Automatic particle picking of biological molecules imaged by electron microscopy

One of the next great challenges of cell biology is the determination of the enormous number of protein structures encoded in genomes. In recent years, advances in electron cryo-microscopy and high-resolution single particle analysis have developed to the point where they now provide a methodology for high resolution structure determination. Using this approach, images of randomly oriented single particles are aligned computationally to reconstruct 3-D structures of proteins and even whole viruses. One of the limiting factors in obtaining high-resolution reconstructions is obtaining a large enough representative dataset ($>100,000$ particles). Traditionally particles have been manually picked which is an extremely labour intensive process. The problem is made especially difficult by the low signal-to-noise ratio of the images. This paper describes the development of automatic particle picking software, which has been tested with both negatively stained and cryo-electron micrographs. This algorithm has been shown to be capable of selecting most of the particles, with few false positives. Further work will involve extending the software to detect differently shaped and oriented particles.

Fractional models for the migration of biological cells in complex spatial domains

Travelling wave phenomena are observed in many biological applications. Mathematical theory of standard reaction-diffusion problems shows that simple partial differential equations exhibit travelling wave solutions with constant wavespeed and such models are used to describe, for example, waves of chemical concentrations, electrical signals, cell migration, waves of epidemics and population dynamics. However, as in the study of cell motion in complex spatial geometries, experimental data are often not consistent with constant wavespeed. Non-local spatial models have successfully been used to model anomalous diffusion and spatial heterogeneity in different physical contexts. In this paper, we develop a fractional model based on the Fisher-Kolmogoroff equation and analyse it for its wavespeed properties, attempting to relate the numerical results obtained from our simulations to experimental data describing enteric neural crest-derived cells migrating along the intact gut of mouse embryos. The model proposed essentially combines fractional and standard diffusion in different regions of the spatial domain and qualitatively reproduces the behaviour of neural crest-derived cells observed in the caecum and the hindgut of mouse embryos during in vivo experiments.

Mass spectrometry-based metabolomics towards understanding of gene functions with a diversity of biological contexts

Currently, mass spectrometry-based metabolomics studies extend beyond conventional chemical categorization and metabolic phenotype analysis to understanding gene function in various biological contexts (e.g., mammalian, plant, and microbial). These novel utilities have led to many innovative discoveries in the following areas: disease pathogenesis, therapeutic pathway or target identification, the biochemistry of animal and plant physiological and pathological activities in response to diverse stimuli, and molecular signatures of host-pathogen interactions during microbial infection. In this review, we critically evaluate the representative applications of mass spectrometry-based metabolomics to better understand gene function in diverse biological contexts, with special emphasis on working principles, study protocols, and possible future development of this technique. Collectively, this review raises awareness within the biomedical community of the scientific value and applicability of mass spectrometry-based metabolomics strategies to better understand gene function, thus advancing this application's utility in a broad range of biological fields

MS-based metabolomics facilitates the discovery of in vivo functional small molecules with a diversity of biological contexts

In vivo small molecules as necessary intermediates are involved in numerous critical metabolic pathways and biological processes associated with many essential biological functions and events. There is growing evidence that MS-based metabolomics is emerging as a powerful tool to facilitate the discovery of functional small molecules that can better our understanding of development, infection, nutrition, disease, toxicity, drug therapeutics, gene modifications and host-pathogen interaction from metabolic perspectives. However, further progress must still be made in MS-based metabolomics because of the shortcomings in the current technologies and knowledge. This technique-driven review aims to explore the discovery of in vivo functional small molecules facilitated by MS-based metabolomics and to highlight the analytic capabilities and promising applications of this discovery strategy. Moreover, the biological significance of the discovery of in vivo functional small molecules with different biological contexts is also interrogated at a metabolic perspective.

The role of biological extracellular matrix scaffolds in vascularized three-dimensional tissue growth in vivo

An in vivo murine vascularized chamber model has been shown to generate spontaneous angiogenesis and new tissue formation. This experiment aimed to assess the effects of common biological scaffolds on tissue growth in this model. Either laminin-1, type I collagen, fibrin glue, hyaluronan, or sea sponge was inserted into silicone chambers containing the epigastric artery and vein, one end was sealed with adipose tissue and the other with bone wax, then incubated subcutaneously. After 2, 4, or 6 weeks, tissue from chambers containing collagen I, fibrin glue, hyaluronan, or no added scaffold (control) had small amounts of vascularized connective tissue. Chambers containing sea sponge had moderate connective tissue growth together with a mild "foreign body" inflammatory response. Chambers containing laminin-1, at a concentration 10-fold lower than its concentration in Matrigel™, resulted in a moderate adipogenic response. In summary, (1) biological hydrogels are resorbed and gradually replaced by vascularized connective tissue; (2) sponge-like matrices with large pores support connective tissue growth within the pores and become encapsulated with granulation tissue; (3) laminin-containing scaffolds facilitate adipogenesis. It is concluded that the nature and chemical composition of the scaffold exerts a significant influence on the amount and type of tissue generated in this in vivo chamber model.

Measurements of Volatile Organic Compounds - from Biogenic Emissions to Concentrations in Ambient Air

Volatile organic compounds (VOCs) affect atmospheric chemistry and thereafter also participate in the climate change in many ways. The long-lived greenhouse gases and tropospheric ozone are the most important radiative forcing components warming the climate, while aerosols are the most important cooling component. VOCs can have warming effects on the climate: they participate in tropospheric ozone formation and compete for oxidants with the greenhouse gases thus, for example, lengthening the atmospheric lifetime of methane. Some VOCs, on the other hand, cool the atmosphere by taking part in the formation of aerosol particles. Some VOCs, in addition, have direct health effects, such as carcinogenic benzene. VOCs are emitted into the atmosphere in various processes. Primary emissions of VOC include biogenic emissions from vegetation, biomass burning and human activities. VOCs are also produced in secondary emissions from the reactions of other organic compounds. Globally, forests are the largest source of VOC entering the atmosphere. This thesis focuses on the measurement results of emissions and concentrations of VOCs in one of the largest vegetation zones in the world, the boreal zone. An automated sampling system was designed and built for continuous VOC concentration and emission measurements with a proton transfer reaction - mass spectrometer (PTR-MS). The system measured one hour at a time in three-hourly cycles: 1) ambient volume mixing-ratios of VOCs in the Scots-pine-dominated boreal forest, 2) VOC fluxes above the canopy, and 3) VOC emissions from Scots pine shoots. In addition to the online PTR-MS measurements, we determined the composition and seasonality of the VOC emissions from a Siberian larch with adsorbent samples and GC-MS analysis. The VOC emissions from Siberian larch were reported for the fist time in the literature. The VOC emissions were 90% monoterpenes (mainly sabinene) and the rest sesquiterpenes (mainly a-farnesene). The normalized monoterpene emission potentials were highest in late summer, rising again in late autumn. The normalized sesquiterpene emission potentials were also highest in late summer, but decreased towards the autumn. The emissions of mono- and sesquiterpenes from the deciduous Siberian larch, as well as the emissions of monoterpenes measured from the evergreen Scots pine, were well described by the temperature-dependent algorithm. In the Scots-pine-dominated forest, canopy-scale emissions of monoterpenes and oxygenated VOCs (OVOCs) were of the same magnitude. Methanol and acetone were the most abundant OVOCs emitted from the forest and also in the ambient air. Annually, methanol and mixing ratios were of the order of 1 ppbv. The monoterpene and sum of isoprene 2-methyl-3-buten-2-ol (MBO) volume mixing-ratios were an order of magnitude lower. The majority of the monoterpene and methanol emissions from the Scots-pinedominated forest were explained by emissions from Scots pine shoots. The VOCs were divided into three classes based on the dynamics of the summer-time concentrations: 1) reactive compounds with local biological, anthropogenic or chemical sources (methanol, acetone, butanol and hexanal), 2) compounds whose emissions are only temperaturedependent (monoterpenes), 3) long-lived compounds (benzene, acetaldehyde). Biogenic VOC (methanol, acetone, isoprene MBO and monoterpene) volume mixing-ratios had clear diurnal patterns during summer. The ambient mixing ratios of other VOCs did not show this behaviour. During winter we did not observe systematical diurnal cycles for any of the VOCs. Different sources, removal processes and turbulent mixing explained the dynamics of the measured mixing-ratios qualitatively. However, quantitative understanding will require longterm emission measurements of the OVOCs and the use of comprehensive chemistry models. Keywords: Hydrocarbons, VOC, fluxes, volume mixing-ratio, boreal forest

Doing marriage and parenthood: The division of household labour across two life course events

The current study is a longitudinal investigation into changes in the division of household labour across transitions to marriage and parenthood in the UK. Previous research has noted a more traditional division of household labour, with women performing the majority of housework, amongst spouses and couples with children. However, the bulk of this work has been cross-sectional in nature. The few longitudinal studies that have been carried out have been rather ambiguous about the effect of marriage and parenthood on the division of housework. Theoretically, this study draws on gender construction theory. The key premise of this theory is that gender is something that is performed and created in interaction, and, as a result, something fluid and flexible rather than fixed and stable. The idea that couples ‘do gender’ through housework has been a major theoretical breakthrough. Gender-neutral explanations of the division of household labour, positing rational acting individuals, have failed to explicate why women continue to perform an unequal share of housework, regardless of socio-economic status. Contrastingly, gender construction theory situates gender as the key process in dividing household labour. By performing and avoiding certain housework chores, couples fulfill social norms of what it means to be a man and a woman although, given the emphasis on human agency in producing and contesting gender, couples are able to negotiate alternative gender roles which, in turn, feed back into the structure of social norms in an ever-changing societal landscape. This study adds extra depth to the doing gender approach by testing whether or not couples negotiate specific conjugal and parent roles in terms of the division of household labour. Both transitions hypothesise a more traditional division of household labour. Data comes from the British Household Panel Survey, a large, nationally representative quantitative survey that has been carried out annually since 1991. Here, data tracks the same 776 couples at two separate time points – 1996 and 2005. OLS regression is used to test whether or not transitions to marriage and parenthood have a significant impact on the division of household labour whilst controlling for host of relevant socio-economic factors. Results indicate that marriage has no significant effect on how couples partition housework. Those couples making the transition from cohabitation to marriage do not show significant changes in housework arrangements from those couples who remain cohabiting in both waves. On the other hand, becoming parents does lead to a more traditional division of household labour whilst controlling for socio-economic factors which accompany the move to parenthood. There is then some evidence that couples use the site of household labour to ‘do parenthood’ and generate identities which both use and inform socially prescribed notions of what it means to be a mother and a father. Support for socio-economic explanations of the division of household labour was mixed although it remains clear that they, alone, cannot explain how households divide housework.

Blue mussel beds as biodiversity hotspots on the rocky shores of the northern Baltic Sea

ABSTRACT The Baltic Sea is a vulnerable ecosystem currently undergoing a number of changes, both natural and human induced. The changes are likely to affect the species found on these shores, e.g. their distribution and interactions with other species. Blue mussels (Mytilus trossulus x Mytilus edulis) provide one of the main biogenic hard structures on the shallow shores of the Baltic Sea where they aggregate into dense beds and provide a number of resources for over 40 associated macrofaunal species, thus functioning as ecosystem engineers. The blue mussel, being a marine species, is highly likely to be affected by any changes in sea water salinity, circulation and/or water balance. These changes could trickle down also to affect the associated macrofaunal communities. The aims of this thesis were three-fold: first, I examined and described the macrofaunal communities found within blue mussel patches since the fauna associated with mussel patches had never been described in the study area prior to this thesis. Second, I explored how changes in mussel density, size as well as patch size and shape would affect the mussel communities. Finally, I tested how general landscape theories derived from terrestrial studies function in blue mussel systems. Theories included the structural heterogeneity hypothesis, species-area relationships, edge effects and patch isolation effects. The work shows that blue mussels in the northern Baltic Sea have an indisputable function as diversity hotspots and that the faunal assemblages found in mussel patches are extremely rich and unique. Further on, it shows that changes in mussel biomass, size, patch size and amount of edge have the potential to alter the faunal assemblages and diversity within patches. Finally, it shows that although some landscape theories, such as the structural heterogeneity hypothesis, seem to apply also in blue mussel communities, others cannot be directly applied due to the different prevailing conditions in the study system. This is a pioneering work looking at diversity shaping processes on the rocky shores of the Gulf of Finland, making up over 40% of the total water basin. A focus on niche construction, positive facilitation effects and ecosystem engineering could provide new insights and methods for conservation biology, but before this can be done, we need to fully understand the circumstances under which a species becomes an ecosystem engineer and recognize the systems in which it functions.

Doing marriage and parenthood: The division of household labour across two life course events

The current study is a longitudinal investigation into changes in the division of household labour across transitions to marriage and parenthood in the UK. Previous research has noted a more traditional division of household labour, with women performing the majority of housework, amongst spouses and couples with children. However, the bulk of this work has been cross-sectional in nature. The few longitudinal studies that have been carried out have been rather ambiguous about the effect of marriage and parenthood on the division of housework. Theoretically, this study draws on gender construction theory. The key premise of this theory is that gender is something that is performed and created in interaction, and, as a result, something fluid and flexible rather than fixed and stable. The idea that couples 'do gender' through housework has been a major theoretical breakthrough. Gender-neutral explanations of the division of household labour, positing rational acting individuals, have failed to explicate why women continue to perform an unequal share of housework, regardless of socioeconomic status. Contrastingly, gender construction theory situates gender as the key process in dividing household labour. By performing and avoiding certain housework chores, couples fulfill social norms of what it means to be a man and a woman although, given the emphasis on human agency in producing and contesting gender, couples are able to negotiate alternative gender roles which, in turn, feed back into the structure of social norms in an ever-changing societal landscape. This study adds extra depth to the doing gender approach by testing whether or not couples negotiate specific conjugal and parent roles in terms of the division of household labour. Both transitions hypothesise a more traditional division of household labour. Data comes from the British Household Panel Survey, a large, nationally representative quantitative survey that has been carried out annually since 1991. Here, data tracks the same 776 couples at two separate time points - 1996 and 2005. OLS regression is used to test whether or not transitions to marriage and parenthood have a significant impact on the division of household labour whilst controlling for host of relevant socio-economic factors. Results indicate that marriage has no significant effect on how couples partition housework. Those couples making the transition from cohabitation to marriage do not show significant changes in housework arrangements from those couples who remain cohabiting in both waves. On the other hand, becoming parents does lead to a more traditional division of household labour whilst controlling for socio-economic factors which accompany the move to parenthood. There is then some evidence that couples use the site of household labour to 'do parenthood' and generate identities which both use and inform socially prescribed notions of what it means to be a mother and a father. Support for socio-economic explanations of the division of household labour was mixed although it remains clear that they, alone, cannot explain how households divide housework.

A report of biological observations at Topanga artificial reef and Santa Monica Bay artificial reef

(Document pdf contains 25 pages)

Rhythms of division of some algae in situ and in laboratory culture. [Translation from: Studii Cerc.Biol.(Bot.) 21, 61-65, 1969. ]

The rhythm of division of 9 species belonging to different groups of algae were analysed in situ and in the laboratory. The research which developed in different environmental conditions attempted to establish the capacity for multiplication and assimilation of chlorophyll on the part of the algae under study with a view to placing them in a culture. The results obtained showed that the green multicellular algae (eg. Ulothrix) and the blue algae (eg. Lyngbya, Oscillatoria) are able to produce an appreciable quantity of dry matter, just as the unicellular algae. At the same time it arises that amongst the numerous factors of the environment, temperature plays one of the most important roles in the process of multiplication.