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RNA-binding proteins play integral roles in the regulation of essential processes in cells and as such are attractive targets for engineering to manipulate gene expression at the RNA level. Expression of transcripts in chloroplasts and mitochondria is heavily regulated by pentatricopeptide repeat (PPR) proteins. The diverse roles of PPR proteins and their naturally modular architecture make them ideal candidates for engineering. Synthetic PPR proteins are showing great potential to become valuable tools for controlling the expression of plastid and mitochondrial transcripts. In this review, by 'synthetic', we mean both rationally modified natural PPR proteins and completely novel proteins designed using the principles learned from their natural counterparts. We focus on the many different applications of synthetic PPR proteins, covering both their use in basic research to learn more about protein–RNA interactions and their use to achieve specific outcomes in RNA processing and the control of gene expression. We describe the challenges associated with the design, construction and deployment of synthetic PPR proteins and provide perspectives on how they might be assembled and used in future biotechnology applications. [ABSTRACT FROM AUTHOR]

Summary: Restorer‐of‐fertility (Rf) genes encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they specifically bind to transcripts that induce cytoplasmic male sterility and repress their expression. In searching for a molecular signature unique to this class of proteins, we found that a majority of known Rf proteins have a distinct domain, which we called RfCTD (Restorer‐of‐fertility C‐terminal domain), and its presence correlates with the ability to induce cleavage of the mitochondrial RNA target.A screen of 219 angiosperm genomes from 123 genera using a sequence profile that can quickly and accurately identify RfCTD sequences revealed considerable variation in RFL/RfCTD gene numbers across flowering plants. We observed that plant genera with bisexual flowers have significantly higher numbers of RFL genes compared to those with unisexual flowers, consistent with a role of these proteins in restoration of male fertility.We show that removing the RfCTD from the RFL protein RNA PROCESSING FACTOR 2‐nad6 prevented cleavage of its RNA target, the nad6 transcript, in Arabidopsis thaliana mitochondria.We provide a simple way of identifying putative Rf candidates in genome sequences, new insights into the molecular mode of action of Rf proteins and the evolution of fertility restoration in flowering plants. [ABSTRACT FROM AUTHOR]

Coxiella burnetii is a Gram-negative intracellular pathogen that causes the debilitating disease Q fever, which affects both animals and humans. The only available human vaccine, Q-Vax, is effective but has a high risk of severe adverse reactions, limiting its use as a countermeasure to contain outbreaks. Therefore, it is essential to identify new drug targets to treat this infection. Macrophage infectivity potentiator (Mip) proteins catalyse the folding of proline-containing proteins through their peptidyl prolyl cis-trans isomerase (PPIase) activity and have been shown to play an important role in the virulence of several pathogenic bacteria. To date the role of the Mip protein in C. burnetii pathogenesis has not been investigated. This study demonstrates that CbMip is likely to be an essential protein in C. burnetii. The pipecolic acid derived compounds, SF235 and AN296, which have shown utility in targeting other Mip proteins from pathogenic bacteria, demonstrate inhibitory activities against CbMip. These compounds were found to significantly inhibit intracellular replication of C. burnetii in both HeLa and THP-1 cells. Furthermore, SF235 and AN296 were also found to exhibit antibiotic properties against both the virulent (Phase I) and avirulent (Phase II) forms of C. burnetii Nine Mile Strain in axenic culture. Comparative proteomics, in the presence of AN296, revealed alterations in stress responses with H2O2 sensitivity assays validating that Mip inhibition increases the sensitivity of C. burnetii to oxidative stress. In addition, SF235 and AN296 were effective in vivo and significantly improved the survival of Galleria mellonella infected with C. burnetii. These results suggest that unlike in other bacteria, Mip in C. burnetii is required for replication and that the development of more potent inhibitors against CbMip is warranted and offer potential as novel therapeutics against this pathogen. Author summary: The bacterium Coxiella burnetii is a highly infectious organism that is found worldwide and can cause debilitating disease in both animals and humans. Treatment of chronic infections remains very difficult and therefore it is essential to identify new drug targets to treat this infection. The Macrophage infectivity potentiator (Mip) protein has been reported as an attractive anti-virulence target in several pathogenic bacteria but its role has not been investigated in C. burnetii. This study demonstrates that inhibitors of the Mip protein from C. burnetii reduce replication inside host cells, increase the sensitivity of the bacteria to oxidative stress, and exhibit antibiotic properties against both the virulent and avirulent forms of C. burnetii. Furthermore, using a moth larvae infection model, the inhibitors demonstrated protective activity. These results suggest that, unlike other studied bacterial pathogens, C. burnetii requires Mip for replication, and that the further development of potent inhibitors against Mip offer potential as novel therapeutics to treat this infection. [ABSTRACT FROM AUTHOR]

A new high-pressure single-crystal diffraction setup has been designed and implemented at the Australian Synchrotron for collecting molecular and protein crystal structures. The setup incorporates a modified micro-Merrill-Bassett cell and holder designed specifically to fit onto the horizontal air-bearing goniometer, allowing high-pressure diffraction measurements to be collected with little to no modification of the beamline setup compared with ambient data collections. Compression data for the amino acid, l-threonine, and the protein, hen egg-white lysozyme, were collected, showcasing the capabilities of the setup. [ABSTRACT FROM AUTHOR]

Decades of research has shown that people are poor at detecting lies. Two explanations for this finding have been proposed. First, it has been suggested that lie detection is inaccurate because people rely on invalid cues when judging deception. Second, it has been suggested that lack of valid cues to deception limits accuracy. A series of 4 meta-analyses tested these hypotheses with the framework of Brunswik's (1952) lens model. Meta-Analysis 1 investigated perceived cues to deception by correlating 66 behavioral cues in 153 samples with deception judgments. People strongly associate deception with impressions of incompetence (r = 0.59) and ambivalence (r = 0.49). Contrary to self-reports, eye contact is only weakly correlated with deception judgments (r = -0.15). Cues to perceived deception were then compared with cues to actual deception. The results show a substantial covariation between the 2 sets of cues (r = 0.59 in Meta-Analysis 2, r = 0.72 in Meta-Analysis 3). Finally, in Meta-Analysis 4, a lens model analysis revealed a very strong matching between behaviorally based predictions of deception and behaviorally based predictions of perceived deception. In conclusion, contrary to previous assumptions, people rarely rely on the wrong cues. Instead, limitations in lie detection accuracy are mainly attributable to weaknesses in behavioral cues to deception. The results suggest that intuitive notions about deception are more accurate than explicit knowledge and that lie detection is more readily improved by increasing behavioral differences between liars and truth tellers than by informing lie-catchers of valid cues to deception. (Contains 1 table, 1 figure, and 3 footnotes.)

The authors report a meta-analysis of individual differences in detecting deception, confining attention to occasions when people judge strangers' veracity in real-time with no special aids. The authors have developed a statistical technique to correct nominal individual differences for differences introduced by random measurement error. Although researchers have suggested that people differ in the ability to detect lies, psychometric analyses of 247 samples reveal that these ability differences are minute. In terms of the percentage of lies detected, measurement-corrected standard deviations in judge ability are less than 1%. In accuracy, judges range no more widely than would be expected by chance, and the best judges are no more accurate than a stochastic mechanism would produce. When judging deception, people differ less in ability than in the inclination to regard others' statements as truthful. People also differ from one another as lie- and truth-tellers. They vary in the detectability of their lies. Moreover, some people are more credible than others whether lying or truth-telling. Results reveal that the outcome of a deception judgment depends more on the liar's credibility than any other individual difference. (Contains 1 table and 4 figures.)

High‐risk neuroblastoma patients have poor survival rates and require better therapeutic options. High expression of a multifunctional DNA and RNA‐binding protein, NONO, in neuroblastoma is associated with poor patient outcome; however, there is little understanding of the mechanism of NONO‐dependent oncogenic gene regulatory activity in neuroblastoma. Here, we used cell imaging, biochemical and genome‐wide molecular analysis to reveal complex NONO‐dependent regulation of gene expression. NONO forms RNA‐ and DNA‐tethered condensates throughout the nucleus and undergoes phase separation in vitro, modulated by nucleic acid binding. CLIP analyses show that NONO mainly binds to the 5′ end of pre‐mRNAs and modulates pre‐mRNA processing, dependent on its RNA‐binding activity. NONO regulates super‐enhancer‐associated genes, including HAND2 and GATA2. Abrogating NONO RNA binding, or phase separation activity, results in decreased expression of HAND2 and GATA2. Thus, future development of agents that target RNA‐binding activity of NONO may have therapeutic potential in this cancer context. Synopsis: NONO protein correlates with poor outcome in neuroblastoma. NONO binds 5′ ends of introns in oncogenic genes, including super‐enhancer‐regulated GATA2 and HAND2, enabling proper RNA processing, via RNA binding and phase separation activities. In neuroblastoma, the multifunctional protein NONO binds to the 5′ intronic regions of pre‐mRNA in non‐paraspeckle nuclear puncta.Some NONO puncta correspond to transcription sites for super‐enhancer regulated GATA2 and HAND2 genes, where NONO enhances RNA processing at the 5′ end, leading to robust gene expression.NONO RNA binding and low‐complexity domains are required for its activity that is also diminished by BRD4 inhibitors, suggesting the puncta are phase separated condensates. [ABSTRACT FROM AUTHOR]

Since 1915, statisticians have been applying Fisher's Z-transformation to Pearson product-moment correlation coefficients. We offer new geometric interpretations of this transformation. (Contains 9 figures.)

Extends the Triadic Relations Model of C. Bond, E. Horn, and D. Kenny (1997) to analyze the covariances between triadic variables. Specifies a bivariate version of the model and presents estimation methods that can be used to decompose the covariance between 2 triadic variables into 33 covariance components. (Author/SLD)

William Henry Bragg moved from Cambridge in Britain to South Australia to take up a professorship at the University of Adelaide in 1885. He brought with him a broad interest in many areas of physics, but when Wilhelm Roentgen discovered X-rays in the 1890s, Bragg's interest was stimulated. William's Australian-born son, Lawrence (WL Bragg), began to share this interest and they worked on the possible applications of X-rays. Together they demonstrated that when X-rays are shined onto a crystal, and the pattern of how the x-rays are scattered (called "diffraction") is examined, information about how the atoms within the crystal are arranged can be gleaned. This Nobel prize-winning "X-ray crystallography" has become the basis for many modern high-technology solutions to challenging problems. This article describes a few examples of the kind of equipment that can be used for crystallography, and the kind of information that can be obtained using them.

The impact of individual differences on the performance of roles of learner and learning facilitator was studied during dyadic cooperative learning with 80 college students in same-sex groups of 4. The learner role accounted for more than 70% of the variance in total recall. The influence of cognitive and rapport factors is discussed. (SLD)

This editorial acknowledges the transformative impact of new machine‐learning methods, such as the use of AlphaFold, but also makes the case for the continuing need for experimental structural biology. [ABSTRACT FROM AUTHOR]

The recombination directionality factors from Mesorhizobium spp. (RdfS) are involved in regulating the excision and transfer of integrative and conjugative elements. Here, solution small‐angle X‐ray scattering, and crystallization and preliminary structure solution of RdfS from Mesorhizobium japonicum R7A are presented. RdfS crystallizes in space group P212121, with evidence of eightfold rotational crystallographic/noncrystallographic symmetry. Initial structure determination by molecular replacement using ab initio models yielded a partial model (three molecules), which was completed after manual inspection revealed unmodelled electron density. The finalized crystal structure of RdfS reveals a head‐to‐tail polymer forming left‐handed superhelices with large solvent channels. Additionally, RdfS has significant disorder in the C‐terminal region of the protein, which is supported by the solution scattering data and the crystal structure. The steps taken to finalize structure determination, as well as the scattering and crystallographic characteristics of RdfS, are discussed. [ABSTRACT FROM AUTHOR]

C. F. Bond and B. M. DePaulo reported a quantitative synthesis of individual differences in judging deception. Here, the authors respond to a pair of commentaries on this synthesis: a statistical critique by T. D. Pigott and M. J. Wu and a narrative reaction by M. O'Sullivan. In response to suggestions made by Pigott and Wu, the authors conduct several alternative analyses of individual differences in judging deception. Without exception, these yield results similar to those that the authors reported earlier. In response to O'Sullivan's questions, the authors point to their meta-analyses of relevant moderator variables. (Contains 1 table.)

Attitude embodiment effects occur when the position or movement of a person's physical body changes the way the person evaluates an object. The present research investigated whether attitude embodiment effects depend more on biomechanical factors or on inferential cues to causal agency. Experiments 1 and 2 showed that actual movements of the physical body are not necessary to create attitude embodiment effects when inferential cues imply agency for another person's physical movements. Experiment 3 showed that actual movements of the physical body are not sufficient to create attitude embodiment effects when inferential cues imply nonagency for those movements. In all 3 experiments, inferential cues to agency played a more important role in attitude embodiment effects than did actual agency, suggesting that theories of embodiment and attitude embodiment need to consider inferential cues to agency alongside biomechanical mechanisms. Keywords: embodiment, attitudes, agency DOI: 10.1037/a0017421

Paraspeckles are ribonucleoprotein bodies found in the interchromatin space of mammalian cell nuclei. These structures play a role in regulating the expression of certain genes in differentiated cells by nuclear retention of RNA. The core paraspeckle proteins (PSF/SFPQ, P54NRB/ NONO, and PSPC1 [paraspeckle protein 1]) are members of the DBHS (Drosophila melanogaster behavior, human splicing) family. These proteins, together with the long nonprotein-coding RNA NEAT1 (MEN-[epsilon]/[beta]), associate to form paraspeckles and maintain their integrity. Given the large numbers of long noncoding transcripts currently being discovered through whole transcriptome analysis, paraspeckles may be a paradigm for a class of sub-nuclear bodies formed around long noncoding RNA.

Background: The macrophage infectivity potentiator (Mip) protein, which belongs to the immunophilin superfamily, is a peptidyl-prolyl cis/trans isomerase (PPIase) enzyme. Mip has been shown to be important for virulence in a wide range of pathogenic microorganisms. It has previously been demonstrated that small-molecule compounds designed to target Mip from the Gram-negative bacterium Burkholderia pseudomallei bind at the site of enzymatic activity of the protein, inhibiting the in vitro activity of Mip.Objectives: In this study, co-crystallography experiments with recombinant B. pseudomallei Mip (BpMip) protein and Mip inhibitors, biochemical analysis and computational modelling were used to predict the efficacy of lead compounds for broad-spectrum activity against other pathogens.Methods: Binding activity of three lead compounds targeting BpMip was verified using surface plasmon resonance spectroscopy. The determination of crystal structures of BpMip in complex with these compounds, together with molecular modelling and in vitro assays, was used to determine whether the compounds have broad-spectrum antimicrobial activity against pathogens.Results: Of the three lead small-molecule compounds, two were effective in inhibiting the PPIase activity of Mip proteins from Neisseria meningitidis, Klebsiella pneumoniae and Leishmania major. The compounds also reduced the intracellular burden of these pathogens using in vitro cell infection assays.Conclusions: These results indicate that Mip is a novel antivirulence target that can be inhibited using small-molecule compounds that prove to be promising broad-spectrum drug candidates in vitro. Further optimization of compounds is required for in vivo evaluation and future clinical applications. [ABSTRACT FROM AUTHOR]

Celebrating 30 years of Acta D and looking forward to the future of structural biology. [ABSTRACT FROM AUTHOR]

The study was conducted to know the effect of metal substitution on the activity and structure of the aminopeptidase P (APPro) from Escherichia coli. The result reveals that excess Zn presence demonstrates a third party metal-binding site, formed by two conserved His residues and the dipeptide inhibitor and Zn atom bound at such a site would stabilize product binding and enhance inhibition.

Oligonucleotides and nucleic acid analogues that alter gene expression are now showing therapeutic promise in human disease. Whilst the modification of synthetic nucleic acids to protect against nuclease degradation and to influence drug function is common practice, such modifications may also confer unexpected physicochemical and biological properties. Gapmer mixed-modified and DNA oligonucleotides on a phosphorothioate backbone can bind non-specifically to intracellular proteins to form a variety of toxic inclusions, driven by the phosphorothioate linkages, but also influenced by the oligonucleotide sequence. Recently, the non-antisense or other off-target effects of 2′ O - fully modified phosphorothioate linkage oligonucleotides are becoming better understood. Here, we report chemistry-specific effects of oligonucleotides composed of modified or unmodified bases, with phosphorothioate linkages, on subnuclear organelles and show altered distribution of nuclear proteins, the appearance of highly stable and strikingly structured nuclear inclusions, and disturbed RNA processing in primary human fibroblasts and other cultured cells. Phosphodiester, phosphorodiamidate morpholino oligomers, and annealed complimentary phosphorothioate oligomer duplexes elicited no such consequences. Disruption of subnuclear structures and proteins elicit severe phenotypic disturbances, revealed by transcriptomic analysis of transfected fibroblasts exhibiting such disruption. Our data add to the growing body of evidence of off-target effects of some phosphorothioate nucleic acid drugs in primary cells and suggest alternative approaches to mitigate these effects. [ABSTRACT FROM AUTHOR]

SUMMARY: KARRIKIN INSENSITIVE2 (KAI2) is an α/β‐hydrolase required for plant responses to karrikins, which are abiotic butenolides that can influence seed germination and seedling growth. Although represented by four angiosperm species, loss‐of‐function kai2 mutants are phenotypically inconsistent and incompletely characterised, resulting in uncertainties about the core functions of KAI2 in plant development. Here we characterised the developmental functions of KAI2 in the grass Brachypodium distachyon using molecular, physiological and biochemical approaches. Bdkai2 mutants exhibit increased internode elongation and reduced leaf chlorophyll levels, but only a modest increase in water loss from detached leaves. Bdkai2 shows increased numbers of lateral roots and reduced root hair growth, and fails to support normal root colonisation by arbuscular‐mycorrhizal (AM) fungi. The karrikins KAR1 and KAR2, and the strigolactone (SL) analogue rac‐GR24, each elicit overlapping but distinct changes to the shoot transcriptome via BdKAI2. Finally, we show that BdKAI2 exhibits a clear ligand preference for desmethyl butenolides and weak responses to methyl‐substituted SL analogues such as GR24. Our findings suggest that KAI2 has multiple roles in shoot development, root system development and transcriptional regulation in grasses. Although KAI2‐dependent AM symbiosis is likely conserved within monocots, the magnitude of the effect of KAI2 on water relations may vary across angiosperms. Significance Statement: KAI2 is an α/β‐hydrolase receptor for abiotic karrikins and yet elusive plant hormones. The roles of KAI2 have been extensively studied in the dicotyledon Arabidopsis. Here we provide a comprehensive characterisation of the roles of KAI2 in the monocotyledon Brachypodium distachyon. [ABSTRACT FROM AUTHOR]