Raphy Zarecki

Raphy Zarecki
Tel Aviv University | TAU · Department of Computer Science

About

37
Publications
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875
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Publications

Publications (37)
Article
Full-text available
Extensive use of agrochemicals is emerging as a serious environmental issue coming at the cost of the pollution of soil and water resources. Bioremediation techniques such as biostimulation are promising strategies used to remove pollutants from agricultural soils by supporting the indigenous microbial degraders. Though considered cost-effective an...
Article
Full-text available
Phenyl urea herbicides are being extensively used for weed control in both agricultural and non-agricultural applications. Linuron is one of the key herbicides in this family and is in wide use. Like other phenyl urea herbicides, it is known to have toxic effects as a result of its persistence in the environment. The natural removal of linuron from...
Article
Full-text available
Atrazine is an herbicide and a pollutant of great environmental concern that is naturally biodegraded by microbial communities. Paenarthrobacter aurescens TC1 is one of the most studied degraders of this herbicide. Here, we developed a genome scale metabolic model for P. aurescens TC1, iRZ1179, to study the atrazine degradation process at organism...
Article
Full-text available
Growing evidence supports the importance of gut microbiota in the control of tumor growth and response to therapy. Here, we select prebiotics that can enrich bacterial taxa that promote anti-tumor immunity. Addition of the prebiotics inulin or mucin to the diet of C57BL/6 mice induces anti-tumor immune responses and inhibition of BRAF mutant melano...
Article
Full-text available
Accumulating evidence points to an important role for the gut microbiome in anti-tumor immunity. Here, we show that altered intestinal microbiota contributes to anti-tumor immunity, limiting tumor expansion. Mice lacking the ubiquitin ligase RNF5 exhibit attenuated activation of the unfolded protein response (UPR) components, which coincides with i...
Preprint
Full-text available
Atrazine is an herbicide and pollutant of great environmental concern that is naturally biodegraded by microbial communities. The efficiency of biodegradation can be improved through the stimulating addition of fertilizers, electron acceptors, etc. In recent years, metabolic modelling approaches have become widely used as an in silico tool for orga...
Article
Microbial communities play a vital role in biogeochemical cycles, allowing the biodegradation of a wide range of pollutants. The composition of the community and the interactions between its members affect degradation rate and determine the identity of the final products. Here, we demonstrate the application of sequencing technologies and metabolic...
Article
Dietary changes are known to affect gut community structure, but questions remain about the mechanisms by which diet induces shifts in microbiome membership. Here we addressed these questions in the rumen microbiome ecosystem - a complex microbial community that resides in the upper digestive tract of ruminant animals and is responsible for the deg...
Article
Full-text available
Recent insights suggest that non-specific and/or promiscuous enzymes are common and active across life. Understanding the role of such enzymes is an important open question in biology. Here we develop a genome-wide method, PROPER, that uses a permissive PSI-BLAST approach to predict promiscuous activities of metabolic genes. Enzyme promiscuity is t...
Data
BLASTP Alignment of hisA and hisH. (TIF)
Data
Evolutionary conservation of the putative pdxS residues in thiG. The residues in thiG that we predict can perform the pdxS function show a high degree of conservation, as shown in the plot. This was generated from the output of ConSurf, set with default settings except for a maximum cutoff of 70% homology in the sequences to be aligned (higher cuto...
Data
Number of replacers per target. (TIF)
Data
Promiscuous functions of metabolic genes tend to be metabolic. All target-replacer pairs predicted by our method were assessed for how often a metabolic target paired with a metabolic replacer, with a non-metabolic replacer, a non-metabolic target with a metabolic replacer, etc. We found that (A) Replacer genes with metabolic primary functions take...
Data
Frequency of usage of Vitamin B6 as a cofactor across pathways. (DOCX)
Data
Inactivating the thiG proposed secondary active site removes its ability to replace pdxB, 48 hour timepoint. Results analogous to those shown in Fig 5 of the main text are shown, but at the 48 hour timepoint (instead of 96 hours as shown in the main text). (A) Ranksum test across all IPTG concentrations in the microwell plate experiment (equivalent...
Data
Supplementary methods and results. (DOCX)
Data
Statistics of gene similarity trees. Histograms are shown of: (A) number of genes represented in each tree; (B) number of unique organisms represented in each tree; (C) number of distinct functions represented in each tree; and (D) number of E. coli metabolic functions present in each tree. (TIF)
Data
BLASTP Alignment of metB and metC. (TIF)
Data
Structural alignments of thiG and pdxS. Multiple alignments are shown. (TIF)
Data
BLASTP Alignment of cysM and ilvA. (TIF)
Data
Sequence analysis of thiG. (A) E. coli thiG is aligned with pdxS, the gene whose function it putatively performs promiscuously. Key residues in both genes are marked, as per the key at the bottom. Two alignments are shown as they came up in BLASTP sequence alignment. (B) The active residues of thiG for its primary function are shown, along with put...
Article
Full-text available
Culturing microorganisms is a critical step in understanding and utilizing microbial life. Here we map the landscape of existing culture media by extracting natural-language media recipes into a Known Media Database (KOMODO), which includes >18,000 strain-media combinations, >3300 media variants and compound concentrations (the entire collection of...
Article
Full-text available
There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different...
Article
Full-text available
Understanding microbial nutritional requirements is a key challenge in microbiology. Here we leverage the recent availability of thousands of automatically generated genome-scale metabolic models to develop a predictor of microbial minimal medium requirements, which we apply to thousands of species to study the relationship between their nutritiona...
Article
Full-text available
Unlabelled: Glycans form the primary nutritional source for microbes in the human gut, and understanding their metabolism is a critical yet understudied aspect of microbiome research. Here, we present a novel computational pipeline for modeling glycan degradation (GlyDeR) which predicts the glycan degradation potency of 10,000 reference glycans ba...
Article
Full-text available
Growth rate has long been considered one of the most valuable phenotypes that can be measured in cells. Aside from being highly accessible and informative in laboratory cultures, maximal growth rate is often a prime determinant of cellular fitness, and predicting phenotypes that underlie fitness is key to both understanding and manipulating life. D...
Article
Full-text available
Gene suppression and overexpression are both fundamental tools in linking genotype to phenotype in model organisms. Computational methods have proven invaluable in studying and predicting the deleterious effects of gene deletions, and yet parallel computational methods for overexpression are still lacking. Here, we present Expression-Dependent Gene...
Article
Full-text available
Revealing the ecological principles that shape communities is a major challenge of the post-genomic era. To date, a systematic approach for describing inter-species interactions has been lacking. Here we independently predict the competitive and cooperative potential between 6,903 bacterial pairs derived from a collection of 118 species' metabolic...

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