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Below are the 20 most recent journal entries recorded in kolbala's LiveJournal:

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Sunday, April 5th, 2015
3:35 pm
1:31 pm
1:26 pm
Saturday, March 7th, 2015
8:49 am
Highly reactive light-dependent monoterpenes in the Amazon

Highly reactive light-dependent monoterpenes in the Amazon

    A. B. Jardine1,*, K. J. Jardine2, J. D Fuentes3, S. T. Martin4, G. Martins1, F. Durgante1, V. Carneiro1, N. Higuchi1, A. O. Manzi1 and J. Q. Chambers2,5

Article first published online: 6 MAR 2015, DOI: 10.1002/2014GL062573

Keywords: secondary organic aerosols; vertical forest structure; ozonolysis; atmospheric oxidation; light-dependent monoterpenes; tropical VOC emissions


Despite orders of magnitude difference in atmospheric reactivity and great diversity in biological functioning, little is known about monoterpene speciation in tropical forests. Here we report vertically resolved ambient air mixing ratios for 12 monoterpenes in a central Amazon rainforest including observations of the highly reactive cis-β-ocimene (160 ppt), trans-β-ocimene (79 ppt), and terpinolene (32 ppt) which accounted for an estimated 21% of total monoterpene composition yet 55% of the upper canopy monoterpene ozonolysis rate. All 12 monoterpenes showed a mixing ratio peak in the upper canopy, with three demonstrating subcanopy peaks in 7 of 11 profiles. Leaf level emissions of highly reactive monoterpenes accounted for up to 1.9% of photosynthesis confirming light-dependent emissions across several Amazon tree genera. These results suggest that highly reactive monoterpenes play important antioxidant roles during photosynthesis in plants and serve as near-canopy sources of secondary organic aerosol precursors through atmospheric photooxidation via ozonolysis.


Sunday, February 1st, 2015
8:45 pm
4:46 pm
2:09 pm
Dynamic Balancing of Isoprene Carbon Sources
Dynamic Balancing of Isoprene Carbon Sources Reflects Photosynthetic and Photorespiratory Responses to Temperature Stress
K. Jardine et. al. 2014, Plant Physiology

The volatile gas isoprene is emitted in teragrams per annum quantities from the terrestrial biosphere and exerts a large effect on atmospheric chemistry. Isoprene is made primarily from recently fixed photosynthate; however, alternate carbon sources play an important role, particularly when photosynthate is limiting. We examined the relative contribution of these alternate carbon sources under changes in light and temperature, the two environmental conditions that have the strongest influence over isoprene emission. Using a novel real-time analytical approach that allowed us to examine dynamic changes in carbon sources, we observed that relative contributions do not change as a function of light intensity. We found that the classical uncoupling of isoprene emission from net photosynthesis at elevated leaf temperatures is associated with an increased contribution of alternate carbon. We also observed a rapid compensatory response where alternate carbon sources compensated for transient decreases in recently fixed carbon during thermal ramping, thereby maintaining overall increases in isoprene production rates at high temperatures. Photorespiration is known to contribute to the decline in net photosynthesis at high leaf temperatures. A reduction in the temperature at which the contribution of alternate carbon sources increased was observed under photorespiratory conditions, while photosynthetic conditions increased this temperature. Feeding [2-13C]glycine (a photorespiratory intermediate) stimulated emissions of [13C1–5]isoprene and 13CO2, supporting the possibility that photorespiration can provide an alternate source of carbon for isoprene synthesis. Our observations have important implications for establishing improved mechanistic predictions of isoprene emissions and primary carbon metabolism, particularly under the predicted increases in future global temperatures.

1:30 pm
Dimethyl Sulfide in the Green Ocean Amazon

Dimethyl sulfide in the Amazon Forest


Surface-to-atmosphere emissions of dimethyl sulfide (DMS) may impact global climate through the formation of gaseous sulfuric acid, which can yield secondary sulfate aerosols and contribute to new particle formation. While oceans are generally considered the dominant sources of DMS, a shortage of ecosystem observations prevents an accurate analysis of terrestrial DMS sources. Using mass spectrometry, we quantified ambient DMS mixing ratios within and above a primary rainforest ecosystem in the central Amazon Basin in real-time (2010–2011) and at high vertical resolution (2013–2014). Elevated but highly variable DMS mixing ratios were observed within the canopy, showing clear evidence of a net ecosystem source to the atmosphere during both day and night in both the dry and wet seasons. Periods of high DMS mixing ratios lasting up to 8 h (up to 160 parts per trillion (ppt)) often occurred within the canopy and near the surface during many evenings and nights. Daytime gradients showed mixing ratios (up to 80 ppt) peaking near the top of the canopy as well as near the ground following a rain event. The spatial and temporal distribution of DMS suggests that ambient levels and their potential climatic impacts are dominated by local soil and plant emissions. A soil source was confirmed by measurements of DMS emission fluxes from Amazon soils as a function of temperature and soil moisture. Furthermore, light- and temperature-dependent DMS emissions were measured from seven tropical tree species. Our study has important implications for understanding terrestrial DMS sources and their role in coupled land-atmosphere climate feedbacks.

Jardine K, Yañez-Serrano A, Williams J, Kunert N, Jardine A, Taylor T, Abrell L, Artaxo P, Guenther A, Hewitt C.N., House E., Florentino A P, Manzi A, Kesselmeier J, Behrendt T, Veres P R, Derstroff B, Fuentes J, Martin S, Andreae M O (2015) Dimethyl Sulfide in the Amazon Forest, Global Biogeochemical Cycles, early view online.
Sunday, May 11th, 2014
9:53 am
Bidirectional exchange of biogenic volatiles with vegetation
Plant Cell Environ. 2014 Mar 17. doi: 10.1111/pce.12322. [Epub ahead of print]
Bidirectional exchange of biogenic volatiles with vegetation: emission sources, reactions, breakdown and deposition.
Niinemets U, Fares S, Harley P, Jardine K

Biogenic volatile organic compound (BVOC) emissions are widely modelled as inputs to atmospheric chemistry simulations. However, BVOC may interact with cellular structures and neighbouring leaves in a complex manner during volatile diffusion from the sites of release to leaf boundary layer and during turbulent transport to the atmospheric boundary layer. Furthermore, recent observations demonstrate that the BVOC emissions are bidirectional, and uptake and deposition of BVOC and their oxidation products are the rule rather than the exception. This review summarizes current knowledge of within-leaf reactions of synthesized volatiles with reactive oxygen species (ROS), uptake, deposition and storage of volatiles, and their oxidation products as driven by adsorption on leaf surface and solubilization and enzymatic detoxification inside leaves. The available evidence indicates that because of the reactions with ROS and enzymatic metabolism, the BVOC gross production rates are much larger than previously thought. The degree to which volatiles react within leaves and can be potentially taken up by vegetation depends upon compound reactivity, physicochemical characteristics, as well as upon their participation in leaf metabolism. We argue that future models should be based upon the concept of bidirectional BVOC exchange and consider modification of BVOC sink/source strengths by within-leaf metabolism and storage.
Link to article
Sunday, April 20th, 2014
1:07 am
Amazon Adventures
Amazon Adventures
2014-04-26 18.03.50 DSC00339 DSC01219 DSC00139
  Rio Urubu (april 2014)                          Rio Preto Da Eva                                                           Rio Uatuma                                                             What SUP?

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      Geco/GoAmazon (2012-2013)                           LBNL-INPA Laboratory (Geco 2013)             Lessons from the Amazon (AMAZE 2008)

DSC04444 Encontro Das Aguas RPXD0497
Vida Brasilera (BrazilianAir 2010-11)       Encontra Das Aguas (2013)                                     GoAmazon Field and Lab Studies (2013)

DSC01103 2014-02-18 18.27.38 2014-03-13 05.56.38-2
Alter do Chão (Natal 2013)             GoAmazon Opening Ceremony       Seasonal Vegetation Dynamics at ZF2

SUP in the flooded forests (2014)
Saturday, October 12th, 2013
11:38 pm
Team Jardine Videos! (last update 11 May 2014)
West Coast Adventures
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                    Berkeley Hillbillies                                                     Re-CALI-bration!                                                 Lost Coast California

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                    Big Sur Wilderness                                       Bird Sanctuary, OR                                 Berkeley-GRC-Yosemite 2014

Canadian Adventures
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          The Golden Orca (British Columbia)             The Hydrologic Cycle (Trans Canada Trail)                     Great Divide Route (Banff to Glacier)

European Adventures
IMAG0615 DSC02214 S3010047 map
30 days Awake (Germany)         North Sea Cycle Route (Norway)                       Tour de Atlantique (France)                                   The Nature (Finland)

Eastern and Northeastern US Adventures
HPIM1691 HPIM1318 HPIM2116
Catamount Trail                                                   The Sun Rises in the East                               Kentucky Dirty

S3010021 HPIM0499
                      Foreverglades                                                       Me, You, and SIKU

Mexico Adventures
google2 S3010155
                    Yucatan bike tour                               Pursuit of Life, Liberty, and Dihydrogen Monoxide

Rockies and Southwest
2500 miles (Great Divide, Mexico to Canada)                 Great Divide, 2007 (New Mexico)                               Las Jardines Javalinas

DCP03610 DSC02506 DSC01906
Rock Climbing (2000-2004)                                             Chicago Basin, CO                                                             Mount Evans

KolbyAngNCARandDchall2004 044 SNV13428
                        Durango Challenge                                                 Babo-Ang                                                           Rap Rock

I-can-tell-U-ride                                                           Mount Baldy
2:05 pm
Tuesday, September 10th, 2013
11:57 pm
Peixe-Bois! What SUP!?
We have been slowly building up our Amazon SUP skills with the goal of multi-day tours through the igapos and rios na Amazônia. This weekend was our longest distance to date - 12.5 km (~7.5 miles) with a break for an amazing regional lunch at the flutuante Peixe-Boi. We paddled quietly and on alert through sections of the flooded forests, swam in the river when the sun overcooked us, white-knuckeled it through high traffic convergence around the marinas, rested in the shade on the beaches now being exposed as the dry season sets in, and watched the skies build convective storms overhead as we made our way south. You can look at the full set of pictures and join us for an adventure if you want to become a peixe-boi and join our meet up group: the Amazonia Exploradores Igapo (SUP)

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DSC00139 PeixeBoi_08Set2013
Saturday, September 7th, 2013
5:10 pm
Plant Cell and Environment article published

Phytogenic biosynthesis and emission of methyl acetate

Acetylation of plant metabolites fundamentally changes their volatility, solubility and activity as semiochemicals. Here we present a new technique termed dynamic
13C-pulse chasing to track the fate of C1–3 carbon atoms of pyruvate into the biosynthesis and emission of methyl acetate (MA) and CO2. 13C-labelling of MA and CO2 branch emissions respond within minutes to changes in 13C-positionally labelled pyruvate solutions fed through the transpiration stream. Strong 13C-labelling of MA emissions occurred only under pyruvate-2-13C and pyruvate-2,3-13C feeding, but not pyruvate-1-13C feeding. In contrast, strong 13CO2 emissions were only observed under pyruvate-1-13C feeding. These results demonstrate that MA (and other volatile and non- volatile metabolites) derive from the C2,3 atoms of pyruvate while the C1 atom undergoes decarboxylation. The latter is a non-mitochondrial source of CO2 in the light generally not considered in studies of CO2 sources and sinks. Within a tropical rainforest mesocosm, we also observed atmospheric concentrations of MA up to 0.6 ppbv that tracked light and temperature conditions. Moreover, signals partially attrib- uted to MA were observed in ambient air within and above a tropical rainforest in the Amazon. Our study highlights the potential importance of acetyl coenzyme A (CoA) biosynthesis as a source of acetate esters and CO2 to the atmosphere.

citation and link to article: Jardine, K., Wegener, F., Ishida, F., Abrell, L., van Haren, J., Werner, C., “Phytogenic Biosynthesis and Emission of Methyl Acetate,” Plant, Cell & Environment, August 13, 2013.
5:04 pm
Real-Time Monitoring of Plant Metabolism with Dynamic 13C-Pulse Tracing

From the Lawrence Berkeley National Labs Technology Transfer and Intellectual Property site:
"Berkeley Lab researcher Kolby Jardine has invented a versatile technology for rapid, in vivo tracking of carbon metabolism in plants using carbon-13 (13C) tracers with optical or mass spectrometry."

Learn more about Kolby's invention here: http://www.lbl.gov/Tech-Transfer/techs/lbnl2013-110.html
Friday, September 6th, 2013
4:45 pm
New publication in: Journal of Experimental Botany
Emissions of putative isoprene oxidation products from mango branches under abiotic stress http://jxb.oxfordjournals.org/content/64/12/3669.1.abstract?keytype=ref&ijkey=UbytJFksydRHSLI

Abstract: Although several per cent of net carbon assimilation can be re-released as isoprene emissions to the atmosphere by many tropical plants, much uncertainty remains regarding its biological significance. In a previous study, we detected emissions of isoprene and its oxidation products methyl vinyl ketone (MVK) and methacrolein (MACR) from tropical plants under high temperature/light stress, suggesting that isoprene is oxidized not only in the atmosphere but also within plants. However, a comprehensive analysis of the suite of isoprene oxidation products in plants has not been performed and production relationships with environmental stress have not been described. In this study, putative isoprene oxidation products from mango (Mangifera indica) branches under abiotic stress were first identified. High temperature/light and freeze–thaw treatments verified direct emissions of the isoprene oxidation products MVK and MACR together with the first observations of 3-methyl furan (3-MF) and 2-methyl-3-buten-2-ol (MBO) as putative novel isoprene oxidation products. Mechanical wounding also stimulated emissions of MVK and MACR. Photosynthesis under 13CO2 resulted in rapid (<30min) labelling of up to five carbon atoms of isoprene, with a similar labelling pattern observed in the putative oxidation products. These observations highlight the need to investigate further the mechanisms of isoprene oxidation within plants under stress and its biological and atmospheric significance.

cicicitation:citaCitation: KJardine, et. al J. Exp. Bot. (2013) 64 (12): 3669-3679. doi: 10.1093/jxb/ert202 First published online: July 23, 2013
Monday, August 19th, 2013
12:54 am
Boas-vindas de volta à floresta da Amazônia!

We have returned to the forest of the central Amazon for two years. We have spent the past year planning and preparing for the GECO project and are now ready to deploy! While here, we hope to explore the forests by foot, tree, and paddle board! Beleza!!

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Sunday, June 9th, 2013
9:58 pm
Ocean-land interface
There is nothing like the pacific ocean to bring peace and wonder to the heart.

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Tuesday, March 19th, 2013
12:24 am
Sunday, March 3rd, 2013
12:21 pm
fevereiro misto de bay
The set of the Berkeley Rep amazing production of "The Wild Bride"

East and west vantages points of the bay.

The little mangsters cranking out the VOCs

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