bluuebunny/crossref_metadata_2025 huggingface dataset:
Fatty Acids and Oxylipins as Antifungal and Anti-Mycotoxin Agents in Food: A Review
Authors: Qiu Mei , Wang Yaling , Sun Lijun , Deng Qi , Zhao Jian
Published: December 2021

Fungal contamination of food, especially by mycotoxigenic fungi, not only reduces the quality of the food, but can also cause serious diseases, thus posing a major food safety challenge to humans. Apart from sound food control systems, there is also a continual need to explore antifungal agents that can inhibit fungal growth and mycotoxin production in food. Many types of fatty acids (FAs) and their oxidized derivatives, oxylipins, have been found to exhibit such effects. In this review, we provide an update on the most recent literature on the occurrence and formation of FAs and oxylipins in food, their effects on fungal growth and mycotoxin synthesis, as well as the genetic and molecular mechanisms of actions. Research gaps in the field and needs for further studies in order to realizing the potential of FAs and oxylipins as natural antifungal preservatives in food are also discussed.
Combined Developmental Toxicity of the Pesticides Difenoconazole and Dimethomorph on Embryonic Zebrafish
Authors: Fan Ruiqi , Zhang Wanjun , Jia Li , Li Lizhong , Zhao Jun , Zhao Zengming , Peng Shuangqing , Chen Yiqiang , Yuan Xiaoyan
Published: December 2021

Difenoconazole (DIF) and dimethomorph (DIM) are widely used pesticides frequently detected together in environmental samples, so the deleterious effects of combined exposure warrant detailed examination. In this study, the individual and combined effects of DIM and DIF on conventional developmental parameters (hatching rate, deformity rate, lethality) and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development, and the most sensitive toxicity index for both was 96 h post-fertilization (hpf) deformity rate (BMDL10 values of 0.30 and 1.10 mg/L, respectively). The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes, cdk1, and cdc20, thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone.
Survey of Freshly Harvested Oat Grains from Southern Brazil Reveals High Incidence of Type B Trichothecenes and Associated Fusarium Species
Authors: Pinheiro Mariana , Iwase Caio H. T. , Bertozzi Bruno G. , Caramês Elem T. S. , Carnielli-Queiroz Lorena , Langaro Nádia C. , Furlong Eliana B. , Correa Benedito , Rocha Liliana O.
Published: December 2021

The current study investigated the fungal diversity in freshly harvested oat samples from the two largest production regions in Brazil, Paraná (PR) and Rio Grande do Sul (RS), focusing primarily on the Fusarium genus and the presence of type B trichothecenes. The majority of the isolates belonged to the Fusarium sambucinum species complex, and were identified as F. graminearum sensu stricto (s.s.), F. meridionale, and F. poae. In the RS region, F. poae was the most frequent fungus, while F. graminearum s.s. was the most frequent in the PR region. The F. graminearum s.s. isolates were 15-ADON genotype, while F. meridionale and F. poae were NIV genotype. Mycotoxin analysis revealed that 92% and 100% of the samples from PR and RS were contaminated with type B trichothecenes, respectively. Oat grains from PR were predominantly contaminated with DON, whereas NIV was predominant in oats from RS. Twenty-four percent of the samples were contaminated with DON at levels higher than Brazilian regulations. Co-contamination of DON, its derivatives, and NIV was observed in 84% and 57.7% of the samples from PR and RS, respectively. The results provide new information on Fusarium contamination in Brazilian oats, highlighting the importance of further studies on mycotoxins.
A Retrospective Review of Calcineurin Inhibitors’ Impact on Cytomegalovirus Infections in Lung Transplant Recipients
Authors: Nogueiras-Álvarez Rita , Mora-Cuesta Víctor , Cifrián Martínez José , de Cos Cossío María , García Sáiz María
Published: December 2021

Immunosuppressive therapy reduces the risk for allograft rejection but leaves recipients susceptible to infections. Cytomegalovirus (CMV) is one of the most frequent causes for infection after transplantation and increases the risk for allograft rejection. As lung transplant recipients (LTRs) need to be under immunosuppression for life, they are a vulnerable group. To determine the potential association between the development of CMV infection and the calcineurin inhibitor (CNI) blood levels within previous 90 days, a retrospective review of LTRs was performed. Data from recipients who underwent a lung transplantation (LTx) at our center from January 2011 to December 2018 were collected. The studied recipients, after case/control matching, included 128 CMV-infection cases. The median time from the transplant to the first positive CMV viral load was 291.5 days. In our study, more patients were treated with tacrolimus (91.9%) than with cyclosporine (8.1%). Drug blood levels at selected timepoints showed no statistically significant difference between cases and controls. However, we found that CMV infection was more frequent in the donor-seropositive/recipient-seronegative group, interstitial lung disease (ILD) recipients, LTRs who underwent basiliximab induction, cyclosporine treated recipients, and LTRs with lymphopenia (at the time of CMV infection and 90 days before). In this review of LTRs, no association between the CNI blood level and CMV infection was seen, although other immunity-related factors were found to be influencing, i.e., basiliximab induction, cyclosporine treatment, and lymphopenia.
The Practicability of the Xpert HCV Viral Load Fingerstick Point-of-Care Assay in Primary Care Settings
Authors: Petroff David , Bätz Olaf , Jedrysiak Katrin , Kramer Jan , Berg Thomas , Wiegand Johannes
Published: December 2021

Linkage to care presents one obstacle toward eliminating HCV, and the current two-step pathway (anti-HCV, followed by HCV-RNA testing) results in the loss of patients. HCV screening was tested in the primary care setting with the fingerstick Xpert HCV viral load point-of-care assay to analyze the practicability of immediate diagnosis. Anti-HCV (Cobas) and HCV-RNA (Cobas Amplicor version 2.0, only performed if anti-HCV was positive) were analyzed centrally as the gold standard. The Xpert assay was performed by 10 primary care private practices. In total, 622 patients were recruited. Five individuals (0.8%) were anti-HCV positive, and one was HCV-RNA positive. The Xpert test was valid in 546/622 (87.8%) patients. It was negative in 544 and positive in 2 cases, both of whom were anti-HCV negative. The HCV-RNA PCR and the Xpert test were both negative in 4/5 anti-HCV-positive cases, and the individual with HCV-RNA 4.5 × 106 IU/mL was not detected by the Xpert test. Primary care physicians rated the Xpert test practicability as bad, satisfactory, or good in 6%, 13%, and 81%, respectively, though 14/29 (48%) bad test ratings were assigned by a single practice. Despite adequate acceptance, interpretability and diagnostic performance in primary care settings should be further evaluated before its use in HCV screening can be recommended.
Analysis of the Physicochemical Properties, Replication and Pathophysiology of a Massively Glycosylated Hepatitis B Virus HBsAg Escape Mutant
Authors: Hossain Md. Golzar , Suwanmanee Yadarat , Du Kaili , Ueda Keiji
Published: December 2021

Mutations in HBsAg, the surface antigen of the hepatitis B virus (HBV), might affect the serum HBV DNA level of HBV-infected patients, since the reverse transcriptase (RT) domain of HBV polymerase overlaps with the HBsAg-coding region. We previously identified a diagnostic escape mutant (W3S) HBV that produces massively glycosylated HBsAg. In this study, we constructed an HBV-producing vector that expresses W3S HBs (pHB-W3S) along with a wild-type HBV-producing plasmid (pHB-WT) in order to analyze the physicochemical properties, replication, and antiviral drug response of the mutant. Transfection of either pHB-WT or W3S into HepG2 cells yielded similar CsCl density profiles and eAg expression, as did transfection of a glycosylation defective mutant, pHB-W3S (N146G), in which a glycosylation site at the 146aa asparagine (N) site of HBs was mutated to glycine (G). Virion secretion, however, seemed to be severely impaired in cases of pHB-W3S and pHB-W3S (N146G), compared with pHB-WT, as determined by qPCR and Southern blot analysis. Furthermore, inhibition of glycosylation using tunicamycinTM on wild-type HBV production also reduced the virion secretion. These results suggested that the HBV core and Dane particle could be formed either by massively glycosylated or glycosylation-defective HBsAg, but reduced and/or almost completely blocked the virion secretion efficiency, indicating that balanced glycosylation of HBsAg is required for efficient release of HBV, and mutations inducing an imbalanced glycosylation of HBs would cause the virion to become stuck in the cells, which might be associated with various pathogeneses due to HBV infection.
Mass Spectrometry-Based System for Identifying and Typing Norovirus Major Capsid Protein VP1
Authors: Chu Pei-Yu , Huang Hui-Wen , Boonchan Michittra , Tyan Yu-Chang , Louis Kevin Leroy , Lee Kun-Mu , Motomura Kazushi , Ke Liang-Yin
Published: December 2021

Norovirus-associated diseases are the most common foodborne illnesses worldwide. Polymerase chain reaction-based methods are the primary diagnostics for clinical samples; however, the high mutation rate of norovirus makes viral amplification and genotyping challenging. Technological advances in mass spectrometry (MS) make it a promising tool for identifying disease markers. Besides, the superior sensitivity of MS and proteomic approaches may enable the detection of all variants. Thus, this study aimed to establish an MS-based system for identifying and typing norovirus. We constructed three plasmids containing the major capsid protein VP1 of the norovirus GII.4 2006b, 2006a, and 2009a strains to produce virus-like particles for use as standards. Digested peptide signals were collected using a nano-flow ultra-performance liquid chromatography mass spectrometry (nano-UPLC/MSE) system, and analyzed by ProteinLynx Global SERVER and TREE-PUZZLE software. Results revealed that the LC/MSE system had an excellent coverage rate: the system detected more than 94% of amino acids of 3.61 femtomole norovirus VP1 structural protein. In the likelihood-mapping analysis, the proportions of unresolved quartets were 2.9% and 4.9% in the VP1 and S domains, respectively, which is superior to the 15.1% unresolved quartets in current PCR-based methodology. In summary, the use of LC/MSE may efficiently monitor genotypes, and sensitively detect structural and functional mutations of noroviruses.
Long-Term Humoral Immune Response against SARS-CoV-2 after Natural Infection and Subsequent Vaccination According to WHO International Binding Antibody Units (BAU/mL)
Authors: Ruetalo Natalia , Flehmig Bertram , Schindler Michael , Pridzun Lutz , Haage Angelika , Reichenbächer Marija , Kirchner Thomas , Kirchner Teresa , Klingel Karin , Ranke Michael B. , Normann Andrea
Published: December 2021

The new WHO reference standard allows for the definition of serum antibodies against various SARS-CoV-2 antigens in terms of binding antibody units (BAU/mL) and thus to compare the results of different ELISA systems. In this study, the concentration of antibodies (ABs) against both the S- and the N-protein of SARS-CoV-2 as well as serum neutralization activity were evaluated in three patients after a mild course of COVID-19. Serum samples were collected frequently during a period of over one year. Furthermore, in two individuals, the effects of an additional vaccination with a mRNA vaccine containing the S1-RBD sequence on these antibodies were examined. After natural infection, the antibodies (IgA, IgG) against the S1-protein remained elevated above the established cut-off to positivity (S-IgA 60 BAU/mL and S-IgG 50 BAU/mL, respectively) for over a year in all patients, while this was not the case for ABs against the N-protein (cut-off N-IgG 40 BAU/mL, N-IgA 256 BAU/mL). Sera from all patients retained the ability to neutralize SARS-CoV-2 for more than a year. Vaccination resulted in a rapid boost of antibodies to S1-protein but, as expected, not to the N-protein. Most likely, the wide use of the WHO reference preparation will be very useful in determining the individual immune status of patients after an infection with SARS-CoV-2 or after vaccination.
Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents
Authors: Happel Anna-Ursula , Balle Christina , Maust Brandon S. , Konstantinus Iyaloo N. , Gill Katherine , Bekker Linda-Gail , Froissart Rémy , Passmore Jo-Ann , Karaoz Ulas , Varsani Arvind , Jaspan Heather
Published: December 2021

The interaction between gut bacterial and viral microbiota is thought to be important in human health. While fluctuations in female genital tract (FGT) bacterial microbiota similarly determine sexual health, little is known about the presence, persistence, and function of vaginal bacteriophages. We conducted shotgun metagenome sequencing of cervicovaginal samples from South African adolescents collected longitudinally, who received no antibiotics. We annotated viral reads and circular bacteriophages, identified CRISPR loci and putative prophages, and assessed their diversity, persistence, and associations with bacterial microbiota composition. Siphoviridae was the most prevalent bacteriophage family, followed by Myoviridae, Podoviridae, Herelleviridae, and Inoviridae. Full-length siphoviruses targeting bacterial vaginosis (BV)-associated bacteria were identified, suggesting their presence in vivo. CRISPR loci and prophage-like elements were common, and genomic analysis suggested higher diversity among Gardnerella than Lactobacillus prophages. We found that some prophages were highly persistent within participants, and identical prophages were present in cervicovaginal secretions of multiple participants, suggesting that prophages, and thus bacterial strains, are shared between adolescents. The number of CRISPR loci and prophages were associated with vaginal microbiota stability and absence of BV. Our analysis suggests that (pro)phages are common in the FGT and vaginal bacteria and (pro)phages may interact.
Viral and Immunologic Factors Associated with Fatal Outcome of Patients with Severe Fever with Thrombocytopenia Syndrome in Korea
Authors: Kwon Ji-Soo , Jin Sol , Kim Ji-Yeun , Ra Sang-Hyun , Kim Taeeun , Park Se-Yoon , Kim Min-Chul , Park Seong-Yeon , Kim Dasarang , Cha Hye-Hee , Lee Hyun-Jung , Kim Min-Jae , Chong Yong-Pil , Lee Sang-Oh , Choi Sang-Ho , Kim Yang-Soo , Lee Keun-Hwa , Kee Sun-Ho , Kim Sung-Han
Published: December 2021

Significant progress has been made on the molecular biology of the severe fever with thrombopenia virus (SFTSV); however, many parts of the pathophysiological mechanisms of mortality in SFTS remain unclear. In this study, we investigated virologic and immunologic factors for fatal outcomes of patients with SFTS. We prospectively enrolled SFTS patients admitted from July 2015 to October 2020. Plasma samples were subjected to SFTSV RNA RT-PCR, multiplex microbead immunoassay for 17 cytokines, and IFA assay. A total of 44 SFTS patients were enrolled, including 37 (84.1%) survivors and 7 (15.9%) non-survivors. Non-survivors had a 2.5 times higher plasma SFTSV load than survivors at admission (p < 0.001), and the viral load in non-survivors increased progressively during hospitalization. In addition, non-survivors did not develop adequate anti-SFTSV IgG, whereas survivors exhibited anti-SFTSV IgG during hospitalization. IFN-α, IL-10, IP-10, IFN-γ, IL-6, IL-8, MCP-1, MIP-1α, and G-CSF were significantly elevated in non-survivors compared to survivors and did not revert to normal ranges during hospitalization (p < 0.05). Severe signs of inflammation such as a high plasma concentration of IFN-α, IL-10, IP-10, IFN-γ, IL-6, IL-8, MCP-1, MIP-1α, and G-CSF, poor viral control, and inadequate antibody response during the disease course were associated with mortality in SFTS patients.
In Silico Identification of Chikungunya Virus B- and T-Cell Epitopes with High Antigenic Potential for Vaccine Development
Authors: Sánchez-Burgos Gilma , Montalvo-Marin Nallely , Díaz-Rosado Edgar , Pérez-Rueda Ernesto
Published: December 2021

Reverse vaccinology is an outstanding strategy to identify antigens with high potential for vaccine development. Different parameters of five prediction programs were used to assess their sensitivity and specificity to identify B-cell epitopes of Chikungunya virus (CHIKV) strains reported in the IEDB database. The results, based on the use of 15 to 20 mer epitopes and the polyproteins to which they belong, were compared to establish the best parameters to optimize the prediction of antigenic peptides of the Mexican strain CHIKV AJV21562.1. LBtope showed the highest specificity when we used the reported epitopes and polyproteins but the worst sensitivity with polyproteins; ABCpred had similar specificity to LBtope only with the epitopes reported and showed moderate specificity when we used polyproteins for the predictions. Because LBtope was more reliable in predicting true epitopes, it was used as a reference program to predict and select six novel epitopes of the Mexican strain of CHIKV according to prediction frequency, viral genome localization, and non-homology with the human proteome. On the other hand, six bioinformatics programs were used with default parameters to predict T-cell epitopes in the CHIKV strains AJV21562.1 and AJV21561.1. The sequences of the polyproteins were analyzed to predict epitopes present in the more frequent HLA alleles of the Mexican population: DQA1*03011, DQA1*0401, DQA1*0501, DQB1*0201, DQB1*0301, DQB1*0302, and DQB1*0402. Fifteen predicted epitopes in the non-structural and 15 predicted epitopes in the structural polyprotein (9- to 16-mers) with the highest scores of each allele were compared to select epitopes with at least 80% identity. Next, the epitopes predicted with at least two programs were aligned to the human proteome, and 12 sequences without identity with the human proteome were identified as potential antigenic candidates. This strategy would be useful to evaluate vaccine candidates against other viral diseases affecting the countries of the Americas and to increase knowledge about these diseases.
Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis
Authors: do Socorro Fôro Ramos Endrya , de Oliveira Ribeiro Geovani , Villanova Fabiola , de Padua Milagres Flávio Augusto , Brustulin Rafael , Araújo Emerson Luiz Lima , Pandey Ramendra Pati , Raj V. Samuel , Deng Xutao , Delwart Eric , Luchs Adriana , da Costa Antonio Charlys , Leal Élcio
Published: December 2021

Metagenomics based on the next-generation sequencing (NGS) technique is a target-independent assay that enables the simultaneous detection and genomic characterization of all viruses present in a sample. There is a limited amount of data about the virome of individuals with gastroenteritis (GI). In this study, the enteric virome of 250 individuals (92% were children under 5 years old) with GI living in the northeastern and northern regions of Brazil was characterized. Fecal samples were subjected to NGS, and the metagenomic analysis of virus-like particles (VLPs) identified 11 viral DNA families and 12 viral RNA families. As expected, the highest percentage of viral sequences detected were those commonly associated with GI, including rotavirus, adenovirus, norovirus (94.8%, 82% and 71.2%, respectively). The most common co-occurrences, in a single individual, were the combinations of rotavirus-adenovirus, rotavirus-norovirus, and norovirus-adenovirus (78%, 69%, and 62%, respectively). In the same way, common fecal-emerging human viruses were also detected, such as parechovirus, bocaporvirus, cosavirus, picobirnavirus, cardiovirus, salivirus, and Aichivirus. In addition, viruses that infect plants, nematodes, fungi, protists, animals, and arthropods could be identified. A large number of unclassified viral contigs were also identified. We show that the metagenomics approach is a powerful and promising tool for the detection and characterization of different viruses in clinical GI samples.
Clinical Picture and Risk Factors of Severe Respiratory Symptoms in COVID-19 in Children
Authors: Mania Anna , Faltin Kamil , Mazur-Melewska Katarzyna , Małecki Paweł , Jończyk-Potoczna Katarzyna , Lubarski Karol , Lewandowska Zuzanna , Cwalińska Agnieszka , Rosada-Kurasińska Jowita , Bartkowska-Śniatkowska Alicja , Figlerowicz Magdalena
Published: December 2021

Children with COVID-19 develop moderate symptoms in most cases. Thus, a proportion of children requires hospital admission. The study aimed to assess the history, clinical and laboratory parameters in children with COVID-19 concerning the severity of respiratory symptoms. The study included 332 children (median age 57 months) with COVID-19. History data, clinical findings, laboratory parameters, treatment, and outcome, were evaluated. Children were compared in the groups that varied in the severity of symptoms of respiratory tract involvement. Children who required oxygen therapy represented 8.73%, and intensive care 1.5% of the whole cohort. Comorbidities were present in 126 patients (37.95%). Factors increasing the risk of oxygen therapy included comorbidities (odds ratio (OR) = 92.39; 95% confidence interval (95% CI) = (4.19; 2036.90); p < 0.00001), dyspnea (OR = 45.81; 95% CI (4.05; 518.21); p < 0.00001), auscultation abnormalities (OR = 34.33; 95% CI (2.59; 454.64); p < 0.00001). Lactate dehydrogenase (LDH) > 280 IU/L and creatinine kinase > 192 IU/L were parameters with a good area under the curve (0.804-LDH) and a positive predictive value (42.9%-CK). The clinical course of COVID-19 was mild to moderate in most patients. Children with comorbidities, dyspnea, or abnormalities on auscultation are at risk of oxygen therapy. Laboratory parameters potentially useful in patients evaluated for the severe course are LDH > 200 IU/L and CK > 192 IU/L.
Clinical Application of Ultraviolet C Inactivation of Severe Acute Respiratory Syndrome Coronavirus 2 in Contaminated Hospital Environments
Authors: Su Wen-Lin , Lin Chih-Pei , Huang Hui-Ching , Wu Yao-Kuang , Yang Mei-Chen , Chiu Sheg-Kang , Peng Ming-Yieh , Chan Ming-Chin , Chao You-Chen
Published: December 2021

To overcome the ongoing coronavirus disease 2019 (COVID-19) pandemic, transmission routes, such as healthcare worker infection, must be effectively prevented. Ultraviolet C (UVC) (254 nm) has recently been demonstrated to prevent environmental contamination by infected patients; however, studies on its application in contaminated hospital settings are limited. Herein, we explored the clinical application of UVC and determined its optimal dose. Environmental samples (n = 267) collected in 2021 were analyzed by a reverse transcription-polymerase chain reaction and subjected to UVC irradiation for different durations (minutes). We found that washbasins had a high contamination rate (45.5%). SARS-CoV-2 was inactivated after 15 min (estimated dose: 126 mJ/cm2) of UVC irradiation, and the contamination decreased from 41.7% before irradiation to 16.7%, 8.3%, and 0% after 5, 10, and 15 min of irradiation, respectively (p = 0.005). However, SARS-CoV-2 was still detected in washbasins after irradiation for 20 min but not after 30 min (252 mJ/cm2). Thus, 15 min of 254-nm UVC irradiation was effective in cleaning plastic, steel, and wood surfaces in the isolation ward. For silicon items, such as washbasins, 30 min was suggested; however, further studies using hospital environmental samples are needed to confirm the effective UVC inactivation of SARS-CoV-2.
Letter to the Editor: SFlt-1 and PlGF Levels in Pregnancies Complicated by SARS-CoV-2 Infection
Authors: Giardini Valentina , Ornaghi Sara , Acampora Eleonora , Vasarri Maria Viola , Arienti Francesca , Gambacorti-Passerini Carlo , Casati Marco , Carrer Andrea , Vergani Patrizia
Published: December 2021

We read with interest the work by Espino-y-Sosa and colleagues [...]
Inhibiting ACSL1-Related Ferroptosis Restrains Murine Coronavirus Infection
Authors: Xia Huawei , Zhang Zeming , You Fuping
Published: December 2021

Murine hepatitis virus strain A59 (MHV-A59) was shown to induce pyroptosis, apoptosis, and necroptosis of infected cells, especially in the murine macrophages. However, whether ferroptosis, a recently identified form of lytic cell death, was involved in the pathogenicity of MHV-A59 is unknown. We utilized murine macrophages and a C57BL/6 mice intranasal infection model to address this. In primary macrophages, the ferroptosis inhibitor inhibited viral propagation, inflammatory cytokines released, and cell syncytia formed after MHV-A59 infection. In the mouse model, we found that in vivo administration of liproxstatin-1 ameliorated lung inflammation and tissue injuries caused by MHV-A59 infection. To find how MHV-A59 infection influenced the expression of ferroptosis-related genes, we performed RNA-seq in primary macrophages and found that MHV-A59 infection upregulates the expression of the acyl-CoA synthetase long-chain family member 1 (ACSL1), a novel ferroptosis inducer. Using ferroptosis inhibitors and a TLR4 inhibitor, we showed that MHV-A59 resulted in the NF-kB-dependent, TLR4-independent ACSL1 upregulation. Accordingly, ACSL1 inhibitor Triacsin C suppressed MHV-A59-infection-induced syncytia formation and viral propagation in primary macrophages. Collectively, our study indicates that ferroptosis inhibition protects hosts from MHV-A59 infection. Targeting ferroptosis may serve as a potential treatment approach for dealing with hyper-inflammation induced by coronavirus infection.
Isolation and Identification of Inter-Species Enterovirus Recombinant Genomes
Authors: Bentley Kirsten , Tee Han Kang , Pearson Ashley , Lowry Kym , Waugh Sheila , Jones Siân , Chan Yoke Fun , Evans David J.
Published: December 2021

Positive-strand RNA virus evolution is partly attributed to the process of recombination. Although common between closely genetically related viruses, such as within species of the Enterovirus genus of the Picornaviridae family, inter-species recombination is rarely observed in nature. Recent studies have shown recombination is a ubiquitous process, resulting in a wide range of recombinant genomes and progeny viruses. While not all recombinant genomes yield infectious progeny virus, their existence and continued evolution during replication have critical implications for the evolution of the virus population. In this study, we utilised an in vitro recombination assay to demonstrate inter-species recombination events between viruses from four enterovirus species, A-D. We show that inter-species recombinant genomes are generated in vitro with polymerase template-switching events occurring within the virus polyprotein coding region. However, these genomes did not yield infectious progeny virus. Analysis and attempted recovery of a constructed recombinant cDNA revealed a restriction in positive-strand but not negative-strand RNA synthesis, indicating a significant block in replication. This study demonstrates the propensity for inter-species recombination at the genome level but suggests that significant sequence plasticity would be required in order to overcome blocks in the virus life cycle and allow for the production of infectious viruses.
Comment on Xu et al. Isolation and Identification of a Novel Phlebovirus, Hedi Virus, from Sandflies Collected in China. Viruses 2021, 13, 772
Authors: Charrel Remi N. , Depaquit Jerome
Published: December 2021

The article from Xu et al. [...]
Norovirus: Facts and Reflections from Past, Present, and Future
Authors: Lucero Yalda , Matson David O. , Ashkenazi Shai , George Sergio , O’Ryan Miguel
Published: December 2021

Human Norovirus is currently the main viral cause of acute gastroenteritis (AGEs) in most countries worldwide. Nearly 50 years after the discovery of the “Norwalk virus” by Kapikian and colleagues, the scientific and medical community continue to generate new knowledge on the full biological and disease spectrum of Norovirus infection. Nevertheless, several areas remain incompletely understood due to the serious constraints to effectively replicate and propagate the virus. Here, we present a narrated historic perspective and summarize our current knowledge, including insights and reflections on current points of interest for a broad medical community, including clinical and molecular epidemiology, viral–host–microbiota interactions, antivirals, and vaccine prototypes. We also include a reflection on the present and future impacts of the COVID-19 pandemic on Norovirus infection and disease.
An Importin-β-like Protein from Nicotiana benthamiana Interacts with the RNA Silencing Suppressor P1b of the Cucumber Vein Yellowing Virus, Modulating Its Activity
Authors: García Beatriz , Bedoya Leonor , García Juan Antonio , Rodamilans Bernardo
Published: December 2021

During a plant viral infection, host–pathogen interactions are critical for successful replication and propagation of the virus through the plant. RNA silencing suppressors (RSSs) are key players of this interplay, and they often interact with different host proteins, developing multiple functions. In the Potyviridae family, viruses produce two main RSSs, HCPro and type B P1 proteins. We focused our efforts on the less known P1b of cucumber vein yellowing virus (CVYV), a type B P1 protein, to try to identify possible factors that could play a relevant role during viral infection. We used a chimeric expression system based on plum pox virus (PPV) encoding a tagged CVYV P1b in place of the canonical HCPro. We used that tag to purify P1b in Nicotiana-benthamiana-infected plants and identified by mass spectrometry an importin-β-like protein similar to importin 7 of Arabidopsis thaliana. We further confirmed the interaction by bimolecular fluorescence complementation assays and defined its nuclear localization in the cell. Further analyses showed a possible role of this N. benthamiana homolog of Importin 7 as a modulator of the RNA silencing suppression activity of P1b.
Genetic Effect and Growth Curve Parameter Estimation under Heat Stress in Slow-Growing Thai Native Chickens
Authors: Boonkum Wuttigrai , Duangjinda Monchai , Kananit Srinuan , Chankitisakul Vibuntita , Kenchaiwong Wootichai
Published: December 2021

Heat stress is becoming a major problem because it limits growth in poultry production, especially in tropical areas. The development of genetic lines of Thai native chickens (TNC) which can tolerate the tropical climate with the least compromise on growth performance is therefore necessary. This research aims to analyze the appropriate growth curve function and to estimate the effect of heat stress on the genetic absolute growth rate (AGR) in TNC and Thai synthetic chickens (TSC). The data comprised 35,355 records for body weight from hatching to slaughtering weight of 7241 TNC and 10,220 records of 2022 TSC. The best-fitting growth curve was investigated from three nonlinear regression models (von Bertalanffy, Gompertz, and logistic) and used to analyze the individual AGR. In addition, a repeatability test-day model on the temperature-humidity index (THI) function was used to estimate the genetic parameters for heat stress. The Gompertz function produced the lowest mean squared error (MSE) and Akaike information criterion (AIC) and highest the pseudo-coefficient of determination (Pseudo-R2) in both chicken breeds. The growth rates in TSC were higher than TNC; the growth rates of males were greater than females, but the age at inflection point in females was lower than in males in both chicken breeds. The THI threshold started at 76. The heritability of the AGR was 0.23 and 0.18 in TNC and TSC, respectively. The additive variance and permanent environmental variance of the heat stress effect increased sharply after the THI of 76. The growth rate decreased more severely in TSC than TNC. In conclusion, the Gompertz function can be applied with the THI to evaluate genetic performance for heat tolerance and increase growth performance in slow-growing chicken.
Analyses of Contact Networks of Community Dogs on a University Campus in Nakhon Pathom, Thailand
Authors: Kittisiam Tipsarp , Phimpraphai Waraphon , Kasemsuwan Suwicha , Thakur Krishna Kumar
Published: December 2021

Free-roaming dogs have been identified as an important reservoir of rabies in many countries including Thailand. There is a need for novel insights to improve current rabies control strategies in these countries. Network analysis is commonly used to study the interactions between individuals or organizations and has been applied in preventive veterinary medicine. However, contact networks of domestic free-roaming dogs are mostly unexplored. The objective of this study was to explore the contact network of free-roaming dogs residing on a university campus. Three one-mode networks were created using co-appearances of dogs as edges. A two-mode network was created by associating the dog with the pre-defined area it was seen in. The average number of contacts a dog had was 6.74. The normalized degree for the weekend network was significantly higher compared to the weekday network. All one-mode networks displayed small-world network characteristics. Most dogs were observed in only one area. The average number of dogs which shared an area was 8.67. In this study, we demonstrated the potential of observational methods to create networks of contacts. The network information acquired can be further used in network modeling and designing targeted disease control programs.
Validation of Digital Applications for Evaluation of Visual Parameters: A Narrative Review
Authors: Mena-Guevara Kevin J. , Piñero David P. , de Fez Dolores
Published: December 2021

The current review aimed to collect and critically analyze the scientific peer-reviewed literature that is available about the use of digital applications for evaluation of visual parameters in electronic devices (tablets and smartphones), confirming if there are studies calibrating and validating each of these applications. Three bibliographic search engines (using the search equation described in the paper) and the Mendeley reference manager search engine were used to complete the analysis. Only articles written in English and that are evaluating the use of tests in healthy patients to measure or characterize any visual function aspects using tablets or smartphones were included. Articles using electronic visual tests to assess the results of surgical procedures or are conducted in pathological conditions were excluded. A total of 19 articles meeting these inclusion and exclusion criteria were finally analyzed. One critical point of all these studies is that there was no mention of the characterization (spatial and/or colorimetrical) of screens and the stimuli used in most of them. Only two studies described some level of calibration of the digital device before the beginning of the study. Most revised articles described non-controlled comparatives studies (73.7%), reporting some level of scientific evidence on the validation of tools, although more consistent studies are needed.
Anthropogenic Disturbances Have Contributed to Degradation of River Water Quality in Arid Areas
Authors: Ji Li , Li Yuan , Zhang Guixiang , Bi Yonghong
Published: December 2021

The earth has been reshaped for millennia. The accelerating pace of anthropogenic activities has generated enormous impacts on the water environment. As one of the main drivers of landscape change, anthropogenic disturbance has brought many negative effects on rivers. Studying the relationship between anthropogenic disturbances and river water quality is of significance for regional conservation and ecosystem management, while the relationship remains poorly understood in the current. In this study, we quantified anthropogenic disturbances by introducing the concept of the hemeroby index and evaluated rivers’ water quality in eight sub-watersheds on the Loess Plateau. The results indicated that 37.5% of the sub-watersheds were in Eutrophic status, and 62.5% were in Marginal water quality index. The river water quality was most poor in the southwestern region near the Yellow River with high-level anthropogenic disturbance. A correlation analysis between water quality indicators and hemeroby suggested that anthropogenic disturbance contributed to a significant water quality deterioration trend (p < 0.01). The river water quality was relatively sensitive to the changes of completely disturbed land-use covers, including urban and industrial land. Our findings provide theoretical guidance for regional water resources conservation and ecosystem management in arid areas.
Exploring the Potential of the Cost-Efficient TAHMO Observation Data for Hydro-Meteorological Applications in Sub-Saharan Africa
Authors: Schunke Julia , Laux Patrick , Bliefernicht Jan , Waongo Moussa , Sawadogo Windmanagda , Kunstmann Harald
Published: December 2021

The Trans-African Hydro-Meteorological Observatory (TAHMO) is a promising initiative aiming to install 20,000 stations in sub-Saharan Africa counteracting the decreasing trend of available measuring stations. To achieve this goal, it is particularly important that the installed weather stations are cost-efficient, appropriate for African conditions, and reliably measure the most important variables for hydro-meteorological applications. Since there exist no performance studies of TAHMO stations while operating in Africa, it is necessary to investigate their performance under different climate conditions. This study provides a first analysis of the performance of 10 selected TAHMO stations across Burkina Faso (BF). More specifically, the analysis consists of missing value statistics, plausibility tests of temperature (minimum, maximum) and precipitation, spatial dependencies (correlograms) by comparison with daily observations from synoptical stations of the BF meteorological service as well as cross-comparison between the TAHMO stations. Based on the results of this study for BF for the period from May 2017 to December 2020, it is concluded that TAHMO potentially offers a reliable and cost-efficient solution for applications in hydro-meteorology. The usage of wind speed measurements cannot be recommended without reservation, at least not without bias correcting of the data. The limited measurement period of TAHMO still prevents its usability in climate (impact) research. It is also stressed that TAHMO cannot replace existing observation networks operated by the local meteorological services, but it can be a complement and has great potential for detailed spatial analyses. Since restricted to BF in this analysis, more evaluation studies of TAHMO are needed considering different environmental and climate conditions across SSA.
The Role of Stakeholder Engagement in Developing New Technologies and Innovation for Nitrogen Reduction in Waters: A Longitudinal Study
Authors: Nygaard Kenneth , Graversgaard Morten , Dalgaard Tommy , Jacobsen Brian H. , Schaper Stefan
Published: December 2021

Better nitrogen management, technologies, and regulation are required to reduce nitrogen losses in the aquatic environment. New innovative technologies can support farmers in a more targeted planning of fertilizer application and crop management at the field level to increase the effect of measures when reducing nitrogen losses. However, if farmers do not perceive the need for such a concept, the demand (market pull) will be minimal, making the implementation of such a technology difficult. The lack of this market pull could, however, be counterbalanced by a market push from research or requirements from public sector stakeholders (regulators). Within this domain, the main objective of this paper was to study technological change over time and identify and understand the crucial stakeholder involvement using the Functions of Innovation Systems Approach. This article shows how stakeholders’ perceptions and participation evolved over a 10-year period. It examines the interplay between technology readiness and the perceived readiness and acceptance by affected stakeholders. We demonstrate how stakeholder engagement was crucial to ensure the development of the technologies by creating marketable options for their future implementation. A key dynamic that emerged in this process was the transition from a research push to a regulator pull. We demonstrate the fact that without the regulatory requirement linked to changes towards more targeting of measures, the technology would not, on its own, be a business case, although it would provide new knowledge, thus representing a gain for society. The specific findings can be used in countries where new technologies need to be developed, and where a link to the regulation can ensure the active use of the new technology and, therefore, make their implementation worthwhile.
A Novel Combined Treatment Process of Hybrid Biosorbent–Nanofiltration for Effective Pb(II) Removal from Wastewater
Authors: Hanif Asma , Ali Shaukat , Hanif Muhammad Asif , Rashid Umer , Bhatti Haq Nawaz , Asghar Muhammad , Alsalme Ali , Giannakoudakis Dimitrios A.
Published: December 2021

The untreated effluents discharged by different industries, such as metallurgy, fertilizers, pesticide, leather, mining, electroplating, surface finishing, aerospace, and electroplating, have increased the risk of the contamination of bodies of water by heavy metals. Herein, hybrid biosorbent–nanofiltration processes for Pb(II) removal from wastewater was studied. The hybrid biosorbent was prepared from date seed waste and Ganoderma lucidum. Hybrid biosorbent characterization was performed by SEM and FTIR. SEM micrographs showed that the HB surface is irregular. For the adsorption studies, various sorption parameters were optimized. The maximum biosorption capacity of immobilized heat-inactivated hybrid biosorbent was 365.9 mg/g, with the Langmuir isotherm model to present the best fit. Desorption experiments were conducted for regenerating immobilized heat-inactivated hybrid biosorbent for three consecutive cycles using different desorption agents, with acetic acid to be the optimum. Going a step further, nanofiltration was also applied as a post-treatment process to elevate the remediation effectiveness for wastewater of high Pb(II) initial concentrations. The reasonably low cost and high removal of Pb(II) make hybrid biosorbent–nanofiltration processes a prosperous and potentially attractive hybrid approach against heavy-metal-polluted wastewater.
Sandtank-ML: An Educational Tool at the Interface of Hydrology and Machine Learning
Authors: Gallagher Lisa K. , Williams Jill M. , Lazzeri Drew , Chennault Calla , Jourdain Sebastien , O’Leary Patrick , Condon Laura E. , Maxwell Reed M.
Published: December 2021

Hydrologists and water managers increasingly face challenges associated with extreme climatic events. At the same time, historic datasets for modeling contemporary and future hydrologic conditions are increasingly inadequate. Machine learning is one promising technological tool for navigating the challenges of understanding and managing contemporary hydrological systems. However, in addition to the technical challenges associated with effectively leveraging ML for understanding subsurface hydrological processes, practitioner skepticism and hesitancy surrounding ML presents a significant barrier to adoption of ML technologies among practitioners. In this paper, we discuss an educational application we have developed—Sandtank-ML—to be used as a training and educational tool aimed at building user confidence and supporting adoption of ML technologies among water managers. We argue that supporting the adoption of ML methods and technologies for subsurface hydrological investigations and management requires not only the development of robust technologic tools and approaches, but educational strategies and tools capable of building confidence among diverse users.
Assessing the Fisheries and Ecosystem Structure of the Largest Greek Lake (Lake Trichonis)
Authors: Petriki Olga , Moutopoulos Dimitrios K. , Tsagarakis Konstantinos , Tsionki Ioanna , Papantoniou Georgia , Mantzouni Irene , Barbieri Roberta , Stoumboudi Maria Th.
Published: December 2021

An Ecopath with Ecosim (EwE) modeling approach was used to explore the ecological structure of the largest lake in Greece (Lake Trichonis). Until the mid-1990s, the lake was receiving a high level of pollution and the fishing pressure was intense, while since the early 2000s, fisheries and other human pressures gradually declined. Nowadays, the lake’s fisheries mainly target Atherina boyeri due to the absence of market demand for the other fish species in the lake, resulting in a low overall fisheries pressure on the fish stocks. The model was built with data collected through: (a) field samplings, (b) in-depth targeted interviews of professional fishermen and (c) historical archive information. The model considered 22 functional groups, while fishing activities were represented by three classes according to the used gears. The outputs of the model revealed that the ecosystem is dominated by low trophic level species (also identified as keystone species), indicating the significance of bottom-up control in the regulation of food web processes. Ecological indicators depicted that the lake’s ecosystem is mature and resilient to external disturbances. The methodological approach used in this study was shown to be helpful for studies addressing ecosystem structure, in particular with limited data availability.
Management of Urban Waters with Nature-Based Solutions in Circular Cities—Exemplified through Seven Urban Circularity Challenges
Authors: Oral Hasan Volkan , Radinja Matej , Rizzo Anacleto , Kearney Katharina , Andersen Theis Raaschou , Krzeminski Pawel , Buttiglieri Gianluigi , Ayral-Cinar Derya , Comas Joaquim , Gajewska Magdalena , Hartl Marco , Finger David C. , Kazak Jan K. , Mattila Harri , Vieira Patrícia , Piro Patrizia , Palermo Stefania Anna , Turco Michele , Pirouz Behrouz , Stefanakis Alexandros , Regelsberger Martin , Ursino Nadia , Carvalho Pedro N.
Published: December 2021

Nature-Based Solutions (NBS) have been proven to effectively mitigate and solve resource depletion and climate-related challenges in urban areas. The COST (Cooperation in Science and Technology) Action CA17133 entitled “Implementing nature-based solutions (NBS) for building a resourceful circular city” has established seven urban circularity challenges (UCC) that can be addressed effectively with NBS. This paper presents the outcomes of five elucidation workshops with more than 20 European experts from different backgrounds. These international workshops were used to examine the effectiveness of NBS to address UCC and foster NBS implementation towards circular urban water management. A major outcome was the identification of the two most relevant challenges for water resources in urban areas: ‘Restoring and maintaining the water cycle’ (UCC1) and ‘Water and waste treatment, recovery, and reuse’ (UCC2). s Moreover, significant synergies with ‘Nutrient recovery and reuse’, ‘Material recovery and reuse’, ‘Food and biomass production’, ‘Energy efficiency and recovery’, and ‘Building system recovery’ were identified. Additionally, the paper presents real-life case studies to demonstrate how different NBS and supporting units can contribute to the UCC. Finally, a case-based semi-quantitative assessment of the presented NBS was performed. Most notably, this paper identifies the most typically employed NBS that enable processes for UCC1 and UCC2. While current consensus is well established by experts in individual NBS, we presently highlight the potential to address UCC by combining different NBS and synergize enabling processes. This study presents a new paradigm and aims to enhance awareness on the ability of NBS to solve multiple urban circularity issues.