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Chapter 7 - CRISPR-Based Tools for Microbial Cell Factories

The development of microbial chassis for the production of a variety of biochemicals and biofuels is a growing area of research. How to efficiently manipulate genetic information to achieve optimal production of these compounds is a key area of focus in the field. In recent years, clustered regularly interspaced palindromic repeats (CRISPR) and its associated proteins (Cas) have become a popular strategy for gene editing and regulation in many organisms due to its versatility and efficacy. Here, we describe methods developed utilizing CRISPR-Cas systems for engineering microbial cell factories (e.g., bacteria and yeast) at the single gene to genome scale for mutagenesis and transcriptional regulation of target genes. Finally, we provide a perspective on the challenges and opportunities for the applications of advanced CRISPR-Cas-based tools for engineering microbial cell factories.

BIOMASS FUELS↗

Exploiting CRIC to streamline the configuration management of GlideinWMS factories for CMS support

GlideinWMS is a workload management and provisioning system that allows sharing computing resources distributed over independent sites. Based on the requests made by GlideinWMS frontends, a dynamically sized pool of resources is created by GlideinWMS pilot factories via pilot job submission to resource sites’ CEs. More than 400 CEs are currently serving more than ten virtual organizations through GlideinWMS, with CMS being the biggest user with 230 CEs. The complex configurations of the parameters defining resource requests, as submitted to those CEs, have been historically managed by manually editing a set of different XML files. New possibilities arise with CMS adopting the CRIC, an information system that collects, aggregates, stores, and exposes, among other things, computing resource data coming from various data providers. The paper will describe the challenges faced when CMS started to use CRIC to automatically generate the GlideinWMS factory configurations. The architecture of the prototype, and the ancillary tools developed to ease this transition, will be discussed. Finally, future plans and milestones will be outlined.

Dost, Jeffrey↗

Experimental quantum Bernoulli factories via Bell-basis measurements

Randomness processing in the Bernoulli factory framework provides a concrete setting in which quantum resources can outperform classical ones. We experimentally demonstrate quantum randomness processing based on Bell-basis measurements of two identical input quoins prepared on IBM superconducting hardware. Using only the measurement outcomes (and no external classical randomness source), we realize the classically inconstructible Bernoulli doubling primitive f(p)=2p, and, as intermediate outputs from the same Bell-measurement statistics, an exact fair coin f(p)=1/2 and the classically inconstructible function f(p)=4p(1−p). We benchmark the measured output biases against ideal predictions and discuss the impact of device noise. Our results establish a simple resource-efficient experimental primitive for quantum-to-classical randomness processing and support the viability of quantum Bernoulli factories for quantum-enhanced stochastic simulation and sampling tasks.

Roy, Tanay [Fermilab] (ORCID:000000019442862X)↗

Testing lepton flavor universality at future Z factories

As one of the hypothetical principles in the Standard Model (SM), lepton flavor universality (LFU) should be tested with a precision as high as possible such that the physics violating this principle can be fully examined. The run of a Z factory at a future e + e − collider, such as the Circular Electron-Positron Collider or Future Circular Collider (electron/positron), provides a great opportunity to perform this task because of the large statistics and high reconstruction efficiencies for b hadrons at the Z pole. In this paper, we present a systematic study on the LFU test in future Z factories. The goal is threefold. First, we study the sensitivities of measuring the LFU-violating observables of b → c τ ν , i.e., R J / ψ , R D s , R D s * , and R Λ c , where τ decays muonically. For this purpose, we develop the strategies for event reconstruction, based on the track information significantly. Second, we explore the sensitivity robustness against detector performance and its potential improvement with the message of event shape or beyond the b -hadron decays. A picture is drawn on the variation of analysis sensitivities with the detector tracking resolution and soft photon detectability, and the impact of Fox-Wolfram moments is studied on the measurement of relevant flavor events. Finally, we interpret the projected sensitivities in the SM effective field theory, by combining the LFU tests of b → c τ ν and the measurements of b → s τ + τ − and b → s ν ¯ ν . We show that the limits on the LFU-violating energy scale can be pushed up to ∼ O ( 10 ) TeV for ≲ O ( 1 ) Wilson coefficients at Tera- Z . Published by the American Physical Society 2024

Astronomy & Astrophysics↗

Acceptance dependence of factorial cumulants, long-range correlations, and the antiproton puzzle

We analyze joint factorial cumulants of protons and antiprotons in relativistic heavy-ion collisions and point out that they obey the scaling Ĉnmp,p¯∝〈Np〉n〈Np¯〉m as a function of acceptance when only long-range correlations are present in the system, such as global baryon conservation and volume fluctuations. This hypothesis can be directly tested experimentally without the need for corrections for volume fluctuations. We show that if correlations among protons and antiprotons are driven by global baryon conservation and volume fluctuations only, the equality Ĉ2p/〈Np〉2=Ĉ2p¯/〈Np¯〉2 holds for large systems created in central collisions. We point out that the experimental data of the STAR Collaboration from phase I of the Relativistic Heavy Ion Collider (RHIC) beam energy scan (BES) are approximately consistent with the scaling Ĉnmp,p¯∝〈Np〉n〈Np¯〉m, but the normalized antiproton correlations are stronger than those of protons, −Ĉ2p¯/〈Np¯〉2>−Ĉ2p/〈Np〉2. Existing theoretical baselines, based on global baryon conservation and volume fluctuations, cannot explain the data, which we refer to as the antiproton puzzle. We also discuss high-order factorial cumulants which can be measured with sufficient precision within phase II of RHIC-BES.

Bzdak, Adam↗

Tau Lepton Physics at a Tau-Charm Factory

A two-day workshop, "The Tau-Charm Factory in the Era of B-factors and CESR," was held at SLAC in August, 1994. This paper summarizes the important research on the tau lepton which could be done at a tau-charm factory in the next decade. It is based on the presentation by the speakers and on the discussions by participants, as well as on published papers.

Perl, M.↗

Container Factories in the Oak Ridge Research Cloud

This technical report describes an implementation of a devops container factory utilizing ORNL ResearchCloud (ORC) birthright resources. Any researcher or project can implement the strategy described here fortheir CI/CD needs. This is a technology demonstration of using rootless podman as a direct replacementfor docker in a GitLab CI/CD context to enhance security. It is also a stepping stone towardsimplementation of the containerized software factory described in the DoD Enterprise DevSecOpsReference Design.

97 MATHEMATICS AND COMPUTING↗

ECFA Higgs, electroweak, and top Factory Study

The ECFA Higgs, electroweak, and top Factory Study ran between 2021 and 2025 as a broad effort across the experimental and theoretical particle physics communities, bringing together participants from many different proposed future collider projects. Activities across three main working groups advanced the joint development of tools and analysis techniques, fostered new considerations of detector design and optimisation, and led to a new set of studies resulting in improved projected sensitivities across a wide physics programme. This report demonstrates the significant expansion in the state-of-the-art understanding of the physics potential of future e+e- Higgs, electroweak, and top factories, and has been submitted as input to the 2025 European Strategy for Particle Physics Update.

Altmann, J. [Monash U.]↗

ILC: Beyond Higgs Factory

The first stage of the International Linear Collider is one of the contenders for a “Higgs factory”, as prioritised by the recent update of the European Strategy for Particle Physics. This article highlights the physics opportunities beyond its Higgs factory program, which is enabled by high luminosity, the polarised beams and the triggerless operation of the detectors, as well as the energy-extendability of the accelerator as key features of Linear Colliders.

List, Jenny↗

Exploring the Potential of Factory Installed Solar + Storage for Homebuilding

In recent years, an increasing number of grid disruptions due to intense weather events, natural disasters, and high peak loads resulted in increased interest in energy-resilient homes. Solar + storage (S+S) as an energy resiliency solution can provide continuity, onsite generation, and backup power during critical events. This project explored factory-installed solar plus storage (FISS) to overcome first cost and installation barriers and bring this resiliency solution to scale for single-family affordable and market-rate homebuyers. Guided by the principles of Lean manufacturing, the team explored how factories building high-performance zero energy modular homes can incorporate S+S into their existing construction system while improving quality and productivity and reducing the costs of the resilient energy system.

ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATION,↗

An argument for using anaerobes as microbial cell factories to advance synthetic biology and biomanufacturing

Anaerobes thrive in the absence of oxygen and are an untapped reservoir of biotechnological potential. Therefore, bioprospecting efforts focused on anaerobic microbial diversity could rapidly uncover new enzymes, pathways, and chassis organisms to drive biotechnology innovation. Despite their potential utility, anaerobic fermenters are viewed as inefficient from a biochemical perspective because their metabolisms produce fewer ATP (~2) per molecule of glucose processed than heterotrophic respirers (~32–38 ATP). While aerobes excel at ATP generation, they are often less efficient than anaerobes at processes that compete with ATP generation for cellular resources. This perspective highlights how anaerobic adaptations are advantageous for synthetic biology and biomanufacturing applications through the engineering of microbial cell factories. We further highlight emerging applications of anaerobic bioprocessing, including the use of anaerobic metabolisms for lignocellulosic bioprocessing, human and environmental health, and value-added bioproduction.

59 BASIC BIOLOGICAL SCIENCES↗

Harnessing selenocysteine to enhance microbial cell factories for hydrogen production

Hydrogen is a clean, renewable energy source, that when combined with oxygen, produces heat and electricity with only water vapor as a biproduct. Furthermore, it has the highest energy content by weight of all known fuels. As a result, various strategies have engineered methods to produce hydrogen efficiently and in quantities that are of interest to the economy. To approach the notion of producing hydrogen from a biological perspective, we take our attention to hydrogenases which are naturally produced in microbes. These organisms have the machinery to produce hydrogen, which when cleverly engineered, could be useful in cell factories resulting in large production of hydrogen. Not all hydrogenases are efficient at hydrogen production, and those that are, tend to be oxygen sensitive. Therefore, we provide a new perspective on introducing selenocysteine, a highly reactive proteinogenic amino acid, as a strategy towards engineering hydrogenases with enhanced hydrogen production, or increased oxygen tolerance.

08 HYDROGEN↗

Multi-track displaced vertices at $B$-factories

We propose a program at B-factories of inclusive, multi-track displaced vertex searches, which are expected to be low background and give excellent sensitivity to non-minimal hidden sectors. Multi-particle hidden sectors often include long-lived particles (LLPs) which result from approximate symmetries, and we classify the possible decays of GeV-scale LLPs in an effective field theory framework. Considering several LLP production modes, including dark photons and dark Higgs bosons, we study the sensitivity of LLP searches with different number of displaced vertices per event and track requirements per displaced vertex, showing that inclusive searches can have sensitivity to a large range of hidden sector models that are otherwise unconstrained by current or planned searches.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DGFRS-2—A gas-filled recoil separator for the Dubna Super Heavy Element Factory

The main goal of development of the new Dubna Gas-Filled Recoil Separator (DGFRS-2) is to sufficiently improve the efficiency of studies on heavy and superheavy nuclei at the Super Heavy Element Factory of the Flerov Laboratory of Nuclear Reactions (FLNR) at the Joint Institute for Nuclear Research. The use of beams with the intensity up to 6×10 13 s -1 (10 pμA) delivered by the DC280 cyclotron requires an effective setup providing high suppression of background reaction products. Additionally, the described gas-filled separator is optimized for synthesis and study of heavy isotopes produced in complete fusion reactions of massive nuclei. Basic characteristics of DGFRS-2, as well as the results of the first test experiments, are presented. In comparison to the DGFRS-1, the transmission efficiency was doubled, and the background was reduced by a factor 200.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Efficiency corrections for factorial moments and cumulants of overlapping sets of particles

In this note we discuss subtleties associated with the efficiency corrections for measurements of off-diagonal cumulants and factorial moments for a situation when one deals with overlapping sets of particles, such as correlations between numbers of protons and positively charged particles. In particular, we discuss the situation commonly encountered in heavy-ion experiments, where first all charges are reconstructed and then protons are selected from these charges by an additional particle identification procedure. We present the efficiency correction formulas for the case when the detection efficiencies follow a binomial distribution.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The role of gas flow distributions on CO 2 mineralization within monolithic cemented composites: coupled CFD-factorial design approach

The carbonation kinetics of monolithic cementing composites are strongly affected by gas transport which is, in turn, influenced by microstructural resistances and the presence of liquid water within pore networks. The non-uniform gas flow distribution within the CO 2 mineralization reactor can impart mass transfer resistance in the monolith microstructure, which affects the uptake of CO 2 (“carbonation”) of the cementing composites. This paper demonstrates how the gas spatial distribution (velocity and flow rate; quantified by CFD analysis) and processing conditions (temperature, relative humidity, and flow rate; quantified by factorial design) affect drying and carbonation, and in turn, the engineering properties of a representative ‘monolithic’ carbonate-cemented concrete component (i.e., herein concrete masonry unit: CMUs, also known as concrete block). It is shown that the gas flow distribution affects drying front penetration and results in moisture and carbonation gradients within the monolith. Particularly, variations in drying kinetics caused by non-uniformity of the contacting gas velocity impose gradients in moisture saturation, which results in increasing microstructural resistance to CO 2 transport. The resultant non-uniform carbonate-mineral formation (i.e., carbonate cementation), if not controlled, can produce gradients in mechanical properties and may alter failure patterns upon loading. Finally, these insights inform the optimal design of gas flow distribution systems and processing conditions within CO 2 mineralization reactors for the manufacturing of low-CO 2 concrete components using CO 2 -dilute industrial flue gas streams.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Towards a modular architecture for science factories

Advances in robotic automation, high-performance computing, and artificial intelligence encourage us to propose large, general-purpose science factories with the scale needed to tackle large discovery problems and to support thousands of scientists.

97 MATHEMATICS AND COMPUTING↗

Lead tungstate calorimeter of the Jefferson Lab Eta Factory experiment

A new electromagnetic calorimeter (ECAL) consisting of 1596 lead tungstate PbWO 4 scintillating crystals has been fabricated and installed in the experimental Hall D at Jefferson Lab (JLab). The highgranularity, high-resolution calorimeter is required by the JLab Eta Factory experiment, whose main physics goal is to study rare decays of eta mesons. The ECAL replaced the inner part of the forward lead glass calorimeter of the GlueX detector. Signals from the detector will be digitized using twelve-bit flash analog-to-digital converters operated at a sampling rate of 250 MHz. The ECAL is integrated into the trigger system of the GlueX detector using electronics modules designed at JLab. The ECAL is currently at the commissioning stage and should be ready for the physics run in January 2025. We will give an overview of the JEF experiment, the design and construction of the ECAL, and the integration of the detector and its infrastructure into the Hall D experimental setup.

Somov, Alexander [Thomas Jefferson National Accele↗