Tables

Authors must use Microsoft word table format only for preparing 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., 3^rd 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., Str^s 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., his_{E. coli} or his_K-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.); P_i (orthophosphate); PP_i (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; AUC_0-24, AUC_0-¥, etc., area under the concentration-time curve from 0 to 24h, 0 h to ¥, etc.; CL, clearance; CL_R, renal clearance; CL_NR, nonrenal clearance; CL_CR, creatinine clearance; C_max, maximum concentration of drug in scrum; T_max, time to maximum concentration of drug in scrum; V_max maximum rate of metabolism; X_u^1-2 , drug concentra­tion in urine between t₁ and t₂, V, volume of distribu­tion; V_ss, volume of distribution at steady state; V₁, volume of distribution of the central compartment; k_el, elimination rate constant; k_ss, 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 as illustrated above.

 

 

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).

 

 

Instructions to Authors

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