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Article ; Online: Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota.

Carasso, Shaqed / Zaatry, Rawan / Hajjo, Haitham / Kadosh-Kariti, Dana / Ben-Assa, Nadav / Naddaf, Rawi / Mandelbaum, Noa / Pressman, Sigal / Chowers, Yehuda / Gefen, Tal / Jeffrey, Kate L / Jofre, Juan / Coyne, Michael J / Comstock, Laurie E / Sharon, Itai / Geva-Zatorsky, Naama

Cell host & microbe

2024 Volume 32, Issue 3, Page(s) 322–334.e9

Abstract: Reversible genomic DNA inversions control the expression of numerous gut bacterial molecules, but how this impacts disease remains uncertain. By analyzing metagenomic samples from inflammatory bowel disease (IBD) cohorts, we identified multiple ... ...

Abstract	Reversible genomic DNA inversions control the expression of numerous gut bacterial molecules, but how this impacts disease remains uncertain. By analyzing metagenomic samples from inflammatory bowel disease (IBD) cohorts, we identified multiple invertible regions where a particular orientation correlated with disease. These include the promoter of polysaccharide A (PSA) of Bacteroides fragilis, which induces regulatory T cells (Tregs) and ameliorates experimental colitis. The PSA promoter was mostly oriented "OFF" in IBD patients, which correlated with increased B. fragilis-associated bacteriophages. Similarly, in mice colonized with a healthy human microbiota and B. fragilis, induction of colitis caused a decline of PSA in the "ON" orientation that reversed as inflammation resolved. Monocolonization of mice with B. fragilis revealed that bacteriophage infection increased the frequency of PSA in the "OFF" orientation, causing reduced PSA expression and decreased Treg cells. Altogether, we reveal dynamic bacterial phase variations driven by bacteriophages and host inflammation, signifying bacterial functional plasticity during disease.
MeSH term(s)	Humans ; Animals ; Mice ; Gastrointestinal Microbiome ; Colitis ; Inflammatory Bowel Diseases/microbiology ; Inflammation ; DNA
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2024-02-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2278004-X
ISSN	1934-6069 ; 1931-3128
ISSN (online)	1934-6069
ISSN	1931-3128
DOI	10.1016/j.chom.2024.02.003
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Gut microbial signatures are associated with Lynch syndrome (LS) and cancer history in Druze communities in Israel.

Naddaf, Rawi / Carasso, Shaqed / Reznick-Levi, Gili / Hasnis, Erez / Qarawani, Amalfi / Maza, Itay / Gefen, Tal / Half, Elizabeth Emily / Geva-Zatorsky, Naama

Scientific reports

2023 Volume 13, Issue 1, Page(s) 20677

Abstract: Lynch syndrome (LS) is a hereditary cancer syndrome caused by autosomal dominant mutations, with high probability of early onset for several cancers, mainly colorectal cancer (CRC). The gut microbiome was shown to be influenced by host genetics and to be ...

Abstract	Lynch syndrome (LS) is a hereditary cancer syndrome caused by autosomal dominant mutations, with high probability of early onset for several cancers, mainly colorectal cancer (CRC). The gut microbiome was shown to be influenced by host genetics and to be altered during cancer development. Therefore, we aimed to determine alterations in gut microbiome compositions of LS patients with and without cancer. We performed fecal microbiome analyses on samples of LS and non-LS members from the Druze ethnoreligious community in Israel, based on both their LS mutation and their cancer history. Our analysis revealed specific bacterial operational taxonomic units (OTUs) overrepresented in LS individuals as well as bacterial OTUs differentiating between the LS individuals with a history of cancer. The identified OTUs align with previous studies either correlating them to pro-inflammatory functions, which can predispose to cancer, or to the cancer itself, and as such, these bacteria can be considered as future therapeutic targets.
MeSH term(s)	Humans ; Colorectal Neoplasms, Hereditary Nonpolyposis/genetics ; Israel/epidemiology ; Gastrointestinal Microbiome/genetics ; Mutation ; DNA Mismatch Repair
Language	English
Publishing date	2023-11-24
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-47723-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Automated device for multi-stage paper-based assays enabled by an electroosmotic pumping valve.

Rofman, Baruch / Naddaf, Rawi / Bar-Dolev, Maya / Gefen, Tal / Ben-Assa, Nadav / Geva-Zatorsky, Naama / Bercovici, Moran

Lab on a chip

2022 Volume 22, Issue 23, Page(s) 4511–4520

Abstract: We leverage electroosmotic-flow generation in porous media in combination with a hydrophobic air gap to create a controllable valve capable of operating in either finite dosing or continuous flow mode, enabling the implementation of multi-step assays on ... ...

Abstract	We leverage electroosmotic-flow generation in porous media in combination with a hydrophobic air gap to create a controllable valve capable of operating in either finite dosing or continuous flow mode, enabling the implementation of multi-step assays on paper-based devices. The hydrophobic air gap between two paper pads creates a barrier keeping the valve nominally closed. Electroosmotic actuation, implemented using a pair of electrodes under the upstream pad, generates sufficient pressure to overcome the barrier and connect the two pads. We present a model describing the flow and governing parameters, including the electric potentials required to open and close the valve and the threshold potential for switching between the modes of operation. We construct the air gap using a hierarchical superhydrophobic surface and study the stability of the closed valve under strenuous conditions and find good agreement between our model and experimental results, as well as stable working conditions for practical applications. We present a straightforward design for a compact and automated device based on paper pads placed on top of printed circuit boards (PCB), equipped with heating and actuation electrodes and additional power and logic capabilities. Finally, we demonstrate the use of the device for amplification of SARS-CoV-2 sequences directly from raw saliva samples, using a loop-mediated isothermal amplification (LAMP) protocol requiring sample lysis followed by enzymatic deactivation and delivery to multiple amplification sites. Since PCB costs scale favorably with mass-production, we believe that this approach could lead to a low-cost diagnostic device that offers the sensitivity of amplification methods.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Nucleic Acid Amplification Techniques ; Molecular Diagnostic Techniques/methods ; Electroosmosis
Language	English
Publishing date	2022-11-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2056646-3
ISSN	1473-0189 ; 1473-0197
ISSN (online)	1473-0189
ISSN	1473-0197
DOI	10.1039/d2lc00572g
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A Protocol for Simple, Rapid, and Direct Detection of SARS-CoV-2 from clinical samples, using Reverse Transcribed Loop-Mediated Isothermal Amplification (RT-LAMP).

Naddaf, Rawi / Ben-Assa, Nadav / Gefen, Tal / Capucha, Tal / Hajjo, Haitham / Mandelbaum, Noa / Elbaum, Lilach / Kaplan, Shai / Rotem, Assaf / Chowers, Michal / Szwarcwort-Cohen, Moran / Paul, Mical / Geva-Zatorsky, Naama

Bio-protocol

2020 Volume 10, Issue 20, Page(s) e3789

Abstract: SARS-CoV-2 has quickly spread all around the globe causing illness and wide damages. Most countries were unprepared for such a rapid spread and crisis. This led to various strategies for effective control of the new pandemic. A key aspect in all ... ...

Abstract	SARS-CoV-2 has quickly spread all around the globe causing illness and wide damages. Most countries were unprepared for such a rapid spread and crisis. This led to various strategies for effective control of the new pandemic. A key aspect in all countries was to effectively test the population for the virus. Most countries chose a lockdown strategy in which many workplaces and activities are completely closed, leading to substantial economy costs. Here, we present a protocol we recently developed that allows rapid and simple detection of SARS-CoV-2 for the large population, eliminating costs and involvement of professional teams and laboratories. This protocol is based on Reverse Transcribed Loop-Mediated Isothermal Amplification (RT-LAMP). We tested this protocol directly on patient samples, both nasal and throat clinical swabs as well as saliva. Notably, this protocol is simple, cheap and can be easily applied to other pathogens as well.
Language	English
Publishing date	2020-10-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833269-6
ISSN	2331-8325 ; 2331-8325
ISSN (online)	2331-8325
ISSN	2331-8325
DOI	10.21769/BioProtoc.3789
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: A Protocol for Simple, Rapid, and Direct Detection of SARS-CoV-2 from clinical samples, using Reverse Transcribed Loop-Mediated Isothermal Amplification (RT-LAMP)

Naddaf, Rawi Ben-Assa Nadav Gefen Tal Capucha Tal Hajjo Haitham Mandelbaum Noa Elbaum Lilach Kaplan Shai Rotem Assaf Chowers Michal Szwarcwort-Cohen Moran Paul Mical Geva-Zatorsky Naama

Bio-Protocol

Abstract: SARS-CoV-2 has quickly spread all around the globe causing illness and wide damages Most countries were unprepared for such a rapid spread and crisis This led to various strategies for effective control of the new pandemic A key aspect in all countries ... ...

Abstract	SARS-CoV-2 has quickly spread all around the globe causing illness and wide damages Most countries were unprepared for such a rapid spread and crisis This led to various strategies for effective control of the new pandemic A key aspect in all countries was to effectively test the population for the virus Most countries chose a lockdown strategy in which many workplaces and activities are completely closed, leading to substantial economy costs Here, we present a protocol we recently developed that allows rapid and simple detection of SARS-CoV-2 for the large population, eliminating costs and involvement of professional teams and laboratories This protocol is based on Reverse Transcribed Loop-Mediated Isothermal Amplification (RT-LAMP) We tested this protocol directly on patient samples, both nasal and throat clinical swabs as well as saliva Notably, this protocol is simple, cheap and can be easily applied to other pathogens as well
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #923008
Database	COVID19

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Article ; Online: A Global Analysis of Kinase Function in

Bar-Yosef, Hagit / Gildor, Tsvia / Ramírez-Zavala, Bernardo / Schmauch, Christian / Weissman, Ziva / Pinsky, Mariel / Naddaf, Rawi / Morschhäuser, Joachim / Arkowitz, Robert A / Kornitzer, Daniel

Frontiers in cellular and infection microbiology

2018 Volume 8, Page(s) 17

Abstract: The human pathogenic ... ...

Abstract	The human pathogenic fungus
MeSH term(s)	Candida albicans/physiology ; Candidiasis/genetics ; Candidiasis/metabolism ; Candidiasis/microbiology ; Endocytosis/genetics ; Endocytosis/immunology ; Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Gene Expression Regulation, Fungal ; Genes, Fungal ; Humans ; Hyphae ; Morphogenesis/genetics ; Phosphotransferases/metabolism
Chemical Substances	Fungal Proteins ; Phosphotransferases (EC 2.7.-)
Language	English
Publishing date	2018-02-08
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2018.00017
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Article ; Online: Direct on-the-spot detection of SARS-CoV-2 in patients.

Ben-Assa, Nadav / Naddaf, Rawi / Gefen, Tal / Capucha, Tal / Hajjo, Haitham / Mandelbaum, Noa / Elbaum, Lilach / Rogov, Peter / King, Daniel A / Kaplan, Shai / Rotem, Assaf / Chowers, Michal / Szwarcwort-Cohen, Moran / Paul, Mical / Geva-Zatorsky, Naama

Experimental biology and medicine (Maywood, N.J.)

2020 Volume 245, Issue 14, Page(s) 1187–1193

Abstract: Impact statement: Humanity is currently experiencing a global pandemic with devastating implications on human health and the economy. Most countries are gradually exiting their lockdown state. We are currently lacking rapid and simple viral detections, ... ...

Abstract	Impact statement: Humanity is currently experiencing a global pandemic with devastating implications on human health and the economy. Most countries are gradually exiting their lockdown state. We are currently lacking rapid and simple viral detections, especially methods that can be performed in the household. Here, we applied RT-LAMP directly on human clinical swabs and self-collected saliva samples. We adjusted the method to allow simple and rapid viral detection, with no RNA purification steps. By testing our method on over 180 human samples, we determined its sensitivity, and by applying it to other viruses, we determined its specificity. We believe this method has a promising potential to be applied world-wide as a simple and cheap surveillance test for SARS-CoV-2.
MeSH term(s)	Betacoronavirus/isolation & purification ; COVID-19 ; Coronavirus Infections/diagnosis ; Humans ; Mass Screening/methods ; Molecular Diagnostic Techniques/methods ; Nucleic Acid Amplification Techniques/methods ; Pandemics ; Pneumonia, Viral/diagnosis ; SARS-CoV-2 ; Saliva/virology ; Sensitivity and Specificity
Keywords	covid19
Language	English
Publishing date	2020-07-16
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	4015-0
ISSN	1535-3699 ; 1525-1373 ; 0037-9727
ISSN (online)	1535-3699 ; 1525-1373
ISSN	0037-9727
DOI	10.1177/1535370220941819
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SARS-CoV-2 On-the-Spot Virus Detection Directly From Patients

Ben-Assa, Nadav / Naddaf, Rawi / Gefen, Tal / Capucha, Tal / Hajjo, Haitham / Mandelbaum, Noa / Elbaum, Lilach / Rogov, Peter / King, Daniel A. / Kaplan, Shai / Rotem, Assaf / Chowers, Michal / Szwarcwort-Cohen, Moran / Paul, Mical / Geva-Zatorsky, Naama

medRxiv

Abstract: Many countries are currently in a lockdown state due to the SARS-CoV-2 pandemic. One key aspect to transition safely out of lockdown is to continuously test the population for infected subjects. Currently, detection is performed at points of care using ... ...

Abstract	Many countries are currently in a lockdown state due to the SARS-CoV-2 pandemic. One key aspect to transition safely out of lockdown is to continuously test the population for infected subjects. Currently, detection is performed at points of care using quantitative reverse-transcription PCR (RT-qPCR) and requires dedicated professionals and equipment. Here, we developed a protocol based on Reverse Transcribed Loop-Mediated Isothermal Amplification (RT-LAMP) for detection of SARS-CoV-2, directly from crude nose and throat swabs. We applied this protocol to over 180 suspected patients, and determined its specificity and sensitivity by comparison to their RT-qPCR results. In addition, we further succeeded to apply the protocol on self-sampled saliva from confirmed cases. Since the proposed protocol provides results on-the-spot, and can detect SARS-CoV-2 from saliva, it can allow simple and continuous surveillance of the community.
Keywords	covid19
Language	English
Publishing date	2020-04-27
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.04.22.20072389
Database	COVID19

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Article: Direct on-the-spot detection of SARS-CoV-2 in patients

Exp Biol Med (Maywood)

Abstract: IMPACT STATEMENT: Humanity is currently experiencing a global pandemic with devastating implications on human health and the economy. Most countries are gradually exiting their lockdown state. We are currently lacking rapid and simple viral detections, ... ...

Abstract	IMPACT STATEMENT: Humanity is currently experiencing a global pandemic with devastating implications on human health and the economy. Most countries are gradually exiting their lockdown state. We are currently lacking rapid and simple viral detections, especially methods that can be performed in the household. Here, we applied RT-LAMP directly on human clinical swabs and self-collected saliva samples. We adjusted the method to allow simple and rapid viral detection, with no RNA purification steps. By testing our method on over 180 human samples, we determined its sensitivity, and by applying it to other viruses, we determined its specificity. We believe this method has a promising potential to be applied world-wide as a simple and cheap surveillance test for SARS-CoV-2.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #646155
Database	COVID19

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Article ; Online: Direct on-the-spot detection of SARS-CoV-2 in patients

Experimental Biology and Medicine

2020 Volume 245, Issue 14, Page(s) 1187–1193

Abstract: Many countries are currently in a state of lockdown due to the SARS-CoV-2 pandemic. One key requirement to safely transition out of lockdown is the continuous testing of the population to identify infected subjects. Currently, detection is performed at ... ...

Abstract	Many countries are currently in a state of lockdown due to the SARS-CoV-2 pandemic. One key requirement to safely transition out of lockdown is the continuous testing of the population to identify infected subjects. Currently, detection is performed at points of care using quantitative reverse-transcription PCR, thus requiring dedicated professionals and equipment. Here, we developed a protocol based on reverse transcribed loop-mediated isothermal amplification for the detection of SARS-CoV-2. This protocol is applied directly to SARS-CoV-2 nose and throat swabs, with no RNA purification step required. We tested this protocol on over 180 suspected patients, and compared the results to those obtained using the standard method. We further succeeded in applying the protocol to self-collected saliva samples from confirmed cases. Since the proposed protocol can detect SARS-CoV-2 from saliva and provides on-the-spot results, it allows simple and continuous surveillance of the community. Impact statement Humanity is currently experiencing a global pandemic with devastating implications on human health and the economy. Most countries are gradually exiting their lockdown state. We are currently lacking rapid and simple viral detections, especially methods that can be performed in the household. Here, we applied RT-LAMP directly on human clinical swabs and self-collected saliva samples. We adjusted the method to allow simple and rapid viral detection, with no RNA purification steps. By testing our method on over 180 human samples, we determined its sensitivity, and by applying it to other viruses, we determined its specificity. We believe this method has a promising potential to be applied world-wide as a simple and cheap surveillance test for SARS-CoV-2.
Keywords	General Biochemistry, Genetics and Molecular Biology ; covid19
Language	English
Publisher	SAGE Publications
Publishing country	us
Document type	Article ; Online
ISSN	1535-3702
DOI	10.1177/1535370220941819
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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