Basem Al-Shayeb
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View article: Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires
Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires Open
Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “ Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new g…
View article: Programmable multi-kilobase RNA editing using CRISPR-mediated trans-splicing
Programmable multi-kilobase RNA editing using CRISPR-mediated trans-splicing Open
Current gene editing approaches in eukaryotic cells are limited to single base edits or small DNA insertions and deletions, and remain encumbered by unintended permanent effects and significant challenges in the delivery of large DNA cargo…
View article: Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires
Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires Open
Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “ Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new g…
View article: Genome expansion by a CRISPR trimmer-integrase
Genome expansion by a CRISPR trimmer-integrase Open
CRISPR–Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity 1 . CRISPR systems maintain genome integrity and avoid aut…
View article: Genome expansion by a CRISPR trimmer-integrase
Genome expansion by a CRISPR trimmer-integrase Open
CRISPR-Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity. CRISPR systems maintain genome integrity and avoid autoim…
View article: Genome editing in plants using the compact editor CasΦ
Genome editing in plants using the compact editor CasΦ Open
Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) systems have been developed as important tools for plant genome engineering. Here, we demonstrate that the hypercompact CasΦ nuclease is …
View article: Genome editing in plants using the compact editor CasΦ
Genome editing in plants using the compact editor CasΦ Open
CRISPR-Cas systems have been developed as important tools for plant genome engineering. Here, we demonstrate that the hypercompact CasΦ nuclease is able to generate stably inherited gene edits in Arabidopsis , and that CasΦ guide RNAs can …
View article: Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors
Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors Open
CRISPR-Cas systems are host-encoded pathways that protect microbes from viral infection using an adaptive RNA-guided mechanism. Using genome-resolved metagenomics, we find that CRISPR systems are also encoded in diverse bacteriophages, whe…
View article: Borgs are giant genetic elements with potential to expand metabolic capacity
Borgs are giant genetic elements with potential to expand metabolic capacity Open
Anaerobic methane oxidation exerts a key control on greenhouse gas emissions 1 , yet factors that modulate the activity of microorganisms performing this function remain poorly understood. Here we discovered extraordinarily large, diverse …
View article: A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters
A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters Open
Bacteria of the phylum Acidobacteria are one of the most abundant groups across soil ecosystems, yet they are represented by comparatively few sequenced genomes, leaving gaps in our understanding of their metabolic diversity. Recently, gen…
View article: Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes
Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes Open
View article: Petabase-scale sequence alignment catalyses viral discovery
Petabase-scale sequence alignment catalyses viral discovery Open
Public databases contain a planetary collection of nucleic acid sequences, but their systematic exploration has been inhibited by a lack of efficient methods for searching this corpus, which (at the time of writing) exceeds 20 petabases an…
View article: Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes
Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes Open
The genetic code is a highly conserved feature of life. However, some “alternative” genetic codes use reassigned stop codons to code for amino acids. Here, we survey stop codon recoding across bacteriophages (phages) in human and animal gu…
View article: The <i>Chloroflexi</i> supergroup is metabolically diverse and representatives have novel genes for non-photosynthesis based CO<sub>2</sub> fixation
The <i>Chloroflexi</i> supergroup is metabolically diverse and representatives have novel genes for non-photosynthesis based CO<sub>2</sub> fixation Open
The Chloroflexi superphylum have been investigated primarily from the perspective of reductive dehalogenation of toxic compounds, anaerobic photosynthesis and wastewater treatment, but remain relatively little studied compared to their clo…
View article: DNA interference states of the hypercompact CRISPR–CasΦ effector
DNA interference states of the hypercompact CRISPR–CasΦ effector Open
View article: Tools for interpretation of wastewater SARS-CoV-2 temporal and spatial trends demonstrated with data collected in the San Francisco Bay Area
Tools for interpretation of wastewater SARS-CoV-2 temporal and spatial trends demonstrated with data collected in the San Francisco Bay Area Open
View article: Borgs are giant extrachromosomal elements with the potential to augment methane oxidation
Borgs are giant extrachromosomal elements with the potential to augment methane oxidation Open
Summary Anaerobic methane oxidation exerts a key control on greenhouse gas emissions 1 , yet factors that modulate the activity of microorganisms performing this function remain little explored. In studying groundwater, sediments, and wetl…
View article: A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters
A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters Open
Bacteria of the phylum Acidobacteria are one of the most abundant bacterial across soil ecosystems, yet they are represented by comparatively few sequenced genomes, leaving gaps in our understanding of their metabolic diversity. Recently, …
View article: Interpretation of temporal and spatial trends of SARS-CoV-2 RNA in San Francisco Bay Area wastewater
Interpretation of temporal and spatial trends of SARS-CoV-2 RNA in San Francisco Bay Area wastewater Open
Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can be integrated with COVID-19 case data to inform timely pandemic response. However, more research is needed to apply and develop systematic met…
View article: Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex
Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex Open
CRISPR-Cas systems provide adaptive immunity in bacteria and archaea, beginning with integration of foreign sequences into the host CRISPR genomic locus and followed by transcription and maturation of CRISPR RNAs (crRNAs). In some CRISPR s…
View article: Interpretation of temporal and spatial trends of SARS-CoV-2 RNA in San Francisco Bay Area wastewater.
Interpretation of temporal and spatial trends of SARS-CoV-2 RNA in San Francisco Bay Area wastewater. Open
*Authors contributed equally to work **Corresponding authors
View article: Interpretation of temporal and spatial trends of SARS-CoV-2 RNA in San Francisco Bay Area wastewater.
Interpretation of temporal and spatial trends of SARS-CoV-2 RNA in San Francisco Bay Area wastewater. Open
*Authors contributed equally to work **Corresponding authors
View article: Interpretation of temporal and spatial trends of SARS-CoV-2 RNA in San Francisco Bay Area wastewater
Interpretation of temporal and spatial trends of SARS-CoV-2 RNA in San Francisco Bay Area wastewater Open
*Authors contributed equally to the work ** Corresponding authors
View article: Sewage, Salt, Silica, and SARS-CoV-2 (4S): An Economical Kit-Free Method for Direct Capture of SARS-CoV-2 RNA from Wastewater
Sewage, Salt, Silica, and SARS-CoV-2 (4S): An Economical Kit-Free Method for Direct Capture of SARS-CoV-2 RNA from Wastewater Open
Wastewater-based epidemiology is an emerging tool to monitor COVID-19 infection levels by measuring the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. There remains a need to improve wastew…
View article: Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater.
Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater. Open
Code and dataset associated with the publication titled Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater.
View article: Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater.
Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater. Open
Code and dataset associated with the publication titled Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater.
View article: Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants
Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants Open
Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients …
View article: Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater
Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater Open
Wastewater-based epidemiology is an emerging tool to monitor COVID-19 infection levels by measuring the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. There remains a need to improve wastew…
View article: V.4 - Direct wastewater RNA capture and purification via the &#34;Sewage, Salt, Silica and SARS-CoV-2 (4S)&#34; method v4
V.4 - Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 Open
This protocol describes the procedure of the "4S" (Sewage, Salt, Silica and SARS-CoV-2) method for SARS-CoV-2 RNA extraction from wastewater. Offering a highly efficient, modular and economical alternative to existing wastewater RNA purifi…
View article: Structural coordination between active sites of a Cas6-reverse transcriptase-Cas1—Cas2 CRISPR integrase complex
Structural coordination between active sites of a Cas6-reverse transcriptase-Cas1—Cas2 CRISPR integrase complex Open
CRISPR-Cas systems provide adaptive immunity in bacteria and archaea by targeting foreign DNA for destruction using CRISPR RNA-guided enzymes. CRISPR immunity begins with integration of foreign sequences into the host CRISPR genomic locus,…