A simulation approach for power calculation in large cohort studies based on multistate models

Realistic power calculations for large cohort studies and nested case control studies are essential for successfully answering important and complex research questions in epidemiology and clinical medicine. For this, we provide a methodical framework for general realistic power calculations via simulations that we put into practice by means of an R‐based template. We consider staggered recruitment and individual hazard rates, competing risks, interaction effects, and the misclassification of covariates. The study cohort is assembled with respect to given age‐, gender‐, and community distributions. Nested case‐control analyses with a varying number of controls enable comparisons of power with a full cohort analysis. Time‐to‐event generation under competing risks, including delayed study‐entry times, is realized on the basis of a six‐state Markov model. Incidence rates, prevalence of risk factors and prefixed hazard ratios allow for the assignment of age‐dependent transition rates given in the form of Cox models. These provide the basis for a central simulation‐algorithm, which is used for the generation of sample paths of the underlying time‐inhomogeneous Markov processes. With the inclusion of frailty terms into the Cox models the Markov property is specifically biased. An “individual Markov process given frailty” creates some unobserved heterogeneity between individuals. Different left‐truncation‐ and right‐censoring patterns call for the use of Cox models for data analysis. p‐values are recorded over repeated simulation runs to allow for the desired power calculations. For illustration, we consider scenarios with a “testing” character as well as realistic scenarios. This enables the validation of a correct implementation of theoretical concepts and concrete sample size recommendations against an actual epidemiological background, here given with possible substudy designs within the German National Cohort.     

厚壳贻贝whirlin类贝壳基质蛋白的重组表达与功能分析

贝壳历来是生物工程和材料学研究的重要对象。贝壳中的贝壳基质蛋白质在贝壳的形成与发育过程中具有重要的调控作用。Whirlin类蛋白质(Whirlin-like protein,WLP)是一种从厚壳贻贝(Mytilus coruscus)中鉴定的新型贝壳基质蛋白质。序列分析结果显示,该蛋白质含有PDZ(postsynaptic density/Discs large/Zonula occludens)结构域,而该结构域对贝壳生物矿化的影响目前尚无报道。为深入了解WLP在贝壳形成中对碳酸钙晶体的影响,在序列分析基础上,采用密码子优化结合原核重组表达,获得其重组表达产物后,开展了重组WLP对碳酸钙晶体形貌及晶型的影响研究,结晶速度抑制以及碳酸钙晶体结合分析。分析结果表明,重组WLP能诱导文石型碳酸钙晶体的形貌和方解石型碳酸钙晶体的晶型发生改变;同时重组WLP对碳酸钙晶体具有结合作用,且能抑制碳酸钙晶体的结晶速度。上述结果表明,WLP对贝壳的形成及发育具有重要影响,并可能在贝壳肌棱柱层的形成中发挥了重要作用。     

DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000.     

The lagena (the third otolith endorgan in vertebrates)

In this review, the structure and functions of the lagena (the third otolith organ) in an evolutionary lineage of the vertebrates are described and discussed. The lagenar macula appears first in the posterior part of the sacculus of elasmobranchs; in these animals, the lagena is considered to be involved in the balance support (orientation with respect to the gravitation force). The lagena as a separate endorgan has been described in teleost fishes; in some species, the lagena is connected with the sacculus, while in other species the interrelations of these structures can be dissimilar. The lagena supplements the functions of the sacculus; in fishes (animals with no special organ of hearing), it is involved in discrimination of sound oscillations, identification of the gravitation vector, and orientation in the course of movements within the vertical plane. In amphibians, the lagena is localized in the posterior part of the sacculus, near the auditory structures; it performs mostly vestibular and (to a much lesser extent) auditory functions. In amniotes, the lagena was first separated from the sacculus; it is localized in the cochlear canal, distally with respect to the hearing organ. Information on the functions of the lagena in amniotes is rather limited and contradictory. Central projections of this organ have been examined practically only in birds. Lagenar afferents project to the vestibular nuclei and cerebellum, while some fibers come to the auditory nuclei of the medulla. The lagena in birds can be related to their navigation abilities (birds are supposed to be capable of orienting within the magnetic field of the Earth due to the magnetic properties of the lagenar otoconia; this structure can also provide detection of movements along the vertical axis. The close proximity between the otolithic and auditory endorgans in the cochlear canal of amniotes can be indicative of the functional significance of these interrelations. This aspect, however, remains at present undiscovered. In mammals (except Monotremata), there is no lagena as an independent endorgan. Neirofiziologiya/Neurophysiology, Vol. 40, No. 2, pp. 160–178, March–April, 2008.     

Stronger dung removal in forests compared with grassland is driven by trait composition and biomass of dung beetles

1. Ecosystem processes depend on the biomass of the involved organisms, but their functional diversity may play an additional role. In particular, the exclusion of key functional groups through habitat disturbance may lead to the breakdown of ecosystem functions. Dung removal is an important process contributing to nutrient cycling and thus productivity in grazed ecosystems. 2. This study investigated the role of different functional groups of dung beetles in dung removal in different habitats within a wood-pasture in two different seasons. An experimental setting with 12 blocks and 108 dung pads was used to investigate short-term dung removal over 1 week of exposure. 3. Dung removal was most strongly affected by habitat type, with almost 40% lower levels in grassland than in adjacent forest and forest gaps. Of all assemblage characteristics, total biomass of tunneller species was the strongest predictor of dung removal, whereas functional diversity showed no significant effect. In accordance with the dung removal pattern at habitat type level, densities of large tunnellers were suppressed in grassland compared with forest. 4. It is concluded that dung removal is habitat-specific and large tunnellers play a disproportionate role in this important ecosystem function in temperate forests.     

Use of tissue culture to bypass wheat hybrid necrosis

Summary Hybrid necrosis in wheat is a barrier to gene transfer in wheat breeding practice. It is based on two complementary genes, Ne1 and Ne2. Recovery mutants (Re1, Re2 and Re3) which can grow to maturity were recovered from immature embryo cultures of necrotic hybrids between T. aestivum and T. durum. Cytological observation demonstrated that Re1 had 34 chromosomes instead of 35. This indicated that one of the chromosomes carrying the Ne genes was lost. Genetic study suggested that for Re1, the lost chromosome was chromosome 5B of the durum parental line. Re mutants are male sterile but can be maintained through a young ear culture method. Re mutants could be successfully pollinated by either parental line and the BC1 progeny is partially fertile. Re mutants were repeatedly induced in about 1% of the regenerated plants from immature embryo culture. This technique provides a practical way to bypass hybrid necrosis.     

Batch production and growth kinetics of hybridomas

Batch cultures of mouse-mouse hybridoma cell lines were carried out and their growth and production kinetics investigated. Three main cell specific production patterns (expressed as pg IgG/cell x hour) were found, which can be used as a classification system for hybridoma cell lines (groups I–III). Cells showing the highest IgG-production at the beginning of the batch culture (during the lag and the onset of the log-phase) were classified as either group I and II. The difference was that cell lines of group II showed a second high cell specific production at the onset of the stationary and death phases. Cell lines of group III had a quite constant production of antibodies during their growth; but IgG secretion completely stopped after the beginning of the stationary phase. The implications of these three production patterns on the design of a production process are discussed.     

Epidermal conductance in different parts of durum wheat grown under Mediterranean conditions: the role of epicuticular waxes and stomata

Abstract. Epidermal (non-stomatally-controlled) conductance from the fourth leaf, first node leaf, flag leaf and ear of durum wheat (Triticum turgidum var durum L.) grown under Mediterranean field conditions has been measured, along with leaf stomatal frequency and the amount and distribution of epicuticular waxes. Measurements were carried out on varieties and land-races from the Middle East, North Africa, ‘Institut National de la Recherche Agricole’ (INRA) and ‘Centra Internacional de Mejora de Maiz y Trigo’ (CIMMYT). Significant differences were observed among genotypes in the epidermal conductances (g_e) of the four organs. For each of the four organs tested, genotypes from the Middle East and CIMMYT showed higher g_e. values than those from North Africa and INRA. Ears showed epidermal conductances that were more than four times higher than those of leaves when g_e. values were expressed per unit dry weight. The amount of epicuticular waxes was higher in the fourth leaves, intermediate in the first node and flag leaves and lower in the ears. For each organ, g_e differences among genotypes were unrelated with the amount of epicuticular waxes. Removal of epicuticular waxes by dipping the organs into chloroform significantly increased the epidermal conductance for the fourth and first node leaves and the ear. However, this did not occur for the flag leaf. For the fourth leaf, g_e of intact leaves and g_e of leaves in which epicuticular waxes were removed were unrelated (r = -0.265). The regression coefficient of this relation for the first node and flag leaves showed values of 0.666 and 0.650 (P > 0.05), respectively, and values were even higher in the ear (r > m 0.892, P > 0.01). Scanning electron microscope analysis showed that wax bloom decreased from the fourth leaf to the flag leaf, whereas the extent of amorphous wax increased. Wax bloom in leaves consisted mainly of deposits of thin wax plates. In the ears and the adaxial surface of flag leaves, fibrillar waxes predominated. In the first node and flag leaves, the wax deposits on the adaxial side cover the surface of the leaf more densely and uniformly than those on the abaxial side. There was no significant correlation between g_e and total stomatal density, or between g_e and either adaxial or abaxial stomatal density for any sample of the three different leaves. The contribution of epicuticular waxes plus total stomatal frequency only explained 42.4, 11.8, 28.3 and 16% of g_e (per unit leaf area) variations for the fourth leaf, first node leaf, flag leaf and the combined variation of the three leaves together, respectively. From these results, it is concluded that complex interrelationship between different morphophysiological characteristics probably control g_e differences among genotypes and that these interrelationships differ for each different plant part.     

Techniques for encapsulating bioactive agents into liposomes

As a prerequisite for the use of liposomes for delivery of biologically active agents, techniques are required for the efficient and rapid entrapment of such agents in liposomes. Here we review the variety of procedures available for trapping hydrophilic and hydrophobic compounds. Considerations which are addressed include factors influencing the choice of a particular liposomal system and techniques for the passive entrapment of drugs in multilamellar vesicles and unilamellar vesicles. Attention is also paid to active trapping procedures relying on the presence of (negatively) charged lipid or transmembrane ion gradients. Such gradients are particularly useful for concentrating lipophilic cationic drugs inside liposomes, allowing trapping efficiencies approaching 100%.     

Isolation of brush-border membranes from rat and rabbit colonocytes: Is alkaline phosphatase a marker enzyme?

Summary A method for the isolation of brush-border membranes of large intestinal epithelial cells was developed, which is based on the purification of intact brush-border caps by Percoll^® density-gradient centrifugation followed by separation of the vesiculated brush-border membranes on sucrose gradients. The procedure has two major advantages in comparison to known methods: 1) its first step does not depend on the determination of marker enzymes and 2) the method is applicable to rats as well as rabbits without major modifications. Due to the lack of an accepted marker for the colonic brush-border membrane the validity of the isolation procedure was tested by its application to the small intestine. Rat small intestinal brush-border membranes were enriched 21-fold when compared to the homogenate. The method was used to evaluate alkaline phosphatase as a marker enzyme for the colonic brush-border membrane. The results suggest that alkaline phosphatase is not exclusively localized in the brush-border membrane since this enzyme was also associated with membranes having different physical properties.