A peptidoform based proteomic strategy for studying functions of post-translational modifications

Protein post-translational modifications (PTMs) generate an enormous, but as yet undetermined, expansion of the produced proteoforms. In this Viewpoint, we firstly reviewed the concepts of proteoform and peptidoform. We show that many of the current PTM biological investigation and annotation studies largely follow a PTM site-specific rather than proteoform-specific approach. We further illustrate a potentially useful matching strategy in which a particular “modified peptidoform” is matched to the corresponding “unmodified peptidoform” as a reference for the quantitative analysis between samples and conditions. We suggest this strategy has the potential to provide more directly relevant information to learn the PTM site-specific biological functions. Accordingly, we advocate for the wider use of the nomenclature “peptidoform” in future bottom-up proteomic studies.     

ATTRIBUTES OF CHLOROCOCCUM SPECIES: A NUMERICAL ANALYSIS2

From previously published data, 73 characteristics of 17 species of Chlorococcum were compiled. Comparisons of character states of each character were made, and simple matching coefficients were calculated for each species by following the procedure of Sokal & Michener. From a data matrix of the matching coefficients, a phenogram was constructed according to the unweighted pair group method of Sokal & Sneath. Arithmetic averages were used in transferring data from one matrix to another. The frequency of each character state was calculated, and the character states of the highest frequency (the modes) were used to describe a “typical” Chlorococcum species. Comparisons were made between the “typical” Chlorococcum species and each of the 17 species studied. Simple matching coefficients were also calculated from these comparisons. All of the species had a relatively high affinity for the data of the calculated “typical”. Suggestions are made about the use of a “typical” taxonomic unit, and questions are raised about the taxonomic relationship among species of the genus Tetracystis and the genus Chlorococcum.     

THE FLAGELLAR APPARATUS OF CHRYSOLEPIDOMONAS DENDROLEPIDOTA (CHRYSOPHYCEAE), A SINGLE-CELLED MONAD COVED WITH ORGANIC SCALES1

The flagellar apparatus of Chrysolepidomonas dedrolepidota Peters et Andersen is similar to that of other members of the Ochromonadales, Chrysophyceae. there are four microtubular roots (R_1-4) and a system II fiber (= rhizoplast). the R₁ root consists of three microtubules that nucleate many cytoplasmic microtubules. One compressed band of 10 or more cytoplasmic microtubules is directed black along the R1 root in an anti-parallel direction. The R₂ root consists of one to two microtubules, and it extends toward the distal end of the R₁ root. The R₃ root consists of six (?seven) microtubules near its proximal end. The “a” and “f” microtubules of the R₃ root are under the short flagellum, and the “f” microtubule loops back and under the basal body, extending down to the nucleus. The R₄ root consists of one to two microtubules extending along the left side of the shot flagellum and curving under the short flagellum where it terminates near the “a” microtubule of R₃ Both flagella have a transitional plate and a transitional helix with five gyres. There is a thin, second plate in the basal body at the level of the distal end of the “c” tubules of the basal body triplets. The tripartite flagellar hairs have long lateral filaments but lack short lateral filaments. We compare the flagellar apparatus with that of other members of the Ochromonadales and members of the Hydrurales and Hibberdiales.     

Improved fruiting of the straw mushroom (Volvariella volvacea) on cotton waste supplemented with sodium acetate

Compared with controls, treatment of the cultivation substrate for Volvariella volvacea with 0.02% NaAc at the “spraying water” stage increased the number of fruiting body primordia by 280, the mushroom yield by 16.25%, the number of fruiting bodies by 35.57%, and the biological efficiency by 16.28%. The average single mushroom weight increased by 19.33%, but there was no significant difference between treatments and controls. A correlation analysis revealed a significant (p < 0.05) positive correlation between the total yield and the number of fruiting bodies. Comparisons of the cost and profit values for the sodium acetate-treated and untreated groups revealed that the former generated a higher income for the grower. Our data indicate that sodium acetate treatment is a promising new method for increasing V. volvacea yields. A possible mechanism whereby sodium acetate increased the mushroom yield is discussed.

     

A mathematical model for malaria involving differential susceptibility,exposedness and infectivity of human host

The main purpose of this article is to formulate a deterministic mathematical model for the transmission of malaria that considers two host types in the human population. The first type is called “non-immune” comprising all humans who have never acquired immunity against malaria and the second type is called “semi-immune”. Non-immune are divided into susceptible, exposed and infectious and semi-immune are divided into susceptible, exposed, infectious and immune. We obtain an explicit formula for the reproductive number, R ₀ which is a function of the weight of the transmission semi-immune-mosquito-semi-immune, R _0a , and the weight of the transmission non-immune-mosquito-non-immune, R _0e . Then, we study the existence of endemic equilibria by using bifurcation analysis. We give a simple criterion when R ₀ crosses one for forward and backward bifurcation. We explore the possibility of a control for malaria through a specific sub-group such as non-immune or semi-immune or mosquitoes.     

Insulin Resistance,Hyperleptinemia, and Obstructive Sleep Apnea in Launois‐Bensaude Syndrome

Objective: Launois‐Bensaude Syndrome (LBS) is a very rare cause of obesity, characterized by a symmetrical accumulation of a very large number of lipomata in different regions of the body, excluding the face, the forearms, and the shanks. Obesity is known to be closely associated with insulin resistance, hyperleptinemia, and obstructive sleep apnea (OSA). We were interested in studying whether these conditions are also present in patients with obesity due to LBS with a similar frequency as in patients with “simple” truncal obesity. Research Methods and Procedures: We performed polysomnography and hyperinsulinemic euglycemic clamp studies and measured serum leptin in three patients with LBS and in six patients with “simple” truncal obesity, matched for sex and body mass index (LBS group, 36.39 kg/m²; controls, 35.82 kg/m²). Results: Polysomnography revealed severe OSA in one LBS patient with marked “horsecollar lipomata.” In the other LBS patients, no OSA could be demonstrated. The leptin levels of the two groups were comparable (LBS group, 36.39 μg/liter; controls, 37.18 μg/liter) and the insulin responsiveness index was also comparable in the two groups (LBS group, 3.47 μmol/kg · minute; controls, 3.79 μmol/kg · minute). Discussion: Patients with LBS demonstrated similar metabolic features in terms of insulin sensitivity and hyperleptinemia as patients with “simple” truncal obesity. LBS is not strictly associated with OSA.     

Extended Rank Analysis of Covariance as a More Efficient Matched Analysis Considering Trend Information

Classical matched analysis, regarded as analysis of covariance (ANOCOVA) in a broad sense, makes no attempt in modeling and may therefore be inefficient. In this paper, we discuss the relative efficiencies of the ERMP (extended rank and matched‐pair) test (Chen and Quade , 2000) to standard matched methods, and extend it to the case of multivariate covariables X . Taking advantage of trend information between the response Y and the covariables X by ranking after matching, ERMP test achieves better efficiency than a proposed class of weighted matched statistics. When Y is dichotomous, the optimal weighted matched statistic is equivalent to the Mantel‐Haenszel statistic. Example and simulation results also suggest the conclusion.     

Estimation of Relative Risk Under M to R Matching

Estimation of the relative risk from a rare disease is carried out using M:R matching. Both conditional and unconditional likelihood methods are used, leading in each case to the same estimate; a non-iterative estimate is always available under M:R matching, M ≦2. The method also enables the testing of homogeneity even when information on the matching variate is unavailable and this is an advantage over logistic regression methods.     

Plasticity for colour adaptation in vertebrates explained by the evolution of the genes pomc,pmch and pmchl

Different camouflages work best with some background matching colour. Our understanding of the evolution of skin colour is based mainly on the genetics of pigmentation (“background matching”), with little known about the evolution of the neuroendocrine systems that facilitate “background adaptation” through colour phenotypic plasticity. To address the latter, we studied the evolution in vertebrates of three genes, pomc, pmch and pmchl, that code for α‐MSH and two melanin‐concentrating hormones (MCH and MCHL). These hormones induce either dispersion/aggregation or the synthesis of pigments. We find that α‐MSH is highly conserved during evolution, as is its role in dispersing/synthesizing pigments. Also conserved is the three‐exon pmch gene that encodes MCH, which participates in feeding behaviours. In contrast, pmchl (known previously as pmch), is a teleost‐specific intron‐less gene. Our data indicate that in zebrafish, pmchl‐expressing neurons extend axons to the pituitary, supportive of an MCHL hormonal role, whereas zebrafish and Xenopus pmch+ neurons send axons dorsally in the brain. The evolution of these genes and acquisition of hormonal status for MCHL explain different mechanisms used by vertebrates to background‐adapt.     

Model-free analysis for large proteins at high magnetic field strengths

Protein backbone dynamics is often characterized using model-free analysis of three sets of ¹⁵N relaxation data: longitudinal relaxation rate (R ₁), transverse relaxation rate (R ₂), and ¹⁵N–{H} NOE values. Since the experimental data is limited, a simplified model-free spectral density function is often used that contains one Lorentzian describing overall rotational correlation but not one describing internal motion. The simplified spectral density function may be also used in estimating the overall rotational correlation time, by making the R ₂/R ₁ largely insensitive to internal motions, as well as used as one of the choices in the model selection protocol. However, such approximation may not be valid for analysis of relaxation data of large proteins recorded at high magnetic field strengths since the contribution to longitudinal relaxation from the Lorentzian describing the overall rotational diffusion of the molecule is comparably small relative to that describing internal motion. Here, we quantitatively estimate the errors introduced by the use of the simplified spectral density in model-free analysis for large proteins at high magnetic field strength.     

The protein–protein interactions required for assembly of the Tn3 resolution synapse

The site-specific recombinase Tn3 resolvase initiates DNA strand exchange when two res recombination sites and six resolvase dimers interact to form a synapse. The detailed architecture of this intricate recombination machine remains unclear. We have clarified which of the potential dimer–dimer interactions are required for synapsis and recombination, using a novel complementation strategy that exploits a previously uncharacterized resolvase from Bartonella bacilliformis (“Bart”). Tn3 and Bart resolvases recognize different DNA motifs, via diverged C-terminal domains (CTDs). They also differ substantially at N-terminal domain (NTD) surfaces involved in dimerization and synapse assembly. We designed NTD-CTD hybrid proteins, and hybrid res sites containing both Tn3 and Bart dimer binding sites. Using these components in in vivo assays, we demonstrate that productive synapsis requires a specific “R” interface involving resolvase NTDs at all three dimer-binding sites in res. Synapses containing mixtures of wild-type Tn3 and Bart resolvase NTD dimers are recombination-defective, but activity can be restored by replacing patches of Tn3 resolvase R interface residues with Bart residues, or vice versa. We conclude that the Tn3/Bart family synapse is assembled exclusively by R interactions between resolvase dimers, except for the one special dimer–dimer interaction required for catalysis.     

Randomization Analysis of Incomplete Data in Some Basic Designs

The first two randomization moments of W = Tt.S.S./(Tt.S.S. + Error S.S.) are derived in case of (a) a completely randomized design with one observation missing using (I) Yates method of fitting constants and (II) the available observations only and in case of (b) a randomized block design in which one treatment is tested twice by mistake in a block and another treatment is not tested at all in that block using (I) all the available observations and (II) the data after deleting the observation due to the treatment tested by mistake in place of another treatment in a block. It is concluded that in each of the two cases for a completely randomized design, the F-test is unbiased whereas in each of the two cases for a randomized block design the F-test is in general not unbiased. However, if one treatment is tested twice by mistake in randomly chosen plots of some block, the F-test is unbiased in both cases for a randomized block design. For a completely randomized design the F-test is found to be a good approximation to the corresponding randomized test if N ≧ 80 in case (I) whereas in case (II) this approximation is of the same accuracy as that of case (I) if N ≧ 90. For a randomized block design it is seen that in case (I), the F-test provides a good approximation to the corresponding randomization test if v≧r≧7 and in case (II) this approximation is of the same accuracy if r≧6 and r(v-1)≧45. The analysis of several uniformity trial data shows that for values of “N” in the neighbourhood of 50 the agreement of the first two moments of “W” under the randomization theory and normal theory are reasonably close in all the four cases considered.     

Perceived psychological stress and serum leptin concentrations in Japanese men

Objective: To examine epidemiologically whether subjects with higher stress perception levels have higher leptin concentrations. Research Methods and Procedures: In this cross‐sectional study, the study population comprised 1062 male workers at local government offices in central Japan. Self‐administered questionnaires were distributed in 1997. Awareness of stress was assessed by the question: “Do you have much stress in your life?” and participants were asked to select from four possible responses: “very much,” “much,” “ordinary,” or “little.” Blood samples were also collected after fasting 12 hours overnight to determine serum leptin concentrations. Results: The mean (standard deviation) age and BMI were 50.2 (6.4) years and 23.3 (2.6) kg/m², respectively. Crude leptin concentrations according to stress categories were 2.86, 3.26, 3.32, and 3.54 ng/mL, respectively, and leptin concentrations adjusted for age, BMI, physical activity, drinking and smoking habits, overtime work, shift work, sleep duration, and availability of confidants were 2.96, 3.24, 3.34, and 3.43 ng/mL for “little,” “ordinary,” “much,” and “very much,” respectively (p = 0.03 by one‐way analysis of covariance; p < 0.01 by test of linear trend). Significant associations were also observed among the level of perceived psychological stress and work‐related stressors, variables related to sleep, and other psychological variables. Discussion: This study showed that subjects who perceived psychological stress had high leptin levels, which provides epidemiological evidence that psychological stress may have the potential effect of increasing blood levels of the pleiotropic peptide, leptin.     

SHORT-TERM IMPACTS OF FORMULATIONS OF BACILLUS THURINGIENSIS VAR. ISRAELENSIS DE BARJAC AND THE ORGANOPHOSPHATE TEMEPHOS,USED IN BLACKFLY (DIPTERA: SIMULIIDAE) CONTROL,ON RHEOPHILIC BENTHIC MACROINVERTEBRATES IN THE MIDDLE ORANGE RIVER,SOUTH AFRICA

Summary

The impacts of larvicides used in the control of blackflies (Diptera: Simuliidae) on macroinvertebrates in the stones-in-current biotope were assessed during 8 field trials in the middle Orange River, South Africa. Two Bacillus thuringiensis var. israelensis (B.t.i.) products (Vectobac^R 12AS and Teknar^R HP-D) and the organophosphate temephos (Abate^R 200EC) were applied at recommended and high dosages to simulate “operational” and “worst-possible” scenario's respectively. Mortality was evaluated either by direct counting of invertebrates on stones before and after application, or by ranking invertebrates on a 4-point relative abundance scale before and after application. In addition, the re-appearance of benthic invertebrate population densities after temephos application was examined.

At the recommended dosage (1.2 ppm/10 min), B.t.i. significantly reduced blackfly larval numbers (P<0.001) and those of the chironomid Rheotanytarsus fuscus Freeman (P<0.05). At high dosage (20 ppm/10 min), numbers of the filter-feeding mayfly Tricorythus discolor (Burmeister) (P<0.01) and the chironomid Cardiocladius sp. (P<0.05) were also significantly reduced. No Simulium predators were directly affected by B.t.i., but there were indications of food shortage amongst Hydropsychidae and Hirudinea.

Temephos caused significant reductions in the relative abundance of 5 taxa at 0.05 ppm, 3 to 6 taxa at 0.1 ppm, and 9 taxa at 1.0 ppm (P<0.05). “Non-target” organisms which were most affected included the chironomid R. fuscus, the mayflies Baetis glaucus Agnew and Choroterpes elegans Barnard, and the caddisflies Cheumatopsyche thomasseti Ulmer and Amphipsyche scottae Kimmins. The mayfly T. discolor was tolerant of temephos, even at high dosage (1.0 ppm/10 min). In winter, most taxa re-appeared within 19 days, and population densities were back to pre-treatment levels within 35 days.

It is concluded that good reduction of blackfly populations may be obtained with minimal direct impact on the “non-target” fauna, provided recommended dosages of temephos are not exceeded. Overdosing with temephos may result in high mortality of “non-target” organisms, including blackfly predators, and should be avoided.     

Phylogeny and evolutionary history of birch mice Sicista Griffith, 1827 (Sminthidae,Rodentia): Implications from a multigene study

Phylogeny of birch mice is estimated using sequences of ten nuclear genes and one mitochondrial gene. Based on the results of tree reconstructions and molecular dating, five major lineages are recognized: “tianschanica,” “concolor,” “caudata,” “betulina,” and “caucasica.” It is established that the three latter lineages constitute a clade and that the long‐tailed birch mouse Sicista caudata is the sister group of the “caucasica” lineage. The “tianschanica” lineage is placed as the sister branch to all other species, however, with insufficient support. The cytochrome b tree is generally concordant with the nuclear topology. The molecular clock results suggest that the radiation among the main lineages occurred in the Late Miocene–Early Pliocene (6.0–4.7 Mya). The correspondence between molecular dating and the fossil record is discussed. Based on nuclear data, a high level of divergence between cryptic species in the “tianschanica” lineage is confirmed. Mitochondrial and nuclear data suggest the existence of a potential cryptic species within Sicista strandi.     

Amyotrophic lateral sclerosis and occupational exposure to electromagnetic fields

In an hypothesis-generating case-control study of amyotrophic lateral sclerosis, lifetime occupational histories were obtained. The patients (n = 28) were clinic based. The occupational exposure of interest in this report is electromagnetic fields (EMFs). This is the first and so far the only exposure analyzed in this study. Occupational exposure up to 2 years prior to estimated disease symptom onset was used for construction of exposure indices for cases. Controls (n = 32) were blood and nonblood relatives of cases. Occupational exposure for controls was through the same age as exposure for the corresponding cases. Twenty (71%) cases and 28 (88%) controls had at least 20 years of work experience covering the exposure period. The occupational history and task data were used to classify blindly each occupation for each subject as having high, medium/high, medium, medium/low, or low EMF exposure, based primarily on data from an earlier and unrelated study designed to obtain occupational EMF exposure information on workers in “electrical” and “nonelectrical” jobs. By using the length of time each subject spent in each occupation through the exposure period, two indices of exposure were constructed: total occupational exposure (E₁) and average occupational exposure (E₂). For cases and controls with at least 20 years of work experience, the odds ratio (OR) for exposure at the 75th percentile of the E₁ case exposure data relative to minimum exposure was 7.5 (P < 0.02; 95% Cl, 1.4–38.1) and the corresponding OR for E₂ was 5.5 (P < 0.02; 95% CI, 1.3–22.5). For all cases and controls, the ORs were 2.5 (P < 0.1; 95% CI, 0.9–8.1) for E₁ and 2.3 (P = 0.12; 95% CI, 0.8–6.6) for E₂. This study should be considered an hypothesis-generating study. Larger studies, using incident cases and improved exposure assessment, should be undertaken. Bioelectromagnetics 18:28–35, 1997. © 1997 Wiley-Liss, Inc.     

On Some Problems in Measuring Change on Ordinal Data

Two designs frequently occurring in biomedicine and social sciences are considered—the “experts”/“objects”—design consisting in ranking M fixed “objects” by each of N “experts” before and after an intervention, and the rating-scale-design in which N judges are asked to assign one of K given lables, constituting the rating-scale, before and after an intervention. Nonparametric test procedures are proposed for evaluating the treatment effect.     

SYNTHETIC HYBRIDS OF NEW WORLD AND OLD WORLD AGROPYRONS II. AGROPYRON RIPARIUM X AGROPYRON REPENS

Five hybrids were obtained from 12 seeds formed in 26 emasculated florets of A. riparium pollinated by A. repens. The hybrid plants were morphologically intermediate between the parents for vegetative and spike characteristics, although they resembled A. repens more closely than A. riparium. The 28-chromosome A. riparium parent behaved cytologically as an allotetraploid and formed an average of 13.98 II and 0.04 I in 94 cells at metaphase I. An average of 20.27 II and 0.36 IV were observed at metaphase I in 55 cells of A. repens, which was designated as a segmental autoallohexaploid. The hybrids contained 35 chromosomes and averaged 6.75 I, 12.49 II, 1.05 III, 0.01 IV, and 0.01 V in 162 cells interpreted at metaphase I. Bivalent chromosome pairing in the hybrids was attributed to autosyndetic pairing of 2 A. repens genomes and allosyndetic pairing between 1 A. riparium genome and 1 A. repens genome. Multivalent chromosome associations were attributed to structural hybridity. A. repens and A. riparium apparently share a genome in common, and this genome is the one responsible for rhizomes in both species. A. riparium was given a genome formula of R₂R₂SS; whereas the A. repens genome formula was written as R₁R₁X₁X₁X₂X₂, and the hybrid genome formula was designated as R₁R₂X₁X₂S. The “S” genome of A. riparium was derived from A. spicatum, and the “R” genome is the genome shared by A. repens and A. riparium. The origin and distribution of the so-called “X” genomes of A. repens remain unknown. The hybrids produced from 3 to 10% stainable pollen; however, no seed was set on the hybrids during 2 years in the field.     

Enantiomer‐Specific In Vitro Biotransformation of Select Pharmaceuticals in Rainbow Trout (Oncorhynchus mykiss)

The occurrence of pharmaceuticals in the environment represents a challenge of emerging concern. Many pharmaceuticals are chiral compounds; however, few studies have examined the relative toxicity of pharmaceutical enantiomers to wildlife. Further, our understanding of stereospecific pharmacokinetics remains largely informed by research on humans and a few well‐studied laboratory test animals, and not by studies conducted with environmentally relevant species, including fish. The objective of this study was to investigate whether rainbow trout display stereospecific in vitro metabolism of three common chiral pharmaceuticals. Metabolism by trout liver S9 fractions was evaluated using a substrate depletion approach, which provides an estimate of intrinsic hepatic clearance (CL_{IN VITRO,INT}). No biotransformation was observed for rac‐, R‐, or S‐fluoxetine. Ibuprofen, including both enantiomers and the racemic mixture, appeared to undergo slow metabolism, but the resulting substrate depletion curves did not differ significantly from those of inactive controls. Contrary to relative clearance rates in humans, S(?)‐propranolol was more rapidly cleared than the R(+)‐ enantiomer. This work demonstrates that relative clearance rates and the effects of racemic mixtures in trout could not have been predicted based on human data. Additional research describing species differences and exploring tools for species extrapolation in biomedical and environmental studies is needed. Chirality 25:763–767, 2013, © 2013 Wiley Periodicals, Inc.