Deep-Learning Convolutional Neural Networks Accurately Classify Genetic Mutations in Gliomas.

BACKGROUND AND PURPOSE: The World Health Organization has recently placed new emphasis on the integration of genetic information for gliomas. While tissue sampling remains the criterion standard, noninvasive imaging techniques may provide complimentary insight into clinically relevant genetic mutations. Our aim was to train a convolutional neural network to independently predict underlying molecular genetic mutation status in gliomas with high accuracy and identify the most predictive imaging features for each mutation. MATERIALS AND METHODS: MR imaging data and molecular information were retrospectively obtained from The Cancer Imaging Archives for 259 patients with either low- or high-grade gliomas. A convolutional neural network was trained to classify isocitrate dehydrogenase 1 (IDH1) mutation status, 1p/19q codeletion, and O6-methylguanine-DNA methyltransferase (MGMT) promotor methylation status. Principal component analysis of the final convolutional neural network layer was used to extract the key imaging features critical for successful classification. RESULTS: Classification had high accuracy: IDH1 mutation status, 94%; 1p/19q codeletion, 92%; and MGMT promotor methylation status, 83%. Each genetic category was also associated with distinctive imaging features such as definition of tumor margins, T1 and FLAIR suppression, extent of edema, extent of necrosis, and textural features. CONCLUSIONS: Our results indicate that for The Cancer Imaging Archives dataset, machine-learning approaches allow classification of individual genetic mutations of both low- and high-grade gliomas. We show that relevant MR imaging features acquired from an added dimensionality-reduction technique demonstrate that neural networks are capable of learning key imaging components without prior feature selection or human-directed training.

The GTP-binding protein RhoA localizes to the cortical granules of Strongylocentrotus purpuratas sea urchin egg and is secreted during fertilization.

The sea urchin egg has thousands of secretory vesicles known as cortical granules. Upon fertilization, these vesicles undergo a Ca2+-dependent exocytosis. G-protein-linked mechanisms may take place during the egg activation. In somatic cells from mammals, GTP-binding proteins of the Rho family regulate a number of cellular processes, including organization of the actin cytoskeleton. We report here that a crude membrane fraction from homogenates of Strongylocentrotus purpuratus sea urchin eggs, incubated with C3 (which ADP-ribosylates specifically Rho proteins) and [32P]NAD, displayed an [32P]ADP-ribosylated protein of 25 kDa that had the following characteristics: i) identical electrophoretic mobility in SDS-PAGE gels as the [32P]ADP-ribosylated Rho from sea urchin sperm; ii) identical mobility in isoelectro focusing gels as human RhoA; iii) positive cross-reactivity by immunoblotting with an antibody against mammalian RhoA. Thus, unfertilized S. purpuratus eggs contain a mammalian RhoA-like protein. Immunocytochemical analyses indicated that RhoA was localized preferentially to the cortical granules; this was confirmed by experiments of [32P]ADP-ribosylation with C3 in isolated cortical granules. Rho was secreted and retained in the fertilization membrane after insemination or activation with A23187. It was observed that the Rho protein present in the sea urchin sperm acrosome was also secreted during the exocytotic acrosome reaction. Thus, Rho could participate in those processes related to the cortical granules, i.e., in the Ca2+-regulated exocytosis or actin reorganization that accompany the egg activation.

Subcellular localization of the GTP-binding protein Rho in the sea urchin sperm.

The Rho proteins are small G-proteins that belong to the Ras superfamily and play an essential role in the organization of the actin cytoskeleton. They are characteristically ADP-ribosylated by the exoenzyme C3 from Clostridium botulinum. Sea urchin sperm contain multiple small G proteins (28-24 kDa) whose identity and function are unknown. Here, we examined whether some of these proteins corresponded to the Rho subfamily. A sperm homogenate incubated with C3 and [32P]NAD revealed, by electrophoresis and autoradiography, a single radiolabeled band with a molecular mass of 25 kDa; this size was identical, under the same conditions, to that displayed by RhoA from human platelets. In flagellar fractions, the 25 kDa protein ADP-ribosylated by C3 localized in the cytosol and in the plasma membrane. In the sperm head, the 25 kDa protein was detected in a membrane preparation enriched in acrosomal and plasma membranes. Separation of these head membranes through a continuous density gradient revealed that both the 25 kDa protein [32P]ADP-ribosylated by C3 and actin had the same localization as bindin, the adhesive protein characteristic of the acrosome. An antibody against RhoB cross-reacted by immunoblotting with the 25 kDa protein and it revealed by both immunofluorescence and immunogold the presence of Rho in the acrosomal region, the middle piece of the head, and in the flagellum. Thus, the results indicate that the G-protein of 25 kDa previously detected in sea urchin sperm is Rho, likely the type B. Based on its cellular localization, Rho may participate in regulating motility and the actin polymerization that accompanies the acrosome reaction.

Molecular characterization of a subtilase from the vascular wilt fungus Fusarium oxysporum.

The gene prt1 was isolated from the tomato vascular wilt fungus Fusarium oxysporum f. sp. lycopersici, whose predicted amino acid sequence shows significant homology with subtilisin-like fungal proteinases. Prt1 is a single-copy gene, and its structure is highly conserved among different formae speciales of F. oxysporum. Prt1 is expressed constitutively at low levels during growth on different carbon and nitrogen sources and strongly induced in medium containing collagen and glucose. As shown by reverse transcription-polymerase chain reaction and fluorescence microscopy of F. oxysporum strains carrying a prt1-promoter-green fluorescent protein fusion, prt1 is expressed at low levels during the entire cycle of infection on tomato plants. F. oxysporum strains transformed with an expression vector containing the prt1 coding region fused to the inducible endopolygalacturonase pg1 gene promoter and grown under promoter-inducing conditions secreted high levels of extracellular subtilase activity that resolved into a single peak of pI 4.0 upon isoelectric focusing. The active fraction produced two clearing bands of 29 and 32 kDa in sodium dodecyl sulfate gels containing gelatin. Targeted inactivation of prt1 in F. oxysporum f. sp. lycopersici had no detectable effect on mycelial growth, sporulation, and pathogenicity on tomato plants.

12-O-tetradecanoyl phorbol-13-acetate interferes with germination of Phycomyces blakesleeanus sporangiospores.

The presence of protein kinase C (PKC), a key enzyme in signal transduction, has not been investigated in fungal cells. The phorbol ester TPA, an activator of PKC, may be used as an indicator of the presence and role of PKC in Phycomyces blakesleeanus spores. Activation of spore germination by acetate was prevented by 6 nM TPA. The TPA analog 4 alpha PDD, an ineffective activator of PKC, did not affect spore germination. 3 mM dbcAMP, on the other hand, reversed the inhibition of germination caused by TPA. TPA-stimulated protein kinase activity was detected in spores. The possible relationship between PKC and the increased levels of cAMP that accompany the induction of spore germination is discussed.

Duplication (5p13 leads to pter): prenatal diagnosis and review of the literature.

We describe a patient with a reciprocal translocation t(5,13) and her three offspring. The chromosome anomaly was ascertained after the birth of her first child, who had the cri-du-chat syndrome. Amniocentesis demonstrated the presence of a dup(5p). The anomalies affecting that fetus are described and compared with the reported phenotypes of dup(5p). The extent of clinical findings in the reported cases depends on the length of the duplicated portion. The larger the duplication (p11 leads to pter), the more pronounced are the clinical signs. Physical signs are nearly absent when 5p14 leads to ter is involved. Also, translocations affecting chromosome 5 have an increased abnormal outcome when compared to D/D Robertsonian translocations. This is the first instance of antenatal diagnosis of trisomy 5p.

Molecular characterisation of a fungal mono(ADP-ribosyl)transferase.

A soluble arginine-specific mono(ADP-ribosyl)transferase was detected in dormant spores of Phycomyces blakesleeanus. Soluble proteins incubated with [32P]NAD revealed, after a two dimensional electrophoretic separation, three major ADP-ribosylated substrates with molecular weights of 38, 37, and 36 kDa and pI values of 6.9, 8.1 and 4.6, respectively. The addition of MgCl2 stimulated the (ADP-ribosyl)transferase activity. This enzymatic activity was stimulated by 250 microM NO-releasing agent sodium nitroprusside and inhibited with 8 mM benzamide, 0.4 mM meta-IodoBenzylGuanidine (MIBG), and 0.5 mM novobiocin. The three ADP-ribosylation inhibitors affected the germination of Phycomyces spores. The concentrations necessary to inhibit 50% of the spore germination of Phycomyces were 0.05 mM, 0.2 mM, and 8 mM for novobiocin, MIBG, and benzamide, respectively. All the above inhibitors affected the germination process to the same extent, that is, they inhibited the tube protuberation, leaving the spores as swollen cells. These data suggest that ADP-ribosylation may be involved in the germination process of Phycomyces, particularly in germ-tube formation.

Interferometric optical signal-to-noise ratio measurements of telecom signals with degraded extinction ratio.

We measure full interferograms of telecom signals impaired by noise and investigate their applicability to in-band optical signal-to-noise ratio (OSNR) monitoring in practical systems. We experimentally establish that the dependence of overall shape of the interferogram on a signal's extinction ratio (ER) is strong but not unique. As the ER is being degraded the interferogram evolves in two distinct ways depending on the modulation conditions. The resulting ambiguity in the interferogram shape prevents OSNR measurements on completely unknown signals and necessitates a calibration for each modulator condition. With appropriate calibration, we experimentally demonstrate reliable OSNR measurements in the 5 to 25 dB range for 42.8 Gb/s nonreturn-to-zero, return-to-zero, and carrier-suppressed return-to-zero on-off-keyed signals.

Entamoeba histolytica: ADP-ribosylation of secreted glyceraldehyde-3-phosphate dehydrogenase.

In addition to its classic glycolytic role, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been implicated in many activities unrelated to glycolysis, such as membrane fusion, binding to host proteins and signal transduction. GAPDH can be the target of several modifications that allow incorporation to membranes and possible regulation of its activity; among these modifications is mono-ADP-ribosylation. This post-translational modification is important for the regulation of many cellular processes and is the mechanism of action of several bacterial toxins. In a previous study, we observed the extracellular ADP-ribosylation of a 37-kDa ameba protein. We report here that GAPDH and cysteine synthase A are the main ADP-ribosylated proteins in Entamoeba histolytica extracellular medium, GAPDH is secreted from ameba at 37 degrees C in a time-dependent manner, and its enzymatic activity is not inhibited by ADP-ribosylation. Extracellular GAPDH from ameba may play an important role in the survival of this human pathogen or in interaction with host molecules, as occurs in other organisms.

Molecular analysis of an NAD-dependent alcohol dehydrogenase from the zygomycete Mucor circinelloides.

NAD-dependent alcohol dehydrogenase (ADH) activity was detected mainly in the cytosol of aerobically cultured mycelium and in anaerobically grown yeast cells of Mucor circinelloides. ADH levels were about 2.5-fold higher in yeast cells than in mycelium; zymogram analysis suggested that the same ADH enzyme is produced in both developmental stages. The enzyme, named ADH1, was purified to homogeneity from yeast cells, using ion-exchange and affinity chromatography. The active ADH1 appears to be a homomeric tetramer of 37,500-kDa subunits. Km values obtained for acetaldehyde, ethanol, NADH and NAD+ indicated that in vivo the enzyme mainly serves to reduce acetaldehyde to ethanol. Amino acid sequences of internal peptides obtained from the purified ADH1 were used to design oligonucleotides that allowed the cloning of the corresponding cDNA by RT-PCR, and the characterization of the genomic DNA sequence. The adh1 ORF is interrupted by two small introns located towards the 5'-end. M. circinelloides adh1 encodes a protein of 348 amino acids, which display moderate to high overall identity to several hypothetical ADH enzymes from the related zygomycete Rhizopus oryzae. adh1 mRNA is expressed at similar levels in aerobic mycelium and anaerobic yeast cells. During exponential growth under aerobic conditions, the level of adh1 transcript was correlated with the glucose concentration in the growth medium.

Y-autosome translocation, gonadal dysgenesis, and gonadoblastoma.

A 5-year-old girl was discovered to have an abnormal karyotype with a translocation involving the Y chromosome. The primary complaint was slight physical growth retardation. Cytogenetic and endocrinologic evaluations were performed. The chromosomal complement exhibited a mosaicism: 45,X,t(Y;18)(q11;p11)/45,X0. The gonads of this patient were typical streaks containing no ova or follicles. A gonadoblastoma was present bilaterally.

Influence of differences in leaf anatomy on net photosynthetic rates of some cultivars of Cassava.

Gas exchange measurements and leaf anatomy of 10 cassava cultivars were conducted to study the interrelationship between the relatively high photosynthetic rates and the factors limiting internal CO2 diffusion. The internal mesophyll surface area per unit leaf surface area (A(mes)/A) and the intracellular components of CO2 diffusion and fixation resistance (R(cell)CO2) were determined. Among the group of cultivars tested net CO2 exchange rates were 26±2.5 µmol CO2 m(-2) s(-1) in normal air and intense light and A(mes)/A ranged from 14 to 38. Estimated R(cell)CO2 ranged from 4300 to 13,000 s m(-1). The combined and compensating effects of A(mes)/A and R(cell)CO2 accounted for both the high net photosynthetic rates (Pn) and the lack of large differences in Pn among cultivars.

Biological properties of a calcium-modulator protein from Phycomyces blakesleeanus.

1. A modulator protein having properties similar to calmodulin-like proteins could be detected in Phycomyces the first day of growth. 2. The modulator protein from Phycomyces was partially purified to a specific activity of 9,000 Units/mg protein. 3. The modulator protein was similar to calmodulin with respect to: (a) the ability to stimulate a calcium-plus-calmodulin-dependent cAMP phosphodiesterase from bovine brain; (b) the inhibitory effect of trifluoperazine in this process; (c) the stimulation of the [Ca2+ + Mg2+)-ATPase from human erythrocyte membranes. 4. Maximum effect of modulator protein in the above mentioned reactions was achieved at micromolar calcium concentrations.

Stabilization of chitin synthetase and purification of chitosomes from several mycelial Mucorales.

Stability of chitin synthetase in cell-free extracts from mycelial fungi was markedly improved by the presence of sucrose in the homogenization media. Breakage of mycelium in sucrose-containing buffer yielded enzyme preparations from which chitosomal chitin synthetase could be purified by a procedure involving ammonium sulfate precipitation, gel filtration and centrifugation in sucrose density gradients. Purified chitosomes catalyzed the synthesis of chitin microfibrils in vitro upon incubation with substrate and activators. Chitosomal chitin synthetase from the filamentous form of M. rouxii was similar to the enzyme from yeast cells, except for the poorer stability and diminished sensitivity to GlcNAc activation of the former.

The GTP-binding protein G alpha s is present in dormant spores and expressed differentially during spore germination of the fungus Phycomyces blakesleeanus.

A DNA sequence homologous to a G alpha s DNA probe, and the corresponding G alpha s protein (stimulatory alpha-subunit of GTP-binding protein) were detected in Phycomyces blakesleeanus. The protein was demonstrated in membrane fractions of dormant spores of this fungus using three different experimental approaches. Photoaffinity-labelling experiments with [alpha-32P]GTP of the membrane fraction revealed two bands, of 56 and 32 kDa. The 56 kDa GTP-binding protein was detected by this method in all the stages of early development and growth investigated. Also, a spore protein of 56 kDa was ADP-ribosylated by cholera toxin, and a 56 kDa protein was detected by Western blotting with a specific antibody against mammalian G alpha s. These results indicate that G alpha s (56 kDa) is present in dormant spores of P. blakesleeanus. Using the ADP-ribosylation and Western blotting assays, G alpha s was detected during all stages of spore germination before the hyphae became highly branched, but it was not detected in the branched hyphae that formed 18 h after the initiation of spore germination. Therefore, G alpha s is expressed differentially during Phycomyces development.

Purification and partial characterization of a chromate reductase from Bacillus.

A soluble NADH-dependent enzyme capable of reducing hexavalent chromium [Cr(VI)] to the trivalent form [Cr(III)] was purified from chromate-resistant Bacillus QC1-2. An enriched single protein band of 24 kDa was observed by SDS-PAGE following HPLC ion-exchange and size-exclusion procedures. In the latter step, the chromate reductase showed a molecular mass of 44 kDa, which suggested that the enzyme consists of two subunits of about 24 kDa. Purified chromate reductase displayed optimal activity at a temperature and pH of 37 degrees C and 7.0, respectively. The enzyme showed a Km of 0.35 mM for chromate and a Vmax of 50 nmol Cr(VI) reduced per minute per mg protein.

Genetic evidence for independence between fermentative metabolism (ethanol accumulation) and yeast-cell development in the dimorphic fungus Mucor rouxii.

Three allyl-alcohol-resistant mutants were isolated in the dimorphic fungus Mucor rouxii and characterized with regard to their alcohol dehydrogenase (ADH) activity in vitro and in vivo as well as their ability to execute the morphological alternatives of dimorphism under different environmental stimuli, either in the absence or in the presence of oxygen. These studies indicated that fermentation and yeast-cell development are independent events and that ADH activity is essential for growth of the fungus in the absence of oxygen. Heterokaryon construction and analysis indicated that in the three mutant strains the corresponding genetic alterations are recessive nuclear mutations which behave as allelic in complementation tests.