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  1. Beyond the Colony-Forming-Unit: Rapid Bacterial Evaluation in Osteomyelitis

    This article has 8 authors:
    1. Qi Sun
    2. Kimberley Huynh
    3. Dzenita Muratovic
    4. Nicholas J. Gunn
    5. Anja R. Zelmer
    6. L. Bogdan Solomon
    7. Gerald J. Atkins
    8. Dongqing Yang
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This useful study addresses discrepancies in determining bacterial burden in osteomyelitis as determined by culture and enumeration using DNA. The authors present compelling data demonstrating the emergence of discrepancies between CFU counts and genome copy numbers detected by PCR in Staphylococcus aureus strains infecting osteocyte-like cells. Whilst the observations may represent a substantial addition to the field of musculoskeletal infection, the broad applicability and clinical benefit are unclear.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  2. RNA polymerase III is involved in regulating Plasmodium falciparum virulence

    This article has 9 authors:
    1. Gretchen Diffendall
    2. Aurélie Claës
    3. Anna Barcons-Simon
    4. Prince Nyarko
    5. Florent Dingli
    6. Miguel Santos
    7. Damarys Loew
    8. Antoine Claessens
    9. Artur Scherf
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This important study links the activity of polymerase III to the regulation of virulence gene expression in the deadliest malaria parasite, Plasmodium falciparum. It identifies Maf1 as a Pol III inhibitor that enables the parasite to respond to external stimuli such as magnesium chloride plasma levels by downregulating Pol III-transcribed ruf6 genes and subsequently regulated var genes. While the evidence presented is generally convincing, some of the results are incomplete, and the mechanistic link between external signals and Maf1 activation remains unknown.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 2 listsLatest version Latest activity
  3. Lipid discovery enabled by sequence statistics and machine learning

    This article has 8 authors:
    1. Priya M. Christensen
    2. Jonathan Martin
    3. Aparna Uppuluri
    4. Luke R. Joyce
    5. Yahan Wei
    6. Ziqiang Guan
    7. Faruck Morcos
    8. Kelli L. Palmer
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study reports important findings on identifying sequence motifs that predict substrate specificity in a class of lipid synthesis enzymes. It sheds light on a mechanism used by bacteria to modify the lipids in their membrane to develop antibiotic resistance. The evidence is convincing, with a careful application of machine learning methods, validated by mass spectrometry-based lipid anlaysis experiments. This interdisciplinary study will be of interest to computational biologists and to the community working on lipids and on enzymes involved in lipid synthesis or modification.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  4. Zika virus remodels and hijacks IGF2BP2 ribonucleoprotein complex to promote viral replication organelle biogenesis

    This article has 12 authors:
    1. Clément Mazeaud
    2. Stefan Pfister
    3. Jonathan E. Owen
    4. Higor Sette Pereira
    5. Zachary E. Robinson
    6. Anaïs Anton
    7. Cheyanne L. Bemis
    8. Aïssatou Aïcha Sow
    9. Trushar R. Patel
    10. Christopher J. Neufeldt
    11. Pietro Scaturro
    12. Laurent Chatel-Chaix
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable study combines multidisciplinary approaches to examine the role of insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) as a potential novel host dependency factor for Zika virus. The main claims are partially supported by the data, but remain incomplete. The evidence would be strengthened by improving the immunofluorescence analyses, addressing the role of IGF2BP2 in "milder" infections, and elucidating the role of IGF2BP2 in the biogenesis of the viral replication organelle. With the experimental evidence strengthened, this work will be of interest to virologists working on flaviviruses.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  5. Fast Evolution of SOS-Independent Multi-Drug Resistance in Bacteria

    This article has 10 authors:
    1. Le Zhang
    2. Yunpeng Guan
    3. Yuen Yee Cheng
    4. Nural N. Cokcetin
    5. Amy L. Bottomley
    6. Andrew Robinson
    7. Elizabeth J. Harry
    8. Antoine van Oijen
    9. Qian Peter Su
    10. Dayong Jin
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This useful study examines how deletion of a major DNA repair gene in bacteria may facilitate the rise of mutations that confer resistance against a range of different antibiotics. Although the phenotypic evidence is intriguing, the interpretation of the phenotypic data presented and the proposed mechanism by which these mutations are generated are incomplete, relying on untested assumptions and suboptimal methodology. If substantially improved, this work could be of interest to microbiologists studying antibiotic resistance, genome integrity, and evolution, but as yet is of unclear significance.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  6. Metabolic disruption impairs ribosomal protein levels, resulting in enhanced aminoglycoside tolerance

    This article has 2 authors:
    1. Rauf Shiraliyev
    2. Mehmet A. Orman
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      The findings of this study are valuable as they challenge the dogma regarding the link between lowered bacterial metabolism and tolerance to aminoglycosides. The authors propose that the well-known tolerance to AG of mutants such as those of complexes I and II is not due to a decrease in the proton motive force and thus antibiotic uptake. The results presented here are solid but incomplete and the conclusions require additional experimental support.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  7. Polysaccharide breakdown products drive degradation-dispersal cycles of foraging bacteria through changes in metabolism and motility

    This article has 10 authors:
    1. Astrid KM Stubbusch
    2. Johannes M. Keegstra
    3. Julia Schwartzman
    4. Sammy Pontrelli
    5. Estelle E. Clerc
    6. Roman Stocker
    7. Cara Magnabosco
    8. Olga T. Schubert
    9. Martin Ackermann
    10. Glen G D’Souza
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This manuscript is a valuable contribution to our understanding of foraging behaviors in marine bacteria. The authors present a conceptual model for how a marine bacterial species consumes an abundant polysaccharide. Using experiments in microfluidic devices and through measurements of motility and gene expression, the authors offer solid evidence that the degradation products of polysaccharide digestion can stimulate motility.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  8. Detecting, mapping, and suppressing the spread of a decade-long Pseudomonas aeruginosa nosocomial outbreak with genomics

    This article has 24 authors:
    1. William Stribling
    2. Lindsey R. Hall
    3. Aubrey Powell
    4. Casey Harless
    5. Melissa J. Martin
    6. Brendan W. Corey
    7. Erik Snesrud
    8. Ana Ong
    9. Rosslyn Maybank
    10. Jason Stam
    11. Katie Bartlett
    12. Brendan T. Jones
    13. Lan N. Preston
    14. Katherine F. Lane
    15. Bernadette Thompson
    16. Lynn M. Young
    17. Yoon I. Kwak
    18. Alice E. Barsoumian
    19. Ana-Elizabeth Markelz
    20. John L. Kiley
    21. Robert J. Cybulski
    22. Jason W. Bennett
    23. Patrick T. Mc Gann
    24. Francois Lebreton
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This important work presents an example of how genomic data can be used to improve understanding of an ongoing, long-term bacterial outbreak in a hospital with an application to multi-drug resistant Pseudomonas aeruginosa, and will be of interest to researchers concerned with the spread of drug-resistant bacteria in hospital settings. The convincing genomic analyses highlight the value of routine surveillance of patients and environmental sampling and show how such data can help in dating the origin of the outbreak and in characterising the epidemic lineages. These findings highlight the importance of understanding environmental factors contributing to the transmission of P. aeruginosa for guiding and tailoring infection control efforts; however, epidemiological information was limited and the sampling methodology was inconsistent, complicating interpretation of inferences about exact transmission routes.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  9. Salmonella-induced SIRT1 and SIRT3 are crucial for maintaining the metabolic switch in bacteria and host for successful pathogenesis

    This article has 5 authors:
    1. Dipasree Hajra
    2. Raju S. Rajmani
    3. Ayushi Devendrasingh Chaudhary
    4. Shashi Kumar Gupta
    5. Dipshikha Chakravortty
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study presents valuable findings on the role of the sirtuins SIRT1 and SIRT3 during Salmonella Typhimurium infection. Although the work increases our understanding of the mechanisms used by this pathogen to interact with its host and may have implications for other intracellular pathogens, the reviewers found that the evidence to support the claims is incomplete. In particular, the discrepancy between results obtained using cultured cell lines and the animal model of infection stands out.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  10. CyAbrB2 is a nucleoid-associated protein in Synechocystis controlling hydrogenase expression during fermentation

    This article has 2 authors:
    1. Ryo Kariyazono
    2. Takashi Osanai
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      The authors provide solid data on a functional investigation of potential nucleoid-associated proteins and the modulation of chromosomal conformation in a model cyanobacterium. While the experiments presented are convincing, the manuscript could benefit from restructuring towards the precise findings; alternatively, additional data buttressing the claims made would significantly enhance the study. These valuable findings will be of interest to the chromosome and microbiology fields.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  11. A chemically-induced attenuated strain of Candida albicans generates robust protective immune response and prevents systemic candidiasis development

    This article has 4 authors:
    1. Swagata Bose
    2. Satya Ranjan Sahu
    3. Abinash Dutta
    4. Narottam Acharya
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study presents a useful strategy in which the authors devised a simple method to attenuate Candida albicans and deliver a live whole-cell vaccine in a mouse model of systemic candidiasis. While a robust candidiasis vaccine will be critical for the field, the study in its current form is incomplete. The strength of the evidence could be augmented with additional experiments to more fully characterize vaccine efficacy and host immune responses.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 2 listsLatest version Latest activity
  12. CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA

    This article has 5 authors:
    1. Ryan T. Bell
    2. Harutyun Sahakyan
    3. Kira S. Makarova
    4. Yuri I. Wolf
    5. Eugene V. Koonin
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This paper marks a fundamental advance in our understanding of prokaryotic Type IV restriction systems. The authors provide an encyclopedic overview of a hitherto uncharacterized branch of these systems, which they name CoCoNuTs, for coiled-coil nuclease tandems. They provide compelling evidence that these nucleases target RNA and are part of an echeloned defense response following viral infection. This article will be of great interest to scientists studying prokaryotic immunity mechanisms, as well as broadly to protein scientists engaged in the analysis, classification, and functional annotation of the proteome of life.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  13. Rifampicin tolerance and growth fitness among isoniazid-resistant clinical Mycobacterium tuberculosis isolates: an in-vitro longitudinal study

    This article has 16 authors:
    1. Vijay Srinivasan
    2. Nguyen Le Hoai Bao
    3. Dao Nguyen Vinh
    4. Le Thanh Hoang Nhat
    5. Do Dang Anh Thu
    6. Nguyen Le Quang
    7. Le Pham Tien Trieu
    8. Hoang Ngoc Nhung
    9. Vu Thi Ngoc Ha
    10. Phan Vuong Khac Thai
    11. Dang Thi Minh Ha
    12. Nguyen Huu Lan
    13. Maxine Caws
    14. Guy E. Thwaites
    15. Babak Javid
    16. Nguyen Thuy Thuong Thuong
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable study demonstrates that there is significant variation in the susceptibility of isoniazid-resistant Mycobacterium tuberculosis clinical isolates to killing by rifampicin, in some cases at the same tolerance levels as bona fide resistant strains. The evidence provided is solid, with no clear genetic marker for increased tolerance, suggesting that there may be multiple routes to achieving this phenotype. The work will be of interest to infectious disease researchers.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  14. Peptidoglycan-Chi3l1 interaction shapes gut microbiota in intestinal mucus layer

    This article has 4 authors:
    1. Yan Chen
    2. Ruizhi Yang
    3. Bin Qi
    4. Zhao Shan
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable study demonstrates that the Chitinase 3-like protein 1 (Chi3l1) interacts with gut microbiota and protects animals from intestinal injury in laboratory colitis model. The evidence supporting the claims of the authors is considered incomplete. The inclusion of consistent in vivo and in vitro data would have strengthened the study. The work will be of interest to scientists studying crosstalk between gut microbiota and inflammatory diseases.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  15. A Remarkable Genetic Shift in a Transmitted/Founder Virus Broadens Antibody Responses Against HIV-1

    This article has 18 authors:
    1. Swati Jain
    2. Gherman Uritskiy
    3. Marthandan Mahalingam
    4. Himanshu Batra
    5. Subhash Chand
    6. Hung V. Trinh
    7. Charles Beck
    8. Woong-Hee Shin
    9. Wadad AlSalmi
    10. Gustavo Kijak
    11. Leigh A. Eller
    12. Jerome Kim
    13. Daisuke Kihara
    14. Sodsai Tovanabutra
    15. Guido Ferrari
    16. Merlin L. Robb
    17. Mangala Rao
    18. Venigalla B. Rao
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study provides a detailed evaluation of how HIV evades nascent immune pressure from people living with HIV followed nearly immediately after infection. There is convincing evidence that H173 mutations in the V2 loop was a key determinant of selection pressure and escape. These data are congruent with protection in the RV144 clinical trial, the only trial that showed protection from infection. Overall, this study is valuable to the field.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  16. Mycobacterium tuberculosis PhoP integrates stress response to intracellular survival by maintenance of cAMP level

    This article has 6 authors:
    1. Hina Khan
    2. Partha Paul
    3. Harsh Goar
    4. Bhanwar Bamniya
    5. Navin Baid
    6. Dibyendu Sarkar
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This important study describes how PhoP regulates cyclic-AMP production in the human pathogen Mycobacterium tuberculosis. The authors provide convincing evidence that PhoP acts as a repressor of the cyclic-AMP-specific phosphodiesterase, Rv0805, which can degrade cyclic-AMP. The work requires substantive revision to clarify the presentation of the data, together with appending conclusions, and will be of interest to bacteriologists.

    Reviewed by eLife

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  17. Infection pressure in apes has driven selection for CD4 alleles that resist lentivirus (HIV/SIV) infection

    This article has 7 authors:
    1. Cody J. Warren
    2. Arturo Barbachano-Guerrero
    3. Vanessa L. Bauer
    4. Alex C. Stabell
    5. Obaiah Dirasantha
    6. Qing Yang
    7. Sara L. Sawyer
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study presents a valuable finding on how lentiviral infection has driven the diversification of the HIV/SIV entry receptor CD4. Using a combination of molecular evolution approaches coupled with functional testing of extant and ancestral reconstructions of great ape CD4, the authors provide solid evidence to support the idea that endemic simian immunodeficiency virus infection in gorillas have selected for gorilla CD4 alleles that are more resistant to SIV infection. However, this conclusion would be supported more strongly with additional functional testing of other great ape CD4 relative to human and ancestral sequences. Additionally, given the difficulty in definitively proving drivers of selection, the current title of the study is considered an overstatement relative to the data presented.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  18. SPARK regulates AGC kinases central to the Toxoplasma gondii asexual cycle

    This article has 4 authors:
    1. Alice L. Herneisen
    2. Michelle L. Peters
    3. Tyler A. Smith
    4. Sebastian Lourido
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study defines a fundamental aspect of protein kinase signalling in the protist parasite Toxoplasma gondii that is required for acute and chronic infections. The authors provide compelling evidence for the role of SPARK/SPARKEL kinases in regulating cAMP/cGMP signalling, although evidence linking the loss of these kinases to changes in the phosphoproteome is incomplete. Overall, this study will be of great interest to those who study Toxoplasma and related apicomplexan parasites.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  19. A conserved cell-pole determinant organizes proper polar flagellum formation

    This article has 7 authors:
    1. Erick Eligio Arroyo-Pérez
    2. John C. Hook
    3. Alejandra Alvarado
    4. Stephan Wimmi
    5. Timo Glatter
    6. Kai M. Thormann
    7. Simon Ringgaard
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This important research uses an elegant combination of protein-protein biochemistry, genetics, and microscopy to demonstrate that the novel bacterial protein FipA is required for polar flagella synthesis and binds to FlhF in multiple bacterial species. This manuscript is convincing, providing evidence for the early stages of flagellar synthesis at a cell pole; however, the protein biochemistry is incomplete and would benefit from additional rigorous experiments. This paper could be of significant interest to microbiologists studying bacterial motility, appendages, and cellular biology.

    Reviewed by eLife

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  20. Akkermansia muciniphila identified as key strain to function in pathogen invasion and intestinal stem cell proliferation through Wnt signaling pathway

    This article has 8 authors:
    1. Xin Ma
    2. Meng Li
    3. Tingting Xu
    4. Xinchen Zhou
    5. Mengqi Qian
    6. Zhiren Yang
    7. Kai Cao
    8. Xinyan Han
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      The work by Han and collaborators describes valuable findings on the role of Akkermansia muciniphila during ETEC infection. If confirmed, these findings will add to a growing list of beneficial properties of this organism. However, as it stands, the strength of the evidence used to justify the conclusions in the manuscript is incomplete.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity