Models for navigating biological complexity in breeding improved crop plants

Progress in breeding higher-yielding crop plants would be greatly accelerated if the phenotypic consequences of making changes to the genetic makeup of an organism could be reliably predicted. Developing a predictive capacity that scales from genotype to phenotype is impeded by biological complexities associated with genetic controls, environmental effects and interactions among plant growth and development processes. Plant modelling can help navigate a path through this complexity. Here we profile modelling approaches for complex traits at gene network, organ and whole plant levels. Each provides a means to link phenotypic consequence to changes in genomic regions via stable associations with model coefficients. A unifying feature of the models is the relatively coarse level of granularity they use to capture system dynamics. Much of the fine detail is not directly required. Robust coarse-grained models might be the tool needed to integrate phenotypic and molecular approaches to plant breeding.     

Motor proteins at the microtubule plus-end

The plus-end of the microtubule has a central role in the interactions that occur between the microtubule and actin cytoskeletons. The recent identification of a family of proteins that congregate at the plus-end is enabling an increased mechanistic understanding of how this cross talk is accomplished. These proteins, termed plus-end tracking proteins because they appear to associate with the plus-end as it grows, have already been shown to regulate microtubule dynamics and to facilitate the formation of connections between the plus-end and the actin-rich cortex. Several motor proteins, including an actin-based motor, microtubule-based motors that move towards either end of the microtubule and microtubule motors that depolymerize microtubule ends, can now be added to the list of plus-end tracking proteins. Here, we discuss how the presence of these motors at the plus-end seems to drive several fundamental cellular processes involving force generation at the interface between microtubule ends and the cortex, vesicle translocation following search and capture, microtubule disassembly and the delivery of signals to the cortex that govern actin assembly and cell polarity.     

Laccase-induced derivatization of unprotected amino acid L-tryptophan by coupling with p-hydroquinone 2,5-dihydroxy-N-(2-hydroxyethyl)-benzamide

Summary. We have studied the enzymatic derivatization of amino acids by use of the polyphenol oxidase laccase. Derivatization of L-tryptophan was achieved by enzymatic crosslinking with the laccase substrate 2,5-dihydroxy-N-(2-hydroxyethyl)-benzamide. The main product (yield up to 70%) was identified as the quinoid compound 2-[2-(2-hydroxy-ethylcarbamoyl)-3,6-dioxo-cyclohexa-1,4-dienylamino]-3-(1H-indol-3-yl)- propionic acid and demonstrates that laccase-catalyzed C–N-coupling occurred on the amino group of the aliphatic side chain. These enzyme based reactions provide a simple and fast method for the derivatization of unprotected amino acids.     

Archaic admixture in the human genome

One of the enduring questions in the evolution of our species surrounds the fate of 'archaic' forms of Homo. Did Neanderthals go extinct without interbreeding with modern humans 25-40 thousand years ago or are their genes present among modern-day Europeans? Recent work suggests that Neanderthals and an as yet unidentified archaic African population contributed to at least 5% of the modern European and West African gene pools, respectively. Extensive sequencing of Neanderthal and other archaic human nuclear DNA has the potential to answer this question definitively within the next few years.     

ApoE receptor 2 controls neuronal survival in the adult brain

A central pathogenic feature of neurodegenerative diseases and neurotrauma is the death of neurons. A mechanistic understanding of the factors and conditions that induce the dysfunction and death of neurons is essential for devising effective treatment strategies against neuronal loss after trauma or during aging. Because Apolipoprotein E (ApoE) is a major risk factor for several neurodegenerative diseases, including Alzheimer's disease , a direct or indirect role of ApoE receptors in the disease process is likely. Here we have used gene targeting in mice to investigate possible roles of ApoE receptors in the regulation of neuronal survival. We demonstrate that a differentially spliced isoform of an ApoE receptor, ApoE receptor 2 (Apoer2), is essential for protection against neuronal cell loss during normal aging. Furthermore, the same splice form selectively promotes neuronal cell death after injury through mechanisms that may involve serine/threonine kinases of the Jun N-terminal kinase (JNK) family. These findings raise the possibility that ApoE and its receptors cooperatively regulate common mechanisms that are essential to neuronal survival in the adult brain.     

Elucidation of ATP-stimulated stress protein expression of RBA-2 type-2 astrocytes: ATP potentiate HSP60 and Cu/Zn SOD expression and stimulates pI shift of peroxiredoxin II

ATP has been shown to mediate stress responses in the brain. The present study examined the ATP-stimulated stress protein expression of RBA-2 type-2 astrocytes. Our results revealed that ATP stimulated HSP60 expression in a dose- and time-dependent manner. The stimulation requires a minimal ATP concentration of 500 microM and high concentration of extracellular ATP (1 mM) stimulated a significant increase of HSP60 expression from 2 to 24 h. In addition, the ATP-stimulated HSP60 expressions were inhibited by inhibitors for protein kinase C (PKC) and phospholipase D (PLD), and by antioxidants, resveratrol, and catalase. Furthermore, ATP stimulated the expression of Cu/Zn superoxide dismutase (SOD). In addition, ATP and P2X7 receptor selective agonist BzATP also decreased mitochondria membrane potential measured by flow cytometry. To further examine the proteins involving in ATP-mediated stress responses, we conducted proteomic analysis. We found that RBA-2 astrocytes possess abundant peroxiredoxin II (Prx II), an antioxidant enzyme. ATP and exogenous H2O2 stimulated Prx II shifting from oxidized form to reduced form. Thus, we concluded that ATP potentiated the expression of HSP60 and Cu/Zn SOD, and decreased mitochondria membrane potential. In addition, RBA-2 astrocytes expressed Prx II that might also serve as a protective mechanism to control the concentration of reactive oxygen species.     

Unexpected NRY chromosome variation in Northern Island Melanesia

To investigate the paternal population history of populations in Northern Island Melanesia, 685 paternally unrelated males from 36 populations in this region and New Guinea were analyzed at 14 regionally informative binary markers and 7 short tandem repeat (STR) loci from the nonrecombining portion of the Y chromosome. Three newly defined binary markers (K6-P79, K7-P117, and M2-P87) aided in identifying considerable heterozygosity that would have otherwise gone undetected. Judging from their geographic distributions and network analyses of their associated STR profiles, 4 lineages appear to have developed in this region and to be of considerable age: K6-P79, K7-P117, M2-P87, and M2a-P22. The origins of K5-M230 and M-M4 are also confirmed as being located further west, probably in New Guinea. In the 25 adequately sampled populations, the number of different haplogroups ranged from 2 in the single most isolated group (the Aita of Bougainville), to 9, and measures of molecular diversity were generally not particularly low. The resulting pattern contradicts earlier findings that suggested far lower male-mediated diversity and gene exchange rates in the region. However, these earlier studies had not included the newly defined haplogroups. We could only identify a very weak signal of recent male Southeast Asian genetic influence (<10%), which was almost entirely restricted to Austronesian (Oceanic)-speaking groups. This contradicts earlier assumptions on the ancestral composition of these groups and requires a revision of hypotheses concerning the settlement of the islands of the central Pacific, which commenced from this region.     

Origin and identity of adrenocortical tumors in inhibin knockout mice: implications for cellular plasticity in the adrenal cortex

Inhibin knockout (Inha-/-) mice develop gonadal sex-cord tumors and--when gonadectomized--adrenocortical tumors. Previous reports demonstrated that adrenocortical tumors from Inha-/- mice produce estrogen and depend on gonadotropin signaling for initiation. Here we show that, in addition to producing estrogen, the adrenocortical tumors display a global change in cellular identity, composed of two unique cell types expressing differing arrays of genes normally restricted to theca and granulosa cells of the ovary. Many of these genes are also induced in wild-type adrenals after gonadectomy or upon chronic gonadotropin stimulation, suggesting that the adrenal cortex normally contains a population of pluripotent cells that can be driven toward an adrenal or gonadal identity given the appropriate pituitary stimuli. A central feature of this altered cellular identity is the switch from predominant expression of Gata6 (endogenous to the adrenal cortex) to Gata4, which defines cellular identity in the ovary. We show that stable transfection of Gata4 in cultured adrenocortical cells is sufficient to activate ovarian-specific genes of both theca and granulose lineages. Spatial analysis of Gata4 expression reveals a distinct pattern of localization to the supcapsular region of the adrenal, which contains undifferentiated progenitor cells that continuously populate the adrenocortical zones. Although both wild-type and Inha-/- mice display this pattern, only Inha-/- mice produce tumors composed of these Gata4-positive cells. These data suggest that Inha-/- adrenocortical tumors cells are derived from pluripotent adrenocortical progenitor cells that adopt a gonadal fate due to the convergent loss of inhibin and chronic exposure to elevated gonadotropins.     

Redundant functions of RIM1alpha and RIM2alpha in Ca(2+)-triggered neurotransmitter release

Alpha-RIMs (RIM1alpha and RIM2alpha) are multidomain active zone proteins of presynaptic terminals. Alpha-RIMs bind to Rab3 on synaptic vesicles and to Munc13 on the active zone via their N-terminal region, and interact with other synaptic proteins via their central and C-terminal regions. Although RIM1alpha has been well characterized, nothing is known about the function of RIM2alpha. We now show that RIM1alpha and RIM2alpha are expressed in overlapping but distinct patterns throughout the brain. To examine and compare their functions, we generated knockout mice lacking RIM2alpha, and crossed them with previously produced RIM1alpha knockout mice. We found that deletion of either RIM1alpha or RIM2alpha is not lethal, but ablation of both alpha-RIMs causes postnatal death. This lethality is not due to a loss of synapse structure or a developmental change, but to a defect in neurotransmitter release. Synapses without alpha-RIMs still contain active zones and release neurotransmitters, but are unable to mediate normal Ca(2+)-triggered release. Our data thus demonstrate that alpha-RIMs are not essential for synapse formation or synaptic exocytosis, but are required for normal Ca(2+)-triggering of exocytosis.