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Biokemistri
Nigerian Society for Experimental Biology
ISSN: 0795-8080


INSTRUCTIONS TO AUTHORS

HOW TO SUBMIT MANUSCRIPTS

Submit manuscripts directly to The Editor, BIOKEMISTRI, c/o Department of Biochemistry, University of Ilorin, P.M.B. 1515, Ilorin, Kwara State, Nigeria, e-mail:editor.biokemistri@gmail.com.

Since all submissions must be processed through this office, alternate routings, will delay initiation of the review process. The manuscript must be accompanied by a covering letter stating the following: the journal to which the manuscript is being submitted, the postal address, e-mail and telephone number of the correspond­ing author, and the former manuscript number and year if it is a resubmission. In addition, include written assurance that permission to cite personal com­munications and preprints has been granted.

Submit three complete computer print copies of each manuscript, including figures and tables. Type every portion of the manuscript double spaced, including figure legends, table footnotes, and Literature Cited, and number all pages in sequence, including the abstract, figure leg­ends, and tables. Place the last two items after the Literature Cited section. See p. iv-v for detailed instructions about illustrations.

Copies of "in press" and "submitted" manuscripts that are important for judgment of the present manu­script should be enclosed to facilitate the review. One copy of each such manuscript should be provided with each copy of the new manuscript.

Authors who are unsure of proper English usage should have their manuscripts checked by someone proficient in the English language. Manuscripts may be rejected on the basis of poor English or lack of conformity to accepted standards of style.

EDITORIAL POLICY

Manuscripts submitted to the journal must represent reports of original research. All authors of a manu­script must have agreed to its submission and are equally responsible for its content, including appropri­ate citations and acknowledgments. By submission of a manuscript to the journal, the authors guarantee that the manuscript, or one substantially the same, was not published previously, is not being considered or pub­lished elsewhere, and was not rejected on scientific grounds by another NISEB publication.

Failure to comply with the above-mentioned policy may result in a 3- to 5-year suspension of publishing privileges in NISEB publications.

Original Publication

The Nigerian Society for Experimental Biology accepts the definition of original publication as follows (i) the first publication of original research results, (ii) in a form whereby peers of the author can repeat the experiments and test the conclusions, and (iii) in a journal or other source document readily available within the scientific community.

A scientific paper published in a conference report, symposium proceeding, technical bulletin, or any other retrievable source is unacceptable for submis­sion to BIOKEMISTRI on grounds of prior publica­tion. A preliminary disclosure of research findings published in abstract form as an adjunct to a meeting, e.g., part of a program, is not considered "prior publication" because it does not meet the criteria for a scientific paper.

Permissions

It is the author's responsibility to obtain permission from the copyright owner to reproduce figures, tables, or quotations of more than 12 lines of text taken intact from previous publications, either his own or those of another author. Note that the journal or publisher (not the author) is the copyright owner; however, as a matter of courtesy the author's permission should be obtained as well.

Authorship

An author is one who made a substantial contribu­tion to the "overall design and execution of the experiments"; therefore, BIOKEMISTRI considers all coauthors equally responsible for the entire paper. Individuals who provided assistance, e.g., supplied strains or reagents or critiqued the paper, should not be listed as authors but may be recognized in the Acknowledg­ment section.

Page Charges

It is anticipated that page charges, will be paid by authors. Having strictly followed the format specified in the current “Instructions to Authors”, our current page charges are as follows: N300.00 per text page, N250.00 per figure (whether within text or not), N250.00 per Table (whether within text or not), N500.00 per black and white plate (whether within text or not) and 20% reduction for NISEB paid-up members or 5% reduction for editorial board members (Biokemistri) or both. The waivers refer only to the corresponding author. The cost of printing color photographs must be borne by the author

Minireviews and Letters to the Editor are also subject to page charges.

A handling fee of N1,000.00 in cash, bank draft or bank teller (original) must accompany all manuscripts submitted to the Editor.  The bank draft or teller must be payable to “Nigerian Society for Experimental Biology”.  Any manuscript that carries the name of a Reviewer to BIOKEMISTRI as author or co-author and not necessarily corresponding author shall receive a waiver from the payment of a handling fee of 1000 Naira per manuscript. The Reviewer must have reviewed and promptly returned a minimum of three reviewed manuscripts in the previous five months to the submission of the manuscript carrying the reviewer’s name. The Editor may use his discretion for this purpose.

Copyright

To maintain and protect the Society's ownership and rights and to protect the original authors from misappropriation of their published work, NISEB re­quires authors to sign a copyright transfer agreement. This agreement form is sent to the submitting author when the manuscript is accepted for publication and should be returned with photocopies of receipts for all payments. Unless this agreement is executed, NISEB will not publish the manu­script.

Scope

BIOKEMISTRI is a journal devoted to the dissemination of knowledge relating to all aspects of biochemistry. These include theoretical biochemistry, Biophysical chemistry, animal and plant biochemistry, microbial biochemistry, clinical and forensic biochemistry, enzymology, Protein chemistry, Analytical biochemistry, nutritional biochemistry, toxicology and xenobiochemistry, molecular biology, genomics and bioinformatics. Within the circumscriptions set forth below, reports involving studies on or with plants, environment, antimi­crobial, antiparasitic, or anticancer agents are within the purview of BIOKEMISTRI. Manuscripts will be rejected if the contents do not sufficiently conform to modern day biochemistry.

NISEB publishes a number of different journals cov­ering various aspects of the field of experimental biology. Each journal has a prescribed scope that must be considered in determining the most appropriate jour­nal for each manuscript. Other journals (and e-mail) of NISEB are African Scientist (africanscientist@yahoo.com), Bioscience Research Communications (biorescom@yahoo.com), NISEB Journal (nisebjournal@yahoo.com). Questions about these guidelines may be directed to the Editor in Chief of the journal being considered.

Culture Deposition

BIOKEMISTRI encourages authors to deposit strains used in therapeutic activity assessments and studies on mech­anisms of action, resistance, and cross resistance in publicly accessible culture collections and to refer to the collections and strain numbers in the text. Since authenticity of subcultures of culture collection spec­imens that are distributed by individuals cannot be assured, authors should indicate laboratory strain des­ignations and donor source as well as original culture collection identification numbers. When authors de­scribe mutants for which genetic stock repositories have not been established or strains that have not been deposited in publicly accessible collections, the jour­nal expects that the authors will make such strains available to other scientists.

Nucleotide Sequences

NISEB requires that the primary nucleotide and/or amino acid sequence data contained in a paper be deposited in a data bank such as GenBank or DDBJ or EMBL Data Library. Accession numbers must be included in the manu­script or be added to the proofs.

Editorial Style

The Editors and the Publica­tions Department reserve the privilege of editing manuscripts to conform to the stylistic conventions set forth in these instructions.

Review Process

All manuscripts are subjected to critical review by the editors, members of the editorial board, or quali­fied ad hoc reviewers. The corresponding author may suggest three to five possible reviewers from among Nigerian University Senior Lecturers /Readers /Professors who are knowledgeable in the subject area.  They should not be in the same institution or city as any of the author(s).  The Name, Rank, Department, Institution, City and e-mail (if available) should be given for each reviewer.  The Editorial Board is not obliged to use any of the suggested reviewers. When a manuscript is submitted to the journal, it is given a manuscript control number and assigned to one of the editors or external reviewers. The authors are notified of this number. It is the responsibility of the corresponding author to inform the coauthors of the manuscript's status throughout the review and publication processes. The reviewers operate under strict guidelines set Forth in "Guidelines for Review­ers" and are expected to complete their reviews within 3 weeks after receiving the manuscript. Authors are notified, generally within 8 weeks after submission, of acceptance, rejection, or the need for modification. When a manuscript is returned to the author for modification, it must be returned to the editor within 2 months; otherwise it may be considered withdrawn.

Notification of Acceptance

When an editor has decided that a manuscript is acceptable for publication on the basis of scientific merit, it is sent to the Publications Department, where it is checked by the production editor. If the manu­script has been prepared according to the criteria set forth in these instructions, it is scheduled for the next available issue and an acceptance letter that indicates the month of publication, approximate page proof dates, and section is mailed to the corresponding author. The editorial staff of the NISEB Publications Department completes the editing of the manuscript to bring it into conformity with prescribed style and English usage.

Page Proofs

The Editor sends page proofs, the copy-edited manuscript, and a page charge form to the author. As soon as the page proofs are corrected (within 48 h), they should be mailed to The Editor, BIOKEMISTRI.

The proof stage is not the time to make extensive corrections, additions, or deletions. Important new information that has become available between accep­tance of the manuscript and receipt of the proofs may be inserted as an Addendum in Proof with the permis­sion of the editor. If references to unpublished data or personal communications are added, include written assurance that permission to cite them has been granted. Limit changes to correction of spelling errors, incorrect data, and serious grammatical errors. "In press" references for which page numbers-have be­come available should be placed in the Literature Cited section as "a" numbers (e.g., 12a). Do not renumber references.

Questions about late proofs and problems in the proofs should be directed to the Editor, biokemistri@yahoo.com

Reprints

One copy of the issue of the journal will be sent to the corresponding author. The price (usually about N1, 500.00) must be paid along with page charges. NISEB paid-up members are entitled to 20% discount.

ORGANIZATION AND FORMAT

Regular Papers

Regular full-length papers should include the ele­ments described in this section.

Title: Each manuscript should present the results of an independent, cohesive study; thus, numbered se­ries titles are not permitted. Exercise care in compos­ing a title. Avoid the main title/subtitle arrangement, and unnecessary articles. On the title page, include the title, running title (not to exceed 54 characters and spaces), full name of each author (surname in block capital), address(es) of the institution(s) at which the work was performed, each author's affiliation, and a footnote indicating the present address of any author no longer at the institution where the work was performed. Place an asterisk after the name of the author to whom inquiries regarding the paper should be directed, and give that author's functional telephone number and e-mail address.

Abstract. Limit the abstract to 250 words or fewer and concisely summarize the basic content of the paper without presenting extensive experimental de­tails. Avoid abbreviations and do not include dia­grams. When it is essential to include a reference, use the literature citation but omit the article title. Because the abstract will be published separately by abstracting services, it must be complete and understandable without reference to the text.

Introduction: The introduction should supply suffi­cient background information to allow the reader to understand and evaluate the results of the present study without referring to previous publications on the topic. The introduction should also provide the ratio­nale for the study. References should be chosen care­fully to provide the most salient background rather than an exhaustive review of the topic.

Materials and Methods: The Materials and Methods section should include sufficient technical information to allow the experiments to be repeated. When centrifugation conditions are critical, give enough infor­mation to enable another investigator to repeat the procedure: make of centrifuge, model of rotor, tem­perature, time at maximum speed, and centrifugal force (x g rather than revolutions per minute). For commonly used materials and methods (e.g., media and protein determinations), a simple reference is sufficient. If several alternative methods are com­monly used, it is helpful to identify the method briefly as well as to cite the reference. For example, it is preferable to state "cells were broken by ultrasonic treatment as previously described (9)" rather than "cells were broken as previously described (9)." The reader should be allowed to assess the method without constant reference to previous publications. Describe new methods completely, and give sources of unusual chemicals, equipment, or microbial strains. When large numbers of microbial strains or mutants are used in a study, include tables identifying the sources and properties of the strains, mutants, bacteriophages, plasmids, etc.

A method, strain, etc., used in only one of several experiments reported in the paper may be described in the Results section or very briefly (one or two sen­tences) in a table footnote or figure legend.

Results. In the Results section, include the rationale or design of the experiments as well as the results; reserve extensive interpretation of the results for the Discussion section. Present the results as concisely as possible in one of the following: text, table(s), or figure(s). Avoid extensive use of graphs to present data that might be more concisely or more quantita­tively presented in the text or tables. Limit photo­graphs (particularly photomicrographs and electron micrographs) to those that are absolutely necessary to show the experimental findings. Number figures and tables in the order which they are cited in the text, and be sure that all figures and tables are cited.

Discussion. The Discussion should provide an inter­pretation of the results in relation to previously pub­lished work and to the experimental system at hand and should not contain extensive repetition of the Results section or reiteration of the introduction. In short papers, the Results and Discussion sections may be combined.

Acknowledgments. Acknowledgments of financial assistance and of personal assistance are given in separate paragraphs.

Appendixes. Appendixes, which contain supplemen­tary material to aid the reader, are permitted. Titles, authors, and Literature Cited sections that are distinct from those of the primary article are not allowed. If it is not feasible to list the author(s) of the appendix in the by-line or the Acknowledgment section of the primary article, rewrite the appendix so that it can be considered for publication as an independent article, either full length or Note style. Equations, tables, and figures should be labeled with the letter "A" preceding the numeral to distinguish them from those cited in the main body of the text.

References. The References section must include all relevant published work, and all listed references must be cited in the text. Arrange the citations and number consecutively. Cite each listed reference by superscript number in the text. Abbreviate journal names ac­cording to Serial Sources for the BIOSIS Data Base, BioSciences Information Service, 1988. BIOKEMISTRI should be cited as biokemistri under References.

The following types of references are not valid for listing: unpublished data, personal communications, website that is not a peer reviewed journal,  manuscripts in preparation, manuscripts submitted, pamphlets, abstracts, patents, unpublished theses, dissertations, newsletters, letters to the editor, editorials, and material that has not been subjected to peer review. References to such sources should be made parenthetically in the text. An "in press" refer­ence to a NISEB. publication should state the manuscript number or the name of the publi­cation if it is a book.

Follow the styles shown in the examples below.

1. Olorunniji, F. J., Malomo, S. O., Adediran, S. A. and Odutuga,  A. A. (2000) Promethazine oxidation by redox mediation in peroxidase reactions. Arch. Biochem. Biophys. 380:251-256.

2. Hofer, A., Ekanem, J. T. and Thelander, L (1998) Allosteric regulation of Trypanosoma brucei ribonucleotide reductase studied in vitro and in vivo. J. Biol. Chem. 273:34098-34104.

3.  Ponka, P. (2002) Iron utilization in erythrocyte formation and hemoglobin synthesis. In: Molecular and cellular iron transport. D. Templeton (ed.), pp. 643-677. Marcel Decker, New York.

4. Leadbetter, E. R. (1974) Order II. Cytophagales nomen novum. In: Bergey's manual of determinative bacteriology (8th ed.). R. E. Buchanan and N. E. Gibbons (eds.), p. 99. The Williams & Wilkins Co., Baltimore.

5. Nolan, D. P., Garcia-Salcedo, J. A., Gueskens, M., Salmon, D., Paturiaux-Hanocq, F., Pays, A., Tebabi, P. and Pays, E. (2001) The endocytic machinery of bloodstream stage African trypanosomes. In: The African trypanosomes (World Class Parasites, Vol.1). S. J. Black & J. R. Seed (eds.), pp. 127-141. Kluwer Academic Publishers, Dordrecht.

Notes

Submit Notes in the same way as full-length papers. They receive the same review, and they are neither published more rapidly than full-length papers nor considered preliminary communications. The Note format is intended for the presentation of brief obser­vations that do not warrant full-length papers.

Each Note must have an abstract of no more than 50 words. Do not use section headings in the body of the Note; report methods, results, and discussion in a single section. Paragraph lead-ins are permissible. The text is not to exceed 1,000 words, and the number of figures and tables should be kept to a minimum. Materials and methods should be described in the text, not in figure legends or table footnotes. Present ac­knowledgments as in full-length papers, but do not use a heading. The Literature Cited section is identical to that of full-length papers.

Minireviews

Minireviews are brief summaries (limit of six printed pages) of developments in fast-moving areas of biochemistry. They must be based on published articles: they are not outlets for unpublished data. They may address any subject within the scope of BIOKEMISTRI. Minireviews may be either solicited or proffered by authors responding to a recognized need. Irrespective of origin, mini-reviews are subject to editorial review.

Letters to the Editor

Letters to the Editor must include data to support the writer's argument and be no more than 500 words long. For letters that refer to arti­cles previously published in BIOKEMISTRI, the editor will solicit a reply from the author of the article. All letters intended for publication must be typed double spaced.

Errata. The Erratum section provides a means of correcting errors (e.g., typographical) in published articles. Changes in data and the addition of new material are not permitted. Send errata directly to the Editor.

Author's Corrections

The Author's Correction section provides a means of adding citations that were overlooked in a published article. The author who failed to cite a reference and the author whose paper was not cited must agree to such a publication; the editor, chairman of the Publications Board, and director of publications will not be involved. Letters from both authors must accompany the author's correction sent to the Editor.

Disclaimers

Statements disclaiming governmental or any other type of endorsement or approval will be deleted from the manuscript.

ILLUSTRATIONS AND TABLES

The figure number and authors' names should be written on all figures, either in the margin or on the back (marked lightly with a soft pencil). For micro­graphs especially, the top should be indicated as well.

Do not clasp figures to each other or to the manu­script with paper clips. Insert small figures in an envelope.

Continuous-Tone and Composite Photographs

When submitting continuous-tone photographs (e.g., polyacrylamide gels), keep in mind the journal page size: 7.5 cm for a single column and 16.5cm for a double column (maximum). Include only the significant portion of an illustration. Photos must be of sufficient contrast to withstand the inevitable loss of contrast and detail inherent in the printing process. Submit one pho­tograph of each continuous-tone figure for each copy of the manuscript; photocopies are not acceptable. If possible, the figures submitted should be the size they will appear when published so that no reduction is needed. If they must be reduced, make sure that all elements, including labeling, can withstand reduction and remain legible.

If a figure is a composite of a continuous-tone photograph and a drawing or labeling, the original composite must be provided for the printer (i.e., not a photograph of the composite). This original, labeled "printer's copy," may be sent with the modified manuscript to the editor.

Electron and light micrographs must be direct cop­ies of the original negative. Indicate the magnification with a scale marker on each micrograph.

Color Photographs

Color photographs are discouraged. However, if they are necessary, include an extra copy so that a cost estimate for printing may be obtained. The cost of printing color photographs must be borne by the author.

Drawings

Submit graphs, charts, complicated chemical or mathematical formulas, diagrams, and other drawings as glossy photographs made from finished drawings not requiring additional artwork or typesetting. Com­puter-generated graphics produced on high-quality la­ser printers are acceptable. No part of the graph or drawing should be handwritten. Both axes of a graph must be labeled. Most graphs will be reduced to one-column width (7.5 cm), and all elements in the drawing should be large enough to withstand this reduction. Avoid heavy letters, which tend to close up when reduced, and unusual symbols, which the printer may not be able to reproduce in the legend.

In figure ordinate and abscissa scales (as well as table column headings), avoid ambiguous use of num­bers with exponents. Usually, it is preferable to use the International System of Units (n for 10-6, m for 10-3, k for 103, M for 106, etc.). A complete listing of SI symbols can be found in the International Union of Pure and Applied Chemistry (IUPAC) "Manual of Symbols and Terminology for Physicochemical Quan­tities and Units" (Pure Appl. Chem. 21:3-44, 1970). Thus, a representation of 20,000 cpm on a figure ordinate should be made by the number 20, accompa­nied by the label kcpm.

When powers of 10 must be used, the journal requires that the exponent power be associated with the number shown. In representing 20,000 cells per ml, the numeral on the ordinate would be "2" and the label would be "104 cells per ml" (not "cells per ml x 10-4"). Likewise, an enzyme activity of 0.06 U/ml would be shown as 6, accompanied by the label "10-4 U/ml." The preferred designation would be "60 mU/ml" (milliunits per milliliter).

Figure Legends

Legends should provide enough information so that the figure is understandable without frequent reference to the text. However, detailed experimental methods must be described in the Materials and Methods section, not in a figure legend. A method that is unique to one of several experiments may be set forth in a legend only if the description is very brief (one or two sentences). Define all symbols and abbreviations used in the figure that have not been defined elsewhere.

Tables

Type each table on a separate page. Arrange the data so that columns of like material read down, not across. The headings should be sufficiently clear so that the meaning of the data will be understandable without reference to the text. See the Abbreviations section of these instructions for those that should be used in tables. Explanatory footnotes are acceptable, but more extensive table "legends" are not. Footnotes should not include detailed descriptions of the exper­iment. Tables must include enough information to warrant table format; those with fewer than six pieces of data may be incorporated into the text by the copy editor.

Avoid tables (or figures) of raw data on drug sus­ceptibility, therapeutic activity, or toxicity. Such data should be analyzed by an approved procedure, and the results should be presented in tabular form.

Tables that can be photographically reproduced for publication without further typesetting or artwork are referred to as "camera ready." They should not be hand lettered and must be carefully prepared to con­form to the style of the .journal. The advantage of submitting camera-ready copy is that the material will appear exactly as envisioned by the author, and no second proofreading is necessary. This is particularly advantageous when there are long, complicated tables and when the division of material and spacing are important. Table 1 is an example of a well-constructed table

TABLE 1. Distribution of protein and ATPase in fractions of dialyzed membranes

Membranes

 

Fraction

 

ATPase

 

 

 

U/mg of protein

 

Total U

 

Control

 

 

 

Depleted

   membrane

Concentrated

   supernatant

0.036

 

0.134

 

2.3

 

4.82

 

El treated

 

 

 

Depleted

   membrane

Concentrated      supernatant

0.034

 

0.11

1.98

 

4.6

"Specific activities of ATPase nondepleted membranes from control and treated bacteria were 0.21 and 0.20, respectively.

NOMENCLATURE

Chemical and Biochemical Nomenclature

The recognized authority for the names of chemical compounds is Chemical Abstracts (Chemical Ab­stracts Service, Ohio State University, Columbus) and its indexes. The Merck Index (10th ed., 1983; Merck & Co., Inc., Rahway, N.J.) is also an excellent source. For guidelines to the use of biochemical terminology, consult the following: Biochemical Nomenclature and Related Documents, 1978, reprinted for The Biochem­ical Society, London; the instructions to authors of the Journal of Biological Chemistry and the Archives of Biochemistry and Biophysics (first issues of each year); and the Handbook of Biochemistry and Molecular Biology (G. D. Fasman, ed., 3rd ed., 1976, CRC Press, Inc.).

Molecular weights should not be expressed in daltons; molecular weight is a unitless ratio. Molecular mass is expressed in daltons.

For enzymes, use the recommended (trivial) name as assigned by the Nomenclature Committee of the International Union of Biochemistry as described in Enzyme Nomenclature (Academic Press, Inc., 1984). If a nonrecommended name is used, place the proper (trivial) name in parentheses at first use in the abstract and text. Use the EC number when one has been assigned, and express enzyme activity either in katals (preferred) or in the older system of micromoles per minute.

Equations

All mathematical equations must be written using Microsoft Equation Editor especially in chemical and enzyme kinetics or pharmacokinetics as well as mathematical modeling equations

Nomenclature of Microorganisms

Binary names, consisting of a generic name and a specific epithet (e.g., Escherichia coli), must be used for all microorganisms. Names of higher categories may be used alone, but specific and subspecific epi­thets may not. A specific epithet must be preceded by a generic name the first time it is used in a paper. Thereafter, the generic name should be abbreviated to the initial capital letter (e.g., E. coli), provided there can be no confusion with other genera used in the paper. Names of all taxa (phyla [for fungi, divisions], classes, orders, families, genera, species, subspecies) are printed in italics and should be so in the manuscript; strain designations and numbers are not.

The spelling of bacterial names should follow the validation lists and relevant articles published in the International Journal of Systematic Bacteriology since 1980. If there is reason to use a name that does not have standing in nomenclature, the name should be enclosed in quota­tion marks and an appropriate statement concerning the nomenclatural status of the name should be made in the text (for an example, see Int. J. Syst. Bacteriol. 30:547-556, 1980).

Genetic Nomenclature

Bacteria. The genetic properties of bacteria are described in terms of phenotypes and genotypes. The phenotype designation describes the observable prop­erties of an organism. The genotype refers to the genetic constitution of an organism, usually in refer­ence to some standard wild type. Use the recommen­dations of Demerec et al. (Genetics 54:61-76, 1966) as a guide to the use of these terms.

(i) Phenotype designations must be used when mu­tant loci have not been identified or mapped. Pheno­type designations generally consist of three-letter sym­bols; these are not italicized and the first letter of the symbol is capitalized. It is preferable to use roman or arabic numerals (instead of letters) to identify a series of related phenotypes. Thus, a series of nucleic acid polymerase mutants might be designated Poll, Pol2, Pol3, etc. Wild-type characteristics can be designated with a superscript plus (Pol+) and, when necessary for clarity, negative superscripts (Pol-) can be used to designate mutant characteristics. Lowercase super­script letters may be used to further delineate pheno­types (e.g., Strs for streptomycin susceptibility). Phe­notype designations should be defined.

(ii) Genotype designations are similarly indicated by three-letter locus symbols. In contrast to phenotype designations, these are lowercase italic (e.g., ara his rps). If several loci govern related functions, these are distinguished by italicized capital letters following the locus symbol (e.g., araA araB araC). Promoter, ter­minator, and operator sites should be indicated as described by Bachmann and Low (Microbiol. Rev. 44:1-56, 1980): e.g., lac2p, lacAt, and lac2o.

(iii) Wild-type alleles are indicated with a super­script plus (ara+ his+). When the genotype of an organism is being specified in a table, a superscript minus is not used to indicate a mutant locus. Else­where, a superscript minus may be used to distinguish between the symbol of a mutant allele and that of a genetic locus. However, this distinction is best made in context, and thus one refers to an ara mutant rather than an ara- strain.

(iv) Mutation sites are designated by placing serial isolation numbers (allele numbers) after the locus symbol (e.g., araA1 araA2). If only a single such locus exists or if it is not known in which of several related loci the mutation has occurred, a hyphen is used instead of the capital letter (e.g., ara-23). It is essential in papers reporting the isolation of new mutants that allele numbers be given to the mutations.

(v) The use of superscripts with genotypes (other than + to indicate wild-type alleles) should be avoided. Designations indicating amber mutations (Am), temperature-sensitive mutations (Ts), constitu­tive mutations (Con), cold-sensitive mutations (Cs), and production of a hybrid protein (Hyb) should follow the allele number [e.g., araA230(Am) hisD2I(Ts)]. All other such designations of phenotype must be defined at the first occurrence. If superscripts must be used, they must be approved by the editor and they must be defined at the first occurrence.

Subscripts may be used in two situations. Subscripts may be used to distinguish between genes (having the same name) from different organisms or strains, e.g., hisE. coli or hisK-12 or strain K-12 in another species or strain, respectively. An abbreviation could also be used if it were explained. Similarly, a subscript can also be used to distinguish between genetic elements that have the same name. For example, the promoters of the gln operon can be designated glnAp1 and glnA2.

(vi) Deletions are indicated by the symbol D placed before the deleted gene or region, e.g., DtrpA432, D(aroP-aceE)419, or Dhis(dhuA hisJ hisQ)1256. Simi­larly, other symbols can be used (with appropriate definition). Thus, a fusion of the ara and lac operons can be shown as F(ara-lac) 95. Similarly, F(araB'-lacZ+) 96 indicates that the fusion results in a truncated araB gene fused to an intact lacZ, and F(malE-lacZ)97(Hyb) shows that a hybrid protein is synthe­sized. An inversion is shown as IN(rrnD-rrnE)1. An insertion of an E. coli his gene into plasmid pSC101 at zero kilobases (0 kb) is shown as pSC101 W(0kb::K-12hisB)4. An alternative designation of an insertion can be used in simple cases, e.g., galT236::Tn5. The number 236 refers to the locus of the insertion, and if the strain carries an additional gal mutation, it is listed separately. It is important in reporting the construction of strains in which a mobile element was inserted and subsequently deleted that this latter fact be noted in the strain table. This can be done by listing the genotype of the strain used as an intermediate, in a table footnote, or by a direct or parenthetical remark in the genotype, e.g., (F-), DMu cts, mal::DMu cts::lac. In setting paren­thetical remarks within the genotype or dividing the genotype into constituent elements, parentheses and square brackets are used without special meaning; square brackets are used outside parentheses. To indicate the presence of an episome, parentheses (or brackets) are used (l, F+). Reference to an integrated episome is indicated as described above for inserted elements, and an exogenote is shown as, for example, W3110/F'8(gal+). Any deviations from standard genetic nomenclature should be explained in Materials and Methods or in a table of strains.

Mutant" vs. "mutation." Keep in mind the distinc­tion between a mutation (an alteration of the primary sequence of the genetic material) and a mutant (a strain carrying one or more mutations). One may speak about the mapping of a mutation, but one cannot map a mutant. Likewise, a mutant has no genetic locus, only a phenotype.

Strain designations. Do not use a genotype as a name (e.g., ". . . subsequent use of leuC6 for transduction . . ."). If a strain designation has not been chosen, select an appropriate word combination (e.g., "an­other strain containing the leuC6 mutation"). For a discussion of the use of patients' initials in strain designations, see Patient Identification below.

Viruses. The genetic nomenclature for viruses dif­fers from that for bacteria. In most instances, viruses have no phenotype, since they have no metabolism outside host cells. Therefore, distinctions between phenotype and genotype cannot be made. Superscripts are used to indicate hybrid genomes. Genetic symbols may be one, two, or three letters. For example, a mutant strain of l might be designated as l Aamll int2 redll4 cI1857; this strain carries mutations in genes cI, int, and red and an amber-suppressible (am) mutation in gene A. A strain designated l att434 imm21 would represent a hybrid of phage l which carries the immu­nity region (imm) of phage 21 and the attachment (att) region of phage 434. Host DNA insertions into viruses should be delineated by square brackets, and the genetic symbols and. designations for such inserted DNA should conform to those used for the host genome.

ABBREVIATIONS AND CONVENTIONS

Patient Identification. When isolates are derived from patients in clinical studies, do not identify them by using the patients' initials, even as part of a strain designation. Change the initials to arabic numerals or use randomly chosen letters. (Note: Established designations of some viruses and cell lines, although they consist of initials, are acceptable [e.g., JC virus, BK virus, HeLa cells].)

Do not identify patients by race, religion, tribe, country or region of origin, or occupation unless the relevance of this information is readily apparent or demonstrated in the text.

Verb Tense. Use the past tense to narrate particular events in the past, including the procedures, observations, and data of the study that you are reporting. Use the present tense for your own general conclusions, the conclu­sions of previous researchers, and generally accepted facts. Thus, most of the abstract. Materials and Meth­ods, and Results sections will be in the past tense, and most of the introduction and some of the Discussion will be in the present tense. Be aware that it may be necessary to vary the tense in a single sentence. For example, it is correct to say "White (30) demonstrated that XYZ cells grow at pH 6.8," "Fig. 2 shows that ABC cells failed to grow at room temperature," and "Air was removed from the chamber and the mice died, which proves that mice require air." In reporting statistics and calculations, it is correct to say “The values for the ABC cells are statistically correct significant, indicating that the drug inhibited …”

Abbreviations

General. Abbreviations should be used as an aid for the reader, rather than as a convenience to the author and therefore their use should be limited. Abbreviations other than those recommended by the IUPAC-IUB (Biochemical Nomenclature and Related Documents, 1978) should be used only when a case can be made for necessity, such as in tables and figures. It is often possible to use pronouns or to paraphrase a long word after its first use (e.g., "the drug," "the substrate"). Standard chemical symbols and trivial names or their symbols (folate, Ala, Leu, etc.) may be used for terms that appear in full in the neighbouring text. It is strongly recommended that all abbreviations except those listed below be introduced in the first paragraph in Materials and Methods. Alternatively, define each abbreviation and introduce it in parentheses the first time it is used; e.g., "cultures were grown in Eagle minimal essential medium (MEM)." Generally, eliminate abbreviations that are not used at least five times in the text (including tables and figure legends).

Not requiring introduction. In addition to abbreviations for standard units of measurement and chemical symbols of the elements, the following should be use without definition in the title, abstract, text, figure legends, and tables: DNA (deoxyribonucleic acid); cDNA (complementary DNA); RNA (ribonucleic acid); cRNA (complementary RNA); RNase (ribonuclease); DNasc (deoxyribonuclease); rRNA (ribosomal RNA); mRNA (messenger RNA); tRNA (transfer RNA); AMP, ADP, ATP, dAMP, ddAT] GTP, etc. (for the respective 5' phosphates of adenosine or other nucleosides) (add 2'-, 3'-, or 5'- when needed for contrast); ATPase, dGTPase, etc. (adenosine triphosphatase, deoxyguanosine triphosphatase, etc.); NAD (nicotinamide adenine dinucleotide NAD+ (nicotinamide adenine dinucleotide, oxidized NADH (nicotinamide adenine dinucleotide, reduced NADP (nicotinamide adenine dinucleotide phosphate); NADPH (nicotinamide adenine dinucleotide phosphate, reduced); poly(A), poly(dT), etc. (polyadenylic acid, polydeoxythymidylic acid, etc.); oligo(dT) etc. (oligodeoxythymidylic acid, etc.); Pi (orthophosphate); PPi (pyrophosphate); UV (ultraviolet); PFU (plaque-forming units); CPU (colony-forming units) MIC (minimal inhibitory concentration); MBC (minimal bactericidal concentration); Tris [tris(hydroxy methyl)aminomethane]; DEAE (diethylaminoethyl); A260 (absorbance at 260 nm); and EDTA (ethylenediaminetetraacetic acid). Abbreviations for cell lines (e.g., HeLa) also need not be denned. The following abbreviations may be used without definition in tables:

amt (amount)                         SE (standard error)

approx (approximately)        SEM (standard error of

avg (average)                                        the mean)

concn (concentration)         sp act (specific activity)

diam (diameter)                     sp gr (specific gravity)

expt (experiment)                  temp (temperature)

exptl (experimental)              tr (trace)

ht (height)                                             vol (volume)

mo (month)                                            vs (versus)

mol wt (molecular weight)                   wk (week)

no. (number)                                         wt (weight)

prepn (preparation)                              yr (year)

SD (standard deviation)

Pharmacokinetic parameters.

Abbreviations and symbols for pharmacokinetic parameters must be in­troduced at their first occurrence in the text. Those most commonly used are:  a (or a phase), distribution phase; b (or b phase), elimination phase; A, zero-time intercept for a phase; B, zero-time intercept for b phase; AUC, area under the concentration-time curve; AUMC, area under the first moment of the concentra­tion-time curve; AUC0-24, AUC0-¥, etc., area under the concentration-time curve from 0 to 24h, 0 h to ¥, etc.; CL, clearance; CLR, renal clearance; CLNR, nonrenal clearance; CLCR, creatinine clearance; Cmax, maximum concentration of drug in scrum; Tmax, time to maximum concentration of drug in scrum; Vmax maximum rate of metabolism; Xu1-2 , drug concentra­tion in urine between t1 and t2, V, volume of distribu­tion; Vss, volume of distribution at steady state; V1, volume of distribution of the central compartment; kel, elimination rate constant; kss, residence rate constant at steady state; t ½ , half-life; t ½a, half-life at a phase; T ½b; half-life at b phase.

Drugs and Pharmaceutical Agents

The use of "nonstandard" abbreviations to desig­nate names of antibiotics and other pharmaceutical agents generally will not be accepted, because the use of different abbreviations for a single agent has often caused confusion. If, on occasion, a nonstandardized abbreviation for a drug or pharmaceutical substance is used, it will be accepted under the following condi­tions: (i) it must be defined in an abbreviation para­graph in Materials and Methods or at the first use in the text; (ii) it must be clear and unambiguous in meaning; and (iii) it must contribute to ease of assim­ilation by readers.

Chemical or generic names of drugs should be used; the use of trade names is not permitted. When code names must be used, the chemical formula of the drug, if known, must be provided at the first occurrence of the code name.

In Vitro Susceptibility Tests 

Tabulate results of determinations of minimal inhibitory and bactericidal concentrations according to the range of concentrations of each antimicrobial agent required to inhibit or kill the members of a species or of each group of microorganisms tested, as well as the corresponding concentrations required to inhibit or kill 50 and 90% of the strains. When only six to nine isolates of a species are tested, tabulate only the MIC range and approximate MIC50,) of each antimicrobial agent tested. When fewer than six isolates of a species are tested, tabulate the MICs for each in a separate table

TABLE 2. MICs isolates

 

Organism

(no. of isolates)

 

MIC for individual

Isolates” (mg/ml)

 

E. ennisi(2) ………………………………….. 0.3, 0.6

E. schmidti (4) …………………………… 0.32, >1002

E. washingtoni (5) ……………. 0.05, 0.1, 0.2, 0.4, 0.8

 The inferior number is the number of isolates with the MIC indicated.

If more than a single drug is studied, insert a column labeled "Test agent" between the present columns and record data for each agent in the same isolate order. Cumulative displays of MICs or MBCs in tables or figures are acceptable only under unusual circum­stances.

Bactericidal tests must be performed with a suffi­cient inoculum (>5 x 105 CFU/ml) and subculture volume (0.01 ml) to ensure accurate determination of the 99 9% killing endpoint. Inoculum size and subculture volume are also critical to studies of combinations of antimicrobial agents. Synergy is defined in two-dimensional or checker­board tests when the fractional inhibitory concentra­tion (FIC) or fractional bactericidal concentration (FBC) index (å) is £0.5. In killing curve tests, synergy is defined as a £³2-log10 decrease in CFU/ml between the combination and its most active constituent after 24 h. At least one of the drugs must be present in a concentration which does not affect the growth curve of the test organism when used alone. Antagonism is defined by a åFIC or åFBC > 4.0.

In killing curve tests, the minimal, accurately detectable number of CFU per milliliter must be stated and the method used for determining this number must be described. In the absence of procedures for drug removal or inactivation, the author must state how drug carryover effects were eliminated. For drugs showing an inoculum effect, mere dilution below the MIC obtained in standard tests is not sufficient.

Sensitivity and Susceptibility to Drugs

Keep in mind that there is a distinction between “sensitivity" and "susceptibility." In general, "sensitivity" should be used in contexts that concern mechanisms of drug action or resistance. "Suscepti­bility" should be used in contexts that concern gross drug-organism interactions, such as death or inhibition of growth.

Reporting Numerical Data

Standard metric units are used for reporting length, weight, and volume. For these units and for molarity, use the prefixes m, m, n, and p for 10-3, 10-6, 10-9, and 10-12, respectively. Likewise, use the prefix k for 103. Avoid compound prefixes such as mm, or mm. Use mg/ml or mg/g in place of mg/liter or mg/kg or the ambiguous ppm. Units of temperature are presented as follows: 37°C or 324 K.

When fractions are used to express units such as enzymatic activities, it is preferable to use whole units, such as g or min, in the denominator instead of fractional or multiple units, such as mg or 10 min. For example, "pmol/min" would be preferable to "nmol/10min," and "mmol/g" would be preferable to "nmol/mg" It is also preferable that an unambiguous form such as the exponential notation be used instead of multiple slashes; for example, "mmol g-1 min-1" is preferable to "mmol/g per min."

Isotopically Labeled Compounds

For simple molecules, labeling is indicated in the chemical formula (e.g., 14CO2, 3H2O, H235SO4). Brackets are not used when the isotopic symbol is attached to a word that is not a specific chemical name (e.g., 131I-labeled protein, 14C-amino acids, 3H-ligands, etc.).

For specific chemicals, the symbol for the isotope introduced is placed in square brackets directly pre­ceding the part of the name that describes the labeled entity. Note that configuration symbols and modifiers precede the isotopic symbol. The following examples illustrate correct usage:

[14C]urea                              UDP-[U-14C]glucose

L-[methyl-14C] methionine  E. coli [32P]DNA

[2,3-3H]serine                      fructose 1,6-[1-32P]bisphospate

[a-14C]lysine

[g-32P]ATP

This journal follows the same conventions for iso­topic labeling as the Journal of Biological Chemistry, and more detailed information can be found in the instructions to authors of that journal (first issue of each year).

© 2004 Nigerian Society for Experimental Biology
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