Features of <Emphasis Type="Italic">Bacillus subtilis</Emphasis> IMB B-7023 and its streptomycin-resistant strain

Features of phosphate-mobilizing bacteria Bacillus subtilis IMB B-7023 and its streptomycin-resistant strain were investigated. While cultivated in medium with glucose and glycerophosphate, the growth rate of the antibiotic-marked strain was approximately similar to this parameter for Bacillus subtilis IMB B-7023 but cell sizes were 1.3-fold less. Both strains significantly stimulated the germinating of plant seeds, attached to their roots, and insignificantly differed in antagonistic activity toward phytopathogens and quantitative content of cell fatty acids and phosphatase activity. Streptomycin-resistant strain may be used for monitoring of Bacillus subtilis introduced to agroecosystem.     

The archaeal triphosphate tunnel metalloenzyme SaTTM defines structural determinants for the diverse activities in the CYTH protein family

CYTH proteins make up a large superfamily that is conserved in all three domains of life. These enzymes have a triphosphate tunnel metalloenzyme (TTM) fold, which typically results in phosphatase functions, e.g., RNA triphosphatase, inorganic polyphosphatase, or thiamine triphosphatase. Some CYTH orthologs cyclize nucleotide triphosphates to 3′,5′-cyclic nucleotides. So far, archaeal CYTH proteins have been annotated as adenylyl cyclases, although experimental evidence to support these annotations is lacking. To address this gap, we characterized a CYTH ortholog, SaTTM, from the crenarchaeote Sulfolobus acidocaldarius. Our in silico studies derived ten major subclasses within the CYTH family implying a close relationship between these archaeal CYTH enzymes and class IV adenylyl cyclases. However, initial biochemical characterization reveals inability of SaTTM to produce any cyclic nucleotides. Instead, our structural and functional analyses show a classical TTM behavior, i.e., triphosphatase activity, where pyrophosphate causes product inhibition. The Ca²⁺-inhibited Michaelis complex indicates a two-metal-ion reaction mechanism analogous to other TTMs. Cocrystal structures of SaTTM further reveal conformational dynamics in SaTTM that suggest feedback inhibition in TTMs due to tunnel closure in the product state. These structural insights combined with further sequence similarity network–based in silico analyses provide a firm molecular basis for distinguishing CYTH orthologs with phosphatase activities from class IV adenylyl cyclases.     

NKp46 O-Glycan Sequences That Are Involved in the Interaction with Hemagglutinin Type 1 of Influenza Virus

Natural killer (NK) cells serve as a crucial first-line defense against tumors and virus-infected cells. We previously showed that lysis of influenza virus (IV)-infected cells is mediated by the interaction between the NK receptor, NKp46, and the IV hemagglutinin (HA) type 1 expressed by the infected cells. This interaction requires the presence of sialyl groups on the NKp46-T225 O-glycoforms. In the current study, we analyzed the O-glycan sequences that are imperative for the interaction between recombinant NKp46 (rNKp46) and IV H1N1 strains. We first showed that rNKp46 binding to IV H1N1 is not mediated by a glycoform unique to the Thr225 site. We then characterized the O-glycan sequences that mediate the interaction of rNKp46 and IV H1N1; we employed rNKp46s with dissimilar glycosylation patterns and IV H1N1 strains with different sialic acid α2,3 and α2,6 linkage preferences. The branched α2,3-sialylated O-glycoform Neu5NAcα2,3-Galβ1,4-GlcNAcβ1,6[Neu5NAcα2,3-Galβ1,3]GalNAc competently mediated the interaction of rNKp46 with IV H1N1, manifesting a preference for α2,3 linkage. In contrast, the linear α2,3-sialylated O-glycoform Neu5NAcα2,3-Galβ1,3-GalNAc was not correlated with enhanced interaction between rNKp46 and IV H1N1 or a preference for α2,3 linkage. The branched α2,3- and α2,6-sialylated O-glycoform Neu5NAcα2,3-Galβ1,3[Neu5NAcα2,6]GalNAc competently mediated the interaction of rNKp46 with IV H1N1, manifesting a preference for α2,6 linkage. Previous viral HA-binding-specificity studies were performed with glycopolymer conjugates, free synthetic sialyl oligosaccharides, and sialidase-treated cells. This study shed light on the O-glycan sequences involved in the interaction of glycoprotein and viral hemagglutinins and may help in the design of agents inhibitory to hemagglutinin for influenza treatment.Hemagglutinin (HA) is the receptor-binding and membrane fusion protein of influenza virus (IV), as well as the target for infectivity-neutralizing antibodies (27). Terminal sialic acids of glycoproteins and glycolipids are the cellular receptors for the IV HA (27). Two major linkages between sialic acid and the penultimate galactose residues of carbohydrate side chains are found in nature, Neu5NAcα(2,3)-Gal and Neu5NAcα(2,6)-Gal (27); different HAs have different recognition specificities for these linkages and the sugar backbone beneath (23, 26, 30). However, all of the HA-binding specificity studies were performed with glycopolymer conjugates, free synthetic sialyl oligosaccharides, and sialidase-treated cells (8, 10, 20, 25). This could be sufficient for the design of IV-inhibitory agents, and yet, it contributes only partially to the understanding of the interaction of IV HAs with glycoproteins and glycolipids. We aimed to further explore the exact glycoform sequences conjugated to a specific glycoprotein''s glycosylation site that is recognized by different IV strains.For this purpose, we took advantage of our findings on the interaction of natural cytotoxicity receptors (NCRs) and IV HAs (2, 3, 13, 18, 19, 22, 34). We showed that the NKp44 and NKp46 NCRs but not the NKp30 NCR interact with IV HAs. This interaction requires the sialylation of NKp44 and NKp46 oligosaccharides, and the binding of these NCRs to viral HA is required for the lysis of virus-infected cells by NK cells (3, 13, 18). NKp46 displays two putative O-linked glycosylation sites at Thr125 and Thr225 and one N-linked glycosylation site at Asn216. In order to determine the specific sugar-carrying residue that is important for the HA1 recognition, site-directed mutagenesis of the three residues was performed to carry the glycan modifications. Only when Thr225 was replaced was a sharp decrease in the enhanced binding to IV HA1 and IV H1N1-infected cells observed (2). Therefore, for the NKp46 receptor, the interaction with IV HA1 is restricted to Thr225, one of its three glycosylation sites (2).We already showed that producing recombinant NKp46 (rNKp46) in different cell lines resulted in dissimilar glycosylation patterns and had a strong effect on the binding to its ligands (11). Therefore, we analyzed the O-glycan patterns of rNKp46 produced from various cell lines and utilized the dissimilar glycosylation patterns to elucidate the NKp46 O-glycan sequences that mediate the interaction with IV H1N1 strains. To associate the results with the IV preference for sialic acid α2,3 and/or α2,6 linkages, we employed A/PR/8/34 (H1N1), A/NC/20/99 (H1N1), and A/Brisbane/59/2007 (H1N1) grown in either hen egg amnion or Madin-Darby canine kidney (MDCK) cells. Our results pointed to two branched O-glycan sequences that mediated the interaction of the NKp46 glycoprotein with IV H1N1 in correlation with the sialic acid linkage preference of the IV strain.     

Functional complexity can mitigate performance trade-offs

Trade-offs are believed to impose major constraints on adaptive evolution, and they arise when modification of a trait improves one aspect of performance but incurs a cost in another. Here we show that performance costs that result from competing demands on one trait can be mitigated by compensatory changes in other traits, so long as performance has a complex basis. Numerical simulations indicate that increases in the number of traits that determine performance decrease the strength of performance trade-offs. In centrarchid fishes, multiple traits underlie suction feeding performance, and experimental data and hydrodynamic modeling show that combinations of traits evolve to increase the ability to feed on attached prey while mitigating costs to performance on evasive prey. Diet data for centrarchid species reveal a weak trade-off between these prey types, corroborating the results based on hydrodynamic modeling and suggesting that complexity in the functional basis of suction feeding performance enhances trophic diversification. Complexity may thus permit the evolution of combinations of high-performance behaviors that appear to violate underlying trade-offs, such as the ability to exert high suction forces with large gape. This phenomenon may promote morphological, functional, and ecological diversification in the face of the myriad selective demands organisms encounter.     

Characteristics of the spawning stock of chinook salmon <Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis> from the Apuka River (northeastern Kamchatka)

Biological features of chinook salmon Oncorhynchus tshawytscha from the Apuka River, the largest river of the northeastern Kamchatka inflowing Olyutorskii Bay of the Bering Sea, are studied. Chinook salmon from the Apuka River spend mainly a year in the river before downstream migration to the sea. The fish live in the sea for 1–4 years. The spawning migration of chinook salmon into the Apuka River begins in late May just after ice melting, and it continues until early August. The main part of the spawners enters the river during June. A hypothesis on the occurrence of two seasonal races in the Apuka River is proposed.     

Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci

BMI1 is required for the self-renewal of stem cells in many tissues including the lung epithelial stem cells, Bronchioalveolar Stem Cells (BASCs). Imprinted genes, which exhibit expression from only the maternally or paternally inherited allele, are known to regulate developmental processes, but what their role is in adult cells remains a fundamental question. Many imprinted genes were derepressed in Bmi1 knockout mice, and knockdown of Cdkn1c (p57) and other imprinted genes partially rescued the self-renewal defect of Bmi1 mutant lung cells. Expression of p57 and other imprinted genes was required for lung cell self-renewal in culture and correlated with repair of lung epithelial cell injury in vivo. Our data suggest that BMI1-dependent regulation of expressed alleles at imprinted loci, distinct from imprinting per se, is required for control of lung stem cells. We anticipate that the regulation and function of imprinted genes is crucial for self-renewal in diverse adult tissue-specific stem cells.     

Effects of sodium sulfate on the freshwater microalga Chlamydomonas moewusii: implications for the optimization of algal culture media

The study of the microalgal growth kinetics is an indispensable tool in all fields of phycology. Knowing the optimal nutrient concentration is an important issue that will help to develop efficient growth systems for these microorganisms. Although nitrogen and phosphorus are well studied for this purpose, sulfur seems to be less investigated. Sulfate is a primary sulfur source used by microalgae; moreover, the concentration of this compound is increasing in freshwater systems due to pollution. The aim of this study was to investigate the effects of different sodium sulfate concentrations in the culture medium on growth and growth kinetics of the freshwater microalga Chlamydomonas moewusii. Production of biomass, chl content, kinetic equations, and a mathematical model that describe the microalgal growth in relation with the concentration of sodium sulfate were obtained. The lowest concentration of sodium sulfate allowing optimal growth was 0.1 mM. Concentrations higher than 3 mM generated a toxic effect. This work demonstrates that this toxic effect was not directly due to the excess of sulfate ion but by the elevation of the ionic strength. An inhibition model was successfully used to simulate the relationship between specific growth rate and sodium sulfate in this microalga.     

Suction feeding mechanics, performance, and diversity in fishes

Despite almost 50 years of research on the functional morphologyand biomechanics of suction feeding, no consensus has emergedon how to characterize suction-feeding performance, or its morphologicalbasis. We argue that this lack of unity in the literature isdue to an unusually indirect and complex linkage between themuscle contractions that power suction feeding, the skeletalmovements that underlie buccal expansion, the sharp drop inbuccal suction pressure that occurs during expansion, the flowof water that enters the mouth to eliminate the pressure gradient,and the forces that are ultimately exerted on the prey by thisflow. This complexity has led various researchers to focus individuallyon suction pressure, flow velocity, or the distance the preymoves as metrics of suction-feeding performance. We attemptto integrate a mechanistic view of the ability of fish to performthese components of suction feeding. We first discuss a modelthat successfully relates aspects of cranial morphology to thecapacity to generate suction pressure in the buccal cavity.This model is a particularly valuable tool for studying theevolution of the feeding mechanism. Second, we illustrate themultidimensional nature of suction-feeding performance in acomparison of bluegill, Lepomis macrochirus, and largemouthbass, Micropterus salmoides, two species that represent oppositeends of the spectrum of performance in suction feeding. As anticipated,bluegills had greater accuracy, lower peak flux into the mouth,and higher flow velocity and acceleration of flow than did bass.While the differences between species in accuracy of strikeand peak water flux were substantial, peak suction velocityand acceleration were only about 50% higher in bluegill, a relativelymodest difference. However, a hydrodynamic model of the forcesthat suction feeders exert on their prey shows that this differencein velocity is amplified by a positive effect of the smallermouth aperture of bluegill on force exerted on the prey. Ourmodel indicates that the pressure gradient in front of a fishthat is feeding by suction, associated with the gradient inwater velocity, results in a force on the prey that is largerthan drag or acceleration reaction. A smaller mouth apertureresults in a steeper pressure gradient that exerts a greaterforce on the prey, even when other features of the suction floware held constant. Our work shows that some aspects of suction-feedingperformance can be determined from morphology, but that thecomplexity of the behavior requires a diversity of perspectivesto be used in order to adequately characterize performance.     

Pain Intensity Recognition Rates via Biopotential Feature Patterns with Support Vector Machines

Background

The clinically used methods of pain diagnosis do not allow for objective and robust measurement, and physicians must rely on the patient’s report on the pain sensation. Verbal scales, visual analog scales (VAS) or numeric rating scales (NRS) count among the most common tools, which are restricted to patients with normal mental abilities. There also exist instruments for pain assessment in people with verbal and / or cognitive impairments and instruments for pain assessment in people who are sedated and automated ventilated. However, all these diagnostic methods either have limited reliability and validity or are very time-consuming. In contrast, biopotentials can be automatically analyzed with machine learning algorithms to provide a surrogate measure of pain intensity.

Methods

In this context, we created a database of biopotentials to advance an automated pain recognition system, determine its theoretical testing quality, and optimize its performance. Eighty-five participants were subjected to painful heat stimuli (baseline, pain threshold, two intermediate thresholds, and pain tolerance threshold) under controlled conditions and the signals of electromyography, skin conductance level, and electrocardiography were collected. A total of 159 features were extracted from the mathematical groupings of amplitude, frequency, stationarity, entropy, linearity, variability, and similarity.

Results

We achieved classification rates of 90.94% for baseline vs. pain tolerance threshold and 79.29% for baseline vs. pain threshold. The most selected pain features stemmed from the amplitude and similarity group and were derived from facial electromyography.

Conclusion

The machine learning measurement of pain in patients could provide valuable information for a clinical team and thus support the treatment assessment.