T3SS and alginate biosynthesis of Pseudomonas aeruginosa impair healing of infected rabbit wounds
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Karna, S. L. Rajasekhar↗
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Evidence that immunization with TP0751, a bipartite Treponema pallidum lipoprotein with an intrinsically disordered region and lipocalin fold, fails to protect in the rabbit model of experimental syphilis
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99 GENERAL AND MISCELLANEOUS↗
Chasing the Rabbit: A Systematic Exploration of Software-Defined HPC storage
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Computer science↗
Rapid Sample Insertion/Extraction Systems for Gamma Irradiation
The Rapid Sample Insertion/Extraction System for Gamma Irradiation, otherwise known as the "rabbit" system, was a four-week long project which included many different aspects; from coding an Arduino to building PVC piping to 3-D printing the "rabbit" capsules. The "rabbit" system is a system of PVC piping that allows a quick and efficient transfer of materials into/out of one of the irradiation chambers in the Gamma Irradiation Facility (GIF) with the use of a 3-D printed "rabbit." This "rabbit" encapsulates material to be irradiated and carries it from a position outside of the irradiation chamber to the basket inside of the chamber. The main purpose of this system is to save time and provide more exact data without any delays that normally occur when a person has to enter the chamber, retrieve data, and then analyze the data. This system should take measurements and retrieve the data instantaneously. The way in which the "rabbit" is sent through the PVC piping is with an advanced bi-directional, high-throughput pneumatic system, or a shop vacuum cleaner. When the vacuum is set to blow or suck then the "rabbit" will be pulled through the PVC piping to its intended destination and will hit sensors along the sides of the tubing when it reaches the end of the piping. These sensors tell the Arduino that the "rabbit" is finished moving throughout the tubing and stops a timer. Another timer is used to see how long the "rabbit" is being irradiated so when the "rabbit" reaches the sensors in the basket in the irradiation chamber another timer is started and it ends when the sensors no longer detect the "rabbit," which means that it has begun its journey back to the starting point.
38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
Additively Manufactured Pressure Limiting Irradiation Capsule for the High Flux Isotope Reactor
The Advanced Materials and Manufacturing Technologies (AMMT) program previously demonstrated an additively manufactured (AM) irradiation capsule (commonly referred to as a “rabbit”) from 316H stainless steel (SS) for insertion into the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL)1. This report details efforts to design and fabricate an AM pressure limiting structure (PLS) into one of the end caps of a rabbit capsule and qualify it for insertion into HFIR. The PLS includes a thin cylindrical rupture wall, a shield, and internal supports to facilitate printing and ensure mechanical integrity. Its overall dimensions are 9-mm tall and 10-mm in diameter— equivalent to about one-fourth of the size of a AAA battery. The PLS maintains safe internal operating pressures for a rabbit capsule while in the reactor. Although this application is specific to HFIR, the approach lends itself to further applications in industrial, aeronautical, advanced space and power generation environments. Several PLS rabbits capsules have been successfully designed, fabricated, pressure tested, and qualified for future insertion into the HFIR for irradiation and post-irradiation evaluation.
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing
Antibody therapeutics are one of the most important classes of drugs. Antibody structures have become an integral part of predicting the behavior of potential therapeutics, either directly or as the basis of modeling. Structures of Fab:antigen complexes have even greater value. While the crystallization and structure determination of Fabs is easy relative to many other protein classes, especially membrane proteins, broad screening and optimization of crystalline hits is still necessary. Through a comprehensive review of rabbit Fab crystal contacts and their incompatibility with human Fabs, we identified a small secondary structural element from the rabbit light chain constant domain potentially responsible for hindering the crystallization of human Fabs. Upon replacing the human kappa constant domain FG loop (HQGLSSP) with the two residue shorter rabbit loop (QGTTS), we dramatically improved the crystallization of human Fabs and Fab:antigen complexes. Our design, which we call “Crystal Kappa”, enables rapid crystallization of human fabs and fab complexes in a broad range of conditions, with less material in smaller screens or from dilute solutions.
59 BASIC BIOLOGICAL SCIENCES↗
Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles
Broad immune responses are needed to mitigate viral evolution and escape. To induce antibodies against conserved receptor-binding domain (RBD) regions of SARS-like betacoronavirus (sarbecovirus) spike proteins that recognize SARS-CoV-2 variants of concern and zoonotic sarbecoviruses, we developed mosaic-8b RBD nanoparticles presenting eight sarbecovirus RBDs arranged randomly on a 60-mer nanoparticle. Mosaic-8b immunizations protected animals from challenges from viruses whose RBDs were matched or mismatched to those on nanoparticles. Here, we describe neutralizing mAbs isolated from mosaic-8b-immunized rabbits, some on par with Pemgarda, the only currently FDA-approved therapeutic mAb. Deep mutational scanning, in vitro selection of spike resistance mutations, and single-particle cryo-electron microscopy structures of spike–antibody complexes demonstrated targeting of conserved RBD epitopes. Rabbit mAbs included critical D-gene segment RBD-recognizing features in common with human anti-RBD mAbs, despite rabbit genomes lacking an equivalent human D-gene segment, thus demonstrating that the immune systems of humans and other mammals can utilize different antibody gene segments to arrive at similar modes of antigen recognition. These results suggest that animal models can be used to elicit anti-RBD mAbs with similar properties to those raised in humans, which can then be humanized for therapeutic use, and that mosaic RBD nanoparticle immunization coupled with multiplexed screening represents an efficient way to generate and select broadly cross-reactive therapeutic pan-sarbecovirus and pan-SARS-CoV-2 variant mAbs.
Science & Technology - Other Topics↗
Subcutaneous power supply by NIR-II light
Implantable medical devices are wished to be recharged via contactless power transfer technologies without interventional operations. Superior to subcutaneous power supply by visible light or electromagnetic wave, second near-infrared (NIR-II) light is predicted to possess 60 times subcutaneous power transmission but hard to be utilized. Here we report a photo-thermal-electric converter via the combination of photothermal conversion and thermoelectric conversion. It is able to generate an output power as high as 195 mW under the coverage of excised tissues, presenting advantages of non-invasion, high output power, negligible biological damage, and deep tissue penetration. As an in vivo demonstration, the output power of a packaged converter in the abdominal cavity of a rabbit reaches 20 mW under NIR-II light irradiation through the rabbit skin with a thickness of 8.5 mm. This value is high enough to recharge an implanted high-power-consumption wireless camera and transfer video signal out of body in real-time.
60 APPLIED LIFE SCIENCES↗
405 nm light microbicidal efficacy on Treponema pallidum spiked in ex vivo human platelets
Abstract Pathogen reduction technologies using chemicals and or UV light have been demonstrated to improve the safety of ex vivo platelets from infectious diseases. However, UV light exposure also may affect the treated products, depending on wavelength and exposure. Alternatively, visible spectra 405 nm violet-blue light has broad-spectrum microbicidal activity. Here we tested the effect of 405 nm light onTreponema pallidum, the bacterium that causes syphilis. We contaminated platelets stored in plasma with two treponemal concentrations (low and high titers) and treated an aliquot with 270 J/cm 2 dose (irradiance = 15 mW/cm 2 ) of 405 nm light while another aliquot remained untreated. Next, we inoculated intradermally an aliquot of both samples into rabbits. Rabbits inoculated with untreated samples developed syphilis while animals inoculated with light-treated samples did not. Thus, inactivation was demonstrated to the limit of detection of the bioassay. We estimated > 2 log 10 and > 4 log 10 reduction in the low and high dose studies, respectively. These results provide proof-of-concept that 405 nm light is effective in reducing syphilis risk in ex vivo platelets.
Science & Technology - Other Topics↗
Structural basis for differential recognition of phosphohistidine-containing peptides by 1-pHis and 3-pHis monoclonal antibodies
In 2015, monoclonal antibodies (mAbs) that selectively recognize the 1-pHis or 3-pHis isoforms of phosphohistidine were developed by immunizing rabbits with degenerate Ala/Gly peptides containing the nonhydrolyzable phosphohistidine (pHis) analog- phosphotriazolylalanine (pTza). Here, we report structures of five rabbit mAbs bound to cognate pTza peptides: SC1-1 and SC50-3 that recognize 1-pHis, and their 3-pHis–specific counterparts, SC39-4, SC44-8, and SC56-2. These cocrystal structures provide insights into the binding modes of the pTza phosphate group that are distinct for the 1- and 3-pHis mAbs with the selectivity arising from specific contacts with the phosphate group and triazolyl ring. The mode of phosphate recognition in the 3-pHis mAbs recapitulates the Walker A motif, as present in kinases. The complementarity-determining regions (CDRs) of four of the Fabs interact with the peptide backbone rather than peptide side chains, thus conferring sequence independence, whereas SC44-8 shows a proclivity for binding a GpHAGA motif mediated by a sterically complementary CDRL3 loop. Specific hydrogen bonding with the triazolyl ring precludes recognition of pTyr and other phosphoamino acids by these mAbs. Kinetic binding experiments reveal that the affinity of pHis mAbs for pHis and pTza peptides is submicromolar. Bound pHis mAbs also shield the pHis peptides from rapid dephosphorylation. The epitope–paratope interactions illustrate how these anti-pHis antibodies are useful for a wide range of research techniques and this structural information can be utilized to improve the specificity and affinity of these antibodies toward a variety of pHis substrates to understand the role of histidine phosphorylation in healthy and diseased states.
59 BASIC BIOLOGICAL SCIENCES↗
Neutralizing Antibodies Induced by First-Generation gp41-Stabilized HIV-1 Envelope Trimers and Nanoparticles
Self-assembling protein nanoparticles (NPs) presenting BG505 envelope (Env) trimers can elicit tier 2 HIV-1-neutralizing antibody (NAb) responses more effectively than soluble trimers. In the present study, monoclonal NAbs were isolated from previously immunized mice and rabbits for structural and functional analyses, which revealed that potent mouse NAbs recognize the C3/V4 region and small NP-elicited rabbit NAbs primarily target known glycan holes on BG505 Env.
59 BASIC BIOLOGICAL SCIENCES↗
Qualification of an Additively Manufactured Irradiation Capsule for the High Flux Isotope Reactor
As part of the Advanced Materials and Manufacturing Technologies (AMMT) Program’s work package Component Manufacturing and Demonstrations from AM 316 SS, irradiation capsules have been additively manufactured (AM) from 316H stainless steel for insertion into the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL). The irradiation capsules (commonly referred to as “rabbits”) have been successfully designed, fabricated, pressure tested, qualified, and inserted into the HFIR for irradiation and post-irradiation evaluation. Each rabbit consists of an AM housing and two standard AM end caps. The design is simple and amenable to geometric and material customization. This demonstration helps pave the way for acceptance of AM safety-critical components for nuclear energy applications.
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
A Single-Board Fermilab Timing Pipeline on the Xilinx KR260: Decode, Timestamp, Publish, Mirror
Full-width abstract \renewcommand{\maketitlehookd}{% \begin{abstract} \noindent Fermilab's accelerator timing links broadcast short event codes to thousands of devices at once, but the links themselves carry no absolute notion of time; that comes separately from a White Rabbit reference. This work builds the piece that ties the two together on a single board. On a Xilinx Kria KR260 (Zynq UltraScale+), the programmable logic decodes a real Fermilab TCLK link, stamps every event with an absolute White-Rabbit \{sec, ns\} UTC time, and reads the timestamped stream out over AXI4-Lite; a thin Linux process on the same die publishes each event into a Redis stream on the control network. To exercise the full chain on one board, the decoded events are re-encoded as gigabit ACLK, transmitted out an SFP+ optical port, looped back over a short fiber jumper, and decoded again on the same timeline, and are additionally mirrored as an ACLK-Lite Manchester waveform for benchtop probing. Across sustained, multi-day testing against real Fermilab TCLK, the pipeline has decoded, timestamped, and published hundreds of millions of events with practically zero loss, and folding the timestamped stream on the 60-second accelerator supercycle recovers the machine's periodic structure directly from the published data.
Rossel, Jacob [UC, Berkeley; Fermilab] (ORCID:0009↗
Mechanistic within-host mathematical model of inhalational anthrax
We present a mathematical model of the dynamics of Bacillus anthracis bacteria within the lymph nodes and blood of a host, following inhalation of an initial dose of spores. We also incorporate the dynamics of protective antigen, which is the binding component of the anthrax toxin produced by the bacteria. The model offers a mechanistic description of the early infection dynamics of inhalational anthrax, while its stochastic nature allows us to study the probabilities of different outcomes (for example, how likely it is that the infection will be cleared for a given inhaled dose of spores) in order to explain dose-response data for inhalational anthrax. The model is calibrated via a Bayesian approach, using in vivo data from New Zealand white rabbit and guinea pig infection studies, enabling within-host parameters to be estimated. We also leverage incubation-period data from the Sverdlovsk 1979 anthrax outbreak to show that the model can accurately describe human time-to-symptoms data under reasonable parameter regimes. Finally, we derive a simple approximate formula for the probability of symptom onset before time t, assuming that the number of inhaled spores has a Poisson distribution.
59 BASIC BIOLOGICAL SCIENCES↗
Use of X-Ray Fluorescence Microscopy for Studies on Research Models of Hepatocellular Carcinoma
Introduction: TheraSphere ® microspheres containing yttrium 90 Y are among many radioembolization agents used clinically to reduce liver tumor burden, and their effects on cancer volume reduction are well-established. At the same time, concerns about off target tissue injury often limit their use. Deeper investigation into tissue distribution and long-term impact of these microspheres could inform us about additional ways to use them in practice. Methods: Healthy rat liver and rabbit liver tumor samples from animals treated with TheraSpheres were sectioned and their elemental maps were generated by X-ray fluorescence microscopy (XFM) at the Advanced Photon Source (APS) synchrotron at Argonne National Laboratory (ANL). Results: Elemental imaging allowed us to identify the presence and distribution of TheraSpheres in animal tissues without the need for additional sample manipulation or staining. Ionizing radiation produced by 90 Y radioactive contaminants present in these microspheres makes processing TheraSphere treated samples complex. Accumulation of microspheres in macrophages was observed. Conclusions: This is the first study that used XFM to evaluate the location of microspheres and radionuclides in animal liver and tumor samples introduced through radioembolization. XFM has shown promise in expanding our understanding of radioembolization and could be used for investigation of human patient samples in the future.
60 APPLIED LIFE SCIENCES↗
Identification of an Attenuated Substrain of Francisella tularensis SCHU S4 by Phenotypic and Genotypic Analyses
Pneumonic tularemia is a highly debilitating and potentially fatal disease caused by inhalation of Francisella tularensis. Most of our current understanding of its pathogenesis is based on the highly virulent F. tularensis subsp. tularensis strain SCHU S4. However, multiple sources of SCHU S4 have been maintained and propagated independently over the years, potentially generating genetic variants with altered virulence. In this study, the virulence of four SCHU S4 stocks (NR-10492, NR-28534, NR-643 from BEI Resources and FTS-635 from Battelle Memorial Institute) along with another virulent subsp. tularensis strain, MA00-2987, were assessed in parallel. In the Fischer 344 rat model of pneumonic tularemia, NR-643 and FTS-635 were found to be highly attenuated compared to NR-10492, NR-28534, and MA00-2987. In the NZW rabbit model of pneumonic tularemia, NR-643 caused morbidity but not mortality even at a dose equivalent to 500x the LD 50 for NR-10492. Genetic analyses revealed that NR-10492 and NR-28534 were identical to each other, and nearly identical to the reference SCHU S4 sequence. NR-643 and FTS-635 were identical to each other but were found to have nine regions of difference in the genomic sequence when compared to the published reference SCHU S4 sequence. Given the genetic differences and decreased virulence, NR-643/FTS-635 should be clearly designated as a separate SCHU S4 substrain and no longer utilized in efficacy studies to evaluate potential vaccines and therapeutics against tularemia. View Full-Text
59 BASIC BIOLOGICAL SCIENCES↗
Modular adjuvant-free pan-HLA-DR-immunotargeting subunit vaccine against SARS-CoV-2 elicits broad sarbecovirus-neutralizing antibody responses
Subunit vaccines typically require co-administration with an adjuvant to elicit protective immunity, adding development hurdles that can impede rapid pandemic responses. To circumvent the need for adjuvant in a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) subunit vaccine, we engineer a thermostable immunotargeting vaccine (ITV) that leverages the pan-HLA-DR monoclonal antibody 44H10 to deliver the viral spike protein receptor-binding domain (RBD) to antigen-presenting cells. X-ray crystallography shows that 44H10 binds to a conserved epitope on HLA-DR, providing the basis for its broad HLA-DR reactivity. Adjuvant-free ITV immunization in rabbits and ferrets induces robust anti-RBD antibody responses that neutralize SARS-CoV-2 variants of concern and protect recipients from SARS-CoV-2 challenge. We demonstrate that the modular nature of the ITV scaffold with respect to helper T cell epitopes and diverse RBD antigens facilitates broad sarbecovirus neutralization. Our findings support anti-HLA-DR immunotargeting as an effective means to induce strong antibody responses to subunit antigens without requiring an adjuvant.
60 APPLIED LIFE SCIENCES↗