The structure of genetic interaction networks predicts that, analogous to synthetic lethal interactions between non-essential genes, combinations of compounds with latent activities may exhibit ...potent synergism. To test this hypothesis, we generated a chemical-genetic matrix of 195 diverse yeast deletion strains treated with 4915 compounds. This approach uncovered 1221 genotype-specific inhibitors, which we termed cryptagens. Synergism between 8128 structurally disparate cryptagen pairs was assessed experimentally and used to benchmark predictive algorithms. A model based on the chemical-genetic matrix and the global genetic interaction network failed to accurately predict synergism. However, a combined random forest and Naïve Bayesian learner that associated chemical structural features with genotype-specific growth inhibition had strong predictive power. This approach identified previously unknown compound combinations that exhibited species-selective toxicity towards human fungal pathogens. This work demonstrates that machine learning methods trained on unbiased chemical-genetic interaction data may be widely applicable for the discovery of synergistic combinations in different species.
To better understand off-target effects of widely prescribed psychoactive drugs, we performed a comprehensive series of chemogenomic screens using the budding yeast Saccharomyces cerevisiae as a ...model system. Because the known human targets of these drugs do not exist in yeast, we could employ the yeast gene deletion collections and parallel fitness profiling to explore potential off-target effects in a genome-wide manner. Among 214 tested, documented psychoactive drugs, we identified 81 compounds that inhibited wild-type yeast growth and were thus selected for genome-wide fitness profiling. Many of these drugs had a propensity to affect multiple cellular functions. The sensitivity profiles of half of the analyzed drugs were enriched for core cellular processes such as secretion, protein folding, RNA processing, and chromatin structure. Interestingly, fluoxetine (Prozac) interfered with establishment of cell polarity, cyproheptadine (Periactin) targeted essential genes with chromatin-remodeling roles, while paroxetine (Paxil) interfered with essential RNA metabolism genes, suggesting potential secondary drug targets. We also found that the more recently developed atypical antipsychotic clozapine (Clozaril) had no fewer off-target effects in yeast than the typical antipsychotics haloperidol (Haldol) and pimozide (Orap). Our results suggest that model organism pharmacogenetic studies provide a rational foundation for understanding the off-target effects of clinically important psychoactive agents and suggest a rational means both for devising compound derivatives with fewer side effects and for tailoring drug treatment to individual patient genotypes.
Vaccinia virus (VACV) is a large, cytoplasmic, double-stranded DNA virus that requires complex interactions with host proteins in order to replicate. To explore these interactions a functional high ...throughput small interfering RNA (siRNA) screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF) influencing the replication and spread of an eGFP-tagged VACV. The experimental design incorporated a low multiplicity of infection, thereby enhancing detection of cellular proteins involved in cell-to-cell spread of VACV. The screen revealed 153 pro- and 149 anti-viral HFs that strongly influenced VACV replication. These HFs were investigated further by comparisons with transcriptional profiling data sets and HFs identified in RNAi screens of other viruses. In addition, functional and pathway analysis of the entire screen was carried out to highlight cellular mechanisms involved in VACV replication. This revealed, as anticipated, that many pro-viral HFs are involved in translation of mRNA and, unexpectedly, suggested that a range of proteins involved in cellular transcriptional processes and several DNA repair pathways possess anti-viral activity. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. This advancement in our understanding of the VACV life cycle provides a reliable knowledge base for the improvement of poxvirus-based vaccine vectors and development of anti-viral theraputics.
The identification of self-renewing and multipotent neural stem cells (NSCs) in the mammalian brain holds promise for the treatment of neurological diseases and has yielded newinsight into brain ...cancer. However, the complete repertoire of signaling pathways that governs the proliferation and self-renewal of NSCs, which we refer to as the ‘ground state’, remains largely uncharacterized. Although the candidate gene approach has uncovered vital pathways in NSC biology, so far only a few highly studied pathways have been investigated. Based on the intimate relationship between NSC self-renewal and neurosphere proliferation,we undertook a chemical genetic screen for inhibitors of neurosphere proliferation in order to probe the operational circuitry of the NSC. The screen recovered small molecules known to affect neurotransmission pathways previously thought to operate primarily in the mature central nervous system; these compounds also had potent inhibitory effects on cultures enriched for brain cancer stem cells. These results suggest that clinically approved neuromodulators may remodel the mature central nervous system and find application in the treatment of brain cancer. (colour figure available in PDF version)
The onset of plant life is characterized by a major phase transition. During early heterotrophic seedling establishment, seed storage reserves fuel metabolic demands, allowing the plant to switch to ...autotrophic metabolism. Although metabolic pathways leading to storage compound mobilization are well-described, the regulatory circuits remain largely unresolved. Using an inducible knockdown approach of the evolutionarily conserved energy master regulator Snf1-RELATED-PROTEIN-KINASE1 (SnRK1), phenotypic studies reveal its crucial function in Arabidopsis thaliana seedling establishment. Importantly, glucose feeding largely restores growth defects of the kinase mutant, supporting its major impact in resource mobilization. Detailed metabolite studies reveal sucrose as a primary resource early in seedling establishment, in a SnRK1-independent manner. Later, SnRK1 orchestrates catabolism of triacylglycerols and amino acids. Concurrent transcriptomic studies highlight SnRK1 functions in controlling metabolic hubs fuelling gluconeogenesis, as exemplified by cytosolic PYRUVATE ORTHOPHOSPHATE DIKINASE (cyPPDK). Here, SnRK1 establishes its function via phosphorylation of the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63), which directly targets and activates the cyPPDK promoter. Taken together, our results disclose developmental and catabolic functions of SnRK1 in seed storage mobilization and describe a prototypic gene regulatory mechanism. As seedling establishment is important for plant vigor and crop yield, our findings are of agronomical importance.
Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant's nutritional ...status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S
-basic-leucine-zipper (S
-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S
-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III
sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase
, involved in N homeostasis, as direct S
-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S
-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.
Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant's nutritional ...status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S1-basic-leucine-zipper (S1-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S1-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III SWEET sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase GLUTAMINE AMIDO-TRANSFERASE 1_2.1, involved in N homeostasis, as direct S1-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S1-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.
Paratesticular fibrous pseudotumors represent benign new growths confined to intrascrotal structures. Both pathogenesis and clinical management are little understood due to the rarity of the lesion, ...with less than 200 cases reported to date. Recently, paratesticular fibrous pseudotumors have been postulated to be immunoglobulin G4-related, pathogenetically. Here we report two cases of patients with paratesticular fibrous pseudotumor to highlight the clinical features of this rare disease and we report the immunohistochemical examinations to support the theory of paratesticular fibrous pseudotumor being an immunoglobulin G4-related disease.
A 28-year-old white man presented with a painless intrascrotal mass. After a clinical examination, a malignant growth was suspected. His ultrasound results revealed a well-demarcated hypoechoic lesion of 1.5cm in diameter at the spermatic cord. Our patient underwent local excision. His follow-up has been uneventful for 12 years. The second case was an 18-year-old white man who presented with a painless scrotal mass suspicious of testicular tumor. A magnetic resonance imaging scan revealed a 3cm mass at the spermatic cord with very low signal density on T2-weighted imaging and a low and inhomogeneous uptake of gadolinium contrast agent on T1-weighted, fat-suppressed imaging. Following local excision, our patient has been well for 18 months.On histological examination, both of the lesions consisted of collagen-rich hyalinized fibrotic tissue with storiform features. There were lymphofollicular infiltrates and, sporadically, also venulitis. The immunoglobulin G4 staining (in case 2) showed an infiltrate of 10 to 15 positive cells per high-power field on average, corresponding to a proportion of 40% in evaluable hot spots. The two patients with paratesticular fibrous pseudotumor presented within a time span of 15 years. During that time, 400 patients with testicular germ cell tumors had been treated in our institution.
The specific histological features documented in our case lend support to the theory of paratesticular fibrous pseudotumor being an immunoglobulin G4-related sclerosing disorder. Paratesticular fibrous pseudotumors usually occur in young adulthood. Clinically, paratesticular fibrous pseudotumor can mimic testicular malignancy. Ultrasonographic findings are largely unspecific, however, scrotal magnetic resonance imaging may aid in discriminating the lesion from malignant tumors. Local excision, whenever technically feasible, is the preferred treatment of paratesticular fibrous pseudotumor.
We present the design and system integration of a hybrid MEMS scanning mirror (MSM) array developed for real-time three-dimensional imaging with a panoramic optical field of view (FOV) of 360 deg × ... 60 deg (horizontal × vertical). The pulsed time-of-flight light detection and ranging (LiDAR) system targets a distance measurement range of 100 m with a video-like frame rate of 10 Hz. The fast vertical scan axis is realized by a synchronous scanning MSM array with large receiver aperture. It increases the scanning rate to 3200 Hz, which is four times faster in comparison with state-of-the-art fast macroscopic polygon scanning systems used in current LiDAR systems. A hybrid assembly of frequency selected scanner elements was chosen instead of a monolithic MEMS array to guaranty high yield of MEMS fabrication and a synchronous operation of all resonant MEMS elements at 1600 Hz with large FOV of 60 deg. The hybrid MSM array consists of a separate emitting mirror for laser scanning of the target and 22 reception elements resulting in a large reception aperture of Deff = 23 mm. All MSM are driven in parametric resonance to enable a fully synchronized operation of all individual MEMS scanner elements. Therefore, piezoresistive position sensors are integrated inside the MEMS chip, used for position feedback of the driving control. We focus on the MEMS system integration including the microassembly of multiple MEMS scanning elements using micromechanical self-alignment. We present technical details to meet the narrow tolerance budgets for (i) microassembly and (ii) synchronous driving of multiple MEMS scanner elements.
PDF
