Water as a complex system: its role in ligand diffusion, general anesthesia, and sleep

The work and inspiration of Robert Rosen is stated and expressed in personal tones. The concept of passages through water (H2O) near protein surfaces is reviewed in terms of its influence on ligand diffusion to an effector. This is offered as a target for interference by a non-specific general anesthetic agent. In view of the similarities between this anesthetic state and sleep, this mechanism is proposed to be operative for the sleep/wake states. Based on this mechanism and other factors, nitrogen (N2) is proposed as an exogenous sleep factor.     

A cellular automata model of ligand passage over a protein hydrodynamic landscape

The subject of ligand passage to an active site on a protein is addressed. Current views on the mechanism and the possible role of surface water are discussed. A theory is presented in which the pattern of hydropathic states of protein surface amino acid side chains is invoked as the influence on the relative hydrophobic effects of nearby water. The theory describes a ligand passage through the hydrodynamic near-surface water which exhibits temporary organized cavities resembling the chreodes introduced by Waddington. The passage of the ligand to the active site is facilitated by this dynamic mechanism. Cellular automata models of preferential directional diffusion through these chreodes support the theory. The theory may be invoked to explain a number of ligand-active site observations and serves as an idea for further studies.     

Sleep, emotions, and visceral control

It is known that sleep is connected with sensory isolation of the brain, inactivation of the consciousness and reorganization of the electrical activity in all cerebral cortical areas. On the other hand, sleep deprivation leads to pathology in visceral organs and finally to the death of animals, while there are no obvious changes in the brain itself. It is still unclear how the changes in the brain activity during sleep could be connected with the visceral health. We assumed that the same brain areas and the same neurons that, in wakefulness, process exteroceptive information, switch, during sleep, to the processing of the interoceptive information. Thus, the central nervous system is involved in regulating the life support functions of the body during sleep. The results of our experiments supported this hypothesis, explained many observations obtained in somnology, and offered mechanisms of several pathological states connected with sleep. However, at the present level of the visceral sleep theory, there is no understanding of the well-known link between the emotional reactions of the body and transition from wakefulness to sleep, and sleep quality. In this study, an attempt is undertaken to combine the visceral theory of sleep with the need-informational theory of emotions proposed by P. Simonov. The visceral theory of sleep assumes that in living organisms there is a constant monitoring of the correspondence of the visceral parameters to the genetically determined values. Mismatch signals evoke the feeling of tiredness and the need of sleep. This sleep need enters the competition with other actual needs of the body. In accordance with the theory of Simonov, emotions connected with a particular need play an important role in their ranking for satisfaction. We propose that emotional estimation of the sleep need based on visceral signals occurs in the same brain structures which undertake this estimation for other behavioral needs in wakefulness. During sleep, the same brain structures involved in estimating emotions continue to rank visceral needs and define their order for processing in the cortical areas and in the highest centers of visceral integration. In the context of the proposed hypothesis, we discuss the results of the studies on the link between sleep and emotions.     

Synthesis, characterization, and in vitro cytotoxic effects of K4 [PtCl2ATP

An antineoplastic agent, cis-K4 [PtCl2ATP] has been synthesized and characterized, using elemental analysis, solution conductance, thermoanalysis, infrared, NMR spectroscopy, and circular dichroism studies. The in vitro cytotoxic effect imparted by this compound on Dalton's Lymphoma cells has been assessed by Trypan blue dye exclusion method and 51Cr release assays.     

Predation risk, stoichiometric plasticity and ecosystem elemental cycling

It is widely held that herbivore growth and production is limited by dietary nitrogen (N) that in turn constrains ecosystem elemental cycling. Yet, emerging evidence suggests that this conception of limitation may be incomplete, because chronic predation risk heightens herbivore metabolic rate and shifts demand from N-rich proteins to soluble carbohydrate-carbon (C). Because soluble C can be limiting, predation risk may cause ecosystem elemental cycling rates and stoichiometric balance to depend on herbivore physiological plasticity. We report on a stoichiometrically explicit ecosystem model that investigates this problem. The model tracks N, and soluble and recalcitrant C through ecosystem compartments. We evaluate how soluble plant C influences C and N stocks and flows in the presence and absence of predation risk. Without risk, herbivores are limited by N and respire excess C so that plant-soluble C has small effects only on elemental stocks and flows. With predation risk, herbivores are limited by soluble C and release excess N, so plant-soluble C critically influences ecosystem elemental stocks flows. Our results emphasize that expressing ecosystem stoichiometric balance using customary C : N ratios that do not distinguish between soluble and recalcitrant C may not adequately describe limitations on elemental cycling.     

Effect of certain herbicides on survival, growth, and nitrogen fixation of blue-green alga Anabaena doliolum Bharadwaja

Growth and fixation of nitrogen were retarded in Anabaena doliolum when grown on elemental nitrogen in presence of four different herbicides. The alga was found to be intolerant to these chemicals under nitrogen fixing conditions even in low concentrations. An inhibition of photosynthesis has been regarded as the main basis of herbicidal activity besides other interactions.     

Melanin standard method: empirical formula.

Melanin isolated from the ink sac of cuttle fish (Sepia melanin) is a proposed standard for natural eumelanin. Sepia melanin isolated by a standard protocol was submitted for both elemental analysis and quantitative amino acid analysis. The contribution of the detected amino acids to the elemental composition is subtracted from the total elemental analysis, and the resultant elemental composition reflects the composition of the Sepia melanin backbone chromophore. The assumption is made that, for eumelanins, there is only one nitrogen atom per monomeric unit, and thus, the empirical formula for the average monomeric Sepia melanin backbone chromophore was determined. Three key parameters can be determined for any melanin sample; namely, the molar C/N for the average monomeric unit, the formula weight of the average monomeric unit, and the total percent composition of amino acid residues. Three commonly used melanin preparations, namely, natural Sepia melanin, melanin prepared by the in vitro tyrosinase catalyzed polymerization of tyrosine (tyrosine-enzymatic melanin), and a polymer synthesized by the peroxide oxidative polymerization of tyrosine (tyrosine-chemical melanin), have been subjected to this standard method of characterization. Tyrosine-enzymatic and Sepia melanin are quite similar and tyrosine-chemical melanin is fundamentally different from the other two melanins.     

Comparison of proprietary elemental and whole-protein diets in unconscious patients with head injury.

Forty men who had sustained head injury were randomly assigned to one of five groups to receive 0.2 g nitrogen/kg body weight/day as either an elemental or a whole-protein diet. Three proprietary elemental and two whole-protein diets were compared. The mean daily nitrogen intake was below 0.2 g/kg in all groups, and was significantly lower in the groups receiving elemental compared with whole-protein diets. Energy intake was significantly different only between one group receiving an elemental and one receiving a whole-protein diet. Mean daily urinary nitrogen excretion was significantly lower in the groups receiving elemental diets, and mean daily nitrogen balance was negative in all groups except one receiving a whole-protein diet. Reduced nitrogen intakes occurred particularly with the elemental diets, which often provoked reflex vomiting or gastric stasis. The need to introduce diets at reduced strength made a negative balance almost inevitable, but nutritional balance seemed to be more readily achieved with the whole-protein diets. More work is needed to assess the relative merits of these proprietary diets compared with tube feeds prepared in hospitals.     

A new nitrogen fixing bacterium from a Danish watercourse

Summary A bacterium, isolated from a Danish watercourse, was studied with special regard to nitrogen fixing ability, and it was found that this strain was able to fix elemental nitrogen in amounts up to 1.6 mg. per g. of carbohydrate decomposed. This nitrogen-fixing ability was confirmed definitively by an isotope experiment. Free oxygen was found to have a clearly depressing effect on nitrogen fixation.The systematic position of this bacterium is difficult to establish with certainty, but in all probability it belongs to the genusAchromobacter Bergey et al., although not identical with any of the species described inBergeys Manual (1948).     

More is not necessarily better: the impact of limiting and excessive nutrients on herbivore population growth rates

Abstract 1. The body tissues of insect herbivores contain higher concentrations of nitrogen and phosphorus than do their host plants, leading to an elemental mismatch that can limit herbivore growth, fecundity and ultimately influence population dynamics. While low nutrient availability can limit herbivore growth and reproduction, nutrient levels that exceed an organism’s nutritional requirements, i.e. an organisms’ threshold elemental ratio, can also decrease performance. 2. We conducted a laboratory experiment to examine the impacts of nitrogen and phosphorus additions on population growth rates of a phloem‐feeding insect herbivore. 3. Herbivore per capita population growth rates were highest at intermediate foliar nitrogen concentrations, indicating a performance cost on the highest nitrogen foliage. While there was no direct effect of foliar phosphorus concentration on insect performance, there was a strong and unexpected indirect effect. High soil phosphorus availability increased both foliar nitrogen concentrations and aphid tissue nitrogen, resulting in low population growth rates when both soil nitrogen and phosphorus availabilities were high. 4. In this study, experimental increases in foliar nitrogen levels led to a decrease in herbivore performance suggesting that excessive nutrient levels can limit herbivore population growth rates.     

An automatic EEG-based sleep staging system with introducing NAoSP and NAoGP as new metrics for sleep staging systems

Different biological signals are recorded in sleep labs during sleep for the diagnosis and treatment of human sleep problems. Classification of sleep stages with electroencephalography (EEG) is preferred to other biological signals due to its advantages such as providing clinical information, cost-effectiveness, comfort, and ease of use. The evaluation of EEG signals taken during sleep by clinicians is a tiring, time-consuming, and error-prone method. Therefore, it is clinically mandatory to determine sleep stages by using software-supported systems. Like all classification problems, the accuracy rate is used to compare the performance of studies in this domain, but this metric can be accurate when the number of observations is equal in classes. However, since there is not an equal number of observations in sleep stages, this metric is insufficient in the evaluation of such systems. For this purpose, in recent years, Cohen’s kappa coefficient and even the sensitivity of NREM1 have been used for comparing the performance of these systems. Still, none of them examine the system from all dimensions. Therefore, in this study, two new metrics based on the polygon area metric, called the normalized area of sensitivity polygon and normalized area of the general polygon, are proposed for the performance evaluation of sleep staging systems. In addition, a new sleep staging system is introduced using the applications offered by the MATLAB program. The existing systems discussed in the literature were examined with the proposed metrics, and the best systems were compared with the proposed sleep staging system. According to the results, the proposed system excels in comparison with the most advanced machine learning methods. The single-channel method introduced based on the proposed metrics can be used for robust and reliable sleep stage classification from all dimensions required for real-time applications.Electronic supplementary materialThe online version of this article (10.1007/s11571-020-09641-2) contains supplementary material, which is available to authorized users.     

Melanin Standard Method: Empirical Formula

Melanin isolated from the ink sac of cuttle fish (Sepia melanin) is a proposed standard for natural eumelanin. Sepia melanin isolated by a standard protocol was submitted for both elemental analysis and quantitative amino acid analysis. The contribution of the detected amino acids to the elemental composition is subtracted from the total elemental analysis, and the resultant elemental composition reflects the composition of the Sepia melanin backbone chromophore. The assumption is made that, for eumelanins, there is only one nitrogen atom per monomeric unit, and thus, the empirical formula for the average monomeric Sepia melanin backbone chromophore was determined. Three key parameters can be determined for any melanin sample; namely, the molar C/N for the average monomeric unit, the formula weight of the average monomeric unit, and the total percent composition of amino acid residues. Three commonly used melanin preparations, namely, natural Sepia melanin, melanin prepared by the in vitro tyrosinase catalyzed polymerization of tyrosine (tyrosine-enzymatic melanin), and a polymer synthesized by the peroxide oxidative polymerization of tyrosine (tyrosine-chemical melanin), have been subjected to this standard method of characterization. Tyrosine-enzymatic and Sepia melanin are quite similar and tyrosine-chemical melanin is fundamentally different from the other two melanins.     

To sleep, to strive, or both: how best to optimize memory

While numerous studies have shown that a night of sleep profits memory relative to wake, we still have little understanding about what factors mediate this effect of sleep. A clear understanding of the dynamics of this effect of sleep beyond the initial night of sleep is also lacking. Here, we examined the effect of extrinsic rewards on sleep-dependent declarative memory processing across 12 and 24 hr training-retest intervals. Subjects were either paid based on their performance at retest ($1 for each correct answer), or received a flat fee for participation. After a 12 hr interval we observed pronounced benefits of both sleep and reward on memory. Over an extended 24 hr interval we found 1) that an initial night of sleep partially protects memories from subsequent deterioration during wake, and 2) that sleep blocks further deterioration, and may even have a restorative effect on memory, when it follows a full day of wake. Interestingly, the benefit imparted to rewarded (relative to unrewarded) stimuli was equal for sleep and wake subjects, suggesting that the sleeping brain may not differentially process rewarded information, relative to wake. However, looking at the overall impact of sleep relative to reward in this protocol, it was apparent that sleep both imparted a stronger mnemonic boost than reward, and provided a benefit to memory regardless of whether it occurred in the first or the second 12 hrs following task training.     

Poly(ethylene glycol)-carboxymethyl chitosan-based pH-responsive hydrogels: photo-induced synthesis, characterization, swelling, and in vitro evaluation as potential drug carriers

In this study, carboxymethyl chitosan was prepared, characterized, and then photo-induced graft copolymerized with poly(ethylene glycol) under a nitrogen atmosphere in aqueous solution using 2,2-dimethoxy-2-phenyl acetophenone (DMPA) as the photo-initiator. The grafting copolymerization process was confirmed and the resulting copolymers were characterized using differential scanning calorimetry (DSC), FTIR spectroscopy, 2D-X ray diffraction, and elemental analysis. The kinetics of the grafting reactions was also studied. Under the applied experimental conditions, the optimum grafting values were obtained at: CMCs = 0.2 g, PEGA = 249 mM, DMPA = 10.4 mM at a 2 h reaction time. Some of the resulting copolymers were selected and used in the presence of methylene bisacrylamide (MBA) as a crosslinking agent to develop pH-responsive hydrogel matrices. The swelling characteristics and the in vitro release profiles of 5-fluorouracil (5-FU), as a model drug, from the hydrogels were investigated. The results revealed that the hydrogel matrices developed in this study can be customized to act as good candidates in drug delivery systems.     

Sleep Promotes the Extraction of Grammatical Rules

Grammar acquisition is a high level cognitive function that requires the extraction of complex rules. While it has been proposed that offline time might benefit this type of rule extraction, this remains to be tested. Here, we addressed this question using an artificial grammar learning paradigm. During a short-term memory cover task, eighty-one human participants were exposed to letter sequences generated according to an unknown artificial grammar. Following a time delay of 15 min, 12 h (wake or sleep) or 24 h, participants classified novel test sequences as Grammatical or Non-Grammatical. Previous behavioral and functional neuroimaging work has shown that classification can be guided by two distinct underlying processes: (1) the holistic abstraction of the underlying grammar rules and (2) the detection of sequence chunks that appear at varying frequencies during exposure. Here, we show that classification performance improved after sleep. Moreover, this improvement was due to an enhancement of rule abstraction, while the effect of chunk frequency was unaltered by sleep. These findings suggest that sleep plays a critical role in extracting complex structure from separate but related items during integrative memory processing. Our findings stress the importance of alternating periods of learning with sleep in settings in which complex information must be acquired.     

Reduction of Selenium Oxyanions in Wastewater Using Two Bacterial Strains

The biological reduction of selenium oxyanions is capable of reducing both selenate and selenite to insoluble elemental selenium. In this process, however, bacteria inevitably require expensive chemicals such as yeast extract in almost all cases. Therefore, the reduction of selenium oxyanions with inexpensive alcohol would be more practical. A Pseudomonas sp. strain 4C‐C isolated from a sludge in a wastewater treatment facility was able to reduce selenate to selenite using ethanol as an electron donor for its anaerobic respiration, but could not reduce selenite to elemental selenium. Paracoccus denitrificans JCM‐6892, on the other hand, was observed to be able to reduce selenite to elemental selenium in the presence of ethanol, but not selenate to selenite. Therefore, a mixture containing a suspension of Pseudomonas sp. strain 4C‐C and P. denitrificans JCM‐6892 cells allowed selenate to be reduced to insoluble elemental selenium via selenite in the presence of ethanol and was also capable of reducing nitrate to nitrogen gas. Aiming at simplicity of the recovery process of insoluble elemental selenium, a polymeric gel immobilized mixture of the two bacterial strains was examined using ethanol as an electron donor. The immobilized mixture could therefore reduce not only selenate to elemental selenium, but also nitrate to nitrogen gas in a single step. The gel that immobilized the microbial mixture changed its color during the process to bright red and no red elemental selenium was left in the wastewater. This indicates that the reduced elemental selenium was completely absorbed in the gel. This simple bacterial combination would therefore be effective in the presence of ethanol to reduce selenium oxyanions in various wastewaters containing selenium and the other oxyanions.     

New methyl pyruvate thiosemicarbazones and their copper and zinc complexes: synthesis, characterization, X-ray structures and biological activity.

By reacting thiosemicarbazides substituted on the aminic nitrogen with both alkyl or aryl groups, and methyl pyruvate a new group of methylpyruvate thiosemicarbazones (Hmpt) derivatives was obtained. These ligands were then treated with copper and zinc inorganic salts. All isolated compounds were characterized using spectroscopic methods. The single crystal structural analysis of the ligands Me-Hmpt x 0.5H2O 1, Et-Hmpt x H2O 2, Ph-Hmpt 5, Meph-Hmpt 6 showed that only compound 6 presents significant deviation from planarity. The X-ray structure of [Zn(Me-Hmpt)Cl2] x H2O 8 showed that in this complex Me-Hmpt behaves as a neutral ligand SNO terdentate and that the penta coordination is achieved by chloride ions according to spectroscopic and elemental analyses. On the basis of the analytical data the same behavior is proposed for the other zinc complexes. All the ligands in copper complexes seem to be monodeprotonated; nevertheless the same SNO behavior is expected. Tests on cell proliferation of human leukemic cell line U937 showed that the copper complex Cu(Et-mpt)Cl x H2O is the most active compound among those reported even though it is not able to induce apoptosis.     

Oxygen protection of bacteriophage T1 against ionizing radiations

Bacteriophage T1 was suspended in distilled water and in phosphate buffer, saturated with oxygen, nitrogen, hydrogen, and carbon monoxide, and irradiated with gamma rays and x-rays. Under the same conditions phage was exposed to hydrogen peroxide. Oxygen acted as a protective agent against both irradiation and hydrogen peroxide inactivation. As a protective agent against irradiation, oxygen was more efficient in distilled water than in buffer. The phage was much more sensitive to irradiation in the presence of hydrogen or nitrogen than in the presence of oxygen. Survivals of phage irradiated in suspensions saturated with hydrogen and with nitrogen did not differ significantly. From this it was concluded that oxygen did not protect T1 by removing atomic hydrogen from the irradiated medium, since the hydrogen-saturated medium increased the yield of atomic hydrogen but did not increase the yield of inactivated phage. It was presumed, therefore, that phage is sensitive to OH radicals and this was confirmed by irradiating phage with UV in the presence of hydrogen peroxide and comparing this survival with the survivals obtained from hydrogen peroxide alone and from UV alone. The combined effect of hydrogen peroxide and UV acting simultaneously was greater than the effect attributable to hydrogen peroxide and UV acting separately. Evidence for sensitivity to HO₂ radicals was considered, and the effect was attributed chiefly to an oxidizing action since phage sensitivity is greater at higher hydrogen ion concentrations, which favor oxidation by HO₂ radicals. Since the OH radical is a more efficient oxidizing agent than O^-, the former being favored in an acid medium, the latter in an alkaline medium, and since the phage is more sensitive in the first situation than in the second, the present tests proved the importance of oxidation as the mechanism of inactivation. Since some inactivation was encountered when phage was exposed to reducing agents, independently of irradiation, it was concluded that phage is somewhat sensitive to reducing agents, but the inactivation attributable to ionizing radiations is due chiefly to oxidation, against which these reducing agents are very efficient protectors. Under no circumstances did hydrogen peroxide protect T1, whether produced by irradiation in the medium or added beforehand to the medium to be irradiated. The first point was investigated by irradiating T1 in the presence of hydrogen and oxygen combined; this produced a higher yield of hydrogen peroxide but a lower survival of T1. In all these tests phage survival under irradiation was directly correlated with oxygen content of the medium rather than with production of hydrogen peroxide. It is proposed that the protective effect of oxygen is due to a reaction between the phage and oxygen, and this complex confers stability upon the phage.     

Enhancement of hexobarbital-induced sleep by lysine and its metabolites

Lysine has been shown to be metabolized in the rat brain to pipecolic acid which is a precursor of piperidine. Lysine and its proposed metabolites in this pathway were studied for the first time for their effect on the sleeping time induced by hexobarbital in the rat. Only $\text{L}$-lysine and $\text{D}$-lysine were found to prolong sleeping time significantly without toxic effect. A 3-day pretreatment with $\text{L}$-lysine produced an even more profound sleep prolongation. In most cases sleep enhancement was accompanied by a significant shortening of the time of sleep onset. Quantification of brain hexobarbital levels in the control and treated rats indicates that prolongation of sleeping time was not produced by inhibition of hexobarbital metabolism. The sleep prolonging effect of lysine, therefore, may be a direct action of lysine, or the metabolite(s) derived $\text{in}$$\text{vivo}$ from lysine, on the central nervous system.     

Effects of pH, Nitrite, and Ascorbic Acid on Nonenzymatic Nitric Oxide Generation and Bacterial Growth in Urine

Nitrite may be generated by bacteria in urine during urinary tract infections. Acidification of nitrite results in the formation of nitric oxide (NO) and other reactive nitrogen oxides, which are toxic to a variety of microorganisms. We have studied NO formation and bacterial growth in mildly acidified human urine containing nitrite and the reducing agent vitamin C. Urine collected from healthy subjects was incubated in closed syringes at different pH values with varying amounts of nitrite and/or ascorbic acid added. NO generation was measured in headspace gas using a chemiluminescence technique. A similar setup was also used to study the growth of three strains of bacteria in urine. Mildly acidified nitrite-containing urine generated large amounts of NO and this production was greatly potentiated by ascorbic acid. The growth of Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus saprophyticus was markedly reduced by the addition of nitrite to acidified urine. This inhibition was enhanced by ascorbic acid. In conclusion, we show that the growth of three common urinary pathogens is markedly inhibited in mildly acidified urine when nitrite is present. The bacteriostatic effect of acidified nitrite is likely related to the release of NO and other toxic reactive nitrogen intermediates. These results may help to explain the well-known beneficial effects of urinary acidification with, e.g., vitamin C in treatment and prevention of urinary tract infection.