Components of a Manuscript/ Research Paper (PART I)- Title, Author detail & Abstract

Scientific articles follow a general pattern. A fairly simple pattern is followed by the vast majority of papers published in scientific journals today. Most papers follow the “IMRAD” format with some variations. IMRAD pattern contains:

Introduction

Method (experiment, theory, design, model)

Results and Discussion

Conclusions

In addition to this main structure, scientific articles will also have the components like Title, Author details, Abstract, Key words, Acknowledgements, References and Footnotes.

All articles begin with a title. In most papers, title is followed by an abstract and ‘key words’. All three of these components describe an article’s content in varying degrees of detail. The purpose of the title is to stimulate the reader’s interest. The abstract summarises the content of the paper. The half-dozen or so key words, also called ‘descriptors’, together with the title and the abstract, facilitate computer-based search and retrieval.

1.        Title

A title will be read by thousands of people and only a few will be reading the entire article. Hence, a good title is required to attract and inform the readers about the content. The title should be accurate and needs to stand out in some way from the other thousands of titles that compete for the reader’s attention. It should also tell the reader what the paper is about. All words in the title should be chosen with great care and they should have association with one another. Titles should not be too long or too short. Titles should not contain abbreviations, chemical formula, proprietary names rather than generic names, jargon etc. Some key words should be included in the title relating to the topic of the paper to facilitate computer-based searches. Also, Indexing and abstracting services are heavily dependent on the accuracy of the title and an improper title may miss the reach of intended audience. 

2.        Author Details

List of authors usually follow the title of a scientific article. List of authors should include those who have actively contributed to the overall design and execution of the particular research work. No authorship issue in the case of single author papers. Two author articles require clarification regarding who comes first. Problem becomes more complicated as the number of authors increase.

·    The sequence of names of the authors to an article must reflect the relative scientific or professional contribution of the authors, irrespective of their academic status.

·   The general rule is that the name of the principal contributor should come first, with subsequent names in order of decreasing contribution.

·       Mere possession of an institutional position on its own, such as Head of the Research team, does not justify authorship.

·       A student should be listed as a principal author on any multi-authored article that is substantially based on the student’s dissertation or thesis.

Sometimes, more than 10 authors will be there for a single paper. Such papers will be quoted in references with the name of first author, followed by et al. Eg:  Stephen et al. Degrees (MD, MS, Ph D etc) or titles (Dr, Mr/Mrs) are not usually added in author details except some medical journals. However, author should go through the “author instructions” provided by the journal before preparing scientific paper to that particular journal. “Author instruction” or “Instruction for authors” of a journal clearly defines the pattern and style to be followed while preparing an article to that specific journal.  

Author name is followed by institutional address of authors where the research work was carried out. If the author has moved to a new institute at the time of publication, then that address is also added as “present address”. Also communication details like e mail address of a “corresponding author” will be added. The “corresponding author” is the one individual who takes primary responsibility for communication with the journal during the manuscript submission, peer review, and publication process.

3.   Abstract

Abstract of an article is placed at the top of the paper immediately after title and authors. However, it is written last by the author as the abstract should summarise the work in limited words. A well prepared abstract enables the reader to identify the basic content of the paper quickly and accurately and thus the author can decide whether they need to read the document entirely.  It is considered as the mini version of the paper and is defined as the summary of the information in the document. It should not exceed 250 words, should clearly define what is dealt with in the paper and should be written in past tense.

Abstracts generally follow the same pattern, summarising the objective and scope of the study, methodology, results and principal conclusions of the study in a very clear and compact manner. Such abstracts are called “informative abstract”.

“Structured abstracts’ are another type now common in medical and many social science articles. Structured abstracts have typically 5 sud-headings, back ground, aim/ objective, method, result & conclusion.  Compared to traditional informative abstracts, structured abstracts contain more information, easier to search, easier to read, facilitated peer review for conferences and also more welcomed by readers and authors.

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 Independent Antigens

During humoral immune response, Ab production is brought about by B lymphocytes. Based on the ability to induce Ab formation, antigens can be classified into T independent and T dependent antigens. Some antigens can directly induce the B cells to produce the Abs and are called T Independent Ans. However, some Ans require the help of T lymohocytes for the production of Abs from B cells. These Ans are called T Dependent Ans.

T Independent (TI) Antigens

Most of the protein Ans require the help of T cells for the production of Abs by B lymphocytes. However, Ans like bacterial capsular polysaccharides and bacterial lipopolysaccharides and some polymeric proteins like flagellar protein flagellin, can directly stimulate the B Cells to produce Abs, without the involvement of T cells. They can directly activate B cells with out An processing and presentation to the T cells.  Such Ans are called T Cell or Thymus Independent (TI) antigens. They are structurally simple and carry repeating epitopes. These repeating epitopes cross link the BCRs and act as first signal of activation. Eventhough T lymphocytes are not involved in Ab production, they assist the B cell proliferation and differentiation. For complete activation of B cells a dual signal is required and the second signal usually comes from T cells. But here, as T cells are not, the second signal should come from other sources.

TI Ans are metabolized slowly and remain in the body for long periods. There are two types of TI Antigens. TI-1 antigens and TI-2 antigens. TI-1 are usually bacterial lipopolysaccharides (LPS) which have mitogenic properties can deliver dual signal to B cells by themselves. First signal by binding to BCR and second by binding to the lipid moiety of LPS whose nature is not well studied.

TI-2 antigens are compounds like polysaccharides without mitogenic properties and activate B cells in another way. They contain multiple repeats of limited number of sugar molecules which will cause excessive cross linking of BCRs. This will deliver strong signals that can compensate the need for co-stimulatory signals from T cells. In this case, the second signal can be the interactions of toll-like receptors (TLRs) with PAMPs or interactions with factors from the complement system.

Toll-like receptors are receptor proteins help in the recognition of wide array of pathogens and are found on the membranes of leukocytes including dendritic cells, macrophages, natural killer cells, immune cells like T cells and B cells, and also on non-immune cells like epithelial and endothelial cells, and fibroblasts.  PAMPs are Pathogen Associated Molecular Patterns found on infectious agents which are recognized by Toll like receptors.  

Once the B cells are activated, they undergo clonal proliferation and daughter cells differentiate into plasma cells. Plasma cells are antibody factories that secrete large quantities of antibodies. Abs produced by TI Ans are mainly IgM Abs. Type switching to IgG can take place with the help of T lymphocytes. Here, there is no production of memory cells and no immunological memory. Hence immune response is effective in primary infection and not effective in secondary infection and also short lived. Also, immune response by TI Ans are dose dependent. Means, too little An is not immunogenic and too much An cause immunological tolerance than immunity.

Cultural Characteristics of Microorganisms on Basal media (Nutrient agar and Nutrient broth)

Isolation of microorganisms in pure culture is necessary to study the relationship between an organism and a disease. Also pure culture isolation is necessary to study about the biochemical properties as well as the susceptibility of the organisms which are essential in diagnosis and prognosis of various diseases.  For this, microorganisms are artificially cultivated on various media in the laboratory. A media usually provides an artificial environment for the growth and multiplication of microbes.

Basal medium or the general purpose media are the ones one which provides all essential nutrients to support the growth of most of the nonfastidious microorganisms.  It will not promote or suppress the growth of one particular organism over the other.  Egs : Nutrient agar, Nutrient broth,  Trypticase Soy agar and Brain Heart Infusion agar.  Nutrient agar and Nutrient broth are the most widely used basal media and the only difference between them is that the former contains agar as the solidifying agent.  The presence or absence of agar in the media will not affect the growth of the organisms as agar has no nutritive value.

Different other types of media are also used in microbiology laboratories based on the requirements. They include special media like enriched media, enrichment media, selective media, differential media, indicator media, sugar media and transport media.

  

Aim  

To demonstrate the cultural characteristics of microorganisms on basal or supportive media for identification and classification of microorganisms into different taxonomic groups.   

Principle

Different growth patterns and cultural characteristics are produced by microorganisms on cultivation on different media which will be useful in their identification. The cultural characteristics for all the microorganisms are well described in Bergey’s Manual of Systematic Bacteriology. Usually cultural characteristics are determined by cultivating the microorganisms on general purpose media like nutrient agar slants and plates, nutrient broth etc.

  

Nutrient agar plates

Microorganisms produce discrete and well defined colonies on nutrient agar plates. The following characteristics can be evaluated from the agar plate cultures:

1. Size: Pinpoint, small, moderate or large.

2. Pigmentation: Color of colony

3. Form: The shape of the colony

     a) Circular: unbroken peripheral edge

     b) Irregular: Indented peripheral edge

     c) Rhizoid: Root like spreading growth

4. Margin: The appearance of the outer edge of the colony is described as follows:

     a) Entire: Sharply defined, even

     b) Lobate: Marked indentations

     c) Undulate: Wavy indentations

     d) Serrate: Toothlike appearance

     e) Filamentous: Thread like spreading edge

5. Elevation: The degree to which colony growth is raised on the agar surface is described as follows:

     a) Flat: No marked elevation from the surface of the medium

     b) Raised: Slightly elevated

     c) Convex: Dome shaped elevation

     d) Umbonate: Raised with elevated convex central region

Nutrient broth cultures

In broth cultures microorganisms do not produce discrete colonies. Increase in turbidity of the broth is the indication of microbial growth. Microorganisms show characteristic growth patterns in nutrient broth which is also considered helpful in the identification of organisms.  They are as follows:

1. Uniform fine turbidity: Finely dispersed growth throughout.

2. Flocculent: Flaky aggregates dispersed throughout

3. Pellicle: Thick, padlike growth on the surface

4. Sediment: Concentration of growth at the bottom of the broth culture which can be granular, flaky or flocculent

Requirements

24 hr nutrient broth cultures of species Bacillus, Streptococcus, Staphylococcus, Pseudomonas and E.coli.

Nutrient agar plates, nutrient broth tubes, Bunsen burner, inoculating loop, glass marking pencil etc.

Procedure

1.  Using sterile techniques, inoculate each of the appropriately marked media as follows:

        a) Nutrient agar plates: Using a sterile loop, prepare a streak plate inoculation of each of the organisms provided on the agar plates for the isolation into discrete colonies.

        b) Nutrient broth tubes: With a sterile loop, inoculate each organism into the tube containing nutrient broth and shake the loop few times to dislodge the inoculum.

2.  Incubate all cultures at 37^oC for 24 hr to 48 hrs.

Results

On nutrient agar plates:

Bacillus sp. - produced irregularly round, raised, dull, opaque and grayish white colonies.

 Streptococcus sp. – produced circular, small, semitransparent and low convex disc like colonies.

Staphylococcus sp. – produced circular, convex, smooth, shiny, opaque and slightly yellow pigmented colonies.

 Pseudomonas sp. – produced large opaque and irregular colonies.

 E.coli.- produced large, thick, moist, white, smooth opaque or partly translucent colonies.

In nutrient broth tubes:

Bacillus sp. – Flocular deposit with little or no turbidity.

Streptococcus sp. – granular turbidity with a powdery deposit. No pellicle.

Staphylococcus sp. – Uniform turbidity.

Pseudomonas sp. – Dense turbidity with a surface pellicle.

E.coli.- General turbidity and a heavy deposit, dispense completely on shaking.

Manuscript Preparation for Journals

1.    Why Write and Publish a Manuscript or Research Paper?

To make publishable results through original research work requires much hard work. Writing a paper and getting it published in a peer-reviewed journal is much harder than that. There are two kinds of motivations behind publishing articles. They are altruism and self-interest, and most authors have combination of both.

1.1.       Altruism (selfless concern for the well-being of others)

Peer-reviewed science publications are the predominant method today for disseminating and archiving scientific advances (books, conference presentations, and university teaching are other common ways). Science grows and advances through a communal collection of knowledge that is constantly being challenged, revised, and expanded. Most scientists have a strong desire to contribute to the advancement of their field, which is often their primary reason for becoming a scientist. Publication is usually the most straightforward way to make such a contribution, and it is thus highly motivating (and satisfying) to most scientists.

1.2.       Self-Interest

Publishing can also bring tangible benefits to an author, thus providing a self-interested motivation for writing and publishing a paper. Publishing may be required for career advancement and is frequently accompanied by direct or indirect monetary rewards. But even without these obvious professional motivations, almost all human beings want recognition for their efforts.

2.        Before starting a Scientific Paper- The Literature Search

A new research project always begins with a literature search. It has to be done before starting the research work as well as before preparing the article. The goal of the search is to evaluate the state of our communal knowledge on a topic before embarking on a quest of adding to that knowledge. Because science is about either confirming or refuting existing knowledge or developing new knowledge. So a thorough understanding of the current state of communal knowledge is essential. A literature search is not about finding relevant papers, it is about reading relevant papers. A thorough literature survey is essential before scientific manuscript preparation.

3.        The Standard Structure of a Scientific Paper

A scientific paper is a written and published report describing original research results. The key characteristic of a scientific paper is its clarity. The words used should be simple, direct and well-ordered as possible. Creativity coupled with critical thinking is the key to successful scientific writing.

There is generally an accepted way of scientific articles. The vast majority of papers published in scientific journals today follow a fairly simple structure. With some variations, most papers use an “IMRAD” format:

Introduction

Method (experiment, theory, design, model)

Results and Discussion

Conclusions

This format is so ubiquitous and there are two main advantages of following the IMRAD structure: it makes it easier for the writer to organize the content of the paper, and it makes it easier for the reader to opportunistically find the information they seek.

Headings and subheadings are an important part of a paper’s organization. Headings are almost always required in science journals, but subheadings are often optional.

References:

1.     Chris A Mack, 2018. How to write a good scientific paper- (ISBN 9781510619135), SPIE Press, USA.

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

Types of Scientific Publications

Scientific publications are of different types. “Scientific paper” is the term used to denote an original research work. Primary publication is the full report (full paper) on an original research work published in peer – reviewed journals.   Review paper, conference report and meeting abstract are also other forms of scientific publications.

Review paper- A review paper summarize, analyse and evaluate the information that has been already published in various journals. Even though these articles are meant for critical review of scientific information published till date on a particular topic, new ideas, new theories and even new paradigms can evolve from a good quality review paper.  

Conference Report- Conference report is the publication in a book or journal which has been published as a part of the proceedings of a national/ international conference, congress etc. Such publications do not qualify as primary publications. They usually contain review papers, discussing recent work by a particular scientist or work in a particular laboratory. Some are in the form of preliminary reports. Such reports also do not qualify as primary publication. Essential experiments has to be conducted and proper mature conclusion has to be arrived with such preliminary works and then it has to be published in a peer reviewed journal to make it valid. Means, original work published as conference report has to be published in an archival journal to be valid as a primary publication.

Meeting abstract – Meeting abstract can be of different types like those published as part of national /international seminars, meetings etc. They are very much similar to conference report, but often contain an original research information. Such abstracts will be summarizing the details of the original research work in one or two paragraphs. These are also not valid as primary publication. Nowadays, extended abstracts are also published in many seminars. Extended abstracts provide much details about the original research work, but differ from full paper in that they lack the experimental details.   Extended abstracts is also not valid as primary publication. 

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.

Demonstration of Bacterial Motility by Stab culture Method

Stab culture method is an indirect way to demonstrate bacterial true motility.  In this method, semisolid agar is used to cultivate the bacteria which allow the movement of the organisms in the medium.

Aim

To demonstrate the bacterial motility by Stab culture method.

Principle

Semisolid nutrient agar is poured into a test tube and allowed to set by keeping in upright position. Broth culture of organism is inoculated to the media by stabbing the culture.  If the organism is motile, it moves through the media and shows growth on the different parts of the media in addition to the line of stab. If non motile, growth can be seen only in the stabbed region of the tube.

Requirements

24 hr culture of E. coli and Staphylococcus spp.

Test tubes, Bunsen burner, straight inoculation needle etc.

Procedure

Prepare nutrient agar with 0.2 % agar concentration, heat to dissolve.

Pour agar approximately up to 10 mm height of the test tubes.

Put the cotton plug and sterilize the medium at 121^o C for 15 min. After sterilization, allow the medium to set in the upright position.

Inoculate the given microorganisms into the agar by stab method with the inoculation needle.

Incubate the tubes at 37^o C for 24 hrs.

Observations

E. coli showed growth throughout the inoculated medium, indicating that the organism is motile.  Staphylococcus sp. showed growth only in the stabbed region of the medium, indicating that it is non motile.

  

Result

In the given cultures, E. coli is motile which showed true motility and Staphylococcus sp. is non motile.

Concept of Biodiversity

Biodiversity means biological diversity.  The term biodiversity was coined by Walter G Rosen in 1985.  Biodiversity is an “umbrella term” used to refer to the number, variety   and variability of living organisms found within the living world.  The International Union for Conservation of Nature (IUCN) defines biodiversity as “the diversity of life on earth including the number, variety and variability of living organisms like animals, plants, microbes etc. and the genetic difference among them and the ecosystem in which they occur”. In simple terms, we can say, biodiversity is the variation in species, genes and ecosystem within an area, biome or planet. 

Biodiversity is the result of billions of years of evolution. Biodiversity is a very vast and complex concept and is generally treated under three fundamental hierarchical levels. Yucel in 2015 divided biodiversity into three main components namely species diversity, genetic diversity and ecosystem diversity.

 1.      Species diversity

Species is a group of living organisms that can interbreed with each other. Species diversity is the different kinds of species within a particular region or it is diversity between species. For example, in a small river there can be plants, frogs, fishes, snakes and so forth, forming the diversity of species. Species diversity is also known as Taxonomic diversity or Organismal diversity. Species diversity is measured as species richness. Species richness is the total count of a species in a defined area. Species abundance refers to the relative number among species. If all species have equal abundance means species variation is high, means high species diversity. Species diversity is dependent on the climatic conditions. 

2.        Genetic diversity 

Genetic diversity is genetic differences within  each species.  Gene is the distinct sequence of DNA forming part of the chromosome which offsprings inherit from their parents. Chromosomes, genes and DNA determine the uniqueness of each individual and each species. Genetic diversity is the variety of genetic information contained in all of the individual plants, animals and microorganisms occurring within the population of a species. In other words,  genetic diversity refers to different types of genes in chromosomes of species and their variations. For example,  within the species of dogs, different varieties like Bulldog, German Shepherd, Great Lane dog etc. are found. It is due to differences in their genes. Even within such varieties, they differ in their  size, shape, colour etc and  this is due to the difference within their genes. 

3.        Ecosystem diversity

Ecosystem diversity is the diversity at ecological or habitat level. Ecosystem is a biological community of animals and plants that interact with each other as well as with their environment in a particular region. Ecosystem diversity refers to a particular assemblage and interaction of a species living together and their physical environment in the given area. It is also called ecological diversity. For example, there may be two different forests in an.area. The species in each ecosystem, natural communities and habitats will be different from each other. This is called ecosystem diversity.

Biodiversity distribution is not uniform on earth. Terrestrial biodiversity is highest near the equator because of warm climate and high primary productivity. Similarly, marine biodiversity is highest along the coast where surface temperature is highest. Biodiversity is the life support system. Organisms depend on it for the air they breathe, for the food they eat and for the water they drink. Biodiversity is the essence of life and human beings form an integral part of it and upon biodiversity we are fully dependent. Hence, the conservation of biodiversity is essential for the existence of living forms including human beings on the earth.

References:

1. Dickson Adom, Krishnan Umachandran, Parisa Ziarati, Barbara Sawicka and Paul Sekyere, 2019. The Concept of Biodiversity and its Relevance to Mankind: A Short Review, Journal of Agriculture and Sustainability, 12 (2); 219-231.
2. Rawat U S and Agarwal N K, 2015. Biodiversity: Concept, threats and conservation, Environment Conservation Journal, 16(3); 19-28.
3. Krishnamurthy K V, 2003. Textbook of Biodiversity, Science Publishers Inc. USA