Optimization of an E. coli L-rhamnose-inducible expression vector: test of various genetic module combinations

<p>Abstract</p> <p>Background</p> <p>A capable expression vector is mainly characterized by its production efficiency, stability and induction response. These features can be influenced by a variation of modifications and versatile genetic modules.</p> <p>Results</p> <p>We examined miscellaneous variations of a <it>rhaP</it>_{<it>BAD </it>}expression vector. The introduction of a stem loop into the translation initiation region of the <it>rhaP</it>_{<it>BAD </it>}promoter resulted in the most significant improvement of <it>eGFP </it>expression. Starting from this plasmid, we constructed a set of expression vectors bearing different genetic modules like <it>rop</it>, <it>ccdAB</it>, <it>cer </it>and combinations thereof, and tested the efficiency of expression and plasmid stability. The plasmid pWA21, containing the stem loop, one <it>cer </it>site and <it>rop</it>, attained high expression levels accompanied by a good stability, and on that score seems to be a well-balanced choice.</p> <p>Conclusion</p> <p>We report the generation of variations of the <it>rhaP</it>_{<it>BAD </it>}expression vector and characterization hereof. The genetic modules showed a complex interplay, therefore two positive effects combined sometimes resulted in a disadvantage.</p

Thermoelastic properties of bridgmanite using Deep Potential Molecular Dynamics

MgSiO_3-perovskite (MgPv) plays a crucial role in the Earth's lower mantle. This study combines deep-learning potential (DP) with density functional theory (DFT) to investigate the structural and elastic properties of MgPv under lower mantle conditions. To simulate complex systems, we developed a series of potentials capable of faithfully reproducing DFT calculations using different functionals, such as LDA, PBE, PBEsol, and SCAN meta-GGA functionals. The obtained predictions exhibit remarkable reliability and consistency, closely resembling experimental measurements. Our results highlight the superior performance of the DP-SCAN and DP-LDA in accurately predicting high-temperature equations of states and elastic properties. This hybrid computational approach offers a solution to the accuracy-efficiency dilemma in obtaining precise elastic properties at high pressure and temperature conditions for minerals like MgPv, which opens a new way to study the Earth's interior state and related processes

Fiat-Shamir for Bounded-Depth Adversaries

We study how to construct hash functions that can securely instantiate the Fiat-Shamir transformation against bounded-depth adversaries. The motivation is twofold. First, given the recent fruitful line of research of constructing cryptographic primitives against bounded-depth adversaries under worst-case complexity assumptions, and the rich applications of Fiat-Shamir, instantiating Fiat-Shamir hash functions against bounded-depth adversaries under worst-case complexity assumptions might lead to further applications (such as SNARG for P, showing the cryptographic hardness of PPAD, etc.) against bounded-depth adversaries. Second, we wonder whether it is possible to overcome the impossibility results of constructing Fiat-Shamir for arguments [Goldwasser, Kalai, FOCS ’03] in the setting where the depth of the adversary is bounded, given that the known impossibility results (against p.p.t. adversaries) are contrived. Our main results give new insights for Fiat-Shamir against bounded-depth adversaries in both the positive and negative directions. On the positive side, for Fiat-Shamir for proofs with certain properties, we show that weak worst-case assumptions are enough for constructing explicit hash functions that give $\mathsf{AC}^0[2]$-soundness. In particular, we construct an $\mathsf{AC}^0[2]$-computable correlation-intractable hash family for constant-degree polynomials against $\mathsf{AC}^0[2]$ adversaries, assuming $\oplus \mathsf{L}/\mathsf{poly} \not\subseteq \widetilde{\mathsf{Sum}}_{n^{-c}} \circ\mathsf{AC}^0[2]$ for some $c > 0$. This is incomparable to all currently-known constructions, which are typically useful for larger classes and against stronger adversaries, but based on arguably stronger assumptions. Our construction is inspired by the Fiat-Shamir hash function by Peikert and Shiehian [CRYPTO ’19] and the fully-homomorphic encryption scheme against bounded-depth adversaries by Wang and Pan [EUROCRYPT ’22]. On the negative side, we show Fiat-Shamir for arguments is still impossible to achieve against bounded-depth adversaries. In particular, • Assuming the existence of $\mathsf{AC}^0[2]$-computable CRHF against p.p.t. adversaries, for every poly-size hash function, there is a (p.p.t.-sound) interactive argument that is not $\mathsf{AC}^0[2]$-sound after applying Fiat-Shamir with this hash function. • Assuming the existence of $\mathsf{AC}^0[2]$-computable CRHF against $\mathsf{AC}^0[2]$ adversaries, there is an $\mathsf{AC}^0[2]$-sound interactive argument such that for every hash function computable by $\mathsf{AC}^0[2]$ circuits the argument does not preserve $\mathsf{AC}^0[2]$-soundness when applying Fiat-Shamir with this hash function. This is a low-depth variant of the result of Goldwasser and Kalai

Continued nucleic acid tests for SARS-CoV-2 following discharge of patients with COVID-19 in Lu’an, China

Background Studies have shown that discharged Coronavirus disease 2019 (COVID-19) patients have retested positive for SARS-CoV-2 during a follow-up RT-PCR test. We sought to assess the results of continued nucleic acid testing for SARS-CoV-2 patients in COVID-19 patients after they were discharged in Lu’an, China. Methods We conducted RT-PCR tests on sputum, throat swabs, fecal or anal swabs, and urine samples collected from 67 COVID-19 patients following discharge. Samples were collected on the 7th and 14th days following discharge. Patients testing positive on the 7th or 14th day were retested after 24 hours until they tested negative twice. Results Seventeen (17/67, 25.4%) discharged COVID-19 patients had a positive RT-PCR retest for SARS-CoV-2. Among them, 14 (82.4%) were sputum positive, five (29.4%) were throat swab positive, seven (41.2%) were fecal or anal swab positive, one (5.9%) was urine sample positive, five (29.4%) were both sputum and throat swab positive, four (23.5%) were both sputum and fecal test positive, and one (5.9%) was positive of all four specimens. The shortest period of time between discharge and the last positive test was 7 days, the longest was 48 days, and the median was 16 days. The proportion of positive fecal or anal swab tests increased from the third week. The median Cq cut-off values after onset were 26.7 after the first week, 37.7 the second to sixth week, and 40 after the sixth week. There were no significant differences between the RT-PCR retest positive group and the unrecovered positive group. Conclusions There was a high proportion of patients who retested positive for COVID-19. Discharge criteria have remained fairly consistent so we encourage regions affected by COVID-19 to appropriately amend their current criteria