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As structure prediction methods are generating millions of publicly available protein structures, searching these databases is becoming a bottleneck. Foldseek aligns the structure of a query protein against a database by describing tertiary amino acid interactions within proteins as sequences over a structural alphabet. Foldseek decreases computation times by four to five orders of magnitude with 86%, 88% and 133% of the sensitivities of Dali, TM-align and CE, respectively. Foldseek speeds up protein structural search by four to five orders of magnitude.

Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same samples agree in principal coordinates space, taxonomy and phenotype effect size when analyzed with the same tree. A comprehensive microbial resource reconciles genomic and 16S rRNA data in a single tree.

ColabFold offers accelerated prediction of protein structures and complexes by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold’s 40−60-fold faster search and optimized model utilization enables prediction of close to 1,000 structures per day on a server with one graphics processing unit. Coupled with Google Colaboratory, ColabFold becomes a free and accessible platform for protein folding. ColabFold is open-source software available at https://github.com/sokrypton/ColabFold and its novel environmental databases are available at https://colabfold.mmseqs.com . ColabFold is a free and accessible platform for protein folding that provides accelerated prediction of protein structures and complexes using AlphaFold2 or RoseTTAFold.

Signal peptides (SPs) are short amino acid sequences that control protein secretion and translocation in all living organisms. SPs can be predicted from sequence data, but existing algorithms are unable to detect all known types of SPs. We introduce SignalP 6.0, a machine learning model that detects all five SP types and is applicable to metagenomic data. A new version of SignalP predicts all types of signal peptides.

Routine haplotype-resolved genome assembly from single samples remains an unresolved problem. Here we describe an algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a haplotype-resolved assembly without the sequencing of parents. Applied to human and other vertebrate samples, our algorithm consistently outperforms existing single-sample assembly pipelines and generates assemblies of similar quality to the best pedigree-based assemblies. Haplotype-resolved genome assemblies are generated by combining HiFi reads with Hi-C long-range interactions.

We are at the beginning of a genomic revolution in which all known species are planned to be sequenced. Accessing such data for comparative analyses is crucial in this new age of data-driven biology. Here, we introduce an improved version of DIAMOND that greatly exceeds previous search performances and harnesses supercomputing to perform tree-of-life scale protein alignments in hours, while matching the sensitivity of the gold standard BLASTP.An updated version of DIAMOND uses improved algorithmic procedures and a customized high-performance computing framework to make seemingly prohibitive large-scale protein sequence alignments feasible.

A previous reconstruction back to 800 ce indicated that the 2000–2018 soil moisture deficit in southwestern North America was exceeded during one megadrought in the late-1500s. Here, we show that after exceptional drought severity in 2021, ~19% of which is attributable to anthropogenic climate trends, 2000–2021 was the driest 22-yr period since at least 800. This drought will very likely persist through 2022, matching the duration of the late-1500s megadrought.Southwestern North America has been experiencing lower than average precipitation and higher temperatures since 2000. This emerging megadrought, spanning 2000–2021, has been the driest 22-year period since the year 800 and 19% of the drought severity in 2021 can be attributed to climate change.

Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa’s fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and similar to BA.2 except for the addition of 69–70 deletion (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild-type amino acid at Q493. The two lineages differ only outside of the spike region. The 69–70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimated growth advantages for BA.4 and BA.5 of 0.08 (95% confidence interval (CI): 0.08–0.09) and 0.10 (95% CI: 0.09–0.11) per day, respectively, over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus. Genomic characterization of the SARS-CoV-2 Omicron lineages BA.4 and BA.5, responsible for the fifth COVID-19 pandemic wave in South Africa, shows continued viral diversification and provides insights into the potential mechanisms underlying the ability of the new lineages to outcompete their predecessors.

TrackMate is an automated tracking software used to analyze bioimages and is distributed as a Fiji plugin. Here, we introduce a new version of TrackMate. TrackMate 7 is built to address the broad spectrum of modern challenges researchers face by integrating state-of-the-art segmentation algorithms into tracking pipelines. We illustrate qualitatively and quantitatively that these new capabilities function effectively across a wide range of bio-imaging experiments. TrackMate 7 combines the benefits of machine and deep learning-based image segmentation with accurate object tracking to enable improved 2D and 3D tracking of diverse objects in biological research.

A 49-year-old male presented with the complaints of sudden-onset redness and watering of both the eyes following the intake of fixed drug combination of ofloxacin-ornidazole for diarrhea. Following this, he developed redness of both the lips and blisters in the upper lip. He also developed erythematous macules in the medial aspects of the right lower thigh and ventral aspects of the right leg. Ocular examination showed conjunctival redness with diffuse corneal punctate epithelial erosions in both the eyes. The patient had a similar history affecting the same region 1 year back following the intake of the same combination medicine. To find out the specific inciting agent and owing to unavailability of Finn chamber, we developed a new modified skin patch test using empty tablet cover with three chambers, incorporated with ornidazole, Vaseline (petroleum jelly), and ofloxacin, respectively, and applied on the healed affected lesions. Modified patch test was positive for ornidazole at 48 h. Ornidazole-induced fixed drug eruption (FDE) affecting cornea is a rare and unique in our case report. The patient was then educated about the offending medication and advised to avoid in the future. We also conducted a systematic review of FDEs associated with ornidazole exposure. We searched PubMed and Google Scholar with specific keywords to finally retrieve 14 case reports of ofloxacin induced FDEs, which were further reviewed.