Discovery of a conserved rule behind the assembly of β-barrel membrane proteins

Gram-negative bacteria, mitochondria and chloroplasts contain β-barrel outer membrane proteins (OMPs). Most OMPs have a “β-signal” imprinted in the final β-strand. In Gram-negative bacteria, the β-barrel assembly machinery (BAM) complex recognize the β-signal for the folding and membrane insertion of the OMP. Here, we identified the “-5 signal”, a novel signal existing in the fifth β-strand from the C-terminus (-5 strand) responsible for the insertion step of the assembly process. We further identified the receptor for the -5 signal as BamD. BamD can recognize both β-signal and -5 signal, marshalling the OMP for assembly. There is sequence similarity in of both signals observed also in mitochondrial OMPs. Therefore, we propose the “-5 rule” repeating a similar sequence in the -5 and last strand, as a conserved feature of the OMP assembly process in bacteria and eukaryotes.

Reference Values of Native T1 at 3T Cardiac Magnetic Resonance—Standardization Considerations between Different Vendors

This study aimed at establishing native T1 reference values for a Canon Vantage Galan 3T system and comparing them with previously published values from different vendors. A total of 20 healthy volunteers (55% Women; 33.9 ± 11.1 years) underwent left ventricular T1 mapping at 3T MR. A MOLLI 5(3)3 sequence was used, acquiring three short-axis slices. Native T1 values are shown as means (±standard deviation) and Student’s independent samples t-test was used to test gender differences in T1 values. Pearson’s correlation coefficient analysis was used to compare two processes of T1 analysis. The results show a global native T1 mean value of 1124.9 ± 55.2 ms (exponential analysis), that of women being statistically higher than men (1163 ± 30.5 vs. 1077.9 ± 39.5 ms, respectively; p < 0.001). There were no specific tendencies for T1 times in different ventricular slices. We found a strong correlation (0.977, p < 0.001) with T1 times derived from parametric maps (1136.4 ± 60.2 ms). Native T1 reference values for a Canon 3T scanner were provided, and they are on par with those already reported from other vendors for a similar sequence. We also found a correlation between native T1 and gender, with higher values for women.

Total Synthesis of 6-Deoxydihydrokalafungin, a Key Biosynthetic Precursor of Actinorhodin, and Its Epimer

In this article, we report the total synthesis of 6-deoxydihydrokalafungin (DDHK), a key biosynthetic intermediate of a dimeric benzoisochromanequinone antibiotic, actinorhodin (ACT), and its epimer, epi-DDHK. Tricyclic hemiacetal with 3-siloxyethyl group was subjected to Et3SiH reduction to establish the 1,3-cis stereochemistry in the benzoisochromane, and a subsequent oxidation/deprotection sequence then afforded epi-DDHK. A bicyclic acetal was subjected to AlH3 reduction to deliver the desired 1,3-trans isomer in an approximately 3:1 ratio, which was subjected to a similar sequence to that used for the 1,3-cis isomer that successfully afforded DDHK. A semisynthetic approach from (S)-DNPA, an isolable biosynthetic precursor of ACT, was also examined to afford DDHK and its epimer, which are identical to the synthetic products.

A Comprehensive Analysis of the Genetic Diversity of Plasmodium falciparum Histidine-Rich Protein 2 (PfHRP2) in the Brazilian Amazon

Early diagnosis and treatment are fundamental to the control and elimination of malaria. In many endemic areas, routine diagnosis is primarily performed microscopically, although rapid diagnostic tests (RDTs) provide a useful point-of-care tool. Most of the commercially available RDTs detect histidine-rich protein 2 (HRP2) of Plasmodium falciparum in the blood of infected individuals. Nonetheless, parasite isolates lacking the pfhrp2 gene are relatively frequent in some endemic regions, thereby hampering the diagnosis of malaria using HRP2-based RDTs. To track the efficacy of RDTs in areas of the Brazilian Amazon, we assessed pfhrp2 deletions in 132 P. falciparum samples collected from four malaria-endemic states in Brazil. Our findings show low to moderate levels of pfhrp2 deletion in different regions of the Brazilian Amazon. Overall, during the period covered by this study (2002-2020), we found that 10% of the P. falciparum isolates were characterized by a pfhrp2 deletion. Notably, however, the presence of pfhrp2-negative isolates has not been translated into a reduction in RDT efficacy, which in part may be explained by the presence of polyclonal infections. A further important finding was the discrepancy in the proportion of pfhrp2 deletions detected using two assessed protocols (conventional PCR versus nested PCR), which reinforces the need to perform a carefully planned laboratory workflow to assess gene deletion. This is the first study to perform a comprehensive analysis of PfHRP2 sequence diversity in Brazilian isolates of P. falciparum. We identified 10 PfHRP2 sequence patterns, which were found to be exclusive of each of the assessed regions. Despite the small number of PfHRP2 sequences available from South America, we found that the PfHRP2 sequences identified in Brazil and neighboring French Guiana show similar sequence patterns. Our findings highlight the importance of continuously monitoring the occurrence and spread of parasites with pfrhp2 deletions, while also taking into account the limitations of PCR-based testing methods associated with accuracy and the complexity of infections.

Associated Gas Utilization Using a Reheat Gas Turbine – Part 1: The Impact of Engine Degradation on the Optimized Power, Energy, and Revenue From Sold Electricity

This study presents a methodology for optimizing the power from a fleet of engines that use associated gas as fuel. The effects of engine degradation on optimized power, energy, and electricity revenue have been evaluated. The Cranfield University TURBOMATCH has been used to simulate a 296MW reheat gas turbine. Four scenarios were considered — clean, optimistic, medium, and pessimistic. Genetic algorithm was used in optimizing the power generated from the fleets. In the sequence of clean, optimistic, medium, and pessimistic fleets, the optimization results show that the total optimized power values are 7324.6, 7245.1, 7164.0, and 7074.4MW respectively. In the same sequence, the total energy generated is 64.2, 63.5, 62.8, and 61.9 billion kWh. In a similar sequence still, the electricity revenue is 8.487, 8.390, 8.298, and 8.192 billion US dollars respectively. In comparison with the clean, engine degradation resulted in a 1.09%, 2.19%, and 3.42% decrease in energy for the optimistic, medium, and pessimistic degraded fleets respectively. In the same sequence as the decrease in energy, degradation resulted in a 1.15%, 2.23%, and 3.48% decrease in electricity revenue. The methodology and results presented in this paper would serve as a guide for associated gas investors in the economic utilization of this fuel resource. This is innovative; it has not been done with the Alstom GT-26 engine.

Adaptive Cartesian and torsional restraints for interactive model rebuilding

When building atomic models into weak and/or low-resolution density, a common strategy is to restrain their conformation to that of a higher resolution model of the same or similar sequence. When doing so, it is important to avoid over-restraining to the reference model in the face of disagreement with the experimental data. The most common strategy for this is the use of `top-out' potentials. These act like simple harmonic restraints within a defined range, but gradually weaken when the deviation between the model and reference grows beyond that range. In each current implementation the rate at which the potential flattens at large deviations follows a fixed form, although the form chosen varies among implementations. A restraint potential with a tuneable rate of flattening would provide greater flexibility to encode the confidence in any given restraint. Here, two new such potentials are described: a Cartesian distance restraint derived from a recent generalization of common loss functions and a periodic torsion restraint based on a renormalization of the von Mises distribution. Further, their implementation as user-adjustable/switchable restraints in ISOLDE is described and their use in some real-world examples is demonstrated.

HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation

Gene expression programs determine cell fate in embryonic development and their dysregulation results in disease. Transcription factors (TFs) control gene expression by binding to enhancers, but how TFs select and activate their target enhancers is still unclear. HOX TFs share conserved homeodomains with highly similar sequence recognition properties, yet they impart the identity of different animal body parts. To understand how HOX TFs control their specific transcriptional programs in vivo, we compared HOXA2 and HOXA3 binding profiles in the mouse embryo. HOXA2 and HOXA3 directly cooperate with TALE TFs and selectively target different subsets of a broad TALE chromatin platform. Binding of HOX and tissue-specific TFs convert low affinity TALE binding into high confidence, tissue-specific binding events, which bear the mark of active enhancers. We propose that HOX paralogs, alone and in combination with tissue-specific TFs, generate tissue-specific transcriptional outputs by modulating the activity of TALE TFs at selected enhancers.