bluuebunny/crossref_metadata_2025 huggingface dataset:
Research on DOA Estimation Based on Acoustic Energy Flux Detection Using a Single MEMS Vector Hydrophone
Authors: Zhang Xiaoyong , Zhang Guojun , Shang Zhenzhen , Zhu Shan , Chen Peng , Wang Renxin , Zhang Wendong
Published: February 2021

The principle of acoustic energy flux detection method using a single micro electromechanical system (MEMS) vector hydrophone is analyzed in this paper. The probability distribution of acoustic energy flux and the weighted histogram algorithm are discussed. Then, an improved algorithm is proposed. Based on the algorithm, the distribution range of the energy is obtained by a sliding window, the energy center of gravity in the range is considered as the result of direction of arrival (DOA) estimation, and it is proved to be the maximum likelihood estimation of the target direction. The simulation results show that, with the signal to noise ratio (SNR) from −10 dB to 10 dB, the root mean square error (RMSE) of the improved algorithm is reduced by 47.8% on average, and is more accurate in the presence of interference. The experimental results of lake test are consistent with the theory analysis and simulation results.
High-Throughput Synthesis of Liposome Using an Injection-Molded Plastic Micro-Fluidic Device
Authors: Woo Sang-Won , Jo Yun Kyong , Yoo Yeong-Eun , Kim Sun Kyoung
Published: February 2021

For mass production of liposomes, we designed a plastic micro-channel device on the basis of 5 μm of micro-nozzle array forming T-junction with 100 μm depth of micro-channel. A micro-channel unit for synthesizing liposomes consisted of two micro-nozzle arrays for mixing two solutions as well as delivery and recovery channels for supplying solutions and collecting liposome suspension. The number of micro-nozzles was approximately 2400 for a micro-channel unit, and seven units were applied independently on a micro-channel plate. The plastic micro-channel plate was injection-molded for mass production using a micro-channel stamper previously fabricated by UV lithography and nickel electroforming process. A plastic cover plate with seven pairs of inlet and outlet ports was machined by mechanical milling and drilling and was assembled with a micro-channel plate using a holder to form a liposome synthesizing device. Flow and mixing of solutions in the micro-channels were tested using colored water to check the micro-fluidic characteristics of the device. Finally, a L-α-phosphatidylcholine (SOY PC) liposome was synthesized using EtOH solution of SOY PC (95%) and saline (0.85% NaOH solution) to find that the liposomes were around 230 and 260 nm in diameter, depending on the flow rate of the lipid solution.
Evaluation and Optimization of a MOEMS Active Focusing Device
Authors: Mescheder Ulrich , Lootze Michael , Aljasem Khaled
Published: February 2021

In this paper we present a detailed evaluation of a micro-opto-electromechanical system (MOEMS) for active focusing which is realized using an electrostatically deformed thin silicon membrane. The evaluation is done using finite element methods and experimental characterization of the device behavior. The devices are realized in silicon on insulator technology. The influence of internal stress especially resulting from the high compressive buried oxide (BOX) layer is evaluated. Additionally, the effect of stress gradients in the crystalline device layer and of high reflective coatings such as aluminum is discussed. The influence of variations of some important process steps on the device performance is quantified. Finally, practical properties such as focal length control, long-term stability, hysteresis and dynamical response are presented and evaluated. The evaluation proves that the proposed membrane focusing device is suitable for high performance imaging (wavefront errors between λ/5–λ/10) with a large aperture (5 mm).
Modelling, Simulation and Dynamic Sliding Mode Control of a MEMS Gyroscope
Authors: Fang Yunmei , Fu Wen , An Cuicui , Yuan Zhuli , Fei Juntao
Published: February 2021

An adaptive dynamic sliding mode control via a backstepping approach for a microelectro mechanical system (MEMS) vibratory z-axis gyroscope is presented in this paper. The time derivative of the control input of the dynamic sliding mode controller (DSMC) is treated as a new control variable for the augmented system which is composed of the original system and the integrator. This DSMC can transfer discontinuous terms to the first-order derivative of the control input, and effectively reduce the chattering. An adaptive dynamic sliding mode controller with the method of backstepping is derived to real-time estimate the angular velocity and the damping and stiffness coefficients and asymptotical stability of the designed systems can be guaranteed. Simulation examples are investigated to demonstrate the satisfactory performance of the proposed adaptive backstepping sliding mode control.
Low Virus-Specific IgG Antibodies in Adverse Clinical Course and Outcome of Tick-Borne Encephalitis
Authors: Bogovič Petra , Lotrič-Furlan Stanka , Avšič-Županc Tatjana , Korva Miša , Lusa Lara , Strle Klemen , Strle Franc
Published: February 2021

Tick-borne encephalitis (TBE) is associated with a range of disease severity. The reasons for this heterogeneity are not clear. Levels of serum IgG antibodies to TBE virus (TBEV) were determined in 691 adult patients during the meningoencephalitic phase of TBE and correlated with detailed clinical and laboratory parameters during acute illness and with the presence of post-encephalitic syndrome (PES) 2–7 years after TBE. Specific IgG antibody levels ranged from below cut-off value (in 32/691 patients, 4.6%), to 896 U/mL (median = 37.3 U/mL). Patients with meningoencephalomyelitis were more often seronegative (24.3%; 9/37) than those with meningoencephalitis (4.7%; 20/428) or meningitis (1.3%; 3/226). Moreover, patients with antibody levels below cut-off had longer hospitalization (13 versus 8 days); more often required intensive care unit treatment (22% versus 8%) and artificial ventilation (71% versus 21%); and had a higher fatality rate (3/32; 9.4% versus 1/659; 0.2%) than seropositive patients. These results were confirmed when antibody levels, rather than cut-off values, were correlated with clinical parameters including the likelihood to develop PES. Low serum IgG antibody responses against TBEV at the onset of neurologic involvement are associated with a more difficult clinical course and unfavorable long-term outcome of TBE, providing a diagnostic and clinical challenge for physicians.
Do Blood Eosinophils Predict in-Hospital Mortality or Severity of Disease in SARS-CoV-2 Infection? A Retrospective Multicenter Study
Authors: Le Borgne Pierrick , Abensur Vuillaume Laure , Alamé Karine , Lefebvre François , Chabrier Sylvie , Bérard Lise , Haessler Pauline , Gennai Stéphane , Bilbault Pascal , Lavoignet Charles-Eric
Published: February 2021

Introduction: Healthcare systems worldwide have been battling the ongoing COVID-19 pandemic. Eosinophils are multifunctional leukocytes implicated in the pathogenesis of several inflammatory processes including viral infections. We focus our study on the prognostic value of eosinopenia as a marker of disease severity and mortality in COVID-19 patients. Methods: Between 1 March and 30 April 2020, we conducted a multicenter and retrospective study on a cohort of COVID-19 patients (moderate or severe disease) who were hospitalized after presenting to the emergency department (ED). We led our study in six major hospitals of northeast France, one of the outbreak’s epicenters in Europe. Results: We have collected data from 1035 patients, with a confirmed diagnosis of COVID-19. More than three quarters of them (76.2%) presented a moderate form of the disease, while the remaining quarter (23.8%) presented a severe form requiring admission to the intensive care unit (ICU). Mean circulating eosinophils rate, at admission, varied according to disease severity (p < 0.001), yet it did not differ between survivors and non-survivors (p = 0.306). Extreme eosinopenia (=0/mm3) was predictive of severity (aOR = 1.77, p = 0.009); however, it was not predictive of mortality (aOR = 0.892, p = 0.696). The areas under the Receiver operating characteristics (ROC) curve were, respectively, 58.5% (CI95%: 55.3–61.7%) and 51.4% (CI95%: 46.8–56.1%) for the ability of circulating eosinophil rates to predict disease severity and mortality. Conclusion: Eosinopenia is very common and often profound in cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Eosinopenia was not a useful predictor of mortality; however, undetectable eosinophils (=0/mm3) were predictive of disease severity during the initial ED management.
Genomic and Phenotypic Characterization of Campylobacter fetus subsp. venerealis Strains
Authors: Silva Marta F. , Pereira Ana L. , Fraqueza Maria J. , Pereira Gonçalo , Mateus Luísa , Lopes-da-Costa Luís , Silva Elisabete
Published: February 2021

The pathogenesis mechanisms of Campylobacter fetus subsp. venerealis (Cfv), the etiologic agent of Bovine Genital Campylobacteriosis remain elusive. This study evaluated the virulence potential and biovar characteristics of Cfv isolates (n = 13) by PCR screening of putative virulence-factor (VF) genes, Multilocus Sequence Typing (MLST) analysis, antimicrobial susceptibility to tetracycline, penicillin, enrofloxacin and streptomycin testing and whole-genome sequencing (WGS; n = 5), also comparing the latter with 26 other whole-genome sequences of Cfv strains. The putative VF genes encoding type IV secretion system of Cfv (virB2-virB11/virD4) were absent in 92% of isolates, including isolates from aborted foetuses, evidencing that these VF genes are not essential for Cfv pathogenicity. The parA gene, used as a Cfv diagnostic molecular target, was detected in only 3 of 13 isolates, invalidating its use for diagnosis purposes. Three novel sequence types were identified by MLST. Although no in vitro antimicrobial resistance was detected, WGS identified antimicrobial resistance-related genes, including those encoding the multidrug efflux pumps CmeABC and YkkCD, indicating that their presence is not enough to provide antimicrobial resistance. The SNP and accessory protein families analysis segregated the Cfv and Cfv biovar intermedius (Cfvi) strains into different clusters. In conclusion, this study evidenced virulence potential and biovar characteristics of Cfv and Cfvi, which are of relevance for the control of Bovine Genital Campylobacteriosis.
The Disordered C-Terminus of the Chaperone DnaK Increases the Competitive Fitness of Pseudomonas putida and Facilitates the Toxicity of GraT
Authors: Rosendahl Sirli , Ainelo Andres , Hõrak Rita
Published: February 2021

Chaperone proteins are crucial for proper protein folding and quality control, especially when cells encounter stress caused by non-optimal temperatures. DnaK is one of such essential chaperones in bacteria. Although DnaK has been well characterized, the function of its intrinsically disordered C-terminus has remained enigmatic as the deletion of this region has been shown to either enhance or reduce its protein folding ability. We have shown previously that DnaK interacts with toxin GraT of the GraTA toxin-antitoxin system in Pseudomonas putida. Interestingly, the C-terminal truncation of DnaK was shown to alleviate GraT-caused growth defects. Here, we aim to clarify the importance of DnaK in GraT activity. We show that DnaK increases GraT toxicity, and particularly important is the negatively charged motif in the DnaK C-terminus. Given that GraT has an intrinsically disordered N-terminus, the assistance of DnaK is probably needed for re-modelling the toxin structure. We also demonstrate that the DnaK C-terminal negatively charged motif contributes to the competitive fitness of P. putida at both high and optimal growth temperatures. Thus, our data suggest that the disordered C-terminal end of DnaK enhances the chaperone functionality.
Hypo- and Hyper-Virulent Listeria monocytogenes Clones Persisting in Two Different Food Processing Plants of Central Italy
Authors: Guidi Fabrizia , Orsini Massimiliano , Chiaverini Alexandra , Torresi Marina , Centorame Patrizia , Acciari Vicdalia Aniela , Salini Romolo , Palombo Barbara , Brandi Giorgio , Amagliani Giulia , Schiavano Giuditta Fiorella , Massacci Francesca Romana , Fisichella Stefano , Domenico Marco Di , Ancora Massimo , Pasquale Adriano Di , Duranti Anna , Cammà Cesare , Pomilio Francesco , Blasi Giuliana
Published: February 2021

A total of 66 Listeria monocytogenes (Lm) isolated from 2013 to 2018 in a small-scale meat processing plant and a dairy facility of Central Italy were studied. Whole Genome Sequencing and bioinformatics analysis were used to assess the genetic relationships between the strains and investigate persistence and virulence abilities. The biofilm forming-ability was assessed in vitro. Cluster analysis grouped the Lm from the meat plant into three main clusters: two of them, both belonging to CC9, persisted for years in the plant and one (CC121) was isolated in the last year of sampling. In the dairy facility, all the strains grouped in a CC2 four-year persistent cluster. All the studied strains carried multidrug efflux-pumps genetic determinants (sugE, mdrl, lde, norM, mepA). CC121 also harbored the Tn6188 specific for tolerance to Benzalkonium Chloride. Only CC9 and CC121 carried a Stress Survival Islet and presented high-level cadmium resistance genes (cadA1C1) carried by different plasmids. They showed a greater biofilm production when compared with CC2. All the CC2 carried a full-length inlA while CC9 and CC121 presented a Premature Stop Codon mutation correlated with less virulence. The hypo-virulent clones CC9 and CC121 appeared the most adapted to food-processing environments; however, even the hyper-virulent clone CC2 warningly persisted for a long time. The identification of the main mechanisms promoting Lm persistence in a specific food processing plant is important to provide recommendations to Food Business Operators (FBOs) in order to remove or reduce resident Lm.
The Global Burden of Meningitis in Children: Challenges with Interpreting Global Health Estimates
Authors: Wright Claire , Blake Natacha , Glennie Linda , Smith Vinny , Bender Rose , Kyu Hmwe , Wunrow Han Yong , Liu Li , Yeung Diana , Knoll Maria Deloria , Wahl Brian , Stuart James M. , Trotter Caroline
Published: February 2021

The World Health Organization (WHO) has developed a global roadmap to defeat meningitis by 2030. To advocate for and track progress of the roadmap, the burden of meningitis as a syndrome and by pathogen must be accurately defined. Three major global health models estimating meningitis mortality as a syndrome and/or by causative pathogen were identified and compared for the baseline year 2015. Two models, (1) the WHO and the Johns Hopkins Bloomberg School of Public Health’s Maternal and Child Epidemiology Estimation (MCEE) group’s Child Mortality Estimation (WHO-MCEE) and (2) the Institute for Health Metrics and Evaluation (IHME) Global Burden of Disease Study (GBD 2017), identified meningitis, encephalitis and neonatal sepsis, collectively, to be the second and third largest infectious killers of children under five years, respectively. Global meningitis/encephalitis and neonatal sepsis mortality estimates differed more substantially between models than mortality estimates for selected infectious causes of death and all causes of death combined. Estimates at national level and by pathogen also differed markedly between models. Aligning modelled estimates with additional data sources, such as national or sentinel surveillance, could more accurately define the global burden of meningitis and help track progress against the WHO roadmap.
Explorative Meta-Analysis of 417 Extant Archaeal Genomes to Predict Their Contribution to the Total Microbiome Functionality
Authors: Starke Robert , Fernandes Maysa Lima Parente , Morais Daniel Kumazawa , Odriozola Iñaki , Baldrian Petr , Jehmlich Nico
Published: February 2021

Revealing the relationship between taxonomy and function in microbiomes is critical to discover their contribution to ecosystem functioning. However, while the relationship between taxonomic and functional diversity in bacteria and fungi is known, this is not the case for archaea. Here, we used a meta-analysis of 417 completely annotated extant and taxonomically unique archaeal genomes to predict the extent of microbiome functionality on Earth contained within archaeal genomes using accumulation curves of all known level 3 functions of KEGG Orthology. We found that intergenome redundancy as functions present in multiple genomes was inversely related to intragenome redundancy as multiple copies of a gene in one genome, implying the tradeoff between additional copies of functionally important genes or a higher number of different genes. A logarithmic model described the relationship between functional diversity and species richness better than both the unsaturated and the saturated model, which suggests a limited total number of archaeal functions in contrast to the sheer unlimited potential of bacteria and fungi. Using the global archaeal species richness estimate of 13,159, the logarithmic model predicted 4164.1 ± 2.9 KEGG level 3 functions. The non-parametric bootstrap estimate yielded a lower bound of 2994 ± 57 KEGG level 3 functions. Our approach not only highlighted similarities in functional redundancy but also the difference in functional potential of archaea compared to other domains of life.
Bacillus amyloliquefaciens TL Downregulates the Ileal Expression of Genes Involved in Immune Responses in Broiler Chickens to Improve Growth Performance
Authors: Hong Yuxuan , Cheng Yang , Guan Leluo , Zhou Zutao , Li Xiaowen , Shi Deshi , Xiao Yuncai
Published: February 2021

Bacillus amyloliquefaciens TL promotes broiler chicken performance by improving nutrient absorption and utilization and reducing intestinal inflammation. In this study, RNA-sequencing (RNA-seq)-based transcriptomes of ileal tissues collected from probiotic-fed and control broiler chickens were analyzed to elucidate the effects of the probiotic B. amyloliquefaciens TL, as a feed additive, on the gut immune function. In total, 475 genes were significantly differentially expressed between the ileum of probiotic-fed and control birds. The expression of genes encoding pyruvate kinase, prothymosin-α, and heat stress proteins was high in the ileum of probiotic-fed birds (FPKM > 500), but not in the control group. The gene ontology functional enrichment and pathway enrichment analyses revealed that the uniquely expressed genes in the control group were mostly involved in immune responses, whereas those in the probiotic group were involved in fibroblast growth factor receptor signaling pathways and positive regulation of cell proliferation. Bacillus amyloliquefaciens TL downregulated the expression of certain proinflammatory factors and affected the cytokine–cytokine receptor interaction pathway. Furthermore, B. amyloliquefaciens TL in broiler diets altered the expression of genes involved in immune functions in the ileum. Thus, it might contribute to improved broiler growth by regulating the immune system and reducing intestinal damage in broilers.
Genetic Characterization of Fungal Biodiversity in Storage Grains: Towards Enhancing Food Safety in Northern Uganda
Authors: Wokorach Godfrey , Landschoot Sofie , Audenaert Kris , Echodu Richard , Haesaert Geert
Published: February 2021

Worldwide fungal contamination leads to both quantitative and qualitative grain losses during crop growth and/or storage. A greater proportion of grains contamination with toxins often occurs in sub-Saharan Africa, where control measures are limited. We determined fungal diversity and their toxin production ability in household grains meant for human consumption to highlight the risk of mycotoxin exposure among people from northern Uganda. The study underlines the high diversity of fungi that group into 15 genera; many of which are plant pathogens with toxigenic potential. Fusarium verticillioides was the most common fungal species isolated from household grains. The study also indicates that northern Uganda is favored by a high proportion of toxigenic isolates of F. verticillioides, F. andiyazi, and F. proliferatum, which are characterized by a high fumonisins production capability. The fumonisins production ability was not dependent on the species, grain types, and haplotype group to which the isolates belong. The contamination of most household grains with fungi capable of producing a high amount of toxin shows that most people are exposed to an elevated amount of mycotoxins, which shows the frequent problems with mycotoxins that have been reported in most parts of sub-Saharan Africa.
Persister Cells Form in the Plant Pathogen Xanthomonas citri subsp. citri under Different Stress Conditions
Authors: Martins Paula M. M. , Wood Thomas K. , de Souza Alessandra A.
Published: February 2021

Citrus canker disease, caused by the bacterium Xanthomonas citri subsp. citri is a constant threat to citrus-producing areas. Since it has no cure, agricultural practices to restrain its dissemination are essential to reduce the economic damage. Hence, increased knowledge of the basic aspects of X. citri biology could lead to more efficient management practices that can eliminate dormant bacteria in the field. The dormant cells, also referred to as persisters, are phenotypic variants with lowered metabolism, which in turn leads to tolerance to antimicrobials and undermines existing control approaches. We show here that X. citri forms persisters, identifying triggers for this phenotype, including antibiotics, high temperature, and metals (copper and zinc), which increase persistence rates by 10–100 times. The antioxidant N-acetylcysteine reduced copper and zinc-induced persisters, but not those induced by tetracycline, indicating that oxidative stress may be an important inducer of X. citri persistence. In addition, we found that metabolism-independent drugs like cisplatin and mitomycin C are able to eliminate X. citri persistent cells, as well as copper, at high concentrations. Specific amino acids like proline and isoleucine interfered with the physiological balance of the dormancy in X. citri, stimulating or preventing persister resuscitation. Taken together, we discover chemicals that can induce, wake, and kill X. citri persister cells; these results provide insights that should be considered for more efficient integrated control management in the field.
Presence of Chromosomal crpP-like Genes Is Not Always Associated with Ciprofloxacin Resistance in Pseudomonas aeruginosa Clinical Isolates Recovered in ICU Patients from Portugal and Spain
Authors: Hernández-García Marta , García-Castillo María , García-Fernández Sergio , López-Mendoza Diego , Díaz-Regañón Jazmín , Romano João , Pássaro Leonor , Paixão Laura , Cantón Rafael
Published: February 2021

CrpP enzymes have been recently described as a novel ciprofloxacin-resistance mechanism. We investigated by whole genome sequencing the presence of crpP-genes and other mechanisms involved in quinolone resistance in MDR/XDR-Pseudomonas aeruginosa isolates (n = 55) with both ceftolozane-tazobactam susceptible or resistant profiles recovered from intensive care unit patients during the STEP (Portugal) and SUPERIOR (Spain) surveillance studies. Ciprofloxacin resistance was associated with mutations in the gyrA and parC genes. Additionally, plasmid-mediated genes (qnrS2 and aac(6′)-Ib-cr) were eventually detected. Ten chromosomal crpP-like genes contained in related pathogenicity genomic islands and 6 different CrpP (CrpP1-CrpP6) proteins were found in 65% (36/55) of the isolates. Dissemination of CrpP variants was observed among non-related clones of both countries, including the CC175 (Spain) high-risk clone and CC348 (Portugal) clone. Interestingly, 5 of 6 variants (CrpP1-CrpP5) carried missense mutations in an amino acid position (Gly7) previously defined as essential conferring ciprofloxacin resistance, and decreased ciprofloxacin susceptibility was only associated with the novel CrpP6 protein. In our collection, ciprofloxacin resistance was mainly due to chromosomal mutations in the gyrA and parC genes. However, crpP genes carrying mutations essential for protein function (G7, I26) and associated with a restored ciprofloxacin susceptibility were predominant. Despite the presence of crpP genes is not always associated with ciprofloxacin resistance, the risk of emergence of novel CrpP variants with a higher ability to affect quinolones is increasing. Furthermore, the spread of crpP genes in highly mobilizable genomic islands among related and non-related P. aeruginosa clones alert the dispersion of MDR pathogens in hospital settings.
Asymptomatic Bacteriuria (ABU) in Elderly: Prevalence, Virulence, Phylogeny, Antibiotic Resistance and Complement C3 in Urine
Authors: Leihof Rikke Fleron , Nielsen Karen Leth , Frimodt-Møller Niels
Published: February 2021

Background: The incidence of asymptomatic bacteriuria (ABU) increases with age and is most common for persons 80 years of age and above and in elderly living in nursing homes. The distinction between ABU and urinary tract infection (UTI) is often difficult, especially in individuals, who are unable to communicate their symptoms, and there is a lack of objective methods to distinguish between the two entities. This can lead to overuse of antibiotics, which results in the selection and dissemination of antibiotic resistant isolates. Materials and methods: From voided midstream urine samples of 211 participants ≥60 years old from nursing homes, an activity center and a general practitioners clinic, we collected 19 ABU, 16 UTI and 22 control urine samples and compared them with respect to levels of complement component C3 in urine as determined by an ELISA assay relative to creatinine levels in the same urine samples, as measured by a creatinine assay. Further, we studied all Escherichia coli isolates for selected virulence genes by multiplex PCR, and by whole-genome sequencing (WGS) for genotypes and phylogenetic clustering. Antibiotic susceptibility was determined by microtiter broth dilution. Results: We identified a prevalence of ABU of 18.9% in nursing home residents, whereas ABU was only found in 4% of elderly living in the community (p < 0.001). E. coli from ABU patients were significantly more antibiotic resistant than E. coli from UTIs (p = 0.01). Prevalence of classical virulence genes, detected by multiplex PCR, was similar in E. coli isolates from ABU and UTI patients. Whole-genome sequencing of the E. coli isolates showed no specific clustering of ABU isolates compared to UTI isolates. Three isolates from three different individuals from one of the nursing homes showed signs of transmission. We demonstrated a significantly increased level of C3/creatinine ratio in ABU and UTI samples compared to healthy controls; however, there was no significant difference between the ABU and UTI group with respect to C3 level, or virulence factor genes. Conclusion: ABU was significantly more prevalent in the elderly residing in nursing homes than in the elderly living at home. Antibiotic resistance was more prevalent in E. coli from nursing homes than in UTI isolates, but there was no difference in prevalence of virulence associated genes between the two groups and no phylogenetic clustering, as determined by WGS relative to the two types of E. coli bacteriuria. The similar complement C3 response in ABU and UTI patients may indicate that ABU should be reconsidered as an infection albeit without symptoms.
From Data Mining of Chitinophaga sp. Genome to Enzyme Discovery of a Hyperthermophilic Metallocarboxypeptidase
Authors: Fernandes Gabriela Cabral , Sierra Elwi Guillermo Machado , Brear Paul , Pereira Mariana Rangel , Lemos Eliana G. M.
Published: February 2021

For several centuries, microorganisms and enzymes have been used for many different applications. Although many enzymes with industrial applications have already been reported, different screening technologies, methods and approaches are constantly being developed in order to allow the identification of enzymes with even more interesting applications. In our work, we have performed data mining on the Chitinophaga sp. genome, a gram-negative bacterium isolated from a bacterial consortium of sugarcane bagasse isolated from an ethanol plant. The analysis of 8 Mb allowed the identification of the chtcp gene, previously annotated as putative Cht4039. The corresponding codified enzyme, denominated as ChtCP, showed the HEXXH conserved motif of family M32 from thermostable carboxypeptidases. After expression in E. coli, the recombinant enzyme was characterized biochemically. ChtCP showed the highest activity versus benziloxicarbonil Ala-Trp at pH 7.5, suggesting a preference for hydrophobic substrates. Surprisingly, the highest activity of ChtCP observed was between 55 °C and 75 °C, and 62% activity was still displayed at 100 °C. We observed that Ca2+, Ba2+, Mn2+ and Mg2+ ions had a positive effect on the activity of ChtCP, and an increase of 30 °C in the melting temperature was observed in the presence of Co2+. These features together with the structure of ChtCP at 1.2 Å highlight the relevance of ChtCP for further biotechnological applications.
Mechanism and Influencing Factors of REY Enrichment in Deep-Sea Sediments
Authors: Ren Jiangbo , Liu Yan , Wang Fenlian , He Gaowen , Deng Xiguang , Wei Zhenquan , Yao Huiqiang
Published: February 2021

Deep-sea sediments with high contents of rare-earth elements and yttrium (REY) are expected to serve as a potential resource for REY, which have recently been proved to be mainly contributed by phosphate component. Studies have shown that the carriers of REY in deep-sea sediments include aluminosilicate, Fe-Mn oxyhydroxides, and phosphate components. The ∑REY of the phosphate component is 1–2 orders of magnitude higher than those of the other two carriers, expressed as ∑REY = 0.001 × [Al2O3] − 0.002 × [MnO] + 0.056 × [P2O5] − 32. The sediment P2O5 content of 1.5% explains 89.1% of the total variance of the sediment ∑REY content. According to global data, P has a stronger positive correlation with ∑REY compared with Mn, Fe, Al, etc.; 45.5% of samples have a P2O5 content of less than 0.25%, and ∑REY of not higher than 400 ppm. The ∑REY of the phosphate component reaches n × 104 ppm, much higher than that of marine phosphorites and lower than that of REY-phosphate minerals, which are called REY-rich phosphates in this study. The results of microscopic observation and separation by grain size indicate that the REY-rich phosphate component is mainly composed of bioapatite. When ∑REY > 2000 ppm, the average CaO/P2O5 ratio of the samples is 1.55, indicating that the phosphate composition is between carbonate fluoroapatite and hydroxyfluorapatite. According to a knowledge map of sediment elements, the phosphate component is mainly composed of P, Ca, Sr, REY, Sc, U, and Th, and its chemical composition is relatively stable. The phosphate component has a negative Ce anomaly and positive Y anomaly, and a REY pattern similar to that of marine phosphorites and seawater. After the early diagenesis process (biogeochemistry, adsorption, desorption, transformation, and migration), the REY enrichment in the phosphate component is completed near the seawater/sediment interface. In the process of REY enrichment, the precipitation and enrichment of P is critical. According to current research progress, the REY enrichment is the result of comprehensive factors, including low sedimentation rate, high ∑REY of the bottom seawater, a non-carbonate depositional environment, oxidation conditions, and certain bottom current conditions.
Supramolecular Assemblies of Dipyrrolyldiketone CuII Complexes
Authors: Haketa Yohei , Maeda Hiromitsu
Published: February 2021

Dipyrrolyldiketones are essential building units of anion-responsive π-electronic molecules and ion-pairing assemblies. Here, we demonstrated that they form complexes with CuII characterized by planar geometries. The solid-state stacking assembled structures, as revealed by single-crystal X-ray analysis, were modulated by the substitution of pyrrole units. The rectangular shapes of the CuII complexes resulted in the formation of mesophases upon introduction of aliphatic chains.
Selected Thoughts on Hydrophobicity in Drug Design
Authors: Lou Lillian L. , Martin John C.
Published: February 2021

The fundamental aim of drug design in research and development is to invent molecules with selective affinity towards desired disease-associated targets. At the atomic loci of binding surfaces, systematic structural variations can define affinities between drug candidates and biomolecules, and thereby guide the optimization of safety, efficacy and pharmacologic properties. Hydrophobic interaction between biomolecules and drugs is integral to binding affinity and specificity. Examples of antiviral drug discovery are discussed.
Molecular and Cellular Effects of Chemical Chaperone—TUDCA on ER-Stressed NHAC-kn Human Articular Chondrocytes Cultured in Normoxic and Hypoxic Conditions
Authors: Kusaczuk Magdalena , Naumowicz Monika , Krętowski Rafał , Cukierman Bartosz , Cechowska-Pasko Marzanna
Published: February 2021

Osteoarthritis (OA) is considered one of the most common arthritic diseases characterized by progressive degradation and abnormal remodeling of articular cartilage. Potential therapeutics for OA aim at restoring proper chondrocyte functioning and inhibiting apoptosis. Previous studies have demonstrated that tauroursodeoxycholic acid (TUDCA) showed anti-inflammatory and anti-apoptotic activity in many models of various diseases, acting mainly via alleviation of endoplasmic reticulum (ER) stress. However, little is known about cytoprotective effects of TUDCA on chondrocyte cells. The present study was designed to evaluate potential effects of TUDCA on interleukin-1β (IL-1β) and tunicamycin (TNC)-stimulated NHAC-kn chondrocytes cultured in normoxic and hypoxic conditions. Our results showed that TUDCA alleviated ER stress in TNC-treated chondrocytes, as demonstrated by reduced CHOP expression; however, it was not effective enough to prevent apoptosis of NHAC-kn cells in either normoxia nor hypoxia. However, co-treatment with TUDCA alleviated inflammatory response induced by IL-1β, as shown by down regulation of Il-1β, Il-6, Il-8 and Cox2, and increased the expression of antioxidant enzyme Sod2. Additionally, TUDCA enhanced Col IIα expression in IL-1β- and TNC-stimulated cells, but only in normoxic conditions. Altogether, these results suggest that although TUDCA may display chondoprotective potential in ER-stressed cells, further analyses are still necessary to fully confirm its possible recommendation as potential candidate in OA therapy.
Conjugate of Thiol and Guanidyl Units with Oligoethylene Glycol Linkage for Manipulation of Oxidative Protein Folding
Authors: Okada Shunsuke , Matsusaki Motonori , Okumura Masaki , Muraoka Takahiro
Published: February 2021

Oxidative protein folding is a biological process to obtain a native conformation of a protein through disulfide-bond formation between cysteine residues. In a cell, disulfide-catalysts such as protein disulfide isomerase promote the oxidative protein folding. Inspired by the active sites of the disulfide-catalysts, synthetic redox-active thiol compounds have been developed, which have shown significant promotion of the folding processes. In our previous study, coupling effects of a thiol group and guanidyl unit on the folding promotion were reported. Herein, we investigated the influences of a spacer between the thiol group and guanidyl unit. A conjugate between thiol and guanidyl units with a diethylene glycol spacer (GdnDEG-SH) showed lower folding promotion effect compared to the thiol–guanidyl conjugate without the spacer (GdnSH). Lower acidity and a more reductive property of the thiol group of GdnDEG-SH compared to those of GdnSH likely resulted in the reduced efficiency of the folding promotion. Thus, the spacer between the thiol and guanidyl groups is critical for the promotion of oxidative protein folding.
Bioinformatics and Functional Analyses Implicate Potential Roles for EOGT and L-fringe in Pancreatic Cancers
Authors: Barua Rashu , Mizuno Kazuyuki , Tashima Yuko , Ogawa Mitsutaka , Takeuchi Hideyuki , Taguchi Ayumu , Okajima Tetsuya
Published: February 2021

Notch signaling receptors, ligands, and their downstream target genes are dysregulated in pancreatic ductal adenocarcinoma (PDAC), suggesting a role of Notch signaling in pancreatic tumor development and progression. However, dysregulation of Notch signaling by post-translational modification of Notch receptors remains poorly understood. Here, we analyzed the Notch-modifying glycosyltransferase involved in the regulation of the ligand-dependent Notch signaling pathway. Bioinformatic analysis revealed that the expression of epidermal growth factor (EGF) domain-specific O-linked N-acetylglucosamine (EOGT) and Lunatic fringe (LFNG) positively correlates with a subset of Notch signaling genes in PDAC. The lack of EOGT or LFNG expression inhibited the proliferation and migration of Panc-1 cells, as observed by the inhibition of Notch activation. EOGT expression is significantly increased in the basal subtype, and low expression of both EOGT and LFNG predicts better overall survival in PDAC patients. These results imply potential roles for EOGT- and LFNG-dependent Notch signaling in PDAC.
Lignans of Sesame (Sesamum indicum L.): A Comprehensive Review
Authors: Andargie Mebeaselassie , Vinas Maria , Rathgeb Anna , Möller Evelyn , Karlovsky Petr
Published: February 2021

Major lignans of sesame sesamin and sesamolin are benzodioxol--substituted furofurans. Sesamol, sesaminol, its epimers, and episesamin are transformation products found in processed products. Synthetic routes to all lignans are known but only sesamol is synthesized industrially. Biosynthesis of furofuran lignans begins with the dimerization of coniferyl alcohol, followed by the formation of dioxoles, oxidation, and glycosylation. Most genes of the lignan pathway in sesame have been identified but the inheritance of lignan content is poorly understood. Health-promoting properties make lignans attractive components of functional food. Lignans enhance the efficiency of insecticides and possess antifeedant activity, but their biological function in plants remains hypothetical. In this work, extensive literature including historical texts is reviewed, controversial issues are critically examined, and errors perpetuated in literature are corrected. The following aspects are covered: chemical properties and transformations of lignans; analysis, purification, and total synthesis; occurrence in Seseamum indicum and related plants; biosynthesis and genetics; biological activities; health-promoting properties; and biological functions. Finally, the improvement of lignan content in sesame seeds by breeding and biotechnology and the potential of hairy roots for manufacturing lignans in vitro are outlined.
Molecules Present in Plant Essential Oils for Prevention and Treatment of Colorectal Cancer (CRC)
Authors: Petrocelli Giovannamaria , Farabegoli Fulvia , Valerii Maria Chiara , Giovannini Catia , Sardo Alberto , Spisni Enzo
Published: February 2021

Essential oils (EOs) are a complex mixture of hydrophobic and volatile compounds synthesized from aromatic plants, commonly present in the human diet. In recent years, many in vitro studies have suggested possible anticancer properties of single EO compounds, on colorectal cancer (CRC) cells. However, the majority of these studies did not compare the effects of these compounds on normal and cancer colon cells. By using NCM-460, a normal human mucosal epithelial cell line, Caco-2, a human colon epithelial adenocarcinoma cell line, and SW-620, colon cancer cells derived from lymph node metastatic site, we identified cinnamaldehyde, derived from cinnamon EO and eugenol, derived from bud clove EO, as compounds with a specific anticancer action selectively targeting the transformed colonic cells. Both cinnamaldehyde (75 µM) and eugenol (800 µM), after 72 h of treatment, were capable to induce apoptosis, necrosis and a cell cycle slowdown in Caco-2 and in SW-620, but not in NCM-460 cells. If associated with a targeted delivery to the colon, these two compounds could prove effective in the prevention or treatment of CRC.
An Estimation Algorithm for General Linear Single Particle Tracking Models with Time-Varying Parameters
Authors: Godoy Boris I. , Vickers Nicholas A. , Andersson Sean B.
Published: February 2021

Single Particle Tracking (SPT) is a powerful class of methods for studying the dynamics of biomolecules inside living cells. The techniques reveal the trajectories of individual particles, with a resolution well below the diffraction limit of light, and from them the parameters defining the motion model, such as diffusion coefficients and confinement lengths. Most existing algorithms assume these parameters are constant throughout an experiment. However, it has been demonstrated that they often vary with time as the tracked particles move through different regions in the cell or as conditions inside the cell change in response to stimuli. In this work, we propose an estimation algorithm to determine time-varying parameters of systems that discretely switch between different linear models of motion with Gaussian noise statistics, covering dynamics such as diffusion, directed motion, and Ornstein–Uhlenbeck dynamics. Our algorithm consists of three stages. In the first stage, we use a sliding window approach, combined with Expectation Maximization (EM) to determine maximum likelihood estimates of the parameters as a function of time. These results are only used to roughly estimate the number of model switches that occur in the data to guide the selection of algorithm parameters in the second stage. In the second stage, we use Change Detection (CD) techniques to identify where the models switch, taking advantage of the off-line nature of the analysis of SPT data to create non-causal algorithms with better precision than a purely causal approach. Finally, we apply EM to each set of data between the change points to determine final parameter estimates. We demonstrate our approach using experimental data generated in the lab under controlled conditions.
Dihydroquinolines, Dihydronaphthyridines and Quinolones by Domino Reactions of Morita-Baylis-Hillman Acetates
Authors: Annor-Gyamfi Joel K. , Ametsetor Ebenezer , Meraz Kevin , Bunce Richard A.
Published: February 2021

An efficient synthetic route to highly substituted dihydroquinolines and dihydronaphthyridines has been developed using a domino reaction of Morita-Baylis-Hillman (MBH) acetates with primary aliphatic and aromatic amines in DMF at 50–90 °C. The MBH substrates incorporate a side chain acetate positioned adjacent to an acrylate or acrylonitrile aza-Michael acceptor as well as an aromatic ring activated toward SNAr ring closure. A control experiment established that the initial reaction was an SN2′-type displacement of the side chain acetate by the amine to generate the alkene product with the added nitrogen nucleophile positioned trans to the SNAr aromatic ring acceptor. Thus, equilibration of the initial alkene geometry is required prior to cyclization. A further double bond migration was observed for several reactions targeting dihydronaphthyridines from substrates with a side chain acrylonitrile moiety. MBH acetates incorporating a 2,5-difluorophenyl moiety were found to have dual reactivity in these annulations. In the absence of O2, the expected dihydroquinolines were formed, while in the presence of O2, quinolones were produced. All of the products were isolated in good to excellent yields (72–93%). Numerous cases (42) are reported, and mechanisms are discussed.
Structure Controlling Factors of Oxido-Bridged Dinuclear Iron(III) Complexes
Authors: Hoshikawa Ryusei , Yoshida Kosuke , Mitsuhashi Ryoji , Mikuriya Masahiro , Okuno Takashi , Sakiyama Hiroshi
Published: February 2021

Oxido bridges commonly form between iron(III) ions, but their bond angles and symmetry vary with the circumstances. A large number of oxido-bridged dinuclear iron(III) complexes have been structurally characterized. Some of them belong to the C2 point group, possessing bent Fe–O–Fe bonds, while some others belong to the Ci symmetry, possessing the linear Fe–O–Fe bonds. The question in this study is what determines the structures and symmetry of oxido-bridged dinuclear iron(III) complexes. In order to gain further insights, three oxido-bridged dinuclear iron(III) complexes were newly prepared with 2,2′-bipyridine (bpy) and 1,10-phenanthroline (phen) ligands: [Fe2OCl2(bpy)4][PF6]2 (1), [Fe2O(NO3)2(bpy)4][PF6]2·0.6MeCN·0.2(2-PrOH) (2), and [Fe2OCl2(phen)4][PF6]2·MeCN·0.5H2O (3). The crystal structures of 1, 2, and 3 were determined by the single-crystal X-ray diffraction method, and all of them were found to have the bent Fe–O–Fe bonds. Judging from the crystal structure, some intramolecular interligand hydrogen bonds were found to play an important role in fixing the structures. Additional density functional theory (DFT) calculations were conducted, also for a related oxido-bridged dinuclear iron(III) complex with a linear Fe–O–Fe bond. We conclude that the Fe–O–Fe bridge tends to bend like a water molecule, but is often stretched by interligand steric repulsion, and that the structures are mainly controlled by the intramolecular interligand interactions.
Limitations of Linear Dichroism Spectroscopy for Elucidating Structural Issues of Light-Harvesting Aggregates in Chlorosomes
Authors: Günther Lisa M. , Knoester Jasper , Köhler Jürgen
Published: February 2021

Linear dichroism (LD) spectroscopy is a widely used technique for studying the mutual orientation of the transition-dipole moments of the electronically excited states of molecular aggregates. Often the method is applied to aggregates where detailed information about the geometrical arrangement of the monomers is lacking. However, for complex molecular assemblies where the monomers are assembled hierarchically in tiers of supramolecular structural elements, the method cannot extract well-founded information about the monomer arrangement. Here we discuss this difficulty on the example of chlorosomes, which are the light-harvesting aggregates of photosynthetic green-(non) sulfur bacteria. Chlorosomes consist of hundreds of thousands of bacteriochlorophyll molecules that self-assemble into secondary structural elements of curved lamellar or cylindrical morphology. We exploit data from polarization-resolved fluorescence-excitation spectroscopy performed on single chlorosomes for reconstructing the corresponding LD spectra. This reveals that LD spectroscopy is not suited for benchmarking structural models in particular for complex hierarchically organized molecular supramolecular assemblies.
Assessing the Functional Properties of TiZr Nanotubular Structures for Biomedical Applications, through Nano-Scratch Tests and Adhesion Force Maps
Authors: Vardaki Maria , Pantazi Aida , Demetrescu Ioana , Enachescu Marius
Published: February 2021

In this work we present the results of a functional properties assessment via Atomic Force Microscopy (AFM)-based surface morphology, surface roughness, nano-scratch tests and adhesion force maps of TiZr-based nanotubular structures. The nanostructures have been electrochemically prepared in a glycerin + 15 vol.% H2O + 0.2 M NH4F electrolyte. The AFM topography images confirmed the successful preparation of the nanotubular coatings. The Root Mean Square (RMS) and average (Ra) roughness parameters increased after anodizing, while the mean adhesion force value decreased. The prepared nanocoatings exhibited a smaller mean scratch hardness value compared to the un-coated TiZr. However, the mean hardness (H) values of the coatings highlight their potential in having reliable mechanical resistances, which along with the significant increase of the surface roughness parameters, which could help in improving the osseointegration, and also with the important decrease of the mean adhesion force, which could lead to a reduction in bacterial adhesion, are providing the nanostructures with a great potential to be used as a better alternative for Ti implants in dentistry.