Measurement of proton relaxation rates in proteins

Summary Five different types of experiment are described which make it possible to measure various relaxation rates of selected protons in crowded spectra of macromolecules such as proteins: longitudinal spin-lattice relaxation rates =1/T₁, transverse relaxation rates =1/T₂ measured under conditions of free precession, transverse relaxation rates ¹ _LOCK=1/T₁ measured under conditions of spin-locking, and transverse relaxation rates ^DQC=1/T₂ ^DQC and ^ZQC=1/T₂ ^ZQC of double- and zero-quantum coherences. The surprisingly large discrepancy between the transverse rates ^t and ^t is discussed in detail. To separate overlapping proton signals, the experimental schemes involve one or several magnetization transfer steps, using a doubly selective homonuclear Hartmann-Hahn method. Numerous variants of the basic ideas can be conceived, depending on the extent of signal overlap and on the topology of the networks of scalar couplings. Applications are shown to H and H of Tyr²³, to H, H and H of Cys³⁰, and to H and H of Ala²⁴ in bovine pancreatic trypsin inhibitor (BPTI).     

Acetylcholine turnover rates in rat brain regions during cocaine self-administration

The involvement of cholinergic neurons in the brain processes underlying reinforcement has been recently demonstrated. This experiment assessed the potential role of cholinergic neurons in cocaine reinforcement by measuring the turnover rates of acetylcholine in brain regions of rats self-administering cocaine and in yoked cocaine and yoked vehicle-infused controls. The activity of cholinergic innervations of and/or interneurons in the olfactory tubercle, caudate putamen, diagonal band-pre-optic region, ventral pallidum, lateral and medial hypothalamus, hippocampus, ventral tegmental area and visual cortices reflected by the turnover rates of acetylcholine were significantly altered in rats self-administering cocaine compared to yoked cocaine infused controls. These changes implicate the involvement of cholinergic neurons with cell bodies in the diagonal band-pre-optic region, the medial septum and several brainstem nuclei and interneurons in the caudate-putamen and ventral pallidum in the processes underlying cocaine self-administration. The identified cholinergic neuronal systems may have a broader role in the brain processes for natural reinforcers (i.e. food, water, etc.) since drugs of abuse are believed to produce reinforcing effects through these systems.     

Differences among dogs in response of their spermatozoa to cryopreservation using various cooling and warming rates

Spermatozoa collected from the caudae epididymides of 16 dogs of various breeds were suspended in an isotonic salt solution (DIMI medium) containing 0.6 M glycerol, frozen in liquid nitrogen, and their "survival" was measured after thawing. In the first experimental series, duplicate samples of spermatozoa from each of 11 dogs were cooled at rates of 0.5, 3, 11, 58, or 209 degrees C/min, stored in liquid nitrogen, and the frozen samples warmed at approximately 830 or at 33 degrees C/min. Sperm "survival" was judged by microscopic assessments of motility and of membrane integrity, the latter as assayed with Fertilight, a double fluorescent stain. Motility of frozen spermatozoa that were thawed rapidly, averaged for 11 dogs, was low at low rates, increased to a maximum at 11 degrees C/min, and then decreased significantly at higher rates (P<0.01). This inverted V-shaped curve was also observed with slow thawing, although the apparent optimum cooling rate ranged from 3 to 11 degrees C/min. The integrity of sperm plasma membranes showed a similar dependence on cooling rate, although the percentages of spermatozoa with intact plasma membranes were higher than the percentages of motile spermatozoa. Motility of spermatozoa, as a function of cooling rate, varied considerably from male to male (P<0.01), whereas membrane integrity was much more consistent among the 11 dogs. In the second experimental series with spermatozoa from 5 dogs, motility of spermatozoa frozen at 0.5 degrees C/min and warmed at 3.6, 33, 140, or 830 degrees C/min also exhibited an inverted V-shaped survival curve, in this case as a function of warming rate. In summary, high survival of frozen-thawed canine epididymal spermatozoa depended on both cooling and warming rates, but spermatozoa from each dog exhibited their own sensitivity to cooling and warming rates.     

Inferring speciation rates from phylogenies

Abstract It is possible to estimate the rate of diversification of clades from phylogenies with a temporal dimension. First, I present several methods for constructing confidence intervals for the speciation rate under the simple assumption of a pure birth process. I discuss the relationships among these methods in the hope of clarifying some fundamental theory in this area. Their performances are compared in a simulation study and one is recommended for use as a result. A variety of other questions that may, in fact, be the questions of primary interest (e.g., Has the rate of cladogenesis been declining?) are then recast as biological variants of the purely statistical question—Is the birth process model appropriate for my data? Seen in this way, a preexisting arsenal of statistical techniques is opened up for use in this area: in particular, techniques developed for the analysis of Poisson processes and the analysis of survival data. These two approaches start from different representations of the data—the branch lengths in the tree—and I explicitly relate the two. Aiming for a synoptic account of useful theory in this area, I briefly discuss some important results from the analysis of two distinct birth‐death processes: the one introduced into this area by Hey (1992) is refitted with some powerful statistical tools.     

Diel changes in copepod respiration rates

Measurements of respiration in adult copepods at optimum concentrations in a respirometer were made at different hours of day; the amperometric method was used to measure dissolved oxygen. The migratory species from the tropical Indian Ocean and from the Black Sea displayed distinct daily variations in respiration rate and considerable difference between averages recorded in day and night hours. Such vertical migrants as Pleuromamma xiphias (Giesbr.) and Calanus euxinus Hulsemann were found to increase respiration rate late in the evening and early in the morning. No statistically reliable daily differences in the estimates of respiration were observed in copepod species like Acatria clausi (Giesbr.) and Temora discaudata (Giesbr.) which do not make long-distance migrations. In these experimental conditions the respiration rate appeared to represent changes in locomotory activity resulting from the sustained natural migratory rhythm and movements in food search. Using data available from the literature, the feeding rhythm and intensity were compared with respiration rate. This suggested that trophic status of the water may indirectly, through locomotory activity, affect the respiration rate. Increased respiration rate was suggested in the Black Sea copepod species in comparison with data obtained in earlier decades. The possibility of changes in respiration caused by changed food conditions of the environment is discussed.     

Measurement of cooling and warming rates in vitrification‐based plant cryopreservation protocols

Cryopreservation protocols include the use of additives and pretreatments aimed to reduce the probability of ice nucleation at all temperatures, mainly through micro‐viscosity increase. Still, there is a risk of ice formation in the temperature region comprised between the equilibrium freezing (T_f) and the glass transition (T_G) temperatures. Consequently, fast cooling and warming, especially in this region, is a must to avoid ice‐derived damage. Vitrification and droplet‐vitrification techniques, frequently used cryopreservation protocols based in fast cooling, were studied, alongside with the corresponding warming procedures. A very fast data acquisition system, able to read very low temperatures, down to that of liquid nitrogen, was employed. Cooling rates, measured between ?20°C and ?120°C, ranged from ca. 5°C s^?1 to 400°C s^?1, while warming rates spanned from ca. 2°C s^?1 to 280°C s^?1, for the different protocols and conditions studied. A wider measuring window (0°C to ?150°C) produced lower rates for all cases. The cooling and warming rates were also related to the survival observed after the different procedures. Those protocols with the faster rates yielded the highest survival percentages. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1177–1184, 2014     

Molecular evolutionary rates of oncogenes

Summary Using nine sets of viral and cellular oncogenes, the rates of nucleotide substitutions were computed by using Gojobori and Yokoyama's (1985) method. The results obtained confirmed our previous conclusion that the rates of nucleotide substitution for the viral oncogenes are about a million times higher than those for their cellular counterparts. For cellular oncogenes and most viral oncogenes, however, the rate of synonymous substitution is higher than that of nonsynonymous substitution. Moreover, the pattern of nucleotide substitutions for viral oncogenes is more similar to that for functional genes (such as cellular oncongenes) than for pseudogenes. This implies that nucleotide substitutions in viral oncogenes may be functionally constrained. Thus, our observation supports that nucleotide substitutions for the oncogenes in those DNA and RNA genomes are consistent with Kimura's neutral theory of molecular evolution (Kimura 1968, 1983).     

Exceptional growth rates of captive loggerhead sea turtles,Caretta caretta

Twelve loggerhead sea turtle hatchlings (Caretta caretta) were removed from a nest site (A) at the Back Bay National Wildlife Refuge (U.S. Fish and Wildlife Service), Virginia Beach, VA. Hatchlings were distributed among study participants, and raised in captivity for a period of two years. Growth of the loggerheads was recorded weekly by straight-line caliper measurements of carapace lengths as well as measurements of total weights. Growth rates from the present study were much greater than those measured in previous studies. Mean weights for Nest A turtles at 1.5 years ranged from 10.3 to 17.6 kg, with one exceptional individual reaching 20.0 kg. The data from this study provide new insights into the early growth potential of loggerhead sea turtles. How this accelerated development may affect sexual maturity and post-release viability remain to be determined. © 1993 Wiley-Liss, Inc.     

Estimation of evacuation rates in the field

Two methods are presented to calculate evacuation rates based on observed diel changes in occurrence and mean mass of prey in predator stomachs. The methods do not require predators to exhibit prolonged non‐feeding periods, but the ingestion of each particular prey type must be restricted to certain diel periods. Data from >7500 whiting Merlangius merlangus collected at five locations in the North Sea were used to demonstrate the methods. The evacuation rates estimated from field data were similar to laboratory results, though a tendency for estimates to exceed literature values slightly was noted. Bias was introduced if a large proportion of the prey was evacuated completely in the interval between subsequent samples and if significant amounts of other food were present in the stomach together with the prey in question. The methods can be used to supplement laboratory estimates of evacuation rates or provide first estimates for species that are not easily maintained in the laboratory.     

Identifying site-specific substitution rates

A maximum likelihood framework for estimating site-specific substitution rates is presented that does not require any prior assumptions about the rate distribution. We show that, when the branching pattern of the underlying tree is known, the analysis of pairs of positions is sufficient to estimate site-specific rates. In the abscense of a known topology, we introduce an iterative procedure to estimate simultaneously the branching pattern, the branch lengths, and site-specific substitution rates. Simulations show that the evolutionary rate of fast-evolving sites can be reliably inferred and that the accuracy of rate estimates depends mainly on the number of sequences in the data set. Thus, large sets of aligned sequences are necessary for reliable site-specific rate estimates. The method is applied to the complete mitochondrial DNA sequence of 53 humans, providing a complete picture of the site-specific substitution rates in human mitochondrial DNA.     

Changes of lipase-catalyzed lipolytic rates in a batch reactor

A dramatic change of the reaction rate was observed for the lipase-catalyzed hyrolysis of tributyrin in a batch reactor. Immediately after the addition of the enzyme, the lipolysis rate increased continuously until a maximal reaction rate was reached. The duration of the induction was mainly controlled by the bulk enzyme concentration and the reactor stirring speed. The reaction rate dropped sharply after reaching its maximal value. The lipolysis decayed at a rate of about 0.012 min(-1), and was not affected by changes of the stirring speed. This decay was attributed to the fast deactivation of the surface-adsorbed lipase, and possibly to the extremely slow desorption of the inactivated species. For reaction time longer than 120 minutes, the lipolysis decreased at a much slower rate. Several mechanisms for the decay of the lipolysis rate were discussed.     

Scaling relationship between tree respiration rates and biomass

The WBE theory proposed by West, Brown and Enquist predicts that larger plant respiration rate, R, scales to the three-quarters power of body size, M. However, studies on the R versus M relationship for larger plants (i.e. trees larger than saplings) have not been reported. Published respiration rates of field-grown trees (saplings and larger trees) were examined to test this relationship. Our results showed that for larger trees, aboveground respiration rates R_A scaled as the 0.82-power of aboveground biomass M_A, and that total respiration rates R_T scaled as the 0.85-power of total biomass M_T, both of which significantly deviated from the three-quarters scaling law predicted by the WBE theory, and which agreed with 0.81–0.84-power scaling of biomass to respiration across the full range of measured tree sizes for an independent dataset reported by Reich et al. (Reich et al. 2006 Nature 439, 457–461). By contrast, R scaled nearly isometrically with M in saplings. We contend that the scaling exponent of plant metabolism is close to unity for saplings and decreases (but is significantly larger than three-quarters) as trees grow, implying that there is no universal metabolic scaling in plants.     

Inverse density dependence of parity rates in the onchocerciasis vector Simulium damnosum s.l.

A correlation between parity rates and an index of adult numbers of Simulium damnosum s.l. (Diptera: Simuliidae) indicates an association, but does not prove causality or show the direction of any causal relationship. The question of whether adult numbers affect parity rates or vice versa is reminiscent of the age‐old query of which of the chicken and the egg came first. A method for resolving such issues based on analyses of pairs of time series was proposed by Granger in 1969. When Granger's method was applied to monthly numbers of adult female S. damnosum s.l. caught attempting to bite humans at Asubende, Ghana, and their parity rates, a significant relationship (P = 0.005) emerged, clearly showing that parity rates were dependent on adult numbers. Implications of this inverse density dependence and the results of analyses of other similar time series are presented and discussed.     

Hydrolysis rates of 1-glucosyl-2-benzoylhydrazines in aqueous solution

A series of substituted 1-glucosyl-2-benzoylhydrazines were synthesized and their pseudo-first-order rate constants for hydrolysis were determined at pH 4, 5, 6 at 50 degrees C. All the compounds hydrolyzed quickly (t(1/2)<3h) at pH 4.0, but were increasingly stable as the pH approached neutrality.     

Distribution of cancer mortality rates by province in South Africa

IntroductionCancer mortality rates are expected to increase in developing countries. Cancer mortality rates by province remain largely unreported in South Africa. This study described the 2014 age standardised cancer mortality rates by province in South Africa, to provide insight for strategic interventions and advocacy.Methods2014 deaths data were retrieved from Statistics South Africa. Deaths from cancer were extracted using 10th International Classification of Diseases (ICD) codes for cancer (C00-C97). Adjusted 2013 mid-year population estimates were used as a standard population. All rates were calculated per 100 000 individuals.ResultsNearly 38 000 (8%) of the total deaths in South Africa in 2014 were attributed to cancer. Western Cape Province had the highest age standardised cancer mortality rate in South Africa (118, 95% CI: 115–121 deaths per 100 000 individuals), followed by the Northern Cape (113, 95% CI: 107–119 per 100 000 individuals), with the lowest rate in Limpopo Province (47, 95% CI: 45–49 per 100 000). The age standardised cancer mortality rate for men (71, 95% CI: 70–72 per 100 000 individuals) was similar to women (69, 95% CI: 68–70 per 100 000). Lung cancer was a major driver of cancer death in men (13, 95% CI: 12.6–13.4 per 100 000). In women, cervical cancer was the leading cause of cancer death (13, 95% CI: 12.6–13.4 per 100 000 individuals).ConclusionThere is a need to further investigate the factors related to the differences in cancer mortality by province in South Africa. Raising awareness of risk factors and screening for cancer in the population along with improved access and quality of health care are also important.     

Nonstochastic variation of species-level diversification rates within angiosperms

Variations in the origination and extinction rates of species over geological time often are linked with a range of factors, including the evolution of key innovations, changes in ecosystem structure, and environmental factors such as shifts in climate and physical geography. Before hypothesizing causality of a single factor, it is critical to demonstrate that the observed variation in diversification is significantly greater than one would expect due to natural stochasticity in the evolutionary branching process. Here, we use a likelihood-ratio test to compare taxonomic rate heterogeneity to a neutral birth-death model, using data on well-supported sister pairs of taxa and their species richness. We test the likelihood that the distribution of extant species among angiosperm genera and families could be the result of constant diversification rates. Results strongly support the conclusion that there is significantly more heterogeneity in diversity at the species level within angiosperms than would be expected due to stochastic processes. This result is consistent in datasets of genus pairs and family pairs and is not affected significantly by degrading pairs to simulate inaccuracy in the assumption of simultaneous origin of sister taxa. When we parse taxon pairs among higher groups of angiosperms, results indicate that a constant rates model is not rejected by rosid and basal eudicot pairs but is rejected by asterid and eumagnoliid pairs. These results provide strong support for the hypothesis that species-level rates of origination and/or extinction have varied nonrandomly within angiosperms and that the magnitude of heterogeneity varies among major groups within angiosperms.     

Estimation of outcrossing rates in Duglas-fir using isozyme markers

Summary Seeds produced under open-pollination were collected from eight natural stands and a plus-tree seed orchard of Douglas-fir. These seeds were germinated and both diploid embryos and haploid gametophytes were analyzed by starch-gel electrophoresis. Eleven variable loci were resolved for both kinds of tissue and used as genetic markers for estimating outcrossing rates. Estimates made with single-locus and multilocus methods both indicated that the proportion of viable embryos resulting from outcrossing is about 0.90 for the natural stands, and for the seed orchard. Comparison of single-locus and multilocus estimates of outcrossing rates indicated that little or no inbreeding other than selfing occurred. Estimated outcrossing rates were higher for seeds from the upper portion of the crown than for seeds from the lower crown. It was also found that some trees selfed at a much higher rate than other trees.     

Flow rate and vertical position influence ingestion rates of colonial zebra mussels (Dreissena polymorpha)

1. Zebra mussels aggregate to form dense colonies where, depending on the flow rate, individuals in different vertical locations within the colony may experience restricted food availability. 2. Using ³²P‐labelled Chlamydomonas angulosa, we found ingestion rates of individual mussels located at the surface to exceed those in the bottom of a 6 cm thick colony by up to 75%. 3. Higher velocities (10 and 20 cm s^?1) increased algal delivery to the colony's middle layer (2–4 cm depth), subsequently increasing ingestion rates to equal those in the surface layer, while increasing ingestion only for the smallest mussels in the bottom (4–6 cm). 4. At all vertical locations within the colonies, smaller mussels showed higher ingestion rates per unit mass than larger mussels, particularly at higher flow rates.     

Species-specific N and P release rates in Daphnia

Bioavailable N and P release rates by juveniles and adults of three Daphnia taxa (D. hyalina, D. galeata and its interspecific hybrids D. hyalina × galeata) were measured to assess the effect of weight and interspecific differences on these rates in Daphnia. Immobilized Scenedesmus obliquus cells were used to estimate the release rates. The specific release rate of N varied between 5.19–5.71 g N mg C^-1 h^-1 for juveniles and 3.00–3.42 g N mg C^-1 h^-1 for adults. P excretion rate ranged between 1.93–2.37 g P mg C^-1 h^-1 for juveniles and 1.00–1.24 g P mg C^-1 h^-1 for adults. Our results show that the taxonomic affiliation of Daphnia individuals did not affect their N and P release rates.