Two different jumping mechanisms of water striders are determined by body size.

Current theory for surface tension-dominant jumps on water, created for small- and medium-sized water strider species and used in bioinspired engineering, predicts that jumping individuals are able to match their downward leg movement speed to their size and morphology such that they maximize the takeoff speed and minimize the takeoff delay without breaking the water surface. Here, we use empirical observations and theoretical modeling to show that large species (heavier than ~80 mg) could theoretically perform the surface-dominated jumps according to the existing model, but they do not conform to its predictions, and switch to using surface-breaking jumps in order to achieve jumping performance sufficient for evading attacks from underwater predators. This illustrates how natural selection for avoiding predators may break the theoretical scaling relationship between prey size and its jumping performance within one physical mechanism, leading to an evolutionary shift to another mechanism that provides protection from attacking predators. Hence, the results are consistent with a general idea: Natural selection for the maintenance of adaptive function of a specific behavior performed within environmental physical constraints leads to size-specific shift to behaviors that use a new physical mechanism that secure the adaptive function.

Dynamics of Bacterial Communities on Eggshells and on Nest Materials During Incubation in the Oriental Tit (Parus minor).

Eggshell bacterial communities may affect hatching success and nestling's condition. Nest materials are in direct contact with the eggshells, but the relationships with the eggshell microbiome during incubation have not been fully elucidated. Here, we characterize eggshell and nest material bacterial communities and their changes during incubation in the Oriental Tit (Parus minor). Bacterial communities on the nest material were relatively stable and remained distinct from the eggshell communities and had higher diversity and greater phylogenetic clustering than the eggshell communities from the same nest, resulting in lower phylogenetic turnover rate of nest material microbiome during incubation than expected by chance. While the species diversity of both communities did not change during incubation, we found significantly greater changes in the structure of bacterial communities on the eggshell than on the nest material. However, eggshell microbiome remained distinct from nest material microbiome, suggesting independent dynamics of the two microbiomes during incubation. We detected an increase in the relative abundance of several bacterial taxa on the eggshell that likely come from the bird's skin, feathers, cloaca/intestine, or uropygial secretion which suggests some exchange of bacteria between the incubating bird and the eggshell. Furthermore, incubation appeared to promote the abundance of antibiotic producing taxa on the eggshell, which may hypothetically inhibit growth of many bacteria including pathogenic ones. Our results suggest that the future studies should focus on simultaneous monitoring of absolute abundance as well as relative abundance in communities on eggshells, nest materials, and the incubating bird's body.

Discovery of small-molecule enzyme activators by activity-based protein profiling.

Activity-based protein profiling (ABPP) has been used extensively to discover and optimize selective inhibitors of enzymes. Here, we show that ABPP can also be implemented to identify the converse-small-molecule enzyme activators. Using a kinetically controlled, fluorescence polarization-ABPP assay, we identify compounds that stimulate the activity of LYPLAL1-a poorly characterized serine hydrolase with complex genetic links to human metabolic traits. We apply ABPP-guided medicinal chemistry to advance a lead into a selective LYPLAL1 activator suitable for use in vivo. Structural simulations coupled to mutational, biochemical and biophysical analyses indicate that this compound increases LYPLAL1's catalytic activity likely by enhancing the efficiency of the catalytic triad charge-relay system. Treatment with this LYPLAL1 activator confers beneficial effects in a mouse model of diet-induced obesity. These findings reveal a new mode of pharmacological regulation for this large enzyme family and suggest that ABPP may aid discovery of activators for additional enzyme classes.

Mechanistic Probes for the Epimerization Domain of Nonribosomal Peptide Synthetases.

Nonribosomal peptide synthetases (NRPSs) are responsible for the synthesis of a variety of bioactive natural products with clinical and economic significance. Interestingly, these large multimodular enzyme machineries incorporate nonproteinogenic d-amino acids through the use of auxiliary epimerization domains, converting l-amino acids into d-amino acids that impart into the resulting natural products unique bioactivity and resistance to proteases. Due to the large and complex nature of NRPSs, several questions remain unanswered about the mechanism of the catalytic domain reactions. We have investigated the use of mechanism-based crosslinkers to probe the mechanism of an epimerization domain in gramicidin S biosynthesis. In addition, MD simulations were performed, showcasing the possible roles of catalytic residues within the epimerization domain.

Molecular and phylogenetic analyses of influenza B viruses isolated from pediatric inpatients in South Korea during the 2011-2012 winter season.

Influenza B virus remains a major cause of respiratory diseases worldwide. Because of limited epidemiological and genetic data, the local and global transmission patterns of influenza B virus are not fully understood. Here we report the molecular and phylogenetic characterization of 163 influenza B virus isolates from pediatric inpatients with influenza-like illness in the winter of 2011-2012 in South Korea. Analysis of haemagglutinin and neuraminidase genes of the influenza B isolates revealed that both B/Victoria (62 %) and B/Yamagata lineages (38 %) co-circulated during that influenza season, and a considerable number of the isolates carried several amino acid substitutions in the four major antigenic epitopes of their haemagglutinin protein.

Assessing dietary specialization to inform the conservation of the fairy pitta (Pitta nympha), an endangered vermivore.

Quantifying the diet of endangered species is crucial for conservation, especially for diet specialists, which can be more susceptible to environmental changes. The vulnerable fairy pitta (Pitta nympha) is considered a specialist that primarily feeds its nestlings with earthworms. However, there have been few studies of the nestling diet provisioned by parents, and no assessments of earthworm proportion in the diet of adults. Our study aimed to fill these gaps, shedding light on crucial factors for conservation. Combining new observations with existing literature, we confirmed a consistent dominance of earthworms in the nestling diet, regardless of rainfall, nestling age, and time of day. We extrapolated the total earthworm consumption during a breeding event, accounting for potential variation in the availability of earthworms and their prevalence in the adult diet. We used literature-based earthworm densities in pitta habitats and our estimates of family earthworm consumption to calculate the habitat area that could provide a pitta family with the number of earthworms consumed during a breeding event. The predictions matched observed pitta home range sizes when assumed that the adult diet is comprised of approximately 70% earthworms. The results highlight the importance of earthworm-rich habitats for conservation planning of the fairy pitta. To mitigate the effects of habitat destruction, we discuss conservation practices that may involve enhancing earthworm abundance in natural habitats and providing vegetation cover for foraging pittas in adjacent anthropogenic habitats rich in earthworms. To guide conservation efforts effectively, future studies should investigate whether previously reported breeding in developed plantation habitats is due to high earthworm abundance there. Future studies should also quantify correlations between local earthworm densities, home range size, and the breeding success of the fairy pitta.

Enhanced selective discrimination of point-mutated viral RNA through false amplification regulatory direct insertion in rolling circle amplification.

Coronaviruses are single-stranded RNA viruses with high mutation rates. Although a diagnostic method for coronaviruses has been developed, variants appear rapidly. Low test accuracy owing to single-point mutations is one of the main factors in the failure to prevent the early spread of coronavirus infection. Although reverse transcription-quantitative polymerase chain reaction can detect coronavirus infection, it cannot exclude the possibility of false positives, and an additional multiplexing kit is needed to discriminate single nucleotide polymorphism (SNP) variants. Therefore, in this study, we introduced a new nucleic acid amplification method to determine whether an infected person has a SNP mutation using a lateral flow assay (LFA) as a point-of-care test. Unlike traditional DNA amplification methods, direct insertion into rolling circle amplification amplifies the target genes without false amplification. After SNP-selective nucleic acid amplification, nuclease enzymes are used to make double-stranded DNA fragments that the LFA can detect, where specific mismatched DNA is found and cleaved to show different signals when a SNP-type is present. Therefore, wild- and SNP-type variants can be selectively detected. In this study, the limit of detection was 400 aM for viral RNA, and we successfully identified a dominant SNP variant selectively. Clinical tests were also conducted.

Erratum: Text Correction. Evaluation of the clinical and radiographic effectiveness of treating peri-implant bone defects with a new biphasic calcium phosphate bone graft: a prospective, multicenter randomized controlled trial.

This corrects the article on p. 306 in vol. 53, PMID: 37524378.

Evaluation of the clinical and radiographic effectiveness of treating peri-implant bone defects with a new biphasic calcium phosphate bone graft: a prospective, multicenter randomized controlled trial.

PURPOSE: Biphasic calcium phosphate (BCP), a widely used biomaterial for bone regeneration, contains synthetic hydroxyapatite (HA) and ß-tricalcium phosphate (ß-TCP), the ratio of which can be adjusted to modulate the rate of degradation. The aim of this study was to evaluate the clinical and radiographic benefits of reconstructing peri-implant bone defects with a newly developed BCP consisting of 40% ß-TCP and 60% HA compared to demineralized bovine bone mineral (DBBM). METHODS: This prospective, multicenter, parallel, single-blind randomized controlled trial was conducted at the periodontology departments of 3 different dental hospitals. Changes in clinical (defect width and height) and radiographic (augmented horizontal bone thickness) parameters were measured between implant surgery with guided bone regeneration (GBR) and re-entry surgery. Postoperative discomfort (severity and duration of pain and swelling) and early soft-tissue wound healing (dehiscence and inflammation) were also assessed. Data were compared between the BCP (test) and DBBM (control) groups using the independent t-test and the χ² test. RESULTS: Of the 53 cases included, 27 were in the test group and 26 were in the control group. After a healing period of 18 weeks, the full and mean resolution of buccal dehiscence defects were 59.3% (n=16) and 71.3% in the test group and 42.3% (n=11) and 57.9% in the control group, respectively. There were no significant differences between the groups in terms of the change in mean horizontal bone augmentation (test group: -0.50±0.66 mm vs. control groups: -0.66±0.83 mm, P=0.133), postoperative discomfort, or early wound healing. No adverse or fatal complications occurred in either group. CONCLUSION: The GBR procedure with the newly developed BCP showed favorable clinical, radiographic, postoperative discomfort-related, and early wound healing outcomes for peri-implant dehiscence defects that were similar to those for DBBM. TRIAL REGISTRATION: Clinical Research Information Service Identifier: KCT0006428.

Unlearned adaptive responses to heterospecific referential alarm calls in two bird species from separate evolutionary lineages.

The interspecific responses to alarm signals may be based on unlearned mechanisms but research is often constrained by the difficulties in differentiating between unlearned and learned responses in natural situations. In a field study of two Paridae species, Parus minor and Sittiparus varius, who originated from a common ancestor 8 million years ago, we found a considerable degree of between-species overlap in acoustic properties of referential snake-alarm calls. Playback of these calls triggered unlearned adaptive fledging behavior in conspecific and heterospecific naive nestlings, suggesting a between-species overlap in the hypothetical unlearned neural templates involved in nestlings' reactions to alarm calls in both species. This suggests that similar calls and similar unlearned sensitivity might have been present in the common ancestor of the two species, and possibly in the ancestor of the whole family Paridae that originated 10-15 million years ago in Asian regions rich in snakes.

Neutralizing Activity against BQ.1.1, BN.1, and XBB.1 in Bivalent COVID-19 Vaccine Recipients: Comparison by the Types of Prior Infection and Vaccine Formulations.

Bivalent COVID-19 vaccines that contain BA.1 or BA.4/BA.5 have been introduced worldwide in response to pandemic waves of Omicron subvariants. This prospective cohort study was aimed to compare neutralizing antibodies (Nabs) against Omicron subvariants (BA.1, BA.5, BQ.1.1, BN.1, and XBB.1) before and 3-4 weeks after bivalent booster by the types of SARS-CoV-2 variants in prior infections and bivalent vaccine formulations. A total of 21 participants were included. Prior BA.1/BA.2-infected, and BA.5-infected participants showed significantly higher geometric mean titers of Nab compared to SARS-CoV-2-non-infected participants after bivalent booster (BA.1, 8156 vs. 4861 vs. 1636; BA.5, 6515 vs. 4861 vs. 915; BQ.1.1, 697 vs. 628 vs. 115; BN.1, 1402 vs. 1289 vs. 490; XBB.1, 434 vs. 355 vs. 144). When compared by bivalent vaccine formulations, Nab titers against studied subvariants after bivalent booster did not differ between BA.1 and BA.4/BA.5 bivalent vaccine (BA.1, 4886 vs. 5285; BA.5, 3320 vs. 4118; BQ.1.1, 311 vs. 572; BN.1, 1028 vs. 1095; XBB.1, 262 vs. 362). Both BA.1 and BA.4/BA.5 bivalent vaccines are immunogenic and provide enhanced neutralizing activities against Omicron subvariants. However, even after the bivalent booster, neutralizing activities against the later Omicron strains (BQ.1.1, BN.1, and XBB.1) would be insufficient to provide protection.

Automated Platform for the Plasmid Construction Process.

There is a growing need for applications capable of handling large synthesis biology experiments. At the core of synthetic biology is the process of cloning and manipulating DNA as plasmids. Here, we report the development of an application named DNAda capable of writing automation instructions for any given DNA construct design generated by the J5 DNA assembly program. We also describe the automation pipeline and several useful features. The pipeline is particularly useful for the construction of combinatorial DNA assemblies. Furthermore, we demonstrate the platform by constructing a library of polyketide synthase parts, which includes 120 plasmids ranging in size from 7 to 14 kb from 4 to 7 DNA fragments.

Pseudo-haptics and self-haptics for freehand mid-air text entry in VR.

Despite the lack of haptic feedback, two-finger typing remains as a common freehand mid-air text entry method in VR. To compensate for this limitation, we investigated the effect of pseudo-haptics and thumb-to-finger pinch self-haptics. Three types of virtual keyboards were developed for comparison: a normal virtual keyboard without any haptic features, a pseudo-haptic keyboard providing a haptic illusion by adding pseudo-haptic features to the normal virtual keyboard, and a pinch keyboard providing passive self-haptic feedback when the index finger touches the thumb to type bubble-shaped keys. A follow-up user study was conducted on the three keyboards to measure typing performance, perceived workload, and user experience. The results showed that the pseudo-haptic and pinch keyboards were comparable to the normal one in typing performance and workload, but beneficial in user experience and preference. The findings suggest that pseudo-haptics and self-haptics could achieve experiential benefits in VR text entry without obtrusive extra devices.

Rapid Extraction of Viral Nucleic Acids Using Rotating Blade Lysis and Magnetic Beads.

The complex and lengthy protocol of current viral nucleic acid extraction processes limits their use outside laboratory settings. Here, we describe a rapid and reliable method for extracting nucleic acids from viral samples using a rotating blade and magnetic beads. The viral membrane can be instantly lysed using a high-speed rotating blade, and nucleic acids can be immediately isolated using a silica magnetic surface. The process was completed within 60 s by this method. Routine washing and eluting processes were subsequently conducted within 5 min. The results achieved by this method were comparable to those of a commercially available method. When the blade-based lysis and magnetic bead adsorption processes were performed separately, the RNA recovery rate was very low, and the Ct value was delayed compared to simultaneous lysis and RNA adsorption. Overall, this method not only dramatically shortens the conventional extraction time but also allows for its convenient use outside the laboratory, such as at remote field sites and for point-of-care testing.

Developing crosslinkers specific for epimerization domain in NRPS initiation modules to evaluate mechanism.

Nonribosomal peptide synthetases (NRPSs) are complex multi-modular enzymes containing catalytic domains responsible for the loading and incorporation of amino acids into natural products. These unique molecular factories can produce peptides with nonproteinogenic d-amino acids in which the epimerization (E) domain catalyzes the conversion of l-amino acids to d-amino acids, but its mechanism remains not fully understood. Here, we describe the development of pantetheine crosslinking probes that mimic the natural substrate l-Phe of the initiation module of tyrocidine synthetase, TycA, to elucidate and study the catalytic residues of the E domain. Mechanism-based crosslinking assays and MALDI-TOF MS were used to identify both H743 and E882 as the crosslinking site residues, demonstrating their roles as catalytic bases. Mutagenesis studies further validated these results and allowed the comparison of reactivity between the catalytic residues, concluding that glutamate acts as the dominant nucleophile in the crosslinking reaction, resembling the deprotonation of the Cα-H of amino acids in the epimerization reaction. The crosslinking probes employed in these studies provide new tools for studying the molecular details of E domains, as well as the potential to study C domains. In particular, they would elucidate key information for how these domains function and interact with their substrates in nature, further enhancing the knowledge needed to assist combinatorial biosynthetic efforts of NRPS systems to produce novel compounds.

Mechanism-based cross-linking probes capture the Escherichia coli ketosynthase FabB in conformationally distinct catalytic states.

Ketosynthases (KSs) catalyse essential carbon-carbon bond-forming reactions in fatty-acid biosynthesis using a two-step, ping-pong reaction mechanism. In Escherichia coli, there are two homodimeric elongating KSs, FabB and FabF, which possess overlapping substrate selectivity. However, FabB is essential for the biosynthesis of the unsaturated fatty acids (UFAs) required for cell survival in the absence of exogenous UFAs. Additionally, FabB has reduced activity towards substrates longer than 12 C atoms, whereas FabF efficiently catalyses the elongation of saturated C14 and unsaturated C16:1 acyl-acyl carrier protein (ACP) complexes. In this study, two cross-linked crystal structures of FabB in complex with ACPs functionalized with long-chain fatty-acid cross-linking probes that approximate catalytic steps were solved. Both homodimeric structures possess asymmetric substrate-binding pockets suggestive of cooperative relationships between the two FabB monomers when engaged with C14 and C16 acyl chains. In addition, these structures capture an unusual rotamer of the active-site gating residue, Phe392, which is potentially representative of the catalytic state prior to substrate release. These structures demonstrate the utility of mechanism-based cross-linking methods to capture and elucidate conformational transitions accompanying KS-mediated catalysis at near-atomic resolution.

Structure and mechanistic analyses of the gating mechanism of elongating ketosynthases.

Ketosynthases (KSs) catalyze carbon-carbon bond forming reactions in fatty acid synthases (FASs) and polyketide synthases (PKSs). KSs utilize a two-step ping pong kinetic mechanism to carry out an overall decarboxylative thio-Claisen condensation that can be separated into the transacylation and condensation reactions. In both steps, an acyl carrier protein (ACP) delivers thioester tethered substrates to the active sites of KSs. Therefore, protein-protein interactions (PPIs) and KS-mediated substrate recognition events are required for catalysis. Recently, crystal structures of Escherichia coli elongating type II FAS KSs, FabF and FabB, in complex with E. coli ACP, AcpP, revealed distinct conformational states of two active site KS loops. These loops were proposed to operate via a gating mechanism to coordinate substrate recognition and delivery followed by catalysis. Here we interrogate this proposed gating mechanism by solving two additional high-resolution structures of substrate engaged AcpP-FabF complexes, one of which provides the missing AcpP-FabF gate-closed conformation. Clearly defined interactions of one of these active site loops with AcpP are present in both the open and closed conformations, suggesting AcpP binding triggers or stabilizes gating transitions, further implicating PPIs in carrier protein-dependent catalysis. We functionally demonstrate the importance of gating in the overall KS condensation reaction and provide experimental evidence for its role in the transacylation reaction. Furthermore, we evaluate the catalytic importance of these loops using alanine scanning mutagenesis and also investigate chimeric FabF constructs carrying elements found in type I PKS KS domains. These findings broaden our understanding of the KS mechanism which advances future engineering efforts in both FASs and evolutionarily related PKSs.

Associations of depression and anxiety with cardiovascular risk among people living with HIV/AIDS in Korea.

OBJECTIVES: As HIV/AIDS is becoming a chronic disease, the risk of developing cardiovascular disease (CVD) among people living with HIV/AIDS is rising. Anxiety and depression, which are common among people living with HIV/AIDS, have been linked with CVD. This study investigated the risk of CVD in people living with HIV/AIDS and explored the effects of depression and anxiety on CVD risk. METHODS: Data were collected for 457 people enrolled in the Korea Cohort HIV/AIDS study after 2010. Framingham risk scores were calculated to quantify the 10-year risk of developing CVD. Depression and anxiety variables were re-coded as a single combined variable. Multivariable logistic regression analysis was performed, adjusting for age, body mass index, low-density lipoprotein (LDL) cholesterol, triglycerides (TG), duration of human immunodeficiency virus (HIV) positivity after entry into the cohort, and depression/anxiety. RESULTS: Participants with both depression and anxiety were 2.28 times more likely than those with neither depression nor anxiety to have moderate/high-risk CVD risk. The 10-year risk of developing CVD was affected by LDL cholesterol, TG, age, and duration of HIV infection. LDL cholesterol and TG levels change according to the duration of HIV infection, and metabolic disorders affect the risk of CVD. Thus, a longer duration of HIV infection is associated with a higher risk of developing CVD. CONCLUSIONS: Screenings for depression and anxiety need to be provided regularly to assess the severity of those symptoms. To help decrease their risk of developing CVD, people living with HIV/AIDS should be offered behavioral modification interventions aimed at developing healthy lifestyle habits.

Microcephaly with altered cortical layering in GIT1 deficiency revealed by quantitative neuroimaging.

G Protein-Coupled Receptor Kinase-Interacting Protein-1 (GIT1) regulates neuronal functions, including cell and axon migration and synapse formation and maintenance, and GIT1 knockout (KO) mice exhibit learning and memory deficits. We noted that male and female GIT1-KO mice exhibit neuroimaging phenotypes including microcephaly, and altered cortical layering, with a decrease in neuron density in cortical layer V. Micro-CT and magnetic resonance microscopy (MRM) were used to identify morphometric phenotypes for the skulls and throughout the GIT1-KO brains. High field MRM of actively-stained mouse brains from GIT1-KO and wild type (WT) controls (n = 6 per group) allowed segmenting 37 regions, based on co-registration to the Waxholm Space atlas. Overall brain size in GIT1-KO mice was ~32% smaller compared to WT controls. After correcting for brain size, several regions were significantly different in GIT1-KO mice relative to WT, including the gray matter of the ventral thalamic nuclei and the rest of the thalamus, the inferior colliculus, and pontine nuclei. GIT1-KO mice had reduced volume of white matter tracts, most notably in the anterior commissure (~26% smaller), but also in the cerebral peduncle, fornix, and spinal trigeminal tract. On the other hand, the basal ganglia appeared enlarged in GIT1-KO mice, including the globus pallidus, caudate putamen, and particularly the accumbens - supporting a possible vulnerability to addiction. Volume based morphometry based on high-resolution MRM (21.5 µm isotropic voxels) was effective in detecting overall, and local differences in brain volumes in GIT1-KO mice, including in white matter tracts. The reduced relative volume of specific brain regions suggests a critical, but not uniform, role for GIT1 in brain development, conducive to brain microcephaly, and aberrant connectivity.