Jarrett

Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules

Nov 30

Arabidopsis KHZ1 and KHZ2, two novel non-tandem CCCH zinc-finger and K-homolog domain proteins, have redundant roles in the regulation of flowering and senescence

Nov 9

Duplication of an upstream silencer of FZP increases grain yield in rice

High throughput shape quantification tool

Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths

Oct 26

Grass inflorescence architecture and meristem determinacy

Small RNAs: Big Impact on Plant Development

unused

The AtMC4 regulates the stem cell homeostasis in Arabidopsis by catalyzing the cleavage of AtLa1 protein in response to environmental hazards

evolution of hermaphroditism in grapes

Oct 12

Reviews:

Stomatal development: focusing on the grasses

Shoot regeneration: a journey from acquisition of competence to completion

Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing

Fall 2017

DELLA genes restrict inflorescence meristem function independently of plant height

Protein has different interaction targets in different tissue, can be used to make dwarf plants with high flowering activity

Distinct genetic architectures for phenotype means and plasticities in Zea mays

GWAS on maize reveals that one can select for plasticity traits independent of other desirable characteristics

Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells

Somehow predict hubs in networks based on expression in stem cells, can we do this for enhancers?

Review

Secondary Growth as a Determinant of Plant Shape and Form

Focuses on CLV1-related LRR-RLKs and their CLEs to regulate development.

June 1

VRS1 also increases leaf primordium size in Barley (preprint)

WUS found to promote SAM stem cell fate by suppressing division, auxin responsiveness, and many differentiation genes.

Plant architectural traits influence residence time of a specialist jumping spider

Epistasis between two tomato MADS-box domestication genes and some workarounds

April 7

CLAVATA1 controls distinct signaling outputs that buffer shoot stem cell proliferation through a two-step transcriptional compensation loop

Maize NOD functions in cellular development, study with mosaic analysis

March 28

Evolution of angiosperm floral quartets from gymnosperm dimers

Polyploidies might be spandrels of asexuality

Shade response in both plant architecture and immunity regulated by same gene networks

High throughput maize architecture phenotyping for QTL

Review of genes and hormones regulating axillary meristem production in angiosperms

Feb 17

DRUS1/2 are FERONIA orthologs in rice; transmit unknown signal to prevent cell death in developing primordia and many tissue types

Feb 10

Review using genomics to examine grass stomata evo-devo

precise deletions in genome editing using low affinity endonuclease fused to cas9

LRR-RLKs in Amborella show that functional families diverged before angiosperm radiation

Using corn-teosinte RILs to map domestication traits in tassel, finds some taseel development genes, misses others

Dec 2

Jatropha domestication

Regeneration of root stem cell niche after damage

Genes regulating asymmetric cell division in epidermis

A regulatory element over 6kb upstream of OsLFY has large effect on floral meristem development

Genome of 5300 year old maize assembled, shows some domestication genes, some not

Affordable technique to improve QTL mapping using bulk segregant RNA-seq

Farming ants

Nitroaromatic detection and infrared communication from wild-type plants using plant nanobionics

Meristem shape can predict QTL for genes controlling development

PhD Dissertation examining CLE40

Cardamine genome assembly

Oct 28

Reviews:

Genetic Control of Lateral Root Formation in Cereals

Plant Enhancers: A Call for Discovery

JULY 22

Recent demography drives changes in linked selection across the maize genome

A look at maize and teosinte genomes to quantify domestication bottlenecks and selection pressures

eLife:

Nucleosome breathing and remodeling constrain CRISPR-Cas9 function

Cas9 not able to act on sequences directly bound to nucleosomes, but can when breathing or chromatin remodeling enzymes are present.

Big picture: CRISPR can only work in vivo under particular circumstances that are difficult to predict, so multiple guides are more likely to succeed.

Gene:

Transcriptomic analysis of Arabidopsis overexpressing flowering locus T driven by a meristem-specific promoter that induces early flowering

FT is produced in mature leaves under long days, is transported to meristems in phloem, and activates MADS-box genes such as SOC1 that initiate inflorescence development. Authors used KNAT1 promoter to drive gene expression, causing early flowering (expected) and significant transcriptomic changes in leaves. Leaves cease expanding early when flowering occur, and many MADS-box TFs are upregulated.

Big picture: signals are flowing proximal from the meristem and influencing other organ transcriptomes

Current Biology:

Diversification of a Transcription Factor Family Led to the Evolution of Antagonistically Acting Genetic Regulators of Root Hair Growth

A study investigating the fates of genes after duplication, how paralogous genes can sub- or neo-functionalize and become antagonistic when ancestral versions were not. Group confirmed that the bHLH TF LRL was originally a single copy in early diverging land plants and is up to 5 copies in Arabidopsis, which form two antagonistic groups. Expression patterns tested with in situs and YFP fusions to show overlapping but distinct LRL expression areas. Over/underexpression of two classes stimulated/suppressed root hair growth, and one class was found to repress the expression of the other.

Other:

The palm family (Arecaceae): a microcosm of sexual system evolution

Review - evo devo of floral sexual type evolution. Not our topic but an interesting tangential to some of our studies.

Aug 19

Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy

Group used both temporal and spatial tracking to model protein movement, and was able to determine protein stoichiometry.

A stochastic multicellular model identifies biological watermarks from disorders in self-organized patterns of phyllotaxis

Produced models of phyllotaxy that incorporate noise of signal diffusion and perception that can recreate some common phenotypes. They also show how patterns of noise propagation through phyllotaxy-determining machinery can give clues about the machinery itself. Super mathy.

Formation of polarity convergences underlying shoot outgrowths

Study on how PIN1 auxin transporters are coordinated to create foci of auxin maxima needed for primordia formation. Testing new model that Pin1 localizes to membrane areas with high auxin flux, not content. Another model that internal cellular components arrange PIN1 and are programmed in polarity by other adjacent cells, kind of like a magnet. This is called tandem alignment, and they used an arabidopsis mutant that forms outgrowths on the abaxial surface of leaves and modeling to support this idea, rather than the up-the-gradient model.

Whole-genome duplication as a key factor in crop domestication

Polyploidy may be an important aspect of domestication, offsetting genetic loss of bottlenecks and increasing adaptability to new contexts. But it also makes fixing traits more difficult and masks underlying recessive alleles. Authors mapped polyploidization events onto many phylogenies and found an association with domestication efforts. They found it preceded domestication, suggesting that it allowed or favored domestication. However many examples exist of post domestication polyploidy such as wheat.

Sept 2

A Secreted Peptide and Its Receptors Shape the Auxin Response Pattern and Leaf Margin Morphogenesis

Leaf tips are caused but axin maxima, initiating higher pace of growth.

EFPL are secreted peptides that regulate many plant features. Ligand and receptor activation causes cells to be insensitive to auxin, cells still sensitive grow and not to produce the ligand. Polar auxin transport initiates auxin peaks, in which the cells are maintained as auxin sensitive while the others are not.

Looks like they made notches in plants expressing GUS constructs to see the gene expression around leaf teeth. They made knockouts as well, auxin maxima couldn't be maintained and tooth dulled.

An Unprecedented Non-canonical Nuclear Genetic Code with All Three Termination Codons Reassigned as Sense Codons

Found in trypanosomatids, protist parasites of insects. UGA encodes tryptophan; UARs encode glutamate or designate translation termination.

Ser70Gly mutation in the eRF1 cause it to DECREASE affinity for UGA, so this codon often codes for Tryptophan.Abundance of trnas to erfs dictates choice. Found through ESTs that contained lots of in frame stop codons, often all three in the same transcript. Found that genes differed in their enrichment for the nonstandard codons, though often they are present in lower copy numbers than expected, and think this is due to age of gene and time allowed for adjustment to new codon reassignment. Other species in genus show various levels of codon reassignments, so this might be ancient. Speculation on what factors influence this and the adaptive advantage this could bring.

Neglecting legumes has compromised human health and sustainable food production

Authors speak about N fixation, global cereal increase, lack of effort to improve legume, impact on climate due to fertilizer and farming, there is great legume diversity in world, "

lobal cereal production has almost tripled over the past 50 years but grain legume production has only increased by about 60%. The relatively low rate of yield improvement in grain legumes versus cereals is at least partly explained by low genetic diversity in grain legume breeding programs46. " Also had impact on health, complete protein (high in lysine),

Sept 16

No plant is an island A cute little essay about how diverse plant interactions are, and an appeal to keep plant science research diverse and open in times of increasing public support for closed-minded politicians.
Genome-Wide Targets Regulated by the OsMADS1 Transcription Factor Reveals Its DNA Recognition Properties Performed CHIP-seq on OsMADS1 to determine genome wide binding affinity. Many mutants have been characterized, and genetic networks identified, phenotypes, but authors wanted to look for more global picture of what this TF was binding downstream. Gained new insights into binding site affinity, sequences, co-affinity with other TFs, and used to provide more complexity and depth to gene interaction networks.
The Myb-domain protein ULTRAPETALA1 INTERACTING FACTOR 1 controls floral meristem activities in Arabidopsis. A protein partner in a dimer that binds WUS regulatory region to supress, triggered by CLV like activities upstream
Plant Stem CellsAn entry level review to the idea of plant stem cells, covers not just SAM but also RAM and a little on lateral stem cells
Regulatory function of homeodomain-leucine zipper (HD-ZIP) family proteins during embryogenesisA review of HD-zips, but focuses mainly on embryogenesis and meristem determination
Control of Anther Cell Differentiation by the Small Protein Ligand TPD1 and Its Receptor EMS1 in ArabidopsisAn LRR-RLK and peptide ligand guide anther cell development - controls division of supporting somatic cells.
Advancing Crop Transformation in the Era of Genome EditingPointing out bottlenecks in bringing advancements to crops. Not really sure who this is written for.
Fatal attraction: the intuitive appeal of GMO oppositionFocus on human guidance by intuition in propelling the anti-gmo movement and how people have used this to exploit people
Mimicry in plantsA quick into into many types of clever plant mimicry - mimicking toxic plants, insect eggs, bird poop, agricultural crops, pollinating insects, dead animals, flowers with nectar, and even sand.

Oct 14

Spiny plants, mammal browsers, and the origin of African savannas An argument towards savanas as being driven by mammals, which in turn are driven by climate change, rather than fire, which is a secondary effect.
A Case for Distributed Control of Local Stem Cell Behavior in Plants An excellent review on arabidopsis root meristem maintenance and genetic control of cell divisions to establish development. By examining features of quiescent center reestablishment and mutants in various other components, they make the argument that genetic control of stem cells is not really being "regulated" in a hierarchical sense, by the QC, but that the QC is more an emergent property of a bunch of other systems that are acting to define regions based on positional cues.
The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection A new genome Brassica juncea, mustard greens/oil, de-novo assembled, allotetraploid mix of two other brassica species. Authors then dig a little into how homoeologous genes from different ancestral chromosomes can exhibit dominance over each other - essentially showing that chromosomes from one species were dominant to others. Showed that genes dominant for glucosinolate production under selection in vegetable varieties, lipid production in oil varieties.