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Unis R, Gnaim R, Kashyap M, Shamis O, Gnayem N, Gozin M, Liberzon A, Gnaim J, Golberg A. Bioconversion of bread waste into high-quality proteins and biopolymers by fermentation of archaea Haloferax mediterranei. Front Microbiol 2024; 15:1491333. [PMID: 39777146 PMCID: PMC11703665 DOI: 10.3389/fmicb.2024.1491333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Accepted: 09/30/2024] [Indexed: 01/11/2025] Open
Abstract
The valorization of bread waste into high-quality protein and biopolymers using the halophilic microorganism Haloferax mediterranei presents a sustainable approach to food waste management and resource optimization. This study successfully coproduced protein and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) biopolymer with a biomass content of 8.0 ± 0.1 g L-1 and a productivity of 11.1 mg L-1 h-1. The fermentation process employed 3.0% w/v of enzymatically hydrolyzed bread waste. The amino acid profile of the cell biomass revealed a total content of 358 g kg-1 of biomass dry weight (DW), including 147 g kg-1 DW of essential amino acids. The protein quality, assessed through in-vitro enzyme digestion, indicated a high-quality protein with a digestibility value of 0.91 and a protein digestibility-corrected amino acid score (PDCAAS) of 0.78. The PHBV biopolymer component (36.0 ± 6.3% w/w) consisted of a copolymer of 3-hydroxybutyrate and 3-hydroxyvalerate in a 91:9 mol% ratio. This bioconversion process not only mitigates food waste but also generates valuable biomaterials.
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Chao LM, Jia L, Wang S, Liberzon A, Ravi S, Couzin ID, Li L. Tailbeat perturbations improve swimming efficiency by reducing the phase lag between body motion and the resulting fluid response. PNAS NEXUS 2024; 3:pgae073. [PMID: 38487161 PMCID: PMC10939483 DOI: 10.1093/pnasnexus/pgae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/02/2024] [Indexed: 03/17/2024]
Abstract
Understanding how animals swim efficiently and generate high thrust in complex fluid environments is of considerable interest to researchers in various fields, including biology, physics, and engineering. However, the influence of often-overlooked perturbations on swimming fish remains largely unexplored. Here, we investigate the propulsion generated by oscillating tailbeats with superimposed rhythmic perturbations of high frequency and low amplitude. We reveal, using a combination of experiments in a biomimetic fish-like robotic platform, computational fluid dynamics simulations, and theoretical analysis, that rhythmic perturbations can significantly increase both swimming efficiency and thrust production. The introduction of perturbations increases pressure-induced thrust, while reduced phase lag between body motion and the subsequent fluid dynamics response improves swimming efficiency. Moreover, our findings suggest that beneficial perturbations are sensitive to kinematic parameters, resolving previous conflicts regarding the effects of such perturbations. Our results highlight the potential benefits of introducing perturbations in propulsion generators, providing potential hypotheses for living systems and inspiring the design of artificial flapping-based propulsion systems.
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Gonzalez-Karlsson A, Golov Y, Steinitz H, Moncaz A, Halon E, Horowitz AR, Goldenberg I, Gurka R, Liberzon A, Soroker V, Jurenka R, Harari AR. Corrigendum to: Males perceive honest information from female released sex pheromone in a moth. Behav Ecol 2022. [DOI: 10.1093/beheco/arac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Gonzalez-Karlsson A, Golov Y, Steinitz H, Moncaz A, Halon E, Horowitz AR, Goldenberg I, Gurka R, Liberzon A, Soroker V, Jurenka R, Harari AR. Males perceive honest information from female released sex pheromone in a moth. Behav Ecol 2021. [DOI: 10.1093/beheco/arab073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
There is accumulating evidence that male insects advertise their quality to conspecific females through pheromones. However, most studies of female released sex pheromone assume information transfer regarding merely the species of the female and her mating status. We show that more information is conveyed through the female sex pheromone, positioning it as an honest sexual trait. We demonstrate that females in bad physical conditions (small, starved, or old) lay significantly fewer eggs than females in good conditions (large, fed, or young). The ratio of components in the sex pheromone blend in gland extracts of the female pink bollworm moths provided honest information on most of the phenotypic conditions tested, whereas the pheromone amount in the glands provided an honest signal of quality for extreme phenotypes only. Moreover, males used the information conveyed by the female pheromone to choose their mates, approaching females that signaled higher reproductive potential. In addition, when simulating the female effect, using the synthetic pheromone blend that represents higher quality females (0.6:0.4 ZZ:ZE), more males were attracted to this blend than to the blend representing the population mean (0.5:0.5 ZZ:ZE). Both, female advertisement for males and the male choosiness, suggest that pheromones have evolved as sexual traits under directional, sexual selection. We suggest that the pheromone blend may serve as a multicomponent signal whereby each component adds information concerning the current condition of the female, and all are necessary to elicit a mate searching response.
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Kogan I, Korolik P, Cartier H, Adhoute H, Liberzon A. In vitro evaluation of aspiration of hyaluronic acid filler with a new saline flashing method. J Cosmet Dermatol 2020; 19:2513-2518. [DOI: 10.1111/jocd.13651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 01/03/2023]
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Liberzon A, Harrington K, Daniel N, Gurka R, Harari A, Zilman G. Moth-inspired navigation algorithm in a turbulent odor plume from a pulsating source. PLoS One 2018; 13:e0198422. [PMID: 29897978 PMCID: PMC5999112 DOI: 10.1371/journal.pone.0198422] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/19/2018] [Indexed: 11/24/2022] Open
Abstract
Some female moths attract male moths by emitting series of pulses of pheromone filaments propagating downwind. The turbulent nature of the wind creates a complex flow environment, and causes the filaments to propagate in the form of patches with varying concentration distributions. Inspired by moth navigation capabilities, we propose a navigation strategy that enables a flier to locate an upwind pulsating odor source in a windy environment using a single threshold-based detection sensor. This optomotor anemotaxis strategy is constructed based on the physical properties of the turbulent flow carrying discrete puffs of odor and does not involve learning, memory, complex decision making or statistical methods. We suggest that in turbulent plumes from a pulsating point source, an instantaneously measurable quantity referred as a “puff crossing time”, improves the success rate as compared to the navigation strategies based on temporally regular zigzags due to intermittent contact, or an “internal counter”, that do not use this information. Using computer simulations of fliers navigating in turbulent plumes of the pulsating point source for varying flow parameters such as turbulent intensities, plume meandering and wind gusts, we obtained statistics of navigation paths towards the pheromone sources. We quantified the probability of a successful navigation as well as the flight parameters such as the time spent searching and the total flight time, with respect to different turbulent intensities, meandering or gusts. The concepts learned using this model may help to design odor-based navigation of miniature airborne autonomous vehicles.
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Habiby O, Nahor O, Israel A, Liberzon A, Golberg A. Exergy efficiency of light conversion into biomass in the macroalga Ulva sp. (Chlorophyta) cultivated under the pulsed light in a photobioreactor. Biotechnol Bioeng 2018. [PMID: 29537063 DOI: 10.1002/bit.26588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Marine macroalgae are a potential feedstock for biorefineries that can reduce dependence on fossil fuels and contribute to bioeconomy. New knowledge and technologies for efficient conversion of solar energy into macroalgae biomass are needed to increase biomass yields and energy conversion efficiency. In this work, we show that the green macroalgae from Ulva sp. can grow under the pulsed light in a photobioreactor with higher exergy conversion efficiency in comparison to cultivation under constant light with the same intensity. In the tested frequencies, 1-40 Hz and duty cycles (DC) 1-100%, DC has a stronger impact on the growth rate than frequency. The efficiency of light transformation into biomass increased with decreasing DC. Pulsating with DC 20% led to 60% of the biomass chemical energy yield for the respective constant light (DC 100%). Models of Ulva sp. growth rate and exergy conversion efficiency as a function of pulsating light parameters were developed. These results open new directions to enhance solar to chemical energy conversion through macroalgae by controlling the light distribution in the macroalgal biomass.
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Stalnov O, Ben-Gida H, Kirchhefer AJ, Guglielmo CG, Kopp GA, Liberzon A, Gurka R. On the Estimation of Time Dependent Lift of a European Starling (Sturnus vulgaris) during Flapping Flight. PLoS One 2015; 10:e0134582. [PMID: 26394213 PMCID: PMC4579066 DOI: 10.1371/journal.pone.0134582] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 07/12/2015] [Indexed: 11/28/2022] Open
Abstract
We study the role of unsteady lift in the context of flapping wing bird flight. Both aerodynamicists and biologists have attempted to address this subject, yet it seems that the contribution of unsteady lift still holds many open questions. The current study deals with the estimation of unsteady aerodynamic forces on a freely flying bird through analysis of wingbeat kinematics and near wake flow measurements using time resolved particle image velocimetry. The aerodynamic forces are obtained through two approaches, the unsteady thin airfoil theory and using the momentum equation for viscous flows. The unsteady lift is comprised of circulatory and non-circulatory components. Both approaches are presented over the duration of wingbeat cycles. Using long-time sampling data, several wingbeat cycles have been analyzed in order to cover both the downstroke and upstroke phases. It appears that the unsteady lift varies over the wingbeat cycle emphasizing its contribution to the total lift and its role in power estimations. It is suggested that the circulatory lift component cannot assumed to be negligible and should be considered when estimating lift or power of birds in flapping motion.
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Guala M, Liberzon A, Lüthi B, Kinzelbach W, Tsinober A. Stretching and tilting of material lines in turbulence: the effect of strain and vorticity. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 73:036303. [PMID: 16605647 DOI: 10.1103/physreve.73.036303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2005] [Indexed: 05/08/2023]
Abstract
The Lagrangian evolution of infinitesimal material lines is investigated experimentally through three dimensional particle tracking velocimetry (3D-PTV) in quasihomogeneous turbulence with the Taylor microscale Reynolds number Re(lambda)=50. Through 3D-PTV we access the full tensor of velocity derivatives du(i)/dx(j) along particle trajectories, which is necessary to monitor the Lagrangian evolution of infinitesimal material lines l. By integrating the effect on l of (i) the tensor du(i)/dx(j), (ii) its symmetric part s(ij), (iii) its antisymmetric part r(ij), along particle trajectories, we study the evolution of three sets of material lines driven by a genuine turbulent flow, by "strain only," or by "vorticity only," respectively. We observe that, statistically, vorticity reduces the stretching rate l(i)l(j)s(ij)/l2, altering (by tilting material lines) the preferential orientation between l and the first (stretching) eigenvector lambda1 of the rate of strain tensor. In contrast, s(ij), in "absence" of vorticity, significantly contributes to both tilting and stretching, resulting in an enhanced stretching rate compared to the case of material lines driven by the full tensor du(i)/dx(j). The same trend is observed for the deformation of material volumes.
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Frenkel V, Gurka R, Liberzon A, Shavit U, Kimmel E. Preliminary investigations of ultrasound induced acoustic streaming using particle image velocimetry. ULTRASONICS 2001; 39:153-156. [PMID: 11349995 DOI: 10.1016/s0041-624x(00)00064-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Particle image velocimetry was used to investigate ultrasound-induced acoustic streaming in a system for the enhanced uptake of substances from the aquatic medium into fish. Four distinct regions of the induced streaming in the system were observed and measured. One of the regions was identified as an preferential site for substance uptake, where the highest velocities in proximity to the fish surface were measured. A positive linear relationship was found between the ultrasound intensity and the maximum streaming velocity, where a unitless geometric factor, specific to the system, was calculated for correcting the numerical relationship between the two parameters. The results are part of a comprehensive study aimed at improving mass transdermal administrations of substances (e.g. vaccines, hormones) into fish from the aquatic medium.
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Zevin-Sonkin D, Liberzon A, Chochikyan A, Hovhannisyan H, Lvovsky L, Ulanovsky L. DENS (differential extension with nucleotide subsets): application to the sequencing of human genomic DNA and cDNA. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 2000; 10:245-54. [PMID: 10727081 DOI: 10.3109/10425179909033953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Here we describe further development of our method of DNA sequencing by Differential Extension with Nucleotide Subsets (DENS) and its application to the sequencing of human genomic DNA and full-insert cDNA. Essentially, DENS is primer walking without custom primer synthesis; instead, DENS uses a presynthesized library of octamer primers degenerate in two positions (4,096 tubes/sequences for a complete library). DENS converts an octamer selected from this library into a long primer on the template, at the intended site only. This is done using a two-step procedure which starts with a limited extension of the octamer (at 20 degrees C) in the presence of only two of the four possible dNTPs. The primer is extended by five bases or more at the intended priming site, which is deliberately selected to maximize the extension length (as are the two-dNTP set and the primer itself). The subsequent termination reaction at 60 degrees C then accepts the primer extended at the intended site, but not at alternative sites, where the initial extension (if any) is generally much shorter. This paper presents a set of rules for selection of DENS priming sites. We also compare different ways of template preparation for DENS sequencing. The data were obtained from primer walking on three human genomic DNA subclones of 3 to 4 kbp and four cDNA clones containing inserts of 1.9, 2.3, 3.8, and 4.9 kbp. Full-length sequences were obtained from both strands of each subclone by automated dye-terminator fluorescent DNA sequencing using DENS with degenerate octamer primers. We compared the following types of DNA templates: single-stranded and double-stranded phagemid DNA, double-stranded PCR products, asymmetric PCR products, and single-stranded DNA produced by digestion with Lambda Exonuclease of double-stranded PCR product phosphorylated at one end (Exo-PCR). While all of the preps were found to work, the best results were obtained with Exo-PCR and phagemid single-stranded DNA. Exo-PCR directly from overnight bacterial culture with no plasmid prep of any kind yielded templates for DENS as good as Exo-PCR from purified DNA. We found that the Tm of the differentially extended octamers is an important factor in the success of DENS. Clustering of successful reactions was clearly distinguished in the Tm range of 50-66 degrees C, with success rates of 70% for Exo-PCR and 65% for ss phagemid templates.
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Lvovsky L, Ioshikhes I, Raja MC, Zevin-Sonkin D, Sobolev IA, Liberzon A, Shwartzburd J, Ulanovsky LE. Interdependence between DNA template secondary structure and priming efficiencies of short primers. Nucleic Acids Res 1998; 26:5525-32. [PMID: 9826780 PMCID: PMC148000 DOI: 10.1093/nar/26.23.5525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Here we analyze the effect of DNA folding on the performance of short primers and describe a simple technique for assessing hitherto uncertain values of thermodynamic parameters that determine the folding of single-stranded DNA into secondary structure. An 8mer with two degenerate positions is extended simultaneously at several complementary sites on a known template (M13mp18) using one, two or three (but never all four) of the possible dNTPs. The length of the extension is site specific because it is limited by the first occurrence in the downstream template sequence of a base whose complementary dNTP is not present. The relative priming efficiencies of different sites are then ranked by comparing their band brightnesses on a gel. The priming efficiency of a short primer (unlike conventional long primers) depends dramatically on the secondary structure of the template at and around the priming site. We calculated the secondary structure and its effect on priming using a simple model with relatively few parameters which were then optimized to achieve the best match between the predictions and the actual rankings of the sites in terms of priming efficiency. This work introduces an efficient and conceptually novel approach that in the future can make use of more data to optimize a larger set of DNA folding parameters in a more refined model. The model we used, however crude it may be, significantly improved the prediction of priming efficiencies of 8mer primers and appreciably raised the success rate of our DNA sequencing technique (from 67 to 91% with a significance of P < 7 x 10(-5)), which uses such primers.
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Shpungin S, Liberzon A, Bangio H, Yona E, Katcoff DJ. Association of yeast SIN1 with the tetratrico peptide repeats of CDC23. Proc Natl Acad Sci U S A 1996; 93:8274-7. [PMID: 8710860 PMCID: PMC38660 DOI: 10.1073/pnas.93.16.8274] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The yeast SIN1 protein is a nuclear protein that together with other proteins behaves as a transcriptional repressor of a family of genes. In addition, sin1 mutants are defective in proper mitotic chromosome segregation. In an effort to understand the basis for these phenotypes, we employed the yeast two-hybrid system to identify proteins that interact with SIN1 in vivo. Here we demonstrate that CDC23, a protein known to be involved in sister chromatid separation during mitosis, is able to directly interact with SIN1. Furthermore, using recombinant molecules in vitro, we show that the N terminal of SIN1 is sufficient to bind a portion of CDC23 consisting solely of tetratrico peptide repeats. Earlier experiments identified the C-terminal domain of SIN1 to be responsible for interaction with a protein that binds the regulatory region of HO, a gene whose transcription is repressed by SIN1. Taken together with the results presented here, we suggest that SIN1 is a chromatin protein having at least a dual function: The N terminal of SIN1 interacts with the tetratrico peptide repeat domains of CDC23, a protein involved in chromosome segregation, whereas the C terminal of SIN1 binds proteins involved in transcriptional regulation.
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Liberzon A, Shpungin S, Bangio H, Yona E, Katcoff DJ. Association of yeast SAP1, a novel member of the 'AAA' ATPase family of proteins, with the chromatin protein SIN1. FEBS Lett 1996; 388:5-10. [PMID: 8654588 DOI: 10.1016/0014-5793(96)00500-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The yeast SIN1 protein is a nuclear protein that together with other proteins behaves as a transcriptional repressor of a family of genes. In addition, sin1 mutants are defective in proper mitotic chromosome segregation. In an effort to understand the basis for these phenotypes, we employed the yeast two-hybrid system to identify proteins that interact with SIN1 in vivo. Here, we demonstrate that SAP1, a novel protein belonging to the 'AAA' family of ATPases, is able to directly interact with SIN1. Furthermore, we show, using recombinant molecules in vitro, that a short 27 amino acid sequence near the N-terminal of SIN1 is sufficient to bind SAP1. Previous experiments defined different domains of SIN that interact with other proteins and with DNA. The C-terminal domain of SIN1 was shown to be responsible for interaction with a protein that binds the regulatory region of HO, a gene whose transcription is repressed by SIN1. The central 'HMG1-like region' of SIN1 binds DNA, while the N-terminal of SIN1 can bind CDC23, a protein that regulates chromosome segregation. These data, taken together with the results presented here, suggest that SIN1 is a multifunctional chromatin protein that can interact with a number of different proteins that are involved in several different cellular functions.
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