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  1. Article ; Online: Hopanoid lipids promote soybean

    Pan, Huiqiao / Shim, Ashley / Lubin, Matthew B / Belin, Brittany J

    mBio

    2024  Volume 15, Issue 4, Page(s) e0247823

    Abstract: The symbioses between leguminous plants and nitrogen-fixing bacteria known as rhizobia are well known for promoting plant growth and sustainably increasing soil nitrogen. Recent evidence indicates that hopanoids, a family of steroid-like lipids, promote ! ...

    Abstract The symbioses between leguminous plants and nitrogen-fixing bacteria known as rhizobia are well known for promoting plant growth and sustainably increasing soil nitrogen. Recent evidence indicates that hopanoids, a family of steroid-like lipids, promote
    A major problem for global sustainability is feeding our exponentially growing human population while available arable land decreases. Harnessing the power of plant-beneficial microbes is a potential solution, including increasing our reliance on the symbioses of leguminous plants and nitrogen-fixing rhizobia. This study examines the role of hopanoid lipids in the symbiosis between
    MeSH term(s) Humans ; Glycine max ; Bradyrhizobium/genetics ; Bradyrhizobium/metabolism ; Symbiosis ; Root Nodules, Plant/microbiology ; Fabaceae/microbiology ; Nitrogen Fixation ; Vegetables ; Rhizobium/genetics ; Rhizobium/metabolism ; Nitrogen/metabolism ; Lipids
    Chemical Substances Nitrogen (N762921K75) ; Lipids
    Language English
    Publishing date 2024-03-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.02478-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Hopanoid lipids promote soybean-

    Pan, Huiqiao / Shim, Ashley / Lubin, Matthew B / Belin, Brittany J

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The symbioses between leguminous plants and nitrogen-fixing bacteria known as rhizobia are well known for promoting plant growth and sustainably increasing soil nitrogen. Recent evidence indicates that hopanoids, a family of steroid-like lipids, promote ! ...

    Abstract The symbioses between leguminous plants and nitrogen-fixing bacteria known as rhizobia are well known for promoting plant growth and sustainably increasing soil nitrogen. Recent evidence indicates that hopanoids, a family of steroid-like lipids, promote
    Importance: A major problem for global sustainability is feeding our exponentially growing human population while available arable land is decreasing, especially in areas with the greatest population growth. Harnessing the power of plant-beneficial microbes has gained attention as a potential solution, including the increasing our reliance on the symbioses of leguminous plants and nitrogen-fixing rhizobia. This study examines the role of hopanoid lipids in the symbiosis between
    Language English
    Publishing date 2023-09-05
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.04.556284
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Engineering Microorganisms for Cancer Immunotherapy.

    Liu, Dingkang / Yu, Lichao / Rong, Haibo / Liu, Lubin / Yin, Jun

    Advanced healthcare materials

    2024  , Page(s) e2304649

    Abstract: Cancer immunotherapy presents a promising approach to fight against cancer by utilizing the immune system. Recently, engineered microorganisms have emerged as a potential strategy in cancer immunotherapy. These microorganisms, including bacteria and ... ...

    Abstract Cancer immunotherapy presents a promising approach to fight against cancer by utilizing the immune system. Recently, engineered microorganisms have emerged as a potential strategy in cancer immunotherapy. These microorganisms, including bacteria and viruses, can be designed and modified using synthetic biology and genetic engineering techniques to target cancer cells and modulate the immune system. This review delves into various microorganism-based therapies for cancer immunotherapy, encompassing strategies for enhancing efficacy while ensuring safety and ethical considerations. The development of these therapies holds immense potential in offering innovative personalized treatments for cancer.
    Language English
    Publishing date 2024-04-10
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 2649576-4
    ISSN 2192-2659 ; 2192-2640
    ISSN (online) 2192-2659
    ISSN 2192-2640
    DOI 10.1002/adhm.202304649
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    In stock of ZB MED Cologne/Königswinter

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  4. Article ; Online: Tactile processing in mouse cortex depends on action context.

    Finkel, Eric A / Chang, Yi-Ting / Dasgupta, Rajan / Lubin, Emily E / Xu, Duo / Minamisawa, Genki / Chang, Anna J / Cohen, Jeremiah Y / O'Connor, Daniel H

    Cell reports

    2024  Volume 43, Issue 4, Page(s) 113991

    Abstract: The brain receives constant tactile input, but only a subset guides ongoing behavior. Actions associated with tactile stimuli thus endow them with behavioral relevance. It remains unclear how the relevance of tactile stimuli affects processing in the ... ...

    Abstract The brain receives constant tactile input, but only a subset guides ongoing behavior. Actions associated with tactile stimuli thus endow them with behavioral relevance. It remains unclear how the relevance of tactile stimuli affects processing in the somatosensory (S1) cortex. We developed a cross-modal selection task in which head-fixed mice switched between responding to tactile stimuli in the presence of visual distractors or to visual stimuli in the presence of tactile distractors using licking movements to the left or right side in different blocks of trials. S1 spiking encoded tactile stimuli, licking actions, and direction of licking in response to tactile but not visual stimuli. Bidirectional optogenetic manipulations showed that sensory-motor activity in S1 guided behavior when touch but not vision was relevant. Our results show that S1 activity and its impact on behavior depend on the actions associated with a tactile stimulus.
    MeSH term(s) Animals ; Mice ; Somatosensory Cortex/physiology ; Male ; Touch/physiology ; Mice, Inbred C57BL ; Optogenetics ; Touch Perception/physiology ; Behavior, Animal ; Female
    Language English
    Publishing date 2024-04-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2024.113991
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  5. Article ; Online: AKT activation because of PTEN loss upregulates xCT via GSK3β/NRF2, leading to inhibition of ferroptosis in PTEN-mutant tumor cells.

    Cahuzac, Kaitlyn M / Lubin, Abigail / Bosch, Kaitlyn / Stokes, Nicole / Shoenfeld, Sarah Mense / Zhou, Royce / Lemon, Haddy / Asara, John / Parsons, Ramon E

    Cell reports

    2023  Volume 42, Issue 5, Page(s) 112536

    Abstract: Here, we show that the tumor suppressor phosphatase and tensin homolog deleted from chromosome 10 (PTEN) sensitizes cells to ferroptosis, an iron-dependent form of cell death, by restraining the expression and activity of the cystine/glutamate antiporter ...

    Abstract Here, we show that the tumor suppressor phosphatase and tensin homolog deleted from chromosome 10 (PTEN) sensitizes cells to ferroptosis, an iron-dependent form of cell death, by restraining the expression and activity of the cystine/glutamate antiporter system X
    MeSH term(s) Animals ; Mice ; Cystine/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; NF-E2-Related Factor 2/genetics ; NF-E2-Related Factor 2/metabolism ; Ferroptosis ; Glycogen Synthase Kinase 3 beta/metabolism ; Fibroblasts/metabolism
    Chemical Substances Cystine (48TCX9A1VT) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; NF-E2-Related Factor 2 ; Glycogen Synthase Kinase 3 beta (EC 2.7.11.1)
    Language English
    Publishing date 2023-05-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2023.112536
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Corrigendum to "Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus" [Heliyon 9(4) (April 2023) e15032].

    Hernandez, Nancy E / Jankowski, Wojciech / Frick, Rahel / Kelow, Simon P / Lubin, Joseph H / Simhadri, Vijaya / Adolf-Bryfogle, Jared / Khare, Sagar D / Dunbrack, Roland L / Gray, Jeffrey J / Sauna, Zuben E

    Heliyon

    2023  Volume 9, Issue 8, Page(s) e17901

    Abstract: This corrects the article DOI: 10.1016/j.heliyon.2023.e15032.]. ...

    Abstract [This corrects the article DOI: 10.1016/j.heliyon.2023.e15032.].
    Language English
    Publishing date 2023-07-06
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2023.e17901
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  7. Article ; Online: A Parametric Rosetta Energy Function Analysis with LK Peptides on SAM Surfaces.

    Lubin, Joseph H / Pacella, Michael S / Gray, Jeffrey J

    Langmuir : the ACS journal of surfaces and colloids

    2018  Volume 34, Issue 18, Page(s) 5279–5289

    Abstract: Although structures have been determined for many soluble proteins and an increasing number of membrane proteins, experimental structure determination methods are limited for complexes of proteins and solid surfaces. An economical alternative or ... ...

    Abstract Although structures have been determined for many soluble proteins and an increasing number of membrane proteins, experimental structure determination methods are limited for complexes of proteins and solid surfaces. An economical alternative or complement to experimental structure determination is molecular simulation. Rosetta is one software suite that models protein-surface interactions, but Rosetta is normally benchmarked on soluble proteins. For surface interactions, the validity of the energy function is uncertain because it is a combination of independent parameters from energy functions developed separately for solution proteins and mineral surfaces. Here, we assess the performance of the RosettaSurface algorithm and test the accuracy of its energy function by modeling the adsorption of leucine/lysine (LK)-repeat peptides on methyl- and carboxy-terminated self-assembled monolayers (SAMs). We investigated how RosettaSurface predictions for this system compare with the experimental results, which showed that on both surfaces, LK-α peptides folded into helices and LK-β peptides held extended structures. Utilizing this model system, we performed a parametric analysis of Rosetta's Talaris energy function and determined that adjusting solvation parameters offered improved predictive accuracy. Simultaneously increasing lysine carbon hydrophilicity and the hydrophobicity of the surface methyl head groups yielded computational predictions most closely matching the experimental results. De novo models still should be interpreted skeptically unless bolstered in an integrative approach with experimental data.
    Language English
    Publishing date 2018-04-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2005937-1
    ISSN 1520-5827 ; 0743-7463
    ISSN (online) 1520-5827
    ISSN 0743-7463
    DOI 10.1021/acs.langmuir.8b00212
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  8. Article: Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus.

    Hernandez, Nancy E / Jankowski, Wojciech / Frick, Rahel / Kelow, Simon P / Lubin, Joseph H / Simhadri, Vijaya / Adolf-Bryfogle, Jared / Khare, Sagar D / Dunbrack, Roland L / Gray, Jeffrey J / Sauna, Zuben E

    Heliyon

    2023  Volume 9, Issue 4, Page(s) e15032

    Abstract: The human infectious disease COVID-19 caused by the SARS-CoV-2 virus has become a major threat to global public health. Developing a vaccine is the preferred prophylactic response to epidemics and pandemics. However, for individuals who have contracted ... ...

    Abstract The human infectious disease COVID-19 caused by the SARS-CoV-2 virus has become a major threat to global public health. Developing a vaccine is the preferred prophylactic response to epidemics and pandemics. However, for individuals who have contracted the disease, the rapid design of antibodies that can target the SARS-CoV-2 virus fulfils a critical need. Further, discovering antibodies that bind multiple variants of SARS-CoV-2 can aid in the development of rapid antigen tests (RATs) which are critical for the identification and isolation of individuals currently carrying COVID-19. Here we provide a proof-of-concept study for the computational design of high-affinity antibodies that bind to multiple variants of the SARS-CoV-2 spike protein using RosettaAntibodyDesign (RAbD). Well characterized antibodies that bind with high affinity to the SARS-CoV-1 (but not SARS-CoV-2) spike protein were used as templates and re-designed to bind the SARS-CoV-2 spike protein with high affinity, resulting in a specificity switch. A panel of designed antibodies were experimentally validated. One design bound to a broad range of variants of concern including the Omicron, Delta, Wuhan, and South African spike protein variants.
    Language English
    Publishing date 2023-04-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2023.e15032
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  9. Article ; Online: Using pre-treatment de novo threat conditioning outcomes to predict treatment response to DCS augmentation of exposure-based CBT.

    Lubin, Rebecca E / Fitzgerald, Hayley E / Rosenfield, David / Carpenter, Joseph K / Papini, Santiago / Dutcher, Christina D / Dowd, Sheila M / Hofmann, Stefan G / Pollack, Mark H / Smits, Jasper A J / Otto, Michael W

    Journal of psychiatric research

    2023  Volume 164, Page(s) 357–363

    Abstract: Background: Over a decade and a half of research has resulted in inconsistent evidence for the efficacy of d-cycloserine (DCS), a partial glutamatergic N-methyl-D-aspartate agonist, for augmenting exposure-based cognitive behavioral therapy (CBT) for ... ...

    Abstract Background: Over a decade and a half of research has resulted in inconsistent evidence for the efficacy of d-cycloserine (DCS), a partial glutamatergic N-methyl-D-aspartate agonist, for augmenting exposure-based cognitive behavioral therapy (CBT) for anxiety- and fear-based disorders. These variable findings have motivated the search for moderators of DCS augmentation efficacy.
    Methods: In this secondary analysis of a previous randomized clinical trial, we evaluated the value of de novo threat conditioning outcomes-degree of threat acquisition, extinction, and extinction retention-for predicting treatment response to exposure-based CBT for social anxiety disorder, applied with and without DCS augmentation in a sample of 59 outpatients.
    Results: We found that average differential skin conductance response (SCR) during extinction and extinction retention significantly moderated the prediction of clinical response to DCS: participants with poorer extinction and extinction retention showed relatively improved treatment response with DCS. No such effects were found for expectancy ratings, consistent with accounts of DCS selectively aiding lower-order but not higher-order extinction learning.
    Conclusions: These findings provide support for extinction and extinction retention outcomes from threat conditioning as potential pre-treatment biomarkers for DCS augmentation benefits. Independent of DCS augmentation, the current study did not support threat conditioning outcomes as useful for predicting response to exposure-based CBT.
    MeSH term(s) Humans ; Anxiety Disorders/drug therapy ; Cognitive Behavioral Therapy/methods ; Combined Modality Therapy ; Cycloserine/therapeutic use ; Extinction, Psychological ; Treatment Outcome
    Chemical Substances Cycloserine (95IK5KI84Z)
    Language English
    Publishing date 2023-06-19
    Publishing country England
    Document type Evaluation Study ; Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 3148-3
    ISSN 1879-1379 ; 0022-3956
    ISSN (online) 1879-1379
    ISSN 0022-3956
    DOI 10.1016/j.jpsychires.2023.06.008
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    In stock of ZB MED Cologne/Königswinter

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  10. Article ; Online: Toluene-mercuric modified USEPA Method 3060A to eliminate interference of sulfide-based reductants with Cr(VI) determination.

    Pang, Jingli / Luo, Yating / Yang, Yuanqiang / Tong, Jianhao / Wang, Lubin / Wu, Hanxin / Shi, Jiyan

    The Science of the total environment

    2023  Volume 887, Page(s) 164209

    Abstract: The validity of USEPA Method 3060A as universal Cr(VI) analysis method for remediated soil is controversial. We investigated soil Cr(VI) remediation performance by commonly used reductants ( ... ...

    Abstract The validity of USEPA Method 3060A as universal Cr(VI) analysis method for remediated soil is controversial. We investigated soil Cr(VI) remediation performance by commonly used reductants (FeSO
    Language English
    Publishing date 2023-05-13
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2023.164209
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    In stock of ZB MED Cologne/Königswinter

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