Highly significant improvement of protein sequence alignments with AlphaFold2.

MOTIVATION: Protein sequence alignments are essential to structural, evolutionary and functional analysis, but their accuracy is often limited by sequence similarity unless molecular structures are available. Protein structures predicted at experimental grade accuracy, as achieved by AlphaFold2, could therefore have a major impact on sequence analysis. RESULTS: Here, we find that multiple sequence alignments estimated on AlphaFold2 predictions are almost as accurate as alignments estimated on experimental structures and significantly closer to the structural reference than sequence-based alignments. We also show that AlphaFold2 structural models of relatively low quality can be used to obtain highly accurate alignments. These results suggest that, besides structure modeling, AlphaFold2 encodes higher-order dependencies that can be exploited for sequence analysis. AVAILABILITY AND IMPLEMENTATION: All data, analyses and results are available on Zenodo (https://doi.org/10.5281/zenodo.7031286). The code and scripts have been deposited in GitHub (https://github.com/cbcrg/msa-af2-nf) and the various containers in (https://cloud.sylabs.io/library/athbaltzis/af2/alphafold, https://hub.docker.com/r/athbaltzis/pred). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Multiple Sequence Alignment Computation Using the T-Coffee Regressive Algorithm Implementation.

Many fields of biology rely on the inference of accurate multiple sequence alignments (MSA) of biological sequences. Unfortunately, the problem of assembling an MSA is NP-complete thus limiting computation to approximate solutions using heuristics solutions. The progressive algorithm is one of the most popular frameworks for the computation of MSAs. It involves pre-clustering the sequences and aligning them starting with the most similar ones. The scalability of this framework is limited, especially with respect to accuracy. We present here an alternative approach named regressive algorithm. In this framework, sequences are first clustered and then aligned starting with the most distantly related ones. This approach has been shown to greatly improve accuracy during scale-up, especially on datasets featuring 10,000 sequences or more. Another benefit is the possibility to integrate third-party clustering methods and third-party MSA aligners. The regressive algorithm has been tested on up to 1.5 million sequences, its implementation is available in the T-Coffee package.

Early Percutaneous Tracheostomy in Coronavirus Disease 2019: Association With Hospital Mortality and Factors Associated With Removal of Tracheostomy Tube at ICU Discharge. A Cohort Study on 121 Patients.

OBJECTIVES: Early tracheotomy, defined as a procedure performed within 10 days from intubation, is associated with more ventilator free days, shorter ICU stay, and lower mortality than late tracheotomy. During the coronavirus disease 2019 pandemic, it was especially important to save operating room resources and to have a shorter ICU stay for patients, when ICUs had insufficient beds. In this context of limited resources, early percutaneous tracheostomy could be an effective way to manage mechanically ventilated patients. Nevertheless, current recommendations suggest delaying or avoiding the tracheotomy in coronavirus disease 2019 patients. Aim of the study was to analyze the hospital mortality of coronavirus disease 2019 patients who had received early percutaneous tracheostomy and factors associated with removal of tracheostomy cannula at ICU discharge. DESIGN: Cohort study. SETTING: Coronavirus disease 2019 ICU. PATIENTS: Adult patients with coronavirus disease 2019 3 days after ICU admission. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Three days after ICU admission, 164 patients were present in ICU and included in the analysis. One-hundred and twenty-one patients (74%) were tracheostomized, whereas the other 43 (26%) were managed with translaryngeal intubation only. In multivariable analysis, early percutaneous tracheostomy was associated with lower hospital mortality. Sixty-six of tracheostomized patients (55%) were discharged alive from the hospital. Age and male sex were the only characteristics that were independently associated with mortality in the tracheostomized patients (45.5% and 62.8% in tracheostomized and nontracheostomized patients, respectively; p = 0.009). Tracheostomy tube was removed in 47 of the tracheostomized patients (71%). The only variable independently associated with weaning from tracheostomy at ICU discharge was a faster start of spontaneous breathing after tracheotomy was performed. CONCLUSIONS: Early percutaneous tracheostomy was safe and effective in coronavirus disease 2019 patients, giving a good chance of survival and of weaning from tracheostomy cannula at ICU discharge.

Large multiple sequence alignments with a root-to-leaf regressive method.

Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf to root, based on a guide tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around from the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes6.

Constraint-based modeling identifies new putative targets to fight colistin-resistant A. baumannii infections.

Acinetobacter baumannii is a clinical threat to human health, causing major infection outbreaks worldwide. As new drugs against Gram-negative bacteria do not seem to be forthcoming, and due to the microbial capability of acquiring multi-resistance, there is an urgent need for novel therapeutic targets. Here we have derived a list of new potential targets by means of metabolic reconstruction and modelling of A. baumannii ATCC 19606. By integrating constraint-based modelling with gene expression data, we simulated microbial growth in normal and stressful conditions (i.e. following antibiotic exposure). This allowed us to describe the metabolic reprogramming that occurs in this bacterium when treated with colistin (the currently adopted last-line treatment) and identify a set of genes that are primary targets for developing new drugs against A. baumannii, including colistin-resistant strains. It can be anticipated that the metabolic model presented herein will represent a solid and reliable resource for the future treatment of A. baumannii infections.

Effects of smoking severity and moderate and severe periodontitis on serum C-reactive protein levels: an age- and gender-matched retrospective cohort study.

BACKGROUND AND PURPOSE: C-reactive protein (CRP) which might affect cardiovascular events can be affected by chronic diseases and smoking. Since the effects of smoking dosage as well as the mutual effect of smoking and periodontitis on CRP levels have not been evaluated, we aimed to assess these. MATERIALS AND METHODS: This retrospective age- and gender-matched study was performed on 120 dental patients. Clinical attachment loss, pocket probing depth (PPD), bleeding on probing (BoP), O'Leary plaque index and serum CRP were recorded. Patients were divided into one control and five cohort groups (n = 20 each) according to smoking severity [pack years (PY) below or above 30] and periodontal condition (healthy periodontium and moderate/severe periodontitis). The effects of clinical measurements, age, gender, smoking and periodontitis on CRP were assessed using one- and two-way analyses of variance, Tukey and Bonferroni post hoc tests, and multiple linear regression (α = 0.05). RESULTS: CRP concentrations were 0.07255 ± 0.009539, 0.09645 ± 0.010625, 0.122235 ± 0.018442, 0.3758 ± 0.187369, 0.81595 ± 0.0410299 and 1.8717 ± 0.652728 mg/l, respectively, in the control (PY ≤ 30 with healthy periodontium), cohort 1 (PY > 30 with healthy periodontium), cohort 2 (PY ≤ 30 with moderate periodontitis), cohort 3 (PY > 30 with moderate periodontitis), cohort 4 (PY ≤ 30 with severe periodontitis) and cohort 5 (PY > 30 with severe periodontitis). The positive effects of age, smoking severity, periodontitis and PPD, on CRP increase were significant (Regression p < 0.02). BoP had a negative effect (p = 0.015). CONCLUSIONS: Clinicians should warn the patients, especially the older ones, about the effects of their gingival health and smoking on their cardiovascular condition.

Association of HLA-DR/DQ polymorphism with Alzheimer's disease.

BACKGROUND: Alzheimer's disease (AD) is a complex disorder, resulting from an interaction between environmental and genetic factors. Several studies have addressed the association of AD with major histocompatibility complex (MHC) polymorphisms without arriving at any definite conclusions. The human leukocyte antigen (HLA) region is the key susceptibility locus in many immunological diseases. The aim of this study was to investigate the probable association between HLA-DR/DQ alleles and AD in Tunisian patients. METHODS: HLA-DR/DQ genotyping was performed using polymerase chain reaction sequence-specific primers with 55 AD patients and 100 healthy individuals serving as the control group. RESULTS: AD in Tunisian patients was found to be associated with the following alleles (Pc denotes Bonferroni corrected probability values): HLA-DRB1*15 (Pc < 10-3), DRB1*04 (Pc = 0.03) and DQB1*06 (Pc < 10-3). Two haplotypes found to be associated with the disease were DRB1*1501/DQB1*0602 (Pc < 10-3) and DRB1*0402/DQB1*0302 (Pc = 0.02). CONCLUSIONS: The authors believe this to be the first research linking the haplotypes DRB1*1501/DQB1*0602 and DRB1*04/DQB1*0302 with AD. Larger studies in other populations will be important to support the present findings of the possible susceptible risk of HLA-DR/DQ in AD.

Association of methylenetetrahydrofolate reductase polymorphisms with susceptibility to Alzheimer's disease.

BACKGROUND: Genetic risk factors play an important role in the pathogenesis of Alzheimer's disease (AD). In this case-control study, we examined the C677T and A1298C polymorphisms in the methylenetetrahydrofolate reductase (MTHFR) gene and their correlation with this pathology. OBJECTIVE: To verify the association between MTHFR C677T and A1298C polymorphisms and Alzheimer's disease. METHOD: This work was conducted as a case-control study. Cases consisted of thirty-eight patients and 100 individuals without dementia constituted the control group. Genotyping of MTHFR polymorphisms was performed on patients and controls. RESULT: Genetic analyses did not indicate a significant association between the MTHFR C677T mutation and AD (C/T: 63.15% versus 39%, p=0.087). However, the genotype prevalence of the missense variant MTHFR A1298C was significantly different between patients and controls (A/C: 55% versus 7%, p<10(-3)). Our data suggest an association between the MTHFR A1298C mutation and AD; however, the MTHFR C677T mutation did not contribute to susceptibility for AD. CONCLUSION: The MTHFR A1298C polymorphism is a possible risk factor for Alzheimer's disease.

Clinically important improvement in the WOMAC and predictor factors for response to non-specific non-steroidal anti-inflammatory drugs in osteoarthritic patients: a prospective study.

BACKGROUND: The aims of the present study were first to detect MCID for WOMAC in a Moroccan population, and second, to identify the best pre-treatment predictors on the change of health after treatment by non-specific, non-steroidal anti-inflammatory drugs (NSAIDs), and to evaluate whether the predictors were dependent on the choice of the response criterion. METHODS: The study involved 173 patients with osteoarthritis in whom primary care physicians decided to start treatment with non-selective NSAIDs. Assessments at admission and after 6 weeks were conducted. In order to determine the threshold levels associated with a definition of clinically important improvement, the receiver operating characteristic method was used. Three different measures of response to a 6-week NSAIDs treatment were used: one indirect measure (MCID in the total WOMAC score), one direct measure (transition question) and a combination of both criteria. RESULTS: Eighty patients (46.3%) reported "a slightly better" general health status compared to that of 6 weeks before NSAIDs treatment. The MCID proportion is a 16.0% reduction in WOMAC. The most stable pre-treatment predictors on the improvement of health after treatment by NSAIDs were the absence of previous knee injury and a high level of education. CONCLUSIONS: In our data, a 16.0% reduction of the total WOMAC score from baseline was associated with the highest degree of improvement on the transition scale category. This cut-off point had good accuracy, and should be appropriate for use in the interpretation of clinical studies results, as well as in clinical care.

Low bone mineral density is related to atherosclerosis in postmenopausal Moroccan women.

BACKGROUND: Some studies have implicated several possible metabolic linkages between osteoporosis and vascular calcification, including estrogen deficiency, vitamin D excess, vitamin K deficiency and lipid oxidation products. Nevertheless, it remains unclear whether osteoporosis and atherosclerosis are related to each other or are independent processes, both related to aging. The aim of this cross-sectional study was to evaluate the correlation between arterial thickening and bone status in a sample of apparently healthy Moroccan women. METHODS: Seventy-two postmenopausal women were studied. All patients were without secondary causes that might affect bone density. Bone status was assessed by bone mineral density (BMD) in lumbar spine and all femoral sites. Arterial wall thickening was assessed by intima-media thickness (IMT) in carotid artery (CA) and femoral artery (FA). Prevalent plaques were categorized into four groups ranging from low echogenicity to high echogenicity. RESULTS: The mean age was 59.2 +/- 8.3 years. 84.7% had at least one plaque. By Spearman Rank correlation, CA IMT was negatively correlated to Femoral total BMD (r = -0.33), Femoral neck BMD (r = -0.23), Ward triangle BMD (r = -0.30) and Trochanter BMD (r = -0.28) while there was no association with lumbar BMD. In multiple regression analysis, CA IMT emerged as an independent factor significantly associated with all femoral sites BMD after adjusting of confounding factors. FA IMT failed to be significantly associated with both Femoral and Lumbar BMD. No significant differences between echogenic, predominantly echogenic, predominantly echolucent and echolucent plaques groups were found concerning lumbar BMD and all femoral sites BMD CONCLUSION: Our results demonstrate a negative correlation between bone mineral density (BMD) qnd carotid intima-media thickness (IMT) in postmenopausal women, independently of confounding factors. We suggest that bone status should be evaluated in patients with vascular disease to assess whether preventive or therapeutic intervention is necessarry.