Network-Free Inference of Knockout Effects in Yeast

Perturbation experiments, in which a certain gene is knocked out and the expression levels of other genes are observed, constitute a fundamental step in uncovering the intricate wiring diagrams in the living cell and elucidating the causal roles of genes in signaling and regulation. Here we present a novel framework for analyzing large cohorts of gene knockout experiments and their genome-wide effects on expression levels. We devise clustering-like algorithms that identify groups of genes that behave similarly with respect to the knockout data, and utilize them to predict knockout effects and to annotate physical interactions between proteins as inhibiting or activating. Differing from previous approaches, our prediction approach does not depend on physical network information; the latter is used only for the annotation task. Consequently, it is both more efficient and of wider applicability than previous methods. We evaluate our approach using a large scale collection of gene knockout experiments in yeast, comparing it to the state-of-the-art SPINE algorithm. In cross validation tests, our algorithm exhibits superior prediction accuracy, while at the same time increasing the coverage by over 25-fold. Significant coverage gains are obtained also in the annotation of the physical network.     

Unusual sequence element found at the end of an amplicon.

In a polyomavirus-transformed rat cell line, designated LPT, the polyomavirus DNA is integrated into a single chromosomal site. Treatment of LPT cells with carcinogens induces amplification of the integrated virus DNA and flanking cellular sequences. We show that the amplification is arrested within a specific cell DNA segment that maps 1.3 to 1.85 kilobases beyond one virus-cell DNA junction, defined as the left junction. We also present the sequence of an 897-base-pair fragment spanning the arrest site. This fragment contains an unusual sequence element, which consists of two contiguous components, a potential cruciform with stems of 6 base pairs and a d(G-A)27 X d(T-C)27 tract, and maps 1,497 to 1,564 nucleotides beyond the left junction. The possibility that this unusual sequence plays a role in the arrest of the amplification process is discussed.     

Correlation between Lack of Receptacle Growth in Response to Auxin and Accumulation of a Specific Polypeptide in a Strawberry (Fragaria ananassa Duch.) Variant Genotype

Receptacle growth in strawberry (Fragaria ananassa Duch. cv.Ozark Beauty) occurred after either pollination or auxin treatment.In a strawberry variant genotype (Washington State UniversitySelection No. 12/13), pollination did not lead to receptaclegrowth but application of -naphthaleneacetic acid (NAA) at anthesisresulted in normal receptacle growth. The receptacles of OzarkBeauty retained their ability to respond to auxin at least upto 36 days after anthesis. However, delay of auxin applicationto the receptacles of the variant genotype resulted in decreasedauxin-responsive growth and auxin application after the 10thday of anthesis led to very little growth. The loss of auxin-responsivegrowth of the receptacle of the variant genotype was not associatedwith any loss of auxin binding activity of receptacle membranes.If auxin was not supplied to the receptacles of the variantgenotype at anthesis, the receptacles did not grow and a polypeptideof 52,000 M_r accumulated. Application of NAA to the receptaclesof the variant genotype at anthesis or on the fifth day afteranthesis resulted in the growth of the receptacle and the 52,000M_r polypeptide did not accumulate. Application of NAA to thereceptacles of the variant genotype on the 10th or the 15thday after anthesis led to very little growth of the receptacleand the 52,000 M_r polypeptide accumulated to high levels. Theseresults suggested a correlation between the lack of receptaclegrowth in response to auxin and accumulation of the 52,000 M_rpolypeptide. ¹ Current adress: The Institute of Applied Research, Ben GurionUniversity of the Negev, Beer-Sheva, Israel. (Received August 6, 1984; Accepted December 11, 1984)     

Effect of Ferricyanide, Ferrocyanide and KCN on Growth and Flowering in the Short-Day Plant Lemna paucicostata 6746

Flowering in the short-day plant Lemna paucicostata 6746 canbe induced under continuous light by the addition of ferricyanie,ferrocyanide or KCN to M-sucrose medium. Each substance is nearly10 times more effective when the flasks are covered by glassbeakers than when cotton plugs are used. By contrast, when floweringis induced under continuous light by copper or by short-daytreatment, neither flowering nor growth are affected by whetherglass beakers or cotton plugs are used. Ferricyanide, ferrocyanideand KCN are also able to induce long-day flowering when theplants are grown on Msucrose medium in small beakers that areplaced in a covered storage dish that also contains a solutionof one of these compounds. Addition of a KOH trap to the storagedish completely blocks the flowering induced by these compounds.If [¹⁴C]ferrocyanide is added to the storage dish both the M-sucrosemedium and the plants contain significant amounts of radioactivity,the amount of radioactivity being proportional to the floweringresponse. These results indicate that ferricyanide, ferrocyanideand KCN break down to release HCN and that it is the HCN whichis responsible for inducing flowering in L. paucicostata 6746under continuous light. ¹Present address: Department of Biology, Osaka Kyoiku University,Ikeda, Osaka 563, Japan. ²Present address: Institute of Horticulture, The Volcani Center,P. O. B. 6, Bet-Dagan, Israel. (Received January 17, 1983; Accepted March 24, 1983)     

Pseudohypoparathyroidism type Ia: two new heterozygous frameshift mutations in exons 5 and 10 of the Gsα gene

Pseudohypoparathyroidism type Ia (PHP-Ia) is a hereditary disease characterized by resistance to PTH and other hormones that act via cAMP. Patients have deficient activity of Gs, the subunit of the G protein, which couples hormone receptors to stimulation of adenylate cyclase. We describe two new mutations discovered in two sporadic patients with PHP-Ia. Using genomic DNA, we have amplified exons 2–13 of the Gs gene (GNAS1) by PCR, and sequenced the resulting products. Both patients had Albright's hereditary osteodystrophy, resistance to multiple hormones, and deficient Gs activity. In the first patient, a deletion of a C in exon 5 at codon 115 was found. In the second patient, an insertion of a C in exon 10 at codon 267 was detected. Both these heterozygous mutations cause frameshift, and predict decreased production of Gs. This report adds two new Gs mutations to the known ten mutations recently described.     

Modulation of small conductance calcium-activated potassium channels in C6 glioma cells

Using the patch clamp technique, we have characterized a small conductance, calcium-activated potassium (SK) channel in the C6 glioma cell line. Elevation of cytosolic Ca²⁺ concentration ([Ca²⁺] _i ) by applications of serotonin or ionomycin induced bursts of channel openings recorded in the cell-attached configuration. These channels underlie the serotonin-induced, [Ca²⁺] _i -activated whole-cell K⁺ conductance described previously. [Ca²⁺] _i directly activated SK channels in inside-out patches with a biphasic concentration dependence. Submicromolar [Ca²⁺] _i induced bursts of channel openings with a unitary conductance of about 25 pS, similar to that of the serotonin-induced channels. Supramicromolar [Ca²⁺] _i caused prolonged openings with a unitary conductance of about 35 pS, resulting in a pronounced increase of the average current in patches exposed to [Ca²⁺] _i above 100 m. The two modes of opening reflect the activity of the same SK channel. The channel conductance depended on external K⁺ concentration with K _Dof 5 m. The channel was slightly permeable to cations other than K⁺, with a permeability ratio for K⁺Ca²⁺Na⁺ of 10.0400.030, respectively. ATP was required to maintain channel activity in outside-out patches but was not essential in inside-out patches. The modulation of SK channels in C6 cells by components in their microenvironment may be related to the role of glial cells in controlling the extracellular milieu in the CNS.The authors are grateful to Dr. M. Segal for continuous support, stimulating discussions and criticism throughout the course of this work, to Dr. I. Steinberg for helpful suggestions and to Dr. H. Jarosch, for helping with the Fortran application. N.M.'s research was supported in part by BARD, the U.S.-Israel Binational Agricultural Research and Development Fund, grant no. IS-1670-89RC.     

Rhipicephalus sanguineus: Observations on the parasitic stage on dogs in the Negev Desert of Israel

Sixteen dogs were studied for infestation with R. sanguineus in Kibbutz Ze'elim in the north-western part of the Negev Desert over a period of one year. The mean number of ticks per dog per month was 16.4. The majority of the ticks were adults: males (48.6%) and females (34.4%). The cars and abdomen of the dog were the predilection sites for the ticks. Male ticks were more abundant on the ears, whereas female ticks were more abundant on the ears and the abdomen. A strong correlation between tick numbers and the ambient temperatures was found. The mean percentage of dogs infested in the winter months was 16.6% and increased in the summer months to 34.4%. During winter, ticks were found more often on the ears and head of their hosts whereas in summer they were distributed mainly on the ears, headd and abdomen. The male: female ratio was higher in winter (2.3:1) than in summer (1.1:1).     

TNF and PGE(2) in human monocyte-derived macrophages infected with Chlamydia trachomatis

In this study levels of prostaglandin E(2) (PGE(2)), tumour necrosis factor (TNF) and interleukin-1 (IL-1) alpha in medium from monocyte derived macrophages (MdM) infected with Chlamydia trachomatis (L(2)/434/Bu or K biovars). TNF and PGE(2) were found in both cases while IL-1 alpha was not detected. Both TNF and PGE(2) levels were higher in the medium of the MdM infected with K biovars. TNF reached maximum levels 24 h postinfection, and then declined, while PGE(2) levels increased continuously during the infection time up to 96 h post-infection. Addition of dexamethasone inhibited production of TNF and PGE(2). Inhibition of PGE(2) production by indomethacin resulted in increased production of TNF, while addition of PGE(2) caused partial inhibition of TNF production from infected MdM.