bluuebunny/crossref_metadata_2025 huggingface dataset:
Coronary Revascularization for Patients with Diabetes Mellitus
Authors: EL-Andari Ryaan , Bozso Sabin J. , Fialka Nicholas M. , Kang Jimmy J. H. , Nagendran Jayan , Nagendran Jeevan
Published: January 2022

Objective:

This systematic review and meta-analysis aims to review the contemporary literature comparing CABG and PCI in diabetic patients providing an up-to-date perspective on the differences between the interventions.

Background:

Diabetes is common and diabetic patients are at a 2-to-4-fold increased risk of developing coronary artery disease. Approximately 75% of diabetic patients die of cardiovascular disease. Previous literature has identified CABG as superior to PCI for revascularization in diabetic patients with complex coronary artery diseas.

Methods:

PubMed and Medline were systematically searched for articles published from January 1, 2015 to April 15, 2021. This systematic review included all retrospective, prospective, and randomized trial studies comparing CABG and PCI in diabetic patients. 1552 abstracts were reviewed and 25 studies were included in this review. The data was analyzed using the RevMan 5.4 software.

Results:

Diabetic patients undergoing CABG experienced significantly reduced rates of 5-year mortality, major adverse cardiovascular and cerebrovascular events, myocardial infarction, and required repeat revascularization. Patients who underwent PCI experienced improved rates of stroke that trended toward significance.

Conclusions:

Previous literature regarding coronary revascularization in diabetic patients has consistently demonstrated superior outcomes for patients undergoing CABG over PCI. The development of 1st and 2nd generation DES have narrowed the gap between CABG and PCI, but CABG continues to be superior. Continued investigation with large randomized trials and retrospective studies including long term follow-up comparing CABG and 2nd generation DES is necessary to confirm the optimal intervention for diabetic patients.
Serum DUPAN-2 could be an Alternative Biological Marker for CA19-9 Nonsecretors with Pancreatic Cancer
Authors: Omiya Kojiro , Oba Atsushi , Inoue Yosuke , Kobayashi Kosuke , Wu Y.H. Andrew , Ono Yoshihiro , Sato Takafumi , Sasaki Takashi , Ozaka Masato , Sasahira Naoki , Ito Hiromichi , Saiura Akio , Takahashi Yu
Published: January 2022

Objective:

This study investigates the use of serum DUPAN-2 in predicting the PC progression in CA19-9 nonsecretors.

Background:

Although we previously reported that serum CA19-9 >500U/ mL is a poor prognostic factor and an indication for enhanced neoadjuvant treatment, there is not a biomarker surrogate that equivalently predicts prognosis for CA19-9 nonsecretors.

Methods:

We evaluated consecutive PC patients who underwent pancreatectomy from 2005 to 2019. All patients were categorized as either nonsecretor or secretor (CA19-9 ≤ or >2.0U/mL).

Results:

Of the 984 resected PC patients, 94 (9.6%) were nonsecretors and 890 (90.4%) were secretors. The baseline characteristics were not statistically different between the 2 groups except for the level of DUPAN-2 (720 vs. 100U/mL, P < 0.001). Survival curves after resection were similar between the 2 groups (29.4 months vs. 31.3 months, P = 0.900). Survival curves of patients with DUPAN-2 >2000U/mL in the nonsecretors and patients with CA19-9 >500U/mL in the secretors were nearly equivalent as well (hazard ratio 2.08 vs. 1.89). In the multivariate analysis, DUPAN-2 >2000U/mL (hazard ratio 2.53, P = 0.010) was identified as independent prognostic factor after resection.

Conclusion:

DUPAN-2 >2000U/mL in CA19-9 nonsecretors can be an unfavorable factor that corresponds to CA19-9 >500U/mL in CA19-9 secretors which is an indicator for enhanced neoadjuvant treatment. The current results shed light on the subset of nonsecretors with poor prognosis that were traditionally categorized in a group with a more favorable prognosis group.
A Population-based Analysis of the COVID-19 Generated Surgical Backlog and Associated Emergency Department Presentations for Inguinal Hernias and Gallstone Disease
Authors: Gomez David , Nantais Jordan , Telesnicki Teagan , de Mestral Charles , Wilton Andrew S. , Stukel Therese A. , Urbach David R. , Baxter Nancy N.
Published: January 2022

Objective:

To evaluate the downstream effects of the COVID-19 generated surgical backlog.

Background:

Delayed elective surgeries may result in emergency department (ED) presentations and the need for urgent interventions.

Methods:

Population-based repeated cross-sectional study utilizing administrative data. We quantified rates of elective cholecystectomy and inguinal hernia repair and rates of ED presentations, urgent interventions, and outcomes during the first and second waves of COVID-19 (March 1, 2020- February 28, 2021) as compared to a 3-year pre-COVID-19 period (January 1, 2017-February 29, 2020) in Ontario, Canada. Poisson generalized estimating equation models were used to predict expected rates during COVID-19 based on the pre-COVID-19 period. The ratio of observed (actual events) to expected rates was generated for surgical procedures (SRRs) and ED visits (ED-RRs).

Results:

We identified 74,709 elective cholecystectomies and 60,038 elective inguinal hernia repairs. During the COVID-19 period, elective inguinal hernia repairs decreased by 21% (SRR 0.791; 0.760–0.824) whereas elective cholecystectomies decreased by 23% (SRR 0.773; 0.732–0.816). ED visits for inguinal hernia decreased by 17% (ED-RR 0.829; 0.786 - 0.874) whereas ED visits for gallstones decreased by 8% (ED-RR 0.922; 0.878 - 0.967). A higher population rate of urgent cholecystectomy was observed, particularly after the first wave (SRR 1.076; 1.000–1.158). No difference was seen in inguinal hernias.

Conclusions:

An over 20% reduction in elective surgeries and an increase in urgent cholecystectomies was observed during the COVID-19 period suggesting a rebound effect secondary to the surgical backlog. The COVID-19 generated surgical backlog will have a heterogeneous downstream effect with significant implications for surgical recovery planning.
Individual and neighborhood level characteristics of pediatric firearm injuries presenting at trauma centers in Colorado
Authors: Stevens Jenny , Leonard Jan , Reppucci Marina L. , Schroeppel Thomas , Bensard Denis , Haasz Maya
Published: January 2022

BACKGROUND

Firearm injuries are the second leading cause of death among children and adolescents in the United States. In Colorado, firearm injuries have surpassed motor vehicle accidents as the leading cause of death in youth. Local research is necessary to characterize risk factors associated with pediatric firearm injuries. We sought to categorize demographics, neighborhood characteristics, and trends in pediatric firearm injuries in Colorado.

METHODS

A review of pediatric firearm-injured patients (18 years or younger) evaluated at four trauma centers in Colorado from 2008 to 2019 was conducted. Clinical information, injury intent, and demographics were collected. Patient addresses were geocoded to census tracts to obtain neighborhood-level characteristics. Annual trends in firearm injury incidence per trauma evaluation were analyzed using regression modeling.

RESULTS

There were 446 firearm injuries during the study period. The median age was 16 years, and 87.0% were male. Assault was the most common injury intent (64.6%), and 92.0% of patients were from metropolitan (rural-urban continuum code 1–3) areas. Neighborhoods associated with firearm injuries were characterized by lower median household income ($47,112 vs. $63,443, p < 0.001) and higher levels of poverty (19.1% vs. 9.4%, p < 0.001) compared with median state levels. There was a 14.0% increase in firearm injuries compared with overall trauma evaluations for each year in the study period (incidence rate ratio, 1.14; 95% confidence interval, 1.08–1.20; p < 0.001).

CONCLUSION

The incidence of pediatric firearm injuries increased significantly from 2008 to 2019 compared with overall trauma evaluations in Colorado. Children and adolescents who live in more socially vulnerable neighborhoods are disproportionately impacted, and injury prevention resources should be focused on these communities.

LEVEL OF EVIDENCE

Prognostic and Epidemiolgic; Level III.
Design and Methods of the Validating Injury to the Renal Transplant Using Urinary Signatures (VIRTUUS) Study in Children
Authors: Kumar Juhi , Contrepois Kévin , Snyder Michael , Grimm Paul C. , Moudgil Asha , Smith Jodi M. , Bobrowski Amy E. , Verghese Priya S. , Hooper David , Ingulli Elizabeth , Lestz Rachel , Weng Patricia , Reason Janaiya L. , Blydt-Hansen Tom D. , Suthanthiran Manikkam , Keating Brendan , Amaral Sandra
Published: January 2022

Background.

Lack of noninvasive diagnostic and prognostic biomarkers to reliably detect early allograft injury poses a major hindrance to long-term allograft survival in pediatric kidney transplant recipients.

Methods.

Validating Injury to the Renal Transplant Using Urinary Signatures Children’s Study, a North American multicenter prospective cohort study of pediatric kidney transplant recipients, aims to validate urinary cell mRNA and metabolite profiles that were diagnostic and prognostic of acute cellular rejection (ACR) and BK virus nephropathy (BKVN) in adult kidney transplant recipients in Clinical Trials in Organ Transplantation-4. Specifically, we are investigating: (1) whether a urinary cell mRNA 3-gene signature (18S-normalized CD3ε, CXCL10 mRNA, and 18S ribosomal RNA) discriminates biopsies with versus without ACR, (2) whether a combined metabolite profile with the 3-gene signature increases sensitivity and specificity of diagnosis and prognostication of ACR, and (3) whether BKV-VP1 mRNA levels in urinary cells are diagnostic of BKVN and prognostic for allograft failure.

Results.

To date, 204 subjects are enrolled, with 1405 urine samples, including 144 biopsy-associated samples. Among 424 urine samples processed for mRNA, the median A260:280 ratio (RNA purity) was 1.91, comparable with Clinical Trials in Organ Transplantation-4 (median 1.82). The quality control failure rate was 10%. Preliminary results from urine supernatant showed that our metabolomics platform successfully captured a broad array of metabolites. Clustering of pool samples and overlay of samples from various batches demonstrated platform robustness. No study site effect was noted.

Conclusions.

Multicenter efforts to ascertain urinary biomarkers in pediatric kidney transplant recipients are feasible with high-quality control. Further study will inform whether these signatures are discriminatory and predictive for rejection and infection.
Turicibacter bilis sp. nov., a novel bacterium isolated from the chicken eggshell and swine ileum
Authors: Maki Joel J. , Looft Torey
Published: January 2022

Three novel, anaerobic, Gram-positive bacteria were isolated from the eggshell of two separate white leghorn chicken flocks and the ileum of a healthy pig, and designated MMM721T, ISU324 and PIG517 respectively. Cells were pleomorphic and capable of forming long chains of rods or coccoid clusters. Phylogenetic analysis of the 16S rRNA gene sequences identified these strains to be within the genus

Turicibacter

, of which only one species,

Turicibacter sanguinis

, has been formally described. However, whole genome sequencing of novel isolates returned a digital DNA–DNA hybridization value of 22.5 % and average nucleotide identity (ANI) values of 76.4 % (ANIb) and 86.0 % (ANIm), indicating divergence between the type strain MMM721T and

T. sanguinis

, suggesting the strains represented a novel species. The major fatty acid methyl esters of strain MMM721T were C16 : 0, C18 : 1 ω7c and C18 : 0. The strains mainly produced the volatile fatty acid lactate, along with smaller amounts of acetate and butyrate. Together, these data indicate that MMM721T, along with ISU324 and PIG517, represent a novel species within the genus

Turicibacter

. We propose the name Turicibacter bilis sp. nov. for the species. The type strain is MMM721T (=ATCC TSD-238T=CCUG 74757T).
Streptomyces caniscabiei sp. nov., which causes potato common scab and is distributed across the world
Authors: Nguyen Hien P. , Weisberg Alexandra J. , Chang Jeff H. , Clarke Christopher R.
Published: January 2022

Fourteen strains of

Streptomyces

isolated from scab lesions on potato are described as members of a novel species based on genetic distance, morphological observation and biochemical analyses. Morphological and biochemical characteristics of these strains are distinct from other described phytopathogenic species. Strain NE06-02DT has white aerial mycelium and grey, cylindrical, smooth spores on rectus-flexibilis spore chains. Members of this species group can utilize most of the International

Streptomyces

Project sugars, utilize melibiose and trehalose, produce melanin, grow on 6–7 % NaCl and pH 5–5.5 media, and are susceptible to oleandomycin (100 µg ml−1), streptomycin (20 µg ml−1) and penicillin G (30 µg ml−1). Though the 16S rRNA gene sequences from several members of this novel species are identical to the

Streptomyces bottropensis

16S rRNA gene sequence, whole-genome average nucleotide identity and multi-locus sequence analysis confirm that the strains are members of a novel species. Strains belonging to this novel species have been isolated from the United States, Egypt and China with the earliest known members being isolated in 1961 from common scab lesions of potato in both California, USA, and Maine, USA. The name Streptomyces caniscabiei sp. nov. is proposed for strain NE06-02DT (=DSM111602T=ATCC TSD-236T) and the other members of this novel species group.
Genome diversity of domesticated Acinetobacter baumannii ATCC 19606T strains
Authors: Artuso Irene , Lucidi Massimiliano , Visaggio Daniela , Capecchi Giulia , Lugli Gabriele Andrea , Ventura Marco , Visca Paolo
Published: January 2022

Acinetobacter baumannii

has emerged as an important opportunistic pathogen worldwide, being responsible for large outbreaks for nosocomial infections, primarily in intensive care units.

A. baumannii

ATCC 19606T is the species type strain, and a reference organism in many laboratories due to its low virulence, amenability to genetic manipulation and extensive antibiotic susceptibility. We wondered if frequent propagation of

A. baumannii

ATCC 19606T in different laboratories may have driven micro- and macro-evolutionary events that could determine inter-laboratory differences of genome-based data. By combining Illumina MiSeq, MinION and Sanger technologies, we generated a high-quality whole-genome sequence of

A. baumannii

ATCC 19606T, then performed a comparative genome analysis between

A. baumannii

ATCC 19606T strains from several research laboratories and a reference collection. Differences between publicly available ATCC 19606T genome sequences were observed, including SNPs, macro- and micro-deletions, and the uneven presence of a 52 kb prophage belonging to genus Vieuvirus. Two plasmids, pMAC and p1ATCC19606, were invariably detected in all tested strains. The presence of a putative replicase, a replication origin containing four 22-mer direct repeats, and a toxin-antitoxin system implicated in plasmid stability were predicted by in silico analysis of p1ATCC19606, and experimentally confirmed. This work refines the sequence, structure and functional annotation of the

A. baumannii

ATCC 19606T genome, and highlights some remarkable differences between domesticated strains, likely resulting from genetic drift.
Do water and host size interactively affect the impact of a native hemiparasite on a major invasive legume?
Authors: Cirocco Robert M. , Facelli Evelina , Facelli José M.
Published: January 2022

It is unknown how the combined effects of host size and water availability influence parasitic plant:host associations. This is a major gap considering that parasitic plants would frequently encounter hosts of different size growing in different water conditions in nature. In a glasshouse experiment, small or largeUlex europaeus(major invasive host) were provided high or low water supply and infected or not with the Australian native shoot hemiparasitic vine,Cassytha pubescens. Infection significantly decreased host total, shoot and root biomass, in both low water and high water conditions but more severely so in the latter. Infection also significantly decreased total biomass of both large and small plants and more severely so for the latter. Infection significantly decreased host foliar nitrogen and potassium concentrations in well-watered but not in low water conditions. Infection significantly suppressed host predawn and midday quantum yield, midday electron transport rates, foliar phosphorus concentration and nodule biomass, irrespective of water conditions or host size. Parasite biomass (including g-1host total biomass) was significantly greater on hosts growing in well-watered than in low water conditions. Our results suggest that some native parasitic plants may effectively control major invasive hosts, particularly in wetter habitats and or when the host is small, leading to enhanced biodiversity protection in those settings.
Hijacking Methyl Reader Proteins for Nuclear-Specific Protein Degradation
Authors: Nalawansha Dhanusha A. , Li Ke , Hines John , Crews Craig M.
Published: January 2022

Targeted protein degradation (TPD) by PROTACs is a promising strategy to control disease-causing protein levels within the cell. While TPD is emerging as an innovative drug discovery paradigm, there are currently only a limited number of E3 ligase: ligand pairs that are employed to induce protein degradation. Herein, we report a novel approach to induce protein degradation by hijacking a methyl reader: E3 ligase complex. L3MBTL3 is a methyl lysine reader protein that binds to the Cul4DCAF5 E3 ligase complex and targets methylated proteins for proteasomal degradation. By co-opting this natural mechanism, we report the design and biological evaluation of L3MBTL3-recruiting PROTACs and demonstrate nuclear-specific degradation of FKBP12 and BRD2. We envision this as a generalizable approach to utilize other reader protein-associated E3 ligase complexes in PROTAC design to expand the E3 ligase toolbox and explore the full potential of TPD.
Antibodies targeting conserved non-canonical antigens and endemic coronaviruses associate with favorable outcomes in severe COVID-19
Authors: Peddireddy Sai Preetham , Rahman Syed A. , Cillo Anthony R. , Vijay Godhev Manakkat , Somasundaram Ashwin , Workman Creg J. , Bain William , McVerry Bryan J. , Methe Barbara , Lee Janet S. , Ray Prabir , Ray Anuradha , Bruno Tullia C. , Vignali Dario A. A. , Kitsios Georgios D. , Morris Alison , Singh Harinder , Sarkar Aniruddh , Das Jishnu
Published: January 2022

While there have been extensive analyses characterizing cellular and humoral responses across the severity spectrum in COVID-19, predictors of outcomes within severe COVID-19 remain to be comprehensively elucidated. Recently, we identified divergent monocyte states as predictors of outcomes within severe COVID-19, but corresponding humoral profiles of risk have not been delineated. Furthermore, the nature of antibodies (Abs) directed against viral antigens beyond the spike protein or endemic coronavirus antigens and their associations with disease severity and outcomes remain poorly defined. We performed deep molecular profiling of Abs directed against a wide range of antigenic specificities in severe COVID-19 patients admitted to the ICU. The profiles consisted of canonical (S, RBD, N) and non-canonical (orf3a, orf8, nsp3, nps13 and M) antigenic specificities. Notably, multivariate machine learning (ML) models, generated using profiles of Abs directed against canonical or non-canonical antigens, were equally discriminative of recovery and mortality COVID-19 outcomes. In both ML models, survivors were associated with increased virus-specific IgA and IgG3 antibodies and with higher antigen-specific antibody galactosylation. Intriguingly, pre-pandemic healthy controls had cross-reactive Abs directed against nsp13 which is a conserved protein in other alpha and beta coronaviruses. Notably, higher levels of nsp13-specific IgA antibodies were associated with recovery in severe COVID-19. In keeping with these findings, a model built on Ab profiles for endemic coronavirus antigens was also predictive of COVID-19 outcome bifurcation, with higher levels of IgA and IgG3 antibodies against OC43 S and NL63 S being associated with survival. Our results suggest the importance of Abs targeting non-canonical SARS-CoV-2 antigens as well as those directed against endemic coronaviruses in favorable outcomes of severe COVID-19.
Dopamine D1-like receptor blockade and stimulation decreases operant responding for nicotine and food in male and female rats
Authors: Chellian Ranjithkumar , Behnood-Rod Azin , Wilson Ryann , Lin Karen , King Grace Wing-Yan , Ruppert-Gomez Marcella , Teter Alexandria Nicole , Bruijnzeel Adriaan W.
Published: January 2022

Dopamine has been implicated in smoking, but there remains a need for a better understanding of the effects of dopamine D1-like receptor agonists on nicotine intake and the role of sex in the effects of dopaminergic drugs on nicotine intake. This work studied the effects of D1-like receptor stimulation and blockade on operant responding for nicotine and food and locomotor activity in male and female rats. The effects of the D1-like receptor antagonist SCH 23390 (0.003, 0.01, 0.03 mg/kg) and the D1-like receptor agonist A77636 (0.1, 0.3, 1 mg/kg) on responding for nicotine and food, and locomotor activity were investigated. The effects of SCH 23390 were investigated 15 min and 24 h after treatment, and the effects of the long-acting drug A77636 were investigated 15 min, 24 h, and 48 h later. Operant responding for nicotine and food was decreased 15 min, but not 24 h, after treatment with SCH 23390. Operant responding for nicotine was decreased 15 min, 24 h, and 48 h after treatment with A77636, and food responding was decreased 15 min and 24 h later. Locomotor activity was decreased 15 min, but not 24 h, after treatment with SCH 23390. A77636 only decreased locomotor activity 48 h after treatment. There were no sex differences in the effects of SCH 23390 or A77636. In conclusions, the D1-like receptor antagonist SCH 23390 reduces nicotine intake and causes sedation in rats. Stimulation of D1-like receptors with A77636 decreases nicotine intake at time points that the drug is not sedative.
Genomic analyses identify significant molecules and biological processes in colorectal cancer cells with DNA damage
Authors: Guo Hongmei , Zhang Mason , Gu Hanming , Liu James
Published: January 2022

Colorectal cancer is a major cause of cancer deaths in the US. DNA damage is considered to be a novel target for the treatment of colorectal cancer. However, the molecular mechanisms and functions are still unclear. In this study, we aim to identify the significant molecules and signaling by analyzing the RNA-seq data. The GSE189366 was created by the BGISEQ-500 (Homo sapiens). The KEGG and GO analyses indicated the p53 signaling pathway and Hippo signaling pathway are major affected processes in colorectal cancer by DNA damage. Furthermore, we identified ten key interactive molecules including CDK1, STAT3, MDM2, CCNB1, CCNA2, CDKN1A, PCNA, AURKA, PLK1, and CDC6. Our study may provide potential drug targets for colorectal cancer.
Seroepidemiological and genomic investigation of COVID-19 spread in North East region of India
Authors: Wahengbam Romi , Bharali Pankaj , Manna Prasenjit , Phukan Tridip , Singh Moirangthem Goutam , Gogoi Gayatri , Tapadar Yasmin Begam , Singh Anil Kumar , Konwar Rituraj , Chikkaputtaiah Channakeshavaiah , Velmurugan Natarajan , Nagamani Selvaraman , Mahanta Hridoy Jyoti , Sarma Himakshi , Sahu Ravi Kumar , Dutta Prachurjya , Wann Sawlang Borsingh , Kalita Jatin , Sastry G Narahari
Published: January 2022

Seroepidemiology and genomics are valuable tools to investigate the transmission of COVID-19. We utilized qRT-PCR, serum antibody immunoassays, and whole genome sequencing to examine the spread of SARS-CoV-2 infections in North East (NE) region of India during the first and second pandemic waves (June 2020 to September 2021). qRT-PCR analysis was performed on a selected population from NE India during June 2020 to July 2021, and metadata were collected for the region. Seroprevalence and neutralizing antibody immunoassay were studied on selected individuals (n=2026) at three time points (August 2020, February 2021 and June 2021), as well as in a cohort (n=35) for a year (August 2020 to August 2021). SARS-CoV-2 genomes of 914 qRT-PCR positive samples (June 2020 to September 2021) were sequenced and assembled, and those obtained from the sequence databases were analyzed. Test positivity rates in first and second waves were 6.34% and 6.64% in the state of Assam, respectively, and a similar pattern was observed in other NE states. Seropositivity in August 2020, February 2021, and June 2021 were 10.63%, 40.3% and 46.33% respectively, and neutralizing antibody prevalence were 90.91%, 52.14%, and 69.30% respectively. The cohort group showed the presence of stable neutralizing antibody throughout the year. Normal variants dominated the first wave, while the variant of concerns (VOCs) B.1.617.2 and AY-sublineages dominated the second wave, and identified mostly among vaccinated individuals. All eight states of NE India reported numerous incidences of SARS-CoV-2 VOCs, especially B.1.617.2 and AY sublineages, and their prevalence co-related well with high TPR and seropositivity rate in the region. High infection and seroprevalence of COVID-19 in NE India during the second wave was associated with the emergence of VOCs. Natural infection prior to vaccination provided higher neutralizing activity than vaccination alone.
Impact of various vaccine boosters on neutralization against Omicron following prime vaccinations with inactivated or adenovirus-vectored vaccine
Authors: Huang Qingrui , Zeng Jiawei , Lang Qingyun , Gao Feng , Liu Dejun , Tian Siyu , Shi Rui , Luo Ling , Wang Hao , Hu Liping , Jiang Linrui , Liu Yawei , Li Kailiang , Wu Yunbo , Xu Junjie , Jiang Wenxi , Guo Ning , Chen Zhihai , Hao Xiaohua , Jin Ronghua , Yan Jinghua , Sun Yufa
Published: January 2022

Since the first report on November 24, 2021, the Omicron SARS-CoV-2 variant is now overwhelmingly spreading across the world. Two SARS-CoV-2 inactivated vaccines (IAVs), one recombinant protein subunit vaccine (PRV), and one adenovirus-vectored vaccine (AdV) have been widely administrated in many countries including China to pursue herd immunity. Here we investigated cross-neutralizing activities in 341 human serum specimens elicited by full-course vaccinations with IAV, PRV and AdV, and by various vaccine boosters following prime IAV and AdV vaccinations. We found that all types of vaccines induced significantly lower neutralizing antibody titers against the Omicron variant than against the prototype strain. For prime vaccinations with IAV and AdV, heterologous boosters with AdV and PRV, respectively, elevated serum Omicron-neutralizing activities to the highest degrees. In a mouse model, we further demonstrated that among a series of variant-derived RBD-encoding mRNA vaccine boosters, it is only the Omicron booster that significantly enhanced Omicron neutralizing antibody titers compared with the prototype booster following a prime immunization with a prototype S-encoding mRNA vaccine candidate. In summary, our systematical investigations of various vaccine boosters inform potential booster administrations in the future to combat the Omicron variant.
On the flexibility of the cellular amination network inE. coli
Authors: Schulz-Mirbach Helena , Müller Alexandra , Wu Tong , Pfister Pascal , Aslan Selçuk , von Borzyskowski Lennart Schada , Erb Tobias J. , Bar-Even Arren , Lindner Steffen N.
Published: January 2022

Ammonium (NH4+) is essential to generate the nitrogenous building blocks of life. It gets assimilated via the canonical biosynthetic routes to glutamate and is further distributed throughout metabolism via a network of transaminases. To study the flexibility of this network, we constructed anEscherichia coliglutamate auxotrophic strain. This strain allowed us to systematically study which amino acids serve as amine source and found that several amino acids complement the auxotrophy, either by producing glutamate via transamination reactions or by their conversion to glutamate. In this network, we identified aspartate transaminase AspC as a major connector between many amino acids and glutamate. Additionally, we extended the transaminase network by the amino acids β-alanine, alanine, glycine and serine as new amine sources and identified D-amino acid dehydrogenase (DadA) as an intracellular amino acid sink removing substrates from transaminase reactions. Finally, ammonium assimilation routes producing aspartate or leucine were introduced. Our study reveals the high flexibility of the cellular amination network, both in terms of transaminase promiscuity and adaptability to new connections and ammonium entry points.
Recommendations for tissue homogenisation and extraction in DNA metabarcoding of Malaise trap samples
Authors: Zizka Vera MA , Geiger Matthias F , Hörren Thomas , Kirse Ameli , Noll Niklas W , Schäffler Livia , Scherges Alice M , Sorg Martin
Published: January 2022

With increased application of DNA metabarcoding in fast and high-resolution biodiversity assessment, various laboratory protocols have been optimised in recent years and their further evaluation is subject of current research. Homogenisation of bulk samples and subsequent DNA extraction from destructed tissue is one way of starting the metabarcoding process. This essential step in the protocol can either be conducted from wet sample material (e.g. bulk insect samples) soaked in fixative or from completely dried individuals. While the latter method appears to produce more consistent results, it is time consuming and more prone to cross-contamination. We tested both homogenisation approaches with regard to time efficiency and biodiversity assessment of complex arthropod bulk samples, in particular how the amount of processed tissue affects taxon recovery. Both approaches reveal similar taxa compositions and detect a similar total OTU diversity in a single extraction reaction. Increased amounts of tissue used in DNA extraction improved OTU diversity detection and recovered particularly specific low-biomass taxa, making this approach valuable for samples with high biomass and/or diversity. Due to less handling time and lower vulnerability for cross-contamination we recommend the processing of wet material when sample homogenisation is applied.
CavitySpace: A database of potential ligand binding sites in the human proteome
Authors: Wang Shiwei , Lin Haoyu , Huang Zhixian , He Yufeng , Deng Xiaobing , Xu Youjun , Pei Jianfeng , Lai Luhua
Published: January 2022

The ligand binding sites of a protein provide useful information to uncover its functions and to direct the structure-based drug design. However, as binding site detection relies on the three-dimensional (3D) structural data of proteins, functional analysis based on protein ligand binding sites is formidable for proteins without structural information. Recent developments in protein structure prediction and the 3D structures built by AlphaFold provide an unprecedented opportunity for analyzing ligand binding sites in human proteins. We have used the reliable ligand binding site detection program CAVITY to analyse all the proteins in the human proteome and constructed the CavitySpace database, which is the first pocket library for predicted protein structures. CavitySpace can be used to predict protein function based on pocket information, to identify new druggable protein targets for drug design, and to search for new binding sites for known drugs for drug repurposing. CavitySpace is freely available at http://www.pkumdl.cn:8000/cavityspace/.
Soft topographical patterns trigger a stiffness-dependent cellular response to contact guidance
Authors: Comelles Jordi , Fernández-Majada Vanesa , Acevedo Verónica , Rebollo-Calderon Beatriz , Martínez Elena
Published: January 2022

Directional migration is involved in multiple physiological and pathological processes. Among other external signals, the architecture of the extracellular matrix can trigger directed cell migration through a phenomenon known as contact guidance: cells elongate, align, and migrate along the direction set by aligned extracellular matrix fibers. This process involves the orientation of focal adhesions, actin, and tubulin cytoskeleton along the direction of those fibers. Contact guidance has been extensively studied on stiff materials with topographical grooved patterns. However, how it translates to softer physiologically relevant compliances is not known. Here we show that substrate stiffness modulates the cellular response to topographical contact guidance. We found that for fibroblasts, while focal adhesions and actin responded to topography independently of the stiffness, microtubules showed a stiffness-dependent response that regulates contact guidance. On the other hand, both clusters and single breast carcinoma epithelial cells displayed stiffness-dependent contact guidance migration, leading to more directional and efficient migration when increasing substrate stiffness. These results suggest that both matrix stiffening and alignment of extracellular matrix fibers cooperate during directional cell migration, and both should be accounted when studying processes such as cancer cell invasion.

Teaser

Changes in the stiffness of topographical patterns modify how mesenchymal and epithelial cells perform contact guidance.
Temporal learning modulates post-interval ERPs in a categorization task with hidden reference durations
Authors: Silvestrin Mateus , Claessens Peter M. E. , Cravo André M.
Published: January 2022

The investigation of time-related activity in human electrophysiological activity has recently expanded from signals during the estimated interval to post-interval activity. Previous findings show timing-associated event-related potentials (ERPs) in both early (∼150ms) and late positive components (LPC; ∼300ms) post-interval signals. However, it is still unclear whether and what aspects of temporal information these different patterns of EEG activity are capturing, especially, if these signals are associated with interval duration or other task parameters. In the present work, we designed a modified temporal categorization task to investigate if participants’ adaptation to a changing decisional context led to changes in post-interval ERPs. Participants had to learn a hidden reference duration on each block to categorize the presented target intervals correctly. We found an early posterior N200 potential correlated to target durations and decisional context. A central LPC, which interacted with duration and learning of the hidden reference, predicted behavioral responses. Our findings add to the current evidence that interval duration modulates post-interval activity in timing categorization tasks and shows that late signals are associated with interval duration and decisional context.
Dexamethasone, a direct modulator of AQP2 in Menière’s disease
Authors: Mom Robin , Robert-Paganin Julien , Mom Thierry , Chabbert Christian , Réty Stéphane , Auguin Daniel
Published: January 2022

Menière’s disease is a chronic illness characterized by intermittent episodes of vertigo associated with fluctuating sensorineural hearing loss, tinnitus and aural pressure. This pathology strongly correlates with a dilatation of the fluid compartment of the endolymph, so-called hydrops. Dexamethasone is one of the therapeutic approaches recommended when conventional antivertigo treatments have failed. Several mechanisms of actions have been hypothesized for the mode of action of dexamethasone such as anti-inflammatory effect or as a regulator of the inner ear water homeostasis. However, none of them have been experimentally confirmed so far. Aquaporins (AQPs) are transmembrane water channels and are hence central in the regulation of trans-cellular water fluxes. In the present study we investigated the hypothesis that dexamethasone could impact water fluxes in the inner ear through direct interaction with AQP2. We addressed this question through molecular dynamics simulations approaches and managed to demonstrate a direct interaction between AQP2 and dexamethasone and its significant impact on the channel water permeability. We also describe the molecular mechanisms involved in dexamethasone binding and in its regulatory action upon AQP2 function.

Highlights

AQP2 water permeability is modulated by dexamethasone at physiological concentrations

The interaction impacts water fluxes through a direct interaction with the extra-cellular surface of the aquaporin

Key interactions implicate conserved residues of the ar/R constriction

New insights on corticosteroids mode of actions in Menière’s disease treatment
The way of the light: how visual information reaches the auditory cortex in congenitally deaf adults
Authors: Giorjiani Giuliana Martinatti , Tal Zohar , Nili Hamed , Yanchao BI , Fang Fang , Almeida Jorge
Published: January 2022

Human and animal studies on cross-modal plasticity under congenital deafness suggest that early auditory cortex plays a significant role in the processing of visual information when congenitally deprived from its typical (auditory) input. However, the pathway by which early auditory cortex is fed with visual information is still understudied. Here we focused on addressing how visual information reaches the auditory cortex under congenital deafness. We put forth a mechanistic model that proposes that different corticocortical and subcortical connections play a central role in rerouting visual information to the early auditory cortex of congenitally deaf individuals. Specifically, we show, using Representational Connectivity Analysis (RCA) and Dynamic Causal Modeling (DCM), that connections from the right superior colliculus to the right inferior colliculus, as well as connections from right early visual cortical regions to the right early auditory cortex play a role in rerouting visual information to early auditory cortex in congenitally deaf individuals. These findings shed light on how visual information reaches the early auditory cortex of deaf individuals - specifically, they suggest that neuroplasticity reshapes subcortical connections in order to re-route visual information to the auditory stream.
Epigenetic Landscape of HIV Infection in Primary Human Macrophage
Authors: Lu Fang , Yi Yanjie , Vladimirova Olga , Zhankharia Urvi , Collman Ronald G. , Lieberman Paul M.
Published: January 2022

HIV-infected macrophages are long-lived cells that sustain persistent virus expression, which is both a barrier to viral eradication and contributor to neurological complications in patients despite antiretroviral therapy (ART). To better understand the regulation of HIV in macrophages, we compared HIV infected primary human monocyte derived macrophages (MDM) to acutely infected primary CD4 T cells and Jurkat cells latently infected with HIV (JLAT 8.4). HIV genomes in MDM were actively transcribed despite enrichment with heterochromatin-associated H3K9me3 across the complete HIV genome in combination with elevated activation marks of H3K9ac and H3K27ac at the LTR. Macrophage patterns contrasted with JLAT cells, which showed conventional bivalent H3K4me3/H3K27me3, and acutely infected CD4 T cells, which showed an intermediate epigenotype. 5‘-methylcytosine (5mC) was enriched across the HIV genome in latently infected JLAT cells, while 5‘-hydroxymethylcytosine (5hmc) was enriched in CD4 and MDM. HIV infection induced multinucleation of MDMs along with DNA damage associate p53 phosphorylation, as well as loss of TET2 and the nuclear redistribution of 5-hydoxymethylation. Taken together, our findings suggest that HIV induces a unique macrophage nuclear and transcriptional profile, and viral genomes are maintained in a non-canonical bivalent epigenetic state.

Importance

Macrophages serve as a reservoir for long-term persistence and chronic production of HIV. We found an atypical epigenetic control of HIV in macrophages marked by heterochromatic H3K9me3 despite active viral transcription. HIV infection induced changes in macrophage nuclear morphology and epigenetic regulatory factors. These findings may identify new mechanisms to control chronic HIV expression in infected macrophage.
A quantitative model for the dynamics of target recognition and off-target rejection by the CRISPR-Cas Cascade complex
Authors: Rutkauskas Marius , Songailiene Inga , Irmisch Patrick , Kemmerich Felix E. , Sinkunas Tomas , Siksnys Virginijus , Seidel Ralf
Published: January 2022

CRISPR-Cas effector complexes recognise nucleic acid targets by base pairing with their crRNA which enables easy re-programming of the target specificity in rapidly emerging genome engineering applications. However, undesired recognition of off-targets, that are only partially complementary to the crRNA, occurs frequently and represents a severe limitation of the technique. Off-targeting lacks comprehensive quantitative understanding and prediction. Here, we present a detailed analysis of the target recognition dynamics by the Cascade surveillance complex on a set of mismatched DNA targets using single-molecule supercoiling experiments. We demonstrate that the observed dynamics can be quantitatively modelled as a random walk over the length of the crRNA-DNA hybrid using a minimal set of parameters. The model accurately describes the recognition of targets with single and double mutations providing an important basis for quantitative off-target predictions. Importantly the model intrinsically accounts for observed bias regarding the position and the proximity between mutations and reveals that the seed length for the initiation of target recognition is controlled by DNA supercoiling rather than the Cascade structure.
Discovery of S-217622, a Non-Covalent Oral SARS-CoV-2 3CL Protease Inhibitor Clinical Candidate for Treating COVID-19
Authors: Unoh Yuto , Uehara Shota , Nakahara Kenji , Nobori Haruaki , Yamatsu Yukiko , Yamamoto Shiho , Maruyama Yuki , Taoda Yoshiyuki , Kasamatsu Koji , Suto Takahiro , Kouki Kensuke , Nakahashi Atsufumi , Kawashima Sho , Sanaki Takao , Toba Shinsuke , Uemura Kentaro , Mizutare Tohru , Ando Shigeru , Sasaki Michihito , Orba Yasuko , Sawa Hirofumi , Sato Akihiko , Sato Takafumi , Kato Teruhisa , Tachibana Yuki
Published: January 2022

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in millions of deaths and threatens public health and safety. Despite the rapid global spread of COVID-19 vaccines, effective oral antiviral drugs are urgently needed. Here, we describe the discovery of S-217622, the first oral non-covalent, non-peptidic SARS-CoV-2 3CL protease inhibitor clinical candidate. S-217622 was discovered via virtual screening followed by biological screening of an in-house compound library, and optimization of the hit compound using a structure-based drug-design strategy. S-217622 exhibited antiviral activity in vitro against current outbreaking SARS-CoV-2 variants and showed favorable pharmacokinetic profiles in vivo for once-daily oral dosing. Furthermore, S-217622 dose-dependently inhibited intrapulmonary replication of SARS-CoV-2 in mice, indicating that this novel non-covalent inhibitor could be a potential oral agent for treating COVID-19.
Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms
Authors: Flynn Julia M. , Samant Neha , Schneider-Nachum Gily , Barkan David T. , Yilmaz Nese Kurt , Schiffer Celia A. , Moquin Stephanie A. , Dovala Dustin , Bolon Daniel N.A.
Published: January 2022

With the continual evolution of new strains of SARS-CoV-2 that are more virulent, transmissible, and able to evade current vaccines, there is an urgent need for effective anti-viral drugs. SARS-CoV-2 main protease (Mpro) is a leading target for drug design due to its conserved and indispensable role in the viral life cycle. Drugs targeting Mpro appear promising but will elicit selection pressure for resistance. To understand resistance potential in Mpro, we performed a comprehensive mutational scan of the protease that analyzed the function of all possible single amino acid changes. We developed three separate high-throughput assays of Mpro function in yeast, based on either the ability of Mpro variants to cleave at a defined cut-site or on the toxicity of their expression to yeast. We used deep sequencing to quantify the functional effects of each variant in each screen. The protein fitness landscapes from all three screens were strongly correlated, indicating that they captured the biophysical properties critical to Mpro function. The fitness landscapes revealed a non-active site location on the surface that is extremely sensitive to mutation making it a favorable location to target with inhibitors. In addition, we found a network of critical amino acids that physically bridge the two active sites of the Mpro dimer. The clinical variants of Mpro were predominantly functional in our screens, indicating that Mpro is under strong selection pressure in the human population. Our results provide predictions of mutations that will be readily accessible to Mpro evolution and that are likely to contribute to drug resistance. This complete mutational guide of Mpro can be used in the design of inhibitors with reduced potential of evolving viral resistance.
X-ray spectroscopic study of chemical state in uranium carbides
Authors: Butorin Sergei M. , Bauters Stephen , Amidani Lucia , Beck Aaron , Weiss Stephan , Vitova Tonya , Tougait Olivier
Published: January 2022

UC and UMeC2 (Me = Fe, Zr, Mo) carbides were studied by the high-energy-resolution fluorescence-detected X-ray absorption (HERFD-XAS) technique at the U M
4 and L
3 edges. Both U M
4 and L
3 HERFD-XAS reveal some differences between UMeC2 and UC; there are differences also between the M
4 and L
3 edge results for both types of carbide in terms of the spectral width and energy position. The observed differences are attributed to the consequences of the U 5f, 6d–4d(3d) hybridization in UMeC2. Calculations of the U M
4 HERFD-XAS spectra were also performed using the Anderson impurity model (AIM). Based on the analysis of the data, the 5f occupancy in the ground state of UC was estimated to be 3.05 electrons. This finding is also supported by the analysis of U N
4,5 XAS of UC and by the results of the AIM calculations of the U 4f X-ray photoelectron spectrum of UC.
Fast crystal growth of amorphous nimesulide: implication of surface effects
Authors: Shi Qin , Wang Yanan , Xu Jia , Liu Ziying , Chin Chai-Yee
Published: January 2022

Understanding crystallization behaviors is of utmost importance for developing robust amorphous pharmaceutical solids. Herein, the crystal growth behaviors of amorphous anti-inflammatory drug nimesulide (NIME) are systemically investigated in the glassy and supercooled liquid state as a function of temperature. A sudden over-tenfold increase is observed in the bulk crystal growth of NIME on cooling below its glass transition temperature (T
g). This fast growth behavior is known as a glass-to-crystal (GC) mode and has been reported in some molecular glasses. Fast surface crystal growth of NIME can persist up to T
g + 57°C with a weak jump in its growth rates at 30–40°C. In addition, surface crystal growth and GC growth of NIME exhibit an almost identical temperature dependence, supporting the view that GC growth is indeed a surface-facilitated process. Moreover, the bubble-induced fast crystal growth of NIME is observed in the interior of its supercooled liquid with approximately the same growth kinetics as surface crystal growth. These findings are relevant for a full understanding of the surface-related crystallization behaviors and physical stability of amorphous pharmaceutical formulations.