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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 reviewers 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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