Insights into electron flux through manipulation of fermentation conditions and assessment of protein expression profiles in Clostridium thermocellum

While annotation of the genome sequence of Clostridium thermocellum has allowed predictions of pathways catabolizing cellobiose to end products, ambiguities have persisted with respect to the role of various proteins involved in electron transfer reactions. A combination of growth studies modulating carbon and electron flow and multiple reaction monitoring (MRM) mass spectrometry measurements of proteins involved in central metabolism and electron transfer was used to determine the key enzymes involved in channeling electrons toward fermentation end products. Specifically, peptides belonging to subunits of ferredoxin-dependent hydrogenase and NADH:ferredoxin oxidoreductase (NFOR) were low or below MRM detection limits when compared to most central metabolic proteins measured. The significant increase in H₂ versus ethanol synthesis in response to either co-metabolism of pyruvate and cellobiose or hypophosphite mediated pyruvate:formate lyase inhibition, in conjunction with low levels of ferredoxin-dependent hydrogenase and NFOR, suggest that highly expressed putative bifurcating hydrogenases play a substantial role in reoxidizing both reduced ferredoxin and NADH simultaneously. However, product balances also suggest that some of the additional reduced ferredoxin generated through increased flux through pyruvate:ferredoxin oxidoreductase must be ultimately converted into NAD(P)H either directly via NADH-dependent reduced ferredoxin:NADP⁺ oxidoreductase (NfnAB) or indirectly via NADPH-dependent hydrogenase. While inhibition of hydrogenases with carbon monoxide decreased H₂ production 6-fold and redirected flux from pyruvate:ferredoxin oxidoreductase to pyruvate:formate lyase, the decrease in CO₂ was only 20 % of that of the decrease in H₂, further suggesting that an alternative redox system coupling ferredoxin and NAD(P)H is active in C. thermocellum in lieu of poorly expressed ferredoxin-dependent hydrogenase and NFOR.     

Neural network‐derived Potts models for structure‐based protein design using backbone atomic coordinates and tertiary motifs

Designing novel proteins to perform desired functions, such as binding or catalysis, is a major goal in synthetic biology. A variety of computational approaches can aid in this task. An energy‐based framework rooted in the sequence‐structure statistics of tertiary motifs (TERMs) can be used for sequence design on predefined backbones. Neural network models that use backbone coordinate‐derived features provide another way to design new proteins. In this work, we combine the two methods to make neural structure‐based models more suitable for protein design. Specifically, we supplement backbone‐coordinate features with TERM‐derived data, as inputs, and we generate energy functions as outputs. We present two architectures that generate Potts models over the sequence space: TERMinator, which uses both TERM‐based and coordinate‐based information, and COORDinator, which uses only coordinate‐based information. Using these two models, we demonstrate that TERMs can be utilized to improve native sequence recovery performance of neural models. Furthermore, we demonstrate that sequences designed by TERMinator are predicted to fold to their target structures by AlphaFold. Finally, we show that both TERMinator and COORDinator learn notions of energetics, and these methods can be fine‐tuned on experimental data to improve predictions. Our results suggest that using TERM‐based and coordinate‐based features together may be beneficial for protein design and that structure‐based neural models that produce Potts energy tables have utility for flexible applications in protein science.     

Effects of the Execution of a Maze Task on Regulatory Mechanisms of the Autonomic Nervous System in Subjects with Different Levels of Nonverbal Intelligence

The effects of spatial task performance on heart rate characteristics were studied taking into account nonverbal intelligence and autonomic balance. Males and females with low nonverbal intelligence according to the Raven test were mostly sympathicotonics, while subjects with high intelligence were mostly vagotonics. A specific emotional response was observed in females with low and high nonverbal IQs immediately after the task completion and increased the stress index (SI). This clearly suggested that the task was stressful for them. Males with low and high nonverbal IQs were characterized by a reduction of the SI, indicating that this task activity was adequate for male subjects.__________Translated from Fiziologiya Cheloveka, Vol. 31, No. 3, 2005, pp. 50–54.Original Russian Text Copyright © 2005 by Grigoryan, Stepanyan, Agababyan, Arakelyan, Arutyunyan.     

Modifications of neuronal activity in the rat hypothalamic supraoptic nucleus after long-lasting vibrational stimulation

We analyzed the background impulse activity (BIA) generated by neurons of the rat hypothalamic supraoptic nucleus in the norm and under conditions of long-lasting vibrational stimulation (exposure 5, 10, or 15 days). Distributions of neurons by the level of regularity, dynamics of discharge trains, form of histograms of interspike intervals (ISIs), as well as distributions of neurons by the BIA frequency ranges, were studied. We also calculated the mean frequency of impulsation of the neurons under study and the coefficient of variation of ISIs. After vibrational influences, we found modifications of both the internal structure of the recorded spike trains and the mean frequency of impulsation within the entire studied group and different frequency subgroups. Neirofiziologiya/Neurophysiology, Vol. 38, No. 3, pp. 224–230, May–June, 2006.     

Aggregation and Adhesion Activity of Lactobacilli Isolated from Fermented Products In Vitro and In Vivo: a Potential Probiotic Strain

Approximately 25 strains of lactobacilli isolated from different dairy products and fermented vegetables were screened according to their possibility to show the high auto-aggregation and co-aggregation. The strains Lactobacillus helveticus INRA-2010-H11, Lactobacillus rhamnosus INA-5.1, and Lactobacillus acidophilus JM-2012 were determined to have the high auto-aggregation (approximately 73, 46, and 70.5% correspondingly). A high co-aggregation capacity (75.53%) for strains INRA-2010-H11 and JM-2012 was shown. The adhesion degree of INRA-2010-H11 on the surface of buccal epithelial cells was 88.23%. The study of INRA-2010-H11, JM-2012, and both strains’ mixture (1:1) adhesion capacity on the surface of epithelial HeLa cells revealed the adhesion of 1.1 × 10⁶, 6.3 × 10⁴, and 2.3 × 10⁵ CFU, respectively, from starter amount of CFU 10⁷ and 10⁸ for both strains. In vivo experiments of LAB adhesion in gastrointestinal tract of mouse revealed the presence of 2.5 × 10⁹, 1.2 × 10⁹, and 1.5 × 10⁹ CFU of LAB in control and groups of mouse, fed by INRA-2010-H11 and mixture, respectively. Feeding by investigated lactobacilli was suggested to lead to microbiota biodiversity reduction in small intestine and colon and its augmentation in stomach. Thus, INRA-2010-H11 demonstrated a high aggregation and adhesion activity so it has the potential as a good probiotic strain.     

Visual Stimuli for P300-Based Brain-Computer Interfaces: Color,Shape, and Mobility

The purpose of this study was to identify the impact of different discriminative features of stimuli in a P300 brain-computer interface paradigm on overall performance and evoked potentials. It has been shown that stimuli sets with a greater number of discriminative features yield better target selection accuracy. Target selection accuracy was significantly higher for the stimuli that differ from each other by color, shape, and semantics. Highest performance was achieved with the stimuli set containing the largest number of discriminative features, namely a set of nine different-colored letters. This result is mainly due to higher mean P300 peak amplitude for stimuli sets that contain more discriminative features. The results of the study can be used for designing a better user experience in brain-computer interfacing (BCI). Motion of the stimuli presentation point and characteristics of this motion (linear or pseudorandom) did not have any impact on BCI performance. This result is promising for future BCI designs with rapid serial visual presentation using mobile robots or augmented reality as stimuli presentation environment.     

“Irregular” visual receptive fields of neurons of the cat lateral geniculate body

Using point-to-point testing, the spatial organization of receptive fields (RF) of the neurons of the lateral geniculate body (LGB) was studied in cats with pretrigeminally transected brainstcm (without general anesthesia). In 60% of studied neurons (96 units of 160 examined), configuration of their RF considerably differed from round or ellipsoid. The shape of such RF was frequently rather complex, and they were qualified as irregular receptive fields (IRF). Presentation of the stable flickering spot throughout the entire surface of 60 IRF (63%) evoked qualitatively similar responses of a neuron, i.e., these IRF were homogeneous. In 29 cells the responses were of theon-off type, 22 neurons generatedoff responses, andon responses were observed in 9 cells. In the rest of the IRF (37%), it was possible to differentiate the subfields, whose stimulation evoked generation of different types of responses, i.e., these IRF were heterogeneous. In the case of moving stimuli, the neurons with homogeneous IRF showed no directional selectivity, while such selectivity was observed in most units with heterogeneous IRF.Neirofiziologiya/Neurophysiology, Vol. 28, No. 1, pp. 7–16, January–February, 1996.     

High regenerative ability of tailed amphibians (Urodela) as a result of the expression of juvenile traits by mature animals

The highest potencies of regeneration in tailed amphibians in comparison with the abilities of organ and tissue restoration in other vertebrates represent the goal of longstanding and intense studies. Accumulated information can half-open some mysteries of cellular and molecular fundamentals of regeneration in Urodela, but it does not explain the maintenance of regenerative abilities in mature, adult animals. The information summarized in the review suggests that the paedomorphosis inherent in this animal group determines the keeping of the juvenile state on all levels of organization—from organismic to molecular. This, in turn, permits and eases initiation and development of regenerative responses to trauma, right up to the epimorphic regeneration of whole organs. As an example, we have traced paedomorphosis-associated cellular and molecular specificities of urodelean eye and brain tissues, which could possibly play a permissive role in their complete regeneration.