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Adey A.,University of Washington | Morrison H.G.,The Marine Biological Laboratory | Asan,BGI Shenzhen | Xun X.,BGI Shenzhen | And 7 more authors.
Genome Biology | Year: 2010

We characterize and extend a highly efficient method for constructing shotgun fragment libraries in which transposase catalyzes in vitro DNA fragmentation and adaptor incorporation simultaneously. We apply this method to sequencing a human genome and find that coverage biases are comparable to those of conventional protocols. We also extend its capabilities by developing protocols for sub-nanogram library construction, exome capture from 50 ng of input DNA, PCR-free and colony PCR library construction, and 96-plex sample indexing.

News Article | November 14, 2016
Site: www.eurekalert.org

WOODS HOLE, Mass. -- While scientists and policy experts debate the impacts of global warming, the Earth's soil is releasing roughly nine times more carbon dioxide to the atmosphere than all human activities combined. This huge carbon flux from soil -- due to the natural respiration of soil microbes and plant roots -- begs one of the central questions in climate change science. As the global climate warms, will soil respiration rates increase, adding even more carbon dioxide to the atmosphere and accelerating climate change? Previous experimental studies of this question have not produced a consensus, prompting Marine Biological Laboratory scientists Joanna Carey, Jianwu Tang and colleagues to synthesize the data from 27 studies across nine biomes, from the desert to the Arctic. Their analysis is published this week in Proceedings of the National Academy of Sciences. This represents the largest dataset to date of soil respiration response to experimental warming. One prediction from this synthesis is that rising global temperatures result in regionally variable responses in soil respiration, with colder climates being considerably more responsive. "Consistently across all biomes, we found that soil respiration increased with soil temperature up to about 25° C (77° F)," says Carey, a postdoctoral scientist in the MBL Ecosystems Center. Above the 25° C threshold, respiration rates decreased with further increases in soil temperature. "That means the Arctic latitudes, where soil temperatures rarely, if ever, reach 25° C , will continue to be most responsive to climate warming. Because there is so much carbon stored in frozen soils of the Arctic, this has really serious repercussions for future climate change," Carey says. The team also found that soil microbes in experimental warming studies showed no sign of adaptation -- meaning a muted respiration response to rising temperatures -- in all of the biomes studied, except desert and boreal forest. This indicates that "soils will typically respond strongly to increasing temperature by releasing more carbon dioxide," says Tang, lead investigator of the study. To understand how global carbon in soils will respond to climate change, the authors stress, more data are needed from under- and non-represented regions, especially the Arctic and the tropics. Other MBL scientists who contributed to this study include Mary Heskel, Jerry Melillo, Edward B. Rastetter, and Gaius R. Shaver. Carey, Joanna A. et al (2016) Temperature response of soil respiration largely unaltered with experimental warming. Proc. Natl. Acad. Sci. DOI: 10.1073/pnas.1605365113 The Marine Biological Laboratory (MBL) is dedicated to scientific discovery - exploring fundamental biology, understanding marine biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.

News Article | December 27, 2016
Site: www.eurekalert.org

WOODS HOLE, MASS. -- One of the most profound changes in the life of an organism is what Antonio Giraldez calls "embryonic puberty": the stage when an early embryo stops taking instructions from its mother on how to develop and activates its own genome to kick out those instructions instead. This critical stage, called the maternal-to-zygote transition, happens in all embryos, from sea anemones to humans. Yet how it is regulated in the embryo is not yet known. This week in Nature Methods, Giraldez and colleagues present a novel way to decipher the genetic code that embryos use to instruct many maternal messages (mRNAs) to be destroyed, and others to become stabilized. Giraldez is a Professor of Genetics at Yale University School of Medicine and was a 2016 Research Awardee in the MBL Whitman Center, where he conducted part of this research. The method, called RESA (RNA Element Selection Assay), has broad applications, Giraldez says. "It's a modular method we can use in many contexts, depending on the question the investigator wants to ask, to dissect the meaning of different parts of the genome. It is a molecular 'Rosetta stone' to help us decode the functional elements within the genome." In this case, they used RESA to detect the stability or decay of millions of RNA fragments in the zebrafish embryo, which in turn gave information about the genes that are shut down or activated during the maternal-to-zygote transition. The team developed RESA in zebrafish, Giraldez says, "but the goal is to use it across many different species, so we can find meaningful 'words' or instructions in the genome from squid to mouse to human." He plans to continue testing RESA in squid and other marine model systems at the MBL next year, such as sea urchin and ctenophores. "That's the part I am most excited about, is the MBL offers us this opportunity to test RESA across many species," Giraldez says. "That is priceless; it's work that cannot be done anywhere else in the world." "The MBL made me realize that we know so much about a few species, and so little about so many other species," Giraldez says. "But now, with new sequencing technologies like RESA, we can really understand biology much more broadly across species. That is really a new revolution." The Marine Biological Laboratory (MBL) is dedicated to scientific discovery - exploring fundamental biology, understanding marine biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.

Jaffe L.F.,The Marine Biological Laboratory
Cell Calcium | Year: 2010

Calcium waves are propagated in five main speed ranges which cover a billion-fold range of speeds. We define the fast speed range as 3-30μm/s after correction to a standard temperature of 20°C. Only waves which are not fertilization waves are considered here. 181 such cases are listed here. These are through organisms in all major taxa from cyanobacteria through mammals including human beings except for those through other bacteria, higher plants and fungi. Nearly two-thirds of these speeds lie between 12 and 24μm/s. We argue that their common mechanism in eukaryotes is a reaction-diffusion one involving calcium-induced calcium release, in which calcium waves are propagated along the endoplasmic reticulum. We propose that the gliding movements of some cyanobacteria are driven by fast calcium waves which are propagated along their plasma membranes. Fast calcium waves may drive materials to one end of developing embryos by cellular peristalsis, help coordinate complex cell movements during development and underlie brain injury waves. Moreover, we continue to argue that such waves greatly increase the likelihood that chronic injuries will initiate tumors and cancers before genetic damage occurs. Finally we propose numerous further studies. © 2010.

Ripps H.,Illinois College | Chappell R.L.,The Marine Biological Laboratory
Molecular vision | Year: 2014

This review covers a broad range of topics related to the actions of zinc on the cells of the vertebrate retina. Much of this review relies on studies in which zinc was applied exogenously, and therefore the results, albeit highly suggestive, lack physiologic significance. This view stems from the fact that the concentrations of zinc used in these studies may not be encountered under the normal circumstances of life. This caveat is due to the lack of a zinc-specific probe with which to measure the concentrations of Zn(2+) that may be released from neurons or act upon them. However, a great deal of relevant information has been garnered from studies in which Zn(2+) was chelated, and the effects of its removal compared with findings obtained in its presence. For a more complete discussion of the consequences of depletion or excess in the body's trace elements, the reader is referred to a recent review by Ugarte et al. in which they provide a detailed account of the interactions, toxicity, and metabolic activity of the essential trace elements iron, zinc, and copper in retinal physiology and disease. In addition, Smart et al. have published a splendid review on the modulation by zinc of inhibitory and excitatory amino acid receptor ion channels.

Ripps H.,Illinois College | Ripps H.,The Marine Biological Laboratory | Shen W.,Florida Atlantic University
Molecular Vision | Year: 2012

Taurine is an organic osmolyte involved in cell volume regulation, and provides a substrate for the formation of bile salts. It plays a role in the modulation of intracellular free calcium concentration, and although it is one of the few amino acids not incorporated into proteins, taurine is one of the most abundant amino acids in the brain, retina, muscle tissue, and organs throughout the body. Taurine serves a wide variety of functions in the central nervous system, from development to cytoprotection, and taurine deficiency is associated with cardiomyopathy, renal dysfunction, developmental abnormalities, and severe damage to retinal neurons. All ocular tissues contain taurine, and quantitative analysis of ocular tissue extracts of the rat eye revealed that taurine was the most abundant amino acid in the retina, vitreous, lens, cornea, iris, and ciliary body. In the retina, taurine is critical for photoreceptor development and acts as a cytoprotectant against stress-related neuronal damage and other pathological conditions. Despite its many functional properties, however, the cellular and biochemical mechanisms mediating the actions of taurine are not fully known. Nevertheless, considering its broad distribution, its many cytoprotective attributes, and its functional significance in cell development, nutrition, and survival, taurine is undoubtedly one of the most essential substances in the body. Interestingly, taurine satisfies many of the criteria considered essential for inclusion in the inventory of neurotransmitters, but evidence of a taurine-specific receptor has yet to be identified in the vertebrate nervous system. In this report, we present a broad overview of the functional properties of taurine, some of the consequences of taurine deficiency, and the results of studies in animal models suggesting that taurine may play a therapeutic role in the management of epilepsy and diabetes. © 2012 Molecular Vision.

Hoang Q.V.,University of Illinois at Chicago | Qian H.,University of Illinois at Chicago | Ripps H.,University of Illinois at Chicago | Ripps H.,The Marine Biological Laboratory
Molecular Vision | Year: 2010

Purpose: The gap junctions (GJs) mediating direct cell-cell interaction are formed by clusters of membrane-spanning proteins known as connexins (Cxs). These channels play a key role in signal transmission, and their permeability, time-, and voltage-dependence are governed by the properties of the specific Cxs forming the gap junctions. Retinal pigment epithelium (RPE) cells express Cx43 and Cx46. Here, we employed a heterologous expression system to explore the functional properties of the hemichannels and GJs that could be formed by different combinations of these Cxs. Specifically, we examined the response kinetics of GJs formed by pairing cells expressing Cx43 or Cx46, or those expressing both, i.e., designated as Cx43·Cx46. Methods: The Xenopus oocyte expression system and a two-electrode voltage clamp technique were used to study the properties of hemichannels and GJs formed in oocytes transfected with Cx43 and/or Cx46 mRNA. Results: Depolarizing voltages activated hemicurrents of similar amplitude from single oocytes transfected with Cx46 or Cx43·Cx46, but not in oocytes expressing Cx43 alone. Incorporating Cx43 with Cx46 altered the gating charge, but not the voltage sensitivity of the hemichannels. In addition, Cx43·Cx46 hemichannel currents exhibited faster activation kinetics than homomeric Cx46 hemichannels. Both homotypic GJs formed by Cx43 and Cx46, and heteromeric Cx43·Cx46 GJs exhibited large junctional conductances with amplitudes of 6.5±3.0 μS (Cx43), 8.9±3.4 μS (Cx46), and 8.5±1.8 μS (Cx43·46); a significantly lower conductance (1.8±0.7 μS) was observed for heterotypic GJs formed by Cx43 and Cx46. There were also differences in their gating kinetics. Whereas the kinetics of homotypic Cx46 could be described by a single exponential function (τ =0.91 s), double exponential functions were required for homotypic Cx43 (τ1=0.24, τ2=3.4 s), heterotypic Cx43/Cx46 (τ1=0.29, τ2=3.6 s), and heteromeric Cx43·Cx46/Cx43·Cx46 (τ1=1.2, τ2=8.1 s) junctions. Conclusions: The failure of oocytes expressing Cx43 to exhibit hemichannel activity is an intrinsic membrane property of this Cx, and cannot be attributed to a lack of expression; western blot analysis showed clearly that Cx43 was expressed in oocytes in which it was injected. Our results provide further evidence that Cx43 and Cx46 form both heterotypic and heteromeric channels when co-expressed, an indication that various combinations of Cxs may participate in gap-junctional communication between RPE cells. © 2010 Molecular Vision.

The Regents Of The University Of California, The Marine Biological Laboratory and The University Of Texas System | Date: 2014-11-07

Methods for the treatment of spinal cord injury or traumatic brain injury are provided. In certain embodiments, the methods include the use of a molecular tweezers and/or nucleobase oligomer capable of inhibiting the accumulation or aggregation of one or more amyloidogenic proteins and/or synuclein proteins. Examples of treatments that may inhibit accumulation or aggregation of one or more amyloidogenic proteins and/or synuclein proteins include treatment with a synuclein antisense nucleobase oligomer or treatment with the molecular tweezers CLR01. These treatments may improve outcomes of spinal cord surgery or traumatic brain injury, including, without limitation, neuronal survival, neuronal regeneration, and recovery of neuronal functions.

The Marine Biological Laboratory | Date: 2011-07-12

A method of identifying the taxonomic or functional classification of cells in situ involves labeling the cells with a set of nucleic acid probes and performing combinatorial fluorescence microscopic imaging. The set of probes contains groups of either two or three probes that bind to a taxon-specific or function-specific nucleotide sequence. Each probe of a group of probes is labeled with a distinct fluorescent label, and each group corresponds to a unique combination of labels, which can be detected across the image and serves to identify cells having a single target sequence, or a set of target sequences, that are characteristic of a unique taxonomic or functional classification. The combinatorial labeling and spectral imaging approach greatly expands the number of different classifications that can be identified simultaneously in a single image of a collection of cells. The methods and probe sets of the invention can be used to rapidly identify microbes, study their ecological relationships, screen for novel antibiotics, and identify pathogens.

The Marine Biological Laboratory | Date: 2014-05-12

Embodiments of various aspects described herein relate to methods and systems for detecting exocytosis or endocytosis of a target molecule from or into a population of cells, in part based on impedance analysis of the population of cells after they are exposed to an alternating current applied at two or more frequencies or to a repetitive voltage waveform. In some embodiments, the methods and systems described herein can be used for assessing viability and/or potency of the population of cells, and/or identifying a secretagogue for the target molecule released from the population of cells.

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