Factors that affect the folding ability of proteins

The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the stability of the native state. We consider a number of estimates of the stability that can be determined without simulation, including the energy gap between the native state and the structurally dissimilar part of the spectrum (Z score) and, for sequences with fully compact native states, the gap in energy between the native and first excited fully compact states. These estimates are found to be more robust predictors of folding ability than a parameter sigma that requires simulation for its evaluation: sigma = 1 - Tf/Ttheta, where Tf is the temperature at which the fluctuation of an order parameter is at its maximum and Ttheta is the temperature at which the specific heat is at its maximum. We show that the interpretation of Ttheta as the collapse transition temperature is not correct in general and that the correlation between sigma and the folding ability arises from the fact that sigma is related to the energy gap (Z score).     

Factors that affect fertility in a feral population of sheep

Feral livestock offer an excellent opportunity lo study factors affecting fertility as the physiology of their husbanded relatives is well known and social and environmental influences can be studied free of man's interference. This is so in the population of about 1250 sheep of the primitive Soay breed on the islands of St Kilda, Scotland. There is a high coincidence of oestrus amongst the ewes in mid November, and the breeding season is constant within a few days, from year to year. The breeding season in other British breeds of sheep demonstrates a strong correlation with latitude. On St Kilda, mortality rates in male sheep are higher than in females so that the ratio of rams to ewes at mating time is about 1:5. Competition amongst rams is intense. The optimal time for mating and the place of ram lambs in the social system are discussed.     

Factors that affect the horizontal transfer of transposable elements

Transposable elements are characterized by their ability to spread within a host genome. Many are also capable of crossing species boundaries to enter new genomes, a process known as horizontal transfer. Focusing mostly on animal transposable elements, we review the occurrence of horizontal transfer and examine the methods used to detect such transfers. We then discuss factors that affect the frequency of horizontal transfer, with emphasis on the mechanism and regulation of transposition. An intriguing feature of horizontal transfer is that its frequency differs among transposable element families. Evidence summarized in this review indicates that this pattern is due to fundamental differences between Class I and Class II elements. There appears to be a gradient in the incidence of horizontal transfer that reflects the presence of DNA intermediates during transposition. Furthermore, horizontal transfer seems to predominate among families for which copy number is controlled predominantly by self-regulatory mechanisms that limit transposition. We contend that these differences play a major role in the observed predominance of horizontal transfer among Class II transposable elements.     

Two-component signal transduction systems in eukaryotic microorganisms

Conserved signal transduction pathways that use phosphorelay from histidine kinases through an intermediate transfer protein (H2) to response regulators have been found in a variety of eukaryotic microorganisms. Several of these pathways are linked to mitogen-activated protein kinase cascades. These networks control different physiological responses including osmoregulation, cAMP levels and cellular morphogenesis.     

Factors that affect the efficiency of cell transfection by immunoporation

Immunoporation is a recently discovered method that is able to transfect various human cell lines efficiently by targeting the cell surface antigens with antibody-coated beads. For this particular study, HL60, a cell line difficult to transfect by other methods, was used as a model to define the various parameters of the cell membrane that determine the efficiency of this method. The level of antigen expression on the cell surface was the first parameter to be analyzed and experiments indicated that there is a close correlation between the level of expression of surface antigens and the efficiency of immunoporation. The mixing speed, the bead to cell ratio, and the mixing time were all found to affect the ability of the antigen-coated beads to pull holes in the cells and it was found that for HL60 cells the optimum mixing speed was 40 rpm and the bead to cell ratio was 20:1 using a mixing time of 6 h.     

Factors that affect transposition mediated by the Tn21 transposase

The frequencies of one-ended transposition mediated by the Tn21 transposase acting on plasmids containing 38-bp inverted repeat sequences (IRs) of both Tn21 and of Tn501/Tn1721 and Tn2501 were measured. The enzyme acted on all these IRs, but more efficiently on the homologous sequences. These differences were magnified when the enzyme acted on plasmids containing two copies of the IRs, inverted with respect to each other. The Tn21 enzyme did not recognize the IR of Tn3. The Tn501 transposase did not mediate measurable one-ended transposition of any of the plasmids used, including those containing an IR of Tn501.     

Factors that affect leaf extracellular ascorbic acid content and redox status

Leaf ascorbic acid content and redox status were compared in ozone-tolerant (Provider) and ozone-sensitive (S156) genotypes of snap bean ( Phaseolus vulgaris L.). Plants were grown in pots for 24 days under charcoal-filtered air (CF) conditions in open-top field chambers and then maintained as CF controls (29 nmol mol⁻¹ ozone) or exposed to elevated ozone (71 nmol mol⁻¹ ozone). Following a 10-day treatment, mature leaves of the same age were harvested early in the morning (06:00–08:00 h) or in the afternoon (13:00–15:00 h) for analysis of ascorbic acid (AA) and dehydroascorbic acid (DHA). Vacuum infiltration methods were used to separate leaf AA into apoplast and symplast fractions. The total ascorbate content [AA + DHA] of leaf tissue averaged 28% higher in Provider relative to S156, and Provider exhibited a greater capacity to maintain [AA + DHA] content under ozone stress. Apoplast [AA + DHA] content was 2-fold higher in tolerant Provider (360 nmol g⁻¹ FW maximum) relative to sensitive S156 (160 nmol g⁻¹ FW maximum) regardless of sampling period or treatment, supporting the hypothesis that extracellular AA is a factor in ozone tolerance. Apoplast [AA + DHA] levels were significantly higher in the afternoon than early morning for both genotypes, evidence for short-term regulation of extracellular ascorbate content. Total leaf ascorbate was primarily reduced with AA/[AA + DHA] ratios of 0.81–0.90. In contrast, apoplast AA/[AA + DHA] ratios were 0.01–0.60 and depended on genotype and ozone treatment. Provider exhibited a greater capacity to maintain extracellular AA/[AA + DHA] ratios under ozone stress, suggesting that ozone tolerance is associated with apoplast ascorbate redox status.     

Factors that affect the type of cell death induced by chemicals

Surveying about 1000 compounds, we found that several low molecular weight alpha, beta-unsaturated ketones induced non-apoptotic cell death characterized by the formation of autophagosomes, occasionally accompanied by mitochondrial shrinkage. The cytotoxic activity of these compounds was significantly reduced by the addition of N-acetyl-L-cysteine, suggesting their interaction with SH groups of intracellular targeted molecules (the so-called "non-sterically hindered Michael acceptor"). This suggests that the nature of the chemical structure as well as the type of target cells is another factor that determines the type of cell death induced by chemicals.     

真菌毒素形成的影响因素

真菌毒素是真菌产生的次级代谢产物,可污染粮食、水果、食品、饲料、中草药等多种农产品。严重威胁食品安全、危害人畜健康,真菌毒素的形成除了受到产毒菌自身遗传因素的调控外,还受到宿主、环境因素的调控。此外,上述的多种因素的交互作用为真菌毒素的产生和调节增加了另一个层次上的多样性和复杂性。为了探究调控真菌毒素形成的因素,本文综述了真菌毒素合成及调控基因、温度、水分活度、光照、渗透压、基质、酸碱度、植物损伤、宿主抗性等因素对真菌毒素形成的影响,同时探讨了真菌毒素的防控,以期为探究真菌毒素形成的调控机制奠定基础,为真菌毒素防控策略的开发提供理论依据。     

Factors that affect hatching asynchrony in the chinstrap penguin (Pygoscelis antarctica)

We examined if laying intervals and hatching asynchronies are related in a chinstrap penguin (Pygoscelis antarctica) population in the South Orkneys. The lack of association between the two variables, as well as data on brood patch development, indicated that incubation did not begin immediately after the first egg was laid. This suggests that longer laying intervals may be compensated by longer delays in the onset of full incubation. Hatching asynchrony increased with within-clutch egg size asymmetry, decreased with breeding date, and was related to the laying order of the eggs according to size. However, only egg-size asymmetry remained significant when controlling for the other variables. We conclude that more asymmetric clutches were more asynchronous, although a large part of the variation in hatching asynchrony remains unexplained.     

Mutations on the external surfaces of adeno-associated virus type 2 capsids that affect transduction and neutralization

Mutations were made at 64 positions on the external surface of the adeno-associated virus type 2 (AAV-2) capsid in regions expected to bind antibodies. The 127 mutations included 57 single alanine substitutions, 41 single nonalanine substitutions, 27 multiple mutations, and 2 insertions. Mutants were assayed for capsid synthesis, heparin binding, in vitro transduction, and binding and neutralization by murine monoclonal and human polyclonal antibodies. All mutants made capsid proteins within a level about 20-fold of that made by the wild type. All but seven mutants bound heparin as well as the wild type. Forty-two mutants transduced human cells at least as well as the wild type, and 10 mutants increased transducing activity up to ninefold more than the wild type. Eighteen adjacent alanine substitutions diminished transduction from 10- to 100,000-fold but had no effect on heparin binding and define an area (dead zone) required for transduction that is distinct from the previously characterized heparin receptor binding site. Mutations that reduced binding and neutralization by a murine monoclonal antibody (A20) were localized, while mutations that reduced neutralization by individual human sera or by pooled human, intravenous immunoglobulin G (IVIG) were dispersed over a larger area. Mutations that reduced binding by A20 also reduced neutralization. However, a mutation that reduced the binding of IVIG by 90% did not reduce neutralization, and mutations that reduced neutralization by IVIG did not reduce its binding. Combinations of mutations did not significantly increase transduction or resistance to neutralization by IVIG. These mutations define areas on the surface of the AAV-2 capsid that are important determinants of transduction and antibody neutralization.     

Factors that affect the binding and uptake of gaba by brain tissue

Abstract— As previously reported, when brain tissue was homogenized in isotonic solution and the suspension was centrifuged, less GABA was found in the sediment if the solution contained only sucrose than if it contained some NaCl. NaBr and Nal were as effective as the chloride. Less effective were Na₂SOi, Na-phosphate, and the chlorides of K, Li, choline, NHt, Ca or Mg. Ouabain and protoveratrine inhibited the extra binding promoted by NaCl in brain suspensions and inhibited the uptake of GABA by respiring slices of cerebral cortex; tetrodotoxin alone had no effect in either case but reversed the effect of protoveratrine. Considerable inhibition of the uptake of GABA by brain slices was observed with glutamic acid, imipramine, chlorpromazine, procaine, xylocaine or picrotoxin but not with acetylcholine, prostigmine, norepinephine, dopamine, chloral hydrate, chloretone, pentylentetrazol or methionine sulphoximine.     

Factors in seminal plasma of bulls that affect the viability and motility of spermatozoa

Bound sialic acids on rat spermatozoa were assayed by oxidation with 1 mM-NaIO4 at 0 degree C, liberating C-9 as formaldehyde which was further quantitated using 3-methyl-2-benzothiazolinone. The mean +/- s.d. (n = 20) content of bound sialic acids of spermatozoa from the caput and cauda epididymidis was 50.9 +/- 8.0 and 25.2 +/- 3.8 nmol/10(8) spermatozoa respectively. About 85% of the former and 75% of the latter could be extracted by 1% Triton X-100 and 2 mM-dithiothreitol. About 70% of the former and 20% of the latter were released by neuraminidase from Vibrio cholerae. About 40% of the former and 30% of the latter were sensitive to trypsin. During sperm maturation, the decrease in the total bound sialic acids was due to the decrease in the neuraminidase-sensitive but not the neuraminidase-resistant sialic acids.     

Factors that affect results of the 13C urea breath test in Japanese patients

Background. The ¹³C urea breath test (UBT) is considered to be the most accurate way of diagnosing Helicobacter pylori infection. Our objective was to investigate the accuracy of the UBT in Japanese patients and the association of UBT values with histological findings.
Materials and Methods. A total of 169 consecutive patients were studied by endoscopy with histology, by serology with IgG antibody and test serum pepsinogen (PG), and by UBT. The association between UBT values and histological findings and the PG I / II ratio were analyzed in H. pylori –positive patients.
Results. Of 169 Japanese patients, 135 were H. pylori –positive on both histology and serology analysis, 27 were H. pylori –negative on both histology and serology analysis, and 7 patients showed differing results. Using a cutoff value of 2.5‰, test sensitivity was 100%, while specificity was 96%. Among the 135 H. pylori –positive patients, a significant relation was observed between UBT value and H. pylori colonization density of the corpus and antrum, neutrophil activity of the antrum, atrophy, and intestinal metaplasia of the corpus in the H. pylori –positive patients. Also, UBT values correlated with the PG I /II ratio. In multivariate analysis, the PG I /II ratio was the most important factor related to UBT values (odds ration [OR], 4.99; 95% confidence interval, 1.60–15.55).
Conclusions. The UBT is an accurate method for detecting H. pylori infection in the Japanese population, which shows a high prevalence of atrophic gastritis. Values are affected by H. pylori infection and by the severity of atrophic gastritis.     

Factors that affect mass transport from drug eluting stents into the artery wall

Coronary artery disease can be treated by implanting a stent into the blocked region of an artery, thus enabling blood perfusion to distal vessels. Minimally invasive procedures of this nature often result in damage to the arterial tissue culminating in the re-blocking of the vessel. In an effort to alleviate this phenomenon, known as restenosis, drug eluting stents were developed. They are similar in composition to a bare metal stent but encompass a coating with therapeutic agents designed to reduce the overly aggressive healing response that contributes to restenosis. There are many variables that can influence the effectiveness of these therapeutic drugs being transported from the stent coating to and within the artery wall, many of which have been analysed and documented by researchers. However, the physical deformation of the artery substructure due to stent expansion, and its influence on a drugs ability to diffuse evenly within the artery wall have been lacking in published work to date. The paper highlights previous approaches adopted by researchers and proposes the addition of porous artery wall deformation to increase model accuracy.     

Factors that affect juvenile emergence in Gammarus palustris (Bousfield, 1969)

In the laboratory, hatched juveniles of the amphipod Gammarus palustris (Bousfield, 1969) emerged from the female's brood pouch at increased rates when the mother was pipetted, fed on mussel meat, or was immersed after a period of exposure to the air. Because juveniles emerged unaided from females feeding on mussel meat, its presence appeared to stimulate the juveniles to emerge.G. palustris is typically found at the high tide mark in the intertidal zone during the reproductive season. Females experience factors similar to those tested in the laboratory only when covered by water; when the tide is out they lie quiescent under rocks and debris. It is hypothesized that in the field juveniles emerge at the greatest rate at the beginning of an incoming tide.     

Factors that affect postnatal bone growth retardation in the twitcher murine model of Krabbe disease

Krabbe disease is an inherited lysosomal disorder in which galactosylsphingosine (psychosine) accumulates mainly in the central nervous system. To gain insight into the possible mechanism(s) that may be participating in the inhibition of the postnatal somatic growth described in the animal model of this disease (twitcher mouse, twi), we studied their femora. This study reports that twi femora are smaller than of those of wild type (wt), and present with abnormality of marrow cellularity, bone deposition (osteoblastic function), and osteoclastic activity. Furthermore, lipidomic analysis indicates altered sphingolipid homeostasis, but without significant changes in the levels of sphingolipid-derived intermediates of cell death (ceramide) or the levels of the osteoclast–osteoblast coupling factor (sphingosine-1-phosphate). However, there was significant accumulation of psychosine in the femora of adult twi animals as compared to wt, without induction of tumor necrosis factor-alpha or interleukin-6. Analysis of insulin-like growth factor-1 (IGF-1) plasma levels, a liver secreted hormone known to play a role in bone growth, indicated a drastic reduction in twi animals when compared to wt. To identify the cause of the decrease, we examined the IGF-1 mRNA expression and protein levels in the liver. The results indicated a significant reduction of IGF-1 mRNA as well as protein levels in the liver from twi as compared to wt littermates. Our data suggest that a combination of endogenous (psychosine) and endocrine (IGF-1) factors play a role in the inhibition of postnatal bone growth in twi mice; and further suggest that derangements of liver function may be contributing, at least in part, to this alteration.