowest cost and most effective agent. The changes of microbial bacteria distribution in different periods of bedding treatment were also detected.

Results

Agent A was eliminated because of poor fermentation effect and low fermentation temperature, which could not achieve the effect of harmless treatment. The other four agents of bacteria achieved a harmless effect, but the bedding treatment effect of agent F was significantly better than agent E, B, and C. In terms of the cost of agents: the cost of agent F required for fermenting 100m³ buffalo manure was the lowest, 1000yuan, followed by E (1200yuan), C (1750yuan), and B (1980yuan). In the process of ectopic fermentation bedding treatment of buffalo manure, Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Chloroflexi were the major bacteria used. The process was divided into three periods; the heating period - high temperature period - cooling period, the high temperature period could reach more than 75°C, and a large number of pathogenic bacteria and harmful bacteria, and other miscellaneous bacteria in the pile were degraded, their species diversity was reduced, and the structure of bacterial flora had significant differences in different treatment periods. In conclusion, this study has provided a guide for the resource utilization of manure in cattle farms and the reduction of manure pollution to the environment.
A gut microbiome tactile teaching tool and guided-inquiry activity promotes student learning
Authors: Shoaf Parker T. , French Katie S. , Clifford Noah J. , McKenney Erin A. , Ott Laura E.
Published: December 2022

The gut microbiome and its physiological impacts on human and animal health is an area of research emphasis. Microbes themselves are invisible and may therefore be abstract and challenging to understand. It is therefore important to infuse this topic into undergraduate curricula, including Anatomy and Physiology courses, ideally through an active learning approach. To accomplish this, we developed a novel tactile teaching tool with guided-inquiry (TTT-GI) activity where students explored how the gut microbiome ferments carbohydrates to produce short chain fatty acids (SCFAs). This activity was implemented in two sections of a large-enrollment Human Anatomy and Physiology course at a research intensive (R1) university in the Spring of 2022 that was taught using a hyflex format. Students who attended class in person used commonly available building toys to assemble representative carbohydrates of varying structural complexity, whereas students who attended class virtually made these carbohydrate structures using a digital learning tool. Students then predicted how microbes within the gut would ferment different carbohydrates into SCFAs, as well as the physiological implications of the SCFAs. We assessed this activity to address three research questions, with 182 students comprising our sample. First, we evaluated if the activity learning objectives were achieved through implementation of a pre-and post-assessment schema. Our results revealed that all three learning objectives of this activity were attained. Next, we evaluated if the format in which this TTT-GI activity was implemented impacted student learning. While we found minimal and nonsignificant differences in student learning between those who attended in-person and those who attended remotely, we did find significant differences between the two course sections, which differed in length and spacing of the activity. Finally, we evaluated if this TTT-GI approach was impactful for diverse students. We observed modest and nonsignificant positive learning gains for some populations of students traditionally underrepresented in STEM (first-generation students and students with one or more disabilities). That said, we found that the greatest learning gains associated with this TTT-GI activity were observed in students who had taken previous upper-level biology coursework.
Identifying circRNA-miRNA interaction based on multi-biological interaction fusion
Authors: Yao Dunwei , Nong Lidan , Qin Minzhen , Wu Shengbin , Yao Shunhan
Published: December 2022

CircRNA is a new type of non-coding RNA with a closed loop structure. More and more biological experiments show that circRNA plays important roles in many diseases by regulating the target genes of miRNA. Therefore, correct identification of the potential interaction between circRNA and miRNA not only helps to understand the mechanism of the disease, but also contributes to the diagnosis, treatment, and prognosis of the disease. In this study, we propose a model (IIMCCMA) by using network embedding and matrix completion to predict the potential interaction of circRNA-miRNA. Firstly, the corresponding adjacency matrix is constructed based on the experimentally verified circRNA-miRNA interaction, circRNA-cancer interaction, and miRNA-cancer interaction. Then, the Gaussian kernel function and the cosine function are used to calculate the circRNA Gaussian interaction profile kernel similarity, circRNA functional similarity, miRNA Gaussian interaction profile kernel similarity, and miRNA functional similarity. In order to reduce the influence of noise and redundant information in known interactions, this model uses network embedding to extract the potential feature vectors of circRNA and miRNA, respectively. Finally, an improved inductive matrix completion algorithm based on the feature vectors of circRNA and miRNA is used to identify potential interactions between circRNAs and miRNAs. The 10-fold cross-validation experiment is utilized to prove the predictive ability of the IIMCCMA. The experimental results show that the AUC value and AUPR value of the IIMCCMA model are higher than other state-of-the-art algorithms. In addition, case studies show that the IIMCCMA model can correctly identify the potential interactions between circRNAs and miRNAs.
The role of ethnicity, biological sex, and psychotropic agents in early and late onset Alzheimer’s disease
Authors: Miller Alyssa , Desai Ashna , Roley Laurie Theriot , Goodwin Richard L. , Nathaniel Adebobola I. , Nathaniel Thomas I.
Published: December 2022

Objective

This study investigates differences in pharmacological and demographic factors among male and female patients with Late-onset Alzheimer’s disease (LOAD) and Early-onset Alzheimer’s disease (EOAD).

Method

Data are from 10,126 AD patients, 9,290 were diagnosed with LOAD, while 836 were diagnosed with EOAD. Data were collected from the Prisma Health Upstate Alzheimer’s patients’ registry between 2016 and 2021. The logistic regression analysis was used to assess the association between pharmacological and demographic factors in males and females with LOAD and EOAD.

Results

In the adjusted analysis for males, patients that were administered memantine [odd ratio (OR) = 1.588, 95% CI, 1.175–2.145, p = 0.003], and buspirone [OR = 1.971, 95% CI, 1.221–3.183, p = 0.006] were more likely to be associated with EOAD, while increasing age [OR = 0.816, 95% CI, 0.799–0.834, p < 0.001] was associated with LOAD. Female patients with a history of alcohol (ETOH) use were more likely to be associated with EOAD while increasing age [OR = 0.845, 95% CI, 0.834–0.857, p < 0.001], treatment with memantine [OR = 0.774, 95% CI, 0.627–0.956, p = 0.017], African Americans [OR = 0.621, 95% CI, 0.462–0.835, p = 0.002] and tobacco use [OR = 0.529, 95% CI, 0.424–0.660, p < 0.001] were associated with LOAD.

Conclusion

Our findings identified specific demographic and pharmacological factors associated with males and females with LOAD and EOAD. These findings suggest the need to develop strategies to eliminate disparity in the care of LOAD or EOAD patients.
Case report: A unusual case of delayed propionic acidemia complicated with subdural hematoma
Authors: Jiang Zongzhi , Fu Yuxin , Wei Xiaojing , Wang Ziyi , Yu Xuefan
Published: December 2022

Background

Propionic acidemia (PA) is an inherited autosomal recessive metabolic disorder that is classified as early-onset or late-onset, depending on the onset time of clinical symptoms. It clinically manifests as numerous lesions in the brain, pancreas, liver, and muscle. Muscle biopsies show myopathic changes, which help to distinguish late-onset propionic acidemia from other metabolic diseases involving muscles.

Case presentation

A 19-year-old Chinese girl was admitted to the hospital because of poor eating and fatigue. Head magnetic resonance imaging suggested metabolic diseases, and we administered symptomatic support treatment. Her symptoms gradually worsened, and she began to show convulsions and disturbances of consciousness. Muscle pathology showed myopathy-like changes. The presence of organic acids in the blood and urine suggested PA. Genetic analyses identified two compound heterozygous mutations in the patient's PCCB gene, confirming the diagnosis of delayed PA.

Conclusions

The muscle pathological examination of late-onset PA provides valuable information that is helpful for distinguishing delayed-onset PA from metabolic diseases. In the absence of a history of trauma, subdural hematoma may be a very rare complication of late-onset PA and can be regarded as a poor prognostic sign; therefore, it is suggested to perform head computed tomography as part of the routine neurological evaluation of PA patients.
Assessing the therapeutic impact of resveratrol in ALS SOD1-G93A mice with electrical impedance myography
Authors: Nagy Janice A. , Semple Carson , Lo PuiChi , Rutkove Seward B.
Published: December 2022

To aid in the identification of new treatments for amyotrophic lateral sclerosis (ALS), convenient biomarkers are needed to effectively and uniformly measure drug efficacy. To this end, we assessed the effects of the nutraceutical resveratrol (RSV) on disease onset and overall survival in SOD1-G93A (ALS) mice and compared several standard biomarkers including body mass, motor score (MS), paw grip endurance (PGE), and compound motor action potential (CMAP) amplitude, with the technique of electrical impedance myography (EIM) to follow disease progression. Eighteen ALS mice (nine females, nine males) received RSV in the chow (dose: 120 mg/kg/day) starting at 8 weeks of age; 19 ALS mice (nine females, 10 males) received normal chow; 10 wild type (WT) littermates (five females, five males) fed standard chow served as controls. Biomarker assessments were performed weekly beginning at 8 weeks. No differences in either disease onset or overall survival were found between RSV-treated and untreated ALS mice of either sex; moreover, all biomarkers failed to identify any beneficial effect of RSV when administered at this dose. Therefore, for the comparative evaluation of the ability of the various biomarkers to detect the earliest symptoms of disease, data from all animals (i.e., RSV-treated and untreated ALS mice of both sexes) were combined. Of the biomarkers tested, EIM impedance values, i.e., surface EIM longitudinal phase at 50 kHz (LP 50 kHz), and CMAP amplitude showed the earliest significant changes from baseline. LP 50 kHz values showed a rate of decline equivalent to that of CMAP amplitude and correlated with both PGE and CMAP amplitude [Spearman rho = 0.806 (p = 0.004) and 0.627 (p = 0.044), respectively]. Consistent with previous work, these findings indicate that surface EIM can serve as an effective non-invasive biomarker for preclinical drug testing in rodent models of ALS.