Rhodopsin-detergent micelles aggregate upon activation of cyclic guanosine monophosphate phosphodiesterase

In the presence of G protein and phosphodiesterase, GTP induces aggregation of phospholipid-free rhodopsin-detergent micelles or rhodopsin reconstituted in phospholipid vesicles. The net electrical charge of the vesicle is not critical to the aggregation process since this phenomenon is not altered by reconstitution with phospholipids with different charge. The aggregation process is observed by monitoring changes in the light-scattering properties of the detergent micelles or vesicle suspension and by phase-contrast microscopy. The lowest light intensity which triggers the aggregation process and concomitant light-scattering changes in a rhodopsin-detergent micellar suspension bleaches 6% rhodopsin. Under these conditions, the signal saturates at 30% rhodopsin bleaching. The aggregation process appears likely to depend on the protein-protein interaction, and the presence of a disk membrane is not necessary for this process.     

Diversity and Evolution of the Marsupial Mandibular Angular Process

A medial inflection of the mandibular angular process is present in most marsupials. The few living marsupials that lack this trait either are very specialized forms (e.g., Tarsipes) or show a medial inflection at some point in development that is lost in later ontogenetic stages (cf. Dactylopsila and Phascolarctos). A medially inflected angular process is not present in any known extant or extinct placental (including all Cretaceous taxa that preserve the back of the dentary bone). Some extant placentals with enlarged auditory bullae evolved a medial flange of the angular process as a strategy to increase gape, but this is not homologous to the marsupial condition. We conclude that the medially inflected angular process is a shared derived trait of extant and extinct marsupials. The significant diversity in the form of the medially inflected mandibular angular process in marsupials, documented here for 53 taxa, shows a general relation to dietary adaptations. Herbivores (with well-developed masseter and medial pterygoid muscles) tend to have a shelf-like angular process, while small, insectivorous marsupials generally have a rod-like angular process. A close connection between the angular process and the ectotympanic is maintained during early postnatal development in all marsupials examined, a relation not seen in the placentals examined. A previous hypothesis suggested that the angular process plays a role in hearing in pouch-young Monodelphis. Data on the maturation of the auditory system does not support this hypothesis. Currently there are no data on differences in muscular anatomy or mastication between marsupials and placentals that could serve as a causal explanation for the difference in adult form of the angular process between the two groups.     

Optimal economic design and operation of single- and multi-column chromatographic processes

Single-column chromatography is widely used in the biopharmaceutical industries, although multi-column alternatives in the form of simulated moving bed (SMB) processes are now emerging. It may be difficult, however, to determine which column alternative will be best suited for a given application, and this work sets out to address this issue. A systematic approach is presented that is based on a full economic appraisal of each process alternative based on an optimization of the net annual profit. Single-column processes with and without recycling are considered, as are both the SMB and the Varicol process. The cyclic steady state for the SMB and Varicol processes is determined directly by complete discretization. The approach is applied to a case study based on a linear isotherm where it is found that for this particular system, a recycling policy is not necessary for the single column. When comparing the single-column process with the multi-column alternatives, the single column is the most economical provided the life time of the project is short; however, the economic benefits of the more capital-intensive multi-column processes are greater if the life time of the project is over 5 years. The SMB process is found to perform marginally better than the Varicol process over 15 years; however, this may be because not all extra degrees of freedom for the Varicol process were considered.     

Are evolutionary rates really variable?

Summary Langley and Fitch (1974, 1976) have shown that the pattern of nucleotide substitutions in proteins is inconsistent with a Poisson process with constant rate. From this they conclude that the rate is temporally heterogeneous. It is pointed out in this note that a process which is temporally homogeneous but not a Poisson process is compatible with the data if the coefficient of variation of the time between substitutions is around 1.63. Furthermore, theoretical analysis of samples from neutral phylogenies shows that these samples should not appear to be samples from a Poisson process, but should deviate from a Poisson process in the same direction, though perhaps not to the same extent, as do the data.     

Oxygen and carbon dioxide in the regulation of respiration.

When a sea-level resident ascends to a high altitude, his breathing immediately increases because of hypoxic stimulation of the peripheral chemoreceptors. In many species the aortic bodies are relatively unimportant in this response compared to the carotid bodies. When the subject stays at that altitude, his breathing increases progressively in the next few hours and days in a process termed ventilatory acclimatization and does not immediately return to control levels when hypoxia is terminated. Evidence is summarized indicating that this chronic process does not depend on the peripheral chemoreceptors or an initial respiratory alkalosis. Historical review indicates that the process of ventilatory acclimatization was initially attributed to renal excretion of plasma bicarbonate with development of a metabolic acidosis; but subsequent measurements indicated this process did not lower the arterial pH sufficiently to account for the ventilatory stimulation. More recently, ventilatory acclimatization has been attributed to accelerated removal of bicarbonate from the cerebrospinal fluid (CSF), producing a metabolic acidosis in the region of the medullary chemoreceptors; but still more recent observations indicate that this process, contrary to earlier observations, does not lower the CSF pH sufficiently to account for the ventilatory stimulation, either. Some other mechanism should be sought.     

A fast algorithm for the exact likelihood of stationary and partially nonstationary vector autoregressive-moving average processes

An expression for the likelihood function of a stationary vectorautoregressive-moving average process is developed. The expressionis very efficient numerically and applies to any stationarybut not necessarily invertible model. In particular, when themultivariate process is autoregressive, the exact likelihoodcan be evaluated with a small number of operations dependingon the order of the autoregressive operator and the processdimension, but not on the size of the observed series. The expressionalso provides an efficient method for the evaluation of theexact likelihood of a partially nonstationary vector autoregressive-movingaverage process, for which the determinant of the autoregressiveoperator has at least one unit root and the remaining rootsare outside the unit circle. This method does not require differencingthe series, so that complications caused by over-differencingthe series, such as noninvertibility and parameter identifiabilityproblems, are avoided. The results for autoregressive modelsare also applied to testing the stationarity and invertibilityof any autoregressive-moving average model with given parametervalues.     

On statistical inference for the random set generated Cox process with set-marking

Cox point process is a process class for hierarchical modelling of systems of non-interacting points in Rd under environmental heterogeneity which is modelled through a random intensity function. In this work a class of Cox processes is suggested where the random intensity is generated by a random closed set. Such heterogeneity appears for example in forestry where silvicultural treatments like harvesting and site-preparation create geometrical patterns for tree density variation in two different phases. In this paper the second order property, important both in data analysis and in the context of spatial sampling, is derived. The usefulness of the random set generated Cox process is highly increased, if for each point it is observed whether it is included in the random set or not. This additional information is easy and economical to obtain in many cases and is hence of practical value; it leads to marks for the points. The resulting random set marked Cox process is a marked point process where the marks are intensity-dependent. The problem with set-marking is that the marks are not a representative sample from the random set. This paper derives the second order property of the random set marked Cox process and suggests a practical estimation method for area fraction and covariance of the random set and for the point densities within and outside the random set. A simulated example and a forestry example are given.     

Discovery of veterinary antiparasitic agents in the 21st Century: A view from industry

Discovery of antiparasitic agents is a challenging process, requiring discovery of molecules with the ability to kill parasites but not their hosts. Customer preference is for fewer doses and ease of application, but this is not always compatible with reduced withdrawal times, human food safety and/or user safety. This article describes some of the difficulties faced by researchers in the search for new antiparasitic agents, while highlighting advances that may improve the discovery process and the chance of success in discovering novel drugs.     

Industrial glucoamylase fed-batch benefits from oxygen limitation and high osmolarity

The market for glucoamylase is large and very competitive and the production process has been optimized through several decades. So far a thorough characterization of the process has not been published, but previous academic reports suggest that the process suffers from severe byproduct formation. In this study we have carried out a thorough characterization of a process as close as possible to the industrial reality. The results show that the oxygen-limited phases of the process have the highest glucoamylase yields on carbon and that the byproducts are efficiently reused in late phases of the process. An alternative process with low glucose concentration show that high osmolarity is beneficial for the process, and we conclude that oxygen limitation, high osmolarity, and the associated byproduct metabolism are important for the efficiency of the process.     

Process development and evaluation for algal glycerol production

This article and develops a process for large-scale production of glycerol by means of a hemophilic algae. The process is shown to be economically and technically feasible. Although the proposed process is extremely capital intensive, the total production cost is competitive with existing glycerol process. In addition, the overall energy requirement is much lower than that of the petrochemical process. This proposed process provides an alternative route for glycerol production that is minimally dependent on fossil fuels and is therefore, less sensitive to crude oil availability and price. The primary raw material carbon dioxide from stack gas, is an inexpensive and renewable resource. Maximal Utilization of solar energy is made not only in the glycerol synthesis steps but also in the product recovery system. Significant improvement in the process economics can be realized through further development of large-scale cultivation technology, and biomass distribution and collection machinery. Due to the labor intensive nature of the proposed algal process, it is particularly suitable for less developed nations with limited fossil fuel resources and lower labor costs.     

氮形态转化途径研究的新进展—厌气铵氧化及其应用前景

20世纪90年代初在污泥处理系统中发现了氮素形态转化的新途径－厌气铵氧化过程,厌气铵氧化过程是铵以亚硝酸根为电子受体在自养细菌参数下氧化成氮气的过程,但目前尚无土壤,河,湖,海底泥等自然系统中是否存在厌氧铵氧化过程的报道,由于该过程无需外加有机碳,耗氧和处理产生污泥少,用于污泥脱氮成本较低,具有很大潜力。     

Parkinson disease: from pathology to molecular disease mechanisms

Parkinson disease (PD) is a complex neurodegenerative disorder with both motor and nonmotor symptoms owing to a spreading process of neuronal loss in the brain. At present, only symptomatic treatment exists and nothing can be done to halt the degenerative process, as its cause remains unclear. Risk factors such as aging, genetic susceptibility, and environmental factors all play a role in the onset of the pathogenic process but how these interlink to cause neuronal loss is not known. There have been major advances in the understanding of mechanisms that contribute to nigral dopaminergic cell death, including mitochondrial dysfunction, oxidative stress, altered protein handling, and inflammation. However, it is not known if the same processes are responsible for neuronal loss in nondopaminergic brain regions. Many of the known mechanisms of cell death are mirrored in toxin-based models of PD, but neuronal loss is rapid and not progressive and limited to dopaminergic cells, and drugs that protect against toxin-induced cell death have not translated into neuroprotective therapies in humans. Gene mutations identified in rare familial forms of PD encode proteins whose functions overlap widely with the known molecular pathways in sporadic disease and these have again expanded our knowledge of the neurodegenerative process but again have so far failed to yield effective models of sporadic disease when translated into animals. We seem to be missing some key parts of the jigsaw, the trigger event starting many years earlier in the disease process, and what we are looking at now is merely part of a downstream process that is the end stage of neuronal death.     

氮形态转化途径研究的新进展──厌气铵氧化及其应用前景

20世纪90年代初在污泥处理系统中发现了氮素形态转化的新途径--厌气铵氧化过程.厌气铵氧化过程是铵以亚硝酸根为电子受体在自养细菌参数下氧化成氮气的过程.但目前尚无土壤、河、湖、海底泥等自然系统中是否存在厌气铵氧化过程的报道.由于该过程无需外加有机碳,耗氧和处理产生污泥少,用于污泥脱氮成本较低,具有很大潜力.     

Zebrafish reproduction: revisiting in vitro fertilization to increase sperm cryopreservation success

Although conventional cryopreservation is a proven method for long-term, safe storage of genetic material, protocols used by the zebrafish community are not standardized and yield inconsistent results, thereby putting the security of many genotypes in individual laboratories and stock centers at risk. An important challenge for a successful zebrafish sperm cryopreservation program is the large variability in the post-thaw in vitro fertilization success (0 to 80%). But how much of this variability was due to the reproductive traits of the in vitro fertilization process, and not due to the cryopreservation process? These experiments only assessed the in vitro process with fresh sperm, but yielded the basic metrics needed for successful in vitro fertilization using cryopreserved sperm, as well. We analyzed the reproductive traits for zebrafish males with a strict body condition range. It did not correlate with sperm volume, or motility (P>0.05), but it did correlate with sperm concentration. Younger males produced more concentrated sperm (P<0.05). To minimize the wastage of sperm during the in vitro fertilization process, 10⁶ cells/ml was the minimum sperm concentration needed to achieve an in vitro fertilization success of ≥ 70%. During the in vitro process, pooling sperm did not reduce fertilization success (P>0.05), but pooling eggs reduced it by approximately 30 to 50% (P<0.05). This reduction in fertilization success was due not to the pooling of the females'' eggs, but to the type of tools used to handle the eggs. Recommendations to enhance the in vitro process for zebrafish include: 1) using males of a body condition closer to 1.5 for maximal sperm concentration; 2) minimizing sperm wastage by using a working sperm concentration of 10⁶ motile cells/ml for in vitro fertilization; and 3) never using metal or sharp-edged tools to handle eggs prior to fertilization.     

THE OUTWARD TRANSPORT OF CORTISOL BY MAMMALIAN CELLS IN VITRO

It has been determined that cortisol and a few other steroids are transported outward from certain mammalian cells growing in vitro. The extrusion process is temperature dependent, glucose dependent, saturable, and operates for only a few selected steroids. Many, but not all, steroids are able to block the extrusion process but are not themselves transported. The outward transport process for steroids has been found in mouse fibroblasts, mouse lymphoma cells, and functional mouse adrenal gland tumor cells growing in vitro. The transport process is not present in two varieties of cells cultured from human sources—HeLa or diploid fibroblasts, WI-38.     

Lag time in microbe growth as an age-dependent branching process with two phase types

We study a two-type, age-dependent branching process in which the branching probabilities of one of the types may vary with time. Specifically this modification of the Bellman-Harris process starts with a Type I particle which may either die or change to a Type II particle depending upon a time varying probability. A Type II particle may either die or reproduce with fixed probabilities but may not return to a particle of Type I. In this way the process models the lag phenomenon observed in microbe growth subsequent to transfer to a new culture medium while the organism is adapting to its new environment. We show that if the mean reproduction rate of Type II particles exceeds 1, then the population size grows exponentially. Further the extinction probability for this process is related to that of the Bellman-Harris process. Finally the governing equations are solved for several choices of the growth parameters and the solutions are graphically displayed showing that a wide variety of behavior can be modeled by this process.     

The calorimetric criterion for a two-state process revisited.

The "calorimetric criterion" is one of the important experimental approaches for determining whether protein folding is an "all-or-none" two-state transition (i.e., whether intermediates are present at equilibrium). The calorimetric criterion states that the equivalence of the "measured" calorimetric enthalpy change and the effective two-state van't Hoff enthalpy change demonstrates that there is a two-state transition. This paper addresses the essential question of whether the calorimetric criterion is a necessary and sufficient condition for a two-state process and shows that it is necessary but not sufficient by means of specific examples. Analysis of simple models indicates that the heat capacity curve, regardless of whether it originates from a two-state process or not, can always be decomposed in such a way that the calorimetric criterion is satisfied. Exact results for a three-state model and a homopolymer tetramer demonstrate that the deviation from the calorimetric criterion is not simply related to the population of intermediate states. Analysis of a three-helix bundle protein model, which has a two-state folding from a random coil to ordered (molten) globule, shows that the calorimetric criterion may not be satisfied if the standard linear interpolation of baselines (weighted or unweighted) is employed. A specific example also suggests that the more recently introduced deconvolution method is not necessarily better than the simple calorimetric criterion for distinguishing a two-state transition from a three-state transition. Although the calorimetric criterion is not a sufficient condition for a two-state process, it is likely to continue to be of practical utility, particularly when its results are shown to be consistent with those from other experimental methods.     

Multivariate PAT solutions for biopharmaceutical cultivation: current progress and limitations

Increasingly elaborate and voluminous datasets are generated by the (bio)pharmaceutical industry and are a major challenge for application of PAT and QbD principles. Multivariate data analysis (MVDA) is required to delineate relevant process information from large multi-factorial and multi-collinear datasets. Here the key role of MVDA for industrial (bio)process data is discussed, with a focus on progress and limitations of MVDA as a PAT solution for biopharmaceutical cultivation processes. MVDA based models were proven useful and should be routinely implemented for bioprocesses. It is concluded that although the highest level of PAT with process control within its design space in real-time during manufacturing is not reached yet, MVDA will be central to reach this ultimate objective for cell cultivations.