bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultramicrobacteria in various fermented cabbages
Authors: Lee Hae-Won , Yoon So-Ra , Dang Yun-Mi , Kang Miran , Lee Kwang Ho , Ha Ji-Hyoung , Bae Jin-Woo 
Published: January 2022

AbstractLittle is known about the ultramicrobial communities of foods. Several bacteria, including pathogenic species, can form ultramicrobial communities when exposed to harsh conditions, making their detection via conventional culture techniques difficult. This study aimed to explore ultramicrobial communities within the microbial communities of fermented cabbage products, such as kimchi, sauerkraut, and suancai, which are produced through specific manufacturing methods based on the laws and culture of respective regions. We used single-molecule real-time sequencing with tangential flow filtration for fermented cabbages after pre-filtration and transmission electron microscopy to confirm the identity of ultramicrobacteria (UMB).To the best of our knowledge, this is the first study to identify the differences between ultramicrobial communities and microbial communities of fermented cabbages. Although the size of the ultramicrobial communities was smaller than that of the latter, their diversity was not lower. In addition, some UMB underwent cell shrinkage due to unfavorable environments, while others maintained their small size regardless. Major pathogens were not detected in the ultramicrobial communities of fermented cabbages. Nevertheless, several suspicious strains were detected. Our method can be used to screen food materials for the presence of UMB undetectable via conventional methods. Ultramicrobial and microbial communities were efficiently separated using tangential flow filtration and analyzed via single-molecule real-time sequencing. The ultramicrobial communities of fermented vegetables were different from conventional microbial communities. This study provides new insights into the ecology of UMB in foods.
Germinal center-derived broadly neutralizing antibodies adapt to SARS-CoV-2 antigenic drift
Authors: Shitaoka Kiyomi , Kawano Yohei , Higashiura Akifumi , Mizoguchi Yoko , Hashiguchi Takao , Nishimichi Norihisa , Huang Shiyu , Ito Ayano , Yamamoto Akima , Ohki Shun , Kanda Miyuki , Taniguchi Tomohiro , Yokosaki Yasuyuki , Okada Satoshi , Sakaguchi Takemasa , Yasuda Tomoharu 
Published: January 2022

AbstractThe outbreak of SARS-CoV-2 variant Omicron which harbors a striking number of mutations in the spike protein has been raising concerns about the effectiveness of vaccines and antibody treatment1. Here, we confirmed a substantial reduction in neutralizing potency against Omicron in all convalescent and vaccinated sera. However, we found that some people infected by the early strain show relatively higher neutralization to Omicron. From those B cells, we developed neutralizing antibodies inhibiting broad variants including Delta and Omicron. Unlike reported antibodies, one had an extremely large interface and widely covered receptor binding motif of spike, thereby interfering with diversified variants. Somatic mutations introduced by long-term germinal center reaction contributed to the key structure of antibodies and the universal interaction with spike variants. Recalling such rare B cells may confer sustainable protection against SARS-CoV-2 variants emerging one after another.
Automated phenol-chloroform extraction of high molecular weight genomic DNA for use in long-read single-molecule sequencing
Authors: Liu Andrew W. , Villar-Briones Alejandro , Luscombe Nicholas M. , Plessy Charles 
Published: January 2022

AbstractIn order to automate the genome sequencing pipeline in our laboratory, we programmed a dual-arm anthropomorphic robot, the Robotic Biology Institute’s Maholo LabDroid, to perform organic solvent-based genomic DNA extraction from cell lysates. To the best of our knowledge, this is the first time that automation of phenol-chloroform extraction has been reported. We achieved routine extraction of high molecular weight genomic DNA (>100 kb) from diverse biological samples including algae cultured in sea water, bacteria, whole insects, and human cell lines. The results of pulse-field electrophoresis size analysis and the N50 sequencing metrics of reads obtained from Nanopore MinION runs verified the presence of intact DNA suitable for direct sequencing. We present the workflow that can be used to program similar robots and discuss the problems and solutions we encountered in developing the workflow. The protocol can be adapted to analogous methods such as RNA extraction, and there is ongoing work to incorporate further post-extraction steps such as library construction. This work shows the potential for automated robotic workflows to free molecular biological researchers from manual interventions in routine experimental work. A time-lapse movie of the entire automated run can be seen at http://doi.org/10.6084/m9.figshare.17097065
Genetic basis and adaptive implications of temperature-dependent and temperature-independent effects of drought on chickpea phenology
Authors: Li Yongle , Lake Lachlan , Chauhan Yashvir S. , Taylor Julian , Sadras Victor O. 
Published: January 2022

AbstractWater deficit often hastens flowering of pulses partially because droughted plants are hotter. Separating temperature-independent and temperature-dependent effects of drought is important to understand, model and manipulate phenology genetically and agronomically.We define a new trait, drought effect on phenology (DEP = difference in flowering time between irrigated and rainfed crops), and use FST genome scan to probe for genomic regions under selection for this trait. Genomic regions overlapping for early- and late-sown crops would associate with temperature-independent effects and non-overlapping genomic regions would associate with temperature-dependent effects.Time to flowering shortened with increasing water stress quantified with carbon isotope composition. Genomic regions on chromosomes 4, 5, 7 and 8 were under selection for DEP. An overlapping region for early and late sowing on chromosome 8 revealed a temperature-independent effect with four candidate genes: BAM1, BAM2, HSL2 and ANT. The non-overlapping regions included six candidate genes: EMF1, EMF2, BRC1/TCP18, BZR1, NPGR1 and ERF1.Modelling to assess DEP adaptive value showed it reduces the likelihood of drought and heat stress at the expense of cold risk. Accounting for DEP would improve phenology models to predict adaptation to future climates and breeding against the combined risks of drought, heat, and cold stress.HighlightPredictive and genetic models that overlook drought effects on phenology can return biased predictions of adaptation to future climates. Here we study the genetic causes and adaptive consequences of hastened flowering under drought.
Parameterization and Application of the General Amber Force Field to Model Fluro Substituted Furanose Moieties and Nucleosides
Authors: Escalante Diego E. , Aldrich Courtney C. , Ferguson David M. 
Published: January 2022

AbstractMolecular mechanics force field calculations have historically shown significant limitations in modeling the energetic and conformational interconversions of highly substituted furanose rings. This is primarily due to the gauche effect that is not easily captured using pairwise energy potentials. In this study, we present a refinement to the set of torsional parameters in the General Amber Force Field (gaff) used to calculate the potential energy of mono, di-, and gem-fluorinated nucleosides. The parameters were optimized to reproduce the pseudorotation phase angle and relative energies of a diverse set of mono- and difluoro substituted furanose ring systems using quantum mechanics umbrella sampling techniques available in the IpolQ engine in the Amber suite of programs. The parameters were developed to be internally consistent with the gaff force field and the TIP3P water model. The new set of angle and dihedral parameters and partial charges were validated by comparing the calculated phase angle probability to those obtained from experimental nuclear magnetic resonance experiments.
Emodin Combined with Multiple Low-frequency Low-intensity Ultrasound to Relieve Osteomyelitis Through Sonoantimicrobial Chemotherapy
Authors: Lu Feng , Wu Xinhui , Hu Huiqun , He Zixuan , Sun Jiacheng , Zhang Jiapeng , Song Xiaoting , Jin Xiangang , Chen Guofu 
Published: January 2022

ABSTRACTTreatment of osteomyelitis is still challenging as conventional antibiotic therapy is limited by the emergence of resistant strains and the formation of biofilms. Sonoantimicrobial chemotherapy (SACT) is a novel therapy of low-frequency and low-intensity ultrasound (LFLIU) combined with sonosensitizer. Therefore, in our study, a sonosensitizer named emodin (EM) was proposed to be combined with LFLIU to relieve acute osteomyelitis caused by Methicillin-resistant Staphylococcus aureus (MRSA) through synergistic antibacterial and anti-biofilm effects. The efficiency of different intensities of ultrasound, single (S-LFLIU, 15 min) and multiple ultrasound (M-LFLIU, 5 min every 4 h, three times) against bacteria and biofilm was compared, contributing to develop the best treatment regimen. Our results demonstrated that EM plus S-LFLIU or M-LFLIU (EM+S-LFLIU or EM+M-LFLIU) have significant synergetic bactericidal and anti-biofilm effects and EM+M-LFLIU exhibits superior performance in anti-biofilm. Furthermore, it was suggested that EM+M-LFLIU could produce a large amount of reactive oxygen species (ROS), destroy the integrity of bacterial membrane and wall, down-regulate the expression of oxidative stress, membrane wall synthesis, bacterial virulence and other related genes (agrB, PBP3, sgtB, GMK, zwf, msrA). In vivo study, micro-CT, H&E staining, ELISA assay and bacterial quantification of bone tissue indicated that EM+M-LFLIU could also relieve osteomyelitis of MRSA infection. Our work proffers an original treating bacterial osteomyelitis approach that weakens drug-resistant bacterial and suppresses biofilm formation through SACT, which may provide new prospects for clinical treatment.
Effect of SARS-CoV-2 spike mutations on its activation by TMPRSS2 and TMPRSS13
Authors: Stevaert Annelies , Van Berwaer Ria , Raeymaekers Valerie , Laporte Manon , Naesens Lieve 
Published: January 2022

ABSTRACTThe continuous emergence of new SARS-CoV-2 variants urges better understanding of the functional motifs in the spike (S) protein and their tolerance towards mutations. We here focus on the S2’ motif which, during virus entry, requires cleavage by a cell surface protease to release the fusion peptide. Though belonging to an immunogenic region, the SARS-CoV-2 S2’ motif (811-KPSKR-815) has shown hardly any variation, with its three basic (K/R) residues being >99.99% conserved thus far. By creating a series of mutant S-pseudotyped viruses, we show that K814, which precedes the scissile R815 residue, is dispensable for SARS-CoV-2 spike activation by TMPRSS2 but not TMPRSS13. The latter protease lost its activity towards SARS-CoV-2 S when the S2’ motif was swapped with that of the low pathogenic 229E coronavirus (685-RVAGR-689) and also the reverse effect was seen. This swap had no impact on TMPRSS2 activation. Also in the MERS-CoV spike, introducing a dibasic scissile motif was fully accepted by TMPRSS13 but less so by TMPRSS2. Our findings are the first to demonstrate which S2’ residues are important for SARS-CoV-2 spike activation by these two airway proteases, with TMPRSS13 exhibiting higher preference for K/R rich motifs than TMPRSS2. This preemptive insight can help to estimate the impact of S2’ motif changes as they may appear in new SARS-CoV-2 variants.IMPORTANCESince the start of the COVID-19 pandemic, SARS-CoV-2 is undergoing worldwide selection with frequent appearance of new variants. The surveillance would benefit from proactive characterization of the functional motifs in the spike protein, the most variable viral factor. This is linked to immune evasion but also influences spike functioning in a direct manner. Remarkably, though located in a strong immunogenic region, the S2’ cleavage motif has, thus far, remained highly conserved. This suggests that its amino acid sequence is critical for spike activation by airway proteases. To investigate this, we assessed which S2’ site mutations affect processing by TMPRSS2 and TMPRSS13, two main activators of the SARS-CoV-2 spike. Being the first in its kind, our study will help to assess the biological impact of S2’ site variations as soon as they are detected during variant surveillance.
Risk factors and survival in patients with COVID-19 in northeastern Brazil
Authors: Fernandes Ana Tereza do N S F , Rodrigues Eujessika K. , Araújo Eder R. , Formiga Magno F. , Sá Horan Priscilla K. , Ferreira Ana Beatriz N. S. , Barbosa Humberto A. , Barbosa Paulo S. 
Published: January 2022

AbstractBACKGROUNDCountries have focused research on developing strategies to fight COVID-19, prevent hospitalizations, and maintain economic activities.OBJECTIVEThis study aimed to establish a survival analysis and identify risk factors for patients with COVID-19 in a upper middle-income city in Brazil.METHODSWe performed a retrospective cohort study with 280 hospitalized patients with COVID-19. The eCOVID platform provided data used to monitor COVID-19 cases and help communication between professionals.RESULTSSurvival analysis showed that age ≥ 65 years was associated with decreased survival (54.8%). Females had lower survival rate than males (p=0.01). Regarding risk factors, urea concentration (p<0.001), hospital LOS (p=0.002), oxygen concentration (p=0.005), and age (p=0.02) were associated with death.CONCLUSIONAge, hospital LOS, high blood urea concentration, and low oxygen concentration were associated with death by COVID-19 in the studied population. These findings corroborate with studies conducted in research centers worldwide.Key FindingsSome parameters assessed during hospital admission may identify patients with COVID-19 with high risk of progressing to severe conditions and early identification of risk factors and continuous monitoring of laboratory tests may prevent progression to severe disease.Key ImplicationsKnowledge regarding main signs and symptoms of COVID-19 and associated risk factors helps the population manage and monitor the disease at home and identify early signs of severity. Also, more information about COVID-19, such as prevalence, specific characteristics in certain regions, and treatments, must become public to encourage the population to participate in the control and contingency of the pandemic.
COVID-19 vaccine attitude and its predictors among people living with chronic health conditions in Ibadan, Nigeria
Authors: Ojewale Lucia Yetunde , Afolabi Rotimi Felix , Ogunniyi Adesola 
Published: January 2022

AbstractsBackgroundGlobally COVID-19 has caused death among millions of people and new cases continue to be reported daily, including in Nigeria. With the efforts of the Nigerian government to ensure everyone gets vaccinated, the vaccination attitude and its predictors among persons with chronic health conditions remains unclear. The study was therefore conducted to assess vaccination attitude and determine its associated factors among people living with chronic health conditions.MethodsA descriptive cross-sectional study was conducted among 423 patients attending the medical outpatient clinic of University College Hospital, Ibadan, Oyo State, Nigeria; before COVID-19 vaccination commencement. Data were collected on socio-demographic and COVID-19 related characteristics, via Open Data Kit (ODK) software. The Vaccine Attitude Examination (Vax) Scale including its four subscales was adopted to assess attitude towards COVID-19 vaccine uptake. The main outcome was vaccine attitude status defined as positive if a VAX sum score was above the median value; otherwise, non-positive’. Data were analysed using Chi-square and multivariate logistic regression analyses at 5% significance level.ResultsHypertension (27.4%), diabetes mellitus (22.0%) and heart conditions/diseases (19.6%) were the top three conditions being managed by the participants. The overall proportion of patients with a positive attitude towards the uptake of COVID-19 vaccination was 46.6%; while 29.6% trusted the vaccine benefit, 46.6% were not worried about the aftermath effect of the vaccine and 11.1% were not concerned about the vaccine commercial profiteering. Factors associated with overall vaccine attitude were level of education, income, knowledge of COVID-19, living room arrangement, and confidence in government (p<0.05). The main influential factor on general vaccine positive attitude and the four subscales was confidence in the government.ConclusionLess than half of people living with a chronic medical condition had a positive attitude towards the COVID vaccine. The attitudes are mediated strongly by confidence in the government and several sociodemographic and COVID related characteristics. A lot still needs to be done to achieve the prescribed herd immunity.
A machine learning approach to identifying important features for achieving step thresholds in individuals with chronic stroke
Authors: Miller Allison E. , Russell Emily , Reisman Darcy S. , Kim Hyosub E. , Dinh Vu 
Published: January 2022

AbstractBackgroundWhile many factors are associated with stepping activity after stroke, there is significant variability across studies. One potential reason for this variability is that there are some characteristics necessary to achieve greater stepping activity that differ from others that may need to be targeted to improve stepping activity.ObjectiveUsing two step thresholds (2500 steps/day, corresponding to home vs. community ambulation and 5500 steps/day, corresponding to achieving physical activity guidelines through walking), we applied 3 different algorithms to determine which predictors are most important to achieve these thresholds.MethodsWe analyzed data from 268 participants with stroke that included 25 demographic, performance-based and self-report variables. Step 1 of our analysis involved dimensionality reduction using lasso regularization. Step 2 applied drop column feature importance to compute the mean importance of each variable. We then assessed which predictors were important to all 3 mathematically unique algorithms.ResultsThe number of relevant predictors was reduced from 25 to 7 for home vs. community and from 25 to 16 for aerobic thresholds. Drop column feature importance revealed that 6 Minute Walk Test and speed modulation were the only variables found to be important to all 3 algorithms (primary characteristics) for each respective threshold. Other variables related to readiness to change activity behavior and physical health, among others, were found to be important to one or two algorithms (ancillary characteristics).ConclusionsAddressing physical capacity is necessary but not sufficient to achieve important step thresholds, as ancillary characteristics, such as readiness to change activity behavior and physical health may also need to be targeted. This delineation may explain heterogeneity across studies examining predictors of stepping activity in stroke.
Application of biophysical methods for improved protein production and characterization: a case study on an HtrA-family bacterial protease
Authors: Ronzetti Michael , Baljinnyam Bolormaa , Jalal Ishrat , Pal Utpal , Simeonov Anton 
Published: January 2022

AbstractThe high temperature requirement A (HtrA) serine protease family presents an attractive target class for antibacterial therapeutics development. These proteins possess dual protease and chaperone functions and contain numerous binding sites and regulatory loops, displaying diverse oligomerization patterns dependent on substrate type and occupancy. HtrA proteins that are natively purified coelute with contaminating peptides and activating species, shifting oligomerization and protein structure to differently activated populations. Here, a redesigned HtrA production results in cleaner preparations with high yields by overexpressing and purifying target protein from inclusion bodies under denaturing conditions, followed by a high-throughput screen for optimal refolding buffer composition using function-agnostic biophysical techniques that do not rely on target-specific measurements. We use the Borrelia burgdorferi HtrA to demonstrate the effectiveness of our function-agnostic approach, while characterization with both new and established biophysical methods shows the retention of proteolytic and chaperone activity of the refolded protein. This systematic workflow and toolset will translate to the production of HtrA-family proteins in higher quantities of pure and monodisperse composition than the current literature standard, with applicability to a broad array of protein purification strategies.StatementThe production of a therapeutically-relevant protein family sensitive to coeluting contaminants is greatly improved by optimized expression and refolding workflow. A miniaturized, high-throughput system supported by a function-agnostic biophysics assay and modified data analysis scripts results in a refolded protein that is highly pure, monodisperse, and retains proteolytic and chaperone activity. This approach has broad applicability towards hard-to-express proteins and proteins sensitive to coeluting species. Additionally, novel methods are presented to characterize protein chaperone activity.
TheVibrio vulnificusstressosome is dispensable in nutrient-replete conditions
Authors: Cutugno Laura , Mc Cafferty Jennifer , Pané-Farré Jan , O’Byrne Conor , Boyd Aoife 
Published: January 2022

ABSTRACTThe stressosome is a protein complex that has been demonstrated to sense environmental stresses and mediate the stress response in several Gram-positive bacteria, through the activation of the alternative sigma factor SigB. The in vivocharacterisation of this complex has never been performed inVibrio vulnificusor any other bacteria that do not possess SigB. The elucidation of the role of the stressosome inV. vulnificuswould provide elements to elaborate a functional model of the complex in a Gram-negative bacterium and identify the regulatory output in the absence of SigB. The stressosome locus is only found in 44% ofVibrio vulnificusisolates raising the question as to whether the role of stressosome is essential or modulatory in this bacterial species.In this work, the expression of the stressosome genes was proven in nutrient-replete conditions and the co-transcription as one operonic unit of the stressosome locus and its putative downstream regulatory locus was demonstrated.Moreover, the construction of a stressosome mutant lacking the four genes constituting the stressosome complex allowed us to examine the role of this complexin vivo. The initial established mutagenesis strategy relied on rifampicin-resistantV. vulnificusto select recombinant bacteria. Our data clearly showed that the influence of the RifRallele on stress and virulence characteristics overshadowed any effects of the stressosome. Therefore, we established an alternative mutagenesis strategy with a non-modifiedV. vulnificusparental strain and a DAP auxotrophicE. colidonor strain. Extensive phenotypic characterisation of the successfully-generated mutant in nutrient-replete conditions showed that the stressosome does not significantly contribute to the growth, ofV. vulnificus. The stressosome did not modulate the response ofV. vulnificusto the range of stresses tested – Ethanol, osmolarity, temperature, and salinity. Furthermore, the stressosome is dispensable for motility and exoenzyme production ofV. vulnificus.