I read this book the same weekend that the Packers took on the Rams, and the experience of the latter event, obviously, colored my judgment. Although I abhor anything that smacks of being a handbook (like, \"How to Earn a Merit Badge in Neurosurgery\") because too many volumes in biomedical science already evince a boyscout-like approach, I must confess that parts of this volume are fast, scholarly, and significant, with certain reservations. I like parts of this well-illustrated book because Dr. Sj6strand, without so stating, develops certain subjects on technique in relation to the acquisition of judgment and sophistication. And this is important! So, given that the author (like all of us) is somewhat deficient in some areas, and biased in others, the book is still valuable if the uninitiated reader swallows it in a general fashion, realizing full well that what will be required from the reader is a modulation to fit his vision, propreception, adaptation and response, and the kind of problem he is undertaking. A major deficiency of this book is revealed by comparison of its use of physics and of chemistry to provide understanding and background for the application of high resolution electron microscopy to problems in biology. Since the volume is keyed to high resolution electron microscopy, which is a sophisticated form of structural analysis, but really morphology in a modern guise, the physical and mechanical background of The instrument and its ancillary tools are simply and well presented. The potential use of chemical or cytochemical information as it relates to biological fine structure , however, is quite deficient. I wonder when even sophisticated morphol-ogists will consider fixation a reaction and not a technique; only then will the fundamentals become self-evident and predictable and this sine qua flon will become less mystical. Staining reactions (the most inadequate chapter) ought to be something more than a technique to selectively enhance contrast of morphological elements; it ought to give the structural addresses of some of the chemical residents of cell components. Is it pertinent that auto-radiography gets singled out for more complete coverage than other significant aspects of cytochemistry by a high resolution microscopist, when it has a built-in minimal error of 1,000 A in standard practice? I don't mean to blind-side (in strict football terminology) Dr. Sj6strand's efforts for what is \"routinely used in our laboratory\"; what is done is usually well done. It's just that …

Methods in Enzymology.

Publisher Summary This chapter examines the range of the variation of secondary structure among the 16-S-like rRNAs. This brings into a larger structural context a recent detailed analysis of the individual helical elements and provides a basis for an accurate alignment of the corresponding regions of different primary structures. Computer-assisted comparative is used in the analysis of aligned sequences to describe the pattern of phylogenetic conservation for each nucleotide position in 16-S rRNA. A search for matching patterns among unpaired positions in the RNA chain then produces a list of candidates for potential base–base tertiary interactions. The completion of nucleotide sequences for 34 16-S-like rRNAs includes 4 eubacteria, 4 chloroplasts, 12 mitochondria, 4 archaebacteria, and 10 eukaryotes. Secondary structure models for these molecules have been developed in the course of refinement of the E. coli model, and have been used to arrive at improved sequence alignments for the 16-S-like rRNAs. Schematic drawings of (1) eubacterial, (2) archaebacterial, (3) eukaryotic cytoplasmic, (4) plant mitochondrial, (5) fungal mitochondrial, and (6) mammalian mitochondrial structures are shown in the chapter.

Comparative Anatomy of 16-S-like Ribosomal RNA

We determined the complete mtDNA sequence of the centipede Lithobius forficatus and found that only one of the 22 inferred tRNA genes encodes a fully paired aminoacyl acceptor stem. The other 21 genes encode tRNAs with up to five mismatches in these stems, and some of these overlap extensively with the downstream genes. Because a well-paired acceptor stem is required for proper tRNA functioning, RNA editing in the products of these genes was suspected. We investigated this hypothesis by studying cDNA sequences from eight tRNAs and found the editing of up to 5 nt at their 3' ends. This editing appears to occur by a novel mechanism with the 5' end of the acceptor stem being used as a template for the de novo synthesis of the 3' end, presumably by an RNA-dependent RNA polymerase. In addition, unusual secondary structures for several tRNAs were found, including those lacking a TPsiC (T) or a dihydrouridine (D) arm, and having an unusual number of base pairs in the acceptor or anticodon stems.

https://www.pnas.org/content/pnas/97/25/13738.full.pdf

A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus

methods of biochemical analysis What to say and what to do when mostly your friends love reading? Are you the one that don't have such hobby? So, it's important for you to start having that hobby. You know, reading is not the force. We're sure that reading will lead you to join in better concept of life. Reading will be a positive activity to do every time. And do you know our friends become fans of methods of biochemical analysis as the best book to read? Yeah, it's neither an obligation nor order. It is the referred book that will not make you feel disappointed.

Methods of Biochemical Analysis.

The evolution of reading frame maintenance must have been an early event, and presumably preceded the emergence of the three domains Archaea, Bacteria and Eukarya. Features evolved early in reading frame maintenance may still exist in present-day organisms. We show that one such feature may be the modified nucleoside 1-methylguanosine (m1G37), which prevents frameshifting and is present adjacent to and 3′ of the anticodon (position 37) in the same subset of tRNAs from all organisms, including that with the smallest sequenced genome (Mycoplasma genitalium), and organelles. We have identified the genes encoding the enzyme tRNA(m1G37)methyltransferase from all three domains. We also show that they are orthologues, and suggest that they originated from a primordial gene. Lack of m1G37 severely impairs the growth of a bacterium and a eukaryote to a similar degree. Yeast tRNA(m1G37)methyltransferase also synthesizes 1-methylinosine and participates in the formation of the Y-base (yW). Our results suggest that m1G37 existed in tRNA before the divergence of the three domains, and that a tRNA(m1G37)methyltrans ferase is part of the minimal set of gene products required for life.

/pdf/a-primordial-trna-modification-required-for-the-evolution-of-1qsqonfeqz.pdf

A primordial tRNA modification required for the evolution of life

A convenient procedure for preparing transfer ribonucleic acid from Escherichia coli

A plural-sample filter device comprises a base plate, a filter plate, a cover plate, and a holding clamp for clamping the parts together with the filter plate interposed between the base and cover plates. The cover plate is formed with a plurality of openings for introducing the samples to be filtered, and the filter plate is provided with a corresponding plurality of aligned perforated areas each adapted to hold a filter disc. The base plate is formed with a plurality of receptacles aligned with the filteres, and is further formed with an outlet adapted to be connected to a pump, and a channel connecting the receptacles to the outlet.

Plural-sample filter device

Properties of the catalytic (αβ)-core complex of chloroplast CF1-ATPase

Comparative studies of free ribosomal RNA and ribosomes were made with two probes, Mg++ ions and ethidium bromide, which interact with RNA in different ways. Mg++. E. coli 16 S rRNA and 30 S ribosomes were equilibrated with four different buffers. Equilibration required several days at 4 degrees and several hours at 37 degrees. In all buffers ribosomes bound more Mg than free rRNA, the difference sometimes reaching 20--30%. Ribosomes were more resistant than free rRNA to heat denaturation and their denaturation was more highly cooperative. Ribosomes that bound more Mg++ had higher denaturation temperatures. Ethidium bromide. Fluorescence enhancement studies of ethidium intercalation showed the free 16 S rRNA to have 50--80 binding sites per molecule. A large fraction of these sites were present and accessible in the ribosome, but their ethidium-binding constants were reduced by an order of magnitude. In addition, free rRNA contained a small number of very strong binding sites that were virtually absent in the ribosomes.

Binding of magnesium ions and ethidium bromide: comparison of ribosomes and free ribosomal RNA

We have attempted to identify long-range interactions in the tertiary structure of RNA in the E. coli 30 S ribosome. Native subunits were cleaved with ribonuclease and separated into nucleoprotein fragments which were deproteinized and fractionated into multi-oligonucleotide complexes under conditions intended to preserve RNA-RNA interactions. The final products were denatured by urea and heat and their constituent oligonucleotides resolved and sequenced. Many complexes contained complementary sequences known to be bound together in the RNA secondary structure, attesting to the validity of the technique. Other co-migrating oligonucleotides, not joined in the secondary structure, contained mutually complementary sequences in locations that allow base-pairing interaction without disrupting pre-existing secondary structure. In seven instances the complementary relationship was found to have been preserved during phylogenetic diversification.

Shlomo Avital

Papers

A convenient procedure for preparing transfer ribonucleic acid from Escherichia coli

Plural-sample filter device

Properties of the catalytic (αβ)-core complex of chloroplast CF1-ATPase

Binding of magnesium ions and ethidium bromide: comparison of ribosomes and free ribosomal RNA

Long range RNA-RNA interactions in the 30 S ribosomal subunit of E. coli