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  1. Article: Host-encoded, cell surface-associated exopolysaccharide required for adsorption and infection by lactococcal P335 phage subtypes.

    Millen, Anne M / Romero, Dennis A / Horvath, Philippe / Magill, Damian / Simdon, Laura

    Frontiers in microbiology

    2022  Volume 13, Page(s) 971166

    Abstract: Lactococcus ... ...

    Abstract Lactococcus lactis
    Language English
    Publishing date 2022-10-04
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2022.971166
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  2. Article ; Online: Functional Study of the Type II-A CRISPR-Cas System of

    Pastuszka, Adeline / Beauruelle, Clémence / Camiade, Emilie / Rousseau, Geneviève M / Moineau, Sylvain / Mereghetti, Laurent / Horvath, Philippe / Lanotte, Philippe

    The CRISPR journal

    2021  Volume 4, Issue 2, Page(s) 233–242

    Abstract: Nearly all strains ... ...

    Abstract Nearly all strains of
    MeSH term(s) Base Sequence ; CRISPR-Cas Systems ; Cloning, Molecular ; Clustered Regularly Interspaced Short Palindromic Repeats ; Genome, Bacterial ; Humans ; Plasmids/genetics ; RNA ; Streptococcus agalactiae/enzymology ; Streptococcus agalactiae/genetics
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2021-04-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 3017891-5
    ISSN 2573-1602 ; 2573-1599
    ISSN (online) 2573-1602
    ISSN 2573-1599
    DOI 10.1089/crispr.2020.0145
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 7195: Show issues Location:
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    Zs.MG 119: Show issues

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  3. Article ; Online: Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages.

    Dion, Moïra B / Shah, Shiraz A / Deng, Ling / Thorsen, Jonathan / Stokholm, Jakob / Krogfelt, Karen A / Schjørring, Susanne / Horvath, Philippe / Allard, Antoine / Nielsen, Dennis S / Petit, Marie-Agnès / Moineau, Sylvain

    The ISME journal

    2024  Volume 18, Issue 1

    Abstract: CRISPR-Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria and archaea. In Escherichia coli, it is generally accepted that CRISPR-Cas systems are inactive in laboratory conditions due to a transcriptional ... ...

    Abstract CRISPR-Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria and archaea. In Escherichia coli, it is generally accepted that CRISPR-Cas systems are inactive in laboratory conditions due to a transcriptional repressor. In natural isolates, it has been shown that CRISPR arrays remain stable over the years and that most spacer targets (protospacers) remain unknown. Here, we re-examine CRISPR arrays in natural E. coli isolates and investigate viral and bacterial genomes for spacer targets using a bioinformatics approach coupled to a unique biological dataset. We first sequenced the CRISPR1 array of 1769 E. coli isolates from the fecal samples of 639 children obtained during their first year of life. We built a network with edges between isolates that reflect the number of shared spacers. The isolates grouped into 34 modules. A search for matching spacers in bacterial genomes showed that E. coli spacers almost exclusively target prophages. While we found instances of self-targeting spacers, those involving a prophage and a spacer within the same bacterial genome were rare. The extensive search for matching spacers also expanded the library of known E. coli protospacers to 60%. Altogether, these results favor the concept that E. coli's CRISPR-Cas is an antiprophage system and highlight the importance of reconsidering the criteria use to deem CRISPR-Cas systems active.
    MeSH term(s) Child ; Humans ; Prophages/genetics ; Escherichia coli/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Bacteriophages/genetics ; Genome, Bacterial ; CRISPR-Cas Systems
    Language English
    Publishing date 2024-02-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 2406536-5
    ISSN 1751-7370 ; 1751-7362
    ISSN (online) 1751-7370
    ISSN 1751-7362
    DOI 10.1093/ismejo/wrae005
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    In stock of ZB MED Bonn / Germany

    Z 7773: Show issues

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  4. Article ; Online: A decade of discovery: CRISPR functions and applications.

    Barrangou, Rodolphe / Horvath, Philippe

    Nature microbiology

    2017  Volume 2, Page(s) 17092

    Abstract: This year marks the tenth anniversary of the identification of the biological function of CRISPR-Cas as adaptive immune systems in bacteria. In just a decade, the characterization of CRISPR-Cas systems has established a novel means of adaptive immunity ... ...

    Abstract This year marks the tenth anniversary of the identification of the biological function of CRISPR-Cas as adaptive immune systems in bacteria. In just a decade, the characterization of CRISPR-Cas systems has established a novel means of adaptive immunity in bacteria and archaea and deepened our understanding of the interplay between prokaryotes and their environment, and CRISPR-based molecular machines have been repurposed to enable a genome editing revolution. Here, we look back on the historical milestones that have paved the way for the discovery of CRISPR and its function, and discuss the related technological applications that have emerged, with a focus on microbiology. Lastly, we provide a perspective on the impacts the field has had on science and beyond.
    Language English
    Publishing date 2017-06-05
    Publishing country England
    Document type Journal Article ; Review
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/nmicrobiol.2017.92
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  5. Article ; Online: Factors contributing to elite athletes' mental health in the junior-to-senior transition: A mixed methods study.

    Ackeret, Nadja / Röthlin, Philipp / Horvath, Stephan

    Psychology of sport and exercise

    2024  Volume 73, Page(s) 102645

    Abstract: The goals of this study were to examine factors that may affect the mental health of elite athletes during their junior-to-senior transition and to explore the types and frequency of facilitators and challenges athletes encounter during this transition. ... ...

    Abstract The goals of this study were to examine factors that may affect the mental health of elite athletes during their junior-to-senior transition and to explore the types and frequency of facilitators and challenges athletes encounter during this transition. Using a cross-sectional, embedded QUAN(qual) mixed methods study design, we surveyed two samples for the study goals. All participants completed demographic data (e.g., gender, age, sports). Sample one (N = 394, M
    Language English
    Publishing date 2024-04-10
    Publishing country Netherlands
    Document type Journal Article
    ISSN 1878-5476
    ISSN (online) 1878-5476
    DOI 10.1016/j.psychsport.2024.102645
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  6. Article ; Online: Shape sensing of optical fiber Bragg gratings based on deep learning

    Samaneh Manavi Roodsari / Antal Huck-Horvath / Sara Freund / Azhar Zam / Georg Rauter / Wolfgang Schade / Philippe C Cattin

    Machine Learning: Science and Technology, Vol 4, Iss 2, p

    2023  Volume 025037

    Abstract: Continuum robots in robot-assisted minimally invasive surgeries provide adequate access to target anatomies that are not directly reachable through small incisions. Achieving precise and reliable shape estimation of such snake-like manipulators ... ...

    Abstract Continuum robots in robot-assisted minimally invasive surgeries provide adequate access to target anatomies that are not directly reachable through small incisions. Achieving precise and reliable shape estimation of such snake-like manipulators necessitates an accurate navigation system, that requires no line-of-sight and is immune to electromagnetic noise. Fiber Bragg grating (FBG) shape sensing, particularly eccentric FBG (eFBG), is a promising and cost-effective solution for this task. However, in eFBG sensors, the spectral intensity of the Bragg wavelengths that carries the strain information can be affected by undesired bending-induced phenomena, making standard characterization techniques less suitable for these sensors. We showed in our previous work that a deep learning model has the potential to extract the strain information from the eFBG sensor’s spectrum and accurately predict its shape. In this paper, we conducted a more thorough investigation to find a suitable architectural design of the deep learning model to further increase shape prediction accuracy. We used the Hyperband algorithm to search for optimal hyperparameters in two steps. First, we limited the search space to layer settings of the network, from which, the best-performing configuration was selected. Then, we modified the search space for tuning the training and loss calculation hyperparameters. We also analyzed various data transformations on the network’s input and output variables, as data rescaling can directly influence the model’s performance. Additionally, we performed discriminative training using the Siamese network architecture that employs two convolutional neural networks (CNN) with identical parameters to learn similarity metrics between the spectra of similar target values. The best-performing network architecture among all evaluated configurations can predict the shape of a 30 cm long sensor with a median tip error of 3.11 mm in a curvature range of 1.4 m ^−1 to 35.3 m ^−1 .
    Keywords supervised deep learning ; shape sensing ; bending birefringence ; bending loss ; eccentric FBG ; fiber sensor ; Computer engineering. Computer hardware ; TK7885-7895 ; Electronic computers. Computer science ; QA75.5-76.95
    Subject code 006
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher IOP Publishing
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Novel Genus of Phages Infecting Streptococcus thermophilus: Genomic and Morphological Characterization.

    Philippe, Cécile / Levesque, Sébastien / Dion, Moïra B / Tremblay, Denise M / Horvath, Philippe / Lüth, Natascha / Cambillau, Christian / Franz, Charles / Neve, Horst / Fremaux, Christophe / Heller, Knut J / Moineau, Sylvain

    Applied and environmental microbiology

    2020  Volume 86, Issue 13

    Abstract: Streptococcus ... ...

    Abstract Streptococcus thermophilus
    MeSH term(s) Microscopy, Electron, Transmission ; Sequence Analysis, DNA ; Siphoviridae/classification ; Siphoviridae/genetics ; Siphoviridae/ultrastructure ; Streptococcus Phages/classification ; Streptococcus Phages/genetics ; Streptococcus Phages/ultrastructure ; Streptococcus thermophilus/virology
    Language English
    Publishing date 2020-06-17
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 223011-2
    ISSN 1098-5336 ; 0099-2240
    ISSN (online) 1098-5336
    ISSN 0099-2240
    DOI 10.1128/AEM.00227-20
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    In stock of ZB MED Cologne/Königswinter

    Zs.B 201: Show issues Location:
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  8. Article ; Online: Reply to "Letter to the Editor on Yurttas C et al. Limitations of laparoscopy to assess the peritoneal cancer index and eligibility for cytoreductive surgery with HIPEC in peritoneal metastasis".

    Yurttas, Can / Königsrainer, Alfred / Horvath, Philipp

    Langenbeck's archives of surgery

    2023  Volume 408, Issue 1, Page(s) 27

    MeSH term(s) Humans ; Peritoneal Neoplasms/drug therapy ; Hyperthermic Intraperitoneal Chemotherapy ; Cytoreduction Surgical Procedures ; Peritoneum/surgery ; Laparoscopy
    Language English
    Publishing date 2023-01-14
    Publishing country Germany
    Document type Letter ; Comment
    ZDB-ID 1423681-3
    ISSN 1435-2451 ; 1435-2443
    ISSN (online) 1435-2451
    ISSN 1435-2443
    DOI 10.1007/s00423-023-02772-0
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    In stock of ZB MED Cologne/Königswinter

    Uk I Zs.10: Show issues Location:
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  9. Article ; Online: Dairy lactococcal and streptococcal phage-host interactions: an industrial perspective in an evolving phage landscape.

    Romero, Dennis A / Magill, Damian / Millen, Anne / Horvath, Philippe / Fremaux, Christophe

    FEMS microbiology reviews

    2020  Volume 44, Issue 6, Page(s) 909–932

    Abstract: Almost a century has elapsed since the discovery of bacteriophages (phages), and 85 years have passed since the emergence of evidence that phages can infect starter cultures, thereby impacting dairy fermentations. Soon afterward, research efforts were ... ...

    Abstract Almost a century has elapsed since the discovery of bacteriophages (phages), and 85 years have passed since the emergence of evidence that phages can infect starter cultures, thereby impacting dairy fermentations. Soon afterward, research efforts were undertaken to investigate phage interactions regarding starter strains. Investigations into phage biology and morphology and phage-host relationships have been aimed at mitigating the negative impact phages have on the fermented dairy industry. From the viewpoint of a supplier of dairy starter cultures, this review examines the composition of an industrial phage collection, providing insight into the development of starter strains and cultures and the evolution of phages in the industry. Research advances in the diversity of phages and structural bases for phage-host recognition and an overview of the perpetual arms race between phage virulence and host defense are presented, with a perspective toward the development of improved phage-resistant starter culture systems.
    MeSH term(s) Dairying ; Host Microbial Interactions/physiology ; Lactococcus/virology ; Streptococcus Phages/pathogenicity ; Streptococcus Phages/physiology
    Language English
    Publishing date 2020-10-04
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 283740-7
    ISSN 1574-6976 ; 0168-6445
    ISSN (online) 1574-6976
    ISSN 0168-6445
    DOI 10.1093/femsre/fuaa048
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2165: Show issues Location:
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  10. Article: Kisspeptin Neurons in the Infundibular Nucleus of Ovariectomized Cats and Dogs Exhibit Unique Anatomical and Neurochemical Characteristics.

    Rumpler, Éva / Takács, Szabolcs / Göcz, Balázs / Baska, Ferenc / Szenci, Ottó / Horváth, András / Ciofi, Philippe / Hrabovszky, Erik / Skrapits, Katalin

    Frontiers in neuroscience

    2020  Volume 14, Page(s) 598707

    Abstract: Neurons co-synthesizing kisspeptin (KP), neurokinin B (NKB), and dynorphin ("KNDy neurons") in the hypothalamic arcuate/infundibular nucleus (INF) form a crucial component of the gonadotropin-releasing hormone (GnRH)/luteinizing hormone (LH) "pulse ... ...

    Abstract Neurons co-synthesizing kisspeptin (KP), neurokinin B (NKB), and dynorphin ("KNDy neurons") in the hypothalamic arcuate/infundibular nucleus (INF) form a crucial component of the gonadotropin-releasing hormone (GnRH)/luteinizing hormone (LH) "pulse generator." The goal of our study was to characterize KP neuron distribution, neuropeptide phenotype and connectivity to GnRH cells in ovariectomized (OVX) dogs and cats with immunohistochemistry on formalin-fixed hypothalamic tissue sections. In both species, KP and NKB neurons occurred in the INF and the two cell populations overlapped substantially. Dynorphin was detected in large subsets of canine KP (56%) and NKB (37%) cells and feline KP (64%) and NKB (57%) cells; triple-labeled ("KNDy") somata formed ∼25% of all immunolabeled neurons. Substance P (SP) was present in 20% of KP and 29% of NKB neurons in OVX cats but not dogs, although 26% of KP and 24% of NKB neurons in a gonadally intact male dog also contained SP signal. Only in cats, cocaine- and amphetamine regulated transcript was also colocalized with KP (23%) and NKB (7%). In contrast with reports from mice, KP neurons did not express galanin in either carnivore. KP neurons innervated virtually all GnRH neurons in both species. Results of this anatomical study on OVX animals reveal species-specific features of canine and feline mediobasal hypothalamic KP neurons. Anatomical and neurochemical similarities to and differences from the homologous KP cells of more extensively studied rodent, domestic and primate species will enhance our understanding of obligate and facultative players in the molecular mechanisms underlying pulsatile GnRH/LH secretion.
    Language English
    Publishing date 2020-12-02
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2411902-7
    ISSN 1662-453X ; 1662-4548
    ISSN (online) 1662-453X
    ISSN 1662-4548
    DOI 10.3389/fnins.2020.598707
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