bluuebunny/crossref_metadata_2025 huggingface dataset:
Siglec-7 represents a glyco-immune checkpoint for non-exhausted effector memory CD8+ T cells with high functional and metabolic capacities
Authors: Haas Quentin , Markov Nikita , Muerner Lukas , Rubino Viviana , Benjak Andrej , Haubitz Monika , Baerlocher Gabriela M. , Ng Charlotte K. Y. , Münz Christian , Riether Carsten , Ochsenbein Adrian F. , Simon Hans-Uwe , von Gunten Stephan
Published: September 2022

While inhibitory Siglec receptors are known to regulate myeloid cells, less is known about their expression and function in lymphocytes subsets. Here we identified Siglec-7 as a glyco-immune checkpoint expressed on non-exhausted effector memory CD8+ T cells that exhibit high functional and metabolic capacities. Seahorse analysis revealed higher basal respiration and glycolysis levels of Siglec-7+ CD8+ T cells in steady state, and particularly upon activation. Siglec-7 polarization into the T cell immune synapse was dependent on sialoglycan interactions in trans and prevented actin polarization and effective T cell responses. Siglec-7 ligands were found to be expressed on both leukemic stem cells and acute myeloid leukemia (AML) cells suggesting the occurrence of glyco-immune checkpoints for Siglec-7+ CD8+ T cells, which were found in patients’ peripheral blood and bone marrow. Our findings project Siglec-7 as a glyco-immune checkpoint and therapeutic target for T cell-driven disorders and cancer.
Basin-scale control on N2O loss rate and emission in the Changjiang River network, China
Authors: Wang Fang , Yu Qibiao , Yan Weijin , Tian Siyu , Zhang Peipei , Wang Jianing
Published: September 2022

Global riverine N2O emissions have been made by several studies with great uncertainty. However, the regional N2O budgets and patterns in large river networks is still unclear, due to the lacking understanding of in-river N2O emission rate and well-classified river network water areas. Furthermore, the mass ratio of N2O emission against nitrogen(N) load in river networks remains controversial. Here we report N2O emissions from the largest river of China, the Changjiang River network, emphasizing the basin-scale control on riverine N2O loss rate in response to increasing N loads and river size. We find the N2O emission rate is negatively related to Strahler river orders, and positively related to N loading. The velocity (Vf) of N conversion into N2O was 0.131-0.436 m yr-1, and N2O loss rate (ζ) was 0.27-37.64 ×10-4 d-1 and declined exponentially with water discharge. Both the loss rate and the mass ratio of N conversion into N2O varied significantly at basin scale, indicating the diminishing capacity of river ecosystems to convert excess DIN into N2O when N load increased as a direct result of human activities. Our study shows N2O emission was 0.66 Gg N2O-N (1Gg=109g) in 1986 and increased to 10.3 Gg N2O-N in 2014 for the whole Changjiang River network. We identified the headwater streams are hotspots of N2O emission across the headwater stream to the estuary aquatic continuum. N2O emission was about 0.82% - 5.31% of global riverine N2O budget during 2010-2014. Our study suggested that an integrated approach in view of the riverine N loads and river hydrology is needed to improve estimates of riverine N2O emissions.
The evolution of predator avoidance in cephalopods: A case of brain over brawn?
Authors: Jaitly Rahul , Ehrnsten Eva , Hedlund Johanna , Cant Michael , Lehmann Philipp , Hayward Alexander
Published: September 2022

Predation is a major evolutionary driver of animal adaptation. However, understanding of anti-predator evolution is biased toward vertebrate taxa. Cephalopoda, a class in the invertebrate phylum Mollusca, are known for their diverse anti-predator strategies, characterised by their behavioural flexibility. While ancestral cephalopods were protected by a hard outer shell, extant cephalopods have greatly reduced their reliance on physical defences. Instead, cephalopods have evolved highly developed senses to identify potential threats, cryptic skin patterns to avoid detection, startle responses to deter attack, and elaborate means of escape. While cephalopod anti-predator repertoires are relatively well described, their evolution, and the selective pressures that shaped them, have received much less attention. This is despite their potential relevance, in turn, to elucidate evolution of the remarkable cognitive abilities of cephalopods. Here, we review cephalopod anti-predator evolution, considering four key aspects: (i) shell reduction and loss; (ii) the skin patterning system; (iii) the ecological context accompanying the evolution of advanced cognit.ive abilities; (iv) why the evolutionary trajectory taken by cephalopods is so unique among invertebrates. In doing so, we consider the unique physiology of cephalopods and discuss how this may have constrained or aided the development of their anti-predator repertoire. In particular, cephalopods are poorly equipped to defend themselves physically and escape predation by fish, due to a lack of comparable weaponry or musculature. We argue that this may have selected for alternative forms of defence, driving an evolutionary trajectory favouring crypsis and complex behaviours, and the promotion of sensory and cognitive adaptations. Unravelling the complexities of cephalopod anti-predator evolution remains challenging. However, recent technological developments available for cephalopod field and laboratory studies, coupled with new genomic data and analysis approaches, offer great scope to generate novel insights.
Dispersion of subsurface lagrangian drifters in the northeastern Gulf of Mexico
Authors: Hancock Cathrine , Speer Kevin , de Souza Joao Marcos Azevedo Correia , Morey Steven L.
Published: September 2022

The dispersion of subsurface Lagrangian floats by eddies was observed directly in DeSoto Canyon, located in the northeastern Gulf of Mexico. Key elements of dispersion include the capture and release of floats by variations in eddy structure and intensity. Two separate eddy events were revealed through 60-day trajectories from five subsurface drifters deployed at 400 m depth in DeSoto Canyon. A changing background flow in DeSoto Canyon allowed for the contraction and expansion of the eddy’s “trap zone,” resulting in the capture and release of several drifters deployed in the area. To investigate the variability of dispersion due to this capture-and-release effect, virtual particle tracks from a 5-year numerical model simulation of the Gulf of Mexico were used. Large interannual variability was observed in eddy activity over the 5-year simulation. When coupled with a variable background flow, this greatly affected Lagrangian particle transport within the entire eastern Gulf of Mexico. During years of increased eddy activity, more virtual particles were “captured” from the along-slope flow and “released” offshore, increasing dispersion and residence time within the eastern Gulf of Mexico. The opposite was observed during minimal eddy activity, where more virtual particles remained within the along-slope flow and thus were funneled toward two main exit points out of the eastern Gulf of Mexico. Regions such as DeSoto Canyon with strong topographic constraints, a highly variable background flow, and considerable eddy activity are likely to spread tracers such as nutrients and contaminants over a substantial area due to this capture-and-release effect.
Does mangrove restoration imply coastal protection? A prospective simulation study
Authors: Juanico Drandreb Earl O.
Published: September 2022

Mangrove restoration in the coastal zones is a concept proposed by environmental conservationists. Among the cited advantages of mangrove restoration are providing socio-economic services and coastal protection. Aware of these advantages, countries in Southeast Asia, such as the Philippines, have been implementing government- or civilian-backed restoration efforts. However, will current practices of restoration lead to the intended results? Also, are claims of coastal protection effects realistic? These two questions underscore the challenges posed by the long gap between the present intervention and future impact. Field evidence of protection may emerge from existing sites, the circumstances of which may not be easily portable onto other sites. This study examines the mangrove restoration practices in the Philippines and proposes the restoration index as a short-term prospective estimate of the future success of the restoration effort. This study also assesses the coastal protection potential of mangroves by examining the “bio-shielding” effect against storm surges driven by category-5 winds. Two coastal sites—Tacloban, Leyte, and Pan de Azucar, Iloilo—in the Philippines along the track of a category-5 storm, were considered. The restoration index was calculated based on the characteristics of Rhizophora mangroves commonly used in restoration programs. The coastal inundation model examined the extent of inland flooding due to storm surges by comparing an actual and hypothetical mangrove scenario for each site. A reasonable value of tree density obtained from the restoration simulations was estimated to determine if and to what degree, do mangroves in both sites offer coastal protection. For Tacloban, the actual mangroves are limited in scope, while the hypothetical scenario assumed a mangrove greenbelt fringing the city’s eastern periphery. For Pan de Azucar, the existing mangroves are dense at the southwestern tip of the island, whereas in the hypothetical scenario, these mangroves are absent. The results, reinforced with a household survey, indicated a positive economic value of mangrove restoration for coastal protection. The restoration index and coastal inundation simulations are prospective tools that will guide the Philippines and Southeast Asia, in general, in formulating impactful mangrove restoration programs.
Environmental DNA (eDNA) for monitoring marine mammals: Challenges and opportunities
Authors: Suarez-Bregua Paula , Álvarez-González Miguel , Parsons Kim M. , Rotllant Josep , Pierce Graham J. , Saavedra Camilo
Published: September 2022

Monitoring marine mammal populations is essential to permit assessment of population status as required by both national and international legislation. Traditional monitoring methods often rely on visual and/or acoustic detections from vessels and aircraft, but limitations including cost, errors in the detection of some species and dependence on taxonomic expertise, as well as good weather and visibility conditions often limit the temporal and spatial scale of effective, long-term monitoring programs. In recent years, environmental DNA (eDNA) has emerged as a revolutionary tool for cost-effective, sensitive, non-invasive species monitoring in both terrestrial and aquatic realms. eDNA is a rapidly developing field and a growing number of studies have successfully implemented this approach for the detection and identification of marine mammals. Here, we review 21 studies published between 2012 and 2021 that employed eDNA for marine mammal monitoring including single species detection, biodiversity assessment and genetic characterization. eDNA has successfully been used to infer species presence (especially useful for rare, elusive or threatened species) and to characterize the population genetic structure, although additional research is needed to support the interpretation of non-detections. Finally, we discuss the challenges and the opportunities that eDNA could bring to marine mammal monitoring as a complementary tool to support visual and acoustic methods.
Dynamic responses of 500-kV transmission line towers under impact force of rockfall in a mountainous area
Authors: Linping Yue , Feng Jiang , Hong Jiang , Wei Jiang , Zhiyong Wang , Zheng Zhou , Jianping Xiong , Tian Wu
Published: September 2022

Since most of the UHV/EHV transmission lines pass through mountainous areas, the impact of rocks caused by landslides or collapses may cause partial deformation of the iron tower, or even collapse, seriously threatening the safety operation of transmission lines. To analyze the dynamic response characteristics and influencing factors of the rolling rock impacting the transmission line tower, a simulation model for the 500-kV steel suspension tower impacted by the falling rock was established by finite element analysis software LS-DYNA in this study, and dynamic response characteristics of the rolling rock impacting the steel tower were analyzed under different conditions. Results show that the stress on the tower foundation is closely related to the mass, volume, and initial velocity of the rolling stone. Under the same rolling stone speed, the stress on the tower foundation increases as the mass of the rolling stone increases. The maximum increase in peak stress generated between the two can reach 110%; when rolling stones of the same size collide with different initial velocities, the location and magnitude of the peak stress of the tower foundation are different. When the initial speed of the rolling stones is more remarkable than 15 m/s, the tower foundation of the hit area increased significantly, causing the tower base to be directly destroyed.
Mesenchymal stem cell therapy on top of triple therapy with remdesivir, dexamethasone, and tocilizumab improves PaO2/FiO2 in severe COVID-19 pneumonia
Authors: Chen Chih-Hao , Chang Kuan-Cheng , Lin Yen-Nien , Ho Mao-Wang , Cheng Meng-Yu , Shih Wen-Hsin , Chou Chia-Huei , Lin Po-Chang , Chi Chih-Yu , Lu Min-Chi , Tien Ni , Wu Mei-Yao , Chang Shih-Sheng , Hsu Wu-Huei , Shyu Woei-Cheang , Cho Der-Yang , Jeng Long-Bin
Published: September 2022

Background

Despite patients with severe coronavirus disease (COVID-19) receiving standard triple therapy, including steroids, antiviral agents, and anticytokine therapy, health condition of certain patients continue to deteriorate. In Taiwan, the COVID-19 mortality has been high since the emergence of previous variants of this disease (such as alpha, beta, or delta). We aimed to evaluate whether adjunctive infusion of human umbilical cord mesenchymal stem cells (MSCs) (hUC-MSCs) on top of dexamethasone, remdesivir, and tocilizumab improves pulmonary oxygenation and suppresses inflammatory cytokines in patients with severe COVID-19.

Methods

Hospitalized patients with severe or critical COVID-19 pneumonia under standard triple therapy were separated into adjuvant hUC-MSC and non-hUC-MSC groups to compare the changes in the arterial partial pressure of oxygen (PaO2)/fraction of inspired oxygen (FiO2) ratio and biological variables.

Results

Four out of eight patients with severe or critical COVID-19 received either one (n = 2) or two (n = 2) doses of intravenous infusions of hUC-MSCs using a uniform cell dose of 1.0 × 108. Both high-sensitivity C-reactive protein (hs-CRP) level and monocyte distribution width (MDW) were significantly reduced, with a reduction in the levels of interleukin (IL)-6, IL-13, IL-12p70 and vascular endothelial growth factor following hUC-MSC transplantation. The PaO2/FiO2 ratio increased from 83.68 (64.34–126.75) to 227.50 (185.25–237.50) and then 349.56 (293.03–367.92) within 7 days after hUC-MSC infusion (P < 0.001), while the change of PaO2/FiO2 ratio was insignificant in non-hUC-MSC patients (admission day: 165.00 [102.50–237.61]; day 3: 100.00 [72.00–232.68]; day 7: 250.00 [71.00–251.43], P = 0.923).

Conclusion

Transplantation of hUC-MSCs as adjunctive therapy improves pulmonary oxygenation in patients with severe or critical COVID-19. The beneficial effects of hUC-MSCs were presumably mediated by the mitigation of inflammatory cytokines, characterized by the reduction in both hs-CRP and MDW.
Genomic profile of SARS-CoV-2 Omicron variant and its correlation with disease severity in Rajasthan
Authors: Sharma Ravi P. , Gautam Swati , Sharma Pratibha , Singh Ruchi , Sharma Himanshu , Parsoya Dinesh , Deeba Farah , Bhomia Neha , Pal Nita , Potdar Varsha , Yadav Pragya D. , Gupta Nivedita , Bhandari Sudhir , Kumar Abhinendra , Joshi Yash , Pandit Priyanka , Malhotra Bharti
Published: September 2022

Background

Omicron, a new variant of Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2), was first detected in November 2021. This was believed to be highly transmissible and was reported to evade immunity. As a result, an urgent need was felt to screen all positive samples so as to rapidly identify Omicron cases and isolate them to prevent the spread of infection. Genomic surveillance of SARS-CoV-2 was planned to correlate disease severity with the genomic profile.

Methods

All the SARS-CoV-2 positive cases detected in the state of Rajasthan were sent to our Lab. Samples received from 24 November 2021 to 4 January 2022 were selected for Next-Generation Sequencing (NGS). Processing was done as per protocol on the Ion Torrent S5 System for 1,210 samples and bioinformatics analysis was done.

Results

Among the 1,210 samples tested, 762 (62.9%) were Delta/Delta-like and other lineages, 291 (24%) were Omicron, and 157 (12.9%) were invalid or repeat samples. Within a month, the proportion of Delta and other variants was reversed, 6% Omicron became 81%, and Delta and other variants became 19%, initially all Omicron cases were seen in international travelers and their contacts but soon community transmission was seen. The majority of patients with Omicron were asymptomatic (56.7%) or had mild disease (33%), 9.2% had moderate symptoms, and two (0.7%) had severe disease requiring hospitalization, of which one (0.3%) died and the rest were (99.7%) recovered. History of vaccination was seen in 81.1%, of the previous infection in 43.2% of cases. Among the Omicron cases, BA.1 (62.8%) was the predominant lineage followed by BA.2 (23.7%) and B.1.529 (13.4%), rising trends were seen initially for BA.1 and later for BA.2 also. Although 8.9% of patients with Delta lineage during that period were hospitalized, 7.2% required oxygen, and 0.9% died. To conclude, the community spread of Omicron occurred in a short time and became the predominant circulating variant; BA.1 was the predominant lineage detected. Most of the cases with Omicron were asymptomatic or had mild disease, and the mortality rate was very low as compared to Delta and other lineages.
MO-MEMES: A method for accelerating virtual screening using multi-objective Bayesian optimization
Authors: Mehta Sarvesh , Goel Manan , Priyakumar U. Deva
Published: September 2022

The pursuit of potential inhibitors for novel targets has become a very important problem especially over the last 2 years with the world in the midst of the COVID-19 pandemic. This entails performing high throughput screening exercises on drug libraries to identify potential “hits”. These hits are identified using analysis of their physical properties like binding affinity to the target receptor, octanol-water partition coefficient (LogP) and more. However, drug libraries can be extremely large and it is infeasible to calculate and analyze the physical properties for each of those molecules within acceptable time and moreover, each molecule must possess a multitude of properties apart from just the binding affinity. To address this problem, in this study, we propose an extension to the Machine learning framework for Enhanced MolEcular Screening (MEMES) framework for multi-objective Bayesian optimization. This approach is capable of identifying over 90% of the most desirable molecules with respect to all required properties while explicitly calculating the values of each of those properties on only 6% of the entire drug library. This framework would provide an immense boost in identifying potential hits that possess all properties required for a drug molecules.
A nationwide survey on the management of the COVID-19 pandemic and respiratory disease in South Korea
Authors: Ang Lin , Yim Mi Hong , Song Eunhye , Lee Hye Won , Lee Hyangsook , Kim Tae-Hun , Willcox Merlin , Hu Xiao-Yang , Houriet Joelle , Graz Bertrand , Lee Je-Won , Jang Yunho , Kim Jung Tae , Kim Eunsop , Park Yong Hee , Lee Myeong Soo
Published: September 2022

Background

This study aimed to explore individual prevalence of respiratory symptoms and to describe the Korean population's treatment approaches, preventive health behaviors, and mental health conditions during the pandemic.

Methods

We analyzed responses from an online nationwide survey, conducted between February 2021 to May 2021, about people's experiences during the pandemic. Statistical analysis was also performed to see if there were any significant differences in treatment and prevention strategies between different groups of respondents (between those had respiratory symptoms, compared with those who did not, and between those tested positive for COVID-19, compared with those who did not).

Results

A total of 2,177 survey respondents completed the survey and, of these, only 142 had experienced symptoms. The most frequently reported respiratory infections related symptoms were runny or blocked nose (47.6%), cough (45.5%), fever (44.1%), sore throat (42.0%), and fatigue (30.1%). More than half of the respondents (53.1%) used complementary and alternative medicine (CAM) approaches as means of preventive measures. In terms of preventive behaviors, the more emphasized behaviors were mask-wearing (58.9%) and hand-washing after coming home (42.7%). The majority of the respondents (64.9%) did not show signs of mental health issues.

Conclusion

In South Korea, conventional medicine was mainly used for COVID-19 treatment whereas CAM was commonly used as preventive measures. COVID-19 was also found to have less impact on the general population's mental health. The findings of this study may shed light on how the pandemic impacted the general population.
Myeloid CD169/Siglec1: An immunoregulatory biomarker in viral disease
Authors: Herzog Silva , Fragkou Paraskevi C. , Arneth Borros M. , Mkhlof Samr , Skevaki Chrysanthi
Published: September 2022

CD169, also known as Siglec1 or Sialoadhesin (Sn), is a surface adhesion molecule on human myeloid cells. Being part of the Siglec family, it acts as a receptor for sialylated molecular structures, which are found among various pathogenic and non-pathogenic ligands. Recent data suggest that CD169 may represent a promising new biomarker in acute respiratory and non-respiratory viral infections, such as SARS-CoV-2, Respiratory syncytial virus (RSV) and Human immunodeficiency virus (HIV). Therein lies a great potential to sufficiently differentiate viral from bacterial infection, which has been an incessant challenge in the clinical management of infectious disease. CD169 equips myeloid cells with functions, reaching far beyond pathogen elimination. In fact, CD169 seems to crosslink innate and adaptive immunity by antigen presentation and consecutive pathogen elimination, embodying a substantial pillar of immunoregulation. Yet, our knowledge about the kinetics, mechanisms of induction, signaling pathways and its precise role in host-pathogen interaction remains largely obscure. In this review, we describe the role of CD169 as a potentially novel diagnostic biomarker for respiratory viral infection by evaluating its strengths and weaknesses and considering host factors that are involved in pathogenesis of virus infection. Finally, this brief review aims to point out shortcomings of available evidence, thus, guiding future work revolving the topic.
Isolation, identification, and biochemical characterization of a novel bifunctional phosphomannomutase/phosphoglucomutase from the metagenome of the brown alga Laminaria digitata
Authors: Jackson Stephen A. , Duan Maohang , Zhang Pengyan , Ihua Maureen W. , Stengel Dagmar B. , Duan Delin , Dobson Alan D. W.
Published: September 2022

Macroalgae host diverse epiphytic bacterial communities with potential symbiotic roles including important roles influencing morphogenesis and growth of the host, nutrient exchange, and protection of the host from pathogens. Macroalgal cell wall structures, exudates, and intra-cellular environments possess numerous complex and valuable carbohydrates such as cellulose, hemi-cellulose, mannans, alginates, fucoidans, and laminarin. Bacterial colonizers of macroalgae are important carbon cyclers, acquiring nutrition from living macroalgae and also from decaying macroalgae. Seaweed epiphytic communities are a rich source of diverse carbohydrate-active enzymes which may have useful applications in industrial bioprocessing. With this in mind, we constructed a large insert fosmid clone library from the metagenome of Laminaria digitata (Ochrophyta) in which decay was induced. Subsequent sequencing of a fosmid clone insert revealed the presence of a gene encoding a bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM) enzyme 10L6AlgC, closely related to a protein from the halophilic marine bacterium, Cobetia sp. 10L6AlgC was subsequently heterologously expressed in Escherichia coli and biochemically characterized. The enzyme was found to possess both PMM and PGM activity, which had temperature and pH optima of 45°C and 8.0, respectively; for both activities. The PMM activity had a Km of 2.229 mM and Vmax of 29.35 mM min−1 mg−1, while the PGM activity had a Km of 0.5314 mM and a Vmax of 644.7 mM min−1 mg−1. Overall characterization of the enzyme including the above parameters as well as the influence of various divalent cations on these activities revealed that 10L6AlgC has a unique biochemical profile when compared to previously characterized PMM/PGM bifunctional enzymes. Thus 10L6AlgC may find utility in enzyme-based production of biochemicals with different potential industrial applications, in which other bacterial PMM/PGMs have previously been used such as in the production of low-calorie sweeteners in the food industry.
Establishment of a reverse transcription real-time quantitative PCR method for Getah virus detection and its application for epidemiological investigation in Shandong, China
Authors: Cao Xinyu , Qiu Xiangshu , Shi Ning , Ha Zhuo , Zhang He , Xie Yubiao , Wang Peng , Zhu Xiangyu , Zhao Wenxin , Zhao Guanyu , Jin Ningyi , Lu Huijun
Published: September 2022

Getah virus (GETV) is a mosquito-borne, single-stranded, positive-sense RNA virus belonging to the genus Alphavirus of the family Togaviridae. Natural infections of GETV have been identified in a variety of vertebrate species, with pathogenicity mainly in swine, horses, bovines, and foxes. The increasing spectrum of infection and the characteristic causing abortions in pregnant animals pose a serious threat to public health and the livestock economy. Therefore, there is an urgent need to establish a method that can be used for epidemiological investigation in multiple animals. In this study, a real-time reverse transcription fluorescent quantitative PCR (RT-qPCR) method combined with plaque assay was established for GETV with specific primers designed for the highly conserved region of GETV Nsp1 gene. The results showed that after optimizing the condition of RT-qPCR reaction, the minimum detection limit of the assay established in this study was 7.73 PFU/mL, and there was a good linear relationship between viral load and Cq value with a correlation coefficient (R2) of 0.998. Moreover, the method has good specificity, sensitivity, and repeatability. The established RT-qPCR is 100-fold more sensitive than the conventional RT-PCR. The best cutoff value for the method was determined to be 37.59 by receiver operating characteristic (ROC) curve analysis. The area under the curve (AUC) was 0.956. Meanwhile, we collected 2,847 serum specimens from swine, horses, bovines, sheep, and 17,080 mosquito specimens in Shandong Province in 2022. The positive detection rates by RT-qPCR were 1%, 1%, 0.2%, 0%, and 3%, respectively. In conclusion, the method was used for epidemiological investigation, which has extensive application prospects.
Phage-prokaryote coexistence strategy mediates microbial community diversity in the intestine and sediment microhabitats of shrimp culture pond ecosystem
Authors: Deng Zhixuan , Zeng Shenzheng , Zhou Renjun , Hou Dongwei , Bao Shicheng , Zhang Linyu , Hou Qilu , Li Xuanting , Weng Shaoping , He Jianguo , Huang Zhijian
Published: September 2022

Emerging evidence supports that the phage-prokaryote interaction drives ecological processes in various environments with different phage life strategies. However, the knowledge of phage-prokaryote interaction in the shrimp culture pond ecosystem (SCPE) is still limited. Here, the viral and prokaryotic community profiles at four culture stages in the intestine ofLitopenaeus vannameiand cultural sediment microhabitats of SCPE were explored to elucidate the contribution of phage-prokaryote interaction in modulating microbial communities. The results demonstrated that the most abundant viral families in the shrimp intestine and sediment were Microviridae, Circoviridae, Inoviridae, Siphoviridae, Podoviridae, Myoviridae, Parvoviridae, Herelleviridae, Mimiviridae, and Genomoviridae, while phages dominated the viral community. The dominant prokaryotic genera wereVibrio,Formosa,Aurantisolimonas,andShewanellain the shrimp intestine, andFormosa,Aurantisolimonas,Algoriphagus,andFlavobacteriumin the sediment. The viral and prokaryotic composition of the shrimp intestine and sediment were significantly different at four culture stages, and the phage communities were closely related to the prokaryotic communities. Moreover, the phage-prokaryote interactions can directly or indirectly modulate the microbial community composition and function, including auxiliary metabolic genes and closed toxin genes. The interactional analysis revealed that phages and prokaryotes had diverse coexistence strategies in the shrimp intestine and sediment microhabitats of SCPE. Collectively, our findings characterized the composition of viral communities in the shrimp intestine and cultural sediment and revealed the distinct pattern of phage-prokaryote interaction in modulating microbial community diversity, which expanded our cognization of the phage-prokaryote coexistence strategy in aquatic ecosystems from the microecological perspective and provided theoretical support for microecological prevention and control of shrimp culture health management.
Control efficiency of hexaconazole-lentinan against wheat sharp eyespot and wheat crown rot and the associated effects on rhizosphere soil fungal community
Authors: Yang Xiu , Zhang Zhongxiao , Yuan Yazhen , Wang Kaiyun , Chen Yuan , Wang Hongyan
Published: September 2022

The use of polysaccharides to induce the systemic immune response of plants for disease resistance has become an effective plant protection measure. Sharp eyespot wheat and crown rot wheat are serious diseases of wheat. In this study, the control effects of hexaconazole and lentinan (LNT) seed dressing of the two wheat diseases were evaluated by field experiments, and the effects of the seed dressing on plant growth, soil enzyme activity, and community diversity in the wheat rhizosphere were discussed. The results showed that the combined seed dressing of hexaconazole at 0.5 a.i. g·100 kg−1 and LNT at 4 a.i. g·100 kg−1 could significantly improve the control effect of the two wheat diseases. The combined treatment of hexaconazole and LNT had little effect on wheat soil enzyme activities. Different seed dressing treatments changed the fungal community structure in the wheat rhizosphere soil, and the combination of LNT and hexaconazole reduced the relative abundance of Rhizoctonia, Cladosporium, Fusarium, Bipolaris, and Gibberella in wheat planting soils. These findings suggested that the combined seed dressing of hexaconazole and LNT could effectively control soilborne diseases of wheat, concurrently could change in rhizosphere fungal community, and reduce in potential soilborne pathogens.
Human Gut Microbiome Across Different Lifestyles: From Hunter-Gatherers to Urban Populations
Authors: Rosas-Plaza Santiago , Hernández-Terán Alejandra , Navarro-Díaz Marcelo , Escalante Ana E. , Morales-Espinosa Rosario , Cerritos René
Published: September 2022

Human lifestyle and its relationship with the human microbiome has been a line of research widely studied. This is because, throughout human history, civilizations have experienced different environments and lifestyles that could have promoted changes in the human microbiome. The comparison between industrialized and non-industrialized human populations in several studies has allowed to observe variation in the microbiome structure due to the population lifestyle. Nevertheless, the lifestyle of human populations is a gradient where several subcategories can be described. Yet, it is not known how these different lifestyles of human populations affect the microbiome structure on a large scale. Therefore, the main goal of this work was the collection and comparison of 16S data from the gut microbiome of populations that have different lifestyles around the world. With the data obtained from 14 studies, it was possible to compare the gut microbiome of 568 individuals that represent populations of hunter-gatherers, agricultural, agropastoral, pastoral, and urban populations. Results showed that industrialized populations present less diversity than those from non-industrialized populations, as has been described before. However, by separating traditional populations into different categories, we were able to observe patterns that cannot be appreciated by encompassing the different traditional lifestyles in a single category. In this sense, we could confirm that different lifestyles exhibit distinct alpha and beta diversity. In particular, the gut microbiome of pastoral and agropastoral populations seems to be more similar to those of urban populations according to beta diversity analysis. Beyond that, beta diversity analyses revealed that bacterial composition reflects the different lifestyles, representing a transition from hunters-gatherers to industrialized populations. Also, we found that certain groups such as Bacteoidaceae, Lanchospiraceae, and Rickenellaceae have been favored in the transition to modern societies, being differentially abundant in urban populations. Thus, we could hypothesize that due to adaptive/ecological processes; multifunctional bacterial groups (e.g., Bacteroidaceae) could be replacing some functions lost in the transition to modern lifestyle.
The Interaction of Influenza A NS1 and Cellular TRBP Protein Modulates the Function of RNA Interference Machinery
Authors: Wang Qi , Wang Jiaxin , Xu Yan , Li Zhe , Wang Binbin , Li Yang
Published: September 2022

Influenza A virus (IAV), one of the most prevalent respiratory diseases, causes pandemics around the world. The multifunctional non-structural protein 1 (NS1) of IAV is a viral antagonist that suppresses host antiviral response. However, the mechanism by which NS1 modulates the RNA interference (RNAi) pathway remains unclear. Here, we identified interactions between NS1 proteins of Influenza A/PR8/34 (H1N1; IAV-PR8) and Influenza A/WSN/1/33 (H1N1; IAV-WSN) and Dicer’s cofactor TAR-RNA binding protein (TRBP). We found that the N-terminal RNA binding domain (RBD) of NS1 and the first two domains of TRBP protein mediated this interaction. Furthermore, two amino acid residues (Arg at position 38 and Lys at position 41) in NS1 were essential for the interaction. We generated TRBP knockout cells and found that NS1 instead of NS1 mutants (two-point mutations within NS1, R38A/K41A) inhibited the process of microRNA (miRNA) maturation by binding with TRBP. PR8-infected cells showed masking of short hairpin RNA (shRNA)-mediated RNAi, which was not observed after mutant virus-containing NS1 mutation (R38A/K41A, termed PR8/3841) infection. Moreover, abundant viral small interfering RNAs (vsiRNAs) were detected in vitro and in vivo upon PR8/3841 infection. We identify, for the first time, the interaction between NS1 and TRBP that affects host RNAi machinery.
Cocktail of isobavachalcone and curcumin enhance eradication of Staphylococcus aureus biofilm from orthopedic implants by gentamicin and alleviate inflammatory osteolysis
Authors: Chen Yan , Hu Hao , Huang Fangli , Ling Zemin , Chen Bolin , Tan Bizhi , Wang Tingxuan , Liu Xiao , Liu Chun , Zou Xuenong
Published: September 2022

Orthopedic device-related infection (ODRI) caused by Staphylococcus aureus, especially methicillin-resistant S. aureus (MRSA) biofilm may lead to persist infection and severe inflammatory osteolysis. Previous studies have demonstrated that both isobavachalcone and curcumin possess antimicrobial activity, recent studies also reveal their antiosteoporosis, anti-inflammation, and immunoregulatory effect. Thus, this study aims to investigate whether the combination of isobavachalcone and curcumin can enhance the anti-S. aureus biofilm activity of gentamicin and alleviate inflammatory osteolysis in vivo. EUCAST and a standardized MBEC assay were used to verify the synergy between isobavachalcone and curcumin with gentamicin against planktonic S. aureus and its biofilm in vitro, then the antimicrobial and immunoregulatory effect of cocktail therapy was demonstrated in a femoral ODRI mouse model in vivo by μCT analysis, histopathology, quantification of bacteria in bone and myeloid-derived suppressor cell (MDSC) in bone marrow. We tested on standard MSSA ATCC25923 and MRSA USA300, 5 clinical isolated MSSA, and 2 clinical isolated MRSA strains and found that gentamicin with curcumin (62.5–250 μg/ml) and gentamicin with isobavachalcone (1.56 μg/ml) are synergistic against planktonic MSSA, while gentamicin (128 μg/ml) with curcumin (31.25–62.5, 250–500 μg/ml) and gentamicin (64–128 μg/ml) with isobavachalcone (1.56–12.5 μg/ml) exhibit synergistic effect against MSSA biofilm. Results of further study revealed that cocktail of 128 μg/ml gentamicin together with 125 μg/ml curcumin +6.25 μg/ml isobavachalcone showed promising biofilm eradication effect with synergy against USA300 biofilm in vitro. Daily intraperitoneal administration of 20 mg/kg/day isobavachalcone, 20 mg/kg/day curcumin, and 20 mg/kg/day gentamicin, can reduce inflammatory osteolysis and maintain microarchitecture of trabecular bone during orthopedic device-related MRSA infection in mice. Cocktail therapy also enhanced reduction of MDSC M1 polarization in peri-implant tissue, suppression of MDSC amplification in bone marrow, and Eradication of USA300 biofilm in vivo. Together, these results suggest that the combination of isobavachalcone and curcumin as adjuvants administrated together with gentamicin significantly enhances its antimicrobial effect against S. aureus biofilm, and can also modify topical inflammation in ODRI and protect bone microstructure in vivo, which may serve as a potential treatment strategy, especially for S. aureus induced ODRI.
Prolactin regulates H3K9ac and H3K9me2 epigenetic marks and miRNAs expression in bovine mammary epithelial cells challenged with Staphylococcus aureus
Authors: Barajas-Mendiola Marco Antonio , Salgado-Lora María Guadalupe , López-Meza Joel Edmundo , Ochoa-Zarzosa Alejandra
Published: September 2022

Epigenetic mechanisms are essential in the regulation of immune response during infections. Changes in the levels of reproductive hormones, such as prolactin, compromise the mammary gland’s innate immune response (IIR); however, its effect on epigenetic marks is poorly known. This work explored the epigenetic regulation induced by bovine prolactin (bPRL) on bovine mammary epithelial cells (bMECs) challenged with Staphylococcus aureus. In this work, bMECs were treated as follows: (1) control cells without any treatment, (2) bMECs treated with bPRL (5 ng/ml) at different times (12 or 24 h), (3) bMECs challenged with S. aureus for 2 h, and (4) bMECs treated with bPRL at different times (12 or 24 h), and then challenged with S. aureus 2 h. By western blot analyses of histones, we determined that the H3K9ac mark decreased (20%) in bMECs treated with bPRL (12 h) and challenged with S. aureus, while the H3K9me2 mark was increased (50%) in the same conditions. Also, this result coincided with an increase (2.3-fold) in HDAC activity analyzed using the cellular histone deacetylase fluorescent kit FLUOR DE LYS®. ChIP-qPCRs were performed to determine if the epigenetic marks detected in the histones correlate with enriched marks in the promoter regions of inflammatory genes associated with the S. aureus challenge. The H3K9ac mark was enriched in the promoter region of IL-1β, IL-10, and BNBD10 genes (1.5, 2.5, 7.5-fold, respectively) in bMECs treated with bPRL, but in bMECs challenged with S. aureus it was reduced. Besides, the H3K9me2 mark was enriched in the promoter region of IL-1β and IL-10 genes (3.5 and 2.5-fold, respectively) in bMECs challenged with S. aureus but was inhibited by bPRL. Additionally, the expression of several miRNAs was analyzed by qPCR. Let-7a-5p, miR-21a, miR-30b, miR-155, and miR-7863 miRNAs were up-regulated (2, 1.5, 10, 1.5, 3.9-fold, respectively) in bMECs challenged with S. aureus; however, bPRL induced a down-regulation in the expression of these miRNAs. In conclusion, bPRL induces epigenetic regulation on specific IIR elements, allowing S. aureus to persist and evade the host immune response.
A review on disinfection methods for inactivation of waterborne viruses
Authors: Lanrewaju Adedayo Ayodeji , Enitan-Folami Abimbola Motunrayo , Sabiu Saheed , Swalaha Feroz Mahomed
Published: September 2022

Water contamination is a global health problem, and the need for safe water is ever-growing due to the public health implications of unsafe water. Contaminated water could contain pathogenic bacteria, protozoa, and viruses that are implicated in several debilitating human diseases. The prevalence and survival of waterborne viruses differ from bacteria and other waterborne microorganisms. In addition, viruses are responsible for more severe waterborne diseases such as gastroenteritis, myocarditis, and encephalitis among others, hence the need for dedicated attention to viral inactivation. Disinfection is vital to water treatment because it removes pathogens, including viruses. The commonly used methods and techniques of disinfection for viral inactivation in water comprise physical disinfection such as membrane filtration, ultraviolet (UV) irradiation, and conventional chemical processes such as chlorine, monochloramine, chlorine dioxide, and ozone among others. However, the production of disinfection by-products (DBPs) that accompanies chemical methods of disinfection is an issue of great concern due to the increase in the risks of harm to humans, for example, the development of cancer of the bladder and adverse reproductive outcomes. Therefore, this review examines the conventional disinfection approaches alongside emerging disinfection technologies, such as photocatalytic disinfection, cavitation, and electrochemical disinfection. Moreover, the merits, limitations, and log reduction values (LRVs) of the different disinfection methods discussed were compared concerning virus removal efficiency. Future research needs to merge single disinfection techniques into one to achieve improved viral disinfection, and the development of medicinal plant-based materials as disinfectants due to their antimicrobial and safety benefits to avoid toxicity is also highlighted.
Integration of metagenomic and metabolomic insights into the effects of microcystin-LR on intestinal microbiota of Litopenaeus vannamei
Authors: Duan Yafei , Xing Yifu , Zeng Shimin , Dan Xueming , Mo Zequan , Zhang Jiasong , Li Yanwei
Published: September 2022

Microcystin-LR (MC-LR) is a hazardous substance that threaten the health of aquatic animals. Intestinal microbes and their metabolites can interact with hosts to influence physiological homeostasis. In this study, the shrimp Litopenaeus vannamei were exposed to 1.0 μg/l MC-LR for 72 h, and the toxic effects of MC-LR on the intestinal microbial metagenomic and metabolomic responses of the shrimp were investigated. The results showed that MC-LR stress altered the gene functions of intestinal microbial, including ABC transporter, sulfur metabolism and riboflavin (VB2) metabolism, and induced a significant increase of eight carbohydrate metabolism enzymes. Alternatively, intestinal metabolic phenotypes were also altered, especially ABC transporters, protein digestion and absorption, and the biosynthesis and metabolism of amino acid. Furthermore, based on the integration of intestinal microbial metagenomic and metabolome, four bacteria species (Demequina globuliformis, Demequina sp. NBRC 110055, Sphingomonas taxi and Sphingomonas sp. RIT328) and three metabolites (yangonin, α-hederin and soyasaponin ii) biomarkers were identified. Overall, our study provides new insights into the effects of MC-LR on the intestinal microbial functions of L. vannamei.
Epidemiological characteristics an outbreak of ST11 multidrug-resistant and hypervirulent Klebsiella pneumoniae in Anhui, China
Authors: He Zhien , Xu Weifeng , Zhao Hang , Li Wei , Dai Yuanyuan , Lu Huaiwei , Zhao Liping , Zhang Changfeng , Li Yujie , Sun Baolin
Published: September 2022

Klebsiella pneumoniae has become a primary threat to global health because of its virulence and resistance. In 2015, China reported multidrug-resistant (MDR) and hypervirulent K. pneumoniae (hvKp) isolates. The emergence of MDR-hvKp poses a significant threat to public health. We collected 76 MDR K. pneumoniae isolates from the same hospital, of which there were a total of six MDR-hvKp isolates. We performed multilocus sequence typing (MLST) and capsular typing, whole genome sequencing, comparative genome analysis, and phylogenetic analysis as well as phenotypic experiments, including growth curves, mucoviscosity assay, Galleria mellonella infection model, human whole blood survival, and human neutrophil bactericidal assay to further characterize the samples. We identified six large plasmids carrying extended spectrum β-lactamase (ESBL) genes or carbapenemase genes (blaCTX–M–65, blaKPC–2, blaSHV–12, blaSHV–158), 9 plasmids containing other drug resistance genes, and 7 hypervirulence plasmids carrying rmpA and rmpA2 in ST11 MDR-hvKp isolates. Some of these plasmids were identical, whereas others differed only by insertion elements. In addition, we identified a plasmid, p21080534_1, that carries hypervirulence genes (iucABCD, iutA, rmpA2), a carbapenemase gene (blaKPC–2), and an ESBL gene (blaSHV–12), as well as MDR-hvKp 21072329, which did not carry rmpA or rmpA2, but exhibited hypervirulence and hypermucoviscosity. ST11 MDR-hvKp derived from hypervirulence and multidrug resistance plasmids not only causes significant treatment difficulties, but also represents an unprecedented challenge to public health. Therefore, urgent measures are needed to limit further spread.