Ambiguities in results obtained with 2D gel replicon mapping techniques.

Recently, two 2-dimensional (2D) gel techniques, termed neutral/neutral and neutral/alkaline, have been developed and employed to map replication origins in eukaryotic plasmids and chromosomal DNA (1-11). The neutral/neutral technique, which requires less DNA for analysis, has been preferentially used in recent studies. We show here that the signal predicted for an origin is not detected using the neutral/neutral technique if the origin is located near the end of the analyzed restriction fragment. We also demonstrate that analysis of the same batch of DNA by the two different mapping techniques can generate apparently contradictory results: in some situations where neutral/alkaline 2D analysis indicates that a certain origin is always used, neutral/neutral 2D analysis suggests that the origin is not always used. Several possible explanations for this type of disagreement between the two techniques are discussed, and we conclude that it is important to use both techniques in combination in order to minimize possible misinterpretations.     

Exploring phenotype space through neutral evolution

RNA secondary-structure folding algorithms predict the existence of connected networks of RNA sequences with identical secondary structures. Fitness landscapes that are based on the mapping between RNA sequence and RNA secondary structure hence have many neutral paths. A neutral walk on these fitness landscapes gives access to a virtually unlimited number of secondary structures that are a single point mutation from the neutral path. This shows that neutral evolution explores phenotype space and can play a role in adaptation. Received: 23 December 1995 / Accepted: 17 March 1996     

Lipid modulation of nicotinic acetylcholine receptor function: the role of neutral and negatively charged lipids.

The effects of negatively charged and neutral lipids on the function of the reconstituted nicotinic acetylcholine receptor from Torpedo californica were determined with two assays using acetylcholine receptor-containing vesicles: the ion flux response and the affinity-state transition. The receptor was reconstituted into three different lipid environments, with and without neutral lipids: (1) phosphatidylcholine/phosphatidylserine; (2) phosphatidylcholine/phosphatidic acid; and (3) phosphatidylcholine/cardiolipin. Analysis of the ion flux responses showed that: (1) all three negatively charged lipid environments gave fully functional acetylcholine receptor ion channels, provided neutral lipids were added; (2) in each lipid environment, the neutral lipids tested were functionally equivalent to cholesterol; and (3) the rate of receptor desensitization depends upon the type of neutral lipid and negatively charged phospholipid reconstituted with the receptor. The functional effects of neutral and negatively charged lipids on the acetylcholine receptor are discussed in terms of protein-lipid interactions and stabilization of protein structure by lipids.     

Prediction of Disease Causing Non-Synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP

We have developed a sequence conservation-based artificial neural network predictor called NetDiseaseSNP which classifies nsSNPs as disease-causing or neutral. Our method uses the excellent alignment generation algorithm of SIFT to identify related sequences and a combination of 31 features assessing sequence conservation and the predicted surface accessibility to produce a single score which can be used to rank nsSNPs based on their potential to cause disease. NetDiseaseSNP classifies successfully disease-causing and neutral mutations. In addition, we show that NetDiseaseSNP discriminates cancer driver and passenger mutations satisfactorily. Our method outperforms other state-of-the-art methods on several disease/neutral datasets as well as on cancer driver/passenger mutation datasets and can thus be used to pinpoint and prioritize plausible disease candidates among nsSNPs for further investigation. NetDiseaseSNP is publicly available as an online tool as well as a web service: http://www.cbs.dtu.dk/services/NetDiseaseSNP     

中性蛋白酶高产菌株的筛选及产酶酶系分析

目的:满足水产中对中性蛋白酶的需求。方法:以实验室保藏的米曲霉ZW为出发菌株,经Co60定向诱变,通过透明圈法初筛、摇瓶发酵复筛,筛选中性蛋白酶活力高的菌株,并对其进行产酶酶系分析。结果:筛选到的米曲霉ZW-06产中性蛋白酶酶活可达15000U/g干曲,比诱变前酶活提高了74%,是目前国内报道的固体发酵产中性蛋白酶活力最高的菌株;经过10代传代之后,酶活力仍保持稳定。通过对米曲霉ZW-06进行产酶酶系分析,发现发酵产物中除了有较高的中性蛋白酶酶活,还有较高的木聚糖酶和酸性纤维素酶酶活,酶活分别达到49879U/g干曲和21099U/g干曲。结论:米曲霉ZW-06在饲料工业中有很大     

Modification of the phylloquinone in the A1 binding site in photosystem I studied using time-resolved FTIR difference spectroscopy and density functional theory

A phylloquinone molecule (2-methyl-3-phytyl-1,4-naphthoquinone) occupies the A1 binding site in photosystem I. Previously, we have obtained A1(-)/A1 FTIR difference spectra using labeled and unlabeled photosystem I particles and proposed assignments for many of the bands in the spectra [Sivakumar, V., Wang, R., and Hastings, G. (2005) Biochemistry 44, 1880-1893]. In particular, we suggested that a negative/positive band at 1654/1495 cm(-1) in A1(-)/A1 FTIR DS is due to a C=O/C-:O mode of the neutral/anionic phylloquinone, respectively. To test this hypothesis, we have obtained A1(-)/A1 FTIR DS for menG mutant PS I particles. In menG mutant PS I, phylloquinone in the A1 binding site is replaced with an analogue in which the methyl group at position 2 of the quinone ring is replaced with a hydrogen atom (2-phytyl-1,4-naphthoquinone). In A1(-)/A1 FTIR DS obtained using menG mutant PS I particles, we find that the 1654/1495 cm(-1) bands are upshifted by approximately 6 cm(-1). To test if such upshifts are likely for C=O/C-:O modes of neutral/anionic phylloquinone, we have used density functional theory to calculate the "anion minus neutral" infrared difference spectra for both phylloquinone and its methyl-less analogue. We have also undertaken calculations in which the C4=O carbonyl group of phylloquinone and its methyl-less analogue are hydrogen bonded (to a water or leucine molecule). We find that, irrespective of the hydrogen bonding state of the C4=O group, the C=O/C-:O modes of neutral/reduced phylloquinone are indeed expected to be upshifted by at least 6 cm(-1) upon replacement of the methyl group at position 2 with hydrogen. The calculations also suggest that certain C=C/C-:C modes of neutral/reduced phylloquinone do not shift upon replacement of the methyl group. On the basis of these calculated results, we suggest which bands in the A1(-)/A1 FTIR DS may be associated with C=C/C-:C modes of neutral/reduced phylloquinone, respectively.     

Studies in Plant Growth Hormones: IV. CHROMATOGRAPHY OF HORMONES AND HORMONE PRECURSORS IN CABBAGE

1. Acid and neutral ethereal fractions and the non-ether-solubleaqueous fraction of an extract of cabbage leaves were chromatographed,and the chromatc-grams assayed using oat coleoptile sections. 2. In the aqueous fraction an acidic precursor of 3-indolylacetonitrile(IAN) was found. When chromatographed in isopropanol/ammonia,the precursor travelled at the position of 3-indolylacetic acid(IAA), but in n-butanol/ammonia it was much closer to the starting-line.IAN is liberated from the precursor under conditions of alkalinehydrolysis including ammoniacal chromatography, and is alsoliberated by heat. Precursor and IAN zones promoted coleoptilegrowth, but the former when sprayed with ferric chloride/perchloricacid or nitrous/nitric acid gave a yellow colour showing thatthere was no free IAN on this part of the chromatogram. Hypothesesto account for this activity are discussed. 3. A neutral inhibitor was present in the aqueous fraction.It is volatile, ether-soluble, and is thought to have been liberatedfrom a water-soluble substance. 4. The neutral fraction, chromatographed in isopropanol/ammonia,contained IAN and a growth promoter at Rf o–o·1:thelatter stimulates cress root growth above that in water. Thispromoter could be formed from a precursor in the aqueous fractionby heat treatment followed by shaking with sodium bicarbonatesolution. It is suggested that this neutral hormone is the accelerator-of Bennet-Clark and Kefford. The data of these workers are analysedto show that this interpretation is consistent with their results. 5. The acid fraction contained IAN but no IAA. The former isthought not to have been liberated from the precursor in thisfraction but to have entered into it from the neutral fractionduring separation with sodium bicarbonate solution. AlthoughIAA may have been absent from the plant material, it is possiblethat any present was destroyed during the process of extraction. 6. Evidence is presented that there are other growth promoterspresent at low concentration in the extract in addition to thosealready mentioned.     

Neurotrophic factors regulate cathepsin S in macrophages and microglia: A role in the degradation of myelin basic protein and amyloid beta peptide.

BACKGROUND: Cathepsin S is a member of the family of cysteine lysosomal proteases preferentially expressed in macrophages and microglia and is active after prolonged incubation in neutral pH. Upon activation of macrophages by a number of inflammatory mediators, there is an increase in secreted cathepsin S activity accompanied by a decrease in cellular cathepsin S activity and protein content, as well as a decrease in cathepsin S mRNA. The decrease in cathepsin S mRNA and protein at the cellular level is in contrast to the response observed in some in vivo scenarios. MATERIALS AND METHODS: We investigated the effect of basic fibroblast growth factor (bFGF) and nerve growth factor (NGF), two growth factors present during cell injury and inflammation but not known to activate macrophages and microglia, on the expression of cathepsin S, cathepsin B, and cathepsin L mRNAs in these cells, and on cathepsin S activity. We then tested the ability of cathepsin S to degrade myelin basic protein, and amyloid beta peptide at both acidic and neutral pH. RESULTS: Basic FGF and NGF treatment of macrophages and microglia significantly increased the levels of cathepsin S, B, and L mRNAs (2- to 5-fold). Basic FGF also increased cathepsin S activity intra- and extracellularly. Recombinant human cathepsin S was able to degrade myelin basic protein and monomeric and dimeric amyloid beta peptide at both acidic and neutral pH, as well as to process human amyloid precursor protein generating amyloidogenic fragments. CONCLUSIONS: These data suggest that bFGF and NGF may be the molecular signals that positively regulate the expression and activity of cysteine lysosomal proteases (cathepsin S in particular) in macrophages and microglia in vivo, and that there is an interplay between these factors and the activators of inflammation. Disruption of the balance between these two categories of signals may underlie the pathological changes that involve cysteine proteases. http://link.springer-ny.com/link/service/journals/00020/bibs /5n5p334. html     

Neutral alpha-D-mannosidase activity in human granulocytes

The presence of neutral soluble alpha-D-mannosidase activity was shown in human granulocytes. For detection of the enzyme different methods were used: addition of stabilizing agents; sorption of acid alpha-D-mannosidase on concanavalin A-sepharose; inhibition of acid alpha-D-mannosidase; determination of neutral alpha-D-mannosidase in granulocytes of patients with inherited defect of acid alpha-D-mannosidase (mannosidosis). The specific activity of neutral alpha-D-mannosidase in granulocytes of donors calculated in nmol/min/mg of protein was near to the activity in lymphocytes. However the activity in granulocytes calculated in nmol/min/10(8) of cells was approximately 3 times lower than that in lymphocytes. The activity of neutral alpha-D-mannosidase in immature myeloid cells of a patient with chronic myeloid leukaemia was 10 times higher than in natural granulocytes of the same patient. This high activity may be in connection with the process of cell differentiation or the result of malignant transformation.     

Selective neutrality and enzyme kinetics

This article appeals to a recent theory of enzyme evolution to show that the properties, neutral or adaptive, which characterize the observed allelic variation in natural populations can be inferred from the functional parameters, substrate specificity, and reaction rate. This study delineates the following relations between activity variables, and the forces—adaptive or neutral—determining allelic variation: (1) Enzymes with broad substrate specificity: The observed polymorphism is adaptive; mutations in this class of enzymes can result in increased fitness of the organism and hence be relevant for positive selection. (2) Enzymes with absolute substrate specificity and diffusion-controlled rates: Observed allelic variation will be absolutely neutral; mutations in this class of enzymes will be either deleterious or have no effect on fitness. (3) Enzymes with absolute or group specificity and nondiffusion-controlled rates: Observed variation will be partially neutral; mutants which are selectively neutral may become advantageous under an appropriate environmental condition or different genetic background. We illustrate each of the relations between kinetic properties and evolutionary states with examples drawn from enzymes whose evolutionary dynamics have been intensively studied. Received: 12 December 1996 / Accepted: 22 April 1997     

Time-of-day effects on anaerobic muscular power in a moderately warm environment

This study evaluated the influence of a neutral vs. a moderately warm environment on the diurnal variation in muscular power. Twelve male subjects [27.0 (+/-4) years] performed two different jump tests [a squat jump (SJ) and a counter-movement jump (CMJ)] and a brief maximal sprint on cycle ergometer (CS) in four different conditions (morning/neutral, morning/moderately warm and humid, afternoon/neutral, and afternoon/moderately warm and humid). The morning experiments were conducted between 07:00 and 09:00 h, and the afternoon experiments were conducted between 17:00 and 19:00 h. The mean laboratory temperatures and humidity were 20 (+/-1) degrees C, 70 (+/-5)% and 29 (+/-1) degrees C, 57 (+/-4)% for the neutral and moderately warm and humid conditions, respectively. Rectal temperature and leg skin temperature were significantly dependent on both time-of-day and ambient temperature. An interaction effect (P < 0.05) was noted between time-of-day and ambient temperature for the power developed for the CMJ, the SJ, and half of a pedal revolution during the cycling sprint. In summary, (i) the same subjects were influenced by time-of-day differently, depending on the ambient temperature during testing; (ii) time-of-day affected muscular performance only in the neutral condition, (iii) the moderately warm and humid condition blunted the diurnal variation in muscular performance, and (iv) the effect of the ambient temperature was dependent on time-of-day.     

Covalent interaction of chloroacetic and acetic acids with cholesterol

The covalent interaction of chloroacetic acid with rat liver lipids was studied in vivo. Rats were given a single oral dose (8.75 mg/kg, 50 microCi) of 1-[14C]chloroacetic acid and sacrificed after 24 hours. Lipids extracted from the livers were separated into neutral lipids and phospholipids by solid-phase extraction using sep-pak silica cartridges. The neutral lipid fraction was further fractionated by preparative thin-layer chromatography followed by reverse-phase high-performance liquid chromatography. The fraction corresponding to the retention time of standard cholesteryl chloroacetate gave a pseudomolecular ion peak at m/z 480/482 ratio: (3:1) on ammonia chemical ionization mass spectrometry, and the fragmentation pattern was found to be similar to that of the standard sample. Under similar conditions, acetic acid resulted in the formation of cholesteryl acetate. The effect of such conjugation reactions on the cell membrane and their contribution to toxicity is presently unknown.     

What Does Brain Response to Neutral Faces Tell Us about Major Depression? Evidence from Machine Learning and fMRI

Introduction

A considerable number of previous studies have shown abnormalities in the processing of emotional faces in major depression. Fewer studies, however, have focused specifically on abnormal processing of neutral faces despite evidence that depressed patients are slow and less accurate at recognizing neutral expressions in comparison with healthy controls. The current study aimed to investigate whether this misclassification described behaviourally for neutral faces also occurred when classifying patterns of brain activation to neutral faces for these patients.

Methods

Two independent depressed samples: (1) Nineteen medication-free patients with depression and 19 healthy volunteers and (2) Eighteen depressed individuals and 18 age and gender-ratio-matched healthy volunteers viewed emotional faces (sad/neutral; happy/neutral) during an fMRI experiment. We used a new pattern recognition framework: first, we trained the classifier to discriminate between two brain states (e.g. viewing happy faces vs. viewing neutral faces) using data only from healthy controls (HC). Second, we tested the classifier using patterns of brain activation of a patient and a healthy control for the same stimuli. Finally, we tested if the classifier’s predictions (predictive probabilities) for emotional and neutral face classification were different for healthy controls and depressed patients.

Results

Predictive probabilities to patterns of brain activation to neutral faces in both groups of patients were significantly lower in comparison to the healthy controls. This difference was specific to neutral faces. There were no significant differences in predictive probabilities to patterns of brain activation to sad faces (sample 1) and happy faces (samples 2) between depressed patients and healthy controls.

Conclusions

Our results suggest that the pattern of brain activation to neutral faces in depressed patients is not consistent with the pattern observed in healthy controls subject to the same stimuli. This difference in brain activation might underlie the behavioural misinterpretation of the neutral faces content by the depressed patients.     

A crystalline lipid phase in a dry biological system: evidence from X-ray diffraction analysis of Typha latifolia pollen

The temperature limits for germination in Typha latifolia pollen lie within the range 4-40 degrees C. These limits correlate at the low-temperature end with the 'crystallization' of endogenous triacylglycerols and on the high-temperature end with the 'melting' of a gel-like lipid component in intact pollen. X-ray diffraction analysis was used to structurally characterize and to trace the latter gel-like lipid from the intact pollen through a range of pollen lipid fractions. We tentatively identify this component as a fatty acyl sterol ester and present evidence that it resides in the exine of the pollen grain. Its thermotropic behavior is insensitive to pollen hydration. The possibility of interpreting a crystalline lipid phase as being membrane-derived when in fact it originates from contaminating non-membranous neutral lipid is discussed. The total lipid content of T. latifolia pollen is 123 mg/g dry weight, of which 37% is polar lipid. The neutral lipid consists primarily of triacylglycerols and of the aforementioned sterol ester, which represents 0.34% (w/w) of pollen dry weight. The polar lipid fraction has phosphatidylcholine, phosphatidylethanolamine and phosphatidic acid as major components with lesser amounts of phosphatidylglycerol and phosphatidylinositol. Palmitic (16:0) and linoleic (18:2) acids, in a 1:2 molar ratio, constitute the major fatty acids of both polar and neutral lipid fractions with lesser amounts of linolenic (18:3), oleic (18:1) and stearic (18:0) acid in evidence.     

Mutation-biased adaptation in a protein NK model

Evolutionary trends responsible for systematic differences in genome and proteome composition have been attributed to GC:AT mutation bias in the context of neutral evolution or to selection acting on genome composition. A possibility that has been ignored, presumably because it is part of neither the Modern Synthesis nor the Neutral Theory, is that mutation may impose a directional bias on adaptation. This possibility is explored here with simulations of the effect of a GC:AT bias on amino acid composition during adaptive walks on an abstract protein fitness landscape called an "NK" model. The results indicate that adaptation does not preclude mutation-biased evolution. In the complete absence of neutral evolution, a modest GC:AT bias of realistic magnitude can displace the trajectory of adaptation in a mutationally favored direction, to such a degree that amino acid composition is biased substantially and persistently. Thus, mutational explanations for evolved patterns need not presuppose neutral evolution.     

Coexistence of nearly neutral species

Aims The neutral theory of biodiversity provides a powerful framework for modeling macroecological patterns and interpreting species assemblages. However, there remain several unsolved problems, including the effect of relaxing the assumption of strict neutrality to allow for empirically observed variation in vital rates and the 'problem of time'—empirically measured coexistence times are much shorter than the prediction of the strictly neutral drift model. Here, we develop a nearly neutral model that allows for differential birth and death rates of species. This model provides an approach to study species coexistence away from strict neutrality.Methods Based on Moran's neutral model, which assumes all species in a community have the same competitive ability and have identical birth and death rates, we developed a model that includes birth–death trade-off but excludes speciation. This model describes a wide range of asymmetry from strictly neutral to nearly neutral to far from neutral and is useful for analyzing the effect of drift on species coexistence. Specifically, we analyzed the effects of the birth–death trade-off on the time and probability of species coexistence and quantified the loss of biodiversity (as measured by Simpson's diversity) due to drift by varying species birth and death rates.Important findings We found (i) a birth–death trade-off operating as an equalizing force driven by demographic stochasticity promotes the coexistence of nearly neutral species. Species near demographic trade-offs (i.e. fitness equivalence) can coexist even longer than that predicted by the strictly neutral model; (ii) the effect of birth rates on species coexistence is very similar to that of death rates, but their compensatory effects are not completely symmetric; (iii) ecological drift over time produces a march to fixation. Trade-off-based neutral communities lose diversity more slowly than the strictly neutral community, while non-neutral communities lose diversity much more rapidly; and (iv) nearly neutral systems have substantially shorter time of coexistence than that of neutral systems. This reduced time provides a promising solution to the problem of time.     

Effect of pulsed electric fields on the activity of neutral trehalase from beer yeast and RSM analysis

The trehalase activity plays an important role in extraction of trehalose from beer yeast. In this study, the effect of pulsed electric field processing on neutral trehalase activity in beer yeast was investigated. In order to develop and optimize a pulsed electric field (PEF) mathematical model for activating the neutral trehalase, we have investigated three variables, including electric field intensity (10-50 kV/cm), pulse duration (2-10 μs) and liquid-solid ratio (20-50 ml/g) and subsequently optimized them by response surface methodology (RSM). The experimental data were fitted to a second-order polynomial equation and profiled into the corresponding contour plots. Optimal condition obtained by RSM is as follows: electric field intensity 42.13 kV/cm, liquid-solid ratio 30.12 ml/g and pulse duration 5.46 μs. Under these conditions, with the trehalose decreased 8.879 mg/L, the PEF treatment had great effect on activating neutral trehalase in beer yeast cells.     

The common patterns of nature

We typically observe large‐scale outcomes that arise from the interactions of many hidden, small‐scale processes. Examples include age of disease onset, rates of amino acid substitutions and composition of ecological communities. The macroscopic patterns in each problem often vary around a characteristic shape that can be generated by neutral processes. A neutral generative model assumes that each microscopic process follows unbiased or random stochastic fluctuations: random connections of network nodes; amino acid substitutions with no effect on fitness; species that arise or disappear from communities randomly. These neutral generative models often match common patterns of nature. In this paper, I present the theoretical background by which we can understand why these neutral generative models are so successful. I show where the classic patterns come from, such as the Poisson pattern, the normal or Gaussian pattern and many others. Each classic pattern was often discovered by a simple neutral generative model. The neutral patterns share a special characteristic: they describe the patterns of nature that follow from simple constraints on information. For example, any aggregation of processes that preserves information only about the mean and variance attracts to the Gaussian pattern; any aggregation that preserves information only about the mean attracts to the exponential pattern; any aggregation that preserves information only about the geometric mean attracts to the power law pattern. I present a simple and consistent informational framework of the common patterns of nature based on the method of maximum entropy. This framework shows that each neutral generative model is a special case that helps to discover a particular set of informational constraints; those informational constraints define a much wider domain of non‐neutral generative processes that attract to the same neutral pattern.