- Yeast strains from the Pfaff collection at UC-Davis were tested for their ability to produce ethanol from switchgrass hydrolysate pretreated with ionic liquids. The highest ethanol yield of 70% theoretical was achieved by Wickerhamomyces anomalus. - Adding 200 mM NaCl to growth media increased E. coli growth and isoprenol production 1.5-13 fold in the presence of imidazolium-based ionic liquids. No comparable increase was observed for E. coli MG1655. - A rice mutant (gs9-1) with shorter grain length but unchanged width was identified. Whole genome sequencing identified the gene as a new allele of gs9 involved in cellulose microf

1. Ethanol production in switchgrass hydrolysate by ionic
liquid-tolerant yeasts
Background
• Ionic liquids (ILs) are a promising pretreatment for the conversion
of plant biomass to biofuels and biochemicals.
• Previous work had identified IL-tolerant yeasts in the Pfaff
collection at UC-Davis.
Approach
• IL-tolerant yeasts previously identified in the Pfaff collection were
tested for the ability to produce ethanol from switchgrass.
hydrolysate obtained by pretreatment with ILs and enzymatic
hydrolysis.
Outcomes and Impacts
• A total of 25 yeast strains including four commercial
ethanologenic Saccharomyces cerevisiae strains were tested to
grow and ferment sugars in stepwise screening tests.
• Four yeast strains produced >10 g/L ethanol in laboratory media
containing [C2C1Im][OAc].
• The highest ethanol yield of 70% of theoretical yield was
achieved by Wickerhamomyces anomalus UCDFST 72-248
when grown in hydrolysate with 3.2% residual IL.
• This study demonstrates the value of microbial collections such
as the Pfaff collection for biotechnology application.
Sitepu
et
al.
(2019
Bioresource
Technology
Reports,
doi.org/10.1016/j.biteb.2019.100275

2. NaCl enhances Escherichia coli growth and isoprenol
production in the presence of imidazolium-based ionic
liquids
Background
• Sustainable production of fuels and value-added chemicals from
lignocellulosic biomass in an integrated biorefinery is extremely
important for both energy security and sustainability. One of the
major steps in the conversion of biomass to fuels is pretreatment,
through which plant polysaccharides are made accessible to the
action of hydrolytic enzymes. The use of certain ionic liquids (ILs)
to process biomass is an emerging pretreatment method.
Approach
• Bacteria are intolerant to high concentrations of imidazolium-based
ILs. The effect of NaCl on IL tolerance was tested to see if
chaotropic effects might improve bacterial tolerance.
Outcomes and Impacts
• Addition of 200 mM NaCl to growth media with 50 mM [C4C1Im]Cl
and 50 mM [C4C1Im][OAc] increased growth of for E. coli DH1 and
MG1655 2-6 fold.
• Addition of 200 mM NaCl increased isoprenol production by E. coli
DH1 1.5-13 fold in the presence of imidazolium Ils.
• No comparable increase was observed under the same conditions
for MG1655.
• The inclusion of NaCl enhances the IL tolerance of E. coli strains,
providing a complement to genetic approaches.
Wang
et
al.
(2019)
Bioresource
Technology
Reports,
doi:
10.1016/j.biteb.2019.01.021

3. Parsons
et
al.
(2019)
The
Plant
Cell,
doi:
10.1105/tpc.19.00081
Separating Golgi Proteins from Cis to Trans Reveals
Underlying Properties of Cisternal Localization
Background
• The order of enzymatic activity across Golgi cisternae is essential for
complex molecule biosynthesis.
• However, an inability to separate Golgi cisternae has meant the
cisternal distribution of most resident proteins, and their underlying
localization mechanisms, are unknown.
• Here, we exploit differences in surface charge of intact cisternae to
perform separation of early to late Golgi sub-compartments.
Approach
• We determine protein and glycan abundance profiles across the Golgi.
• Over 390 resident proteins are identified, including 136 new additions,
with over 180 cisternal assignments.
• These assignments provide a means to better understand the
functional roles of Golgi proteins and how they operate sequentially.
Outcomes and Impacts
• This work reveals distinct functional compartmentalization among
resident Golgi proteins.
• Analysis of transmembrane proteins shows several sequence-based
characteristics relating to isoelectric point, hydrophobicity, serine
abundance, and phenylalanine bilayer asymmetry that change across
the Golgi.
• Overall our results suggest that a continuum of features, rather than
discrete rules, guide proteins to earlier or later locations within the
Golgi stack.
Schematic overview of electrophoretic separation profile
analysis of Arabidopsis endomembrane proteins. (A)
Samples enriched in intact endomembranes were separated
by using free-flow electrophoresis (FFE). (B) Total protein
content of FFE fractions was determined via absorption at
280 nm. (C) Endomembrane fractions investigated using
shotgun proteomics. (D) Average FFE abundance profiles for
resident proteins from Golgi, ER and other organelles.

4. Whole-Genome Sequencing Identifies gs9-1
involved in cellulose microfibril deposition
Outcomes
• Identified a rice mutant (gs9-1) whose grain length is shorter
than wild type, but whose grain width remains unchanged.
• Identified the gene associated with the phenotype as a new
allele of the gs9 (Grain Shape gene on Chromosome 9) gene.
Background
• Grain weight is an important agronomic trait for crop
genetic improvement.
• Grain weight encompasses length, width, length-to-
width ratio, and thickness.
• Traditional map-based cloning is very time-
consuming and labor-intensive.
Significance
• Whole genome sequencing facilitated the quick identification of
the gs9-1 allele.
• gs9-1 is a new allele of the BC12/GDD1/MTD1 gene that
encodes a kinesin-like protein involved in cell-cycle progression,
cellulose microfibril deposition and gibberellic acid biosynthesis.
Approach
• Screened a whole-genome-sequenced, fast-neutron-
induced rice mutant population to identify mutants in
grain length..
• Quickly identified the responsible gene using Kitbase
Jiang
et
al.
(2019)
Rice,
doi:
10.1186/s12284-­‐019-­‐0308-­‐8.
G r a i n , p a n i c l e a n d p l a n t
morphology of Kitaake and gs9–1
plants. a. Grains of gs9–1 are
shorter than those of Kitaake
while grain width is slightly
increased. b. The culm brittle
phenotype of gs9–1. c. gs9–1 has
a smaller plant stature than
Kitaake. d. Panicles of gs9–1 are
shorter than those of Kitaake. e.
Quantitative plant height. **
indicates a significant difference
(P < 0.01) using the unpaired
Student’s t-test.
Cell size and number of
grain glume. a. Horizontal
and vertical cell length of
grain glume. b. Horizontal
and vertical cell number of
grain glume epidermis. c
and d. Scanning electron
microscopy of epidermal
cells. (Å~ 300). ** indicates
an extremely significant
d i f f e r e n c e u s i n g t h e
unpaired Student’s t-test

5. Opportunities at the Intersection of Synthetic
Biology, Machine Learning, and Automation
Background
• Our inability to predict the behavior of biological
systems severely hampers progress in
bioengineering and biomedical applications.
Approach
• Machine learning techniques recently reached a
new level of maturity, and are capable of providing
the needed predictive power without a detailed
mechanistic understanding.
• However, they require large amounts of data to be
trained.
• The amount and quality of data required can only
be produced through a combination of synthetic
biology and automation.
Outcomes and Impact
• A sustained investment in the intersection of
synthetic biology, machine learning, and
automation will drive forward predictive biology,
and produce improved machine learning algorithms.
Carbonell
et
al.
(2019)
ACS
Synthe:c
Biology,
doi:
10.1021/acssynbio.8b00540
Machine
learning
and
automaLon
can
be
used
to
improve
the
basic
syntheLc
biology
Design-­‐Build-­‐Test-­‐Learn
(DBTL)
cycle
in
different
ways
SyntheLc
biology,
machine
learning,
and
automaLon
complement
each
other
naturally

6. Outcomes and Impacts
• Up to 85.7% of glucose and 57% of xylose were extracted from MSW
paper/corn stover blend
• The low toxicity of bionic liquids enabled the high efficiency of the
fermentable sugar conversion for six MSW-biomass blends. The obtained
hydrolysates were readily utilized by E. coli to produce MKs with a
maximum titer of 1145 mg/L at 0.2 L scale
• The TEA highlighted that the MK yield cannot be compromised regardless
of the mode of operation (i.e., batch, fed-batch, or even continuous) to
ensure that the MFSP is less than $4/gal.
Background
• There is a significant amount of municipal solid waste (MSW)
produced daily. These MSW supplies are typically less expensive and
could potentially be used as a stand-alone feedstock or as a blending
agent to supplement other biomass inputs
• Saturated and monounsaturated aliphatic MKs in the C11 to C15
length range compatible with diesel engines have been produced
using an engineered E. coli strain
Approach
• Formulated six MSW-biomass blends, including corn stover,
switchgrass, air classified grass clippings, and non-recyclable
paper, and evaluated the sugar yields and MK production resulting
from the bionic liquid-based conversion process.
Process overview of the conversion process
Methyl Ketone from Municipal Solid Waste/Lignocellulosic
Biomass Blends by One-pot Ionic Liquid Pretreatment,
Enzymatic Saccharification, and Escherichia coli
Fermentation
Yan
et
al.
(2019)
ChemSusChem,
doi:
10.1002/cssc.201901084
MK production from the hydrolysates

7. Gupta
et
al.
(2019)
J.
Biol.
Chem.,
doi:
10.1074/jbc.RA119.009239
Water molecules mediate zinc mobility in the bacterial
zinc diffusion channel ZIPB
Background
• Regulated ion diffusion across biological membranes is vital to cell function.
• In a nanoscale ion channel, the active role of discrete water molecules in
modulating hydrodynamic behaviors of individual ions is poorly understood
because of the technical challenge of tracking water molecules through the
channel.
• Here, we report on the results of a hydroxyl radical x-ray footprinting analysis of
water molecules associated with the zinc-selective channel ZIPB from the
Gram-negative bacterium Bordetella bronchiseptica.
Approach
• Irradiating ZIPB by microsecond X-ray pulses activated water molecules to
form covalent hydroxyl radical adducts at nearby residues, which were
identified by bottom-up proteomics to detect residues that interact either with
zinc or water in response to zinc binding.
Outcomes and Impacts
• We found a series of residues exhibiting reciprocal changes in water
accessibility attributed to alternating zinc and water binding (Figure 1).
• We identified a water-reactive pathway that superimposed upon a zinc
translocation pathway consisting of two binuclear metal centers and an interim
zinc-binding site (Figure 2).
• The co-translocation of zinc and water suggested that pore-lining residues
undergo a mode switch between zinc coordination and water binding to confer
zinc mobility.
Key residues involved in metal binding and water interactions.
The residues are mapped in the crystal structure of ZIPB(5) and
colored in red and blue for decreased or increased water
accessibility. Bound Zn, Cd and water molecules are shown in
slate grey, orange and cyan spheres, respectively. (A) The
central binuclear metal center viewed from the extracellular side.
(B) The peripheral binuclear metal center viewed from the
cytoplasmic side. (C) Extracellular entrance viewed
approximately along the arrow as indicated in B. Residues
sealing the channel opening on the extracellular surface are
drawn in sticks and excluded from the protein surface drawing.
Water and zinc m
P a g e 15
Fig. 4. Key residues involved in metal binding and water interactions. The residues are map
the crystal structure of ZIPB(5) and colored in red and blue for decreased or increased water acces
as shown in Fig 3. Bound Zn, Cd and water molecules are shown in slate grey, orange and cyan sp
respectively. A. The central binuclear metal center viewed from the extracellular side. A pair of Z
Cd ion is bridged by E181 and E211. Note the clustering of modified residues with reciprocal chan
water accessibility is associated with crystallographic water molecules. B. The peripheral binuclea
center viewed from the cytoplasmic side. The TM3-TM4 and TM7-TM8 loops are shown in a
conformations. The dotted line indicates a plausible zinc translocation pathway from the central bin
metal center through an intermediate zinc binding site at E276 toward the peripheral binuclear
center near the cytoplasmic exit. C. Extracellular entrance viewed approximately along the ar
indicated in B. Residues sealing the channel opening on the extracellular surface are drawn in stic
excluded from the protein surface drawing.
Water and zinc mobility
Fig 5. Schematic diagram of water-mediated zinc transport. Multiple bound Zn/Cd ions in the crystal
structure of ZIPB(5) define a zinc translocation pathway for zinc movement down a concentration gradient
from an extracellular entrance marked by S106 to a cytoplasmic exit capped by two cytosolic loops not
atUniversityofCalifornia,BerkeleyonAugust5,2019http://www.jbc.org/Downloadedfrom
Schematic diagram of water-
mediated zinc transport. Multiple
bound Zn/Cd ions in the crystal
structure of ZIPB define a zinc
translocation pathway for zinc
movement down a concentration
gradient from an extracellular
entrance marked by S106 to a
cytoplasmic exit capped by two
cytosolic loops not resolved in the
crystal structure. Red, blue and
g r e y a r e f o r p r o t e c t e d ,
hyperreactive and unmodified
residues. Bound Zn, Cd and water
molecules are shown in slate grey,
orange and cyan spheres,
respectively. Yellow dotted lines
show the distances, which are
within 2.0 - 3.3 Å, between
crystallographic water molecules,
metal ions and coordinating

8. Sommer
et
al.
(2019)
Plant
Physio.,
doi:
10.1104/pp.18.01190
Heterohexamers Formed by CcmK3 and CcmK4
Increase the Complexity of Beta Carboxysome Shells
Background
• Bacterial microcompartments (BMCs) encapsulate enzymes within a selectively
permeable, proteinaceous shell.
• Carboxysomes are BMCs containing ribulose-1,5-bisphosphate carboxylase
oxygenase and carbonic anhydrase that enhance carbon dioxide fixation.
• The carboxysome shell consists of three structurally characterized protein types:
BMC-H (hexamer), BMC-P (pentamer), and BMC-T (trimer).
• Here, we studied the function of the BMC-H proteins CcmK3 and CcmK4.
Approach
• We made single and double deletion mutants of ccmK3 and ccmK4 in
Synechococcus elongatus PCC7942.
• The oligomeric state of heterologously expressed and purified CcmK3 and
CcmK4 was determined by size exclusion chromatography and we
characterized the interprotein interactions using hydroxyl radical x-ray
footprinting coupled to LC-MS.
• We successfully determined the structure CcmK4 at a resolution of 1.8 Å.
Outcomes and Impacts
• Growth analysis of deletion mutants shows that CcmK3 and CcmK4 are not
redundant and that CcmK3 is a component of the carboxysome that is
expendable under ideal growth conditions.
• CcmK3 does not form homohexamers when expressed recombinantly, but
CcmK3 and CcmK4 form a heterohexameric complex (Fig. 2) that can further
form dodecamers under certain conditions.
• Overall, our results suggest that heterohexamer formation could provide a
means of fine-tuning carboxysome shell permeability.
Model of the beta carboxysome shell. Selective permeability of
each pore type is represented by dashed lines and spheres in
shades of green. Proposed capping of carboxysome facet
CcmK4 hexamers by CcmK3-CcmK4 heterohexamers is
indicated with red arrows. Altered metabolite flux after capping
is represented in red.
facets of BMC shells are comprised of a monolayer of
these proteins, with their concave face exposed to the
cytosol, punctuated by a subset of BMC-T pseudohex-
amers that form stacked oligomers (dimers of trimers,
referred to as BMC-Td) (Sutter et al., 2017) (Fig. 1).
Pores, typically at the cyclic axes of symmetry of the
oligomers, are the conduits for substrates and products.
There are two types of carboxysomes, distinguished
by the form of Rubisco they encapsulate: Form IA in
a-carboxysomes and Form IB in b-carboxysomes
(Tabita, 1999; Rae et al., 2013; Zarzycki et al., 2013;
Kerfeld and Melnicki, 2016). Accordingly, cyanobacte-
rial species encoding each carboxysome type were
termed a- and b-cyanobacteria (Badger et al., 2002).
a-cyanobacterial strains occupy the open ocean (Pro-
chlorococcus and the marine Synechococcus), and their
carboxysomes are encoded in a single genomic locus
(Badger et al., 2006; Roberts et al., 2012). In contrast,
b-cyanobacteria inhabit a variety of dynamic habitats.
Most b-carboxysome genes, including the genes en-
coding the BMC-H proteins CcmK1 and CcmK2, are
situated in the main carboxysome locus and are con-
stitutively expressed across a wide range of conditions
(Billis et al., 2014; Hernández-Prieto et al., 2016). But all
b-cyanobacterial genomes also contain varying num-
bers of additional CcmK paralogs (CcmK3-CcmK6) in
satellite loci (Sommer et al., 2017). It has been hypoth-
esized that the different CcmK paralogs have differing
metabolite selectivities (Kerfeld et al., 2005; Rae et al.,
2013; Sommer et al., 2017).
Two of these paralogs, CcmK3 and CcmK4, are pre-
sent in ;90% of all sequenced b-cyanobacterial genomes
(Sommer et al., 2017). Gene deletion of ccmK3 and ccmK4
has been shown to cause impaired growth, although
carboxysomes are still formed (Rae et al., 2012). Whereas
the exact function of CcmK3 and CcmK4 remains un-
known, Rae et al. (2012) found that the genes of both
ccmK3 and ccmK4 must be knocked out in Synechococcus
elongatus PCC7942 (Syn7942) to cause a slow-growth
phenotype, and they thus concluded that the gene pro-
ducts act redundantly. However, deletion of only ccmK4
was sufficient to produce a slow-growth phenotype in
Synechocystis sp. PCC 6803 (Syn6803) (Zhang et al., 2004).
A recent comprehensive survey of carboxysome genes in
b-cyanobacteria showed that ccmK3 and ccmK4 genes
always co-occur; it was suggested that the proteins are
not redundant but are functionally linked (Sommer et al.,
2017). Because our understanding of BMC hexamers is
based on crystal structures of purified BMC-H proteins
of a single type, we hypothesized that the functional
interdependence may involve heterohexamer formation.
In this study, we investigated the function of the
satellite locus-encoded proteins CcmK3 and CcmK4.
Growth analysis of deletion mutants shows that CcmK3
and CcmK4 are not redundant and that CcmK3 is a
component of the b-carboxysome that is expendable
under ideal growth conditions. CcmK3 does not form
Figure 1. Model of the beta carboxysome shell. Selective permeability
of each pore type is represented by dashed lines and spheres in shades of
green. Proposed capping of carboxysome facet CcmK4 hexamers by
CcmK3-CcmK4 heterohexamers is indicated with red arrows. Altered
metabolite flux after capping is represented in red.
1
This work was supported by the Deutsche Forschungsgemein-
schaft (DFG) (to M.So.) and the Office of Science, Office of Basic En-
ergy Sciences, of the U.S. Department of Energy (DOE) (award
number DE–FG02–91ER20021) with infrastructure support from
Michigan State University AgBioResearch (to C.A.K.). This work
used resources of the Advanced Light Source, the Joint BioEnergy
Institute, and the National Energy Research Scientific Computing
Center, all supported by the Office of Science, Office of Basic Energy
Heterohexamers of the Carboxysome Shell
(Left) Concave surface of a CcmK3 model replacing a protomer
of a CcmK4 hexamer. Blue coloring shows residues in CcmK3
buried upon inter- action with CcmK4 as determined by de-
creased dose response. (Right) Structural model of a CcmK3-
CcmK4 heterohexamer (assuming 1:2 ratio and symmetrical
distribution). Two residues involved in interoligomer contacts in
CcmK4 (D50, R81) are colored in green, and the residues
replacing them in CcmK3 are in red.
Halothece for reference. Conserved residues
involved in interoligomer (lateral tiling) con-
tacts are shaded brown, and those facing the
intermonomer interface are yellow. Asterisks
indicate substitutions of conserved residues at
the interoligomer surface in CcmK3. Num-
bering below follows Halothece CcmK3.
Boxes highlight important regions. B, Ratio of
dose response to irradiation of CcmK3 resi-
dues, comparing a CcmK3-CcmK4 hetero-
complex to isolated CcmK3. C, Concave
surface of a CcmK3 model replacing a pro-
tomer of a CcmK4 hexamer. Blue coloring
shows residues in CcmK3 buried upon inter-
action with CcmK4 as determined by de-
creased dose response. D, Structural model of
a CcmK3-CcmK4 heterohexamer (assuming
1:2 ratio and symmetrical distribution). Two
residues involved in interoligomer contacts in
CcmK4 (D50, R81) are colored in green, and
the residues replacing them in CcmK3 are
in red.
160
wwon August 5, 2019 - Published byDownloaded from
Copyright © 2019 American Society of Plant Biologists. A
CcmK4 is equivalent to 1.9 CcmK3 monomers per
hexamer of the mixed complex. To confirm the
results from the dot blot with a further indepen-
dent method, we performed quantitative analysis
of the heterocomplex via liquid chromatography
and mass spectrometry (LC-MS/MS). This also resulted
in 1.9 CcmK3 monomers per hexamer (Supplemental
Table S2).
Characterization of the Interaction between CcmK3-
CcmK4 in the Heterohexamers
Because we were unable to crystallize the CcmK3-
CcmK4 complex, we characterized the interprotein
interactions using hydroxyl radical x-ray footprinting
coupled to LC-MS (Fig. 4, A–C; Xu and Chance, 2007).
The relative oxidation of residues by hydroxyl radi-
cals measured in x-ray footprinting mass spectrom-
etry (XFMS) correlates to solvent accessibility of a
residue; profiles were collected for purified CcmK3 and
for the CcmK3-CcmK4 complex. In isolated CcmK3,
25 residues were susceptible to oxidation. Of these,
nine showed a decreased solvent accessibility (dose
response) in the presence of CcmK4. In a model as-
suming a typical hexameric assembly consisting of
CcmK3 and CcmK4 (Fig. 4C), the CcmK3 residues with
a decrease in solvent accessibility in the presence of
CcmK4 map to the intermonomer surface (V5, F13, L31,
F34) or the concave surface (T30, V32, S33, F42), with
the exception of M23, which points into the hydro-
phobic core between the beta sheet and alpha helices of
the BMC fold. Notably, solvent accessibility of residues
at the convex side surface (V53, E54, R55, M77, M89,
I91), the hexamer perimeter (P2, V3, P49, E52), and the
central pore (K36, R39) remained unchanged. This
finding indicates that CcmK3 only forms the typical
intermonomer interactions observed within hexamers
in the presence of CcmK4.
Figure 4. Interactions between CcmK3 and
CcmK4 in heterohexamers determined by
XFMS. A, Alignment of the sequences of
CcmK2, CcmK3, and CcmK4 of Syn7942 and
Halothece for reference. Conserved residues
involved in interoligomer (lateral tiling) con-
tacts are shaded brown, and those facing the
intermonomer interface are yellow. Asterisks
indicate substitutions of conserved residues at
the interoligomer surface in CcmK3. Num-
bering below follows Halothece CcmK3.
Boxes highlight important regions. B, Ratio of
dose response to irradiation of CcmK3 resi-
dues, comparing a CcmK3-CcmK4 hetero-
complex to isolated CcmK3. C, Concave
surface of a CcmK3 model replacing a pro-
tomer of a CcmK4 hexamer. Blue coloring
shows residues in CcmK3 buried upon inter-
action with CcmK4 as determined by de-
creased dose response. D, Structural model of
a CcmK3-CcmK4 heterohexamer (assuming
1:2 ratio and symmetrical distribution). Two
residues involved in interoligomer contacts in
CcmK4 (D50, R81) are colored in green, and
the residues replacing them in CcmK3 are
in red.
160 Plant Physiol. Vol. 179, 2019
www.plantphysiol.orgon August 5, 2019 - Published byDownloaded from
Copyright © 2019 American Society of Plant Biologists. All rights reserved.

9. Roth
et
al.
(2019)
Plant
Cell,
doi:
10.1105/tpc.18.00742
Regulation of oxygenic photosynthesis during trophic
transitions in the green alga Chromochloris zofingiensis
Background
• Regulation of oxygenic photosynthesis and primary carbon metabolism in algae
and plants is critical for net primary production of biomass on a global scale.
• Algae can regulate photosynthesis and metabolism in response to changes in
light and nutrient availability.
• Recently, the connection between the accumulation of TAGs and astaxanthin in
C. zofingiensis has become of interest to improve commercialization of this alga.
Approach
• Using cellular physiology analyses, transcriptomics, lipid analyses, transmission
electron microscopy, soft x-ray tomography, and structured illumination
microscopy, we provide insight into glucose-dependent repression and
activation of oxygenic photosynthesis that occurs in C. zofingiensis during
trophic transitions
• Monitor reversible glucose-dependent repression/activation of oxygenic
photosynthesis in the unicellular green alga C. zofingiensis.
Outcomes and Impacts
• C. zofingiensis is emerging as a new model for oleaginous algae.
• C. zofingiensis can be exploited as an experimental organism for investigating
glucose responses, carbon metabolism and partitioning, disassembly and
reassembly of the photosynthetic apparatus, astaxanthin biosynthesis, as well
as TAG accumulation and remobilization from cytoplasmic oil bodies.
• Understanding these fundamental processes in C. zofingiensis will enable
bioengineering approaches to enhance production of biofuel precursors and
high-value products from microalgae.
(B) Representative cryo-SXT of cells showing orthoslices, segmented
chloroplasts containing starch granules and nucleus, mitochondrial
networks and nuclei, lipid bodies and nuclei, and fully segmented
cells. Nucleus, purple; chloroplast, green; mitochondria, red; lipid
bodies, yellow; starch granules within the chloroplast, blue. Scale bar
= 2 µm. (C) Changes in intracellular morphology with glucose as
determined by cryo-SXT. Data represent means ± SD (n = 8-11
technical replicates). (D) Heat map TAG abundance plotted as log2-
transformed fold change in comparisons of glucose versus
photoautotrophic control and glucose removal versus heterotrophic
control at each time point. Lipids are normalized to AFDW. Data
represent means (n = 3-4 biological replicates).

10. Isolation and characterization of bacterial cellulase
producers for biomass deconstruction: a microbiology
laboratory course
Background
• At JBEI, we have demonstrated that a complex, open-ended,
inquiry-based course can be appropriate and highly beneficial for
students at an early stage of their scientific training. Over the past
ten years, we have administered a program that targets an
underrepresented segment of the future STEM workforce as a
means to increase its diversity.
Approach
• This paper describes the eight week curriculum for this program,
called iCLEM (Introductory College Level Experience in
Microbiology), which has occurred every summer since 2008 and
targets underrepresented high school students in the San Francisco
Bay Area.
Outcomes and Impacts
• The iCLEM curriculum involves a number of laboratory experiments
to isolate, identify and characterize cellulolytic bacteria from
environmental samples.
• Students develop practical laboratory skills as well as being taught
the fundamental concepts behind the experiments they perform.
• iCLEM has eight students each year who are chosen from 50-100
applicants.
• >95% of the iCLEM students go to four year colleges.
Barajas
et
al.
(2019)
Journal
of
Microbiology
&
Biology
Educa:on
doi:10.1128/jmbe.v20i2.1723.