bluuebunny/crossref_metadata_2025 huggingface dataset:
Fungal foraging behaviour and hyphal space exploration in micro-structured Soil Chips
Authors: Aleklett Kristin , Ohlsson Pelle , Bengtsson Martin , Hammer Edith C
Published: January 2021

How do fungi navigate through the complex microscopic maze-like structures found in the soil? Fungal behaviour, especially at the hyphal scale, is largely unknown and challenging to study in natural habitats such as the opaque soil matrix. We monitored hyphal growth behaviour and strategies of seven Basidiomycete litter decomposing species in a micro-fabricated “Soil Chip” system that simulates principal aspects of the soil pore space and its micro-spatial heterogeneity. The hyphae were faced with micrometre constrictions, sharp turns and protruding obstacles, and the species examined were found to have profoundly different responses in terms of foraging range and persistence, spatial exploration and ability to pass obstacles. Hyphal behaviour was not predictable solely based on ecological assumptions, and our results obtained a level of trait information at the hyphal scale that cannot be fully explained using classical concepts of space exploration and exploitation such as the phalanx/guerrilla strategies. Instead, we propose a multivariate trait analysis, acknowledging the complex trade-offs and microscale strategies that fungal mycelia exhibit. Our results provide novel insights about hyphal behaviour, as well as an additional understanding of fungal habitat colonisation, their foraging strategies and niche partitioning in the soil environment.
Efficient clofilium tosylate-mediated rescue of POLG-related disease phenotypes in zebrafish
Authors: Facchinello Nicola , Laquatra Claudio , Locatello Lisa , Beffagna Giorgia , Brañas Casas Raquel , Fornetto Chiara , Dinarello Alberto , Martorano Laura , Vettori Andrea , Risato Giovanni , Celeghin Rudy , Meneghetti Giacomo , Santoro Massimo Mattia , Delahodde Agnes , Vanzi Francesco , Rasola Andrea , Dalla Valle Luisa , Rasotto Maria Berica , Lodi Tiziana , Baruffini Enrico , Argenton Francesco , Tiso Natascia
Published: January 2021

The DNA polymerase gamma (Polg) is a nuclear-encoded enzyme involved in DNA replication in animal mitochondria. In humans, mutations in the POLG gene underlie a set of mitochondrial diseases characterized by mitochondrial DNA (mtDNA) depletion or deletion and multiorgan defects, named POLG disorders, for which an effective therapy is still needed. By applying antisense strategies, ENU- and CRISPR/Cas9-based mutagenesis, we have generated embryonic, larval-lethal and adult-viable zebrafish Polg models. Morphological and functional characterizations detected a set of phenotypes remarkably associated to POLG disorders, including cardiac, skeletal muscle, hepatic and gonadal defects, as well as mitochondrial dysfunctions and, notably, a perturbed mitochondria-to-nucleus retrograde signaling (CREB and Hypoxia pathways). Next, taking advantage of preliminary evidence on the candidate molecule Clofilium tosylate (CLO), we tested CLO toxicity and then its efficacy in our zebrafish lines. Interestingly, at well tolerated doses, the CLO drug could successfully rescue mtDNA and Complex I respiratory activity to normal levels, even in mutant phenotypes worsened by treatment with Ethidium Bromide. In addition, the CLO drug could efficiently restore cardio-skeletal parameters and mitochondrial mass back to normal values. Altogether, these evidences point to zebrafish as a valuable vertebrate organism to faithfully phenocopy multiple defects detected in POLG patients. Moreover, this model represents an excellent platform to screen, at the whole-animal level, candidate molecules with therapeutic effects in POLG disorders.
Plasma membrane integrity in health and disease: significance and therapeutic potential
Authors: Dias Catarina , Nylandsted Jesper
Published: January 2021

Maintenance of plasma membrane integrity is essential for normal cell viability and function. Thus, robust membrane repair mechanisms have evolved to counteract the eminent threat of a torn plasma membrane. Different repair mechanisms and the bio-physical parameters required for efficient repair are now emerging from different research groups. However, less is known about when these mechanisms come into play. This review focuses on the existence of membrane disruptions and repair mechanisms in both physiological and pathological conditions, and across multiple cell types, albeit to different degrees. Fundamentally, irrespective of the source of membrane disruption, aberrant calcium influx is the common stimulus that activates the membrane repair response. Inadequate repair responses can tip the balance between physiology and pathology, highlighting the significance of plasma membrane integrity. For example, an over-activated repair response can promote cancer invasion, while the inability to efficiently repair membrane can drive neurodegeneration and muscular dystrophies. The interdisciplinary view explored here emphasises the widespread potential of targeting plasma membrane repair mechanisms for therapeutic purposes.
Concomitant control of mechanical properties and degradation in resorbable elastomer-like materials using stereochemistry and stoichiometry for soft tissue engineering
Authors: Wandel Mary Beth , Bell Craig A. , Yu Jiayi , Arno Maria C. , Dreger Nathan Z. , Hsu Yen-Hao , Pitto-Barry Anaïs , Worch Joshua C. , Dove Andrew P. , Becker Matthew L.
Published: January 2021

Complex biological tissues are highly viscoelastic and dynamic. Efforts to repair or replace cartilage, tendon, muscle, and vasculature using materials that facilitate repair and regeneration have been ongoing for decades. However, materials that possess the mechanical, chemical, and resorption characteristics necessary to recapitulate these tissues have been difficult to mimic using synthetic resorbable biomaterials. Herein, we report a series of resorbable elastomer-like materials that are compositionally identical and possess varying ratios of cis:trans double bonds in the backbone. These features afford concomitant control over the mechanical and surface eroding degradation properties of these materials. We show the materials can be functionalized post-polymerization with bioactive species and enhance cell adhesion. Furthermore, an in vivo rat model demonstrates that degradation and resorption are dependent on succinate stoichiometry in the elastomers and the results show limited inflammation highlighting their potential for use in soft tissue regeneration and drug delivery.
A wheat cysteine-rich receptor-like kinase confers broad-spectrum resistance against Septoria tritici blotch
Authors: Saintenac Cyrille , Cambon Florence , Aouini Lamia , Verstappen Els , Ghaffary Seyed Mahmoud Tabib , Poucet Théo , Marande William , Berges Hélène , Xu Steven , Jaouannet Maëlle , Favery Bruno , Alassimone Julien , Sánchez-Vallet Andrea , Faris Justin , Kema Gert , Robert Oliver , Langin Thierry
Published: January 2021

The poverty of disease resistance gene reservoirs limits the breeding of crops for durable resistance against evolutionary dynamic pathogens. Zymoseptoria tritici which causes Septoria tritici blotch (STB), represents one of the most genetically diverse and devastating wheat pathogens worldwide. No fully virulent Z. tritici isolates against synthetic wheats carrying the major resistant gene Stb16q have been identified. Here, we use comparative genomics, mutagenesis and complementation to identify Stb16q, which confers broad-spectrum resistance against Z. tritici. The Stb16q gene encodes a plasma membrane cysteine-rich receptor-like kinase that was recently introduced into cultivated wheat and which considerably slows penetration and intercellular growth of the pathogen.
Ionic liquid enables highly efficient low temperature desalination by directional solvent extraction
Authors: Guo Jiaji , Tucker Zachary D. , Wang Yu , Ashfeld Brandon L. , Luo Tengfei
Published: January 2021

Seawater desalination plays a critical role in addressing the global water shortage challenge. Directional Solvent Extraction (DSE) is an emerging non-membrane desalination technology that features the ability to utilize very low temperature waste heat (as low as 40 °C). This is enabled by the subtly balanced solubility properties of directional solvents, which do not dissolve in water but can dissolve water and reject salt ions. However, the low water yield of the state-of-the-art directional solvent (decanoic acid) significantly limits its throughput and energy efficiency. In this paper, we demonstrate that by using ionic liquid as a new directional solvent, saline water can be desalinated with much higher production rate and thus significantly lower the energy and exergy consumptions. The ionic liquid identified suitable for DSE is [emim][Tf2N], which has a much (~10×) higher water yield than the currently used decanoic acid. Using molecular dynamics simulations with Gibbs free energy calculations, we reveal that water dissolving in [emim][Tf2N] is energetically favorable, but it takes significant energy for [emim][Tf2N] ions to dissolve in water. Our findings may significantly advance the DSE technology as a solution to the challenges in the global water-energy nexus.
Passerini-type reaction of boronic acids enables α-hydroxyketones synthesis
Authors: Yang Kai , Zhang Feng , Fang Tongchang , Li Chaokun , Li Wangyang , Song Qiuling
Published: January 2021

Multicomponent reactions (MCRs) facilitate the rapid and diverse construction of molecular scaffolds with modularity and step economy. In this work, engagement of boronic acids as carbon nucleophiles culminates in a Passerini-type three-component coupling reaction towards the synthesis of an expanded inventory of α-hydroxyketones with skeletal diversity. In addition to the appealing features of MCRs, this protocol portrays good functional group tolerance, broad substrate scope under mild conditions and operational simplicity. The utility of this chemistry is further demonstrated by amenable modifications of bioactive products and pharmaceuticals as well as in the functionalization of products to useful compounds.
Clostridioides difficile exploits toxin-mediated inflammation to alter the host nutritional landscape and exclude competitors from the gut microbiota
Authors: Fletcher Joshua R. , Pike Colleen M. , Parsons Ruth J. , Rivera Alissa J. , Foley Matthew H. , McLaren Michael R. , Montgomery Stephanie A. , Theriot Casey M.
Published: January 2021

Clostridioides difficile is a bacterial pathogen that causes a range of clinical disease from mild to moderate diarrhea, pseudomembranous colitis, and toxic megacolon. Typically, C. difficile infections (CDIs) occur after antibiotic treatment, which alters the gut microbiota, decreasing colonization resistance against C. difficile. Disease is mediated by two large toxins and the expression of their genes is induced upon nutrient depletion via the alternative sigma factor TcdR. Here, we use tcdR mutants in two strains of C. difficile and omics to investigate how toxin-induced inflammation alters C. difficile metabolism, tissue gene expression and the gut microbiota, and to determine how inflammation by the host may be beneficial to C. difficile. We show that C. difficile metabolism is significantly different in the face of inflammation, with changes in many carbohydrate and amino acid uptake and utilization pathways. Host gene expression signatures suggest that degradation of collagen and other components of the extracellular matrix by matrix metalloproteinases is a major source of peptides and amino acids that supports C. difficile growth in vivo. Lastly, the inflammation induced by C. difficile toxin activity alters the gut microbiota, excluding members from the genus Bacteroides that are able to utilize the same essential nutrients released from collagen degradation.
Host development overwhelms environmental dispersal in governing the ecological succession of zebrafish gut microbiota
Authors: Xiao Fanshu , Zhu Wengen , Yu Yuhe , He Zhili , Wu Bo , Wang Cheng , Shu Longfei , Li Xinghao , Yin Huaqun , Wang Jianjun , Juneau Philippe , Zheng Xiafei , Wu Yongjie , Li Juan , Chen Xiaojuan , Hou Dongwei , Huang Zhijian , He Jianguo , Xu Guohuan , Xie Liwei , Huang Jie , Yan Qingyun
Published: January 2021

Clarifying mechanisms underlying the ecological succession of gut microbiota is a central theme of gut ecology. Under experimental manipulations of zebrafish hatching and rearing environments, we test our core hypothesis that the host development will overwhelm environmental dispersal in governing fish gut microbial community succession due to host genetics, immunology, and gut nutrient niches. We find that zebrafish developmental stage substantially explains the gut microbial community succession, whereas the environmental effects do not significantly affect the gut microbiota succession from larvae to adult fish. The gut microbiotas of zebrafish are clearly separated according to fish developmental stages, and the degree of homogeneous selection governing gut microbiota succession is increasing with host development. This study advances our mechanistic understanding of the gut microbiota assembly and succession by integrating the host and environmental effects, which also provides new insights into the gut ecology of other aquatic animals.
Tumour inflammation signature and expression of S100A12 and HLA class I improve survival in HPV-negative hypopharyngeal cancer
Authors: Mints Michael , Landin David , Näsman Anders , Mirzaie Leila , Ursu Ramona Gabriela , Zupancic Mark , Marklund Linda , Dalianis Tina , Munck-Wikland Eva , Ramqvist Torbjörn
Published: January 2021

Hypopharyngeal squamous cell carcinoma (HPSCC) has a very poor prognosis. Local surgery may increase survival, but is often avoided due to significant post-op co-morbidities. Since prognostic markers are lacking, the aim was to find predictive biomarkers that identify patients whose response to oncological treatment is poor and who may benefit from primary surgery to increase survival. Pretreatment biopsies from 23 HPSCC patients, 3 human papillomavirus (HPV) positive and 20 HPV-negative, were analyzed for expression of 750 mRNAs using the Nanostring nCounter IO360 panel in relation to 3-year survival. Validation was performed through immunohistochemistry (IHC) for HLA class I and S100A12 in 74 HPV-negative HPSCC samples. Clustering identified a subset of HPV-negative HPSCC with favorable prognosis and a gene expression signature overexpressing calgranulins and immune genes, distinct from that of HPV-positive HPSCC. Enrichment analysis showed immune signaling, including the tumor inflammation signature, to be enriched in surviving patients. IHC validation confirmed high S100A12 and HLA class I expression to correlate with survival in HPV-negative HPSCC. This shows that immune activity is strongly related to survival in HPV-negative HPSCC. Enrichment of the tumor inflammation signature indicates a potential benefit of immunotherapy. Low expression of both HLA class I and S100A12 could be used to select patients for local surgery.
Cellulose acetate based Complexation-NF membranes for the removal of Pb(II) from waste water
Authors: Idress H. , Zaidi S. Z. J. , Sabir A. , Shafiq M. , Khan R. U. , Harito C. , Hassan S. , Walsh F. C.
Published: January 2021

This study investigates the removal of Pb(II) using polymer matrix membranes, cellulose acetate/vinyl triethoxysilane modified graphene oxide and gum Arabic (GuA) membranes. These complexation-NF membranes were successfully synthesized via dissolution casting method for better transport phenomenon. The varied concentrations of GuA were induced in the polymer matrix membrane. The prepared membranes M-GuA2–M-GuA10 were characterized by Fourier transform infrared spectroscopy, scanning electron microscopy, transmission electron microscopy, atomic force microscope and bio-fouling studies. Thermal stability of the membranes was determined by thermogravimetric analysis under nitrogen atmosphere. Dead end nanofiltration was carried out to study the perm- selectivity of all the membranes under varied pressure and concentration of Pb(NO3)2. The complexation-NF membrane performances were significantly improved after the addition of GuA in the polymer matrix membrane system. M-GuA8 membrane showed optimum result of permeation flux 8.6 l m−2 h−1. Rejection of Pb(II) ions was observed to be around 97.6% at pH 9 for all the membranes due to electrostatic interaction between CA and Gum Arabic. Moreover, with the passage of time, the rate of adsorption was also increased up to 15.7 mg g−1 until steady state was attained. Gum Arabic modified CA membranes can open up new possibilities in enhancing the permeability, hydrophilicity and anti-fouling properties.
Detection of QTNs for kernel moisture concentration and kernel dehydration rate before physiological maturity in maize using multi-locus GWAS
Authors: Li Shufang , Zhang Chunxiao , Yang Deguang , Lu Ming , Qian Yiliang , Jin Fengxue , Liu Xueyan , Wang Yu , Liu Wenguo , Li Xiaohui
Published: January 2021

Maize is China’s largest grain crop. Mechanical grain harvesting is the key technology in maize production, and the kernel moisture concentration (KMC) is the main controlling factor in mechanical maize harvesting in China. The kernel dehydration rate (KDR) is closely related to the KMC. Thus, it is important to conduct genome-wide association studies (GWAS) of the KMC and KDR in maize, detect relevant quantitative trait nucleotides (QTNs), and mine relevant candidate genes. Here, 132 maize inbred lines were used to measure the KMC every 5 days from 10 to 40 days after pollination (DAP) in order to calculate the KDR. These lines were genotyped using a maize 55K single-nucleotide polymorphism array. QTNs for the KMC and KDR were detected based on five methods (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, and ISIS EM-BLASSO) in the package mrMLM. A total of 334 significant QTNs were found for both the KMC and KDR, including 175 QTNs unique to the KMC and 178 QTNs unique to the KDR; 116 and 58 QTNs were detected among the 334 QTNs by two and more than two methods, respectively; and 9 and 5 QTNs among 58 QTNs were detected in 2 and 3 years, respectively. A significant enrichment in cellular component was revealed by Gene Ontology enrichment analysis of candidate genes in the intervals adjacent to the 14 QTNs and this category contained five genes. The information provided in this study may be useful for further mining of genes associated with the KMC and KDR in maize.
Possible pairing mechanism switching driven by structural symmetry breaking in BiS2-based layered superconductors
Authors: Yamashita Aichi , Usui Hidetomo , Hoshi Kazuhisa , Goto Yosuke , Kuroki Kazuhiko , Mizuguchi Yoshikazu
Published: January 2021

Investigation of isotope effects on superconducting transition temperature (Tc) is one of the useful methods to examine whether electron–phonon interaction is essential for pairing mechanisms. The layered BiCh2-based (Ch: S, Se) superconductor family is a candidate for unconventional superconductors, because unconventional isotope effects have previously been observed in La(O,F)BiSSe and Bi4O4S3. In this study, we investigated the isotope effects of 32S and 34S in the high-pressure phase of (Sr,La)FBiS2, which has a monoclinic crystal structure and a higher Tc of ~ 10 K under high pressures, and observed conventional-type isotope shifts in Tc. The conventional-type isotope effects in the monoclinic phase of (Sr,La)FBiS2 are different from the unconventional isotope effects observed in La(O,F)BiSSe and Bi4O4S3, which have a tetragonal structure. The obtained results suggest that the pairing mechanisms of BiCh2-based superconductors could be switched by a structural-symmetry change in the superconducting layers induced by pressure effects.
Integrated photothermal decontamination device for N95 respirators
Authors: Muñoz Marcelo , Comtois-Bona Maxime , Cortes David , Cimenci Cagla Eren , Du Qiujiang , Thompson Collin , Figueroa Juan David , Franklin Vivian , Liu Peter , Alarcon Emilio I.
Published: January 2021

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the COVID-19 global pandemic has infected over 25 million people worldwide and resulted in the death of millions. The COVID-19 pandemic has also resulted in a shortage of personal protective equipment (PPE) in many regions around the world, particularly in middle- and low-income countries. The shortages of PPE, such as N95 respirators, is something that will persist until an effective vaccine is made available. Thus, devices that while being easy to operate can also be rapidly deployed in health centers, and long-term residences without the need for major structural overhaul are instrumental to sustainably use N95 respirators. In this report, we present the design and validation of a decontamination device that combines UV-C & B irradiation with mild-temperature treatment. The device can decontaminate up to 20 masks in a cycle of < 30 min. The decontamination process did not damage or reduce the filtering capacity of the masks. Further, the efficacy of the device to eliminate microbes and viruses from the masks was also evaluated. The photothermal treatment of our device was capable of eradicating > 99.9999% of the bacteria and > 99.99% of the virus tested.
A stable spin-structure found in a 3-body system with spin-3 cold atoms and its role in N-body condensates
Authors: Liu Y. M. , He Y. Z. , Bao C. G.
Published: January 2021

We have found a stable spin-structure of N $$=$$
=
3 system in which three spin-3 atoms are trapped and coupled to total spin S $$=$$
=
3. We have proved that a pair of this structure is nearly an exact solution for N $$=$$
=
6 systems in a very broad district in the parameter-space. Comparing with the well-known singlet pairs, this pair is a more promising candidate to serve as a building block for large N systems with spin-3 atoms. This is because the spin-structure of the latter can be modified depending on the interactions to reduce the energy while the singlet pairs can not. In fact, we have proved that, for a specific set of strengths (a point in the parameter-space) the product state based on this pair is an exact solution of the N-body Hamiltonian. Thus, in the neighborhood of this point, the product state will appear as an approximate solution. However, how broad this neighborhood would be remains to be clarified.
[18F]-sodium fluoride autoradiography imaging of nephrocalcinosis in donor kidneys and explanted kidney allografts
Authors: Benjamens Stan , Antunes Ines F. , Hillebrands Jan-Luuk , Reijrink Melanie , Bulthuis Marian L. C. , Berger Stefan P. , Moers Cyril , de Borst Martin H. , Slart Riemer H. J. A. , Pol Robert A.
Published: January 2021

Nephrocalcinosis is present in up to 43% of kidney allograft biopsies at one-year after transplantation and is associated with inferior graft function and poor graft survival. We studied [18F]-sodium fluoride ([18F]-NaF) imaging of microcalcifications in donor kidneys (n = 7) and explanted kidney allografts (n = 13). Three µm paraffin-embedded serial sections were used for histological evaluation of calcification (Alizarin Red; Von Kossa staining) and ex-vivo [18F]-NaF autoradiography. The images were fused to evaluate if microcalcification areas corresponded with [18F]-NaF uptake areas. Based on histological analyses, tubulointerstitial and glomerular microcalcifications were present in 19/20 and 7/20 samples, respectively. Using autoradiography, [18F]-NaF uptake was found in 19/20 samples, with significantly more tracer activity in kidney allograft compared to deceased donor kidney samples (p = 0.019). Alizarin Red staining of active microcalcifications demonstrated good correlation (Spearman’s rho of 0.81, p < 0.001) and Von Kossa staining of consolidated calcifications demonstrated significant but weak correlation (0.62, p = 0.003) with [18F]-NaF activity. This correlation between ex-vivo [18F]-NaF uptake and histology-proven microcalcifications, is the first step towards an imaging method to identify microcalcifications in active nephrocalcinosis. This may lead to better understanding of the etiology of microcalcifications and its impact on kidney transplant function.
Incorporating social opinion in the evolution of an epidemic spread
Authors: Carballosa Alejandro , Mussa-Juane Mariamo , Muñuzuri Alberto P.
Published: January 2021

The evolution of the COVID19 pandemic worldwide has shown that the most common and effective strategy to control it used worldwide involve imposing mobility constrains to the population. A determinant factor in the success of such policies is the cooperation of the population involved but this is something, at least, difficult to measure. In this manuscript, we propose a method to incorporate in epidemic models empirical data accounting for the society predisposition to cooperate with the mobility restriction policies.
Clinical and laboratory features of hypercoagulability in COVID-19 and other respiratory viral infections amongst predominantly younger adults with few comorbidities
Authors: Tan Chuen Wen , Tan Jing Yuan , Wong Wan Hui , Cheong May Anne , Ng Ian Matthias , Conceicao Edwin Philip , Low Jenny Guek Hong , Ng Heng Joo , Lee Lai Heng
Published: January 2021

COVID-19 caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) and other respiratory viral (non-CoV-2-RV) infections are associated with thrombotic complications. The differences in prothrombotic potential between SARS-CoV-2 and non-CoV-2-RV have not been well characterised. We compared the thrombotic rates between these two groups of patients directly and further delved into their coagulation profiles. In this single-center, retrospective cohort study, all consecutive COVID-19 and non-CoV-2-RV patients admitted between January 15th and April 10th 2020 were included. Coagulation parameters studied were prothrombin time and activated partial thromboplastin time and its associated clot waveform analysis (CWA) parameter, min1, min2 and max2. In the COVID-19 (n = 181) group there were two (1.0 event/1000-hospital-days) myocardial infarction events while one (1.8 event/1000-hospital-day) was reported in the non-CoV-2-RV (n = 165) group. These events occurred in patients who were severely ill. There were no venous thrombotic events. Coagulation parameters did not differ throughout the course of mild COVID-19. However, CWA parameters were significantly higher in severe COVID-19 compared with mild disease, suggesting hypercoagulability (min1: 6.48%/s vs 5.05%/s, P < 0.001; min2: 0.92%/s2 vs 0.74%/s2, P = 0.033). In conclusion, the thrombotic rates were low and did not differ between COVID-19 and non-CoV-2-RV patients. The hypercoagulability in COVID-19 is a highly dynamic process with the highest risk occurring when patients were most severely ill. Such changes in haemostasis could be detected by CWA. In our population, a more individualized thromboprophylaxis approach, considering clinical and laboratory factors, is preferred over universal pharmacological thromboprophylaxis for all hospitalized COVID-19 patients and such personalized approach warrants further research.
Washing with alkaline solutions in protein A purification improves physicochemical properties of monoclonal antibodies
Authors: Imura Yuichi , Tagawa Toshiaki , Miyamoto Yuya , Nonoyama Satoshi , Sumichika Hiroshi , Fujino Yasuhiro , Yamanouchi Masaya , Miki Hideo
Published: January 2021

Protein A affinity chromatography has been widely used for both laboratory scale purification and commercial manufacturing of monoclonal antibodies and Fc-fusion proteins. Protein A purification is specific and efficient. However, there still remain several issues to be addressed, such as incomplete clearance of impurities including host cell proteins, DNA, aggregates, etc. In addition, the effects of wash buffers in protein A purification on the physicochemical characteristics of antibodies have yet to be fully understood. Here we found a new purification protocol for monoclonal antibodies that can improve physicochemical properties of monoclonal antibodies simply by inserting an additional wash step with a basic buffer after the capture step to the conventional protein A purification. The effects of the alkaline wash on monoclonal antibodies were investigated in terms of physicochemical characteristics, yields, and impurity clearance. The simple insertion of an alkaline wash step resulted in protection of antibodies from irreversible aggregation, reduction in free thiols and impurities, an improvement in colloidal and storage stability, and enhanced yields. This new procedure is widely applicable to protein A affinity chromatography of monoclonal antibodies.
Direct and Indirect endocrine-mediated suppression of human endometrial CD8+T cell cytotoxicity
Authors: Shen Z. , Rodriguez-Garcia M. , Patel M. V. , Wira C. R.
Published: January 2021

Regulation of endometrial (EM) CD8+T cells is essential for successful reproduction and protection against pathogens. Suppression of CD8+T cells is necessary for a tolerogenic environment that promotes implantation and pregnancy. However, the mechanisms regulating this process remain unclear. Sex hormones are known to control immune responses directly on immune cells and indirectly through the tissue environment. When the actions of estradiol (E2), progesterone (P) and TGFβ on EM CD8+T cells were evaluated, cytotoxic activity, perforin and granzymes were directly suppressed by E2and TGFβ but not P. Moreover, incubation of polarized EM epithelial cells with P, but not E2, increased TGFβ secretion. These findings suggest that E2acts directly on CD8+T cell to suppress cytotoxic activity while P acts indirectly through induction of TGFβ production. Understanding the mechanisms involved in regulating endometrial CD8+T cells is essential for optimizing reproductive success and developing protective strategies against genital infections and gynecological cancers.
A diabetes risk score for Qatar utilizing a novel mathematical modeling approach to identify individuals at high risk for diabetes
Authors: Awad Susanne F. , Dargham Soha R. , Toumi Amine A. , Dumit Elsy M. , El-Nahas Katie G. , Al-Hamaq Abdulla O. , Critchley Julia A. , Tuomilehto Jaakko , Al-Thani Mohamed H. J. , Abu-Raddad Laith J.
Published: January 2021

We developed a diabetes risk score using a novel analytical approach and tested its diagnostic performance to detect individuals at high risk of diabetes, by applying it to the Qatari population. A representative random sample of 5,000 Qataris selected at different time points was simulated using a diabetes mathematical model. Logistic regression was used to derive the score using age, sex, obesity, smoking, and physical inactivity as predictive variables. Performance diagnostics, validity, and potential yields of a diabetes testing program were evaluated. In 2020, the area under the curve (AUC) was 0.79 and sensitivity and specificity were 79.0% and 66.8%, respectively. Positive and negative predictive values (PPV and NPV) were 36.1% and 93.0%, with 42.0% of Qataris being at high diabetes risk. In 2030, projected AUC was 0.78 and sensitivity and specificity were 77.5% and 65.8%. PPV and NPV were 36.8% and 92.0%, with 43.0% of Qataris being at high diabetes risk. In 2050, AUC was 0.76 and sensitivity and specificity were 74.4% and 64.5%. PPV and NPV were 40.4% and 88.7%, with 45.0% of Qataris being at high diabetes risk. This model-based score demonstrated comparable performance to a data-derived score. The derived self-complete risk score provides an effective tool for initial diabetes screening, and for targeted lifestyle counselling and prevention programs.
Increased colonic K+ excretion through inhibition of the H,K-ATPase type 2 helps reduce plasma K+ level in a murine model of nephronic reduction
Authors: Walter Christine , Rafael Chloé , Genna Anthony , Baron Stéphanie , Crambert Gilles
Published: January 2021

Hyperkalemia is frequently observed in patients at the end-stage of chronic kidney disease (CKD), and has possible harmful consequences on cardiac function. Many strategies are currently used to manage hyperkalemia, one consisting of increasing fecal K+ excretion through the administration of cation-exchange resins. In this study, we explored another more specific method of increasing intestinal K+ secretion by inhibiting the H,K-ATPase type 2 (HKA2), which is the main colonic K+ reabsorptive pathway. We hypothetised that the absence of this pump could impede the increase of plasma K+ levels following nephronic reduction (N5/6) by favoring fecal K+ secretion. In N5/6 WT and HKA2KO mice under normal K+ intake, the plasma K+ level remained within the normal range, however, a load of K+ induced strong hyperkalemia in N5/6 WT mice (9.1 ± 0.5 mM), which was significantly less pronounced in N5/6 HKA2KO mice (7.9 ± 0.4 mM, p < 0.01). This was correlated to a higher capacity of HKA2KO mice to excrete K+ in their feces. The absence of HKA2 also increased fecal Na+ excretion by inhibiting its colonic ENaC-dependent absorption. We also showed that angiotensin-converting-enzyme inhibitor like enalapril, used to treat hypertension during CKD, induced a less severe hyperkalemia in N5/6 HKA2KO than in N5/6 WT mice. This study therefore provides the proof of concept that the targeted inhibition of HKA2 could be a specific therapeutic maneuver to reduce plasma K+ levels in CKD patients.
Alteration of coastal productivity and artisanal fisheries interact to affect a marine food web
Authors: Ávila-Thieme M. Isidora , Corcoran Derek , Pérez-Matus Alejandro , Wieters Evie A. , Navarrete Sergio A. , Marquet Pablo A. , Valdovinos Fernanda S.
Published: January 2021

Top-down and bottom-up forces determine ecosystem function and dynamics. Fisheries as a top-down force can shorten and destabilize food webs, while effects driven by climate change can alter the bottom-up forces of primary productivity. We assessed the response of a highly-resolved intertidal food web to these two global change drivers, using network analysis and bioenergetic modelling. We quantified the relative importance of artisanal fisheries as another predator species, and evaluated the independent and combined effects of fisheries and changes in plankton productivity on food web dynamics. The food web was robust to the loss of all harvested species but sensitive to the decline in plankton productivity. Interestingly, fisheries dampened the negative impacts of decreasing plankton productivity on non-harvested species by reducing the predation pressure of harvested consumers on non-harvested resources, and reducing the interspecific competition between harvested and non-harvested basal species. In contrast, the decline in plankton productivity increased the sensitivity of harvested species to fishing by reducing the total productivity of the food web. Our results show that strategies for new scenarios caused by climate change are needed to protect marine ecosystems and the wellbeing of local communities dependent on their resources.
Antimicrobial effects of syndiotactic polypeptides
Authors: Hazam Prakash Kishore , Phukan Chimanjita , Akhil R. , Singh Anjali , Ramakrishnan Vibin
Published: January 2021

We present design and antibacterial studies of stereochemically diversified antimicrobial peptides against multidrug-resistant bacterial pathogens. Syndiotactic polypeptides are polymers of alternating L and D amino acids with LDLD or DLDL backbone stereochemical sequence, which can form stable gramicidin like helical conformations. We designed, synthesized and characterized eight model molecular systems with varied electrostatic fingerprints, modulated through calibrated sequence positioning. Six out of eight model systems showed very impressive antimicrobial activity against three difficult to treat bacterial species, Gentamicin resistant MRSA, E. coli and Mycobacterium. More importantly, the designed LDLD peptides were equally potent in serum, an important drawback of poly L peptide sequences due to enzyme mediated degradation and ion sensitivity. Further, we tested the activity of the designed peptides against drug-resistant clinical isolates of Staphylococcus aureus and Escherichia coli. Molecular dynamics simulation studies suggest formation of an assembly of individual peptides, preceding the membrane interaction and deformation. The activity estimates are comparable with the available peptide based antimicrobials, and are also highly specific and less toxic as per standard estimates. Incorporation of D amino-acids can significantly expand the peptide design space, which can in turn manifest in future biomaterial designs, especially antimicrobials.
Transperineal ultrasound as a reliable tool in the assessment of membranous urethra length in radical prostatectomy patients
Authors: Piotr Kania , Rafał Mieleszko , Marcin Kuligowski , Karol Dudka , Monika Kuca , Jakub Biedrzycki , Bartosz Zwolan , Tadeusz Dmowski , Maciej Salagierski
Published: January 2021

To evaluate the usefulness of transperineal ultrasound (TPUS) as a method of membranous urethra length (MUL) measurement and investigate whether preoperative (MULpre) and postoperative (MULpost) would be associated with the degree and time of urinary continence recovery after laparoscopic radical prostatectomy (LRP). 84 patients who underwent LRP between January 2017 and December 2018 were selected for final analysis. All patients had preoperative and postoperative measurement of MUL in TPUS. Urinary continence was defined as no pad or a safety pad. Recovery of continence was assessed at 1, 3, 6 and 12 months after catheter removal. We prospectively analyzed correlation of MULpre, MULpost and a percent change in membranous urethral length (MULratio) with the urinary continence status. 69 (82%) patients regained continence in the follow-up of 12 months. MULpre, MULpost and MULratio assessed in TPUS were larger in subgroups of patients who regained continence earlier and in the entire continent group. Spearman rank test showed strong correlations between MULpost and MULratio (R—0.6 and R—0.56, respectively, p < 0.0001) with the time to continence recovery in the cumulative 12 months follow-up. TPUS allowed a reliable measurement of MUL before and after LRP. MULpre, MULpost as well as MULratio are related with time to regain continence and recovery rate after LRP. Sparing longest possible sphincteric urethra, with respect to oncological outcomes is a key factor in recovering continence after prostate cancer surgery.
A finite element analysis of relationship between fracture, implant and tibial tunnel
Authors: Wang Yiqun , Qi Erpeng , Zhang Xiaojun , Xue Lu , Wang Lianyou , Tian Jiahe
Published: January 2021

The purpose of this article was to use finite element analysis (FEA) to study the relationship of tibial tunnel (TT) with fracture pattern and implants. A computed tomography scan of full-length tibia and fibula was obtained. Models were built after three-dimensional reconstruction. The corresponding plates and screws were constructed and assembled together with fracture models. FEA was performed and contourplots were output. The Von Mises stresses of nodes and displacements of elements were extracted. Student’s t test was used to compare the values of Von Mises stresses and displacements between corresponding models. Differences in Von Mises stresses and displacements of fragments and implants between models with and without TT were nearly all statistically significant. However, the displacements of fragments and implants for all models were < 2 mm. TT in fracture models had larger Von Mises stresses than TT in intact tibial model. However, displacements of TT in fracture models showed similar or even smaller results to those in intact tibial model. Although almost all the tested parameters were statistically significant, differences were small and values were all below the clinical threshold. This study could promote open reduction and internal fixation with one-stage reconstruction for treatment of tibial plateau fractures associated with anterior cruciate ligament (ACL) ruptures.
Enzyme and lateral flow monoclonal antibody-based immunoassays to simultaneously determine spirotetramat and spirotetramat-enol in foodstuffs
Authors: Cevallos-Cedeño Ramón E. , Agulló Consuelo , Abad-Fuentes Antonio , Abad-Somovilla Antonio , Mercader Josep V.
Published: January 2021

Spirotetramat is employed worldwide to fight insect pests due to its high efficiency. This chemical is quickly metabolized by plants into spirotetramat-enol, so current regulations establish that both compounds must be determined in foodstuffs for monitoring purposes. Nowadays, immunochemical methods constitute rapid and cost-effective strategies for chemical contaminant analysis at trace levels. However, high-affinity binders and suitable bioconjugates are required. In this study, haptens with opposite functionalisation sites were synthesized in order to generate high-affinity monoclonal antibodies. A direct competitive enzyme-linked immunosorbent assay with an IC50 value for the sum of spirotetramat and spirotetramat-enol of 0.1 μg/L was developed using selected antibodies and a novel heterologous bioconjugate carrying a rationally-designed hapten. Studies with fortified grape, grape juice, and wine samples showed good precision and accuracy values, with limits of quantification well below the maximum residue limits. Excellent correlation of results was observed with a standard reference chromatographic method. As a step forward, a lateral flow immunoassay was developed for onsite screening analysis of spirotetramat in wine. This assay was successfully validated according to Regulation 519/2014/EU for semi-quantitative methods at concentrations in line with the legal levels of spirotetramat and spirotetramat-enol in grapes, with a satisfactory false suspect rate below 2%.
TNFα promotes oral cancer growth, pain, and Schwann cell activation
Authors: Salvo Elizabeth , Tu Nguyen H. , Scheff Nicole N. , Dubeykovskaya Zinaida A. , Chavan Shruti A. , Aouizerat Bradley E. , Ye Yi
Published: January 2021

Oral cancer is very painful and impairs a patient’s ability to eat, talk, and drink. Mediators secreted from oral cancer can excite and sensitize sensory neurons inducing pain. Cancer mediators can also activate Schwann cells, the peripheral glia that regulates neuronal function and repair. The contribution of Schwann cells to oral cancer pain is unclear. We hypothesize that the oral cancer mediator TNFα activates Schwann cells, which further promotes cancer progression and pain. We demonstrate that TNFα is overexpressed in human oral cancer tissues and correlates with increased self-reported pain in patients. Antagonizing TNFα reduces oral cancer proliferation, cytokine production, and nociception in mice with oral cancer. Oral cancer or TNFα alone increases Schwann cell activation (measured by Schwann cell proliferation, migration, and activation markers), which can be inhibited by neutralizing TNFα. Cancer- or TNFα-activated Schwann cells release pro-nociceptive mediators such as TNFα and nerve growth factor (NGF). Activated Schwann cells induce nociceptive behaviors in mice, which is alleviated by blocking TNFα. Our study suggests that TNFα promotes cancer proliferation, progression, and nociception at least partially by activating Schwann cells. Inhibiting TNFα or Schwann cell activation might serve as therapeutic approaches for the treatment of oral cancer and associated pain.
Circulator function in a Josephson junction circuit and braiding of Majorana zero modes
Authors: Kim Mun Dae
Published: January 2021

We propose a scheme for the circulator function in a superconducting circuit consisting of a three-Josephson junction loop and a trijunction. In this study we obtain the exact Lagrangian of the system by deriving the effective potential from the fundamental boundary conditions. We subsequently show that we can selectively choose the direction of current flowing through the branches connected at the trijunction, which performs a circulator function. Further, we use this circulator function for a non-Abelian braiding of Majorana zero modes (MZMs). In the branches of the system we introduce pairs of MZMs which interact with each other through the phases of trijunction. The circulator function determines the phases of the trijunction and thus the coupling between the MZMs to gives rise to the braiding operation. We modify the system so that MZMs might be coupled to the external ones to perform qubit operations in a scalable design.
Retraction Note: Facile design of an ultra-thin broadband metamaterial absorber for C-band applications
Authors: Hoa Nguyen Thi Quynh , Tuan Tran Sy , Hieu Lam Trung , Giang Bach Long
Published: January 2021

This Article has been retracted. Please
see the Retraction Note for more detail: https://doi.org/10.1038/s41598-021-81808-1.
A generic approach to study the kinetics of liquid–liquid phase separation under near-native conditions
Authors: Van Lindt Joris , Bratek-Skicki Anna , Nguyen Phuong N. , Pakravan Donya , Durán-Armenta Luis F. , Tantos Agnes , Pancsa Rita , Van Den Bosch Ludo , Maes Dominique , Tompa Peter
Published: January 2021

Understanding the kinetics, thermodynamics, and molecular mechanisms of liquid–liquid phase separation (LLPS) is of paramount importance in cell biology, requiring reproducible methods for studying often severely aggregation-prone proteins. Frequently applied approaches for inducing LLPS, such as dilution of the protein from an urea-containing solution or cleavage of its fused solubility tag, often lead to very different kinetic behaviors. Here we demonstrate that at carefully selected pH values proteins such as the low-complexity domain of hnRNPA2, TDP-43, and NUP98, or the stress protein ERD14, can be kept in solution and their LLPS can then be induced by a jump to native pH. This approach represents a generic method for studying the full kinetic trajectory of LLPS under near native conditions that can be easily controlled, providing a platform for the characterization of physiologically relevant phase-separation behavior of diverse proteins.
Optimal combination treatment regimens of vaccine and radiotherapy augment tumor-bearing host immunity
Authors: Zhang Fayun , Zheng Zifeng , Barman Apurba Kumar , Wang Zihao , Wang Luyao , Zeng Wenfeng , Wang Luoyang , Qin Yan , Pandey Asmita , Zhang Chunling , Liang Wei
Published: January 2021

A major obstacle to immunotherapy is insufficient infiltration of effector immune cells into the tumor microenvironment. Radiotherapy greatly reduces tumor burden but relapses often occur. Here we show that the immunosuppressive tumor microenvironment was gradually established by recruiting Tregs after radiation. Despite tumors being controlled after depletion of Tregs in the irradiated area, improvement of mice survival remained poor. A much better antitumor effect was achieved with vaccination followed by radiation than other treatments. Vaccination followed by radiation recruited more effector T cells in tumor regions, which responded to high levels of chemokines. Sequential combination of vaccination and radiotherapy could elicit distinct host immune responses. Our study demonstrated that optimal combination of irradiation and vaccination is required to achieve effective antitumor immune responses. We propose a combination regimen that could be easily translated into the clinic and offer an opportunity for rational combination therapies design in cancer treatment.