Examination of the seasonal variation in the abundance of Crangon shrimp and its relationship to the presence of the green sturgeon (Acipenser medirostris).pdf

A better understanding of the distribution and spawning behavior of Crangon shrimp and their relationship with their predators, including the green sturgeon, Acipenser medirostris, is an important step toward the larger goal to understand food webs of the nearshore continental shelf of the northeastern Pacific. Here, I examined how the biomass and energetics of two species of Crangon varied seasonally and by depth and the relationship between those patterns and the modeled distribution of A. medirostris, hypothesizing that the predicted presence of sturgeon would show a positive relationship with Crangon. With the help of Larkin Loewenherz, a colleague, I also examined the assemblage and spawning behavior of Crangon species across several habitat types in Yaquina Bay, Oregon, hypothesizing that C. franciscorum would dominate the bay while C. alaskensis would be most common offshore, and that these species would be of larger average mass offshore due to mature individuals moving down the salinity gradient. This latter investigation, dealing with spawning and assemblage, was presented to a public audience as the final project for the spring term 2014 BI 450 Marine Biology course at Hatfield Marine Science Center. Crangon samples were collected via beam trawl near Newport, Oregon, in 15 months over a span of 3 years (2010-2013). The presence of A. medirostris was predicted with help from Dr. David Huff, using a model based on data from coastal hydrophone arrays tracking acoustically tagged sturgeon, that included a number of physical covariates. For spawning and assemblage, samples were trawled from two stations in the river channel of Yaquina Bay and collected from two beach stations by seine net during spring 2014, and compared with offshore samples taken the previous year. Subsequent analyses found that for the most part, biomass density of Crangon was higher in fall and late summer than in winter or spring, driven by the more abundant C. alaskensis. Alternatively, Crangon stylirostris was most abundant in February and at shallower depths. Energetics of individual C. alaskensis was higher in winter than in fall and at shallower depths, and energetics of C. stylirostris showed no effect from month or depth. Biomass density of Crangon and calorimetry of C. alaskensis were both tested as explanatory variables for A. medirostris, but no relationship was found between these quantities and A. medirostris presence. For assemblage and spawning, we found that species assemblage differed between habitat types, but there was no significant difference in mean individual biomass between the channel and offshore habitats. We also found that there was no significant difference in average proportion of gravid C. alaskensis females between the channel and offshore habitats, leaving the question of where they go to spawn unanswered. We did find a positive correlation between the average total length and the percentage of gravid females. The observed patterns in Crangon abundance and energetics could be explained either by seasonal fluctuation of nutrients caused by upwelling, or by reproductive migration of individual shrimp once they reached sexual maturity. The lack of any correlation between Crangon distribution and A. medirostris presence doesn’t rule out some relationship between the two, but a larger spatial area of Crangon sampling might be required to detect those patterns if they exist. From our findings regarding assemblage and spawning, one of two possible interpretations exists: either salinity is not sufficiently different between the bay and the offshore area - or more likely, salinity is not a useful predictor of gravidity in Crangon. This study was important because it aimed to shed some light on the habits of an oft-overlooked group of animals, which likely play a significant role in coastal food webs. By sharing our work with an audience that extended beyond our immediate colleagues and included people outside of our field, our hope was that we would open the eyes of some of the public to just how many questions about the denizens of the supposedly familiar near-shore and estuarine environments still wait to be answered.Keywords: sturgeon, Biology, acipenser, medirostris, Shrimp, Marine, Gravidity, Population, Spawning, Gravid, Crangon, Hatfield, Estuary, Ecology, calorimetry, green, Pacific, Yaquina, Estuarine, Benthic, Caride

Investigation of Crangon species assemblage and spawning patterns in Yaquina Bay, OR.pdf

A better understanding of the distribution and spawning behavior of Crangon shrimp and their relationship with their predators, including the green sturgeon, Acipenser medirostris, is an important step toward the larger goal to understand food webs of the nearshore continental shelf of the northeastern Pacific. Here, I examined how the biomass and energetics of two species of Crangon varied seasonally and by depth and the relationship between those patterns and the modeled distribution of A. medirostris, hypothesizing that the predicted presence of sturgeon would show a positive relationship with Crangon. With the help of Larkin Loewenherz, a colleague, I also examined the assemblage and spawning behavior of Crangon species across several habitat types in Yaquina Bay, Oregon, hypothesizing that C. franciscorum would dominate the bay while C. alaskensis would be most common offshore, and that these species would be of larger average mass offshore due to mature individuals moving down the salinity gradient. This latter investigation, dealing with spawning and assemblage, was presented to a public audience as the final project for the spring term 2014 BI 450 Marine Biology course at Hatfield Marine Science Center. Crangon samples were collected via beam trawl near Newport, Oregon, in 15 months over a span of 3 years (2010-2013). The presence of A. medirostris was predicted with help from Dr. David Huff, using a model based on data from coastal hydrophone arrays tracking acoustically tagged sturgeon, that included a number of physical covariates. For spawning and assemblage, samples were trawled from two stations in the river channel of Yaquina Bay and collected from two beach stations by seine net during spring 2014, and compared with offshore samples taken the previous year. Subsequent analyses found that for the most part, biomass density of Crangon was higher in fall and late summer than in winter or spring, driven by the more abundant C. alaskensis. Alternatively, Crangon stylirostris was most abundant in February and at shallower depths. Energetics of individual C. alaskensis was higher in winter than in fall and at shallower depths, and energetics of C. stylirostris showed no effect from month or depth. Biomass density of Crangon and calorimetry of C. alaskensis were both tested as explanatory variables for A. medirostris, but no relationship was found between these quantities and A. medirostris presence. For assemblage and spawning, we found that species assemblage differed between habitat types, but there was no significant difference in mean individual biomass between the channel and offshore habitats. We also found that there was no significant difference in average proportion of gravid C. alaskensis females between the channel and offshore habitats, leaving the question of where they go to spawn unanswered. We did find a positive correlation between the average total length and the percentage of gravid females. The observed patterns in Crangon abundance and energetics could be explained either by seasonal fluctuation of nutrients caused by upwelling, or by reproductive migration of individual shrimp once they reached sexual maturity. The lack of any correlation between Crangon distribution and A. medirostris presence doesn’t rule out some relationship between the two, but a larger spatial area of Crangon sampling might be required to detect those patterns if they exist. From our findings regarding assemblage and spawning, one of two possible interpretations exists: either salinity is not sufficiently different between the bay and the offshore area - or more likely, salinity is not a useful predictor of gravidity in Crangon. This study was important because it aimed to shed some light on the habits of an oft-overlooked group of animals, which likely play a significant role in coastal food webs. By sharing our work with an audience that extended beyond our immediate colleagues and included people outside of our field, our hope was that we would open the eyes of some of the public to just how many questions about the denizens of the supposedly familiar near-shore and estuarine environments still wait to be answered.Keywords: Caridea, Gravidity, Hatfield, Estuary, Marine, Population, Biology, Ecology, green, Shrimp, Gravid, medirostris, calorimetry, acipenser, Spawning, Benthic, Crangon, sturgeon, Estuarine, Pacific, Yaquin

RHEBI Expression in Embryonic and Postnatal Mouse

Ras homolog enriched in brain (RHEB1) is a member within the superfamily of GTP-binding proteins encoded by the RAS oncogenes. RHEB1 is located at the crossroad of several important pathways including the insulin-signaling pathways and thus plays an important role in different physiological processes. To understand better the physiological relevance of RHEB1 protein, the expres- sion pattern of RHEB1 was analyzed in both embryonic (at E3.5–E16.5) and adult (1-month old) mice. RHEB1 immu- nostaining and X-gal staining were used for wild-type and Rheb1 gene trap mutant mice, respectively. These inde- pendent methods revealed similar RHEB1 expression pat- terns during both embryonic and postnatal developments. Ubiquitous uniform RHEB1/β-gal and/or RHEB1 expres- sion was seen in preimplantation embryos at E3.5 and post- implantation embryos up to E12.5. Between stages E13.5 and E16.5, RHEB1 expression levels became complex: In particular, strong expression was identified in neural tis- sues, including the neuroepithelial layer of the mesenceph- alon, telencephalon, and neural tube of CNS and dorsal root ganglia. In addition, strong expression was seen in certain peripheral tissues including heart, intestine, muscle, and urinary bladder. Postnatal mice have broad spatial RHEB1 expression in different regions of the cerebral cortex, sub- cortical regions (including hippocampus), olfactory bulb, medulla oblongata, and cerebellum (particularly in Purkinje cells). Significant RHEB1 expression was also viewed in internal organs including the heart, intestine, urinary blad- der, and muscle. Moreover, adult animals have complex tis- sue- and organ-specific RHEB1 expression patterns with different intensities observed throughout postnatal develop- ment. Its expression level is in general comparable in CNS and other organs of mouse. Thus, the expression pattern of RHEB1 suggests that it likely plays a ubiquitous role in the development of the early embryo with more tissue-specific roles in later development

RHEB1 Expression in Embryonic and Postnatal Mouse

Ras homolog enriched in brain (RHEB1) is a member within the superfamily of GTP-binding proteins encoded by the RAS oncogenes. RHEB1 is located at the crossroad of several important pathways including the insulin-signaling pathways and thus plays an important role in different physiological processes. To understand better the physiological relevance of RHEB1 protein, the expres-sion pattern of RHEB1 was analyzed in both embryonic (at E3.5–E16.5) and adult (1-month old) mice. RHEB1 immu-nostaining and X-gal staining were used for wild-type and Rheb1 gene trap mutant mice, respectively. These inde-pendent methods revealed similar RHEB1 expression pat-terns during both embryonic and postnatal developments. Ubiquitous uniform RHEB1/β-gal and/or RHEB1 expres-sion was seen in preimplantation embryos at E3.5 and post-implantation embryos up to E12.5. Between stages E13.5 and E16.5, RHEB1 expression levels became complex: In particular, strong expression was identified in neural tis-sues, including the neuroepithelial layer of the mesenceph-alon, telencephalon, and neural tube of CNS and dorsal root ganglia. In addition, strong expression was seen in certain peripheral tissues including heart, intestine, muscle, and urinary bladder. Postnatal mice have broad spatial RHEB1 expression in different regions of the cerebral cortex, sub-cortical regions (including hippocampus), olfactory bulb, medulla oblongata, and cerebellum (particularly in Purkinje cells). Significant RHEB1 expression was also viewed in internal organs including the heart, intestine, urinary blad-der, and muscle. Moreover, adult animals have complex tis-sue- and organ-specific RHEB1 expression patterns with different intensities observed throughout postnatal develop-ment. Its expression level is in general comparable in CNS and other organs of mouse. Thus, the expression pattern of RHEB1 suggests that it likely plays a ubiquitous role in the development of the early embryo with more tissue-specific roles in later development

Possible origins of macroscopic left-right asymmetry in organisms

I consider the microscopic mechanisms by which a particular left-right (L/R) asymmetry is generated at the organism level from the microscopic handedness of cytoskeletal molecules. In light of a fundamental symmetry principle, the typical pattern-formation mechanisms of diffusion plus regulation cannot implement the "right-hand rule"; at the microscopic level, the cell's cytoskeleton of chiral filaments seems always to be involved, usually in collective states driven by polymerization forces or molecular motors. It seems particularly easy for handedness to emerge in a shear or rotation in the background of an effectively two-dimensional system, such as the cell membrane or a layer of cells, as this requires no pre-existing axis apart from the layer normal. I detail a scenario involving actin/myosin layers in snails and in C. elegans, and also one about the microtubule layer in plant cells. I also survey the other examples that I am aware of, such as the emergence of handedness such as the emergence of handedness in neurons, in eukaryote cell motility, and in non-flagellated bacteria.Comment: 42 pages, 6 figures, resubmitted to J. Stat. Phys. special issue. Major rewrite, rearranged sections/subsections, new Fig 3 + 6, new physics in Sec 2.4 and 3.4.1, added Sec 5 and subsections of Sec

The Maternal-Effect Gene cellular island Encodes Aurora B Kinase and Is Essential for Furrow Formation in the Early Zebrafish Embryo

Females homozygous for a mutation in cellular island (cei) produce embryos with defects in cytokinesis during early development. Analysis of the cytoskeletal events associated with furrow formation reveal that these defects include a general delay in furrow initiation as well as a complete failure to form furrow-associated structures in distal regions of the blastodisc. A linkage mapping-based candidate gene approach, including transgenic rescue, shows that cei encodes the zebrafish Aurora B kinase homologue. Genetic complementation analysis between the cei mutation and aurB zygotic lethal mutations corroborate gene assignment and reveal a complex nature of the maternal-effect cei allele, which appears to preferentially affect a function important for cytokinesis in the early blastomeres. Surprisingly, in cei mutant embryos a short yet otherwise normal furrow forms in the center of the blastodisc. Furrow formation is absent throughout the width of the blastodisc in cei mutant embryos additionally mutant for futile cycle, which lack a spindle apparatus, showing that the residual furrow signal present in cei mutants is derived from the mitotic spindle. Our analysis suggests that partially redundant signals derived from the spindle and astral apparatus mediate furrow formation in medial and distal regions of the early embryonic blastomeres, respectively, possibly as a spatial specialization to achieve furrow formation in these large cells. In addition, our data also suggest a role for Cei/AurB function in the reorganization of the furrow-associated microtubules in both early cleavage- and somite-stage embryos. In accordance with the requirement for cei/aurB in furrow induction in the early cleavage embryo, germ plasm recruitment to the forming furrow is also affected in embryos lacking normal cei/aurB function

A direct role for SNX9 in the biogenesis of filopodia.

Filopodia are finger-like actin-rich protrusions that extend from the cell surface and are important for cell-cell communication and pathogen internalization. The small size and transient nature of filopodia combined with shared usage of actin regulators within cells confounds attempts to identify filopodial proteins. Here, we used phage display phenotypic screening to isolate antibodies that alter the actin morphology of filopodia-like structures (FLS) in vitro. We found that all of the antibodies that cause shorter FLS interact with SNX9, an actin regulator that binds phosphoinositides during endocytosis and at invadopodia. In cells, we discover SNX9 at specialized filopodia in Xenopus development and that SNX9 is an endogenous component of filopodia that are hijacked by Chlamydia entry. We show the use of antibody technology to identify proteins used in filopodia-like structures, and a role for SNX9 in filopodia

Femtosecond laser scribing of sapphire at wavelength 1040 and 520 nm

Резка сапфира в настоящее время является одной из крупнейшей развивающейся области лазерной обработки материалов. Сапфир является одним из самых твердых прозрачных материалов. Его механические и оптические свойства сделали его идеальной и ценной основой для создания различных устройств, например, таких как защитные стекла для часов, дисплеи мобильных устройств, защитные стекла для камер и подложки для светодиодов и транзисторов. Среди существующих способов резки с помощью лазерных или алмазных инструментов, фемтосекундное лазерное скрайбирование является ногообещающей технологией, поскольку эта технология обладает уникальной способностью производить высоколокализованную объемную модификацию благодаря нелинейному поглощению. Резка сапфира твердотельными лазерами хорошо известна уже в течение многих лет и стала современным промышленным процессом. Однако скорость и качество процесса резки до сих пор ограничены, а эксплуатационные расходы относительно высоки. Целью работы, результаты которой представлены в рамках данной статьи, является улучшение скорости и качества резки. В статье описаны результаты исследования фемтосекундного лазерного скрайбирования сапфира при длинах волн 1040 и 520 нм с последующим жидкостным травлением в смеси азотной и плавиковой кислот для выявления формирующихся дефектов и трещин. Морфология поверхности сапфира, подвергнутого лазерной абляции, оценена методом сканирующей электронной микроскопии. Показано, что на основной частоте материал эффективно удаляется с поверхности, однако при этом формируются расходящиеся по поверхности трещины на расстояние до 40 мкм. Использование второй гармоники дало более аккуратные и глубокие резы по сравнению с основной частотой при той же энергии импульса, что обусловлено меньшей размерностью многофотонных процессов. При этом формируются анизотропные трещины, расходящиеся в объем материала. Таким образом, показаны возможности применения фемтосекундной лазерной абляции в технологических процессах скрайбирования для изготовления устройств на основе сапфира. Sapphire cutting is one of the largest markets in laser materials processing. Since sapphire is one of the hardest transparent materials its mechanical and optical properties made it the ideal choice for use in the production of various devices, such as LEDs and transistors, cover glasses of watches and mobile devices. Among existing laser- or diamond-based tools solutions, femtosecond laser scribing appear as a promising technology since this technology has the unique capacity to produce highly localized bulk modification owing to non-linear absorption. Sapphire cutting with solid-state lasers is well known for many years and has become a modern industrial process. However, achievable process speed and cut quality are still limited. The femtosecond laser scribing of sapphire was studied at wavelengths of 1040 and 520 nm, followed by wet etching in HNO3/HF solution to identify emerging defects. The morphology of the laser ablated sapphire surface was evaluated by scanning electron microscopy. It was shown that at the wavelength of 1040nm, the material was effectively removed from the surface; however, cracks on the surface were formed. The use of the second harmonic gave more accurate and deep cuts compared with the main frequency at the same conditions. At the wavelength of 520 nm, the cracks were formed anisotropically inside the volume of the material. Therefore, there is a potential application of the femtosecond laser scribing for the fabrication of sapphire-based devices

Low Frequency Vibrations Disrupt Left-Right Patterning in the Xenopus Embryo

The development of consistent left-right (LR) asymmetry across phyla is a fascinating question in biology. While many pharmacological and molecular approaches have been used to explore molecular mechanisms, it has proven difficult to exert precise temporal control over functional perturbations. Here, we took advantage of acoustical vibration to disrupt LR patterning in Xenopus embryos during tightly-circumscribed periods of development. Exposure to several low frequencies induced specific randomization of three internal organs (heterotaxia). Investigating one frequency (7 Hz), we found two discrete periods of sensitivity to vibration; during the first period, vibration affected the same LR pathway as nocodazole, while during the second period, vibration affected the integrity of the epithelial barrier; both are required for normal LR patterning. Our results indicate that low frequency vibrations disrupt two steps in the early LR pathway: the orientation of the LR axis with the other two axes, and the amplification/restriction of downstream LR signals to asymmetric organs