bluuebunny/crossref_metadata_2025 huggingface dataset:
Drivers of Soil Total Nitrogen and Phosphorus Storage in Alpine Wetland Across the Three Rivers Source Region on the Qinghai-Tibetan Plateau
Authors: Nie Xiuqing , Wang Dong , Zhou Guoying , Xiong Feng , Ren Lining , Chen Yongzhe , Ma Kali , Zhong Zebing , Du Yangong
Published: March 2022

Although soil total nitrogen (STN) and soil total phosphorus (STP) play significant roles in terrestrial ecosystem function, their storage and driving factors in the alpine wetlands of the Qinghai-Tibetan Plateau remain unclear. In this study, we estimated STN and STP storage and their controlling factors, including vegetation, soil, and climate characteristics, using data collected from 50 sites across the wetlands in the Three Rivers Source Region. STN and STP storage in the top 30 cm of soil were 62.12 ± 37.55 Tg N and 9.24 ± 2.90 Tg P, respectively. Although STN density did not differ significantly for different vegetation types (i.e., alpine meadow and alpine wetland), belowground biomass showed a positive relationship with STN density. Mean annual precipitation (MAP) showed a significant positive relationship with STN density, whereas the effects of mean annual temperature on STN density were minor. Compared with the effects of vegetation and climatic factors, soil characteristics were found to not only exert a significant effect on STN density, but also influence the effects of climate and vegetation on STN density. For STP density, soil characteristics were found to be a significant controlling factor, whereas the effects of biomass and climatic factors were minor. The studied climate, soil, and vegetation characteristics jointly explained ∼54% of STN variance, whereas soil characteristics explained only 20% of STP variation. MAP indirectly affected STN density via effects on vegetation and soil, and its direct effect on STN density was minor. This indicated a strong relationship between biotic and abiotic effects and STN density. Identification of the factors influencing STN and STP variance in alpine wetlands contributes to our understanding of the biogeochemical cycle in high-altitude regions.
Evaluation of Agricultural Sustainable Development Based on Resource Use Efficiency: Empirical Evidence From Zhejiang Province, China
Authors: Fu Linlin , Mao Xiaobao , Mao Xiaohong , Wang Jin
Published: March 2022

Improving resource use efficiency is an effective way to accelerate the realization of “carbon emission peak” and “carbon neutrality.” To perform a thorough analysis of the temporal and spatial variations in Zhejiang’s agricultural sustainable development, the present study adopted the entropy weight TOPSIS method and built a RUE-based evaluation index system for sustainable agriculture. The system covered six evaluation aspects: agricultural resource endowment, the agricultural production and agricultural science and technology levels, and ecological, economic, and social benefits. Based hereon, the present study evaluated the agricultural sustainable development of Zhejiang province from 2013 to 2019, and that of its 11 prefecture-level cities and 25 national agricultural sustainable development pilot demonstration zones in 2019. The results showed that chronologically, Zhejiang made steady progress in its agricultural sustainable development from 2013 to 2019, despite slight fluctuations, and spatially, evident regional disparities were found across its 11 prefecture-level cities and 25 pilot demonstration zones. Moreover, resource use efficiency had a significant impact on agricultural sustainable development. Zhejiang’s practices in the efficient use of cultivated land, water resources, forest resources, agricultural labor force, agricultural material goods, and agricultural science and technology offer valuable references for sustainable agriculture worldwide.
Mammal Taphonomy in a Cave Deposit From Quaternary of Brazil
Authors: Trifilio Lucas Henrique Medeiros da Silva , Araújo-Júnior Hermínio Ismael de , Porpino Kleberson de Oliveira , Barbosa Fernando Henrique de Souza
Published: March 2022

In Brazil, the Quaternary caves of the Brazilian Intertropical Region (BIR) host important fossiliferous deposits of terrestrial vertebrates, whose fossil content is taxonomically well known. Here, we conducted a taphonomic analysis based on macroscopic and microscopic features of 543 specimens collected in the F3 cave, a fossiliferous deposit located in the municipality of Baraúna, northeast of Brazil. This deposit encompasses 17 taxa, but it is dominated by fossils of Eremotherium laurillardi. Most bones were buried in less than a year, but the taphonomic history of this deposit was governed by alternation of dry and wet cycles. This led us to recognize four taphonomic modes, that differ according to the climatic conditions in which the bones were preserved as well as the time interval between the accumulation and the final burial of the remains.
A Gene Panel for Early Identification of Future Responders to Immune Checkpoint Blockade
Authors: Panda Anshuman , Betigeri Anil , Ganesan Shridar
Published: March 2022

Immune checkpoint blockade (ICB), therapies that target the PD-1 pathway, CTLA-4 pathway, and other checkpoint pathways, lead to durable responses in many cancer types. Since only a minority of patients respond to ICB, it may be useful to identify the future responders early in the course of treatment. In this study we evaluated a small (15 genes) biologically motivated panel, consisting of genes involved in immune activation and checkpoint pathways, for early identification of future responders to ICB. The panel passed consistency check, pathological and in-silico validations, and was an excellent predictor (area under ROC curve >0.95) of eventual response to ICB, both CTLA-4 and PD-1 blockade, when applied to metastatic melanoma patients undergoing ICB (i.e., “on-treatment”) in a publicly available dataset. These results suggest that this small biologically motivated panel may be useful for early identification of future responders to ICB.
MAP3K1 Variant Causes Hyperactivation of Wnt4/β-Catenin/FOXL2 Signaling Contributing to 46,XY Disorders/Differences of Sex Development
Authors: Chen Hong , Chen Qingqing , Zhu Yilin , Yuan Ke , Li Huizhu , Zhang Bingtao , Jia Zexiao , Zhou Hui , Fan Mingjie , Qiu Yue , Zhuang Qianqian , Lei Zhaoying , Li Mengyao , Huang Wendong , Liang Li , Yan Qingfeng , Wang Chunlin
Published: March 2022

Background: 46,XY disorders/differences of sex development (46,XY DSD) are congenital conditions that result from abnormal gonadal development (gonadal dysgenesis) or abnormalities in androgen synthesis or action. During early embryonic development, several genes are involved in regulating the initiation and maintenance of testicular or ovarian-specific pathways. Recent reports have shown that MAP3K1 genes mediate the development of the 46,XY DSD, which present as complete or partial gonadal dysgenesis. Previous functional studies have demonstrated that some MAP3K1 variants result in the gain of protein function. However, data on possible mechanisms of MAP3K1 genes in modulating protein functions remain scant.

Methods: This study identified a Han Chinese family with the 46,XY DSD. To assess the history and clinical manifestations for the 46,XY DSD patients, the physical, operational, ultra-sonographical, pathological, and other examinations were performed for family members. Variant analysis was conducted using both trio whole-exome sequencing (trio WES) and Sanger sequencing. On the other hand, we generated transiently transfected testicular teratoma cells (NT2/D1) and ovary-derived granular cells (KGN), with mutant or wild-type MAP3K1 gene. We then performed functional assays such as determination of steady-state levels of gender related factors, protein interaction and luciferase assay system.

Results: Two affected siblings were diagnosed with 46,XY DSD. Our analysis showed a missense c.556A > G/p.R186G variant in the MAP3K1 gene. Functional assays demonstrated that the MAP3K1R186G variant was associated with significantly decreased affinity to ubiquitin (Ub; 43–49%) and increased affinity to RhoA, which was 3.19 ± 0.18 fold, compared to MAP3K1. The MAP3K1R186G led to hyperphosphorylation of p38 and GSK3β, and promoted hyperactivation of the Wnt4/β-catenin signaling. In addition, there was increased recruitment of β-catenin into the nucleus, which enhanced the expression of pro-ovarian transcription factor FOXL2 gene, thus contributing to the 46,XY DSD.

Conclusion: Our study identified a missense MAP3K1 variant associated with 46,XY DSD. We demonstrated that MAP3K1R186G variant enhances binding to the RhoA and improves its own stability, resulting in the activation of the Wnt4/β-catenin/FOXL2 pathway. Taken together, these findings provide novel insights into the molecular mechanisms of 46,XY DSD and promotes better clinical evaluation.
Comparative Transcriptomic Analysis Reveals the Regulated Expression Profiles in Oreochromis niloticus in Response to Coinfection of Streptococcus agalactiae and Streptococcus iniae
Authors: Cui Miao , Wang Zibin , Yang Yongchun , Liu Ru , Wu Min , Li Yujie , Zhang Qizhong , Xu Delin
Published: March 2022

Tilapia (Oreochromis sp.) is one of the important economical fishes in the world. Streptococcosis is commonly found in tilapia, causing severe and devastating effects in tilapia cultures. Streptococcus agalactiae and Streptococcus iniae are the predominant pathogens causing tilapia streptococcosis. To understand the molecular mechanisms underlying differential streptococcal infection patterns, Nile tilapias (Oreochromis niloticus) were infected by 1 × 107 CFU/mL S. agalactiae, 1 × 107 CFU/mL S. iniae, and 1 × 107 CFU/mL S. agalactiae and S. iniae (1:1), respectively, and transcriptome analysis was conducted to the intestine samples of Nile tilapia (Oreochromis niloticus) at 6, 12, 24 h, and 7 days post-infection. A total of 6,185 genes that differentially expressed among groups were identified. Eight differentially expressed genes (DEGs) including E3 ubiquitin-protein ligase TRIM39-like, C-X-C motif chemokine 10-like(CXCL 10), C-C motif chemokine 19-like, interleukin-1 beta-like, IgM heavy chain VH region, partial, IgG Fc-binding protein, proteasome subunit beta type-8 (PSMB8), and ATP synthase F(0) complex subunit B1, mitochondrial that involved in the immune system were selected, and their expression levels in the coinfection group were significantly higher than those in either of the single infection groups. These genes were associated with four different KEGG pathways. Additionally, the differential expression of eight DEGs was validated by using the RT-qPCR approach, and their immunological importance was discussed. The results provided insights into the responses of tilapia against S. agalactiae and S. iniae at the transcriptome level, promoting our better understanding of immune responses for aquatic animal against Streptococcus.
The Evolutionary Advantage in Mammals of the Complementary Monoallelic Expression Mechanism of Genomic Imprinting and Its Emergence From a Defense Against the Insertion Into the Host Genome
Authors: Kaneko-Ishino Tomoko , Ishino Fumitoshi
Published: March 2022

In viviparous mammals, genomic imprinting regulates parent-of-origin-specific monoallelic expression of paternally and maternally expressed imprinted genes (PEGs and MEGs) in a region-specific manner. It plays an essential role in mammalian development: aberrant imprinting regulation causes a variety of developmental defects, including fetal, neonatal, and postnatal lethality as well as growth abnormalities. Mechanistically, PEGs and MEGs are reciprocally regulated by DNA methylation of germ-line differentially methylated regions (gDMRs), thereby exhibiting eliciting complementary expression from parental genomes. The fact that most gDMR sequences are derived from insertion events provides strong support for the claim that genomic imprinting emerged as a host defense mechanism against the insertion in the genome. Recent studies on the molecular mechanisms concerning how the DNA methylation marks on the gDMRs are established in gametes and maintained in the pre- and postimplantation periods have further revealed the close relationship between genomic imprinting and invading DNA, such as retroviruses and LTR retrotransposons. In the presence of gDMRs, the monoallelic expression of PEGs and MEGs confers an apparent advantage by the functional compensation that takes place between the two parental genomes. Thus, it is likely that genomic imprinting is a consequence of an evolutionary trade-off for improved survival. In addition, novel genes were introduced into the mammalian genome via this same surprising and complex process as imprinted genes, such as the genes acquired from retroviruses as well as those that were duplicated by retropositioning. Importantly, these genes play essential/important roles in the current eutherian developmental system, such as that in the placenta and/or brain. Thus, genomic imprinting has played a critically important role in the evolutionary emergence of mammals, not only by providing a means to escape from the adverse effects of invading DNA with sequences corresponding to the gDMRs, but also by the acquisition of novel functions in development, growth and behavior via the mechanism of complementary monoallelic expression.
Genetic Parameters of White Striping and Meat Quality Traits Indicative of Pale, Soft, Exudative Meat in Turkeys (Meleagris gallopavo)
Authors: Vanderhout Ryley J. , Leishman Emily M. , Abdalla Emhimad A. , Barbut Shai , Wood Benjamin J. , Baes Christine F.
Published: March 2022

Due to the increasing prevalence of growth-related myopathies and abnormalities in turkey meat, the ability to include meat quality traits in poultry breeding strategies is an issue of key importance. In the present study, genetic parameters for meat quality traits and their correlations with body weight and meat yield were estimated using a population of purebred male turkeys. Information on live body, breast, thigh, and drum weights, breast meat yield, feed conversion ratio, breast lightness (L*), redness (a*), and yellowness (b*), ultimate pH, and white striping (WS) severity score were collected on 11,986 toms from three purebred genetic lines. Heritability and genetic and partial phenotypic correlations were estimated for each trait using an animal model with genetic line, hatch week-year, and age at slaughter included as fixed effects. Heritability of ultimate pH was estimated to be 0.34 ± 0.05 and a range of 0.20 ± 0.02 to 0.23 ± 0.02 for breast meat colour (L*, a*, and b*). White striping was also estimated to be moderately heritable at 0.15 ± 0.02. Unfavorable genetic correlations were observed between body weight and meat quality traits as well as white striping, indicating that selection for increased body weight and meat yield may decrease pH and increase the incidence of pale meat with more severe white striping. The results of this analysis provide insight into the effect of current selection strategies on meat quality and emphasize the need to include meat quality traits into future selection indexes for turkeys.
The Prognostic Value of Integrated Analysis of Inflammation and Hypoxia-Related Genes in Idiopathic Pulmonary Fibrosis
Authors: Liu Jun , Gu Liming , Li Wenli
Published: March 2022

Currently, the aetiology and pathogenesis of idiopathic pulmonary fibrosis (IPF) are still largely unclear. Moreover, patients with IPF exhibit a considerable difference in clinical presentation, treatment, and prognosis. Optimal biomarkers or models for IPF prognosis are lacking. Therefore, this study quantified the levels of various hallmarks using a single-sample gene set enrichment analysis algorithm. The hazard ration was calculated using Univariate Cox regression analysis based on the transcriptomic profile of bronchoalveolar lavage cells and clinical survival information. Afterwards, weighted Gene Co-expression Network Analysis was performed to construct a network between gene expression, inflammation response, and hypoxia. Subsequently, univariate Cox, random forest, and multivariate Cox regressions were applied to develop a robust inflammation and hypoxia-related gene signature for predicting clinical outcomes in patients with IPF. Furthermore, a nomogram was constructed to calculate risk assessment. The inflammation response and hypoxia were identified as latent risk factors for patients with IPF. Five genes, including HS3ST1, WFDC2, SPP1, TFPI, and CDC42EP2, were identified that formed the inflammation-hypoxia-related gene signature. Kaplan-Meier plotter showed that the patients with high-risk scores had a worse prognosis than those with low-risk scores in training and validation cohorts. The time-dependent concordance index and the receiver operating characteristic analysis revealed that the risk model could accurately predict the clinical outcome of patients with IPF. Therefore, this study contributes to elucidating the role of inflammation and hypoxia in IPF, which can aid in assessing individual prognosis and personalised treatment decisions.
Impact of HLA Epitope Matching on Outcomes After Unrelated Bone Marrow Transplantation
Authors: Iwasaki Makoto , Kanda Junya , Tanaka Hidenori , Shindo Takero , Sato Takahiko , Doki Noriko , Fukuda Takahiro , Ozawa Yukiyasu , Eto Tetsuya , Uchida Naoyuki , Katayama Yuta , Kataoka Keisuke , Ara Takahide , Ota Shuichi , Onizuka Makoto , Kanda Yoshinobu , Ichinohe Tatsuo , Atsuta Yoshiko , Morishima Satoko
Published: March 2022

The significance of antibody-identified epitopes stimulating humoral alloimmunity is not well understood in the identification of non-permissive human leukocyte antigen (HLA) mismatching patterns in hematopoietic stem cell transplantation (HSCT). This was a retrospective study in a cohort of 9,991 patients who underwent their first HSCT for hematologic malignancies from unrelated bone marrow donors in the Transplant Registry Unified Management Program (TRUMP). HLA eplet mismatches (EMM) were quantified using HLAMatchmaker (HLAMM). The median age of patients was 48 years (range, 16 to 77). The number of EMM in recipient-donor pairs in our study population ranged from 0 to 37 in HLA class I (median, 0) and 0 to 60 in HLA class II (median, 1). In addition to the known high-risk mismatch patterns in the Japanese cohort, HLA-C EMM in the GVH direction was associated with a significantly higher risk for grade III-IV aGVHD, leading to a higher risk of non-relapse mortality and lower overall survival (compared with HLA-C matched patients, HR 1.67, 95% CI 1.44–1.95; HR 1.39, 95% CI 1.25–1.54; HR 1.20, 95% CI 1.10–1.30, respectively). HLAMM-based epitope matching might be useful for identifying patients who are at high risk for serious complications after HSCT from HLA mismatched unrelated donors.
5-Methylcytosine Related LncRNAs Reveal Immune Characteristics, Predict Prognosis and Oncology Treatment Outcome in Lower-Grade Gliomas
Authors: Zhang Jiheng , Wang Nan , Wu Jiasheng , Gao Xin , Zhao Hongtao , Liu Zhihui , Yan Xiuwei , Dong Jiawei , Wang Fang , Ba Yixu , Ma Shuai , Jin Jiaqi , Du Jianyang , Ji Hang , Hu Shaoshan
Published: March 2022

5-Methylcytosine (m5C) methylation is an important RNA modification pattern that can participate in oncogenesis and progression of cancers by affecting RNA stability, expression of oncogenes, and the activity of cancer signaling pathways. Alterations in the expression pattern of long non-coding RNAs (lncRNAs) are potentially correlated with abnormalities in the m5C regulation features of cancers. Our aim was to reveal the mechanisms by which lncRNAs regulated the m5C process, to explore the impact of aberrant regulation of m5C on the biological properties of lower-grade gliomas (LGG), and to optimize current therapeutic. By searching 1017 LGG samples from the Cancer Genome Atlas and Chinese Glioma Genome Atlas, we first clarified the potential impact of m5C regulators on LGG prognosis in this study and used univariate Cox analysis and least absolute shrinkage and selection operator regression to explore clinically meaningful lncRNAs. Consequently, we identified four lncRNAs, including LINC00265, CIRBP-AS1, GDNF-AS1, and ZBTB20-AS4, and established a novel m5C-related lncRNAs signature (m5CrLS) that was effective in predicting prognosis. Notably, mutation rate, WHO class II, IDH mutation, 1p/19q co-deletion and MGMT promoter methylation were increased in the low m5CrLS score group. Patients with increased m5CrLS scores mostly showed activation of tumor malignancy-related pathways, increased immune infiltrating cells, and decreased anti-tumor immune function. Besides, the relatively high expression of immune checkpoints also revealed the immunosuppressed state of patients with high m5CrLS scores. In particular, m5CrLS stratification was sensitive to assess the efficacy of LGG to temozolomide and the responsiveness of immune checkpoint blockade. In conclusion, our results revealed the molecular basis of LGG, provided valuable clues for our understanding of m5C-related lncRNAs, and filled a gap between epigenetics and tumor microenvironment.
Monomeric C-Reactive Protein: Current Perspectives for Utilization and Inclusion as a Prognostic Indicator and Therapeutic Target
Authors: Slevin Mark , Heidari Nima , Azamfirei Leonard
Published: March 2022

Monomeric C-reactive protein (mCRP), once thought to be a figment of the imagination and whose biological activity was ascribed to its sodium azide preservative, has now pronounced itself as a critical molecule playing a direct role in mediating many of the acute and chronic aberrant pathological responses to inflammation. In this focused mini review, we describe the currently attributed pathobiological interactions of mCRP in disease, where its tissue and cellular distribution and deposition have recently been clearly characterized and linked to inflammation and other pathway-associated progression of neurological and cardiovascular complications and deleterious outcomes. and focus upon current opinions as to the diagnostic and prognostic potential of mCRP-plasma circulating protein and define the possible future therapeutics including ongoing research attempting to block CRP dissociation with small molecule inhibitors or prevention of cell surface binding directly using antibodies or modified orphan drug targeting directed towards CRP, inhibiting its cellular interactions and signaling activation. There is no doubt that understanding the full influence of the biological power of mCRP in disease development and outcome will be considered a critical parameter in future stratified treatment.
Space and Habitat Utilization of the Red King Crab (Paralithodes camtschaticus) in a Newly Invaded Fjord in Northern Norway
Authors: Aune Magnus , Jensen Jenny L. A. , Siikavuopio Sten I. , Christensen Guttorm N. , Nilsen Kåre Tormod , Merkel Benjamin , Renaud Paul E.
Published: March 2022

The red king crab (RKC, Paralithodes camtschaticus) was introduced to the southern Barents Sea in the 1960s with the aim to develop a new, commercially attractive stock of the species. In the subsequent decades, the stock has indeed become abundant and widespread, but the species’ presence also implies intense predation on benthic biota and thereby severe degradation of benthic ecosystems. Our capacity to monitor and harvest the species efficiently is therefore imperative. Yet, fishermen report highly variable catches despite little variation in the timing and location of fishing, possibly induced by the species’ migratory behavior, which makes the search for crab aggregations time consuming and expensive. Previous studies have shown that the RKC is capable of conducting long-distance migrations, and suggest that the species conduct seasonal migrations between shallow (winter- and springtime) and deep waters (summer and autumn). Here, we applied telemetry to investigate the migratory behavior and habitat utilization of 37 adult individuals of the RKC in a relatively shallow fjord in northern Norway from late May until early November. Approximately half of the crabs (n = 16) left the study area early during the study period, but some individuals (n = 3) were recaptured between 53 and 147 km away from the study area, confirming that the RKC may conduct long-distance migrations. In contrast to expectations, most of the remaining individuals of RKC (n = 16) stayed for a prolonged summer and autumn period and used a limited portion of the fjord. These crabs responded quickly to changes in ambient water temperature, seeking deeper and colder waters masses when the temperature in shallower waters increased. Several individuals showed nearly identical spatio-temporal distributions, which supports earlier observations of crab aggregations. Our data indicates that the area utilization of the RKC is affected by trade-offs between biotic and abiotic factors, in which sub-optimal water temperatures may be tolerated provided appropriate access to food. Thus, our findings suggest that the current knowledge of RKC seasonal migration patterns may need to be revised, which in turn will have implications for managers and the fishing industry. This study demonstrates the high potential of telemetry studies to yield new, high-resolution data and knowledge of species’ ecology.
Fish Assemblages of a Sub-Arctic Fjord Show Early Signals of Climate Change Response Contrary to the Benthic Assemblages
Authors: Mérillet Laurène , Skogen Morten D. , Vikebø Frode , Jørgensen Lis Lindal
Published: March 2022

Arctic benthic ecosystems are facing high-speed environmental changes, such as decreased sea ice coverage, increased temperature and precipitations, as well as the invasion by non-indigenous species. Few sub-arctic fjords have the particularity to have an inner-most part forming a basin in which water remains very cold. Those fjords may offer a refugee for cold-water arctic species as well as a small-scale “laboratory” of the changes that arctic assemblages located at higher latitudes might face soon. The Porsangerfjord in Northern Norway is a sub-arctic fjord with an inner arctic part and face red king crabs Paralithodes camtchasticus invasion since the end of the 1990s. It offers a case study of the dynamics of arctic ecosystems facing multiple stressors, i.e., climate change and invasive species. Based on a time series of megabenthic invertebrates and bentho-demersal fishes over 2007–2019, a complex multivariate analysis (STATICO) was used to identify the trends in the relationship between taxa and the environment. We showed the main environmental changes in the fjord were the freshening of the water, the increase of the seabed current, and the decrease of the maximum sea ice extent. A strong along-fjord gradient was visible for both benthic and fish assemblages. Species richness and Shannon diversity of fishes significantly increased into the fjord, due to the arrival of warm-water species over time that overlapped with cold-water species that have seen their biomass significantly reduced. No significant decrease in the biomass of the cold-water benthic species was visible, which could indicate an efficient refugee effect of the inner fjord. Yet, this refugee effect could be unbalanced by the red king crab invasion as it is a predator of several arctic species. In the Porsangerfjord, fish species thus respond to climate change while megabenthic assemblages are more threatened by invasive species.
DNA Barcoding Identifies Endangered Sharks in Pet Food Sold in Singapore
Authors: French Ian , Wainwright Benjamin J.
Published: March 2022

Shark populations have declined by more than 70% over the past 50 years. These declines have largely been attributed to increases in fishing efforts. Despite increased public awareness surrounding the conservation of sharks, three-quarters of all oceanic shark species are currently considered at risk of extinction. Here, we use DNA barcoding to identify shark DNA found in pet food purchased within Singapore. We identified a number of sharks that have some degree of control over their trade exerted under the auspices of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), or through their classification as threatened by the International Union for Conservation of Nature (IUCN). The most commonly identified shark was the blue shark, Prionace glauca, a species that is not listed in CITES or classified as threatened by the IUCN, but one which scientific evidence suggests is overexploited and should have its catch regulated. The second most commonly encountered species was the CITES Appendix II listed silky shark, Carcharhinus falciformis. None of the products specifically listed shark as an ingredient, listing only generic terms, such as “ocean fish,” “white fish,” and “white bait.” The vague terminology used to describe pet food ingredients, and in some cases, the mislabeling of contents, prevents consumers – in this case, pet owners – from making informed and environmentally conscious decisions; consequently, pet owners and animal lovers may unwittingly be contributing to the overfishing of endangered sharks.
Ecophysiological Responses of Five Mangrove Species (Bruguiera gymnorrhiza, Rhizophora stylosa, Aegiceras corniculatum, Avicennia marina, and Kandelia obovata) to Chilling Stress
Authors: Wang Shu-Min , Wang You-Shao , Su Bo-Yu , Zhou Yue-Yue , Chang Li-Fang , Ma Xiao-Yu , Li Xiao-Mei
Published: March 2022

Although the low temperature is a critical growth constraint on plants, the physiological mechanism remains unclear, especially in mangrove plants. Hence, the morphological characteristics of five mangrove plants (Bruguiera gymnorrhiza, Rhizophora stylosa, Aegiceras corniculatum, Avicennia marina, and Kandelia obovata) were compared under chilling stress. The contents of hydrogen peroxide (H2O2), malondialdehyde (MDA), and proline were tested. Activities of reactive oxygen species (ROS)-scavenging enzyme [superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)] were also measured after chilling stress. It was concluded that K. obovata can well tolerate chilling stress, and B. gymnorrhiza suffered the most severe chilling damage. Leaf-morphology observation exhibited that K. obovata and A. corniculatum can sustain chilling stress, while B. gymnorrhiza wilted and A. marina turned brown. The content of H2O2 increased at first and subsequently decreased in all plants. MDA increased instantaneously in B. gymnorrhiza and R. stylosa but changed slowly in K. obovata and A. corniculatum. The high content of proline accumulated in B. gymnorrhiza and K. obovata. The activities of the SOD, POD, and CAT increased at first and then decreased in all mangrove species. The antioxidants maintained high activity in K. obovata while decreasing earliest in A. marina exposed to the long-term chilling stress. Principal component analysis (PCA) indicated that high antioxidant enzyme activities play key roles in chilling tolerance for mangrove plants. The longer-term chilling tolerance of K. obovata may be related to the high antioxidant enzyme activities and proline accumulation. Lower H2O2 and MDA contents strengthen the anti-chilling ability of A. corniculatum. Further investigation on the molecular mechanisms will facilitate the understanding of the anti-chilling ability of mangrove plants.
Ocular Surface Ion-Channels Are Closely Related to Dry Eye: Key Research Focus on Innovative Drugs for Dry Eye
Authors: Yang Shuo , Wu Yaying , Wang ChunYang , Jin Xiuming
Published: March 2022

Abundant ion-channels, including various perceptual receptors, chloride channels, purinergic receptor channels, and water channels that exist on the ocular surface, play an important role in the pathogenesis of dry eye. Channel-targeting activators or inhibitor compounds, which have shown positive effects in in vivo and in vitro experiments, have become the focus of the dry eye drug research and development, and individual compounds have been applied in clinical experimental treatment. This review summarized various types of ion-channels on the ocular surface related to dry eye, their basic functions, and spatial distribution, and discussed basic and clinical research results of various channel receptor regulatory compounds. Therefore, further elucidating the relationship between ion-channels and dry eye will warrant research of dry eye targeted drug therapy.
Screening of Long Non-coding RNAs Biomarkers for the Diagnosis of Tuberculosis and Preliminary Construction of a Clinical Diagnosis Model
Authors: Chen Juli , Wu Lijuan , Lv Yanghua , Liu Tangyuheng , Guo Weihua , Song Jiajia , Hu Xuejiao , Li Jing
Published: March 2022

Background

Pathogenic testing for tuberculosis (TB) is not yet sufficient for early and differential clinical diagnosis; thus, we investigated the potential of screening long non-coding RNAs (lncRNAs) from human hosts and using machine learning (ML) algorithms combined with electronic health record (EHR) metrics to construct a diagnostic model.

Methods

A total of 2,759 subjects were included in this study, including 12 in the primary screening cohort [7 TB patients and 5 healthy controls (HCs)] and 2,747 in the selection cohort (798 TB patients, 299 patients with non-TB lung disease, and 1,650 HCs). An Affymetrix HTA2.0 array and qRT-PCR were applied to screen new specific lncRNA markers for TB in individual nucleated cells from host peripheral blood. A ML algorithm was established to combine the patients’ EHR information and lncRNA data via logistic regression models and nomogram visualization to differentiate PTB from suspected patients of the selection cohort.

Results

Two differentially expressed lncRNAs (TCONS_00001838 and n406498) were identified (p < 0.001) in the selection cohort. The optimal model was the “LncRNA + EHR” model, which included the above two lncRNAs and eight EHR parameters (age, hemoglobin, lymphocyte count, gamma interferon release test, weight loss, night sweats, polymorphic changes, and calcified foci on imaging). The best model was visualized by a nomogram and validated, and the accuracy of the “LncRNA + EHR” model was 0.79 (0.75–0.82), with a sensitivity of 0.81 (0.78–0.86), a specificity of 0.73 (0.64–0.79), and an area under the ROC curve (AUC) of 0.86. Furthermore, the nomogram showed good compliance in predicting the risk of TB and a higher net benefit than the “EHR” model for threshold probabilities of 0.2–1.

Conclusion

LncRNAs TCONS_00001838 and n406498 have the potential to become new molecular markers for PTB, and the nomogram of “LncRNA + EHR” model is expected to be effective for the early clinical diagnosis of TB.
First Detection of Mukawa Virus in Ixodes persulcatus and Haemaphysalis concinna in China
Authors: Wang Yu-Na , Jiang Rui-Ruo , Ding Heng , Zhang Xiao-Long , Wang Ning , Zhang Yun-Fa , Li Yue , Chen Jin-Jin , Zhang Pan-He , Li Hao , Jiang Jia-Fu , Liu Lan-Zheng , Yu Meng-bin , Wang Gang , Zhang Xiao-Ai , Liu Wei
Published: March 2022

Mukawa virus (MKWV), a novel tick-borne virus (TBV) of the genus Phlebovirus of family Phenuiviridae, has been firstly reported in Ixodes persulcatus in Japan. In this study, we made an epidemiological investigation in China to obtain the geographic distribution and genetic features of this virus outside Japan. We screened 1,815 adult ticks (665 I. persulcatus, 336 Dermacentor silvarum, 599 Haemaphysalis longicornis, 170 Rhipicephalus microplus, 45 Haemaphysalis concinna) and 805 wild small mammals collected from eight provinces. The positive rate of 6.77% (45/665, including 18 female and 27 male I. persulcatus) and 2.22% (1/45, 1 male H. concinna) were obtained from I. persulcatus and H. concinna in Heilongjiang province, respectively. No evidence of MKWV infection was found in other three tick species or any of the mammalian species. The virus can infect the Vero cells successfully, indicating the ability of MKWV to replicate in mammalian cells. A phylogenetic tree based on the nucleotide sequences of L, M, and S segments demonstrated that the Japanese MKWV variant, our two MKWV variants, and KURV were clustered with the members of the mosquito/sandfly-borne phleboviruses and distant from other tick-borne phenuiviruses. A phylogenetic analysis based on 895 bp partial L gene sequences (n = 46) showed that all MKWV sequences were separated into three lineages. Our results showed the presence of MKWV in I. persulcatus and H. concinna in northeast of China, highlighting the necessity of epidemiological study in wider regions. Due to the ability of MKWV to replicate in mammalian cells, the potential for zoonosis, and wide distribution of I. persulcatus and H. concinna in China, the important vectors of MKWV, further screening to more tick species, wild animals, domestic animals, and humans raises up practical significance.
Increase in Viral Load in Patients With SARS-CoV-2 Delta Variant Infection in the Republic of Korea
Authors: Kim Jeong-Min , Rhee Jee Eun , Yoo Myeongsu , Kim Heui Man , Lee Nam-Joo , Woo Sang Hee , Jo Hye-Jun , Kwon Donghyok , Lee Sangwon , Yoo Cheon Kwon , Kim Eun-Jin
Published: March 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread rapidly, causing in COVID-19 being declared a global pandemic by the World Health Organization. The key variants include alpha, beta, gamma, and delta; these exhibit high viral transmission, pathogenicity, and immune evasion mechanisms. The delta variant, first confirmed in India, was detected in the majority of COVID-19 patients at the recent wave in the Republic of Korea. Here, the features of the delta variant were compared to the earlier waves, with focus on increased transmissibility. The viral load, from the initial days of infection to 14 days later, was compared based on epidemiological data collected at the time of confirmed diagnosis. The increased viral load observed in the delta variant-led infections influences the scale of the wave, owing to the increased rate of transmission. Infections caused by the delta variant increases the risk of hospitalization within 14 days after symptom onset, and the high viral load correlates with COVID-19 associated morbidity and mortality. Therefore, the future studies should compare the trend of disease severity caused by the high viral load of delta variant with previous waves and analyze the vaccine effects in light of the delta variant of fourth wave.
Cr(VI) Removal by Recombinant Escherichia coli Harboring the Main Functional Genes of Sporosarcina saromensis M52
Authors: An Qiuying , Zhang Min , Guo Dongbei , Wang Guangshun , Xu Hao , Fan Chun , Li Jiayao , Zhang Wei , Li Yi , Chen Xiaoxuan , You Wanting , Zhao Ran
Published: March 2022

Hexavalent chromium [Cr(VI)], a recognized heavy metal pollutant, has attracted much attention because of its negative impact on the ecological environment and human health. A chromium-resistant strain, Sporosarcina saromensis M52, was discovered, and the functional genes orf2987, orf3015, orf0415, and orf3237 were identified in the strain by genomics. With the advancement of DNA recombination and gene-splicing technology, genetic engineering technology was used to produce recombinant strains 2987, 3015, 0415, and 3237. The study revealed Cr(VI) tolerance in the order of M52 ≈ 2987 > 3015 ≈ 0415 > 3237 and reduction abilities in the order of M52 ≈ 2987 > 3015 > 0415 ≈ 3237. SEM-EDS, XRD, FT-IR and XPS were utilized to examine the surface structure of the recombinant strains and analyze the surface components and main functional groups. A comprehensive review of the recombinant strains’ capacity to tolerate and reduce Cr(VI) revealed that orf2987 and orf0415 were the main functional genes in Sporosarcina saromensis M52, which may play a key role in removing Cr(VI) and protecting the strain, respectively. The optimum pH for recombinant strains 2987 and 0415 was 7.5–8.5, and the optimum temperature was 37°C. Cu2+ had the greatest promotional effect when Cr(VI) was removed by them, while SDS had an inhibitory effect. This research provided the foundation for further study into the mechanism of Cr(VI) reduction in Sporosarcina saromensis M52, as well as a theoretical basis for the development of effective engineered strains to repair Cr(VI) contamination.
β-Glucuronidase Pattern Predicted From Gut Metagenomes Indicates Potentially Diversified Pharmacomicrobiomics
Authors: Candeliere Francesco , Raimondi Stefano , Ranieri Raffaella , Musmeci Eliana , Zambon Alfonso , Amaretti Alberto , Rossi Maddalena
Published: March 2022

β-glucuronidases (GUS) of intestinal bacteria remove glucuronic acid from glucoronides, reversing phase II metabolism of the liver and affecting the level of active deconjugated metabolites deriving from drugs or xenobiotics. Two hundred seventy-nine non-redundant GUS sequences are known in the gut microbiota, classified in seven structural categories (NL, L1, L2, mL1, mL2, mL1,2, and NC) with different biocatalytic properties. In the present study, the intestinal metagenome of 60 healthy subjects from five geographically different cohorts was assembled, binned, and mined to determine qualitative and quantitative differences in GUS profile, potentially affecting response to drugs and xenobiotics. Each metagenome harbored 4–70 different GUS, altogether accounting for 218. The amount of intestinal bacteria with at least one GUS gene was highly variable, from 0.7 to 82.2%, 25.7% on average. No significant difference among cohorts could be identified, except for the Ethiopia (ETH) cohort where GUS-encoding bacteria were significantly less abundant. The structural categories were differently distributed among the metagenomes, but without any statistical significance related to the cohorts. GUS profiles were generally dominated by the category NL, followed by mL1, L2, and L1. The GUS categories most involved in the hydrolysis of small molecules, including drugs, are L1 and mL1. Bacteria contributing to these categories belonged to Bacteroides ovatus, Bacteroides dorei, Bacteroides fragilis, Escherichia coli, Eubacterium eligens, Faecalibacterium prausnitzii, Parabacteroides merdae, and Ruminococcus gnavus. Bacteria harboring L1 GUS were generally scarcely abundant (<1.3%), except in three metagenomes, where they reached up to 24.3% for the contribution of E. coli and F. prausnitzii. Bacteria harboring mL1 GUS were significantly more abundant (mean = 4.6%), with Bacteroides representing a major contributor. Albeit mL1 enzymes are less active than L1 ones, Bacteroides likely plays a pivotal role in the deglucuronidation, due to its remarkable abundance in the microbiomes. The observed broad interindividual heterogeneity of GUS profiles, particularly of the L1 and mL1 categories, likely represent a major driver of pharmacomicrobiomics variability, affecting drug response and toxicity. Different geographical origins, genetic, nutritional, and lifestyle features of the hosts seemed not to be relevant in the definition of glucuronidase activity, albeit they influenced the richness of the GUS profile.
The Emergence of Viral Encephalitis in Donkeys by Equid Herpesvirus 8 in China
Authors: Wang Tongtong , Hu Leyu , Liu Mengyuan , Wang Tianjiao , Hu Xinyao , Li Ying , Liu Wenqiang , Li Yubao , Wang Yonghui , Ren Huiying , Zhang Wei , Wang Changfa , Li Liangliang
Published: March 2022

The equine herpesvirus type 8 (EHV-8) can cause significant economic losses in the global horses and donkey industry. The disease has been associated with abortion and respiratory symptoms. However, it is rare for a study to be reported about donkeys with neurological diseases induced by EHV-8 infection. In the present study, one 2-year-old male donkey, from a large-scale donkey farm in China, died with a severe neurological disorder. The causative agent, donkey/Shandong/10/2021 (GenBank accession:OL856098), was identified and isolated from the brain tissue of the dead donkey. Meanwhile, BALB/c mice were used as an animal model to evaluate the pathogenicity of the EHV-8 isolate. Our data showed that EHV-8 was positive in brains by PCR and immunohistochemistry, which induced typical viral encephalitis lesions in both donkey and mice consistent with clinical signs. For the first time, we reported that EHV-8 had been isolated from donkeys with a neurological illness in China, which is helpful to reveal the pathogenicity of EHV-8 in the donkey.
Systems Biology of Gut Microbiota-Human Receptor Interactions: Toward Anti-inflammatory Probiotics
Authors: Koduru Lokanand , Lakshmanan Meiyappan , Hoon Shawn , Lee Dong-Yup , Lee Yuan Kun , Ow Dave Siak-Wei
Published: March 2022

The incidence and prevalence of inflammatory disorders have increased globally, and is projected to double in the next decade. Gut microbiome-based therapeutics have shown promise in ameliorating chronic inflammation. However, they are largely experimental, context- or strain-dependent and lack a clear mechanistic basis. This hinders precision probiotics and poses significant risk, especially to individuals with pre-existing conditions. Molecules secreted by gut microbiota act as ligands to several health-relevant receptors expressed in human gut, such as the G-protein coupled receptors (GPCRs), Toll-like receptor 4 (TLR4), pregnane X receptor (PXR), and aryl hydrocarbon receptor (AhR). Among these, the human AhR expressed in different tissues exhibits anti-inflammatory effects and shows activity against a wide range of ligands produced by gut bacteria. However, different AhR ligands induce varying host responses and signaling in a tissue/organ-specific manner, which remain mostly unknown. The emerging systems biology paradigm, with its powerful in silico tool repertoire, provides opportunities for comprehensive and high-throughput strain characterization. In particular, combining metabolic models with machine learning tools can be useful to delineate tissue and ligand-specific signaling and thus their causal mechanisms in disease and health. The knowledge of such a mechanistic basis is indispensable to account for strain heterogeneity and actualize precision probiotics.
Detection of the Disorders of Glycerophospholipids and Amino Acids Metabolism in Lung Tissue From Male COPD Patients
Authors: Huang Qian , Wu Xiaojie , Gu Yiya , Wang Ting , Zhan Yuan , Chen Jinkun , Zeng Zhilin , Lv Yongman , Zhao Jianping , Xie Jungang
Published: March 2022

Background: At present, few studies have reported the metabolic profiles of lung tissue in patients with COPD. Our study attempted to analyze the lung metabolome in male COPD patients and to screen the overlapping biomarkers of the lung and plasma metabolomes.

Methods: We performed untargeted metabolomic analysis of normal lung tissue from two independent sets (the discovery set: 20 male COPD patients and 20 controls and the replication set: 47 male COPD patients and 27 controls) and of plasma samples from 80 male subjects containing 40 COPD patients and 40 controls.

Results: We found glycerophospholipids (GPs) and Amino acids were the primary classes of differential metabolites between male COPD patients and controls. The disorders of GPs metabolism and the valine, leucine and isoleucine biosynthesis metabolism pathways were identified in lung discovery set and then also validated in the lung replication set. Combining lung tissue and plasma metabolome, Phytosphingosine and l-tryptophan were two overlapping metabolites biomarkers. Binary logistic regression suggested that phytosphingosine together with l-tryptophan was closely associated with male COPD and showed strong diagnostic power with an AUC of 0.911 (95% CI: 0.8460-0.9765).

Conclusion: Our study revealed the metabolic perturbations of lung tissues from male COPD patients. The detected disorders of GPs and amino acids may provide an insight into the pathological mechanism of COPD. Phytosphingosine and l-tryptophan were two novel metabolic biomarkers for differentiating COPD patients and controls.