Components of Manuscript/ Research Paper (Part III)- Results, Discussion, Conclusion, Acknowledgement & References

 

1.   Results

Results forms the core or data of the manuscript. This section has two components. Initially the overall description of experiments have to be provided without repeating the minor details of experiments as explained in Materials & Methods part. Second part is the presentation of findings or data of the analysis in past tense. In this part, first the   main findings of the study in order, relating them in turn to the hypotheses and methods used are presented.  Followed by stating the subsidiary findings, relating them in turn to the hypotheses and methods used. Negative results should be also stated.

If one or only a few determinations are to be presented, it can be included in the descriptive part of results. If repetitive determinations are made, data have to be tabulated and presented as graphs and tables. Figures could be added if required to explain the results. Do not verbose in citing graphs, figures and tables. For eg: “It is clearly shown in Table 1 that Penicillin could inhibit the growth of N.gonorrhoea”- Wrong usage.

“Penicillin inhibited the growth of N.gonorrhoea (Table 1)”- Correct usage.

Statistical analysis of results have to be also performed.

Result section should be short and without verbiage. Results should be stated clearly and simply because this part includes the new knowledge you are contributing to the world. Results should be presented with crystal clarity because the stand or fall of the whole paper is decided on the basis of result section.

2.             Discussion 

Discussion part is the hardest section to write. Discussion sections are long and verbose.

   ·       Restate the findings and accomplishments. State principles, relationships and generalisations shown by the results.

·       Evaluate how the results agree with the previous findings – do

they contradict, qualify, agree or go beyond them?

·       Offer an interpretation/explanation of these results and ward off

counter-claims.

·       List potential limitations to the study.

·       State the theoretical implications as well as potential applications and recommend further research.

3.             Conclusion

Summarise the major findings in simple and effective manner. Should be a short brief paragraph. In some journals, it forms the last part of Result & Discussion section. In some, it comes under separate head.

  4.             Acknowledgements

It is courteous to thank sources of financial support (funding agencies), and colleagues and referees for their help during work as well as in improving articles.

·     Financial (recognition of extramural or internal funding);

·     Instrumental/technical (providing access to tools, technologies, facilities, and also furnishing technical expertise, such as statistical analysis);

·     Conceptual (source of inspiration, idea generation, critical insight, intellectual guidance, assistance of referees etc.);

·     Editorial (providing advice on manuscript preparation, submission, bibliographic assistance etc.)

·     Moral (recognising the support of family, friends etc.).

Eg: Portions of this research were funded by a grant from the National

Institutes of Health (MH53291). We would like to thank Greg Hixon, Amy Kaderka and Girish Tembe for their assistance on this project and

Amie Green, Timothy Loving, Mathew Newman, William Swann, and Simine Vazire for their helpful comments on an earlier draft of this article.

(Slatcher and Pennebaker, 2006, p. 663)

5.             References

References serve many purposes in a scientific manuscript. References should include details like author name, year of publication, topic of paper, Journal name, volume, issue, page number etc.

They:

• Establish where ideas came from
• Give evidence for claims
• Connect readers to other research
• Provide a context for your work
• Show that there is interest in this field of research

Many different styles of referencing have developed over the years. Journals considerably vary in the style of reference section. Currently there are four main styles.

1.       The APA style. This system is also known as the Harvard or, more colloquially, as the ‘name (date)’ system. This is because an author’s surname in the text is followed by the date of the publication in brackets.

Eg: Zammuner, V. L. (1995). Individual and co-operative computer writing and revising: Who gets the best results? Learning and Instruction, 5(2), 101–24.

 

2.     The Modern Languages Association (MLA) style. In this version the authors’ surnames (with or without the dates) appear in the text and the first author’s surname comes first in the reference list.

 

Eg: Speck, Bruce W., Teresa R. Johnson, Catherine Dice, and Leon B. Heaton. Collaborative Writing: An Annotated Bibliography. Westport, Connecticut: Greenwood Press, 1999. 

 

3.      The Institute of Electronic and Electrical Engineers (IEEE) style. Here, the authors in the text are numbered in order of their appearance in the text, sometimes without their names, and the numbers are enclosed in square brackets. The reference list is then numbered sequentially.

    Eg: [1] V. L. Zammuner, ‘Individual and co-operative computer writing and revising: Who           gets the best results?’ Learning and Instruction, vol. 5, no.2, pp. 101–24, 1995.

 

4.   The Vancouver style- popular in medical journals. the authors are numbered in the text in order of their appearance, and the numbers are enclosed in square brackets. The reference list is numbered sequentially, but the authors are listed surnames first, followed by their initials. Again the dates of publications are given after journal titles, or at the ends of the references for books etc

 

Eg:

1.   Speck BWM, Johnson TR, Dice CP, Heaton LB. Collaborative    writing: an annotated bibliography. Westport, CT: Greenwood Press, 1999.

References:

1.             James Hartely, 2008. Academic writing and publishing-A practical handbook (ISBN 0-203-92798-2), Routledge Taylor & Francis Group, New York

2.             Robert A Day and Barbara Gastel, 2012. How to write and publish a scientific paper (ISBN 978-1-107-67074-7), Cambridge University press, UK.

 

Cultural characteristics of microorganisms on special media- Differential/ selective media

 Differentiation of microorganisms which are morphologically and biochemically related is quite difficult.  The use of special media such as differential, selective, enriched and enrichment media is found to make the identification process much easier.  Selective media are used to select specific groups of bacteria.  They incorporate chemical substances that inhibit the growth of one type of bacteria while permitting growth of another, thus facilitating bacterial isolation.  Differential media incorporate chemical compounds that, following inoculation and incubation, produce a characteristic change in the appearance of bacterial growth and/or the medium surrounding the colonies, which permit differentiation. Eg: Mannitol salt agar, MacConkey agar, Eosin-methylene blue (EMB) agar.  

 Aim

To differentiate and identify microorganisms on the basis of the cultural characteristics on differential/ selective media.

 Principle

Special purpose media usually contain the necessary nutrients for growth as well as one or more chemical substances that are essential for the functional specificity of the microorganism.  Mannitol salt agar contains a high salt concentration (7.5 %) which is inhibitory to most of the bacteria except Staphylococci. This medium also helps to differentiate between mannitol fermenting and non fermenting Staphylococci.  The indicator phenol red, in the medium detects the presence of acid produced by the mannitol fermenting Staphylococci which produce a yellow zone surrounding its growth.  Non fermenting Staphylococci will not show change in coloration. 

Mac Conkey agar contains crystal violet which is inhibitory to gram positive bacteria.  The medium also contains the carbohydrate lactose, bile salts and pH indicator neutral red. This medium is useful to differentiate enteric bacteria on the basis of their ability to ferment lactose.  On this basis, enteric bacteria can be separated into Coliform bacilli and Dysentery, typhoid and paratyphoid bacilli.  Coliform bacilli ferment lactose and the acid produced will change the color of indicator.  E.coli produce large amount of acid than other coliform.  Hence, the medium surrounding the growth also becomes red as the acid precipitates bile salts, followed by absorption of the neutral red.

Eosin-methylene blue (Levine) agar contains lactose and the dyes eosin and methylene blue that permit differentiation between  enteric lactose fermenters and nonfermenters as well as identification of the colon bacillus, E.coli.  The E.coli colonies are blue black with a metallic green sheen caused by the large quantity of acid produced and that precipitates the dyes on to the growth surface.  Other coliforms such as Enterobacter aerogenes, produce thick mucoid, pink colonies on this medium.  Enteric bacteria that do not ferment lactose produce colorless colonies, which, because of their transparency, appear to take on the purple color of the medium.  This medium is also partially inhibitory to the gram positive organisms.

Mannitol salt agar, MacConkey agar and   Eosin-methylene blue agar can be considered as the selective as well as differential media.

 Requirements

24 to 48 hr broth culture of species Bacillus, Staphylococcus, Streptococcus, Pseudomonas and E.coli.

Mannitol salt agar, MacConkey agar and   Eosin-methylene blue agar plates,Bunsen burner, inoculating loop, glass marking pencil etc.

Procedure

The given bacterial cultures are inoculated into the special media as follows:

1.  Appropriately label each of the plates.  Divide each of the petridishes into two sections (one section for each different organism) by marking the bottom of the plate.

2.  Inoculate each of the different media with the following:

      Mannitol salt agar:  Bacillus, E coli and Staphylococcus sp.

     MacConkey agar:   Streptococcus, Pseudomonas and E.coli

     Eosin-methylene blue agar: Bacillus, Pseudomonas and E.coli

                                                                                                                                                                Using sterile technique, inoculate all plates with the designated organisms by making a single line of inoculation of each organism in its appropriate section.  Flame inoculating loop between inoculations of different organisms.

3.  Incubate the plates in an inverted position for 24 to 48 hrs at 37^o C.

 Observation

On Mannitol salt agar:  Bacillus and E coli produced no growth.  Staphylococcus sp. produced characteristic colonies on the medium.  The organism exhibited yellow zone surrounding their growth indicating acid production as a part of mannitol fermentation.

On MacConkey agar:   Streptococcus sp. produced no growth. Pseudomonas sp. produced colorless colonies on the medium. E.coli showed pink colored colonies due to lactose fermentation.

EMB agar : Bacillus sp. showed no growth on the medium. Pseudomonas sp., produced colorless colonies. E.coli produced blue black colonies with a metallic sheen.

 Results

Mannitol salt agar:  Bacillus and E coli are non- halophiles and Staphylococcus sp. is halophile.

MacConkey agar:   Streptococcus and Pseudomonas sp. are non lactose fermenters and E.coli is lactose fermenter.

EMB agar:                Bacillus and Pseudomonas sp. are non lactose fermenters and E.coli is an enteric lactose fermenter.

Components of a Manuscript/ Research Paper (PART II)- Key words , Introduction, Materials & Methods

1.   Key words

Importance of Key words:

1.   Allow readers to judge whether or not an article contains material relevant to their interests

2.   Provide readers with suitable terms to use in web-based searches to find out other materials on the same or similar topics

3.   Help indexers/editors to group together related materials. For eg: the end of-year issues of a particular journal or a set of conference proceedings etc.

A wise choice of key words might increase the probability of retrieval and reading of that particular paper and thereby potentially improve its citation counts and thus journal impact factors.

2.   Introduction

First section of a paper is introduction. Purpose of the introduction is to provide the reader with sufficient background information to understand and evaluate results of the present study without the need to refer previous publications in the concerned field. Carefully choose and add references in introduction to provide the most important and relevant background information. Introduction should state the rationale of the present study. Author should briefly and clearly state the purpose of writing this paper. Introduction should be written in present tense as we are discussing the present investigation and correlating it with previous literature. A good introduction should follow the rules like:

·         Should clearly state the nature and scope of the problem investigated

·         Should review the pertinent literature to orient the reader

·         Should briefly state the method of investigation

·         Should state the principal results of the study

·         Should state the principal conclusions as suggested by the results.

3.   Materials & Methods

In this section, full details about the methodology followed is to be given and should be written in past tense. The main purpose of the section is to describe the experimental design with enough details so a competent worker can repeat the experiments. When your paper is subjected to peer review, the good reviewer will carefully go through the materials & methods. Authors are supposed to write their method sections in such a way that readers can repeat the method from the descriptions given. Means, the methods mentioned should be repeatable and should reproduce the same results. If not so, then the reviewer will suggest the rejection of paper.

Most method sections are usually subdivided into three sections, as follows:

1. Participants

2. Measures

3. Procedure(s).

If no participants are involved, then the method simply describes the measures and procedures. Method sections may be brief and succinct when the methods used are well known and standardized or quite lengthy, when the methods used are new or different and thus require careful elaboration.

References:

1.             James Hartely, 2008. Academic writing and publishing-A practical handbook (ISBN 0-203-92798-2), Routledge Taylor & Francis Group, New York

2.             Robert A Day and Barbara Gastel, 2012. How to write and publish a scientific paper (ISBN 978-1-107-67074-7), Cambridge University press, UK.

T Dependent (TD) Antigens

Ø  T Dependent (TD) Antigens require the participation of T lymphocytes for the stimulation of B cells to produce Abs. T cells are of two types. Helper T cells (T_H) or CD 4+ cells and cytotoxic T cells (T_C) or CD 8+ cells. T_H cells are involved in B cell activation by TD antigens.

Ø  TD antigens are structurally complex molecules like serum proteins, protein-hapten complex, erythrocytes etc. Activation of B cells by TD antigens is more complex, but results in stronger response with immunological memory. TD antigens have to be first processed by the An processing/ presenting cells (APC).

Ø  Macrophages, dendritic cells and B cells usually act as An processing/presenting cells. These cells capture An and present them to T lymphocytes. APCs have 2 unique properties.

1.      They express MHC Class II molecules on their surface.

2.      They can also produce co-stimulatory signals necessary to activate T_H cells

APCs first internalize the An by phagocytosis or endocytosis. Then APCs display part of An bound to MHC Class II molecules on their surface membrane.  T_H cells can recognise only those Ans that are presented or attached to MHC class II.

·         I signal - If B cell is acting as the APC, then the first signal is binding of An and BCR. B cell will then internalise the An, process it and present part of An on it surface along with MHC Class II which will be recognized by  T_H cells.

·         II signal - T Cell Receptor (TCR)-CD3 complex on the surface of T Cell recognize and bin to the MHC Class II + An expressed on the surface of B cells. CD4 molecule of T cell also bind to a specific portion on the MHC molecule of B cell to make the binding more  effective. This binding of B cell/APC to T_H cell is called “linked recognition”.

Ø  Additional activation of T_H cells are brought about co-stimulatory signals produced by the APCs. A number of co-stimulatory molecules are involved in T cell activation.  

Co-stimulatory signals

·      CD 28 on T_H cells binds to CD 80 (B7-1) or CD86 (B7-2) membrane proteins on APC. This interaction will activate the T_H cells to secrete various cytokines.

·       T_H cells also start expressing CD40 Ligand (CD40L) which will interact with complementary CD40 of the B cell. This interaction is essential for the survival of B cells and also for germinal centre formation for the secretion of memory cells.

Ø Activated T_H cells secrete T cell growth factor or Interleukin-2 (IL-2) which will act on the T_H cell itself and initiate its proliferation. Proliferated T_H cells are called naïve T cells or T_H0 cells.

Ø Proliferated T_H cells secrete IL-2, IL-4, IL-5, IFN-γ etc. B cells begin to express receptors for various cytokines, bind to cytokines released by T_H cells and thus B cells get activated.

Ø The activated B-cell clonally proliferates to produce a population of plasma cells (Effector B cells) and secrete Abs against the An which had initiated all these process. Initially IgM are the Abs produced by plasma cells. After several rounds of proliferation, B cells differentiate to form memory B cells which will act during secondary response.   

Ø After initial secretion of IgM, cytokines secreted by T_H2 cells stimulate the plasma cells to switch from IgM production to production of IgG, IgA, or IgE. This process is called class switching or isotype switching. By class switching, plasma cells produced from the same B cell could produce a variety of antibody classes with the same epitope specificity. Class switching is due to genetic rearrangement of gene segments encoding the constant region of Abs which determines the antibody type or class.

Ø Differences between TI & TD Antigens

TI Antigens	TD Antigens
Structurally simple & composed of limited number of repeating epitopes	Structurally complex
Molecules like bacterial capsular polysaccharides, bacterial lipopolysaccharides and  some polymeric proteins like flagellar protein flagellin	Molecules like serum proteins, protein-hapten complex, erythrocytes etc
Immune response is dose dependent. Too little An is non- immunogenic & too much An cause immunological tolerance	Immunogenic over wide dose range. Do not readily cause tolerance
Do not require preliminary processing by APCs	Require preliminary processing by APCs and presented along with MHC class II molecules on the surface of APC
Ab response limited to IgM and no isotype switching	Isotype switching occurs and induce formation of almost all isotypes like IgM, IgG, IgA &IgE
Week response & no immunological memory	Strong response with immunological memory
Metabolized slowly and remain in body for long periods	Metabolized rapidly in the body