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Kim, Lee, Cho, Chung, Park, and Jung: RNA-seq Gene Profiling Reveals Transcriptional Changes in the Late Phase during Compatible Interaction between a Korean Soybean Cultivar (Glycine max cv. Kwangan) and Pseudomonas syringae pv. syringae B728a
RNA-seq Gene Profiling Reveals Transcriptional Changes in the Late Phase during Compatible Interaction between a Korean Soybean Cultivar (Glycine max cv. Kwangan) and Pseudomonas syringae pv. syringae B728a
Myoungsub Kim1,†, Dohui Lee1,†, Hyun Suk Cho1, Young-Soo Chung1, Hee Jin Park2,3,* , Ho Won Jung4,*
1Department of Applied Bioscience, Dong-A University, Busan 49315, Korea
2Department of Molecular Genetics, Dong-A University, Busan 49315, Korea
3Department of Biological Sciences, Chonnam National University, Gwangju 61186, Korea
4Institute of Agricultural Life Science, Dong-A University, Busan 49315, Korea
*Co-corresponding authors: H. J. Park, Phone) +82-62-530-3410, FAX) +82-62-530-3409, E-mail) hjpark_bio@jnu.ac.kr. H. W. Jung, Phone) +82-51-200-7546, FAX) +82-51-200-7505, E-mail) hwjung@dau.ac.kr
† These authors contributed equally to this work.
Handling Editor: Sang-Wook Han
(Received on August 25, 2022; Revised on September 23, 2022; Accepted on September 26, 2022)
Soybean (Glycine max (L) Merr.) provides plant-derived proteins, soy vegetable oils, and various beneficial metabolites to humans and livestock. The importance of soybean is highly underlined, especially when carbon-negative sustainable agriculture is noticeable. However, many diseases by pests and pathogens threaten sustainable soybean production. Therefore, understanding molecular interaction between diverse cultivated varieties and pathogens is essential to developing disease-resistant soybean plants. Here, we established a pathosystem of the Korean domestic cultivar Kwangan against Pseudomonas syringae pv. syringae B728a. This bacterial strain caused apparent disease symptoms and grew well in trifoliate leaves of soybean plants. To examine the disease susceptibility of the cultivar, we analyzed transcriptional changes in soybean leaves on day 5 after P. syringae pv. syringae B728a infection. About 8,900 and 7,780 differentially expressed genes (DEGs) were identified in this study, and significant proportions of DEGs were engaged in various primary and secondary metabolisms. On the other hand, soybean orthologs to well-known plant immune-related genes, especially in plant hormone signal transduction, mitogen-activated protein kinase signaling, and plant-pathogen interaction, were mainly reduced in transcript levels at 5 days post inoculation. These findings present the feature of the compatible interaction between cultivar Kwangan and P. syringae pv. syringae B728a, as a hemibiotroph, at the late infection phase. Collectively, we propose that P. syringae pv. syringae B728a successfully inhibits plant immune response in susceptible plants and deregulates host metabolic processes for their colonization and proliferation, whereas host plants employ diverse metabolites to protect themselves against infection with the hemibiotrophic pathogen at the late infection phase.
Keywords: bacterial brown spot, compatible interaction, mRNA-seq, Pseudomonas syringae pv. syringae B728a, soybean
Soybean (Glycine max (L) Merr.), an edible legume, is one of the most important crops as an excellent source of plant-based oils, vegetable proteins, and secondary metabolites. Wild soybean (G. soja) was domesticated to G. max in Northeast Asia, including Korea, China, and Japan. So far, over 60,000 varieties have been developed and cultivated in different countries (Carter et al., 2004; Li et al., 2020). Since a reference genome of cultivated accession Williams 82 was published, functional studies of soybean are accelerating, and the pan-genome of soybean was also analyzed (Liu et al., 2015b, 2020; Schmutz et al., 2010; Wang and Tian, 2015). A Korean soybean cultivar (cv.), Kwangan, also known as 'Kwangankong' (Suwon No. 159), was bred by crossing a high-protein Japanese cv. Dongsan (Touzan) 69 with a virus disease-resistant Korean cv. Hwangkeum (Suwon No. 97), and largely cultivated in the Central and Southern regions of Korea (Kim et al., 2011; Lee et al., 2015; Soybean Breeding Team, Upland Crop Div., Crop Experiment and Experiment Station, 1994). The soybean cv. Kwangan exhibits good crop traits such as high protein content and seed yield and relatively higher resistance against pests and pathogens than other Korean sprout soybean cultivars (Kim et al., 2011; Soybean Breeding Team, Upland Crop Div., Crop Experiment and Experiment Station, 1994).
Like other crops and vegetables, the productivity and quality of soybean rely on disease management. Indeed, the average soybean yield loss due to pests and pathogens was 21.4% (11.0-32.4%) from 2010 to 2014 globally (Savary et al., 2019). Worldwide, cyst nematode (Heterodera glycines), white mold (Sclerotinia sclerotiorum), and soybean rust (Phakopsora pachyrhizi) are the most destructive pathogens in soybean, and many fungi, oomycetes, and nematodes also cause severe yield loss of soybean (Savary et al., 2019). Additionally, bacterial blight and bacterial pustule, the major bacterial diseases in fields, are caused by Pseudomonas syringae pv. glycinea and Xanthomonas axonopodis pv. glycines, respectively (Faske et al., 2014; Hartman et al., 2015). Even though agricultural practices such as aggressive usage of agricultural chemicals, crop rotation, and tillage, have been performed to avoid primary and secondary inoculum from previously infected crop residues, disease management of soybean is primarily dependent on cultivating disease-resistant plants (Faske et al., 2014). Thus, considering eco-friendly and sustainable food supply, previously unidentified genetic resources have to be unveiled and applied to molecular breeding to increase disease resistance in soybean plants.
P. syringae pv. syringae among more than 60 pathovars of P. syringae exhibits polyphagous bacterium with a broad-spectrum host range (Kennelly et al., 2007). P. syringae pv. syringae can infect soybean leaves and pods, and consequently cause necrotic lesions surrounded by chlorotic zones (Gnanamanickam and Ward, 1982). The genome sequence of P. syringae pv. syringae B728a (PssB728a), a representative strain of P. syringae pv. syringae that was firstly isolated from a snap bean (Phaseolus vulgaris) leaflet in Wisconsin, USA, was complete (Feil et al., 2005; Loper and Lindow, 1987). PssB728a retains an effector repertoire secreted into its host plants through its type III secretion system (Vinatzer et al., 2006). In the field, this bacterium can multiply and survive for many generations on the (non)host leaf surfaces as an epiphyte (Ercolani et al., 1974; Hirano and Upper, 1990; Lindemann et al., 1984). The size of the epiphytic population increases upon heavy rains, promoting the bacteria's rapid multiplication (Hirano et al., 1994, 1996). Thus, it is considered an intriguing source to study the molecular interaction between host plants and parasitic microbes (Vinatzer et al., 2006).
Recently, (molecular) components of soybeans associated with biotic stress response have been identified (Cooper et al., 2013; Delgado-Cerrone et al., 2018; Helm et al., 2019; Liu et al., 2015b; Pottinger et al., 2020; Russell et al., 2015; Wei et al., 2020; Yuan et al., 2020). Thus, we felt it is necessary to fill the knowledge gap in a Korean soybean accession. In this study, we evaluated the bacterial disease in the soybean cv. Kwangan inoculated with PssB728a and analyzed transcriptional change in soybean plants to identify genes involved in pathogenesis and immune response against a virulent Pseudomonas infection. In the infected soybean leaves, 8,902 and 7,786 genes were up- and down-regulated, respectively, at the late phase of infection. They appeared to be associated and involved in mainly biological pathways, including metabolic pathways, secondary metabolites, hormonal signal transduction, and plant-pathogen interaction upon PssB728a bacterial infection. Taken together, this pathosystem shows that the expression of soybean orthologs to well-known plant immune-related genes, especially in plant hormone signal transduction, MITOGEN-ACTIVATED PROTEIN KINASE (MAPK) signaling, and plant-pathogen interaction, is reduced during a compatible interaction. In contrast, soybean genes involved in the biosynthesis of primary and secondary metabolites are strongly expressed by PssB728a infection. This finding can help understand how PssB728a suppresses the plant immunity in the susceptible cultivar. We propose a few signaling pathways primarily affected by a virulent bacterial infection during a compatible interaction.
Plant material and growth conditions
G. max cv. Kwangan was used for this study. Soybean seeds were sterilized with chlorine gas (100 ml of 5.25% NaOCl supplemented with 3 ml of 12 N HCl) in a fume-hood overnight and sowed on soils (Nongwoo Bio, Suwon, Korea). Soybean plants grew under long-day conditions (25°C, 16 h light/8 h dark, 120 μmol/m2/s) in a walk-in growth chamber.
Bacterial strain and inoculation
The second trifoliate leaves of 3-week-old soybean plants were inoculated with PssB728a. We sprayed PssB728a suspension (OD600 = 0.01) in 10 mM MgSO4 containing 0.01% Silwet L-77 to the abaxial and adaxial side of leaves and kept the infected plants in the dark conditions with high humidity during the indicated periods. At least eight leaf discs were taken from infected leaves, and the number of bacteria in the leaf disc was counted using the typical serial dilution method. To analyze the epiphytic growth of PssB728a in plants, leaf discs of infected leaves with PssB728a were washed thoroughly with 10 mM MgSO4, in which bacterial growth was counted. The washed leaves were then soaked in 70% ethanol during several seconds for surface sterilization and were ground in 10 mM MgSO4 to measure the endophytic growth of PssB728a (Lee et al., 2012).
Transcriptome analysis
Trifoliate leaf tissues of soybean plants (~1 g) were harvested on the 5 days after spray-inoculation with 10 mM MgSO4 (2 of the control group) and PssB728a (OD600 = 0.01) (2 of treatment group) for the extraction of total RNA. RNA purification using RNeasy spin column (Qiagen, Hilden, Germany) was then conducted following the manufacturer's instruction. After confirming the RNA quality (Bioanalyzer, Agilent, Palo Alto, CA, USA), the total RNA was subject to construct mRNA sequencing libraries using a TruSeq Stranded Total RNA LT Sample Prep Kit (Plant) according to the manufacturer's instruction (Illumina, San Diego, CA, USA) (Martin and Wang, 2011). Each library from two biological replicates per treatment (total 4 libraries) was sequenced for 101 bp paired-end reads with a HiSeq 2500 platform (Illumina) serviced by Macrogen in Seoul, Korea.
The RNA-seq data were processed by TopHat2 and Bowtie2 (Langmead and Salzberg, 2012; Trapnell et al., 2009). After quality control of raw sequence reads, provided by Phred quality score and FastQC, adaptor sequences were trimmed using the Trimmomatic program to generate trimmed data (Bolger et al., 2014). The trimmed reads were aligned and assembled with the G. max v2.1 gene model (https://www.ncbi.nlm.nih.gov/assembly/GCA_000004515.4/) using the HISAT2 and StringTie (Kim et al., 2019; Pertea et al., 2015, 2016). The raw read counts, FPKM (fragments per kilobase of transcript per million mapping reads), TPM (transcripts per million), and simple description of the mapped transcripts to known soybean genes were presented in Supplementary Table 1.
Followed by the normalization by trimmed mean of M-values in edgeR, differentially expressed genes (DEGs) in infected plants were determined by two statistical outputs (|fold change (FC)| ≥ 2 and exactTest raw. P < 0.05) compared with the mock-inoculated plants (Chen et al., 2016). FC (infected samples/non-infected samples) and related statistical data of each DEG were listed in Supplementary Table 2.
Functional classification and enrichment analyses of DEGs
The DEGs were used for gene ontology (GO) enrichment analysis using Protein Analysis Through Evolutionary Relationships (PANTHER) (Mi et al., 2019; Thomas et al., 2003) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis (Kanehisa et al., 2007). The GO terms and KEGG pathways with P < 0.01 and Q < 0.01 were considered to be significantly enriched in DEGs. The list of enriched GO terms and KEGG pathways related to each DEG were shown in Supplementary Tables 3 and 4. We can share detailed analysis procedures under a request.
The soybean cv. Kwangan owns good agronomic features such as high resistance to soybean mosaic virus and high protein quality (Kim et al., 2011; Lee et al., 2015; Soybean Breeding Team, Upland Crop Div., Crop Experiment and Experiment Station, 1994). Therefore, the cv. Kwangan was broadly cultivated in Korea and used as a well-established parental plant to develop the Biotech soybean (Kim et al., 2012; Yeom et al., 2020). However, the molecular response of cv. Kwangan to bacterial disease, especially bacteria brown spot caused by P. syringae pv. syringae, has not been done. This study focused on the transcriptional changes in susceptible response in soybean plants upon PssB728a infection.
Growth of P. syringae pv. syringe B728a in trifoliate leaves of soybean plants
PssB728a exploits two different habitats (leaf surface and apoplast) as a phytopathogenic bacterium. The epiphytic PssB728a population acts as an inoculum to infect host plants successfully (Hirano and Upper, 2000). The epiphytic bacterial growth was counted every 2 days after a spray-inoculation of PssB728a. The number of bacteria on the leaf surface increased 2 days post inoculation (dpi), and the bacterial growth was saturated on the 4th day and 6th day (4 and 6 dpi) with populations of 106 colony forming unit (cfu) per leaf disc (Fig. 1A, left). Consistently, the endophytic bacterial population reached > 108 cfu per leaf disc at 4 dpi (Fig. 1A, right), and the lesion increased in size as time progressed (Fig. 1B). The bacterial growth assay reveals that PssB728a causes a compatible interaction with soybean cv. Kwangan.
DEGs during P. syringae pv. syringe B728a infection
Transcriptome sequencing libraries were made with total RNA from soybean leaves collected on day 5 after inoculation with 10 mM MgSO4 (non-infected sample, NI) and PssB728a (infected sample, IF). Among 60,506 known soybean transcripts, 31,608 genes, except 28,898 not detected in at least one sample, were used in the transcriptome analysis. The correlation matrix of Pearson's coefficient among four samples (NI_1, NI_2, IF_1, and IF_2) indicated that two independent biological replicates were highly reproducible (Fig. 2A). In addition, multidimensional scaling analysis showed that NIs and IFs were separately clustered, and components I and II reflected a 97.4% and 2.1% difference among samples, respectively (data not shown). These statistical analyses show that the transcriptome-seq data can represent the transcriptional reprogramming occurring in infected soybean leaves with PssB728a at 5 dpi.
In a volcano plot, the up-regulated and down-regulated genes with |FC| ≥ 2 and P < 0.05 were displayed on the right (brown dots) and the left (blue dots) sides, respectively (Fig. 2B). About 8,900 up-regulated genes (14.7% of known soybean transcripts) and 7,780 down-regulated genes (12.9%) were assigned as DEGs in infected leaves with PssB728a (Fig. 2C). Hierarchical clustering of expression levels of DEGs (up to 3,000 of 16,680 genes) indicated that two biological replicates for non-infected plants and infected plants had also been done reproducibly (Fig. 2D). Therefore, we suggest that DEGs' information obtained from the transcriptome analysis helps us to understand the transcriptional changes at 5 dpi in susceptible soybean plants to PssB728a infection. Whole lists of DEGs were presented in Supplementary Table 2.
The enriched GO terms of DEGs
The cellular and physiological processes of plants are altered upon pathogen infection. Molecular networks composed of complex interactions between/among genes, proteins, and metabolic compounds are involved especially in plant immune signaling, transcription of immune-related genes, and biosynthesis of phytohormones and secondary metabolites, as the outcome of a plant-microbe interaction (Delplace et al., 2022). A compatible interaction between host and pathogen leads to successful infection and disease (Glazebrook, 2005). Different from an incompatible interaction accompanying a hypersensitive response due to intensified immune responses, the compatible interaction entails interruption of plant immunity by effectors and toxins derived from pathogens, resulting in suppression of immune responses during pathogenesis (Chisholm et al., 2006; Dangl and Jones, 2001; Dodds and Rathjen, 2010; Jones and Dangl, 2006). To analyze which biological processes and molecular functions of DEGs were implicated in the compatible interaction between cv. Kwangan and PssB728a, the GO enrichment analysis was accomplished, which explains the associations between gene products and GO terms using the PANTHER classification system.
First, all up-regulated and down-regulated genes were subjected to GO analysis (GO biological process) to point out biological processes in which DEGs are involved. The top 10 categories exhibiting the lowest P-values were listed with the fold enrichments determined by the ratio of the number of observed genes versus that of expected genes (Fig. 3A and B). The up-regulated DEGs were enriched in 'small molecule metabolic process (GO:0044281)', 'child terms of organonitrogen compound metabolic process (GO:1901564) and cellular amide metabolic process (GO:0043603)', and 'generation of precursor metabolites and energy (GO:0006091)' (Fig. 3A). On the other hand, certain kinds of genes involved in 'regulation of metabolic process (GO:0019222)', 'macromolecule metabolic process (GO:0043170)', and 'protein modification process (GO:0006464)' were significantly down-regulated by PssB728a at 5 dpi (Fig. 3B). In addition, large sets of genes associated with RNA biological process appeared to be influenced by pathogen infection, because the expression of those genes involved in RNA biosynthesis, RNA metabolic process, mRNA metabolic process, and regulation of RNA biosynthetic process decreased upon bacterial infection (Supplementary Table 3). In the same line with it, the number of observed genes related to transcription was significantly less in the infected plants compared with that of expected genes of the soybean genome (Fig. 3C). Supporting this, the expression of 99 genes which are implicated in the metabolism of purines (heterocyclic aromatic organic compound consisting of two rings fused, adenine and guanine here), essential building block components for DNA and RNA, was altered by PssB728a infection (Supplementary Table 4). Second, we also analyzed the molecular function of DEGs' products (GO molecular function and GO-slim molecular function). Both up- and down-regulated DEGs were significantly enriched in 62 GO terms, including transferase activity, catalytic activity, kinase activity, and small molecule binding (Supplementary Table 3). These results suggest that primary and secondary metabolisms are mainly affected by PssB728a infection, whereas transcriptional activity decreased at 5 dpi.
Numerous genes encoding enzymes such as hydrolases, lyases, transferase, and metabolite interconversion enzymes were expressed highly upon bacterial infection (Fig. 4A). In contrast, a large number of genes encoding kinases, especially non-receptor serine/threonine protein kinases (about more than 150 genes) and protein modifying enzymes such as ubiquitin-protein ligases, expressed lower in infected soybean plants than mock-inoculated plants (Fig. 4B). In fact, KEGG pathway analysis revealed that the high population of DEGs was mostly associated with metabolic pathways (carbonate, secondary metabolite, starch and sucrose, amino sugar metabolism) and protein processing (Supplemental Table 4).
The KEGG pathways related to DEGs
Transcriptional profiles of several crop plants after pathogen infections clarified particular metabolic and signaling pathways tightly related to compatible and incompatible interaction (Cregeen et al., 2015; Gyetvai et al., 2012; Meng et al., 2021; Sonah et al., 2016; van Esse et al., 2009; Wang et al., 2010).
Using 3,775 genes mapped in KEGG pathways (http://www.kegg.jp/kegg/pathway.html) among 16,688 DEGs, gene-set enrichments were analyzed to examine which pathways were activated or suppressed at 5 dpi in infected leaves (Kanehisa et al., 2022). Fig. 5 presents the top 15 pathways with P-values < 7.47E-45 and Q-values < 6.63E-44 as follows; metabolic pathways, biosynthesis of secondary metabolite, carbon metabolism, plant hormone signal transduction, MAPK signaling pathway, plant-pathogen interaction, photosynthesis, protein processing in the endoplasmic reticulum (ER), purine metabolism, pyruvate metabolism, etc. Many genes were mapped simultaneously into different pathways. For example, among 137 genes in the category of glycolysis [7], whose expressions were affected upon bacterial infection, 49 genes (about 36%) participate in the pyruvate metabolism [15]; 50% of genes (49 genes) in pyruvate metabolism work at glycolysis-related pathway as well.
Cellular detoxification of reactive oxygen species (ROS) formed from different metabolic pathways and upon various unfavorable stress conditions is an essential biological process in living organisms to maintain homeostasis (Huang et al., 2019). Upon bacterial infection, expression of the biosynthetic genes of antioxidant compounds appeared to be increased as expected. For instance, the expression of genes encoding enzymes involved in ascorbate biosynthesis, such as mannose-6-phosphate isomerase 1 (EC: 5.3.1.8, Entrez_Gene_ID: 100815644), phosphomannomutase (EC: 5.4.2.8, Entrez_Gene_ID: 732605), and mannose-1-phosphate guanylyltransferase 1-like (EC: 2.7.7.13, Entrez_Gene_ID: 100777120), increased during infection (Supplementary Table 4). In addition, numerous glutathione S-transferases, which function as one of the major detoxifying enzymes by conjugating tripeptide (γ-Glu-Cys-Gly) glutathione to various hydrophobic and electrophilic substrates (Liu et al., 2015a), were actively transcribed in the leaves infected with PssB728a (Supplementary Table 4).
Furthermore, a variety of genes related to an ER stress response, which occurs when the capacity of the ER to fold proteins becomes saturated and leads to activation of stress-adaptive response called unfolded protein response (UPR) (Bao and Howell, 2017; Ruberti et al., 2015), showed the altered transcription patterns under PssB728a infection. Three soybean orthologs of an ER stress sensor, the ER-resident transmembrane protein inositol-requiring enzyme 1 (serine/threonine-protein kinase/endoribonuclease IRE1, EC: 2.7.11.1 or EC: 3.1.26, Entrez_Gene_IDs: 100785904, 100788389, 102661527), reduced their mRNA expression upon bacterial infection (Supplemental Table 4). An ortholog of another ER-resident transmembrane protein ER stress sensor, PERK (eukaryotic translation initiation factor 2-alpha kinase 4/eIF-2-alpha kinase GCN2 isoform X1 (EC:2.7.11.1, Entrez_Gene_ID: 100797996), which has been characterized as an ER stress sensor in animal cells but not identified experimentally in plant cells (Park and Park, 2019), also showed the reduced expression in infected leaves. In contrast, several ER-stress responsive genes and genes whose products participate in the protein secretion process exhibited higher expression upon bacterial infection (Supplemental Table 4). An ER stress-inducing compound, tunicamycin enhanced the susceptibility to P. syringae pv. tomato DC3000 in Arabidopsis while gene expression of PR1 and FLS2-mediated PTI such as callose deposition increased (Chakraborty et al., 2017). ire1 and bzip60 mutants, which are deficient in IRE1, an ER stress sensor activating UPR and its splicing target bZIP-transcription factor, bZIP60, respectively, were more susceptible to P. syringae pv. maculicola (Moreno et al., 2012). Consistently, knock-down tobacco plants of IRE1 and bZIP60 via virus-induced gene silencing were more sensitive to the necrotic fungal pathogen, Alternaria alternata (Xu et al., 2019). The transcriptome profile of soybean plants infected with PssB728a suggests that ER-mediated biological process is significantly affected in a compatible interaction (Saijo et al., 2009).
Among the top 15 pathways (Fig. 5), we analyzed further details about plant hormone signal transduction [5], MAPK signaling pathway-plant [10], and plant-pathogen interaction [11]. Genes participating in auxin- and cytokinin-mediated signaling were up-regulated in soybean leaves under PssB728a infection, whereas ethylene (ET)-, jasmonic acid (JA)-, and salicylic acid (SA)-mediated signaling seemed to be down-regulated in PssB728a-infected leaves (Supplementary Fig. 1). In the hormone-biosynthetic aspects, transcript levels of genes participating in the last half of α-linolenic acid metabolic pathway for JA biosynthesis decreased by more than 2-folds in the infected plant (Supplementary Fig. 2). On the other side, soybean orthologs encoding three critical enzymes for the ET biosynthesis, S-ADENOSYLMETHIONINE SYNTHETASE (SAM), 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE (ACS), and AMINOCYCLOPROPANECARBOXYLATE OXIDASE (ACO) were actively transcribed under PssB728a infection (Supplementary Table 4). Additionally, a putative ortholog of Arabidopsis ISOCHORISMATE SYNTHASE1 (ICS1), ICS was strongly transcribed in the infected leaves (EC:5.4.4.2, Entrez_Gene_ID: 100799025) albeit genes involved in shikimate pathway did not show any trends on transcriptional change under infection (Supplementary Table 4). Note that we do not have any experimental clues on the dynamics of these hormones in the infected plants. To measure hormone levels during infection will be necessary to understand the compatible interaction. Taken together, we assume that PssB728a successfully suppresses plant immune signaling activated by ET, JA, and SA and employs growth-related hormone signaling for their colonization.
MAPK signal cascades consisting of three sequential serine/threonine kinases (MAPKKK → MAPKK → MAPK) transmit environmental and developmental signals upon a range of stresses, including pathogen infection, heat, freezing, ROS, drought, and wounding (Meng and Zhang, 2013). Various hormones such as auxin, abscisic acid (ABA), JA, SA, and ET affect the MAPK signaling pathway (Jagodzik et al., 2018). Upon PssB728a infection, ABA receptors PYRABACTIN RESISTANCE 1 (PYR1)/PYRABACTIN RESISTANCE 1-LIKE (PYL) and its downstream signaling components type 2C protein phosphatases (PP2C), negative regulators of ABA signaling, displayed higher mRNA expression. In contrast, the expressions of MAPK signaling components were reduced, probably leading to a non-efficient and unsuccessful stress-adaptive response with disease increase (Supplementary Fig. 3). MAPK pathway relays signals from membrane-residing immune receptors to downstream components for defense activation in plants (Thulasi Devendrakumar et al., 2018). Most of the MAPKKKs, MAPKKs, and MAPKs detected in this study were down-regulated in the transcript levels on day 5 after PssB728a infection (Supplementary Fig. 3). Besides MAPK signaling cascades, genes encoding extracellular (co)receptors, CYCLIC NUCLEOTIDE GATED CHANNELs, and Ca2+-signaling proteins were weakly expressed in the infected leaves of soybean (Supplementary Fig. 4). However, a soybean ortholog of FLAGELLIN-SENSITIVE 2 (FLS2) showed increased mRNA expression in the soybean leaves infected with PssB728a. However, its downstream pathways, MEKK1-MKK4/5-MPK3/6 and MPK4, reduced their transcription. In addition, soybean homologous genes of well-identified defense regulators in Arabidopsis and tomato, such as EDS1, RIN4, SGT1, and Pti1/5/6, displayed reduced mRNA levels in the infected leaves (Supplementary Fig. 4). This KEGG pathway analysis suggests that the plant immune responses of soybean cv. Kwangan are compromised by PssB728a.
In this study, we developed a pathosystem between soybean cv. Kwangan and PssB278a, a causal pathogen of bacterial brown spot disease, and presented the transcriptional changes in soybean leaves on day 5 after PssB728a infection. Unexpectedly, mRNA expression of homologous genes to well-identified immune-related genes in model and other crop plants decreased or was not dramatically altered in soybean leaves on day 5 after infection. In contrast, primary and secondary metabolisms underwent a change in PssB728a-infected conditions. Thus, these analyses represent the transcriptional changes at the late phase of a compatible interaction and reflect the suppression of plant immunity in susceptible plants by virulent pathogen infection. Furthermore, this study identifies large number of candidates for future functional analyses and provides a foundation to understand molecular mechanisms implicated in the compatible interaction of a susceptible Korean soybean cultivar and bacterial brown spot disease.
This work was supported by the New Breeding Technologies Development Program of the Rural Development Administration (PJ01477702 and PJ01653304) (Ho Won Jung), the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Republic of Korea (2020R1A6A1A03047729) (Ho Won Jung and Hee Jin Park), and the Green Fusion Technology Graduate School Program of the Ministry of Environment (Myoungsub Kim, Dohui Lee).
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Disease symptom development and bacterial growth in leaves of soybean cv. Kwangan infected with Pseudomonas syringae pv. syrinage (Pss) B728a. (A) The epiphytic and endophytic bacterial growths were tested on infected soybean leaves. At least eight leaf discs were used to count the endophytic and epiphytic bacterial growth of PssB728a on the indicated day post inoculation (dpi). The bars present the mean ± standard error. (B) The second trifoliate leaves from 3-week-old soybean plants grown in long-day conditions were spray-inoculated with 10 mM MgSO4 (mock) and PssB728a (OD600 = 0.01) and incubated under dark conditions with high humidity and 25°C during the experiment. Disease symptoms were taken in photographs 0, 3, and 5 dpi.
Quality of RNA-seq analysis and number of differentially expressed genes (DEGs) in infected soybean leaves with Pseudomonas syringae pv. syringae B728a. (A) Correlation matrix of Pearson's coefficient (-1 ≤ r ≤ 1) to determine the similarity of each sample. NI and IF mean samples from non-infected and PssB728a-infected leaves of soybean plants, respectively. A closer value to r = 1 presents a higher similarity between samples. (B) A volcano plot to verify DEGs in PssB728a-infected plants versus non-infected soybean. Blue and brown dots indicate genes displaying fold change (FC) ≤ −2 and FC ≥ 2 with P < 0.05, respectively. Vertical dotted lines showed the |FC| = 2 and a horizontal dotted line indicates P = 0.05. (C) Numbers of genes whose FC is up- and down-regulated on day 5 after PssB728a infection. (D) Heat map showing the expression pattern of DEGs in two biological replications of non-infected (NI) leaves and PssB728a-infected (IF) leaves. Genes are grouped according to hierarchical clustering analysis (Euclidean distance, complete linkage). Rows are clustered using distance and average linkage. The color gradient represents the Z-score for log2 FC-based normalized values.
Enriched gene ontology (GO) terms of differentially expressed genes (DEGs) in infected soybean plants. (A, B) Top 10 GO biological process terms based on the number of observed genes in this analysis among up-regulated DEGs (A) and down-regulated DEGs (B). The numeric on the right side of the bars shows the exact numbers of observed genes. Fold enrichment was calculated by the ratio of observed gene versus expected gene. (C) Terms of GO-slim molecular function showing fold enrichment < 1, P < 0.005, and Q < 0.05 in up-regulated DEGs. The whole GO biological process, cellular component, and molecular function terms for each DEG were presented in Supplementary Table 3. FDR, false discovery rate.
Enriched gene ontology (GO) protein class terms of differentially expressed genes (DEGs) in infected soybean plants. (A, B) Top 10 GO protein class terms based on the number of observed genes in this analysis among up-regulated DEGs (A) and down-regulated DEGs (B). Up-regulated (8,902 genes, A) and down-regulated (7,786 genes, B) genes were applied to GO enrichment protein class analysis. For each protein, class GO term, the expected (empty) and observed gene (filled) numbers whose P-values are lower than 0.01 (statistical significance) are presented. No. of observed genes, number of DEGs associated with a GO term for protein class; no. of expected genes, number of genes expected for each GO term in the genome after normalization of the whole number of genes analyzed in this analysis (8,902 and 7,786).
The top 15 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in which differentially expressed genes (DEGs) are participating. Each protein ID of DEGs was converted to KEGG gene ID using a biological DataBase network (bioDBnet, https://biodbnet-abcc.ncifcrf.gov/) and the converted KEGG gene IDs were used for the KEGG pathway analysis (KEGG Mapper-Color). The top 15 pathways were presented here with the exact number of genes. The whole KEGG pathways related to each DEG were listed in Supplementary Table 4.
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Supplement1
Hee Jin Park
Ho Won Jung


Liz Chen, a doctoral student in health behavior, is leveraging mobile technologies to transform health education and support adolescent well-being. Jessica Shor, a master of business administration student, works full-time within renewable energy and wants to increase opportunities for women in the industry.
The two University of North Carolina at Chapel Hill students recently received American Association of University Women (AAUW) awards focused on "expanding women's potential and supporting their future promise." In total, the AAUW provided fellowships and grants to 250 women and community projects for academic year 2018-19.
Chen receives an AAUW American Dissertation Fellowship. Named a Forbes 2018 "30 Under 30" social entrepreneur, Chen is working with colleagues to develop a mobile application in which teens can share stories and read information on topics such as puberty, healthy relationships and bullying. For her dissertation research, Chen is developing a scale to measure the acceptability of mobile health (mHealth) interventions among teens.
Shor receives an AAUW Career Development Grant. As finance manager for Enel Green Power North America, Shor manages a project finance team and works with investors to secure funding for the company's large-scale wind and solar energy projects.
Jennifer Gerz-Escandón, associate dean for interdisciplinary education and fellowship programs at The Graduate School, said the AAUW American Dissertation Fellowship and Career Development Grant awards affirm the timely and important research and professional goals Chen and Shor are pursuing at Carolina.
"Each year, AAUW funding plays a valuable role in increasing the number of females completing doctorates and enhancing women's career advancement prospects. For Liz and Jessie, the impact of these generous awards begins with degree funding and will continue to be felt professionally for years to come," she added.


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Archive for the 'Home' Category
Blowing Smoke: Netflix promises to douse smoking lamp
Today's non-story concerns some do-gooder consumer group and our very own Netflix, based in Los Gatos.
Seems the streaming behemoth has too many movies and series featuring chain smokers and/or vapers. And this according to the DC-based Truth Initiative is bad for impressionable teens who binge on "Stranger Things," "Orange Is the New Black" and other home entertainment cash cows.
Without contesting the yawn-inducing findings, a contrite Netflix promises to do better in the future and start monitoring material rated TV-14 or PG-13. Unless of course we're talking about shows like "Stranger Things" and Prime's "The Marvelous Mrs. Maisel" that take place in some bygone era and depend on cigs for period authenticity.
C'mon, guys, the argument seems to go. Would anybody buy "Mad Men" or Tarantino's upcoming "Once Upon a Time in Hollywood" without that tell-tale blue haze.
With that barn-size caveat, which falls under directorial discretion, the streaming service, in essence, promises to comply. "We … recognize that smoking is harmful and when portrayed positively on screen can adversely influence young people," the company hedged in a statement to Variety.
Before we rush to congratulate Netflix for its benevolence, its fair's fair civic-mindedness, remember this: the old school studios and networks have been regularly promising to clean up their butt-festooned back lots for years. It makes good copy. And better publicity.
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Stanley Donen (1924 – 2019): Dancer, director proved a nimble pragmatist
"I can't change the world," said a typically stoic Stanley Donen, recipient of a lifetime achievement award at the San Francisco International Film Festival in 1995.
Movie buffs begged to disagree. As proof they pointed to the director- choreographer's "On the Town," "Seven Brides for Seven Brothers" and, of course, "Singin' in the Rain" (co-directed with Gene Kelly), and reminded Donen his name had been affixed to some of the most stylish and scintillating entertainment of all time.
It was this body of work, which ranged from trend-bucking musicals to sparkling comedy capers, that brought Donen to San Francisco's Castro Theatre. The then-71-year-old film maker received SFIFF's coveted Akira Kurosawa Award. A Q&A followed a screening of his never-more-entrancing "Funny Face" (1957), a May-December romance with Audrey Hepburn, Fred Astaire and some of George and Ira Gershwin's best love songs.
Donen, a dyed-in-the-woof New Yorker, died last Thursday in Manhattan. He was 94.
Donen's "Singin' in the Rain" (1952), "Charade" (1963) and "Bedazzled" (1968) were slated for later in the festival. "Singin' in the Rain," a musical-comedy about Hollywood's reluctant transition to "talkies," has long topped fan-mag polls. Its only competition: "Casablanca."
"Who knew it was going to be revered all these years later?" Donen shrugged. "When it opened, it was just another movie. The reviews referred to it as 'this very nice MGM musical.' Bosley Crowther of the New York Times half dismissed it. He thought it was fair."
To what, then, did the dancer-turned-choreographer-turned-director attribute its growing appeal?
"It's full of energy — everybody was young and lively and at the peak of their powers," replied Donen, who when the cameras started rolling was a 27-year-old veteran with 10 years' experience and 50 movie-musical sequences behind him. "Also, it's unusually earthy for a musical. . . . It tells it like it is, or was, with a funny attitude."
The sequence everyone recalls has Kelly splashing happily through the rain to the title tune. Donen recalled the number with a shrug and a smile.
"We always knew what we had to do. We said, 'Gene's going to dance in the rain, and the place for him to do that is when he's happiest, when he's in love.' No great inspiration. It took 2 1/2 days to shoot."
While awaiting his next movie — which turned out to be A.R. Gurney's two-character "Love Letters," released in 1999 — Donen spent a lot of time in the dark, watching movies. He saw Woody Allen's "Bullets Over Broadway" four times and continued to search retrospectives for the names Ingmar Bergman, Kurosawa and Orson Welles. He loved Quentin Tarantino's "Pulp Fiction": "It's fresh, inventive . . . constantly surprising."
Donen stayed in the game by "constantly reinventing myself." He made his Broadway directorial debut in late '93, with the calamitous "The Red Shoes." (It closed in three days.) When we talked he was considering other stage projects.
"But between talking about it and getting it on is a large hiccup," he allowed. "We need to get the score, the cast, the money. Doing a movie or a show is like moving a snowball up a mountain."
Ironically, the man who refused to bow to protestations of "… but it's never been done!" — remember the Jerry Mouse – Gene Kelley routine in "Anchors Aweigh" and Astaire as human fly in the "Royal Wedding"? — was, at heart, a bottom-line pragmatist. It didn't bother him that movies cost more (as much as $175 million, if the rumors surrounding Kevin Costner's "Waterworld" were to be believed). "Show business is two words — partly show, partly business. If they (the producers) think they can satisfy the business side, God speed. I hope every movie is a hit. The more hits, the better for everybody."
Donen's last crowd-pleaser was 1963's "Charade," a sleek, Paris-set murder mystery with an unforgettable Henry Mancini score. He still winces when critics refer to it as "an homage to Hitchcock."
"He isn't the sole owner of the mystery-romance genre any more than I'm the sole owner of the musical film," Donen said.
Donen considered "Two for the Road," with Albert Finney and Audrey Hepburn, his last great picture. The critics agree, pointing to its Antonioni- like time shifts and brittle dissection of what at first looks like a fairy-tale romance. "Many people have said, 'I got married or I got divorced after seeing that movie.' But I don't believe it."
Though it now has a cult following, "Two for the Road" also flopped.
"We'd all like our movies to gross $325 million, like 'Forrest Gump,' " Donen acknowledged. "It's like Samuel Goldwyn said, 'If people don't want to go to your movie, nothing can stop them.' "
This article was originally published in April, 1995.
Contact Glenn Lovell at glovell@aol.com
Short-form Fright by Two Masters
CinemaDope is rewatching two horror anthologies this afternoon — Masaki Kobayashi's "Kwaidan" and the Franco-Italian homage to Poe, "Spirits of the Dead" — well, the Fellini-directed episode of the latter "Toby Dammit." My kind of ghostly anthologies. Smart, scary, wickedly sardonic. Eat your hearts out Miike & Tim Burton!
The only thing that comes close is Fellini's "Toby Dammit," kicker to "Spirits of the Dead," a 1968 Poe-inspired trilogy. Terence Stamp plays a happily out-of-it star who agrees to appear at a debauched awards show (think Oscars hosted by Caligula) for the ultimate swag, a gold Ferrari sports car. Maybe the most audacious of the maestro's life-as-cavalcade satires, this one comes with blackbird nuns, Sgt Peppers era Beatles, sycophantic studio types, and a coquettish Death in party smock. Here's a taste of Ennio Morricone's puckish piano score.
Hard to believe "Kwaidan's" distributor, concerned about the 2 hr-plus running length, lopped off the haunting "Woman of the Snow" segment for the US premiere. Shot entirely on two studio soundstages, thereby ensuring total stylization, this tale of a young woodcutter who enters into a pact with a snow witch has always been my favorite exercise in the supernatural —
Scott 'Hershel' Wilson (1942-2018): Anonymous character actor stayed course & found second-time-around cult status
By nature soft-spoken and introverted, some called him temperamental, Scott Wilson had, ironically, one of Hollywood's splashier sendoffs. He made his big screen debut as the Mississippi drifter falsely accused of murder in 1967's powerful "In the Heat of the Night," starring Sidney Poitier and Rod Steiger. Wilson's character is introduced running across a long bridge. Director Norman Jewison wanted to try something new. He filmed bridge and fugitive in extreme long shot, as Sheriff Gillespie (Steiger) in squad car methodically closes in on the panicked suspect. The scene is imaginatively backed by Quincy Jones' scat music, which slows to raspy crawl as Wilson's fugitive tires and surrenders.
Wilson didn't know it at the time but that extreme long shot would become a metaphor of sorts for a career that began in closeup — with a decade of leads in such cult favorites as "In Cold Blood," "The Grissom Gang" and, opposite Burt Lancaster and Gene Hackman, "The Gypsy Moths" — but was for the most part taken for granted, viewed from the wrong end of a telescope by producers and casting agents.
I met Wilson, who died last week at age 76, when I was on sabbatical at USC and freelancing for the LA Times. I had just seen Tim Robbins' powerful anti-capital punishment docudrama "Dead Man Walking" with Sean Penn as a killer on death row, Susan Sarandon as activist Sister Helen Prejean … and, in a role so brief if you blinked you missed it, a rheumy Scott Wilson as the cynical prison chaplain. I remember thinking, 'I know that guy — he's good, he's always been good. Why isn't he getting better roles.' I decided to find out why.
After the story (below) ran, Wilson called to say thanks. "It got me an agent," he said, appreciatively. We stayed in touch by phone. I used him as a grounded Hollywood source on more than one occasion. He often talked about his work as a SAG activist. He read for but lost the beekeeper lead to Peter Fonda in Victor Nunez's "Ulee's Gold." That one hurt; Fonda's Oscar nomination should have been his. And he continued to operate just under the radar, picking up the occasional studio gig but mostly roles in small independent releases like "Monster" and "Junebug." He played the apoplectic father in a remake of "The Heartbreak Kid," a window-dressing general in Michael Bay's "Pearl Harbor," and, of course, the bearded Hershel, Rick & Co's patriarch-conscience, in three seasons of "The Walking Dead."
Special to The Times
Scott Wilson made the cover of Life Magazine in 1967. To prove it, as much to himself as visitors, he has a framed copy of the May 12 issue hanging in his study. It depicts Wilson, then 24, Robert Blake and Truman Capote–stars and author of "In Cold Blood"–posing on a lonely stretch of Kansas highway.
Un der the words "Nightmare Revisited" is a caption that would portend much to come in Wilson's 30 frustrating years as one of Hollywood's most respected but least utilized character actors: "Truman Capote stands between actors playing killers in movie of his book."
Who are these anonymous actors? You have to look inside. No cover ID. Director-screenwriter Richard Brooks wanted it that way. He wanted to further his film's documentary-like realism by making the public think Wilson and Blake were Dick Hickock and Perry Smith, the young drifters executed in 1965 for murdering a Kansas farm family.
He succeeded only too well in Wilson's case.
"Every actor in the English-speaking world wanted those two roles, including Newman and McQueen," recalls Wilson, who plays the prison chaplain in the current "Dead Man Walking," another Oscar-nominated film about capital punishment. "Brooks hired two 'unknowns' and he wanted to keep it that way. We were treated like two killers he had somehow run across."
Verisimilitude was pushed to absurd lengths in promoting the crime thriller. It wasn't enough to have the young stars' eyes glowering down from a Sunset Boulevard billboard: "Brooks had the poster with our eyes taken down and replaced with one of the real killers' eyes.
Wilson, cautiously mounting a comeback at 53, says he never saw himself as "star material." He was always introverted, temperamental, distrustful of authority.
"It was the late '60s," he explains, drawing on a cigarette. "I was anti-establishment, anti-Vietnam."
Never trust anyone over 30, right?
"Yeah, I took the sound bite and went with it."
Wilson applied his generation's motto to the Hollywood bureaucracy, which insisted upon typecasting him as Dick Hickock's evil twin.
"I didn't handle things well," he acknowledges during an interview at the West Hollwood apartment he shares with his artist wife, Heavenly. "There were some dark holes in my–I don't know if you want to call it 'a career'–in my time out here."
After "In Cold Blood" and two offbeat but unsuccessful follow-ups (Sydney Pollack's "Castle Keep," John Frankenheimer's "The Gypsy Moths"), Wilson couldn't find work–at least not on his terms. It was a calamitous turn of events for someone now recalled by a director friend as "the Sean Penn of his day." Penn and co-star Susan Sarandon are nominated for Oscars for "Dead Man Walking"; he plays a silver-tongued death-row inmate, a role that might have been modeled on Wilson's Hickock.
Wilson is flattered and made uneasy by the comparison. "I do see some of myself in Sean. He doesn't play the game," observes the Georgia-born actor, who will next be seen in "The Grass Harp" (another Capote adaptation) and "Shiloh" (from the award-winning children's book).
When the conversation turns to his best qualities, Wilson looks away, kneads the back of his neck.
"I think you always get a credibility out of me," he finally offers. "I think you always get a believability out of me."
Wilson's directors–including Walter Hill, Steve Kloves and Richard Fleischer (who cast Wilson as the disillusioned rookie in 1972's "The New Centurions")–agree with this self-assessment. They also think Wilson is scandalously under-employed.
Says Kloves, who used Wilson as a penny-ante thief in "Flesh and Bone": "Scott is one of those guys who's powerful, perversely, because he doesn't call attention to himself. . . . I'd love to find something just for him, to write a movie where he's the guy."
Action director Hill relied on Wilson for key moments in "Johnny Handsome" and "Geronimo." "Scott brings a quality of both anxiety and pain to his parts," Hill observes. "I don't know where he gets it from, but there's a kind of melancholy he brings to things."
In the upcoming "Shiloh," directed by Dale Rosenbloom and featuring Michael Moriarty and Rod Steiger, Wilson handles villain chores. He plays Judd, the West Virginia hunter who mistreats the hound dog of the title.
Rosenbloom didn't want a stereotypical bad guy. Wilson delivered a villain with a past. "It's the eyes," he says. "There are stories in those eyes."
Charlie Matthau cast Wilson as a grieving father in "The Grass Harp." "You instantly see the grief in Scott's face," he says. "He conveyed everything in a look."
The "look" to which many allude could come from years of rejection and disappointment. Or it may just be, as Robert Blake would have it, "your basic dark side, man."
This article first appeared in the LA Times on March 17, 1996.
Burt Reynolds (1936-2018): More Gator than Gable
Though he appeared in a handful of action classics, including "Deliverance" and "The Longest Yard," Reynolds will be remembered by fans for his crass crash comedies. He turned down leads in "Star Wars" and "Die Hard" and admitted to being a "lousy" judge of his own talent.
Burt "Buddy" Reynolds — the good ol' boy hero in a slew of demo-derby epics, including the roisterous "Smokey and the Bandit" — gave arguably three great performances in a wildly uneven film and TV career that spanned six decades. Make that four performances if you count his popular guest-hosting stints for the vacationing Johnny Carson on "The Tonight Show." I do.
Reynolds died Thursday (9/6/18) in Jupiter, FL, of what's being reported as cardiac arrest. He was 82 and for years had looked alarmingly gaunt.
As Entertainment Editor at the Fort Lauderdale Sun-Sentinel, I crossed paths with the sometimes defensive and prickly leading man several times, starting with the Atlanta premiere of "Smokey and the Bandit" and including the New Orleans press sendoff for "Semi-Tough" and the gala opening of the Burt Reynolds Dinner Theatre in Jupiter. (Reynolds, Liza Minnelli, Martin Sheen and others taught at the theater's drama school, where student actors earned Equity cards.)
Reynolds grew up nearby, in Riviera Beach and attended Palm Beach High School. An All-State fullback, he earned an athletic scholarship to Florida State, where his dreams of a pro career were soon dashed by a knee injury. He changed his major to drama and, after paying dues in summer stock, made his Broadway debut in 1961. A revival of "Mister Roberts" starring Charlton Heston led to TV offers and recurring roles on "Riverboat" and "Gunsmoke." Often compared to Brando (not favorably), the swarthy Reynolds did a dead-on caricature of the mumbling Method icon on "The Twilight Zone."
Universal signed him to a six-year contract but cut him after a year. "They fired Clint Eastwood, David Janssen and me at the same time," he recalled in Atlanta. "They said Clint's Adam's Apple was to big and he had to have it operated on. They said Janssen's ears were too big and he sounded too much like another Gable. And they told me I was incorrigible, which was their way of saying I was untalented."
After a handful of low-budget actioners, including Sam Fuller's "Shark," Reynolds got his big break in "Deliverance," based on the James Dickey bestseller about four Atlanta friends on a weekend canoeing trip that turns deadly. Reynolds was paid $50,000 for the plum part of Lewis, the poseur survivalist. Next came the coveted title role in "The Man Who Loved Cat Dancing," a big-budget adaptation that costarred Sarah Miles and drew attention in the tabloids for the stars' steamy behind-the-scenes romance and the suicide of Miles' personal assistant.
Along with "Deliverance," Reynolds best performances came in Robert Aldrich's "The Longest Yard" and Paul Thomas Anderson's "Boogie Nights." For the former he didn't have to reach far to play a fallen gridiron star who lands in prison where he's forced to don helmet and pads for a high-stakes scrimmage. In "Boogie Nights" (1997), he appeared as a San Fernando Valley porn director who's surrogate father to cast and crew. He was ballyhooed as a shoo-in for Oscar nominations for "Deliverance" and "The Longest Yard." Almost a quarter century later, he received one for "Boogie Nights," an adult "family movie" he didn't pretend to like or understand.
Peter Bogdanovich saw Reynolds as the modern-day incarnation of the ah-shucks hayseed often played by Gary Cooper and Joel McCrea. He cast him first as a hammy matinee idol in "Nickelodeon," his Valentine to the early days of picture-making, and then as a tux-and-tails sophisticate in "At Long Last Love," a tone-deaf musical costarring Cybill Shepherd. The stars sang and danced to Cole Porter. Badly.
Reynolds also costarred with Gene Hackman in "Lucky Lady" and Clint Eastwood in "City Heat." Both period buddy pictures tanked.
When the mainstre am studio films didn't pan out, Reynolds returned to his southern rural base, which couldn't get enough of the unapologetically crass interplay between Jackie Gleason's sputtering sheriff and Reynolds' legendary bad boy in the first two "Smokey and the Bandit" movies. Much in the same vein were "White Lightning," "Gator," "Hooper," "Stroker Ace" and "The Cannonball Run," a mostly improvised cross-country race for which the star was paid a then-record $5 million. The even less organized "Cannonball Run 2," likened at the time to "a Texas barbecue with a hundred of your closest friends," co-starred Reynolds' pals Dom DeLuise, Marilu Henner and Mel Tillis. Aging Rat Packers Frank Sinatra, Dean Martin, Sammy Davis Jr., Henry Silva and Shirley MacLaine dropped by for cameos.
Reynolds knew the slapstick comedies hurt his reputation, but they paid the rent. When we sat down, he was in a been-there-done-that mood and more than ready to segue into something more challenging. His next films: the underrated "Semi-Tough," based on the Dan Jenkins' outrageous novel about the NFL, and "The End," a leaden attempt at a Woody Allen dark comedy. Reynolds, prone to dizziness and anxiety attacks, identified with the latter's hapless hypochondriac.
" 'Smokey' will probably be the last of the chase films," said Reynolds, who ruled the box office with "Smokey II" and its ilk from 1978 to 1982. "I don't think anybody will be able to top it. I think we said it all."
On five feature films and a ton of TV episodes Reynolds called the shots behind the camera. While hardly a great director, he was a decent one, especially on "Sharky's Machine" (1981), a grim, surprisingly cynical cop thriller.
Reynolds, who lived a stone's throw from the National Enquirer, was perfect tabloid fodder. His always seemed in the midst of relationship and money woes. Though he played the womanizer in Blake Edwards "The Man Who Loved Women" and other films, he was in fact an old-fashioned romantic who tended to carry a torch for his true loves — singer-TV host Dinah Shore, 20 years his senior, and Sally Field, who rode shotgun in "Smokey and the Bandit I & II." (Reynolds admitted jealousy over her Oscar win for "Norma Rae" led to their breakup.)
"I'd be lying if I said (the tabloid gossip) didn't bother me,
he said in the spring of 1977. "If I were married and running around, I would deserve to be called a womanizer. But I'm a bachelor and that means I should be able to go out with whomever I choose — a different lady every night if I want.
"But all the press puts a lot of pressure on my relationships; it scares the ladies off. Where can we go so we won't get that kind of pressure? The public library?"
Reynolds again became tabloid fodder during his acrimonious split from second wife Loni Anderson. He wrote about the divorce and protracted custody battle in his 1994 memoir, "My Life." On the book tour Reynolds sat with KGO radio's Ronn Owens for an interview that quickly went from uncomfortable to hostile when a caller asked the star, "What species of wig do you have on? Chipmunk?"
The top box office draw for five consecutive years always seemed one residual check from bankruptcy. In recent years he sold movie memorabilia to settle debts. Which explains why he worked right up until the end. He's in two upcoming releases, including Quentin Tarantino's Charles Manson movie, "Once Upon a Time in Hollywood."
Who Benefits from New Oscar Category? You or Disney?
AMPAS announced Thursday (9/7/18) that because of negative response to last month's announcement of changes to the Academy Awards, it would huddle longer and might not implement the Outstanding Achievement in Popular Film category after all.
If the Academy Awards were telecast tomorrow instead of March 4, the five "nominees" for the newly minted Outstanding Achievement in Popular Film would be, in descending order: "Black Panther" (Disney), "Avengers: Infinity War" (Disney), "Incredibles 2" (Disney), "Jurassic World: Fallen Kingdom" (Universal), and "Deadpool 2" (Fox). (Of course one or two of these titles could be muscled out of contention with "Creed II" and DC's "Aquaman" around the corner.)
So much for suspense. So much for variety. So much for a healthy mix of studio and indie releases. So much for avoiding perceived conflicts of interest.
The hydra-like Disney Company owns ABC, which as the network that televises the Academy Awards recommended the change, which will most benefit … you got it, Disney!
By adding this new category, Oscar has inched closer to the dumbest of dumb awards shows, the People's Choice Awards, where bes t is synonymous with most popular. Past Favorite Movie winners: "Pretty Woman," "Rocky II," "Top Gun," "Liar Liar," "Twilight."
Two questions about the new category loom:
Can a movie like "Black Panther" be nominated in both Best Picture and Outstanding Achievement in Popular Film? The Academy says yes. Doesn't this, as others have opined, dilute or cheapen a best picture nomination?
Also, what happens when one of the years most popular films also happens to be really bad or politically embarrassing, like, say, Mike Todd's moribund "Around the World in 80 Days" or John Wayne's rightwing "The Green Berets" or Mel Gibson's anti-Semitic "The Passion of the Christ," which at least one critic (myself) likened to "a religious snuff film"?
ABC suggested the new category because, in the network's opinion, Oscar was in danger of becoming irrelevant. Top grossers like "Star Wars: The Last Jedi," "Captain America" and "Guardians of the Galaxy," coincidentally all Disney releases, were being all but overlooked when it came time to divvy up the gold-plated hardware. ("Last Jedi" was nominated for f/x, music, and the two sound awards – losing in all four categories. "Guardians" was nominated for f/x, makeup and hairstyling.)
The argument went something like: Year in and year out, members of the Academy of Motion Pictures Arts & Sciences favor offbeat, relatively low-budget film like "There Will be Blood," "American Hustle," "Birdman," "12 Years a Slave," "The Shape of Water," "Three Billboards," "Moonlight," "Manchester by the Sea," "I, Tanya," and so on.
Unquestionably audacious, these films are usually dark, depressing … unpopular. Mainstream audiences prefer upbeat, exhilarating, action-packed, i.e. the latest Marvel or DC superhero mashup.
And because their type of film isn't rewarded come Oscar time, Hollywood's target audience (male and somewhere between 14 and 35 year olds) could care less about who wins. Hence, the precipitous drop in viewership. According to the folks at Nielsen, the 90th Oscars attracted 26.5 million viewers worldwide, a drop of almost 20 percent from 2017 and, according to the trades, the worse turnout in the show's history.
As a journalist who over the years deadlined backstage at either the Music Center or Shrine Auditorium, the Oscars, which could take almost four hours, seemed like a feat of stamina. So I applaud the Academy's decision to hold the show to a strict three-hour format during which some of the less popular technical awards will be presented during commercial breaks and announced later. I've never cared much about the documentary short or sound mixing categories.
In 2020, the Oscar telecast will move to early February, further closing the gap between the Academy Awards and the Foreign Press's more raucous and freewheeling Golden Globes (Jan. 6) and avoiding the dreaded awards-season burnout.
Bradbury torched (well, kinda) early draft of HBO's dystopian "F-451"
CinemaDope scored one of the last interviews with Ray Bradbury. We talked to the author about HBO's proposed adaptation of his never-more-prescient "Fahrenheit 451," published in 1953, when the stench of Nazi book burnings was still in the air.
In the telefilm, scheduled for this weekend, Michael B. Jord an ("Creed") plays protagonist Montag, a fallen-away fireman in a near future society that has outlawed the printed word as seditious. Near future? Sounds more like the here-and-now.
If the scripts Bradbury sampled were any indication, the new version would be less successful than Francois Truffaut's sadly neglected 1966 adaptation, starring Oskar Werner, Julie Christie (as both member of the book underground and Montag's horny wife), and one of Bernard Herrmann's most evocative scores.
A bookseller friend in Atlanta had somehow come into possession of draft No. 6 of the script, commissioned by Mel Gibson's Icon Films. He sent it to Bradbury, who — curmudgeonly under the best of circumstances — let out a loud Yeeech!
"I was afraid to open it. Finally I turned to page 42, very gingerly. It's where Fire Chief Beatty comes to Montag's house and Mildred asks, 'Would you like some coffee?' Beatty replies, 'D oes a bear s— in the woods?' I closed the script and didn't read the rest. I couldn't believe it."
He then, fittingly, fed it to his backyard barbecue. (Not really, but he thought about it.)
Bradbury remained dumbfounded that Hollywood kept screwing up his dystopian classic. "It's stupid," he said, all they have to do is shoot the pages."
Back then, Tom Hanks and Frank Darabont ("The Shawshank Redemption") were connected to the project, as well as a proposed $70-million HBO serialization of Bradbury's "The Martian Chronicles." Bradbury thought Darabont a good choice. "He's does beautiful work. When I saw 'The Green Mile,' I called him and said, 'Is the ending a Bradbury ending?' He said, 'Yes, I read you in high school.' "
Darabont and Hanks eventually left the project.
When 'No' Meant 'Maybe'
What Movies Taught Us About Sexual Misconduct
As new allegations of sexual misconduct arrive daily — from the high-tech sector, academia, state and national politics — it's time to circle back and ask: What role have the movies played in conditioning a generation of men to believe, no matter the resistance, that they are entitled to sexual favors from interns, colleagues and fans.
With apologies to Rodgers and Hammerstein, a variation on their show tune about prejudice keeps playing in my head:
Men have to be taught from year to year /
That sexual harassment is nothing to cheer /
They've got to be carefully taught.
Examples of men physically abusing women in the movies abound. We can trace them to D.W. Griffith's silent "Broken Blossoms" and, later, "Public Enemy" (Cagney using Mae Clarke's face as a grapefruit juicer) and "The Philadelphia Story" (Cary Grant shoving Katherine Hepburn backward through her front door).
Since many of the alleged abusers now in the news — from fallen studio exec Harvey Weinstein to TV host Charlie Rose to actors Kevin Spacey and Richard Dreyfuss — are roughly Boomer age, they most likely were reared on movies from the 1950s and '60s, when limits were less well-defined and "no" sometimes meant "maybe."
This, of course, can never be taken as justification for sexual harassment or assault. Hollywood has always been a lousy source of advice on how to conduct yourself in real-world relationships, where "no" means just that.
The movies of Weinstein's and Spacey's youths trafficked in a troubling double-standard: When an alpha male demanded affection screen, it was exhilarating and romantic, perfectly normal. When an aggressive female demanding attention, alarm bells sounded. "Alert! Alert! Aberrant personality!"
In "The Graduate," Dustin Hoffman's Ben Braddock follows Elaine Robinson to UC Berkeley. In 1966, we applauded his determination. He was a die-hard romantic who wouldn't take "no" for an answer. When Jessica Walter pursues Clint Eastwood's Carmel disc jockey with a bit more fervor in "Play Misty for Me," she's an out-and-out loony, every red-blooded male's worst nightmare.
When Charles Grodin in "The Heartbreak Kid" abandons his new wife on their Miami Beach honeymoon to pursue a spoiled sun goddess (Cybill Shepherd), he's an incorrigible cad, yes, but one who's living the American Dream.
And so it goes …
I saw Hitchcock's "Marnie" when it opened in 1964. I was 15. Sean Connery, working the sang froid that had served him as agent 007, hires a private eye to find Tippi Hedren's troubled title character, an d when he runs her to ground, he sounds much like a big game hunter who has bagged a trophy antelope: "I've tracked you and caught you and, by God, I'm going to keep you!"
I can still remember the rush I got from Connery's snarled pronouncement. It reinforced the sense of entitlement that we Boomer males learned from the movies, where persistence that at times amounted to societal-sanctioned rape was rewarded. Indeed, later in the same film, Connery, claiming his matrimonial prerogative, rapes Marnie on their cruise-ship honeymoon.
A decade earlier, in "On the Waterfront," Eva Marie Saint's Edie attempts to fend off Marlon Brando's Terry Malloy. He breaks down her door and pins her to the wall; her pounding fists and cries of "Stay away from me!" soon give way to an embrace. This forced compliance was considered so exciting at the time the scene made it into the trailer.
It's no coincidence that Toback, Dreyfuss, Steven Segal and others who have been accused of sexual harassment and assault are in the late 60s or early 7s. Producer Harvey Weinstein, in a statement following the New York Times's publication of allegations by Ashley Judd and Rose McGowan, used this as his defense. "I came of age in the '60s and '70s, when all the rules about behavior and workplaces were different," he wrote. "That was the culture then."
Dustin Hoffman was recently accused of inappropriate sexual overtures toward a 17-year-old production assistant during the filming of a 1985 TV adaptation of "Death of a Salesman." Ironic, no? His Braddock character in "The Graduate" was once embraced as a counterculture icon for turning his back on his parents' materialism and hypocrisy. Now, as we wince through Ben's public shaming of Elaine (at a strip club, no less) and his dogged pursuit of her in Berkeley, the character seems more alienating than alienated. Once condoned as funny and irreverent his behavior today would qualify as stalking and warrant a restraining order or jail time.
Glenn Lovell has written about film for the Boston Globe, Los Angeles Times and Variety. He teaches film studies at De Anza College.
Published in San Francisco Chronicle (11-20-17)
Mickey Malice — The Trump Years
Emboldened by Trump's "Fake News" Campaign, Disney Blacklists L.A. Times. Media Fight Back with United Front. It Wasn't Always Thus. A Backstory.
Hollywood's most vengeful and manipulative studio?
Fanfare, please. Dun-daah-DUNN! Winner and still champion: Disney. Tweak the Mouse's nose with negative reviews and/or news stories and you'll likely regret it.
That's what I found when I conducted a national film critics survey. Everyone from T ime magazine's Richard Schickel to Chicago Sun-Times's Roger Ebert to The New Yorker's Pauline Kael and Wall Street Journal's Joe Morgenstern participated. A questionnaire went out from USC's Annenberg School of Communication & Journalism, where I was on sabbatical from my job as film critic for the San Jose Mercury News.
The results — published in an arts journal in 1996 as "Caught in the Machinery: How Hollywood Subverts the Media" – caused what then passed for a media storm. CNN, Ebert and Columbia Journalism Review reported on the findings. Matt Drudge predicted the author "would not only never eat lunch in (Hollywood) again … if he's not careful, he may find himself turning into the main course for some very hungry Dalmatians."
More than 50 critics, entertainment editors and film writers weighed in. And when the numbers were crunched Disney outranked the competition as, in the eyes of critics and editors, the "most manipulative" studio, followed closely by Warner Bros., Miramax (then a subsidiary of Disney), and Universal. MGM and 20th Century Fox were adjudged the least manipulative.
The survey grew out of my personal experience. I was blacklisted by Disney in the spring of 1993, cut from screenings, junkets and interviews. Why? The studio had found the "tone" o f my coverage (reviews, columns, features) not to its liking. Asked for something more concrete, like factual errors or a star who had been misquoted, nothing was forthcoming. My boss, Robin Doussard, told Disney's front office, "Lovell's our critic. Want coverage? Deal with him." (Note: When this happened, the Merc was a paper to be reckoned with, one of the 10 best papers in the country, according to Time magazine.)
In less than two weeks, Disney reversed itself. All's forgiven, if not forgotten, I was told through an intermediary. Let's move on.
Why this unpleasant amble down memory lane? Because Disney recently went after the L.A. Times for what it called a "biased and inaccurate" investigative piece on the studio's one-sided business dealings with the city of Anaheim, home to Disneyland. The ban from screenings and interviews lasted four days.
The big difference between what I and others (like Jami Bernard of the Daily News had experienced at the hands of Disney? Back then, when the Internet was in its infancy and print was still paramount, individual papers and their critics were left to turn in the wind. Colleagues were just pleased it wasn't them. If a studio came down on a critic, there was probably good reason. "Lovell's notoriously 'difficult,' always demanding the sun and moon. He probably got what he deserved, etc., etc." (Then, as now, I wore the "Scarlet D" with pride.)
Twenty years later, the L.A. Times's East Coast competition jumped to, lined up behind one of their number under fire. Deny our brethren access to "Star Wars VIII: The Last Jedi" screenings, the New York Film Critics Circle and the other critics groups threatened, we'll hit you where it hurts; we'll stamp your films "ineligible" for year-end honors.
Little wonder Fantasyland hoisted a white flag.
Can we chalk up this once-unheard-of show of solidarity to Trump and the current administration's war on the First Amendment? Has Disney, controlling under the best of circumstances, been emboldened to follow the president's lead and dismiss coverage it dislikes as "fake news." Sounds reasonable.
And has the media, likewise, been emboldened to join arms and present a united front? Those writing about entertainment certainly feel a new sense of urgency. Under assault politically, we are, across the board, more sensitive to outside manipulation. And whether the bully sports orange comb-over or mouse ears, he must be faced down. What was once tolerated as all part of the game, collateral damage, if you will, is now seen as intolerable.
Critic-author Glenn Lovell teaches film studies at De Anza College and other Bay Area schools.
Are Media Outlets Inflating Toback's Credentials to Advance Harassment Story?
The New York Times incorrectly ID'd him as "an executive." The San Francisco Chronicle referred to him as "the latest powerful man in Hollywood" to be accused of sexual harassment. And the L.A. Times, which broke the Weinstein-Lite exposé, inflated his credentials, overselling the all-but-forgotten screenwriter-director as a Hollywood insider, a player.
If that weren't enough both the Washington Post and SF Chron erroneous ly reported that James Toback won an Oscar for the Warren Beatty vehicle "Bugsy." (He was nominated, but, appropriately, lost out to Callie Khouri for "Thelma & Louise.")
What's behind such careless entertainment coverage? Circulation numbers and ratings, of course, fueled by a newsroom directive to keep "our readers" hanging on every sordid disclosure. After the New York Times embarrassed the L.A. Times by breaking the Harvey Weinstein story, a story the hometown Hollywood paper should have been all over, the L.A. Times has been playing catch-up. Which must have played into the decision to oversell Toback, pass off a small-fry as a trophy catch.
Last I looked screenwriter-director Toback, 72, was a struggling fringe-dweller, a talented but marginal indie filmmaker who, throughout his career, has complained of barely having two nickels to rub together.
You wouldn't know this from media fallout following the L.A. Times' Sunday story headlined "38 Women have come forward to accuse director James Toback of sexual harassment." (This number has, in a few days, swelled to almost two hundred, including Oscar-winner Julianne Moore.)
Little wonder the NBC and CBS News anchors who over the weekend reported on the "scoop" couldn't help looking off-camera for clarification: James who? He directed what?
The best the L.A. Times could come up with to help readers ID Toback we re decades-old credits starring the pre-Iron Man Robert Downey Jr. – "The Pick-Up Artist" (1987) and "Two Girls and a Guy" (1997). More recently Toback was involved in a sympathetic documentary on heavyweight champ-convicted rapist Mike Tyson. (The Times reporter coyly lumped the original 1974 "The Gambler,'' starring James Caan, with Toback's directing credits. That film was directed by England's Karel Reisz; Toback did the original screenplay.)
We're not disputing that reporting on Hollywood's endemic mistreatment of women, countenanced by men as an OT perk, is an important story, and that the longer this story remains front and center the more women will feel emboldened and come forward with their stories.
But in the rush to one-up the competition, guys, let's not oversell what we have, fudge on the facts and reporting. (Where in last Sunday's story were the comments from longtime Toback friend Downey? Even a "no comment" from the actor's agent would have helped.) Anyone with even a passing knowledge of the independent film scene knows Toback resides half-a-rung up from Russ "Supervixens" Meyer, a sad, sleazy throwback to the days of the casting-couch audition. He has openly bragged about same.
But in terms of play and importance this bottom feeder doesn't belong on Page 1 with producer-studio chief Weinstein, only too happy to share the spotlight, I'm guessing. Toback, who denies he forced himself on anyone — and supports these protestations with a doctor's note (diebetic, he is incapable of maintaining an erection) — is symptomatic of a misogynistic culture that has festered for far too long; Weinstein, a hydra-like producer-exec, hires and fires the likes of Toback. He is illustrative of something deeper, more pervasive and dangerous.
Comments? glovell@aol.com

redpajama_set_name: RedPajamaCommonCrawl


text:
From journals and scientific sources
Tansey, 2012 Genetic predictors of response to serotonergic and noradrenergic antidepressants in major depressive disorder...
By Altostrata,
November 11, 2012 in From journals and scientific sources
No such genetic predictors exist, concludes the most authoritative study to date.
PLoS Med. 2012 Oct;9(10):e1001326. doi: 10.1371/journal.pmed.1001326. Epub 2012 Oct 16.
Genetic predictors of response to serotonergic and noradrenergic antidepressants in major depressive disorder: a genome-wide analysis of individual-level data and a meta-analysis.
Tansey KE, Guipponi M, Perroud N, Bondolfi G, Domenici E, Evans D, Hall SK, Hauser J, Henigsberg N, Hu X, Jerman B, Maier W, Mors O, O'Donovan M, Peters TJ, Placentino A, Rietschel M, Souery D, Aitchison KJ, Craig I, Farmer A, Wendland JR, Malafosse A, Holmans P, Lewis G, Lewis CM, Stensbøl TB, Kapur S, McGuffin P, Uher R.
Institute of Psychiatry, King's College London, London, United Kingdom.
Abstract and full text at http://www.ncbi.nlm.nih.gov/pubmed/23091423
It has been suggested that outcomes of antidepressant treatment for major depressive disorder could be significantly improved if treatment choice is informed by genetic data. This study aims to test the hypothesis that common genetic variants can predict response to antidepressants in a clinically meaningful way.
METHODS AND FINDINGS:
The NEWMEDS consortium, an academia-industry partnership, assembled a database of over 2,000 European-ancestry individuals with major depressive disorder, prospectively measured treatment outcomes with serotonin reuptake inhibiting or noradrenaline reuptake inhibiting antidepressants and available genetic samples from five studies (three randomized controlled trials, one part-randomized controlled trial, and one treatment cohort study). After quality control, a dataset of 1,790 individuals with high-quality genome-wide genotyping provided adequate power to test the hypotheses that antidepressant response or a clinically significant differential response to the two classes of antidepressants could be predicted from a single common genetic polymorphism. None of the more than half million genetic markers significantly predicted response to antidepressants overall, serotonin reuptake inhibitors, or noradrenaline reuptake inhibitors, or differential response to the two types of antidepressants (genome-wide significance p<5×10(-8)). No biological pathways were significantly overrepresented in the results. No significant associations (genome-wide significance p<5×10(-8)) were detected in a meta-analysis of NEWMEDS and another large sample (STAR*D), with 2,897 individuals in total. Polygenic scoring found no convergence among multiple associations in NEWMEDS and STAR*D.
No single common genetic variant was associated with antidepressant response at a clinically relevant level in a European-ancestry cohort. Effects specific to particular antidepressant drugs could not be investigated in the current study. Please see later in the article for the Editors' Summary.
From the paper:
Editors' Summary
Genetic and environmental factors can influence a person's response to medications. Taking advantage of the recent advancements in genetics, scientists are working to match specific gene variations with responses to particular medications. Knowing whether a patient is likely to respond to a drug or have serious side effects would allow doctors to select the best treatment up front. Right now, there are only a handful of examples where a patient's version of a particular gene predicts their response to a particular drug. Some scientists believe that there will be many more such matches between genetic variants and treatment responses. Others think that because the action of most drugs is influenced by many different genes, a variant in one of those genes is unlikely to have measurable effect in most cases.
Why Was This Study Done?
One of the areas where patients' responses to available drugs vary widely is severe depression (or major depressive disorder). Prescription of an antidepressant is often the first step in treating the disease. However, less than half of patients get well taking the first antidepressant prescribed. Those who don't respond to the first drug need to, together with their doctors, try multiple courses of treatment to find the right drug and the right dose for them. For some patients none of the existing drugs work well.
To see whether genetic information could help improve the choice of antidepressant, researchers from universities and the pharmaceutical industry joined forces in this large study. They examined two ways to use genetic information to improve the treatment of depression. First, they searched all genes for common genetic variants that could predict which patients would not respond to the two major groups of antidepressants (serotonin reuptake inhibitors, or SRIs, and noradrenaline reuptake inhibitors, or NRIs). They hoped that this would help with the development of new drugs that could help these patients. Second, they looked for common genetic variants in all genes that could identify patients who responded to one of the two major groups of antidepressants. Such predictors would make it possible to know which drug to prescribe for which patient.
What Did the Researchers Do and Find?
The researchers selected 1,790 patients with severe depression who had participated in one of several research studies; 1,222 of the patients had been treated with an SRI, the remaining 568 with an NRI, and it was recorded how well the drugs worked for each patient. The researchers also had a detailed picture of the genetic make-up of each patient, with information for over half a million genetic variants. They then looked for an association between genetic variants and responses to drugs.
They found not a single genetic variant that could predict clearly whether a person would respond to antidepressants in general, to one of the two main groups (SRIs and NRIs), or much better to one than the other. They also didn't find any combination of variants in groups of genes that work together that could predict responses. Combining their data with those from another large study did not yield any robust predictors either.
What Do These Findings Mean?
This study was large enough that it should have been possible to find common genetic variants that by themselves could predict a clinically meaningful response to SRIs and/or NRIs, had such variants existed. The fact that the study failed to find such variants suggests that such variants do not exist. It is still possible, however, that variants that are less common could predict response, or that combinations of variants could. To find those, if they do exist, even larger studies will need to be done.