Search

Gene structure and expression regulation mechanism are the research hotspots and focus of modern life sciences. The lac operon is a cluster of genes through which Escherichia coli catabolizes lactose. It was first proposed by F. Jacob and J. Monod, who were also awarded the Nobel Prize in Physiology or Medicine in 1965 for their contributions. Thereafter, the lac operon has become the classic teaching case of the gene regulation mechanism in microbiology, genetics and molecular biology, and been highly valued by teachers and students alike. Although the conclusion is easy to follow and memorize, its rich connotation and esoteric reasoning has rendered it difficult to understand, neither is it easy for teachers to fully exploit the advantages of this teaching case. Therefore it is necessary to have an in-depth understanding of the genetic structure and working principle of the lac operon, especially the scientific background and thinking process through which scientists revealed these mysteries. In this paper, the historical discovery and analysis process of the E. coli lac operon was reviewed by following their footprints, listening to their analysis of experimental results. Based on the DNA sequences, the reasons for several unusual phenomena of lac operon expression were also discussed to exemplify the teaching value of the classic cases in genetics and molecular biology.

A critical aspect of science is the clear communication of complicated matters. However, language is often ambiguous, and the message can get lost in the telling. In particular, genetic terms can have different meanings for different people. Here, I discuss this problem and suggest remedies to clarify the message., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Large lecture classes and standardized laboratory exercises are characteristic of introductory biology courses. Previous research has found that these courses do not adequately convey the process of scientific research and the excitement of discovery. Here we propose a model that provides beginning biology students with an inquiry-based, active learning laboratory experience. The Dynamic Genome course replicates a modern research laboratory focused on eukaryotic transposable elements where beginning undergraduates learn key genetics concepts, experimental design, and molecular biological skills. Here we report on two key features of the course, a didactic module and the capstone original research project. The module is a modified version of a published experiment where students experience how virtual transposable elements from rice (Oryza sativa) are assayed for function in transgenic Arabidopsis thaliana. As part of the module, students analyze the phenotypes and genotypes of transgenic plants to determine the requirements for transposition. After mastering the skills and concepts, students participate in an authentic research project where they use computational analysis and PCR to detect transposable element insertion site polymorphism in a panel of diverse maize strains. As a consequence of their engagement in this course, students report large gains in their ability to understand the nature of research and demonstrate that they can apply that knowledge to independent research projects.

Many students do not recognize that individual organisms within populations vary, and this may make it difficult for them to recognize the essential role variation plays in natural selection. Also, many students have weak scientific reasoning skills, and this makes it difficult for them to recognize misconceptions they might have. This paper describes a 2-h laboratory for college students that introduces them to genetic diversity and gives them practice using hypothetico-deductive reasoning. In brief, the lab presents students with DNA sequences from Africans, Europeans, and Asians, and asks students to determine whether people from each continent qualify as distinct "races." Comparison of the DNA sequences shows that people on each continent are not more similar to one another than to people on other continents, and therefore do not qualify as distinct races. Ninety-four percent of our students reported that the laboratory was interesting, and 79% reported that it was a valuable learning experience. We developed and used a survey to measure the extent to which students recognized variation and its significance within populations and showed that the lab increased student awareness of variation. We also showed that the lab improved the ability of students to construct hypothetico-deductive arguments.

We report a thematic sequence of directed inquiry-based labs taking students from bacterial mutagenesis and phenotypic identification of their own self-created mutant, through identification of mutated genes by biochemical testing, to verification of mutant alleles by complementation, and finally to mutant allele characterization by DNA sequence analysis. The lab utilizes UV mutagenesis with wild-type Escherichia coli and a UV-sensitive isogenic derivative optimized for undergraduate use. The labs take advantage of the simplicity of E. coli in a realistic genetic investigation using safe UV irradiation methods for creation and characterization of novel mutants. Assessment data collected over three offerings of the course suggest that the labs, which combine original investigation in a scientifically realistic intellectual environment with learned techniques and concepts, were instrumental in improving students' learning in a number of areas. These include the development of critical thinking skills and understanding of concepts and methods. Student responses also suggest the labs were helpful in improving students' understanding of the scientific process as a rational series of experimental investigations and awareness of the interdisciplinary nature of scientific inquiry.

Background: Animal mitochondrial genomes are physically separate from the much larger nuclear genomes and have proven useful both for phylogenetic studies and for understanding genome evolution. Within the phylum Arthropoda the subphylum Crustacea includes over 50,000 named species with immense variation in body plans and habitats, yet only 23 complete mitochondrial genomes are available from this subphylum., Results: I describe here the complete mitochondrial genome of the crustacean Squilla mantis (Crustacea: Malacostraca: Stomatopoda). This 15994-nucleotide genome, the first described from a hoplocarid, contains the standard complement of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding AT-rich region that is found in most other metazoans. The gene order is identical to that considered ancestral for hexapods and crustaceans. The 70% AT base composition is within the range described for other arthropods. A single unusual feature of the genome is a 230 nucleotide non-coding region between a serine transfer RNA and the nad1 gene, which has no apparent function. I also compare gene order, nucleotide composition, and codon usage of the S. mantis genome and eight other malacostracan crustaceans. A translocation of the histidine transfer RNA gene is shared by three taxa in the order Decapoda, infraorder Brachyura; Callinectes sapidus, Portunus trituberculatus and Pseudocarcinus gigas. This translocation may be diagnostic for the Brachyura. For all nine taxa nucleotide composition is biased towards AT-richness, as expected for arthropods, and is within the range reported for other arthropods. Codon usage is biased, and much of this bias is probably due to the skew in nucleotide composition towards AT-richness., Conclusion: The mitochondrial genome of Squilla mantis contains one unusual feature, a 230 base pair non-coding region has so far not been described in any other malacostracan. Comparisons with other Malacostraca show that all nine genomes, like most other mitochondrial genomes, share a bias toward AT-richness and a related bias in codon usage. The nine malacostracans included in this analysis are not representative of the diversity of the class Malacostraca, and additional malacostracan sequences would surely reveal other unusual genomic features that could be useful in understanding mitochondrial evolution in this taxon.

AcNPV (Autographa californica nuclear polyhedrosis virus) and BmNPV(Bombyx mori nuclear polyhedrosis virus) are two principal insect-baculovirus expression systems, each having different characteristics. AcNPV has a wider host range and can infect a series of cell lines thus making it suitable for cell suspension culture expression, but the small size of the host insect, A. californica, makes AcNPV less suitable for large scale protein synthesis. In contrast, BmNPV can only infect the silkworm, Bombyx mori, which is well-known for its easy rearing and large size. These characteristics make the BmNPV system especially suitable for large-scale industrial expression. To utilize the advantages of both AcNPV and BmNPV, we tried to expand their host range through homologous recombination and successfully constructed a hybrid baculovirus of AcNPV and BmNPV, designated as HyNPV. The hybrid baculovirus can infect the hosts of both AcNPV and BmNPV. Taking the human basic fibroblast growth factor (bFGF) gene as an application example, we constructed a recombinant, HyNPV-bFGF. This construct is able to express the bFGF protein both in silkworm larvae and in common-use cell lines, sf21, sf9 and High-five. Moreover, to reduce the loss of recombinant protein due to degradation by proteases that are simultaneously expressed by the baculovirus, we knocked out the cysteinase gene coding for one of the most important baculovirus proteases. This knockout mutation improves the production efficiency of the bFGF recombinant protein.

Over the past century researchers have identified normal genetic variation and studied that variation in diverse human populations to determine the amounts and distributions of that variation. That information is being used to develop an understanding of the demographic histories of the different populations and the species as a whole, among other studies. With the advent of DNA-based markers in the last quarter century, these studies have accelerated. One of the challenges for the next century is to understand that variation. One component of that understanding will be population genetics. We present here examples of many of the ways these new data can be analyzed from a population perspective using results from our laboratory on multiple individual DNA-based polymorphisms, many clustered in haplotypes, studied in multiple populations representing all major geographic regions of the world. These data support an "out of Africa" hypothesis for human dispersal around the world and begin to refine the understanding of population structures and genetic relationships. We are also developing baseline information against which we can compare findings at different loci to aid in the identification of loci subject, now and in the past, to selection (directional or balancing). We do not yet have a comprehensive understanding of the extensive variation in the human genome, but some of that understanding is coming from population genetics.

Genome sequencing has revolutionized all fields of life sciences. Bioinorganic chemistry is certainly not immune to this influence, which is presenting unprecedented challenges. A new goal for bioinorganic chemistry is the investigation of the linkages between inorganic elements and genomic information. This requires new advancements andor the development of new expertise in fields such as bioinformatics and genetics but also provides a driving force to push forward the exploitation of traditional analytical techniques and spectroscopic tools. The "case study" of metal homeostasis in cells is discussed to provide a flavor of the current evolution of the field.

Comparative sequence analyses of eukaryotic genes and genomic regions are beginning to provide a wealth of information that is directly relevant to human biology. Functional changes that set us apart from apes are identifiable, as are functional constraints in proteins and genomic elements that arose in our relatively distant phylogenetic past.

The human body is becoming hot property, a resource to be "mined," "harvested," patented, and traded commercially for profit as well as scientific and therapeutic advances. Under the new entrepreneurial approach to the body old tensions take on new dimensions -- about consent, the fair distribution of tissues and products developed from them, the individual and cultural values represented by the body, and public policy governing the use of organs and tissues.

Research on genetic markers in the fields of forensic medicine and human genetics did not begin in earnest until 1968. Study of an extended family in Wakayama Prefecture resulted in the discovery of the variant Bm type in the ABO blood group system. This family of nearly 40 members composed of Group A, B, O and AB spouses and type Bm monozygotic twins provided the best research material possible. An extremely rare case of an individual with type O red blood cells but no anti-A or anti-B antibodies led to the discovery of type AmBm. Fishman and Mitsuhashi advocated the concept of immunogenetic RNA. We attempted to examine the immunogenetic RNA function by isolating RNA from the human spleen but obtained no definitive results. Many researchers had since examined the genetic markers in erythrocytes, leukocytes, serum proteins and blood cell enzymes, but research on genetic marker in saliva had not been advanced. We searched for genetic markers in the parotid saliva and developed the PmF and Ph systems. A salivary amylase variant and acid phosphatase polymorphism were also discovered. We elucidated the genetic structure and geographic gradinet of the salivary genetic markers, such as the Pa, Pb, Pr, Db and PIF systems, in Japanese. The genetic markers in the tear and saliva of mice and rats were also detected. We demonstrated RFLP polymorphism using an amylase cDNA probe. Our report was one of the first on polymorphism in the field of forensic medicine in Japan. Interest was also directed to polymorphism in platelet and we employed two-dimensional electrophoresis to establish the ThA and ThB systems which are controlled by autosomal codominant genes. Regarding the research on monoclonal antibody production and their application in forensic medicine, we cloned and produced antibodies for ABO, MN and Lewis grouping. Anti-glycopholin-A, anti-glycopholin-B and anti-glycolipid monoclonal antibodies were also produced and used to divide the red blood cell antigens roughly into three classes; the glycopholin-A (MN), glycopholin-B (Ss. Duffy Kell-Cellano, Lutheran, Diego, Xg) and the glycolipid (ABO, Lewis, P) classes. Red blood cell protein membrane proteases were also isolated from Nepenthes alata extract and lectin which are used in grouping animal blood cells. In the research on erythrocyte differentiation and erythrocyte group substance expression, we established a selective two phase liquid culture system for culturing precursor cells of peripheral erythrocytes, and demonstrated the expression of red blood cell antigens such as ABO, Rh and Duffy antigens in the early period (4 to 9 days) of Phase 2. Recently, research on identifying the genes which code for polymorphism in erythrocytes or erythrocyte enzymes is making progress. For example, a study indicated a possible relationship between an isoform of the glycophorin A gene and the MN variant. In the cDNA sequence of the Fy (a-b+) and (a + b-) types in the Duffy system, a GAT (Asp) to GGT (Gly) substitution in the codon for residual 44 was detected. Research on the Rh gene is being pursued energetically. Two clones of the Rh gene have been isolated; Rh Pl composed of 1251 bases, and Rh Pll estimated to be Ph PI with a base substitution at position 41 and an amino acid substitution at position 31. Seven isoforms of Ph Pl and 5 isoforms of Ph Pll have been obtained. The delineation of the Rh gene which contains as many as 50 types of Rh antigen genes is in progress. The red blood cell enzyme EsD system is also used commonly in the field of forensic genetics. In EsD polymorphism, type EsD1 contains G at base 569, type EsD2 contains A and type EsD1-2 shows a heterologous conjugation of G and A. Due to the development of immunosuppressive agents, bone marrow transplant can now be conducted even when the ABO and Rh systems are not compatible, as long as the HLA is compatible. In this case, all the erythrocyte polymorphic types or erythrocyte enzyme polymorphic types are transformed to t

Conclusion: Genetic knowledge is now in the public domain and its interpretation by the media and the citizens brings the issues into the public forum of discussion for the necessary ethical, legal and socio-cultural evaluation of its application. Science is being perceived by some as dangerous and as requiring international regulation. Others feel that genetic knowledge will be the breakthrough that will permit medical progress and individual autonomy with regards to personal health and lifestyle choices. The mapping of the human genome has already yielded valuable information on an increasing number of diseases and their variants. Prevailing popular and journalistic archetypes ("imaginaires") used in the media are perceived by the producers as slowing down the possible application of genetic knowledge. The answers to these dilemmas are not readily apparent nor are they prescribed by classical philosophy of medicine. Since genetic knowledge eventually resides with the individual who carries the genes of disease and/or susceptibility, a logical approach to integration of this knowledge at a societal level would seem to reside with individual education and decision-making. The politics of the ensuing social debate could transform the current social contract since an individual's interests need to be balanced against those of his or her immediate family in the sharing of information. The ethical foundations of such a contract requires the genetic education of "Everyone" as a matter of urgent priority. Genetic education should not serve ideological power struggles between the medical establishment and the ethical-legal alliance. Instead, it should ensure the transfer of knowledge to physicians, to patients, to users, to planners, to social science and humanities researchers and to politicians, so that they may make "informed" and free decisions....

In this article it is suggested that the first coding system started from specific interactions between the nucleotide part of nucleotidic cofactors and enzymes. These interactions generated a first primitive code of four words of one letter each for the four primittive amino acids (phenylalanine, lysine, glycine and proline); when the triplet code (which allowed the integration of 20 amino acids into proteins) progressively appeared, it must have been modulated by the existence of this first coding system.

Conducting computer simulations, Nei and Tateno (1978) have shown that Jukes and Holmquist's (1972) method of estimating the number of nucleotide substitutions tends to give an overestimate and the estimate obtained has a large variance. Holmquist and Conroy (1980) repeated some parts of our simulation and claim that the overestimation of nucleotide substitutions in our paper occurred mainly because we used selected data. Examination of Holmquist and Conroy's simulation indicates that their results are essentially the same as ours when the Jukes-Holmquist method is used, but since they used a different method of computation their estimates of nucleotide substitutions differed substantially from ours. Another problem in Holmquist and Conroy's Letter is that they confused the expected number of nucleotide substitution with the number in a sample. This confusion has resulted in a number of unnecessary arguments. They also criticized our X2 measure, but this criticism is apparently due to a misunderstanding of the assumptions of our method and a failure to use our method in the way we described. We believe that our earlier conclusions remain unchanged.

The origin of the degree and type of order found in biological macromolecules is not adequately explained solely as an accumulation of genetic restrictions acquired through natural selection from otherwise unrestricted primeval sequences capable of self-replication, since the biological process of replication is itself dependent on the pre-existence of such order, and since the number of sequences that could have ever been tested by selection on the earth is an insignificant fraction of the number of unrestricted sequences which would be possible. Therefore the hypothesis is considered that replication and selection began from well ordered sequences, rather than random sequences. It is shown how the Turing concept of computation in fed-back, discrete-state automata can lead to the generation of order withour pre-existing instructions, and how this computation can result in self-repeating, random-like, but well ordered sequences of great length. Macromolecular models of such computers are suggested on the basis of mechanisms proposed for the growth of eutactic polymers. Such self-replicating, mutable sequences may then evolve genetic control which is sufficient to accommodate the information accumulated by natural selection. The structure and function of enzymes and structural proteins is related to this model, and statistical evidence from known amino acid sequences is shown to be consistent with some degree of non-genetic ordering.

The genetic map of T4 (and T2) bacteriophage is circular but the DNA molecule that is liberated by phenol extraction is a linear duplex of polynucleotide chains. If the genetic map is related to the physical structure of the DNA molecule, the problem arises as to how a linear molecule can give rise to a circular map. An explanation can be made on the basis that the bacteriophage liberate molecules which have nucleotide sequences which are circular permutations of each other. Thus, markers which are most distant on one molecules are closest together on another. To test this hypothesis, the middles of T2 and T5 DNA molecules were mechanically deleted and the absence of certain nucleotide sequences was tested by "renaturation" or "reannealing" experiments using columns containing denatured DNA immobilized in agar beads. The results indicate that when the middles are deleted from the T5 DNA molecule, some special sequences are removed; whereas, when the middles are deleted from the T2 DNA molecule, no special group of sequences is removed. This would indicate that T2 molecules begin at different points in their nucleotide sequence, while T5 molecules all begin at the same point. It is likely that this permutation of sequences of T2(T4) molecules is related to the circularity of their genetic map.

Doi, Roy H. (Syracuse University, Syracuse, N.Y.), and Richard T. Igarashi. Conservation of ribosomal and messenger ribonucleic acid cistrons in Bacillus species. J. Bacteriol. 90:384-390. 1965.-Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) fractions from various Bacillus species were tested for interspecies DNA-RNA hybrid formation. DNA preparations from B. subtilis, B. cereus, B. megaterium, B. stearothermophilus, and B. macerans, whose base composition varied from 33 to 50% guanylate + cytidylate content, were used in the hybrid annealing mixtures with pulse-labeled RNA from sporulating cells and from log-phase cells of B. subtilis and B. cereus. Efficient hybridization in these cases was obtained only in homologous annealing situations. When heterologous DNA and RNA preparations were tested for hybrid formation, only 1 to 6% of the homologous hybridization was obtained. Although the efficiency of hybrid formation was low, the results were reproducible. No difference in efficiency of hybrid formation was observed between the messenger RNA from sporulating cells and that from log-phase cells. When B. subtilis ribosomal RNA was placed in annealing mixtures with heterologous DNA, 47.5 to 62.9% of the homologous hybridization was obtained. These results suggest that a small number of identical sequences are present among the Bacillus species. Furthermore, the ribosomal RNA cistrons appear to be more highly conserved relative to other genetic sequences.

Because the cancerous change in cells appears to be a permanent alteration, handed on to daughter cells through innumerable divisions, it seems probable that it reflects an abnormality in the transfer of information from cell to daughter cells. Transfer of information in cells is believed to depend on their genetic apparatus, and transfer of abnormal information implies that the genetic apparatus is not functioning normally. Abnormalities in genetic material, whether induced by ionizing radiation, chemical compounds or viruses, would, if reproduced at cell division, reappear in daughter cells. If such abnormalities lead to cancerous change in cells, any one of these primary incitants might be effective. Under such circumstances, the nature of the primary incitant may not be the most important question, and definition of the nature of the abnormality in the genetic material may become the central problem. It may ultimately be feasible to explain the cancerous change in cells in chemical terms and to find that it represents a molecular disease which takes its origin from the emergence of abnormal nucleotide sequences in the genetic material. In biological terms this would correspond with an induced mutation which is heritable at the level of the somatic cell.