cdna sequence and expression pattern of the putative

Size: px
Start display at page:

Download "cdna sequence and expression pattern of the putative"

Transcription

1 Proc. Natl. Acad. Sci. USA Vol. 92, pp , March 1995 Biochemistry cdna sequence and expression pattern of the putative pheromone carrier aphrodisin (lipocalin/hamster/vagina/bartholin's glands) HANS-JURGEN MAGERT*t, THORSTEN HADRYS*, ALEXANDRA CIESLAK*, ANJA GROGER*, STEPHAN FELLERt, AND WOLF-GEORG FORSSMANN* *Lower Saxony Institute for Peptide Research, Feodor-Lynen-Strasse 31, Hannover, Germany; and tdepartment of Molecular Oncology, Rockefeller University, York Avenue, New York, NY Communicated by M. Lindauer, Universitat Wurzburg, Wurzburg, Germany, October 5, 1994 ABSTRACT The cdna sequence for aphrodisin, a lipocalin from hamster vaginal discharge which is involved in pheromonal activity, has been determined. Corresponding genomic clones were isolated and the promoter region was identified. Primer extension analysis revealed an adenosine residue as the main transcription initiation site, located 50 bp upstream of the translation start codon ATG, which is surrounded by a typical Kozak sequence. However, data from polymerase chain reaction analysis suggest the existence of at least one alternative transcription initiation site. The aphrodisin cdna is 732 bp long and codes for the mature 151-aa aphrodisin and an additional N-terminal 16-aa secretory signal peptide. The 3' nontranslated region is 228 bp long. Among the known sequences, the aphrodisin cdna shares the highest homology with the rat odorant-binding protein cdna (45%), which verifies the protein data. Vaginal tissue and Bartholin's glands are the main aphrodisin gene-expressing tissues of the female hamster genital tract, as demonstrated by Northern blot analysis. Under less stringent hybridization conditions, RNA isolated from rat Bartholin's glands also showed a signal, indicating the occurrence of aphrodisinrelated mrna in this species. The so-called lipocalins (lipocalycins) are a superfamily of structurally related proteins in the size range of kda which typically consist of two sets of four antiparallel,3-strands arranged in two orthogonally stranded (3-sheets (1-3). The resulting tertiary structure is comparable to a coffee filter containing an apolar pocket for the noncovalent binding of small hydrophobic molecules such as lipids, steroids, odorants, bilins, and retinoids (3). Most of the lipocalins are known to serve as carriers for the mentioned ligands. However, one of these proteins, prostaglandin D synthase, exhibits enzymatic activity (4, 5). The specificity of the lipocalins for certain ligands is probably determined by the composition of the amino acids within the binding pocket (6). Nevertheless, some lipocalins-for instance,,b-lactoglobulin and mouse major urinary protein-are capable of binding several different ligands (6, 7). The mechanisms of interaction of the lipocalin/ ligand complexes with specific receptors have not been well investigated. In the case of human serum retinol-binding protein, it has been demonstrated that certain parts of the loops connecting the (B-strands are essential for the interaction with an additional protein called transthyretin and a membrane receptor of the target cells. Further, it is proposed that the release of retinol from the binding pocket is triggered by some kind of conformational change in the retinol-binding protein after binding to the receptor (8). Aphrodisin, a 17-kDa glycoprotein of the lipocalin family, has been purified from hamster vaginal discharge (9). It The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C solely to indicate this fact. consists of 151 aa and contains two disulfide bonds which connect the cysteine residues at positions 38 and 42 and at positions 57 and 149. Its N terminus is blocked by a pyroglutamate residue, indicating the occurrence of a larger primary translational product (10). Acting via the vomeronasal organ (11), aphrodisin elicits copulatory behavior in male hamsters. At this time it is not quite clear whether an additional ligand is required for biological activity but, if this should be the case, it must be bound very tightly to the protein (12). On the other hand, proteolytic or heat degradation of aphrodisincontaining fractions leads to a loss of activity (9). Functions as pheromone-binding proteins have also been discussed for two other lipocalins, the mouse major urinary protein and a-2u globulin (6, 13). Among the known proteins, rat odorant-binding protein (ROBP) shares the highest sequence homology with aphrodisin (40%). It occurs in nasal mucosa of rats and seems to be responsible for the binding of odorant molecules (refs. 14 and 15; for review see ref. 16). Here we report the nucleotide sequence of a 732-bp aphrodisin precursor cdna which codes for the mature protein and an additional N-terminal secretory signal peptide of 16 aa. PCR amplifications of different cdna fragments indicate the existence of at least two transcriptional initiation sites. We show by Northern hybridization that vaginal tissue and Bartholin's glands are the main aphrodisin gene-expressing tissues of the female hamster genital tract. Under less stringent conditions we also obtained a hybridization signal in the expected size range from rat Bartholin's glands, suggesting the synthesis of a related protein. MATERIALS AND METHODS Polymerase Chain Reaction. Total RNA was purified from one female hamster genital tract by means of an automatic nucleic acid extractor (model 340; Applied Biosystems). Five micrograms of the total RNA was subjected to reverse transcription using Moloney murine leukemia virus reverse transcriptase and a synthetic oligo(dt) universal primer (UNIP-2; Fig. 1). One-thirtieth of the cdna mixture was then used for each of the three-step-cycle PCRs (17) in a model 480 thermocycler with Amplitaq DNA polymerase (both from Perkin- Elmer) and synthetic primers (Fig. 1). Cloning of PCR Fragments. PCR fragments were separated in 3% NuSieve GTG agarose gels (Biozyme, Oldendorf, Germany) and purified with a Qiaex kit (Qiagen, Hilden, Germany). The ends of the PCR fragments were cleaved with Xba I, whose recognition sequence was included in the PCR primers. After the short cleavage products were removed by Abbreviation: ROBP, rat odorant-binding protein. tto whom reprint requests should be addressed. I The sequence reported in this paper has been deposited in the GenBank data base (accession no. X65238). 2091

2 2092 Biochemistry: Magert et al. AP-1 AP-2 AP-3 AP-4 AP-5 AP-6 AP-7 AP-8 AP-9 RAP-1 RAP-2 UNIP CCCTCTAGAA TTCARGGNAARTGGTAYACNAT CCTCTA GAA TTCTAYGTNATHACNAAYAAYCARTG AA TCTA GAA TCTMNCCYTCRAAYTGNGTYTG A CTCTA GAA TTCTTYTTYTCRTGNGCRAAYTGNAC AAA TCTA GAA TTCAGTGCTCCAAGACCACAGTCATTGG CGGTCTA GAA TTCGGAAATGGAACYTACCAAACCCAGTTTG TCCTGAGCATGAGCCAGA GCAG1TTTTATAACAATCAATATG CGGTCTAGAA7TCTATCTM1ICAAGATTGTCAGCAGC GCTTTGTCAGTTGAGTTCTTTTC GGAAAAGCAAAGTCAGGCACC poly(a)tail CCTGAA TTCTA GA GCTCA (T) 17 FIG. 1. Nucleotide sequences (in 5' -- 3' orientation) of primers. The positions of the primers within the presented cdna sequence are indicated. Italic regions do not correspond to the cdna sequence but contain recognition sites for restriction endonucleases (Xba I, EcoRI, and, in the case of UNIP-2, also Sst I) which enable easy cloning of the obtained PCR fragments. Proc. Natl. Acad Sci. USA 92 (1995) centrifugation in Centricon filters (Amicon), the fragments were ligated with Xba I-cleaved plasmid puc18 (18). Escherichia coli JM109 cells (18) were transformed with the ligation products by the PEG method (19). Genomic Library Screening. A Golden hamster (Mesocricetus auratus) genomic library in A Fix II (Stratagene) was screened (20) with the 407-bp AP-1/AP-4 aphrodisin cdna PCR fragment, which had been labeled with [a-32p]dctp by use of a random-primer labeling kit (Boehringer Mannheim). Primer Extension Analysis. Total RNA was extracted from Golden hamster vagina and brain as described above. A synthetic antisense oligonucleotide primer (AP-7; Fig. 1) was 5'-end labeled with 32P by use of [,y-32p]atp and T4 polynucleotide kinase and hybridized to 5,ug of total RNA. After the extension reaction (21), the products together with labeled size markers were separated by electrophoresis in a denaturing 8% polyacrylamide gel, which was subsequently exposed to x-ray film (Kodak XAR-5). DNA Sequencing. Nucleotide sequences were determined according to the method of Sanger et al. (22) by means of an automatic fluorescence sequencer (model 373A; Applied Biosystems) (23). To avoid sequence errors caused by misincorporation of nucleotides during PCR, at least three independent clones of each fragment were sequenced. Uncloned PCR fragments were also directly sequenced after agarose gel electrophoresis and purification with Ultrafree-MC filter columns (first 0.45-,um Durapore, then PTTK polysulfone membrane; Millipore) using the PCR primers as sequencing primers Ṅorthern and Southern Blotting. Total RNA was glyoxylated and electrophoretically separated as described (24). RNA and PCR fragments were transferred from the gel to Hybond N+ membrane (Amersham) by use of a PosiBlot pressure blotting apparatus (Stratagene). The nucleic acids were fixed to the membranes according to the manufacturer's instructions. Northern blots were hybridized to the same 32P-labeled PCR fragment, AP-1/AP-4, that was used for genomic library screening. PCR Southern blots (25) were hybridized to a synthetic oligonucleotide (AP-7; Fig. 1) that had been 5'-end labeled with 32p. DNA Sequence Comparisons. Homology searches in the EMBL nucleic acid sequence database, sequence alignments, and other kinds of sequence analyses were performed on an Apple SE 30 computer using the MACMOLLY program package (Soft Gene, Berlin). RESULTS Aphrodisin cdna Sequence. From the already known aphrodisin protein sequence, four degenerate PCR primers were constructed (sense, AP-1 and AP-2; antisense, AP-3 and AP-4; Figs. 1 and 2) and used for the amplification of aphrodisin-specific cdna fragments from total RNA of female hamster genital tract. Four homogeneous PCR fragments were obtained, all of them in the expected size range. The largest fragment (AP-1/AP-4) was cloned in puc18 and three independent clones (ppet1-3) were sequenced. Translation of the cdna into protein sequence and comparison with the aphrodisin amino acid sequence verified the cloning of an aphrodisin-specific partial cdna. By means of this sequence, two highly specific primers (AP-5 and AP-6; Fig. 1) were constructed and used together with the oligo(dt) primer UNIP-2 (Fig. 1) for amplification of the rest of the 3'-terminal cdna (preamplification with AP-5/UNIP-2, final amplification with AP-6/UNIP-2). The 500-bp cdna fragment obtained was cloned in puc18 and five independent clones (ppet11-15) were sequenced. From the partial gene (see below) and cdna sequence, two additional primers (RAP-2 and AP-8; Fig. 1) were derived for the amplification of the rest of the 5'-terminal cdna. The 198-bp fragment obtained was sequenced directly and, by means of overlapping regions, the I-> secretory signal peptide I> mature aphrodisin AP-1 > Met Val Lys Ile Leu Leu Leu Ala Leu Val Phe Ser Leu Ala His Ala Gln Asp Phe Ala Glu Leu Gln Gly Lys Trp Tyr Thr Ile Val Ile Ala Ala Asp Asn Leu Glu Lys Ile acc AM GTA AAG ATU CTG CTG CTG GCT TTG GTC mtt AGT CTG GCT CAT GCT CAG GAT UTT GCA GAG CUT CAA GGA AAA TGG TAT ACC ATU GTC ATT GCT GCT GAC AAT CUT GAA AAG ATA AP-5 AP-2 Glu Glu Gly Gly Pro Leu Arg Phe Tyr Phe Arg His Ile Asp Cys Tyr Lys Asn Cys Ser Glu Met Glu Ile Thr Phe Tyr Val Ile Thr Asn Asn Gln Cys Ser Lys Thr Thr Val Ile GAA GAA GGA GGA CCA CTG AGA TTC TAT UT CGT CAT ATU GAT TGT TAT AAA AAC TGC AGT GAA ATG GAA ATC ACA UT TAT GTC ATT ACA AAC AAC CAG TGC TCC AAG ACC ACA GTC ATT * * 0* _, AP-6 AP-3 Gly Tyr Leu Lys Gly Asn Gly Thr Tyr Gln Thr Gln Phe Glu Gly Asn Asn Ile Phe Gln Pro Leu Tyr Ile Thr Ser Asp Lys Ile Phe Phe Thr Asn Lys Asn Met Asp Arg Ala Gly GGG TAC TUG AM GG AAT GGA ACC TAC CAA ACC CAG UT GAA GGT AAC MT ATA UTT CAA CCT TTG TAT ATA ACA TCA GAC AAG ATT TUC m ACC AAC AAG AAC ATG GAT AGA GCT GGC c - AP-4 Gln Glu Thr Asn Met Ile Val Val Ala Gly Lys Gly Asn Ala Leu Thr Pro Glu Glu Asn Glu Ile Leu Val Gln Phe Ala His Glu Lys Lys Ile Pro Val Glu Asn Ile Leu Asn Ile CAG GAA ACG AAC ATG ATT GTT GUT GCT GGA AAA GGT AAT GCT TUG ACA CCT GAA GAA AAT GM ATA CTT GTG CAAm GCr CAT GAA AAG AAA ATT CCA GTG GAA AAC ATT CTC AAT ATT * * * 0 Leu Ala Thr Asp Thr Cys Pro Glu STOP CUT GCT ACA GAT ACT TGT CCT GAA TAA aggcmttccgtaggtgagacaggotggcaottaggcotcatctcttgotcotggoatcagcatcacaeatoootcaccotttcattctocatgaettgtccatctcctgtagogccag ap jp W-- V-. 'IF... 9 FIG. 2. Nucleotide sequence of the hamster aphrodisin precursor cdna. The deduced amino acid sequence is shown in the three-letter code. The translational start codon and the polyadenylylation signal are underlined. Positions of PCR primers are marked with arrows. Distances of 30 bp are indicated with black dots. 732

3 Biochemistry: Mdgert et al complete aphrodisin cdna sequence (EMBL data library, accession number X65238) (Fig. 2) was assembled. The amplified coding region of the cdna and the 3' nontranslated region together have a size of 732 bp. The cdna codes for the 151-aa mature aphrodisin and a typical N- terminal 16-aa secretory signal peptide (26). No deviation of the translated cdna sequence from the published protein sequence of mature aphrodisin was detected. The 3' nontranslated region is 228 bp long and contains a typical AATAAA polyadenylylation signal (27, 28) at its 3' terminus. Comparisons with known cdna sequences revealed the highest homology (45% nucleotide sequence identity) with the ROBP cdna (15). This is in accordance with comparisons at the protein level (40% identity). Identification of the Aphrodisin Gene Promoter Region and Transcription Initiation Site. After screening of 400,000. plaques of the Golden hamster genomic library, 4 independent clones were isolated. As determined by restriction analysis, 1 clone, compared with the other 3 clones, contained a slightly shifted part of the same genomic region as the insert. PCR amplifications of partial insert fragments using primers (not listed) derived from the incomplete gene sequence and the 3'-terminal end of the cdna indicated the cloning of the complete gene in all cases. It has a size of '6000 bp (data not shown). Sst I and Xba I fragments of the gene were subcloned in puc18 and partially sequenced. One of the obtained sequences contains a CCAAT-box motif (29) in reverse complementary orientation and a TATA-box motif (for review see refs. 30 and 31) near potential transcription start sites, followed in the 3' direction by a region that codes for a typical secretory signal peptide (26) and the first 5 aa of mature aphrodisin (Fig. 3). These features strongly fit those expected for the 5' end of the aphrodisin gene. The first exon is then interrupted by the 448-bp intron I, which is followed by a sequence expected for exon II. Our sequence data allow the conclusion that the aphrodisin gene consists of at least five exons and four introns (data not shown). From the partial gene sequence an antisense primer (AP-7; Figs. 1 and 3) was derived and used for primer extension analysis of Golden hamster vaginal and brain RNA. In the first case we obtained a 103-nt extension product (Fig. 4), whereas we obtained none in the second case (negative control). The extension product correlates with a pair of adenosines located 29 and 30 bp downstream from the second thymidine of the above-mentioned TATA-box motif. Forty-nine base pairs downstream of the first potential transcription start site, an ATG in the correct frame appears, surrounded by nucleotides matching the Kozak sequence (CCRCCATGG) (32) typical for highly efficient eukaryotic translational start codons (Fig. 1). Proc. NatL Acad Sci USA 92 (1995) 2093 Brain agin S Size (Nucleotides) so _ * ~- 78 * FIG. 4. Primer extension analysis of hamster aphrodisin mrna. The size of the extension product obtained by using the primer AP-7 and vaginal total RNA is calculated as 103 bp. Thus, the most probable transcription start site is the adenosine in position 1 of Fig. 3. To verify the detected transcription start site by an alternative method, we performed cdna PCRs with two different sense primers located upstream (RAP-1) and downstream (RAP-2; Fig. 1) of the identified transcription start site. To enable us to distinguish between amplified cdna and gene fragments, we used antisense primers (AP-8 and AP-9; Fig. 1) located behind the first intron (Fig. 3). Surprisingly, all primer combinations led to the amplification of fragments which fit the sizes expected for cdna. Using the internal primer AP-7 as a probe, we verified the amplification of aphrodisin-specific fragments by Southern blot analysis (Fig. 5). Despite the fact that we obtained just one signal from the primer extension analysis, these results indicate an alternative transcription initiation of the aphrodisin gene. Distribution ofaphrodisin mrna Within the Female Hamster Genital Tract. To identify tissues expressing the aphrodisin gene, we analyzed total RNA from various parts of the female hamster genital tract (ovaries, fallopian tubes, uterus, vaginal tissue, and Bartholin's glands) by Northern blot analysis. Under stringent conditions we obtained single signals only from hamster vaginal tissue and Bartholin's glands (Fig. 6), both in comparable intensity. CAAT-Box -160 gctaatcacattagtttttgagatatgaggtcatacatcatttggcagggccaaagaggaaacactagacagatgtagcttagtgtagatcaaactgattottccgtgaaactccctct -41 * * * TATA-Box **Exn I > RAP-i >* aactatctg±ttaaaa gctttgtcagttgagttcttttcggccactcacctcttcgagcttctgt +103 <-Ex2n II < 'AP-7 (ILi 11 Phe Ser Leu Ala His Ala Gln Asp Phe Ala Glul +81 AGT CTG GCT CAT GCT CAG GAT TTT GCA GAG gtaaattcatttgct. 000 RAP-2 > Met Val Lys Ile Leu Val Leu Ala Leu Val tggaaaagcaaagtcaggcarccac_atg.gta AAG ATT CTG GTG CTG GCT TTG GTC 0 O6 tron I 448 bp) - I ILeu Gln Gly Lys Trp Tyr Thr Ile Val... tgttgcttttttcag CT CMA GGA MA TGG TAT ACC AU GTC. <- AP-9 AP-8 31 Ile Ala Ala Asp Asn Leu Glu Lys Ile Glu Glu Gly Gly Pro Leu Arg Phe Tyr Phe Arg His Ile Asp Cys Tyr Lys Asn Cys Ser Glu Met Glu ATT GCT GCT GAC AAT CUT GAA AAG ATA GA GAA GGA GGA CCA CTG AGA TTC TAT m CGT CAT ATT GAT TGT TAT AAA AAC TGC AGT GMA ATG GAA +236 FIG. 3. Part of the Golden hamster (Mesocricetus auratus) aphrodisin gene showing the transcription start site and the position of the primers used for primer extension analysis (AP-7) and PCR amplifications of 5'-terminal portions of the cdna (RAP-1, RAP-2, AP-8, AP-9). The putative CAAT box in reverse complementary orientation, the TATA box, the transcription start site, and the Kozak sequence surrounding the ATG start codon are underlined. The two adenosines which correspond to the transcription start site are additionally marked with asterisks (the more probable start site is marked with two asterisks). The codon for valine, differing from the codon for leucine in the case of hamster (Cricetus cricetus), is marked with diamonds. Distances of 30 bp are indicated with black dots. Intron I was not included in the numeration

4 2094 Biochemistry: Miigert et al _' -qj fe' Size (bp) 247 ~~~_ ~ ~ J"' FIG. 5. PCR Southern blot analysis of the transcription start site of the hamster aphrodisin gene with different sets of primers (see text and Fig. 3). After 35 PCR cycles, all primer combinations revealed DNA fragments in the size range expected for cdna (RAP-1/AP-8, 247 bp; RAP-2/AP-8, 198 bp; RAP-1/AP-9, 203 bp; RAP-2/AP-9, 154 bp). Southern blotting and hybridization with the internal oligonucleotide AP-7 verified the amplification of aphrodisin-specific cdna fragments in all cases. Under less stringent conditions we performed Northern hybridization experiments with the corresponding tissues of several other species, including rat, pig (data not shown), guinea pig (data not shown), tupaia, and human (Fig. 6). We obtained a signal in the expected size range only from rat Bartholin's glands. Tupaia vaginal and Bartholin's gland tissue (mixed) and human Bartholin's glands showed long signal smears between the 28S and 18S rrna and below the 18S rrna. DISCUSSION Since the presented cdna sequence was determined by sequencing PCR products, we had to identify the region of 0 47Z3 e Hamster Rat Human Tupaia -_*--28 S S FIG. 6. Northern hybridization with the radioactive-labeled aphrodisin cdna PCR fragment AP-1/AP-4. Five micrograms of total RNA was applied per lane. Hybridization was performed under conditions of high stringency (hamster) [5X standard saline citrate (SSC)/5x Denhardt's solution/0.1% SDS/50% formamide at 42 C, with washes in 2x SSC/0.1% SDS twice for 10 min at room temperature and 0.5x SSC/0.1% SDS once for 10 min at 65 C] or low stringency (rat, human, tupaia) (1 M NaCl/50 mm Tris-HCl ph 7.5/0.1% SDS/10% dextran sulfate at 45 C, with two 5-min washes in 6x SSC/0.1% SDS at room temperature). RNA samples from hamster vagina and Bartholin's glands show a strong hybridization signal even under highly stringent conditions. Under conditions of low stringency a signal in the expected size range was obtained from rat Bartholin's glands. RNA from mixed tissue of tupaia vagina and Bartholin's glands and from human Bartholin's glands gave long signal smears. Under conditions of low stringency rrna from all tissues showed crosshybridization with the aphrodisin probe. Positions of 28S and 18S rrna and aphrodisin (AP) RNA are indicated. _- AP Proc. NatL Acad Sci USA 92 (1995) transcription initiation by primer extension analysis. For this purpose, and in order to clone the corresponding gene, we have screened a Golden hamster genomic library in A phage. Assuming that the differences between aphrodisin genespecific sequences of hamster (Cricetus cricetus) and Golden hamster (Mesocricetus auratus) are only slight, we have chosen a library of the latter species because of its easy commercial availability. Indeed, during the not yet completed sequence determination of the gene, we have detected just one deviating nucleotide in the region coding for the putative secretory signal peptide of the aphrodisin precursor. This deviation leads to a predicted valine in position 6 of the Golden hamster aphrodisin precursor instead of leucine as in the case of the hamster (Fig. 3). By primer extension analysis, we obtained an extension product which correlates with a pair of adenines (see Figs. 3 and 4), identified as potential transcription start sites by both their ideal distance from a TATA-box motif and their location within a polypyrimidine tract. In two independent experiments, we obtained a single extension product which has been determined as 103 nt by means of logarithmic regression. These results suggest that the first adenine of the mentioned pair represents the real transcription initiation point. A further indication for the correct detection of this locus is the fact that the first ATG which follows in the 3' direction is surrounded by a Kozak sequence (see above) which is typical for highly efficient eukaryotic translational start points (32). It is the beginning of the region coding for a putative 16-aa secretory signal peptide, which ends before the codon for the first amino acid (Gln) of mature aphrodisin. Comparison of the deduced signal peptide to that from ROBP revealed a slight homology, especially within the first 9 aa (Fig. 7). However, the PCR experiments indicated the existence of at least one additional alternative transcription initiation site. This phenomenon is also known for some other genes-for instance, the renin gene (33). Since no alternative transcript has been detected by primer extension, it must appear in a much lower concentration than the predominant transcript. Northern blot analysis revealed vaginal tissue and Bartholin's glands (glandulae vestibulares majores) as the main aphrodisin mrna-synthesizing tissues of the female hamster genital tract. Taking into account that we used total RNA and that only relative short exposure times were necessary to obtain strong signals, the expression of the gene in these tissues would seem to be abundant. Whether the expression in vaginal tissue is due to an activity of the glandulae vestibulares minores, which are homologous to Bartholin's glands but much smaller, has to be investigated by in situ hybridization experiments or immunocytochemistry. To totally clarify the tissue distribution of aphrodisin-specific mrna, other tissues also have to be analyzed, preferably by using the more sensitive poly(a)+ RNA Northern blot or the nuclease S1 protection assay. Because aphrodisin acts via the vomeronasal organ (34) and is probably a carrier for an additional ligand, salivary glands are also potential candidates as loci of synthesis. Less stringent Northern hybridizations revealed signals from Bartholin's glands of other species, including rat, tupaia (mixed vaginal and Bartholin's gland tissue), and human. In the rat, the signal obtained was in the same size range as for aphrodisin mrna, suggesting the synthesis of an aphrodisinrelated protein. We now have to determine by cdna cloning and sequence analysis whether the signal is due to a novel mrna or to an expression of the gene for ROBP normally Aphrodisin I7V LLA VF s L- A ROBP F FLLI V.:A L G V SCH E N L FIG. 7. Comparison of the proaphrodisin signal peptide with the ROBP signal peptide (15). Identical regions are boxed.

5 Biochemistry: Mdgert et al. occurring in nasal mucosa (14, 15). In the case of Tupaia belangeri (a putative primate) and humans, we obtained long signal smears from Bartholin's glands instead of distinct signal bands. We first supposed this to be due to experimental artifacts, but this stands in contradiction to the fact that only specimens which contained RNA from Bartholin's glands behaved in this way. Further, the RNA used was absolutely undegraded and the signals cannot be explained by effects of concentration as in the case of 28S and 18S rrna, because no additional dominant bands corresponding to the signals were visible in the ethidium bromide-stained gel (data not shown). Signals from vaginal tissue could not be obtained from species other than hamster or Golden hamster. In summary, the results of Northern hybridization indicate high expression of the aphrodisin gene in hamster Bartholin's glands and vaginal tissue and suggest the synthesis of mrna species with at least a slight homology to the aphrodisin mrna in Bartholin's glands of rat, tupaia, and human. Whether these mrna species are related to lipocalins acting as pheromone carriers has to be investigated. Indications for the occurrence of primate sex pheromones in vaginal discharge already exist (35). Also, the occurrence of the vomeronasal organ in humans (36, 37) and its ability to perceive putative pheromones (38) have been demonstrated. The cloned aphrodisin cdna fragments as well as the gene will now serve as potentially useful tools for the investigation of aphrodisin/ lipocalin-related pheromone systems and their regulation in mammals. We thank G. Schmeding, H. Stober, H. Schindler, and W. Posselt for their excellent technical assistance; I. Kunstyr, A. Bub, M. Meyer, and E. Fuchs for tissue specimens and helpful advice; and G. Klock for the partial sequence analysis. This work was supported by a grant from the Deutsche Forschungsgemeinschaft (Ma 1605/1-1). 1. Pervaiz, S. & Brew, K. (1987) FASEB J. 1, Godovac-Zimmermann, J. (1988) Trends Biochem. Sci. 13, Akerstrom, B. & Logdberg, L. (1990) Trends Biochem. Sci. 15, Peitsch, M. C. & Boguski, M. S. (1991) Trends Biochem. Sci. 16, Igarashi, M., Nagata, A., Toh, H., Urade, Y. & Hayaishi, 0. (1992) Proc. Natl. Acad. Sci. USA 89, Bocskei, Z., Groom, C. R., Flower, D. R., Wright, C. E., Phillips, S. E. V., Cavaggioni, A., Findlay, J. B. C. & North, A. C. T. (1992) Nature (London) 360, Papiz, M. Z., Sawyer, L., Eliopoulos, E. E., North, A. C. T., Findley, J. B. C., Sivaprasadarao, R., Jones, T. A., Newcomer, M. E. & Kraulis, P. J. (1986) Nature (London) 324, Sivaprasadarao, A., Boudjelal, M. & Findley, J. B. (1993) Biochem. Soc. Trans. 21, Proc. NatL Acad Sci. USA 92 (1995) Singer, A. G., Macrides, F., Clancy, A. N. & Agosta, W. C. (1986) J. Biol. Chem. 261, Henzel, W. J., Rodriguez, H., Singer, A. G., Stults, J. T., Macrides, F., Agosta, W. C. & Niall, H. (1988) J. Biol. Chem. 263, Clancy, A. N., Macrides, F., Singer, A. G. & Agosta, W. C. (1984) Physiol. Behav. 33, Singer, A. G. (1991) J. Steroid Biochem. Mol. Biol. 39, Mancini, M. A., Majumdar, D., Chatterjee, B. & Roy, A. K. (1989) J. Histochem. Cytochem. 37, Pevsner, J., Trifiletti, R. R., Strittmatter, S. M. & Snyder, S. H. (1985) Proc. Natl. Acad. Sci. USA 82, Pevsner, J., Reed, R. R., Feinstein, P. G. & Snyder, S. H. (1988) Science 241, Snyder, S. H., Sklar, P. B. & Pevsner, J. (1988) J. Biol. Chem. 263, Saiki, R. K., Gelfand, D. H., Stoffel, S., Scharf, S. J., Higuchi, R., Horn, G. T., Mullis, K. B. & Erlich, H. A. (1988) Science 239, Yanish-Perron, C., Vieira, J. & Messing, J. (1985) Gene 33, Nishimura, A., Morita, M., Nishimura, Y. & Sugino, Y. (1990) Nucleic Acids Res. 18, Benton, W. D. & Davis, R. W. (1977) Science 196, Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Lab. Press, Plainview, NY). 22. Sanger, F., Nicklen, S. & Coulson, A. R. (1977) Proc. Natl. Acad. Sci. USA 74, Smith, L. M., Sanders, J. Z., Kaiser, R. J., Hughes, P., Dodd, C., Connell, C. R., Heiner, C., Kent, S. B. H. & Hood, L. E. (1986) Nature (London) 321, McMaster, G. K. & Carmichael, G. G. (1977) Proc. Natl. Acad. Sci. USA 74, Southern, E. M. (1975) J. Mol. Biol. 98, von Heijne, G. (1983) Eur. J. Biochem. 133, Proudfoot, N. J. & Brownlee, G. G. (1976) Nature (London) 263, Proudfoot, N. J. (1984) Nature (London) 307, Benoist, C., O'Hare, K., Breathnach, R. & Chambon, P. (1980) Nucleic Acids Res. 8, Breathnach, R. & Chambon, P. (1981) Annu. Rev. Biochem. 50, Wingender, E. (1988) Nucleic Acids Res. 16, Kozak, M. (1989) J. Cell Biol. 108, Paul, M., Burt, D. W., Krieger, J. E., Nakamura, N. & Dzau, V. J. (1992) Am. J. Physiol. 262, E644-E Jacobson, L. (1811) Ann. Mus. Hist. Natn. Paris 18, Michael, R. P. & Keverne, E. B. (1970) Nature (London) 225, Garcia-Velasco, J. & Mondragon, M. (1991) J. Steroid Biochem. Mol. Biol. 39, Moran, D. T., Jafek, B. W. & Rowley, J. C., III (1991) J. Steroid Biochem. Mol. Biol. 39, Monti-Bloch, L. & Grosser, B. I. (1991) J. Steroid Biochem. Mol. Biol. 39,

UNIVERSITETET I OSLO Det matematisk-naturvitenskapelige fakultet

UNIVERSITETET I OSLO Det matematisk-naturvitenskapelige fakultet 1 UNIVERSITETET I OSLO Det matematisk-naturvitenskapelige fakultet Exam in: MBV4010 Arbeidsmetoder i molekylærbiologi og biokjemi I MBV4010 Methods in molecular biology and biochemistry I Day of exam:.

More information

pcas-guide System Validation in Genome Editing

pcas-guide System Validation in Genome Editing pcas-guide System Validation in Genome Editing Tagging HSP60 with HA tag genome editing The latest tool in genome editing CRISPR/Cas9 allows for specific genome disruption and replacement in a flexible

More information

GENEWIZ, Inc. DNA Sequencing Service Details for USC Norris Comprehensive Cancer Center DNA Core

GENEWIZ, Inc. DNA Sequencing Service Details for USC Norris Comprehensive Cancer Center DNA Core DNA Sequencing Services Pre-Mixed o Provide template and primer, mixed into the same tube* Pre-Defined o Provide template and primer in separate tubes* Custom o Full-service for samples with unknown concentration

More information

(http://genomes.urv.es/caical) TUTORIAL. (July 2006)

(http://genomes.urv.es/caical) TUTORIAL. (July 2006) (http://genomes.urv.es/caical) TUTORIAL (July 2006) CAIcal manual 2 Table of contents Introduction... 3 Required inputs... 5 SECTION A Calculation of parameters... 8 SECTION B CAI calculation for FASTA

More information

Part ONE. a. Assuming each of the four bases occurs with equal probability, how many bits of information does a nucleotide contain?

Part ONE. a. Assuming each of the four bases occurs with equal probability, how many bits of information does a nucleotide contain? Networked Systems, COMPGZ01, 2012 Answer TWO questions from Part ONE on the answer booklet containing lined writing paper, and answer ALL questions in Part TWO on the multiple-choice question answer sheet.

More information

Inverse PCR & Cycle Sequencing of P Element Insertions for STS Generation

Inverse PCR & Cycle Sequencing of P Element Insertions for STS Generation BDGP Resources Inverse PCR & Cycle Sequencing of P Element Insertions for STS Generation For recovery of sequences flanking PZ, PlacW and PEP elements E. Jay Rehm Berkeley Drosophila Genome Project I.

More information

Hands on Simulation of Mutation

Hands on Simulation of Mutation Hands on Simulation of Mutation Charlotte K. Omoto P.O. Box 644236 Washington State University Pullman, WA 99164-4236 omoto@wsu.edu ABSTRACT This exercise is a hands-on simulation of mutations and their

More information

DNA Sample preparation and Submission Guidelines

DNA Sample preparation and Submission Guidelines DNA Sample preparation and Submission Guidelines Requirements: Please submit samples in 1.5ml microcentrifuge tubes. Fill all the required information in the Eurofins DNA sequencing order form and send

More information

10 µg lyophilized plasmid DNA (store lyophilized plasmid at 20 C)

10 µg lyophilized plasmid DNA (store lyophilized plasmid at 20 C) TECHNICAL DATA SHEET BIOLUMINESCENCE RESONANCE ENERGY TRANSFER RENILLA LUCIFERASE FUSION PROTEIN EXPRESSION VECTOR Product: prluc-c Vectors Catalog number: Description: Amount: The prluc-c vectors contain

More information

The p53 MUTATION HANDBOOK

The p53 MUTATION HANDBOOK The p MUTATION HANDBOOK Version 1. /7 Thierry Soussi Christophe Béroud, Dalil Hamroun Jean Michel Rubio Nevado http://p/free.fr The p Mutation HandBook By T Soussi, J.M. Rubio-Nevado, D. Hamroun and C.

More information

(A) Microarray analysis was performed on ATM and MDM isolated from 4 obese donors.

(A) Microarray analysis was performed on ATM and MDM isolated from 4 obese donors. Legends of supplemental figures and tables Figure 1: Overview of study design and results. (A) Microarray analysis was performed on ATM and MDM isolated from 4 obese donors. After raw data gene expression

More information

SERVICES CATALOGUE WITH SUBMISSION GUIDELINES

SERVICES CATALOGUE WITH SUBMISSION GUIDELINES SERVICES CATALOGUE WITH SUBMISSION GUIDELINES 3921 Montgomery Road Cincinnati, Ohio 45212 513-841-2428 www.agctsequencing.com CONTENTS Welcome Dye Terminator Sequencing DNA Sequencing Services - Full Service

More information

a. Ribosomal RNA rrna a type ofrna that combines with proteins to form Ribosomes on which polypeptide chains of proteins are assembled

a. Ribosomal RNA rrna a type ofrna that combines with proteins to form Ribosomes on which polypeptide chains of proteins are assembled Biology 101 Chapter 14 Name: Fill-in-the-Blanks Which base follows the next in a strand of DNA is referred to. as the base (1) Sequence. The region of DNA that calls for the assembly of specific amino

More information

Table S1. Related to Figure 4

Table S1. Related to Figure 4 Table S1. Related to Figure 4 Final Diagnosis Age PMD Control Control 61 15 Control 67 6 Control 68 10 Control 49 15 AR-PD PD 62 15 PD 65 4 PD 52 18 PD 68 10 AR-PD cingulate cortex used for immunoblot

More information

Molecular analyses of EGFR: mutation and amplification detection

Molecular analyses of EGFR: mutation and amplification detection Molecular analyses of EGFR: mutation and amplification detection Petra Nederlof, Moleculaire Pathologie NKI Amsterdam Henrique Ruijter, Ivon Tielen, Lucie Boerrigter, Aafke Ariaens Outline presentation

More information

Mutations and Genetic Variability. 1. What is occurring in the diagram below?

Mutations and Genetic Variability. 1. What is occurring in the diagram below? Mutations and Genetic Variability 1. What is occurring in the diagram below? A. Sister chromatids are separating. B. Alleles are independently assorting. C. Genes are replicating. D. Segments of DNA are

More information

2. The number of different kinds of nucleotides present in any DNA molecule is A) four B) six C) two D) three

2. The number of different kinds of nucleotides present in any DNA molecule is A) four B) six C) two D) three Chem 121 Chapter 22. Nucleic Acids 1. Any given nucleotide in a nucleic acid contains A) two bases and a sugar. B) one sugar, two bases and one phosphate. C) two sugars and one phosphate. D) one sugar,

More information

Title : Parallel DNA Synthesis : Two PCR product from one DNA template

Title : Parallel DNA Synthesis : Two PCR product from one DNA template Title : Parallel DNA Synthesis : Two PCR product from one DNA template Bhardwaj Vikash 1 and Sharma Kulbhushan 2 1 Email: vikashbhardwaj@ gmail.com 1 Current address: Government College Sector 14 Gurgaon,

More information

Molecular Facts and Figures

Molecular Facts and Figures Nucleic Acids Molecular Facts and Figures DNA/RNA bases: DNA and RNA are composed of four bases each. In DNA the four are Adenine (A), Thymidine (T), Cytosine (C), and Guanine (G). In RNA the four are

More information

http://www.life.umd.edu/grad/mlfsc/ DNA Bracelets

http://www.life.umd.edu/grad/mlfsc/ DNA Bracelets http://www.life.umd.edu/grad/mlfsc/ DNA Bracelets by Louise Brown Jasko John Anthony Campbell Jack Dennis Cassidy Michael Nickelsburg Stephen Prentis Rohm Objectives: 1) Using plastic beads, construct

More information

pcmv6-neo Vector Application Guide Contents

pcmv6-neo Vector Application Guide Contents pcmv6-neo Vector Application Guide Contents Package Contents and Storage Conditions... 2 Product Description... 2 Introduction... 2 Production and Quality Assurance... 2 Methods... 3 Other required reagents...

More information

Supplementary Online Material for Morris et al. sirna-induced transcriptional gene

Supplementary Online Material for Morris et al. sirna-induced transcriptional gene Supplementary Online Material for Morris et al. sirna-induced transcriptional gene silencing in human cells. Materials and Methods Lentiviral vector and sirnas. FIV vector pve-gfpwp was prepared as described

More information

Pipe Cleaner Proteins. Essential question: How does the structure of proteins relate to their function in the cell?

Pipe Cleaner Proteins. Essential question: How does the structure of proteins relate to their function in the cell? Pipe Cleaner Proteins GPS: SB1 Students will analyze the nature of the relationships between structures and functions in living cells. Essential question: How does the structure of proteins relate to their

More information

Coding sequence the sequence of nucleotide bases on the DNA that are transcribed into RNA which are in turn translated into protein

Coding sequence the sequence of nucleotide bases on the DNA that are transcribed into RNA which are in turn translated into protein Assignment 3 Michele Owens Vocabulary Gene: A sequence of DNA that instructs a cell to produce a particular protein Promoter a control sequence near the start of a gene Coding sequence the sequence of

More information

Gene Synthesis 191. Mutagenesis 194. Gene Cloning 196. AccuGeneBlock Service 198. Gene Synthesis FAQs 201. User Protocol 204

Gene Synthesis 191. Mutagenesis 194. Gene Cloning 196. AccuGeneBlock Service 198. Gene Synthesis FAQs 201. User Protocol 204 Gene Synthesis 191 Mutagenesis 194 Gene Cloning 196 AccuGeneBlock Service 198 Gene Synthesis FAQs 201 User Protocol 204 Gene Synthesis Overview Gene synthesis is the most cost-effective way to enhance

More information

Essentials of Real Time PCR. About Sequence Detection Chemistries

Essentials of Real Time PCR. About Sequence Detection Chemistries Essentials of Real Time PCR About Real-Time PCR Assays Real-time Polymerase Chain Reaction (PCR) is the ability to monitor the progress of the PCR as it occurs (i.e., in real time). Data is therefore collected

More information

Next Generation Sequencing

Next Generation Sequencing Next Generation Sequencing 38. Informationsgespräch der Blutspendezentralefür Wien, Niederösterreich und Burgenland Österreichisches Rotes Kreuz 22. November 2014, Parkhotel Schönbrunn Die Zukunft hat

More information

HiPer RT-PCR Teaching Kit

HiPer RT-PCR Teaching Kit HiPer RT-PCR Teaching Kit Product Code: HTBM024 Number of experiments that can be performed: 5 Duration of Experiment: Protocol: 4 hours Agarose Gel Electrophoresis: 45 minutes Storage Instructions: The

More information

RT-PCR: Two-Step Protocol

RT-PCR: Two-Step Protocol RT-PCR: Two-Step Protocol We will provide both one-step and two-step protocols for RT-PCR. We recommend the twostep protocol for this class. In the one-step protocol, the components of RT and PCR are mixed

More information

Provincial Exam Questions. 9. Give one role of each of the following nucleic acids in the production of an enzyme.

Provincial Exam Questions. 9. Give one role of each of the following nucleic acids in the production of an enzyme. Provincial Exam Questions Unit: Cell Biology: Protein Synthesis (B7 & B8) 2010 Jan 3. Describe the process of translation. (4 marks) 2009 Sample 8. What is the role of ribosomes in protein synthesis? A.

More information

expressed histone genes have intervening sequences and encode polyadenylylated mrnas

expressed histone genes have intervening sequences and encode polyadenylylated mrnas Proc. Natl. Acad. Sci. USA Vol. 82, pp. 2834-2838, May 1985 Genetics Structure of a human histone cdna: Evidence that basally expressed histone genes have intervening sequences and encode polyadenylylated

More information

Characterization of cdna clones of the family of trypsin/a-amylase inhibitors (CM-proteins) in barley {Hordeum vulgare L.)

Characterization of cdna clones of the family of trypsin/a-amylase inhibitors (CM-proteins) in barley {Hordeum vulgare L.) Characterization of cdna clones of the family of trypsin/a-amylase inhibitors (CM-proteins) in barley {Hordeum vulgare L.) J. Paz-Ares, F. Ponz, P. Rodríguez-Palenzuela, A. Lázaro, C. Hernández-Lucas,

More information

ISTEP+: Biology I End-of-Course Assessment Released Items and Scoring Notes

ISTEP+: Biology I End-of-Course Assessment Released Items and Scoring Notes ISTEP+: Biology I End-of-Course Assessment Released Items and Scoring Notes Page 1 of 22 Introduction Indiana students enrolled in Biology I participated in the ISTEP+: Biology I Graduation Examination

More information

DNA Fingerprinting. Unless they are identical twins, individuals have unique DNA

DNA Fingerprinting. Unless they are identical twins, individuals have unique DNA DNA Fingerprinting Unless they are identical twins, individuals have unique DNA DNA fingerprinting The name used for the unambiguous identifying technique that takes advantage of differences in DNA sequence

More information

Mir-X mirna First-Strand Synthesis Kit User Manual

Mir-X mirna First-Strand Synthesis Kit User Manual User Manual Mir-X mirna First-Strand Synthesis Kit User Manual United States/Canada 800.662.2566 Asia Pacific +1.650.919.7300 Europe +33.(0)1.3904.6880 Japan +81.(0)77.543.6116 Clontech Laboratories, Inc.

More information

Peptide bonds: resonance structure. Properties of proteins: Peptide bonds and side chains. Dihedral angles. Peptide bond. Protein physics, Lecture 5

Peptide bonds: resonance structure. Properties of proteins: Peptide bonds and side chains. Dihedral angles. Peptide bond. Protein physics, Lecture 5 Protein physics, Lecture 5 Peptide bonds: resonance structure Properties of proteins: Peptide bonds and side chains Proteins are linear polymers However, the peptide binds and side chains restrict conformational

More information

Protein Physics. A. V. Finkelstein & O. B. Ptitsyn LECTURE 1

Protein Physics. A. V. Finkelstein & O. B. Ptitsyn LECTURE 1 Protein Physics A. V. Finkelstein & O. B. Ptitsyn LECTURE 1 PROTEINS Functions in a Cell MOLECULAR MACHINES BUILDING BLOCKS of a CELL ARMS of a CELL ENZYMES - enzymatic catalysis of biochemical reactions

More information

Forensic DNA Testing Terminology

Forensic DNA Testing Terminology Forensic DNA Testing Terminology ABI 310 Genetic Analyzer a capillary electrophoresis instrument used by forensic DNA laboratories to separate short tandem repeat (STR) loci on the basis of their size.

More information

Drosophila NK-homeobox genes

Drosophila NK-homeobox genes Proc. Natl. Acad. Sci. USA Vol. 86, pp. 7716-7720, October 1989 Biochemistry Drosophila NK-homeobox genes (NK-1, NK-2,, and DNA clones/chromosome locations of genes) YONGSOK KIM AND MARSHALL NIRENBERG

More information

Recombinant DNA & Genetic Engineering. Tools for Genetic Manipulation

Recombinant DNA & Genetic Engineering. Tools for Genetic Manipulation Recombinant DNA & Genetic Engineering g Genetic Manipulation: Tools Kathleen Hill Associate Professor Department of Biology The University of Western Ontario Tools for Genetic Manipulation DNA, RNA, cdna

More information

Bio 102 Practice Problems Recombinant DNA and Biotechnology

Bio 102 Practice Problems Recombinant DNA and Biotechnology Bio 102 Practice Problems Recombinant DNA and Biotechnology Multiple choice: Unless otherwise directed, circle the one best answer: 1. Which of the following DNA sequences could be the recognition site

More information

Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals

Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals Xiaohui Xie 1, Jun Lu 1, E. J. Kulbokas 1, Todd R. Golub 1, Vamsi Mootha 1, Kerstin Lindblad-Toh

More information

First Strand cdna Synthesis

First Strand cdna Synthesis 380PR 01 G-Biosciences 1-800-628-7730 1-314-991-6034 technical@gbiosciences.com A Geno Technology, Inc. (USA) brand name First Strand cdna Synthesis (Cat. # 786 812) think proteins! think G-Biosciences

More information

June 09, 2009 Random Mutagenesis

June 09, 2009 Random Mutagenesis Why Mutagenesis? Analysis of protein function June 09, 2009 Random Mutagenesis Analysis of protein structure Protein engineering Analysis of structure-function relationship Analysis of the catalytic center

More information

RevertAid Premium First Strand cdna Synthesis Kit

RevertAid Premium First Strand cdna Synthesis Kit RevertAid Premium First Strand cdna Synthesis Kit #K1651, #K1652 CERTIFICATE OF ANALYSIS #K1651 Lot QUALITY CONTROL RT-PCR using 100 fg of control GAPDH RNA and GAPDH control primers generated a prominent

More information

The Biotechnology Education Company

The Biotechnology Education Company EDVTEK P.. Box 1232 West Bethesda, MD 20827-1232 The Biotechnology 106 EDV-Kit # Principles of DNA Sequencing Experiment bjective: The objective of this experiment is to develop an understanding of DNA

More information

TITRATION OF raav (VG) USING QUANTITATIVE REAL TIME PCR

TITRATION OF raav (VG) USING QUANTITATIVE REAL TIME PCR Page 1 of 5 Materials DNase digestion buffer [13 mm Tris-Cl, ph7,5 / 5 mm MgCl2 / 0,12 mm CaCl2] RSS plasmid ptr-uf11 SV40pA Forward primer (10µM) AGC AAT AGC ATC ACA AAT TTC ACA A SV40pA Reverse Primer

More information

Recombinant DNA Unit Exam

Recombinant DNA Unit Exam Recombinant DNA Unit Exam Question 1 Restriction enzymes are extensively used in molecular biology. Below are the recognition sites of two of these enzymes, BamHI and BclI. a) BamHI, cleaves after the

More information

NimbleGen SeqCap EZ Library SR User s Guide Version 3.0

NimbleGen SeqCap EZ Library SR User s Guide Version 3.0 NimbleGen SeqCap EZ Library SR User s Guide Version 3.0 For life science research only. Not for use in diagnostic procedures. Copyright 2011 Roche NimbleGen, Inc. All Rights Reserved. Editions Version

More information

Molecular Biology Techniques: A Classroom Laboratory Manual THIRD EDITION

Molecular Biology Techniques: A Classroom Laboratory Manual THIRD EDITION Molecular Biology Techniques: A Classroom Laboratory Manual THIRD EDITION Susan Carson Heather B. Miller D.Scott Witherow ELSEVIER AMSTERDAM BOSTON HEIDELBERG LONDON NEW YORK OXFORD PARIS SAN DIEGO SAN

More information

The nucleotide sequence of the gene for human protein C

The nucleotide sequence of the gene for human protein C Proc. Natl. Acad. Sci. USA Vol. 82, pp. 4673-4677, July 1985 Biochemistry The nucleotide sequence of the gene for human protein C (DNA sequence analysis/vitamin K-dependent proteins/blood coagulation)

More information

Nucleic Acid Techniques in Bacterial Systematics

Nucleic Acid Techniques in Bacterial Systematics Nucleic Acid Techniques in Bacterial Systematics Edited by Erko Stackebrandt Department of Microbiology University of Queensland St Lucia, Australia and Michael Goodfellow Department of Microbiology University

More information

Protein Synthesis. Page 41 Page 44 Page 47 Page 42 Page 45 Page 48 Page 43 Page 46 Page 49. Page 41. DNA RNA Protein. Vocabulary

Protein Synthesis. Page 41 Page 44 Page 47 Page 42 Page 45 Page 48 Page 43 Page 46 Page 49. Page 41. DNA RNA Protein. Vocabulary Protein Synthesis Vocabulary Transcription Translation Translocation Chromosomal mutation Deoxyribonucleic acid Frame shift mutation Gene expression Mutation Point mutation Page 41 Page 41 Page 44 Page

More information

IV. -Amino Acids: carboxyl and amino groups bonded to -Carbon. V. Polypeptides and Proteins

IV. -Amino Acids: carboxyl and amino groups bonded to -Carbon. V. Polypeptides and Proteins IV. -Amino Acids: carboxyl and amino groups bonded to -Carbon A. Acid/Base properties 1. carboxyl group is proton donor! weak acid 2. amino group is proton acceptor! weak base 3. At physiological ph: H

More information

Gene Expression Assays

Gene Expression Assays APPLICATION NOTE TaqMan Gene Expression Assays A mpl i fic ationef ficienc yof TaqMan Gene Expression Assays Assays tested extensively for qpcr efficiency Key factors that affect efficiency Efficiency

More information

Introduction to Perl Programming Input/Output, Regular Expressions, String Manipulation. Beginning Perl, Chap 4 6. Example 1

Introduction to Perl Programming Input/Output, Regular Expressions, String Manipulation. Beginning Perl, Chap 4 6. Example 1 Introduction to Perl Programming Input/Output, Regular Expressions, String Manipulation Beginning Perl, Chap 4 6 Example 1 #!/usr/bin/perl -w use strict; # version 1: my @nt = ('A', 'C', 'G', 'T'); for

More information

Thermo Scientific DyNAmo cdna Synthesis Kit for qrt-pcr Technical Manual

Thermo Scientific DyNAmo cdna Synthesis Kit for qrt-pcr Technical Manual Thermo Scientific DyNAmo cdna Synthesis Kit for qrt-pcr Technical Manual F- 470S 20 cdna synthesis reactions (20 µl each) F- 470L 100 cdna synthesis reactions (20 µl each) Table of contents 1. Description...

More information

Molecular Characterization of the Llamas (Lama glama) Casein Cluster Genes Transcripts (CSN1S1, CSN2, CSN1S2, CSN3) and Regulatory Regions

Molecular Characterization of the Llamas (Lama glama) Casein Cluster Genes Transcripts (CSN1S1, CSN2, CSN1S2, CSN3) and Regulatory Regions RESEARCH ARTICLE Molecular Characterization of the Llamas (Lama glama) Casein Cluster Genes Transcripts (CSN1S1, CSN2, CSN1S2, CSN3) and Regulatory Regions Alfredo Pauciullo 1,2 *, Georg Erhardt 2 1 Department

More information

GenBank, Entrez, & FASTA

GenBank, Entrez, & FASTA GenBank, Entrez, & FASTA Nucleotide Sequence Databases First generation GenBank is a representative example started as sort of a museum to preserve knowledge of a sequence from first discovery great repositories,

More information

2. True or False? The sequence of nucleotides in the human genome is 90.9% identical from one person to the next. False (it s 99.

2. True or False? The sequence of nucleotides in the human genome is 90.9% identical from one person to the next. False (it s 99. 1. True or False? A typical chromosome can contain several hundred to several thousand genes, arranged in linear order along the DNA molecule present in the chromosome. True 2. True or False? The sequence

More information

Chapter 9. Applications of probability. 9.1 The genetic code

Chapter 9. Applications of probability. 9.1 The genetic code Chapter 9 Applications of probability In this chapter we use the tools of elementary probability to investigate problems of several kinds. First, we study the language of life by focusing on the universal

More information

EU Reference Laboratory for E. coli Department of Veterinary Public Health and Food Safety Unit of Foodborne Zoonoses Istituto Superiore di Sanità

EU Reference Laboratory for E. coli Department of Veterinary Public Health and Food Safety Unit of Foodborne Zoonoses Istituto Superiore di Sanità Identification and characterization of Verocytotoxin-producing Escherichia coli (VTEC) by Real Time PCR amplification of the main virulence genes and the genes associated with the serogroups mainly associated

More information

Supplementary Information. Binding region and interaction properties of sulfoquinovosylacylglycerol (SQAG) with human

Supplementary Information. Binding region and interaction properties of sulfoquinovosylacylglycerol (SQAG) with human Supplementary Information Binding region and interaction properties of sulfoquinovosylacylglycerol (SQAG) with human vascular endothelial growth factor 165 revealed by biosensor based assays Yoichi Takakusagi

More information

Biotechnology: DNA Technology & Genomics

Biotechnology: DNA Technology & Genomics Chapter 20. Biotechnology: DNA Technology & Genomics 2003-2004 The BIG Questions How can we use our knowledge of DNA to: diagnose disease or defect? cure disease or defect? change/improve organisms? What

More information

Appendix 2 Molecular Biology Core Curriculum. Websites and Other Resources

Appendix 2 Molecular Biology Core Curriculum. Websites and Other Resources Appendix 2 Molecular Biology Core Curriculum Websites and Other Resources Chapter 1 - The Molecular Basis of Cancer 1. Inside Cancer http://www.insidecancer.org/ From the Dolan DNA Learning Center Cold

More information

How To Clone Into Pcdna 3.1/V5-His

How To Clone Into Pcdna 3.1/V5-His pcdna 3.1/V5-His A, B, and C Catalog no. V810-20 Rev. date: 09 November 2010 Manual part no. 28-0141 MAN0000645 User Manual ii Contents Contents and Storage... iv Methods... 1 Cloning into pcdna 3.1/V5-His

More information

From DNA to Protein. Proteins. Chapter 13. Prokaryotes and Eukaryotes. The Path From Genes to Proteins. All proteins consist of polypeptide chains

From DNA to Protein. Proteins. Chapter 13. Prokaryotes and Eukaryotes. The Path From Genes to Proteins. All proteins consist of polypeptide chains Proteins From DNA to Protein Chapter 13 All proteins consist of polypeptide chains A linear sequence of amino acids Each chain corresponds to the nucleotide base sequence of a gene The Path From Genes

More information

2006 7.012 Problem Set 3 KEY

2006 7.012 Problem Set 3 KEY 2006 7.012 Problem Set 3 KEY Due before 5 PM on FRIDAY, October 13, 2006. Turn answers in to the box outside of 68-120. PLEASE WRITE YOUR ANSWERS ON THIS PRINTOUT. 1. Which reaction is catalyzed by each

More information

Transcriptional repressor CopR: dissection of stabilizing motifs within the C terminus

Transcriptional repressor CopR: dissection of stabilizing motifs within the C terminus Microbiology (2001), 147, 3387 3392 Printed in Great Britain Transcriptional repressor CopR: dissection of stabilizing motifs within the C terminus Kornelia Kuhn, 1 Katrin Steinmetzer 2 and Sabine Brantl

More information

(c) How would your answers to problem (a) change if the molecular weight of the protein was 100,000 Dalton?

(c) How would your answers to problem (a) change if the molecular weight of the protein was 100,000 Dalton? Problem 1. (12 points total, 4 points each) The molecular weight of an unspecified protein, at physiological conditions, is 70,000 Dalton, as determined by sedimentation equilibrium measurements and by

More information

Advanced Medicinal & Pharmaceutical Chemistry CHEM 5412 Dept. of Chemistry, TAMUK

Advanced Medicinal & Pharmaceutical Chemistry CHEM 5412 Dept. of Chemistry, TAMUK Advanced Medicinal & Pharmaceutical Chemistry CHEM 5412 Dept. of Chemistry, TAMUK Dai Lu, Ph.D. dlu@tamhsc.edu Tel: 361-221-0745 Office: RCOP, Room 307 Drug Discovery and Development Drug Molecules Medicinal

More information

Becker Muscular Dystrophy

Becker Muscular Dystrophy Muscular Dystrophy A Case Study of Positional Cloning Described by Benjamin Duchenne (1868) X-linked recessive disease causing severe muscular degeneration. 100 % penetrance X d Y affected male Frequency

More information

DNA Sequencing of the eta Gene Coding for Staphylococcal Exfoliative Toxin Serotype A

DNA Sequencing of the eta Gene Coding for Staphylococcal Exfoliative Toxin Serotype A Journal of General Microbiology (1988), 134, 71 1-71 7. Printed in Great Britain 71 1 DNA Sequencing of the eta Gene Coding for Staphylococcal Exfoliative Toxin Serotype A By SUSUMU SAKURA, HTOSH SUZUK

More information

restriction enzymes 350 Home R. Ward: Spring 2001

restriction enzymes 350 Home R. Ward: Spring 2001 restriction enzymes 350 Home Restriction Enzymes (endonucleases): molecular scissors that cut DNA Properties of widely used Type II restriction enzymes: recognize a single sequence of bases in dsdna, usually

More information

PRACTICE TEST QUESTIONS

PRACTICE TEST QUESTIONS PART A: MULTIPLE CHOICE QUESTIONS PRACTICE TEST QUESTIONS DNA & PROTEIN SYNTHESIS B 1. One of the functions of DNA is to A. secrete vacuoles. B. make copies of itself. C. join amino acids to each other.

More information

Introduction to Bioinformatics (Master ChemoInformatique)

Introduction to Bioinformatics (Master ChemoInformatique) Introduction to Bioinformatics (Master ChemoInformatique) Roland Stote Institut de Génétique et de Biologie Moléculaire et Cellulaire Biocomputing Group 03.90.244.730 rstote@igbmc.fr Biological Function

More information

A. A peptide with 12 amino acids has the following amino acid composition: 2 Met, 1 Tyr, 1 Trp, 2 Glu, 1 Lys, 1 Arg, 1 Thr, 1 Asn, 1 Ile, 1 Cys

A. A peptide with 12 amino acids has the following amino acid composition: 2 Met, 1 Tyr, 1 Trp, 2 Glu, 1 Lys, 1 Arg, 1 Thr, 1 Asn, 1 Ile, 1 Cys Questions- Proteins & Enzymes A. A peptide with 12 amino acids has the following amino acid composition: 2 Met, 1 Tyr, 1 Trp, 2 Glu, 1 Lys, 1 Arg, 1 Thr, 1 Asn, 1 Ile, 1 Cys Reaction of the intact peptide

More information

Part A: Amino Acids and Peptides (Is the peptide IAG the same as the peptide GAI?)

Part A: Amino Acids and Peptides (Is the peptide IAG the same as the peptide GAI?) ChemActivity 46 Amino Acids, Polypeptides and Proteins 1 ChemActivity 46 Part A: Amino Acids and Peptides (Is the peptide IAG the same as the peptide GAI?) Model 1: The 20 Amino Acids at Biological p See

More information

Rapid Acquisition of Unknown DNA Sequence Adjacent to a Known Segment by Multiplex Restriction Site PCR

Rapid Acquisition of Unknown DNA Sequence Adjacent to a Known Segment by Multiplex Restriction Site PCR Rapid Acquisition of Unknown DNA Sequence Adjacent to a Known Segment by Multiplex Restriction Site PCR BioTechniques 25:415-419 (September 1998) ABSTRACT The determination of unknown DNA sequences around

More information

APOT - Assay. Protocol for HPV16 and 18. Amplification of Papilloma Virus Oncogene Transcripts HPV. E6 E7 E1 Zelluläre DNA poly(a)

APOT - Assay. Protocol for HPV16 and 18. Amplification of Papilloma Virus Oncogene Transcripts HPV. E6 E7 E1 Zelluläre DNA poly(a) E5 E2 E1 APOT - Assay Amplification of Papilloma Virus Oncogene Transcripts URR E6 E7 L1 HPV L2 E4 E6 E7 E1 Zelluläre DNA poly(a) Protocol for HPV16 and 18 Brief summary of the APOT assay Fig.1A shows

More information

Molecular Genetics. RNA, Transcription, & Protein Synthesis

Molecular Genetics. RNA, Transcription, & Protein Synthesis Molecular Genetics RNA, Transcription, & Protein Synthesis Section 1 RNA AND TRANSCRIPTION Objectives Describe the primary functions of RNA Identify how RNA differs from DNA Describe the structure and

More information

Gene Finding CMSC 423

Gene Finding CMSC 423 Gene Finding CMSC 423 Finding Signals in DNA We just have a long string of A, C, G, Ts. How can we find the signals encoded in it? Suppose you encountered a language you didn t know. How would you decipher

More information

DNA Sequence Analysis

DNA Sequence Analysis DNA Sequence Analysis Two general kinds of analysis Screen for one of a set of known sequences Determine the sequence even if it is novel Screening for a known sequence usually involves an oligonucleotide

More information

Mutation. Mutation provides raw material to evolution. Different kinds of mutations have different effects

Mutation. Mutation provides raw material to evolution. Different kinds of mutations have different effects Mutation Mutation provides raw material to evolution Different kinds of mutations have different effects Mutational Processes Point mutation single nucleotide changes coding changes (missense mutations)

More information

--not necessarily a protein! (all proteins are polypeptides, but the converse is not true)

--not necessarily a protein! (all proteins are polypeptides, but the converse is not true) 00Note Set 5b 1 PEPTIDE BONDS AND POLYPEPTIDES OLIGOPEPTIDE: --chain containing only a few amino acids (see tetrapaptide, Fig 5.9) POLYPEPTIDE CHAINS: --many amino acids joined together --not necessarily

More information

Recombinant DNA and Biotechnology

Recombinant DNA and Biotechnology Recombinant DNA and Biotechnology Chapter 18 Lecture Objectives What Is Recombinant DNA? How Are New Genes Inserted into Cells? What Sources of DNA Are Used in Cloning? What Other Tools Are Used to Study

More information

Genomic DNA Clean & Concentrator Catalog Nos. D4010 & D4011

Genomic DNA Clean & Concentrator Catalog Nos. D4010 & D4011 Page 0 INSTRUCTION MANUAL Catalog Nos. D4010 & D4011 Highlights Quick (5 minute) spin column recovery of large-sized DNA (e.g., genomic, mitochondrial, plasmid (BAC/PAC), viral, phage, (wga)dna, etc.)

More information

PyroPhage 3173 DNA Polymerase, Exonuclease Minus (Exo-)

PyroPhage 3173 DNA Polymerase, Exonuclease Minus (Exo-) PyroPhage 3173 DNA Polymerase, Exonuclease Minus (Exo-) FOR RESEARCH USE ONLY. NOT FOR HUMAN OR DIAGNOSTIC USE Lucigen Corporation 2905 Parmenter St, Middleton, WI 53562 USA Toll Free: (888) 575-9695 (608)

More information

CompleteⅡ 1st strand cdna Synthesis Kit

CompleteⅡ 1st strand cdna Synthesis Kit Instruction Manual CompleteⅡ 1st strand cdna Synthesis Kit Catalog # GM30401, GM30402 Green Mountain Biosystems. LLC Web: www.greenmountainbio.com Tel: 800-942-1160 Sales: Sales@ greenmountainbio.com Support:

More information

Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources

Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources 1 of 8 11/7/2004 11:00 AM National Center for Biotechnology Information About NCBI NCBI at a Glance A Science Primer Human Genome Resources Model Organisms Guide Outreach and Education Databases and Tools

More information

HCS604.03 Exercise 1 Dr. Jones Spring 2005. Recombinant DNA (Molecular Cloning) exercise:

HCS604.03 Exercise 1 Dr. Jones Spring 2005. Recombinant DNA (Molecular Cloning) exercise: HCS604.03 Exercise 1 Dr. Jones Spring 2005 Recombinant DNA (Molecular Cloning) exercise: The purpose of this exercise is to learn techniques used to create recombinant DNA or clone genes. You will clone

More information

Chem 465 Biochemistry II

Chem 465 Biochemistry II Chem 465 Biochemistry II Name: 2 points Multiple choice (4 points apiece): 1. Formation of the ribosomal initiation complex for bacterial protein synthesis does not require: A) EF-Tu. B) formylmethionyl

More information

Global MicroRNA Amplification Kit

Global MicroRNA Amplification Kit Global MicroRNA Amplification Kit Store kit at -20 C on receipt (ver. 3-060901) A limited-use label license covers this product. By use of this product, you accept the terms and conditions outlined in

More information

IIID 14. Biotechnology in Fish Disease Diagnostics: Application of the Polymerase Chain Reaction (PCR)

IIID 14. Biotechnology in Fish Disease Diagnostics: Application of the Polymerase Chain Reaction (PCR) IIID 14. Biotechnology in Fish Disease Diagnostics: Application of the Polymerase Chain Reaction (PCR) Background Infectious diseases caused by pathogenic organisms such as bacteria, viruses, protozoa,

More information

Introduction To Real Time Quantitative PCR (qpcr)

Introduction To Real Time Quantitative PCR (qpcr) Introduction To Real Time Quantitative PCR (qpcr) SABiosciences, A QIAGEN Company www.sabiosciences.com The Seminar Topics The advantages of qpcr versus conventional PCR Work flow & applications Factors

More information

Application Guide... 2

Application Guide... 2 Protocol for GenomePlex Whole Genome Amplification from Formalin-Fixed Parrafin-Embedded (FFPE) tissue Application Guide... 2 I. Description... 2 II. Product Components... 2 III. Materials to be Supplied

More information

Recap. Lecture 2. Protein conformation. Proteins. 8 types of protein function 10/21/10. Proteins.. > 50% dry weight of a cell

Recap. Lecture 2. Protein conformation. Proteins. 8 types of protein function 10/21/10. Proteins.. > 50% dry weight of a cell Lecture 2 Protein conformation ecap Proteins.. > 50% dry weight of a cell ell s building blocks and molecular tools. More important than genes A large variety of functions http://www.tcd.ie/biochemistry/courses/jf_lectures.php

More information

Real-Time PCR Vs. Traditional PCR

Real-Time PCR Vs. Traditional PCR Real-Time PCR Vs. Traditional PCR Description This tutorial will discuss the evolution of traditional PCR methods towards the use of Real-Time chemistry and instrumentation for accurate quantitation. Objectives

More information

Amino Acids, Peptides, Proteins

Amino Acids, Peptides, Proteins Amino Acids, Peptides, Proteins Functions of proteins: Enzymes Transport and Storage Motion, muscle contraction Hormones Mechanical support Immune protection (Antibodies) Generate and transmit nerve impulses

More information

Methods for Protein Analysis

Methods for Protein Analysis Methods for Protein Analysis 1. Protein Separation Methods The following is a quick review of some common methods used for protein separation: SDS-PAGE (SDS-polyacrylamide gel electrophoresis) separates

More information