Article
Biochemical Research Methods
Yunda Si, Chengfei Yan
Summary: AlphaFold2 is able to predict protein complex structures using multiple sequence alignments of interologs. A simplified phylogeny-based approach was applied to generate the alignments, resulting in successful predictions for a high percentage of bacterial and eukaryotic protein-protein interactions. Restricting the interologs to specific taxonomic ranks further improved the success rates.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
SeyedMohsen Hosseini, Lucian Ilie
Summary: The article introduces a deep learning model, PITHIA, for predicting protein interaction sites. This model, which combines multiple sequence alignments and learning attention, outperforms existing models. New test datasets were introduced to provide meaningful comparisons.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Editorial Material
Biochemical Research Methods
Lin Tang
Summary: Progressive Cactus allows reference-free multiple-genome alignment for massive datasets.
Article
Biochemical Research Methods
Soren M. Karst, Ryan M. Ziels, Rasmus H. Kirkegaard, Emil A. Sorensen, Daniel McDonald, Qiyun Zhu, Rob Knight, Mads Albertsen
Summary: High-throughput amplicon sequencing of large genomic regions remains challenging for short-read technologies. Here, a new approach combining unique molecular identifiers (UMIs) with Oxford Nanopore Technologies (ONT) or Pacific Biosciences circular consensus sequencing was reported, achieving high-accuracy single-molecule consensus sequences. The method was successfully applied to sequence ribosomal RNA operon amplicons and genomic sequences of microbial communities, showing a very low chimera rate.
Article
Infectious Diseases
Daniel Bravo-Barriga, Martina Ferraguti, Sergio Magallanes, Pilar Aguilera-Sepulveda, Francisco Llorente, Elisa Perez-Ramirez, Ana Vazquez, Fatima Guerrero-Carvajal, Maria Paz Sanchez-Seco, Miguel Angel Jimenez-Clavero, Carlos Mora-Rubio, Alfonso Marzal, Eva Frontera, Florentino de Lope
Summary: Usutu virus (USUV) has caused an increasing number of animal and human cases in Europe. The circulation of USUV in Extremadura, Spain was investigated through mosquito and bird sampling. USUV was detected in two pools of Culex pipiens mosquitoes, and USUV-specific antibodies were found in 17 wild birds from eight species. This indicates active circulation of USUV and a potential risk of exposure for the human population.
TRANSBOUNDARY AND EMERGING DISEASES
(2023)
Article
Multidisciplinary Sciences
Aashish Jain, Genki Terashi, Yuki Kagaya, Sai Raghavendra Maddhuri Venkata Subramaniya, Charles Christoffer, Daisuke Kihara
Summary: The application of deep learning methods in protein structure prediction continuously improves prediction accuracy. Additionally, combining MSAs generated with different E-values in a single model can increase co-evolutionary information. Studies show that combining multiple MSAs with different E-value cutoffs, as well as adding an attention layer and extra prediction tasks, can significantly enhance the model's performance.
SCIENTIFIC REPORTS
(2021)
Article
Biology
Zi Liu, Yi-Heng Zhu, Long-Chen Shen, Xuan Xiao, Wang-Ren Qiu, Dong-Jun Yu
Summary: Accurately identifying inter-chain contacts is crucial for determining protein complex structures and understanding biological functions. We proposed a new deep learning method, ICCPred, which predicts inter-chain contacts based on protein complex amino acid sequences. Experimental results on 709 benchmark protein complexes showed that ICCPred significantly outperformed state-of-the-art approaches in contact prediction accuracy. Detailed data analyses revealed that ICCPred's advantage lies in its utilization of pre-trained language models to extract complementary co-evolution diversity from multiple sequence alignments (MSAs), and its designed deep residual network which enhances the correlation between co-evolution diversity and inter-chain contact patterns.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Plant Sciences
Manuel Anguita-Maeso, Carmen Haro, Juan A. Navas-Cortes, Blanca B. Landa
Summary: This study evaluated the effects of extraction methods, plant age, and PCR primers on the characterization of xylem bacterial communities. Different extraction methods and PCR primers resulted in significant biases in describing the bacterial community. The relative importance of dominant bacterial genera varied depending on the primers and extraction methods used.
Article
Multidisciplinary Sciences
Umberto Lupo, Damiano Sgarbossa, Anne-Florence Bitbol
Summary: Self-supervised neural language models with attention have been applied to biological sequence data, advancing structure, function, and mutational effect prediction. This study demonstrates that protein language models can encode detailed phylogenetic relationships and can distinguish correlations caused by structural constraints from those caused by phylogeny.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Andrew F. Neuwald, Bryan D. Kolaczkowski, Stephen F. Altschul
Summary: eCOMPASS tackles the issue of constructing large and accurate multiple sequence alignments by utilizing a statistical measure of relative alignment quality based on direct coupling analysis (DCA). It computes the statistical significance of the congruence between high scoring directly coupled pairs and 3D contacts in corresponding structures, depending on properly aligned homologous residues. This approach is illustrated using both simulated and real MSAs.
Article
Microbiology
Youssuf Ahmed Gherbawy, Yassmin Mohamed Shebany, Eman Gamal Abd Elnaser Mohamed El-Dawy
Summary: The study investigated the occurrence and genetic diversity of Stachybotrys chartarum isolates from faba beans dust during threshing in Upper Egypt. It found low counts of Stachybotrys with six isolates identified through morphological and molecular methods. All tested isolates were positive for the Tri5 gene, indicating the potential for toxin synthesis. Further taxonomic study of S. chartarum and the possibility of subspecies presence based on morphological variations confirmed by molecular techniques is necessary.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Yohan Charbonnier, Daciana Papura, Olivier Touzot, Noriane Rhouy, Gilles Sentenac, Adrien Rusch
Summary: The study found that bats increase their hunting activity significantly when European grapevine moths are present in vineyards. Molecular analysis shows that at least 10 species of bats prey on the three grapevine moth species. This suggests that bats can be natural enemies of grape pests in vineyard landscapes.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2021)
Article
Plant Sciences
Gi Yoon Shin, Amy Smith, Teresa A. Coutinho, Bhabesh Dutta, Brian H. Kvitko
Summary: Species of Pantoea are plant pathogenic bacteria that infect economically important plant species. This study evaluated the specificity of different primers for rapid identification of Pantoea species and found that some primers showed high specificity and accuracy.
Article
Medicine, General & Internal
Agnieszka Sroka-Oleksiak, Wojciech Pabian, Joanna Sobonska, Kamil Drozdz, Tomasz Bogiel, Monika Brzychczy-Wloch
Summary: The aim of this study was to evaluate the sensitivity of group B Streptococcus (GBS) detection using polymerase chain reaction primers and a preincubation step. Vaginal and rectal swabs were collected from 97 pregnant women and subjected to enrichment broth culture-based diagnostics and amplification using specific primers. The preincubation step increased the sensitivity of GBS detection, and additional GBS cases were identified using nucleic acid amplification techniques. The atr gene primers showed the highest number of true positive results compared to other primers.
Article
Biology
Damiano Sgarbossa, Umberto Lupo, Anne-Florence Bitbol
Summary: Computational models based on protein sequences can capture protein families and learn constraints associated with their structure and function, enabling the generation of novel sequences. MSA Transformer, a protein language model trained on multiple sequence alignments, is shown to be effective in this task.
Article
Virology
Philippe Colson, Philippe Gautret, Jeremy Delerce, Herve Chaudet, Pierre Pontarotti, Patrick Forterre, Raphael Tola, Marielle Bedotto, Lea Delorme, Wahiba Bader, Anthony Levasseur, Jean-Christophe Lagier, Matthieu Million, Nouara Yahi, Jacques Fantini, Bernard La Scola, Pierre-Edouard Fournier, Didier Raoult
Summary: This study investigated the dynamics of the French variant Marseille-4 of SARS-CoV-2 over a 10-month period, identifying two subvariants and analyzing their mutations and lifetimes. The findings suggest that beneficial mutations can initiate new outbreaks, while the accumulation of other mutations can result in the disappearance of lineages.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Virology
Nathalie Wurtz, Maelle Boussier, Louis Souville, Gwilherm Penant, Alexandre Lacoste, Philippe Colson, Bernard La Scola, Sarah Aherfi
Summary: This study aimed to find a simple method for detecting and monitoring SARS-CoV-2 variants in wastewater. Through evaluation and comparison of sample preservation strategies and concentration methods, an optimal protocol was identified. This protocol was successfully applied to monitor the emergence of the Omicron variant in wastewater samples from Marseille, France.
Article
Critical Care Medicine
Roberto Lorusso, Maria Elena De Piero, Silvia Mariani, Michele Di Mauro, Thierry Folliguet, Fabio Silvio Taccone, Luigi Camporota, Justyna Swol, Dominik Wiedemann, Mirko Belliato, Lars Mikael Broman, Alain Vuylsteke, Yigal Kassif, Anna Mara Scandroglio, Vito Fanelli, Philippe Gaudard, Stephane Ledot, Julian Barker, Udo Boeken, Sven Maier, Alexander Kersten, Bart Meyns, Matteo Pozzi, Finn M. Pedersen, Peter Schellongowski, Kaan Kirali, Nicholas Barrett, Jordi Riera, Thomas Mueller, Jan Belohlavek, EuroECMO COVID Study Grp
Summary: This study aimed to investigate in-hospital outcomes in patients who received ECMO during the first wave of COVID-19 and found that factors such as patient's age, timing of cannulation, and use of medication were associated with higher in-hospital mortality. Despite favorable post-discharge survival, some patients still require long-term rehabilitation.
LANCET RESPIRATORY MEDICINE
(2023)
Article
Infectious Diseases
Lise Cuzin, Philippe Flandre, Clotilde Allavena, Romain Palich, Claudine Duvivier, Agathe Becker, Helene Laroche, Pascal Pugliese, Andre Cabie, Dat'AIDS Study Grp
Summary: This study analyzed the occurrence of virological failure (VF) in patients starting ART with an integrase strand transfer inhibitor (INSTI)-based regimen in recent years and its relationship with previous episodes of low-level viral load (LLVL). The results showed that LLVL was associated with VF, and even in the absence of subsequent failure, LLV episodes have a cost. Therefore, any viral load value above 50 copies/mL should lead to enhanced adherence counseling.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Virology
Anna Julienne Selbe Ndiaye, Mamadou Beye, Gora Lo, Idir Kacel, Aissatou Sow, Nafissatou Leye, Abdou Padane, Aminata Mboup, Halimatou Diop-Ndiaye, Cheikh Sokhna, Coumba Toure Kane, Philippe Colson, Florence Fenollar, Souleymane Mboup, Pierre-Edouard Fournier
Summary: We used whole genome sequencing to analyze mutations in SARS-CoV-2 during the deadliest wave of the COVID-19 epidemic in Senegal. A total of 291 genotypable consensus genome sequences were obtained, revealing diversification and the presence of a Senegalese strain belonging to the P.1.14 sublineage of the Brazilian P.1 lineage. This study highlights the significant genomic variations of SARS-CoV-2 in Senegal.
Article
Microbiology
Valerie Moal, Margaux Valade, Celine Boschi, Thomas Robert, Nicolas Orain, Audrey Bancod, Sophie Edouard, Philippe Colson, Bernard La Scola
Summary: Kidney transplant recipients (KTRs) are at high risk of severe COVID-19 and additional booster vaccinations or passive immunization are recommended to improve their protection. The study found that a significant proportion of vaccinated KTRs had poor neutralization of SARS-CoV-2 variants, with only 46% able to neutralize all five variants. Cross-neutralization was observed against Delta and Omicron variants in the majority of serum samples.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Nasserdine Papa Mze, Idir Kacel, Mamadou Beye, Raphael Tola, Mariema Sarr, Leonardo Basco, Herve Bogreau, Philippe Colson, Pierre-Edouard Fournier
Summary: A rapid and cost-effective sequencing protocol is proposed to validate its reliability by comparing the SARS-CoV-2 genome sequences obtained using the modified Illumina COVIDSeq protocol with the standard protocol. The modified protocol saves time and costs, providing high-quality results comparable to the standard protocol.
Letter
Infectious Diseases
Hubert Bassene, Masse Sambou, Marielle Bedetto, Philippe Colson, Oleg Mediannikov, Ndiaw Goumballa, Georges Diatta, Philippe Gautret, Florence Fenollar, Cheikh Sokhna
NEW MICROBES AND NEW INFECTIONS
(2023)
Article
Immunology
Lise Cuzin, Adeline Morisot, Clotilde Allavena, France Lert, Pascal Pugliese
Summary: The study found significant reductions in transition time through the cascade of care, contributing to a shorter transmission period after each new infection. However, delayed diagnosis remains the primary obstacle to ending AIDS in the next decade.
CLINICAL INFECTIOUS DISEASES
(2023)
Letter
Virology
Nhu Ngoc Nguyen, Linda Houhamdi, Line Meddeb, Philippe Colson, Philippe Gautret
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Virology
Coline Mortier, Herve Tissot-Dupont, Florian Cardona, Christiane Bruel, Salima Lahouel, Hanane Lasri, Karim Bendamardji, Celine Boschi, Philippe Parola, Matthieu Million, Philippe Colson, Philippe Brouqui, Bernard La Scola, Jean-Christophe Lagier, Nadim Cassir
Summary: In the current global outbreak of mpox, the clinical presentation is poorly specific and reinforces the importance of microbiological confirmation. Symptomatic patients who test negative for the virus should undergo a broad differential diagnosis.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Editorial Material
Virology
Philippe Colson, Bernard La Scola, Mamadou Beye, Jeremy Delerce, Didier Raoult, Jacques Fantini
Summary: The emergence of the Omicron BA.2.86 variant with 39 additional mutations in the spike protein is a major event in the genetic evolution of SARS-CoV-2. This study provides insights into the phylogeny, mutation positions and frequencies, and structural model of the spike protein in BA.2.86.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Immunology
Philippe Charlier, Anais Augias, Raphael Weil, Francoise Bouchet, Joel Poupon, Maria Speranta Popescu, Philippe Decloquement, Said Azza, Emmanouil Angelakis, Pascale Richardin, Philippe Colson, Gregory Dubourg, Matthieu Million, Didier Raoult
Summary: Analysis of the relics of King Saint-Louis suggests that he may have died from scurvy and inflammatory jaw disease, with infection by oral commensals potentially being the main cause of the illness.
MICROBIAL PATHOGENESIS
(2023)
Article
Virology
Lucille Claire De Maria, Philippe Colson, Aurelie Morand, Noemie Vanel, Didier Stoupan, Bernard La Scola, Celine Boschi
Summary: This article studied the epidemiology of respiratory syncytial virus(RSV) in university hospitals of Marseille, France, from 2020 to 2023. The results showed an atypical evolution of the RSV incidence, with a 4-month delay in the onset of the epidemic compared to previous years, and a peak in March 2021. There was a significant increase in RSV-positive cases during summer 2021, while the incidence during winter 2022 was not significantly higher compared to previous winters. The study also identified high-risk populations, including patients over 65 years old. These findings demonstrate the unpredictability of RSV infection and infectious disease epidemiology.
Article
Public, Environmental & Occupational Health
Xuan Duong Tran, Van Thuan Hoang, Thi Thuy Duong Dang, Thi Phuong Vu, Minh Manh To, Trong Kiem Tran, Manh Dung Do, Duy Cuong Nguyen, Quoc Tien Nguyen, Philippe Colson, Philippe Parola, Pierre Marty, Philippe Gautret
Summary: This study investigated the causes of acute undifferentiated fever (AUF) in children under five in Vietnam. Real-time PCR testing of blood samples revealed that 53.9% of children were positive for at least one pathogen. During hospitalization, children presented with various symptoms including respiratory tract infections, hand, foot and mouth disease, chickenpox, central nervous system infections, and gastrointestinal infections. Ultimately, 23.1% of patients were diagnosed with AUF.
JOURNAL OF EPIDEMIOLOGY AND GLOBAL HEALTH
(2023)
