Molecular mechanisms underlying gene regulatory variation of maize metabolic traits.

Variation in gene expression levels is pervasive among individuals and races or varieties, and has substantial agronomic consequences, for example, by contributing to hybrid vigor. Gene expression level variation results from mutations in regulatory sequences (cis) and/or transcription factor (TF) activity (trans), but the mechanisms underlying cis and/or trans-regulatory variation of complex phenotypes remain largely unknown. Here, we investigated gene expression variation mechanisms underlying the differential accumulation of the insecticidal compounds maysin and chlorogenic acid in silks of two widely used maize (Zea mays) inbreds, B73 and A632. By combining transcriptomics and cistromics, we identified 1,338 silk direct targets of the maize R2R3-MYB TF Pericarp color1 (P1), consistent with it being a regulator of maysin and chlorogenic acid biosynthesis. Among these P1 targets, 464 showed allele-specific expression (ASE) between B73 and A632 silks. Allelic DNA-affinity purification sequencing identified 34 examples in which P1 allelic specific binding (ASB) correlated with cis-expression variation. From previous yeast one-hybrid studies, we identified nine TFs potentially implicated in the control of P1 targets, with ASB to 83 out of 464 ASE genes (cis) and differential expression of 4 out of 9 TFs between B73 and A632 silks (trans). These results provide a molecular framework for understanding universal mechanisms underlying natural variation of gene expression levels, and how the regulation of metabolic diversity is established.

ABCG2 Mediates Resistance to the Dual EGFR and PI3K Inhibitor MTX-211 in Cancer Cells.

MTX-211 is a first-in-class dual inhibitor of epidermal growth factor receptor (EGFR) and phosphoinositide-3 kinase (PI3K) signaling pathways with a compelling pharmaceutical profile and could enhance the effectiveness of mitogen-activated protein kinase kinase (MEK) inhibitor therapy in colorectal tumors with KRAS mutations. However, the specific mechanisms contributing to the acquired resistance to MTX-211 in human cancers remain elusive. Here, we discovered that the overexpression of the ATP-binding cassette (ABC) drug transporter ABCG2, a prevalent mechanism associated with multidrug resistance (MDR), could diminish the effectiveness of MTX-211 in human cancer cells. We showed that the drug efflux activity of ABCG2 substantially decreased the intracellular accumulation of MTX-211 in cancer cells. As a result, the cytotoxicity and effectiveness of MTX-211 in suppressing the activation of the EGFR and PI3K pathways were significantly attenuated in cancer cells overexpressing ABCG2. Moreover, the enhancement of the MTX-211-stimulated ATPase activity of ABCG2 and the computational molecular docking analysis illustrating the binding of MTX-211 to the substrate-binding sites of ABCG2 offered a further indication for the interaction between MTX-211 and ABCG2. In summary, our findings indicate that MTX-211 acts as a substrate for ABCG2, underscoring the involvement of ABCG2 in the emergence of resistance to MTX-211. This finding carries clinical implications and merits further exploration.

Exploring Camelina sativa lipid metabolism regulation by combining gene co-expression and DNA affinity purification analyses.

Camelina (Camelina sativa) is an annual oilseed plant that is gaining momentum as a biofuel cover crop. Understanding gene regulatory networks is essential to deciphering plant metabolic pathways, including lipid metabolism. Here, we take advantage of a growing collection of gene expression datasets to predict transcription factors (TFs) associated with the control of Camelina lipid metabolism. We identified approximately 350 TFs highly co-expressed with lipid-related genes (LRGs). These TFs are highly represented in the MYB, AP2/ERF, bZIP, and bHLH families, including a significant number of homologs of well-known Arabidopsis lipid and seed developmental regulators. After prioritizing the top 22 TFs for further validation, we identified DNA-binding sites and predicted target genes for 16 out of the 22 TFs tested using DNA affinity purification followed by sequencing (DAP-seq). Enrichment analyses of targets supported the co-expression prediction for most TF candidates, and the comparison to Arabidopsis revealed some common themes, but also aspects unique to Camelina. Within the top potential lipid regulators, we identified CsaMYB1, CsaABI3AVP1-2, CsaHB1, CsaNAC2, CsaMYB3, and CsaNAC1 as likely involved in the control of seed fatty acid elongation and CsaABI3AVP1-2 and CsabZIP1 as potential regulators of the synthesis and degradation of triacylglycerols (TAGs), respectively. Altogether, the integration of co-expression data and DNA-binding assays permitted us to generate a high-confidence and short list of Camelina TFs involved in the control of lipid metabolism during seed development.

Effect of energy per atom (E/n) on the Ar gas cluster ion beam (Ar-GCIB) and O2+ cosputter process.

Gas cluster ion beam (GCIB) is a promising technique for preserving molecular structures during ion sputtering and successfully profiling biological and soft materials. However, although GCIB yields lower damage accumulation compared with C60+ and monoatomic ion beams, the inevitable alteration of the chemical structure can introduce artifacts into the resulting depth profile. To enhance the ionization yield and further mask damage, a low-energy O2+ (200-500 V) cosputter can be applied. While the energy per atom (E/n) of GCIB is known to be an important factor influencing the sputter process, the manner through which E/n affects the GCIB-O2+ cosputter process remains unclear. In this study, poly(ethylene terephthalate) (PET) was used as a model material to investigate the sputter process of 10-20 kV Ar1000-4000+ (E/n = 2.5-20 eV per atom) with and without O2+ cosputter at different energies and currents. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) with Bi32+ as the primary ion was used to examine surfaces sputtered at different fluences. The sputter craters were also measured by alpha-step and atomic force microscopy in quantitative imaging mode. The SIMS results showed that the steady-state cannot be obtained with E/n values of less than 5 eV per atom due to damage accumulation using single GCIB sputtering. With a moderate E/n value of 5-15 eV per atom, the steady-state can be obtained, but the ∼50% decay in intensity indicated that damage cannot be masked completely despite the higher sputter yield. Furthermore, the surface Young's modulus decreased with increasing E/n, suggesting that depolymerization occurred. At an E/n value of 20 eV per atom, a failed profile was obtained with rapidly decreased sputter rate and secondary ion intensity due to the ion-induced crosslink. With O2+ cosputtering and a moderate E/n value, the oxidized species generated by O2+ enhanced the ionization yield, which led to a higher ion intensity at steady-state in general. Because higher kinetic energy or current density of O2+ led to a larger interaction volume and more structural damage that suppressed molecular ion intensity, the enhancement from O2+ was most apparent with low-energy-high-current (200 V, 80 µA cm-2) or high-energy-low-current (500 V, 5 µA cm-2) O2+ cosputtering with 0.5 µA cm-2 GCIBs. In these cases, little or no intensity drop was observed at the steady-state.

Improvement of the gas cluster ion beam-(GCIB)-based molecular secondary ion mass spectroscopy (SIMS) depth profile with O2(+) cosputtering.

Over the last decade, cluster ion beams have displayed their capability to analyze organic materials and biological specimens. Compared with atomic ion beams, cluster ion beams non-linearly enhance the sputter yield, suppress damage accumulation and generate high mass fragments during sputtering. These properties allow successful Secondary Ion Mass Spectroscopy (SIMS) analysis of soft materials beyond the static limit. Because the intensity of high mass molecular ions is intrinsically low, enhancing the intensity of these secondary ions while preserving the sample in its original state is the key to highly sensitive molecular depth profiles. In this work, bulk poly(ethylene terephthalate) (PET) was used as a model material and analyzed using Time-of-Flight SIMS (ToF-SIMS) with a pulsed Bi3(2+) primary ion. The optimized hardware of a 10 kV Ar2500(+) Gas Cluster Ion Beam (GCIB) with a low kinetic energy (200-500 V) oxygen ion (O2(+)) as a cosputter beam was employed for generating depth profiles and for examining the effect of beam parameters. The results were then quantitatively analyzed using an established erosion model. It was found that the ion intensity of the PET monomer ([M + H](+)) and its large molecular fragment ([M - C2H4O + H](+)) steadily declined during single GCIB sputtering, with distortion of the distribution information. However, under an optimized GCIB-O2(+) cosputter, the secondary ion intensity quickly reached a steady state and retained >95% intensity with respect to the pristine surface, although the damage cross-section was larger than that of single GCIB sputtering. This improvement was due to the oxidation of molecules and the formation of -OH groups that serve as proton donors to particles emitted from the surface. As a result, the ionization yield was enhanced and damage to the chemical structure was masked. Although O2(+) is known to alter the chemical structure and cause damage accumulation, the concurrently used GCIB could sufficiently remove the surface layer and allow the damage to be masked by the enhanced ionization yield when the ion-solid interaction volume was kept shallow with a low O2(+) energy. This low O2(+) energy (200 V) cosputtering also produced a smoother surface than a single GCIB. Because the oxidized species were produced by O2(+) and removed by GCIB simultaneously, a sufficiently high O2(+) current density was required to produce adequate enhancements. Therefore, it was found that 10 kV with 2 × 10(-6) A per cm(2) Ar2500(+) and 200 V with 3.2 × 10(-4) A per cm(2) O2(+) produced the best profile.

Effect of surface potential on extracellular matrix protein adsorption.

Extracellular matrix (ECM) proteins, such as fibronectin, laminin, and collagen IV, play important roles in many cellular behaviors, including cell adhesion and spreading. Understanding their adsorption behavior on surfaces with different natures is helpful for studying the cellular responses to environments. By tailoring the chemical composition in binary acidic (anionic) and basic (cationic) functionalized self-assembled monolayer (SAM)-modified gold substrates, variable surface potentials can be generated. To examine how surface potential affects the interaction between ECM proteins and substrates, a quartz crystal microbalance with dissipation detection (QCM-D) was used. To study the interaction under physiological conditions, the ionic strength and pH were controlled using phosphate-buffered saline at 37 °C, and the ζ potentials of the SAM-modified Au and protein were determined using an electrokinetic analyzer and phase analysis light scattering, respectively. During adsorption processes, the shifts in resonant frequency (f) and energy dissipation (D) were acquired simultaneously, and the weight change was calculated using the Kelvin-Voigt model. The results reveal that slightly charged protein can be adsorbed on a highly charged SAM, even where both surfaces are negatively charged. This behavior is attributed to the highly charged SAM, which polarizes the protein microscopically, and the Debye interaction, as well as other short-range interactions such as steric force, hydrogen bonding, direct bonding, charged domains within the protein structure, etc., that allow adsorption, although the macroscopic electrostatic interaction discourages adsorption. For surfaces with a moderate potential, proteins are not significantly polarized by the surface, and the interaction can be predicted through simple electrostatic attraction. Furthermore, surface-induced self-assembly of protein molecules also affects the adsorbed structures and kinetics. The adsorbed layer properties, such as rigidity and packing behaviors, were further investigated using the D-f plot and phase detection microscopy (PDM) imaging.

Sunlight enhanced the formation of tribromomethane from benzotriazole degradation during the sunlight/free chlorine treatment in the presence of bromide.

The coexistence of free chlorine and bromide under sunlight irradiation (sunlight/FC with Br-) is unavoidable in outdoor seawater swimming pools, and the formation of brominated disinfection byproducts could act more harmful than chlorinated disinfection byproducts. In this study, benzotriazole was selected as a model compound to investigate the degradation rate and the subsequent formation of disinfection byproducts via sunlight/FC with Br- process. The rate constants for the degradation of benzotriazole under pseudo first order conditions in sunlight/FC with Br- and sunlight/FC are 2.3 ± 0.07 × 10-1 min-1 and 6.0 ± 0.7 × 10-2 min-1, respectively. The enhanced degradation of benzotriazole can be ascribed to the generation of HO•, bromine species, and reactive halogen species (RHS) during sunlight/FC with Br-. Despite the fact that sunlight/FC with Br- process enhanced benzotriazole degradation, the reaction results in increasing tribromomethane (TBM) formation. A high concentration (37.8 µg/L) of TBM was detected in the sunlight/FC with Br-, which was due to the reaction of RHS. The degradation of benzotriazole was notably influenced by the pH value (pH 4 - 11), the concentration of bromide (0 - 2 mM), and free chlorine (1 - 6 mg/L). Furthermore, the concentration of TBM increased when the free chlorine concentrations increased, implying the formation potential of harmful TBM in chlorinated seawater swimming pools.

Leveraging a rationally designed veliparib-based anilide eliciting anti-leukemic effects for the design of pH-responsive polymer nanoformulation.

Careful recruitment of the components of the HDAC inhibitory template culminated in veliparib-based anilide 8 that elicited remarkable cell growth inhibitory effects against HL-60 cell lines mediated via dual modulation of PARP [(IC50 (PARP1) = 0.02 nM) and IC50 (PARP2) = 1 nM)] and HDACs (IC50 value = 0.05, 0.147 and 0.393 µM (HDAC1, 2 and 3). Compound 8 downregulated the expression levels of signatory biomarkers of PARP and HDAC inhibition. Also, compound 8 arrested the cell cycle at the G0/G1 phase and induced autophagy. Polymer nanoformulation (mPEG-PCl copolymeric micelles loaded with compound 8) was prepared by the nanoprecipitation technique. The mPEG-PCL diblock copolymer was prepared by ring-opening polymerization method using stannous octoate as a catalyst. The morphology of the compound 8@mPEG-PCL was examined using TEM and the substance was determined to be monodispersed, spherical in form, and had an average diameter of 138 nm. The polymer nanoformulation manifested pH-sensitive behaviour as a greater release of compound 8 was observed at 6.2 pH as compared to 7.4 pH mimicking physiological settings. The aforementioned findings indicate that the acidic pH of the tumour microenvironment might stimulate the nanomedicine release which in turn can attenuate the off-target effects precedentially claimed to be associated with HDAC inhibitors.

Prioritizing Metabolic Gene Regulators through Multi-Omic Network Integration in Maize.

Elucidating gene regulatory networks (GRNs) is a major area of study within plant systems biology. Phenotypic traits are intricately linked to specific gene expression profiles. These expression patterns arise primarily from regulatory connections between sets of transcription factors (TFs) and their target genes. In this study, we integrated publicly available co-expression networks derived from more than 6,000 RNA-seq samples, 283 protein-DNA interaction assays, and 16 million of SNPs used to identify expression quantitative loci (eQTL), to construct TF-target networks. In total, we analyzed ~4.6M interactions to generate four distinct types of TF-target networks: co-expression, protein-DNA interaction (PDI), trans-expression quantitative loci (trans-eQTL), and cis-eQTL combined with PDIs. To improve the functional annotation of TFs based on its target genes, we implemented three different strategies to integrate these four types of networks. We subsequently evaluated the effectiveness of our method through loss-of function mutant and random networks. The multi-network integration allowed us to identify transcriptional regulators of hormone-, metabolic- and development-related processes. Finally, using the topological properties of the fully integrated network, we identified potentially functional redundant TF paralogs. Our findings retrieved functions previously documented for numerous TFs and revealed novel functions that are crucial for informing the design of future experiments. The approach here-described lays the foundation for the integration of multi-omic datasets in maize and other plant systems.

Mutator transposon insertions within maize genes often provide a novel outward reading promoter.

The highly active family of Mutator (Mu) DNA transposons has been widely used for forward and reverse genetics in maize. There are examples of Mu-suppressible alleles that result in conditional phenotypic effects based on the activity of Mu. Phenotypes from these Mu-suppressible mutations are observed in Mu-active genetic backgrounds, but absent when Mu activity is lost. For some Mu-suppressible alleles, phenotypic suppression likely results from an outward-reading promoter within Mu that is only active when the autonomous Mu element is silenced or lost. We isolated 35 Mu alleles from the UniformMu population that represent insertions in 24 different genes. Most of these mutant alleles are due to insertions within gene coding sequences, but several 5' UTR and intron insertions were included. RNA-seq and de novo transcript assembly were utilized to document the transcripts produced from 33 of these Mu insertion alleles. For 20 of the 33 alleles, there was evidence of transcripts initiating within the Mu sequence reading through the gene. This outward-reading promoter activity was detected in multiple types of Mu elements and does not depend on the orientation of Mu. Expression analyses of Mu-initiated transcripts revealed the Mu promoter often provides gene expression levels and patterns that are similar to the wild-type gene. These results suggest the Mu promoter may represent a minimal promoter that can respond to gene cis-regulatory elements. Findings from this study have implications for maize researchers using the UniformMu population, and more broadly highlight a strategy for transposons to co-exist with their host.

The Role of Nonapoptotic Programmed Cell Death - Ferroptosis, Necroptosis, and Pyroptosis - in Pancreatic Ductal Adenocarcinoma Treatment.

Pancreatic ductal adenocarcinoma (PDAC) is the most lethal cancer, with a dismal 5-year survival rate of less than 10%. It is estimated that approximately 80% of pancreatic ductal carcinoma (PDAC) patients are diagnosed at an advanced or metastatic stage. Hence, most patients are not appropriate candidates for surgical resection and therefore require systemic chemotherapy. However, it has been reported that most patients develop chemoresistance within several months, partly because of antiapoptotic mechanisms. Hence, inducing alternative programmed cell death (PCD), including ferroptosis, necroptosis or pyroptosis, seems to be a promising strategy to overcome antiapoptosis-mediated chemoresistance. In this review, we shed light on the molecular mechanisms of ferroptosis, necroptosis and pyroptosis and suggest several potential strategies (e.g., compounds and nanoparticles [NPs]) that are capable of triggering nonapoptotic PCD to suppress PDAC progression. In conclusion, these strategies might serve as adjuvants in combination with clinical first-line chemotherapies to improve patient survival rates.

Rapid Detection of Gut Microbial Metabolite Trimethylamine N-Oxide for Chronic Kidney Disease Prevention.

The gut microbiota plays a critical role in chronic kidney disease (CKD) and hypertension. Trimethylamine-N-oxide (TMAO) and trimethylamine (TMA) are gut microbiota-derived metabolites, and both are known uraemic toxins that are implicated in CKD, atherosclerosis, colorectal cancer and cardiovascular risk. Therefore, the detection and quantification of TMAO, which is a metabolite from gut microbes, are important for the diagnosis of diseases such as atherosclerosis, thrombosis and colorectal cancer. In this study, a new "colour-switch" method that is based on the combination of a plasma separation pad/absorption pad and polyallylamine hydrochloride-capped manganese dioxide (PAH@MnO2) nanozyme was developed for the direct quantitative detection of TMAO in whole blood without blood sample pretreatment. As a proof of concept, a limit of quantitation (LOQ) of less than 6.7 µM for TMAO was obtained with a wide linear quantification range from 15.6 to 500 µM through quantitative analysis, thereby suggesting potential clinical applications in blood TMAO monitoring for CKD patients.

The third-generation EGFR inhibitor almonertinib (HS-10296) resensitizes ABCB1-overexpressing multidrug-resistant cancer cells to chemotherapeutic drugs.

The overexpression of the human ATP-binding cassette (ABC) drug transporter ABCB1 (P-glycoprotein, P-gp) or ABCG2 (breast cancer resistance protein, BCRP) in cancer cells often contributes significantly to the development of multidrug resistance (MDR) in cancer patients. Previous reports have demonstrated that some epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) could modulate the activity of ABCB1 and/or ABCG2 in human cancer cells, whereas some EGFR TKIs are transport substrates of these transporters. Almonertinib (HS-10296) is a promising, orally available third-generation EGFR TKI for the treatment of EGFR T790M mutation-positive non-small cell lung cancer (NSCLC) in patients who have progressed on or after other EGFR TKI therapies. Additional clinical trials are currently in progress to study almonertinib as monotherapy and in combination with other agents in patients with NSCLC. In the present work, we found that neither ABCB1 nor ABCG2 confers significant resistance to almonertinib. More importantly, we discovered that almonertinib was able to reverse MDR mediated by ABCB1, but not ABCG2, in multidrug-resistant cancer cells at submicromolar concentrations by inhibiting the drug transport activity of ABCB1 without affecting its expression level. These findings are further supported by in silico docking of almonertinib in the drug-binding pocket of ABCB1. In summary, our study revealed an additional activity of almonertinib to re-sensitize ABCB1-overexpressing multidrug-resistant cancer cells to conventional chemotherapeutic drugs, which may be beneficial for cancer patients and warrant further investigation.

Tomato locule number and fruit size controlled by natural alleles of lc and fas.

Improving yield by increasing the size of produce is an important selection criterion during the domestication of fruit and vegetable crops. Genes controlling meristem organization and organ formation work in concert to regulate the size of reproductive organs. In tomato, lc and fas control locule number, which often leads to enlarged fruits compared to the wild progenitors. LC is encoded by the tomato ortholog of WUSCHEL (WUS), whereas FAS is encoded by the tomato ortholog of CLAVATA3 (CLV3). The critical role of the WUS-CLV3 feedback loop in meristem organization has been demonstrated in several plant species. We show that mutant alleles for both loci in tomato led to an expansion of the SlWUS expression domain in young floral buds 2-3 days after initiation. Single and double mutant alleles of lc and fas maintain higher SlWUS expression during the development of the carpel primordia in the floral bud. This augmentation and altered spatial expression of SlWUS provided a mechanistic basis for the formation of multilocular and large fruits. Our results indicated that lc and fas are gain-of-function and partially loss-of-function alleles, respectively, while both mutations positively affect the size of tomato floral meristems. In addition, expression profiling showed that lc and fas affected the expression of several genes in biological processes including those involved in meristem/flower development, patterning, microtubule binding activity, and sterol biosynthesis. Several differentially expressed genes co-expressed with SlWUS have been identified, and they are enriched for functions in meristem regulation. Our results provide new insights into the transcriptional regulation of genes that modulate meristem maintenance and floral organ determinacy in tomato.

Integration of paper-based microarray and time-of-flight secondary ion mass spectrometry (ToF-SIMS) for parallel detection and quantification of molecules in multiple samples automatically.

With its low-cost fabrication and ease of modification, paper-based analytical devices have developed rapidly in recent years. Microarrays allow automatic analysis of multiple samples or multiple reactions with minimal sample consumption. While cellulose paper is generally used, its high backgrounds in spectrometry outside of the visible range has limited its application to be mostly colorimetric analysis. In this work, glass-microfiber paper is used as the substrate for a microarray. The glass-microfiber is essentially chemically inert SiOx, and the lower background from this inorganic microfiber can avoid interference from organic analytes in various spectrometers. However, generally used wax printing fails to wet glass microfibers to form hydrophobic barriers. Therefore, to prepare the hydrophobic-hydrophilic pattern, the glass-microfiber paper was first modified with an octadecyltrichlorosilane (OTS) self-assembled monolayer (SAM) to make the paper hydrophobic. A hydrophilic microarray was then prepared using a CO2 laser scriber that selectively removed the OTS layer with a designed pattern. One microliter of aqueous drops of peptides at various concentrations were then dispensed inside the round patterns where OTS SAM was removed while the surrounding area with OTS layer served as a barrier to separate each drop. The resulting specimen of multiple spots was automatically analyzed with a time-of-flight secondary ion mass spectrometer (ToF-SIMS), and all of the secondary ions were collected. Among the various cluster ions that have developed over the past decade, pulsed C60+ was selected as the primary ion because of its high secondary ion intensity in the high mass region, its minimal alteration of the surface when operating within the static-limit and spatial resolution at the ∼µm level. In the resulting spectra, parent ions of various peptides (in the forms [M+H]+ and [M+Na]+) were readily identified for parallel detection of molecules in a mixture. By normalizing the ion intensity of peptides with respect to the glass-microfiber matrix ([SiOH]+), a linear calibration curve for each peptide was generated to quantify these components in a mixture.

Effect of surface potential on epithelial cell adhesion, proliferation and morphology.

Cell adhesion is the basis of individual cell survival, division and motility. Hence, understanding the effects that the surface properties have on cell adhesion, proliferation and morphology are crucial. In particular, surface charge/potential has been identified as an important factor that affects cell behavior. However, how cells respond to incremental changes in surface potential remains unclear. By using binary self-assembled monolayer (SAM) modified Au surfaces that are similar in mechanical/chemical properties and provide a series of surface potentials, the effect of surface potential on the behavior of cells can be studied. In this work, the effect of surface potential on epithelial cells, including human embryonic kidney (HEK293T) and human hepatocellular carcinoma (HepG2), were examined. The results showed that the adhesion density of epithelial cells increased with increasing surface potential, which is similar to but varied more significantly compared with fibroblasts. The proliferation rate is found to be independent of surface potential in both cell types. Furthermore, epithelial cells show no morphological change with respect to surface potential, whereas the morphology of the fibroblasts clearly changed with the surface potential. These differences between the cell types were rationalized by considering the difference in extracellular matrix composition. Laminin-dominant epithelial cells showed higher adhesion density and less morphological change than did fibronectin-dominant fibroblasts because the more significant adsorption of positively charged laminin on the surface enhanced the adhesion of epithelial cells. In contrast, due to the dominance of negatively charged fibronectin that adsorbed weakly on the surface, fibroblasts had to change their morphology to fit the inhomogeneous fibronectin-adsorbed area.

A cascade of arabinosyltransferases controls shoot meristem size in tomato.

Shoot meristems of plants are composed of stem cells that are continuously replenished through a classical feedback circuit involving the homeobox WUSCHEL (WUS) gene and the CLAVATA (CLV) gene signaling pathway. In CLV signaling, the CLV1 receptor complex is bound by CLV3, a secreted peptide modified with sugars. However, the pathway responsible for modifying CLV3 and its relevance for CLV signaling are unknown. Here we show that tomato inflorescence branching mutants with extra flower and fruit organs due to enlarged meristems are defective in arabinosyltransferase genes. The most extreme mutant is disrupted in a hydroxyproline O-arabinosyltransferase and can be rescued with arabinosylated CLV3. Weaker mutants are defective in arabinosyltransferases that extend arabinose chains, indicating that CLV3 must be fully arabinosylated to maintain meristem size. Finally, we show that a mutation in CLV3 increased fruit size during domestication. Our findings uncover a new layer of complexity in the control of plant stem cell proliferation.

What lies beyond the eye: the molecular mechanisms regulating tomato fruit weight and shape.

Domestication of fruit and vegetables resulted in a huge diversity of shapes and sizes of the produce. Selections that took place over thousands of years of alleles that increased fruit weight and altered shape for specific culinary uses provide a wealth of resources to study the molecular bases of this diversity. Tomato (Solanum lycopersicum) evolved from a wild ancestor (S. pimpinellifolium) bearing small and round edible fruit. Molecular genetic studies led to the identification of two genes selected for fruit weight: FW2.2 encoding a member of the Cell Number Regulator family; and FW3.2 encoding a P450 enzyme and the ortholog of KLUH. Four genes were identified that were selected for fruit shape: SUN encoding a member of the IQD family of calmodulin-binding proteins leading to fruit elongation; OVATE encoding a member of the OVATE family proteins involved in transcriptional repression leading to fruit elongation; LC encoding most likely the ortholog of WUSCHEL controlling meristem size and locule number; FAS encoding a member in the YABBY family controlling locule number leading to flat or oxheart shape. For this article, we will provide an overview of the putative function of the known genes, when during floral and fruit development they are hypothesized to act and their potential importance in regulating morphological diversity in other fruit and vegetable crops.

MRI/SPECT-based diagnosis and CT-guided high-intensity focused-ultrasound treatment system in MPTP mouse model of Parkinson's disease.

Single-photon emission computed tomography (SPECT) of dopamine transporters with (99m)Tc-TRODAT-1 has recently been proposed to offer valuable information for the diagnosis of Parkinson's disease (PD). Furthermore, High-intensity focused ultrasound (HIFU) is a newly developed technique in which the energy of ultrasound wave is directed to a focused spot for the purpose treatment of PD. This study presents a diagnosis and image-guided system using HIFU to treat the mouse with PD under a designed stereotactic frame. The system comprises two key components: an automatic atlas-based SPECT/MRI image registration module for diagnosis and a stereotactic CT-guided module for HIFU treatment. The SPECT/MR image registration here is important in the non-invasive examination of the dopamine concentration in vivo. From the experimental results, the image registration module proves to have comparable performance to that derived from manual drawing by experts. In addition, the stereotactic CT-guided module achieved a positioning accuracy to within 2mm on the average, which is acceptable for the purpose of HIFU treatment.

Multi-image registration for evaluating the 99mTc-TRODAT-1 of Parkinson's rat model.

Study on small animal model using multiple imaging is an important procedure in medicine and physiology. Recently, Single Photon Emission Computed Tomography (SPECT) of dopamine transporter with (99cm)Tc-TRODA-1 has been proved to be a valuable and feasible mean of assessing the integrity of dopamine neurons. In this paper, an image registration algorithm for MRI and SPECT is proposed to evaluate the changes of a Parkinson's rat in brain organization and function. In addition, an automatic labeling algorithm which highlights striatum is necessary because manually segmenting these tissues from MRI is usually time consuming. As a result, we have built a computer-aid clinical diagnosis system which automates all the processes. This paper provides effective evaluation of Parkinson's symptoms by calculating the values of binding potentials for dopamine for quantification. Experimental result shows that the performance of the proposed method is better than the previous approach based on automated image registration.