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

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Wednesday, February 3rd, 2016
10:56 am
SBU Alum Looks Deep in the Amazon for Clues to Climate Change
Stony Brook University, Kolby's PhD alma mater recently created this nice feature about our research in the Amazon forest.
10:52 am
Bem Vindo 2016!
We said goodbye to 2015 and welcomed in 2016 in our favorite way - with our beloved best friends and puppies camping, exploring, and stand up paddling (SUP) on an enchanted ephemeral island in Anavilhana's National Park, a massive fresh water archipeligo on the Rio Negro, Amazônia.
Wednesday, November 18th, 2015
7:52 pm
Caras de Caxiuãna - a science adventure
After three years and two countries, the epic 3 year adventure called the GoAmazon GECO 2014/5 project came to a close this month. We celebrated in style with one last field campaign in Caxiuãna - a 2 day boat trip from Belem, Pará into the heart of the eastern Amazon. This project marks many epic milestones for us individually, together as a family, and scientifically. Here is the 17 minute tribute: https://www.dropbox.com/s/gtmr7bpu7fq3san/caras_de_caxiuana_oct2015.mov?dl=0

Sunday, October 4th, 2015
8:22 am
On Friday, 2 Oct 2015, the US Ambassador to Brazil came to see Kolby's lab and learn about his group's research!
Her name is Liliana Ayalde (http://brazil.usembassy.gov/about-us/the-ambassador.html). At the white board, Kolby described some cool new research we are working on, and then showed her one of the methods he developed to collect samples in the field.
8:17 am
Searching the Amazon for Climate change clues
Links to the articles published about the GoAmazon GECO and NGEE Tropics projects, their goals, and their science.

8:13 am
Green Leaf Volatile Emissions during High Temp and Drought Stress in a Central Amazon Rainforest
Prolonged drought stress combined with high leaf temperatures can induce programmed leaf senescence involving lipid peroxidation, and the loss of net carbon assimilation during early stages of tree mortality. Periodic droughts are known to induce widespread tree mortality in the Amazon rainforest, but little is known about the role of lipid peroxidation during drought-induced leaf senescence. In this study, we present observations of green leaf volatile (GLV) emissions during membrane peroxidation processes associated with the combined effects of high leaf temperatures and drought-induced leaf senescence from individual detached leaves and a rainforest ecosystem in the central Amazon. Temperature-dependent leaf emissions of volatile terpenoids were observed during the morning, and together with transpiration and net photosynthesis, showed a post-midday depression. This post-midday depression was associated with a stimulation of C5 and C6 GLV emissions, which continued to increase throughout the late afternoon in a temperature-independent fashion. During the 2010 drought in the Amazon Basin, which resulted in widespread tree mortality, green leaf volatile emissions (C6 GLVs) were observed to build up within the forest canopy atmosphere, likely associated with high leaf temperatures and enhanced drought-induced leaf senescence processes. The results suggest that observations of GLVs in the tropical boundary layer could be used as a chemical sensor of reduced ecosystem productivity associated with drought stress.

Full article: http://www.mdpi.com/2223-7747/4/3/678

Kolby J. Jardine 1,*, Jeffrey Q. Chambers 1,2,†, Jennifer Holm 1,†, Angela B. Jardine 3,†, Clarissa G. Fontes 2,†, Raquel F. Zorzanelli 3,†, Kimberly T. Meyers 4,†, Vinicius Fernadez de Souza 3,†, Sabrina Garcia 3,†, Bruno O. Gimenez 3,†, Luani R. de O. Piva 3,†, Niro Higuchi 3,†, Paulo Artaxo 5,†, Scot Martin 6,7,† and Antônio O. Manzi 3,†
8:10 am
Atmospheric benzenoid emissions from plants rival those from fossil fuels
Despite the known biochemical production of a range of aromatic compounds by plants and the presence of benzenoids in floral scents, the emissions of only a few benzenoid compounds have been reported from the biosphere to the atmosphere. Here, using evidence from measurements at aircraft, ecosystem, tree, branch and leaf scales, with complementary isotopic labeling experiments, we show that vegetation (leaves, flowers, and phytoplankton) emits a wide variety of benzenoid compounds to the atmosphere at substantial rates. Controlled environment experiments show that plants are able to alter their metabolism to produce and release many benzenoids under stress conditions. The functions of these compounds remain unclear but may be related to chemical communication and protection against stress. We estimate the total global secondary organic aerosol potential from biogenic benzenoids to be similar to that from anthropogenic benzenoids (~10 Tg y(-1)), pointing to the importance of these natural emissions in atmospheric physics and chemistry.
Atmospheric benzenoid emissions from plants rival those from fossil fuels (PDF Download Available). Available from: http://www.researchgate.net/publication/280027378_Atmospheric_benzenoid_emissions_from_plants_rival_those_from_fossil_fuels [accessed Oct 4, 2015].

Misztal, P. K., Hewitt, C. N., Wildt, J., Blande, J. D., Eller, A. S. D., Fares, S., Gentner, D. R., Gilman, J. B., Graus, M., Greenberg, J., Guenther, A. B., Hansel, A., Harley, P., Huang, M., Jardine, K., Karl, T., Kaser, L., Keutsch, F. N., Kiendler-Scharr, A., Kleist, E., Lerner, B. M., Li, T., Mak, J., Nölscher, A. C., Schnitzhofer, R., Sinha, V., Thornton, B., Warneke, C., Wegener, F., Werner, C., Williams, J., Worton, D. R., Yassaa, N., and Goldstein, A. H. Scientific Reports, 5, 12064, 10.1038/srep12064, 2015.
8:02 am
Kolby interview for Brazilian Medical TV series
Kolby and his students' parts are from ~16-21 minutes. The video intro shows Manaus life, the famous Theatre Amazônas, and the historic fish market showing some of the many fresh daily catches from the great rivers that surround the city. The overall context of this episode is the mysteries that the Amazon forest has and how these discoveries may apply to modern medicine:
7:38 am
Great Allegheny Passage and C&O Towpath (July 2015)
The GAP-CO Trail runs from 340 miles from Pittsburg, PA to Washington, D.C. across historic and beautiful lands in the eastern US. The GAP covers the first 150 miles and is a rails to trails masterpiece! The C&O is more wild and rugged with wagon wheel 2 tracks dating back to George Washington's days and concrete pathways that hang out over the river.
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?

IMAG1710 RPXD0545 SNV10288
      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
IMAG1302 IMAG0925 DSC00929
                    Berkeley Hillbillies                                                     Re-CALI-bration!                                                 Lost Coast California

DSC00485 DSC01003 DSC01368
                    Big Sur Wilderness                                       Bird Sanctuary, OR                                 Berkeley-GRC-Yosemite 2014

Canadian Adventures
DSC00896 DSC02234 DSCN3069
          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
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