THE "PROTEUS PROJECT"
WEBPAGE No.3.
THE "PROTEUS PROJECT IN THE TREBIŠNJICA RIVER BASIN"
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"A JOINT STRATEGY FOR THE PROTECTION OF THE ENDANGERED UNDERGROUND ENDEM Proteus anguinus AND ITS NATURAL KARST HABITAT IN THE TREBIŠNJICA RIVER BASIN."
Eastern Hercegovina and the Hercegovinian Littoral, Bosnia & Hercegovina;  Dalmatian & Dubrovnik Littoral and Konavle, Croatia;  Old Hercegovina, Montenegro.
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"Zajednička Strategija za Zaštitu Ugroženog Podzemnog Endem Čovječje Ribice (Proteus anguinus) i Njezinog Prirodnog Krškog Staništa u Slivu Rijeke Trebišnjice."
Istočna Hercegovina, Bosna i Hercegovina.
"Заједничка Стратегијаза Заштите Угроженог Подземног Ендема Човјечије Рибице(Proteus anguinus) и Његовог Природног Кршког Станишта у Сливу Ријеке Требишњице."
Источна Херцеговина, Босна и Херцеговина.
"Együttműködési Stratégia a Veszélyeztetett Barlangi Vakgőte (Proteus anguinus) Természetes Karsztos Élőhelyének Védelmére a Trebišnjica Folyó Völgyében."
Kelet- Hercegovina, Bosznia - Hercegovina.
"The Proteus Project in the Trebišnjica River Basin" - Webpage 3. for INFORMATION SECTIONS 3. to 5.
Text Updated.09 January 2017.
.(undergoing major updating)
.....PROTEUS PROJECT WEBPAGE [3.] CONTENTS :-
.....Click on the underlined Links below to move down to the Sections more quickly.
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.....NOTE: This "Proteus Project" Webpage [3] has started to undergo a substantive revision, whereby some of the former Information Sections have now been removed, are being updated and are being placed in a 4th Webpage of this Series and
.....where the remaining Information Sections are currently being updated.
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.....Section 3...Broad Aims and Objectives of the Project.
.....Section 4...Theoretical and Practical Fieldwork support Documentation for Project Research Assistants :
.....Section 5...Glossary of Biological Terms used in the text of the 5-part Webpages, together with General Speleobiological Terms :
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.....Click on the underlined Links below to navigate to the other "Proteus Project" Webpages more quickly.
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.....Link to. "Proteus Project" Introductory Webpage :
.....Link to. "Proteus Project" Webpage [1.] :
.....Link to. "Proteus Project" Webpage [2.] :
.....Link to. "Proteus Project" Webpage [4.]: (Active but under initial development)
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Section 3....BROAD AIMS AND OBJECTIVES OF THE "PROTEUS PROJECT".
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Groundwater is the main drinking water reservoir on earth and is also a major ecosystem in terms of biological diversity.
Maintaining groundwater quality and conserving its biodiversity are converging goals because their level of biodiversity attests the healthy functioning of these systems. 
The "Proteus Project" has been planned to be implemented through three ten-year Phases, with the flexibility for a substantial cross-over between and during each Phase of work.
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"PROTEUS PROJECT" PHASE 1. (2000-2010) :
......i)..Partnerships:
.............To set up and undertake the Project in Partnership with a selected Voluntary Sector speleological society in each of the governing political and administrative entities within the geographical area of the Project,
thus maximizing the use of the locally available resources, skills and expertise.
Where resources, skills and expertise are not available either locally or elsewhere in BiH, out-sourcing will be undertaken and used, until such time that they do become available locally or in elsewhere BiH.
In connection with this, the UK Project Co-ordinator Group will be responsible for enabling the training of the Voluntary Sector Partners to become proficient in any skills necessary to undertake the Project.
....ii)..Proteus anguinus Habitat Locations:
..........-  To identify and locate all presently and previously known habitat locations of Proteus anguinus at the local level and to search for other potential habitat locations and to initialize an interim version of a Gazeteer containing such information;
..........-  To undertake a thorough speleological, hydrological, hydro-physico-chemical and biological assessment of each previously known and presently known habitat location, for a comparative study of identifying the parameters and conditions that constitute a.viable habitat location for Proteus anguinus.
....iii)..Identification and Spatial Characterisation of Karst Conduit-aquifer Ecosystems:
..........-..To undertake a thorough hydrological and hydrogeological assessment of the relevant parent hypogean Karst Conduit-aquifers to determine the spatial extent and physical disposition of the ecosystems.
..........-  To assign each Proteus habitat location to a Karst Conduit-aquifer Ecosystem;
..........-  To determine the areal extent of the surface rainfall catchment associated with each Karst Conduit-aquifer Ecosystem;
..........-  Initialization of relevant interim versions of Project Documentation, including guidelines for methodology, best practice and results.
.............The results may help in determining why Proteus can be seen at some locations and never at others and why is has disappeared from some former locations where it was once prolific.
....iv)..Qualitative and Quantitative Hypogean Species Inventories in the Proteus anguinus Habitats:
..........-  To access all presently and previously known habitat locations of Proteus anguinus and begin to qualitatively and quantitatively monitor for the presence / absence of this and all other hypogean species, together with a relative assessment of species population numbers;
..........-  Initialization of relevant interim versions of Project Documentation.
....v)..Habitat Restoration & Protection:
..........-  To instigate unilateral environmental "clean-ups" of individual actual, potential and ex- Proteus anguinus habitat locations, as, when and where necessary and to formalize associated "best practice" into the Project Documentation.
..........-  To attempt to make contact with the relevant Local Governmental and BiH-Entity Government Institutions and Ministries to form working partnerships with the objective of obtaining Government Protection for Proteus anguinus and its hypogean habitat locations.
...vi)..Public Education Programme:
.............To start up the on-going facilitation of a high profile Public Education Programme to promote the importance of the concept of "clean water through a clean karst environment" at every opportunity and by any means possible, aimed at the National, Regional and Local Governments and the general population; engagement with the Press and Media must be established in order to disseminate the necessary information as widespread as possible.
...vii)..Promotion of Nature Protection and Conservation Laws :
..........To promote the introduction of Laws in Bosnia and Hercegovina which will provide effective legal protection for karst aquifer ecosystems, caves, cave habitats and cave flora and fauna and which will provide penalties for those who contaminate or destroy caves, cave habitats and cave flora and fauna. 
Such Laws must also outlaw the trading or export, for any reason, of cave speleothems and all species of underground flora and fauna and provide effective penalties for those attempting to do so.
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"PROTEUS PROJECT" PHASE 2. (2011-2020) :
....i)..Proteus aguinus Habitat Locations:
.............To continue with the identification process of all presently and previously known habitat locations of Proteus anguinus and to continue the search for other potential habitat locations and to formalize a definitive illustrated version of a Gazeteer containing such information;
...ii)..Identification and Spatial Characterisation of Karst Conduit-aquifer Ecosystems:
..........-..To continue the work detailed above in Phase 1., and to produce the relevant formal definitive documentation on guidelines to methodology, best practice and on-going results.
..iii)..Qualitative and Quantitative Hypogean Species Inventories in the Proteus anguinus Habitats:
..........- To continue to access all presently and previously known habitat locations of Proteus anguinus and to continue to qualitatively and quantitatively monitor for the presence / absence of this and all other hypogean species;
..........- To devise and implement methods of in situ biometric assay for Proteus anguinus specimens;
..........- To devise and implement in situ trial programmes of tagging of Proteus anguinus specimens;
..........- To undertake detailed identification of all hypogean species;
..........- To produce the relevant formal definitive documentation on guidelines to methodology, best practice and on-going results.
..iv)..Behavioural Studies of Proteus anguinus in its Natural Habitat:
..........- To devise and implement in situ trial programmes of zero-impact observation of Proteus anguinus specimens in their natural habitats;
..........- To produce the relevant formal definitive versions of documentation on guidelines to methodology, best practice and on-going results;
...v)..Habitat Restoration & Protection:
.............To continue with the work detailed in Para (v) above in Phase 1. 
..vi)..Public Education Programme:
.............To continue with and extend the scope of the work detailed in Para (vi) above in Phase 1.
..vii)..Publication of a "Proteus Project" Monograph Series:
.............To produce at least a first Volume of Spelæobiologica Bosniæ et Hercegovinæ, detailing current results about the work on one named karst conduit-aquifer hypogean ecosystem. 
..viii)..Publication of a "Proteus Project" Occasional Series of Periodicals:
.............To produce at least 3 Issues annually of Observations in Speleology, detailing current results about the work on karst conduit-aquifer hypogean ecosystems occupied by Proteus in each of the river basins in BiH.. 
..ix)..RS-BiH Entity Level Nature Protection and Conservation of Selected Karst Conduit-aquifer Hypogean Ecosystems:
.............- Assist the RS-BiH Entity Government in the selection of Karst Conduit-aquifer Hypogean Ecosystems for eventual BiH-Entity Level Nature Protection as Biosphere Reserves and to assist in the drafting of all relevant documentation.
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"PROTEUS PROJECT" PHASE 3. (2021-2030) :
.....i)..RS-BiH Entity-Level Nature Protection and Conservation of Selected Karst Conduit-aquifer Hypogean Ecosystems:
.............- To achieve legal protection of increasing numbers of selected Karst Conduit-aquifer Hypogean Ecosystems by the RS-BiH Ministry responsible for Nature Protection."
.............- To achieve and ensure the viability of such Nature Protection Orders through engagement with and active participation by other relevant Government and non-Governmental Agencies at local, regional and BiH-Entity Government levels.
.............This to be achieved locally at RS-BiH Municipality Level by the formation of Conservation Management Boards to implement Conservation Management Plans. 
.............By this means and through additional engagement with, and participation by local populations and their elected representatives, all stakeholders can be empowered to care for their natural heritage.
...ii)...Habitat & Hypogean Species Conservation and Public & Touristic Education:
.............-..To promote concepts and identify practical methods for the preservation, conservation, research and study of the karst habitat locations of Proteus anguinus and for the conservation of the species itself and
.............-..To ensure and assist with the future survival of the hypogean species by promoting a long-term programme for the study of the local variety of Proteus anguinus, within a combined Speleobiological Laboratory to be constructed in the 
.............Trebinje area as an integral part of a local Proteus anguinus karst habitat location, adapted and maintained for the purpose. Such a Facility must include a substantial Lecture Theatre and a permanent exhibition to support the 
.............Public Education Objectives and Tourism.
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Section 4....THEORETICAL AND PRACTICAL FIELDWORK SUPPORT-DOCUMENTATION FOR THE "PROTEUS PROJECT".
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Due to the immense success of the field-work, the "Proteus Project" is generating a large quantity of Archive Documentation relating to each sub-Project Report.
As a result of this, there has now been a change in the documentation content style, such that, with effect from July 2006., Site Citation Reports will be incorporated into the Part 1. Documentation of each sub-Project Report, to reduce
duplication of information. 
Master copies of individual sub-Project Reports are kept in the Archives of the UK Project Co-ordinator Group, The Devon Karst Research Society, and in due course, will also be kept locally by the Local.Project Co-ordinator Group RS-BiH.
For reasons explained in more detail below, we have decided not to make the sub-Project Reports.accessible via Links on this webpage.
If Project Research Assistants in BiH require hard-copies of these Reports but are locally unable to produce hard-copy printouts, please e-mail to the UK Project Co-ordinator Group requesting the appropriate hardcopy documentation.
The Group's Project-Administrator will forward any requested documentation by Post. Please remember that it currently takes 6 days for despatch from the UK to delivery in RS-BiH.
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The selection of Primary Documents listed below are for use by Project Research Assistants and Project Workers and provide a measure of technical support.
These two Batches of Documentation relate solely to Theoretical and Practical Fieldwork Information and the massive amount of detailed information is being developed to publication-ready standards of format and presentation.
Project Research Assistants have full access to this information. Please note that these documents can no longer be directly accessed from this website.
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Batch Type-7. Primary Documentation available to "Proteus Project" Research Assistants.
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....7.1...Geographical Scope of the Project Area,.(Illustrated version 3.1.) :
...This document presents details of the constraint line boundary of the "Proteus Project" Area in Eastern Hercegovina and the Hercegovinian Littoral, (both of which are wholly within the Territory of Bosnia & Hercegovina);
...in Old Hercegovina within Montenegro and in the areas of the Dalmatian Littoral and Konavle within Croatia.
...In recent years, the boundary line has been adjusted ever outwards to include more karst territory, reflecting the geographical distribution of Proteus anguinus within the catchment and drainage areas of the Trebišnjica River Basin
...and of the "palaeo-Trebišnjica River Basin" in the Mt. Orjen direction.
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....7.2...The Proteus anguinus Habitat Locations, Part 1...(Illustrated Version T21.0. with an Appendix on Type Localities for Hypogean Species in Hercegovina.) :
...This full-scale Illustrated version is the Definitive Primary Document for locational information relating to all known and highly-probable Proteus anguinus Habitats within the Geographical range of the "Proteus Project" Area.
....This version includes information such as Specific Locational Data; Location Descriptive text; a Location-specific Hydrological Synopsis, with details of any installed hydrometric infrastructure and also offers a speleobiological
...assessment of each location, with qualitative and quantitative details of resident hypogean species.
....The data is useful in evaluating population densities and the geographical distribution of hypogean species. The document also attributes each location to a particular Karst Conduit-aquifer Ecosystem wherever possible.
....This version includes Location Recognition Images of each location, which are supplemented by BiH State Aerial Photogrammetry Images and where possible, by Map extracts derived from the BiH National 1 : 25 000.; 1 : 2 500. and
...1 : 1 000 Scale Maps. When brought fully up-to-date, this lengthy document of currently 380 pages, will replace the Text-only version.
.Trebišnjica River Basin.
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Batch Type-9. Primary and Other Documentation available to "Proteus Project" Research Assistants.
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.......9.1.1..Habitat Karst Water-Quality Database and Species Sightings Records.
.......This document is the "Proteus Project's" central spreadsheet / database for storing all physico-chemical karst water analyses data obtained by Project Research Assistants and Project Workers.
.......At present, it is only produced in a digital format using MS Excel software.
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......Standards and Field Methodology for the  Determination of Karst Water Quality, (Combined Document).
.......9.1.2. - 9.1.3. - 9.1.6. - 9.1.8...
.......This is a research-support document available to all Project Research Assistants and Project Workers concerned with the acquisition of raw hydro-physico-chemical data in the field.
.......The document also gives detailed methodologies and procedures for data acquisition using the Project's portable analytical equipment. 
.......- 9.1.2...The Determination of Eh and pH Values in Karst Water; the general relationship of the Eh (Oxidation-Reduction Potential) with the pH Value and the Oxygen Values and what the Values can Indicate
.......................about the Quality of a Karst Water Habitat.
.......The document explains the relevance of the terms pH and Eh together with the concepts behind the acquisition of these two values and their relevance in monitoring the quality of the hypogean aquatic habitat.
.......The document also gives a detailed methodology of data acquisition using the Project's portable electronic instrumentation.
.......- 9.1.3...The Determination of Carbonate Values in Karst Water.
.......The Rapid EDTA Complexometric Titrimetric Determination of Calcium Hardness and Total Hardness in Karst Water.
.......The Quantitative Determination of the Carbonate-saturation Value in Karst Water.
.......The Rapid EDTA Complexometric Titrimetric Determination of Magnesium Hardness in Karst Water.
.......The Qualitative Determination of Dissolved Strontium and Barium in Karst Water.
.......Notes on the Determination of Alkalinity Values and on Interferences by other Ion Species on The EDTA Methods Herein.
.......Conversion Factors for Equivalent Values of International Units of Water Hardness.
.......- 9.1.4...Commissioned Bacteriological Examination Reports of Karst Water in Proteus anguinus Habitat Locations & Costings.
.......This is a reporting document available to all Project Research Assistants and Project Workers concerned with the safety and microbiological quality of water in the aquatic hypogean habitat prior to partial or 
.......complete immersion in the habitat for investigative work. This documentation is particularly relevant to the Project's cave divers.
.......The document explains some of the problems associated with biologically-contaminated water and then presents the reports of commissioned micro-biological analyses undertaken by an approved competent laboratory.
.......- 9.1.6...The Determination of Dissolved Oxygen and Oxygen Saturation Values in Karst Water.
.......General Explanation of the Terms, their Determination and what the Values can Indicate about the Quality of a Karst Water Habitat.
.......- 9.1.7...Karst & Cave Water Analysis Reporting Sheet.
........For recording all physico-chemical karst water analyses data obtained by Project Research Assistants and Project Workers during locational field-work.
.......- 9.1.8...The Determination of the Turbidity Value in Karst Water.
.......General Explanation of the Parameter, its Determination and what it can Indicate about the Quality of a Karst Water Habitat.
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.......9.1.5....Proteus anguinus anguinus (Laurenti 1768) :  Biomorphic and Bio-Morphometric Data from Specimens in their Natural Hypogean Habitats in Eastern Hercegovina, Bosnia & Hercegovina.
............9.1.5.1...Part 1...Standards and Guidelines for Working in or Around Hypogean Karst Ecosystems and for Working with Proteus anguinus in its Natural Karst Habitats. 
..............................-..The Prime Directive and An Ethical Code of Practice;
..............................-..Standard Operational Protocols;
..............................-..Procedures and Methodology for Obtaining Biometric and Bio-Morphometric Data from Specimens in their Natural Hypogean Habitats in Eastern Hercegovina, Bosnia & Hercegovina.
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............9.1.5.2...Part 2...Illustrated Field-Results Database, Together with any Relevant Implications for Habitat Conservation Management. 
.............................This contains Biometric data arising from the practical application of methodologies in Document 9.1.5.1. above.
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............9.1.5.3...Proteus anguinus anguinus (Laurenti 1768) :
.............................Potential Problems Associated with the Re-introduction (Translocation) of the Species into its Former Habitat Locations.
.............................Interim Guidelines & Procedures and Future Research Requirements.
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............9.1.5.4...Proteus anguinus anguinus (Laurenti 1768) :
............................Tagging and Tracking of Live Proteus in Their Natural Hypogean Habitats Using the Visible Implant Elastomer (VIE) Method, Eastern Hercegovina, Bosnia & Hercegovina.
............................- Methodology and its Practical Application.
............................- Observations on the Positions and Movements of the Tagged Proteus Specimens, together with any relevant Implications for Habitat Conservation Management.
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............9.1.5.5...Methodology for the Sampling of Hypogean Phytoplankton and Zooplankton Protozoa and Metazoa in Karst Ecosystems, together with the Results obtained from Samples submitted for
.............................Microbiological Examination.
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....9.2....Sub-Project Reports for Project Research Assistants :
......An Index of sub-Project Reports has been produced to enable Project Research Assistants and Project Workers to access the actual Reports more easily for reference purposes.
.......-.9.2.1..The Current Index of sub-Project Reports.
.......These are produced by the UK Project Co-ordinator Group as stand-alone, publication-ready, fully illustrated documents, issued in hard-copy form to the Project Co-ordinator Groups and permanently stored in both digital and hard-copy formats.
.......They present the core results of all observations and investigations obtained from individual habitat locations in a generic presentational format. They often contain cave surveys and karst hydrogeological charts.
........Many of these Reports are produced in Parts, and may be accompanied by additional data on a separate CD or DVD.
........Please also note that the Part 1. Documents of individual site-specific sub-Project Reports now incorporate the Site Citation information.
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....9.4....Other Internal Information Resources Available to Project Research Assistants for Promoting the "Proteus Project" in the realm of Public Education  :
.......9.4.1....The "Proteus Project's" established Annual "Stevo Čučković Memorial Lecture" in the Museum of Hercegovina, (Muzej Hercegovine), Trebinje, has provided a wonderful opportunity, not only to promote the Project itself,
but also for all those working in the Project to be able to connect directly with all levels of Hercegovinian Society, from the ordinary citizens to the Regional, National and International Press & Media.
This extremely popular Series of Lectures, each of which has a slightly different "theme of approach" and which are always delivered by Brian Lewarne, aided by others from the Local Project Co-ordinator Group and the Project's
Hungarian cave diving & technical support team, "Caudata Hungarian Cave Research", has largely outgrown the venue kindly provided free of charge by the Museum.
In 2011., the next in this series of free public lectures will again be held in the Museum but will also be repeated in other local or regional venues at about the same time to ensure that all those who are interested can have the opportunity to attend.
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The Muzej Hercegovine Website in the "Početna" section, describes our previous "Proteus Project" lectures delivered in August 2008 and September 2009. 
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The August 2008 Lecture was titled "The Private Life of the Human Fish", thus :-
"ČOVJEČIJA RIBICA PROJEKAT".  Napredak od 2007. i "PRIVATNI ŽIVOT ČOVJEČIJE RIBICE"
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U petak, 29. avgusta, 2008.godine, u Muzeju Hercegovine Trebinje održana je prezentacija pod naslovom „Privatni život čovječije ribice“.
Prezentacija je izvedena u saradnji „Devon Karst Research Society, Plymouth“ i Speleološkog društva „Zelena brda“ iz Trebinja, a u čast i sjećanje na velikog trebinjskog prirodnjaka
i istraživača čovječije ribice pok. Steva Čučkovića.
U toku prezentacije, koju je vodio Brian Lewarne, publika je mogla da uživa u ljepotama podzemnih voda i obilju života čija je jedinstvenost u činjenici da podzemne životinje možemo naći
samo na ograničenim područjima, a svaka za sebe ima ograničeno rasprostranjenje.
Tu je, prije svih, čuvena čovječija ribica (Proteus anguinus), zatim neke vrste slijepih rakušaca, roda Niphargus, kao i mnogi drugi."

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.The September 2009 Lecture was titled "Problems of Survival of the Human Fish", thus :-
"ČOVJEČIJA RIBICA PROJEKAT".  Napredak od 2008. i "PROBLEM PREŽIVLJAVANJA ČOVJEČIJE RIBICE"
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U srijedu, 2. septembra 2009.godine, u Muzeju Hercegovine Trebinje održana je prezentacija pod naslovom „Problem preživljavanja čovječije ribice“. Godišnje predavanje u Trebinju, posvećeno
sjećanju na prof. Steva Čučkovića i njegov speleo-biološki istraživački rad izvedeno je u saradnji Društva za istraživanje krša „Devon Karst Research Society, Plymouth“ i
Speleološkog društva „Zelena brda“ iz Trebinja.  U toku prezentacije, koju je vodio Brian Lewarne, stručnjak iz Društva za istraživanje krša "Devon" (Plymouth, Engleska, UK) predstavljeni su 
rezultati rada na projektu zaštite ovog podzemnog endema u poslednjih godinu dana.
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"Napredak u odnosu na proteklu godinu je očigledan u tehničkom smislu proučavanja čovječije ribice. Moramo biti jako pametni da bismo proučavali ovu komplikovanu vrstu u njenom prirodnom, takođe komplikovanom staništu. Zato smo počeli da koristimo kamere sa infra-crvenim zracima, tako da čovječija ribica uopšte i ne primjećuje naše prisustvo. Takođe je napravljen pomak u biometrijskom proučavanju, tako da sada određujemo težinu, dužinu i ostale parametre za svaki primjerak. Naša laboratorija je područje cijele Hercegovine, i u Republici Srpskoj i u BiH. Ipak, najveće probleme u opstanku čovječije ribice stvara sam čovjek svojim nepromišljenim djelovanjem u prirodi"  istakao je B. Lewarne u toku svog predavanja. Još je naveo da se nada da će u saradnji sa Speleološkim društvom "Zelena brda" iz Trebinja pokušati izdati knjigu, kako bi svi zainteresovani mogli saznati mnoge interesantne stvari o čovječijoj ribici, te da će u narednom periodu pokrenuti inicijativu za otvaranje svojevrsnog centra za proučavanje ove vrste. "U narednoj fazi ići ćemo na detaljnije proučavanje navika čovječije ribice, jer je ova prva bila bazirana na lokacije gdje se ova vrsta može pronaći i na broj primjeraka. Da bismo to uradili biće nam potrebna podrška lokalnih vlasti, koju smo i do sada imali".
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This lecture was given as a multimedia presentation in an experimental format simultaneously using 3 Digital Projectors + 3 Projector Screens. The event was a success and preparations are now underway to construct a large portable cinema-style
screen to support future multimedia presentations, not only in the Trebinje Museum, but also in venues across the "Proteus Project" area.
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Section 5a....GLOSSARY OF BIOLOGICAL TERMS & DEVELOPMENTAL-BIOLOGY TERMINOLOGY, together with GENERAL SPELEOBIOLOGICAL TERMS
used in the main text of the 5-part Webpages and in the text of attached documents :
[in alphabetical order]
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ANOXIC (syn. Hypoxic) :...Description of a habitat where there is a deficiency in oxygen for normal respiration by the resident species.
ANTERIOR :...At, in or towards the front end or front side. Forward of the rear end. [opposite = Posterior].
APICAL :...Of, pertaining to, located at, or constituting the apex.
BENTHIC :...The benthic zone is the ecological region at the lowest level of a body of water such as a lake, including the sediment surface and some sub-surface layers. Organisms living in this zone are called benthos.
....................They generally live in close relationship with the substrate bottom; many such organisms are permanently attached to the bottom.
....................The superficial layer of the soil lining the given body of water is an integral part of the benthic zone, as it influences greatly the biological activity which takes place there.
....................For comparison, the pelagic zone is the descriptive term for the ecological region above the benthos, including the water-column up to the surface.
....................Depending on the water-body, the benthic zone may include areas which are only a few inches below water, such as a stream or shallow pond.
BIOCENOLOGY :...The branch of biology dealing with the study of biological communities and the interactions among their members.
BIOCENOSIS :...Association of living creatures in a certain or specified area. Also, a self-sufficient community of naturally occurring organisms occupying and interacting within a specific biotope.
..........................A group of interacting organisms that live in a particular habitat and form an ecological community.  This is a particularly relevant phenomenom in cave habitats.
BIOME :...Habitat.
BRANCHIAL CHAMBER :...The chamber containing the gills or similar breathing organ.
CANNULA :...A tube inserted into a bodily cavity to drain fluid, tissue or to insert medication.
CAPILLARIES :...The small blood vessels that form an intricate network of the circulatory system throughout the body, for the interchange of various substances, such as oxygen and carbon dioxide between the blood and tissue cells.
CARAPACE :...A hard bony or chitinous outer covering, such as the covering of the head and thorax of a crustacean, usually enclosing the branchial chamber.
CATABOLISM :...The metabolic change of complex into simple molecules with the release of energy.
CAVERNICOLE :...A species which lives in a cave habitat and can complete its life-cycle there.
CHELA (pl. CHELAE) :...A pincer-like claw of arthropods as, for example, in crustaceans.
CHELATE :...Having, or characteristic of, a chela.
CIRCADIAN :...Of or pertaining to endogenous or exogenous processes that exhibit approximately 24 hour periodicity.
CLOACA :...The common cavity into which the intestinal, genital and urinary tracts open in vertebrates such as amphibians, fish, reptiles, birds and some primitive mammals.
CONSPECIFICS :...Of the same species.
DIFFERENTIATION :...The process of forming a specific type of cell. This occurs through a series of steps in which cells become increasingly restricted in the range of possible types that they can form.
DNA (deoxyribonucleic acid) :...(see also Gene expression.) Genes are made of DNA. DNA is comprised of four types of chemicals ('bases', abbreviated as A, T, G and C) linked to each other in a long chain.
......................Two strands of DNA are twined in a helix in which due to their complementary shape A in one strand pairs with T in the other, and G pairs with C.
......................The sequence of one strand (such as AATGCC...) is therefore complementary to the other (TTACGG...).
......................One DNA molecule is replicated to form two DNA molecules by separation of the strands, each of which is a template for synthesising a new complementary chain.
......................During 'transcription', one of the DNA strands is used as a template to form a complementary sequence of RNA, comprised of a chain of four types of chemicals (abbreviated A, U, G, C) closely related to those in DNA.
DNA SEQUENCING :...Techniques used to deduce the sequence of a DNA chain. Nowadays carried out using machines that in a single day can determine sequences that are many thousands in length.
DORSAL :...Pertaining or belonging to the back, or that part facing away from the ground. [ppposite = Ventral].
ECDYSIS :...The shedding of an outer integument or layer of skin, as by insects, crustaceans and snakes.
ENDEMIC :...In ecological terms, native or confined to a certain region; having a comparatively restricted distribution.
ENDOGEAN :....That which lies on the surface of the earth. Endogean species are sometimes Facultative Cave Dwellers.
ENZYME :....Most enzymes are proteins that due to their shape and chemical properties bind and promote chemical reactions of specific molecules, such as cleaving them or linking two molecules into one. Some enzymes are made of RNA or a combination of protein and RNA.
FACULTATIVE :...Not obligatory; Optional and thus capable of living in different environmental conditions.
GENE CLONING :...Techniques in which large amounts of a single gene are made by replicating the DNA molecule in large numbers of cells. Usually carried out in bacteria that carry special DNA molecules capable of being replicated, into which any other DNA sequence can be inserted.
GENE EXPRESSION :...The process by which the DNA sequence of genes is used to create the sequence of RNAs and proteins whose functions underlie or control the properties of cells.
.......................The switching on or off of a specific gene is controlled by binding of transcription factor proteins in the vicinity of that gene.
.......................During transcription, one of the strands of the DNA helix is used as a template to form a complementary sequence of RNA , comprised of a chain of four chemical 'bases' closely related to those in DNA.
.......................In some cases the RNA is then modified by precise removal of specific internal sequences (known as 'splicing').
.......................Some RNAs are parts of enzymes that promote specific chemical reactions. Messenger RNAs (mRNAs) are translated by a molecular machine (a ribosome, made of protein and RNA) that reads the RNA sequence to form the amino acid sequence of a protein.
.......................This involves a genetic code in which each of the 64 combinations of three bases (AUG GGC CAA ...) specifies the addition of one of the 20 different types of amino acid, or termination of the protein chain.
GENETICS, GENETIC SCREENS :...The study and identification of genes by detecting alterations in the structure or functioning of cells or organisms that have been caused by changes in the genome.
.......................Typically is carried out by using a chemical 'mutagen' that causes random changes in the DNA sequence, then screening many individuals for any changes in their development or adult anatomy.
.......................Once an altered organism is found, various techniques can be used to identify the mutant gene that is responsible for the change.
.......................Genetic screens have the important advantage that they specifically find genes based upon them having a function in a particular process.
.......................However, some genes are hard to find because two different genes making related proteins carry out the same function, and one of them is enough.
.......................During evolution, many genes have been multiplied to become families, and although some duplicated genes later diverge in function, others do not.
.......................Consequently, extra genome duplications, for example in many fishes compared with human, mouse and Xenopus tropicalis , can obscure some genes involved in development.
.......................Because different duplicated genes have diverged in function or been deleted during evolution, genetic screens in multiple species can identify different and overlapping subsets of the genes required for development.
GLUCIDIC  (adjective) :...characteristics of something containing any of various organic compounds that consist of or contain a carbohydrate. 
HYPOGEAN :..That which lies beneath the surface of the earth, including the soil, rocks and any air- or water-filled spaces within them. 
........................In the case of any body of water (fresh, salt or frozen), the Hypogean realm begins at the top of whatever medium lies underneath the water mass.
HYPORHEIC :..When studying the catchment as the source of solutes to a stream, the hyporheic zone is simply the sub-water surface interface between stream water and subsurface water in streambed sediments, effectively a membrane, often reactive and of no physical dimension.
........................When applied to caves, cave-streams / cave-rivers and their streambed sediment loads, this becomes a complex area to study.
........................Hyporheic zones, at whatever scale, are part of a continuum of stream-catchment connections between stream water and soil water, root-zone water, riparian water, quick-flow, delayed-flow, macropore flow and so on to including base flow.
........................Hyporheic zone respiration is often an important component of stream ecosystem metabolism and may be influenced by the magnitude of exchange between sub-water surface and water surface.
HYPOXIA :...Deficiency in available oxygen such that respiration of the resident species cannot be supported.
HYPOXIC (syn. Anoxic) :...Description of a habitat where there is a deficiency in oxygen for respiration by the resident species.
LARVA :...The stage in an animal's life cycle after it hatches from the egg. Larvae are typically very different in appearance to that of the adult. They are able to feed and move around but are usually unable to reproduce.
LIPIDS :....A fatty or waxy organic compound that is readily soluble in nonpolar solvent (e.g. ether) but not in polar solvent (e.g water). Its major biological functions involve energy storage, structural component of cell membrane, and cell signalling.
........................Examples of lipids are waxes, oils, sterols, cholesterol, fat-soluble vitamins, monoglycerides, diglycerides, triglycerides (fats), and phospholipids. 
MAXILLIPEDS :...The first pair or first three pairs of thoracic appendages in crustaceans, situated behing the maxillae and used for feeding.
METAMORPHOSIS :...An abrupt physical change from the larval to the adult form. 
MOLECULAR BIOLOGY :...Term used broadly to describe the field of studying biology at the molecular level, and the techniques involved such as gene cloning and manipulation.
NEOTENY:...The retention of larval features in the adult form of an animal, without an abrupt metamorphosis from the larval to the adult stages.
OBLIGATE :...(eg. Obligate Cave Dweller). Obliged without an option. Able to survive in only one kind of environment.
OXIC:...Describes conditions in a habitat where there is plenty of available oxygen for respiration.
POSTERIOR :...At, in or towards the rear end or rear side. To the Rear of the front end. [opposite = Anterior].
PROTEIN :...(See also Gene expression.) Proteins are made of a chain of amino acids. There are twenty types of amino acids, each with different chemical properties.
.......................The sequence of amino acids in a protein causes it to fold up into a particular shape, with chemical properties such as charged groups located at specific positions, and these underlie how it functions by interacting with other molecules. 
.......................Proteins are the main workers of the cell, and many assemble with each other to form molecular machines.
.......................For example, they enable chemical reactions (enzymes); form physical scaffolding between and within cells; transmit signals between and within cells; bind to DNA and switch genes on or off; transcribe DNA into RNA, and translate RNA into protein.
.......................The activity of some proteins is increased or decreased by attachment of specific chemicals, such as phosphate onto particular amino acids. The control of protein activity by these modifications is one of the ways that signals are transmitted within cells.
REVERSE GENETICS :...A range of techniques that enable going from an identified gene to finding its function (whereas genetics goes from detecting an altered function to identifying the underlying gene).
.......................Includes targeted deletion ('knockout') or alteration of the DNA sequence of a gene, and targeted inhibition of translation or degradation of specific RNAs.
.......................All of these techniques rely upon the specificity of interactions between complementary DNA or RNA sequences. Sophisticated techniques have been devised in fruitflies and mice in which a gene can be deleted in particular cell types and at a specific time.
.......................Similar techniques can be used to switch on a reporter gene in specific cells.
RNA, mRNA :...(See also Gene expression.) Ribonucleic acid. A chemical with a chain of bases (G,C,U,A) whose sequence is determined by a DNA template based upon the complementarity of double stranded nucleic acids.
.......................Some RNAs interact with specific proteins to form molecular machines, such as ribosomes. The sequence of a messenger RNA (mRNA) is read by ribosomes to specify the amino acid sequence of proteins.
ROSTRUM :...In crustaceans, a beak-like or snout-like projection on the front or top of the head.
SESSILE :......Sedentary.
SETA (pl. SETAE) :...A stiff hair, bristle or bristle-like growth or organ.
SOMITE :...A body segment.
SPERMATOPHORE :...A gelatinous jelly-like cone with a sperm cap, deposited by a male during courtship and picked up by the cloacal lips of the female.
STYGOBIONT  :...Fauna with stygobiotic adaptations to subterranean environments, (white, blind, low metabolism, infrequent reproduction, low fecundity, reduced fright/flight response, long time to first reproduction, and long life) are elements of a strategy
.......................for energy and matter efficiency suited to low risk/low payoff cave environments. Stygobionts also have small population sizes, and limited genetic diversity, vagility, predator defences, and tolerance of environmental change.
.......................These characteristics coupled with the insular nature of cave habitats places them at risk of extinction. This natural situation is exacerbated by anthropogenic disturbances to physical, chemical, and biological attributes of cave ecosystems, including surface recharge areas of aquifers.
.......................Such physical changes include altered hydrology, mining, and opening and closing of entrances. Chemical changes include organic enrichment and toxins. Extended longevity provides more time for bioaccumulation of toxins, but biomagnification is not indicated.
.......................Management of cave ecosystems requires control of activities in the upstream surface recharge zone for the cave aquifers. Controlling access to cave interiors is important, but effective management of recharge areas is absolutely essential.
STYGOBITE :...An aquatic Troglobite.
STYGOFAUNA :...Any fauna that live within groundwater systems, such as caves and aquifers, or more specifically small, aquatic groundwater invertebrates, though terrestrial air-breathing subterranean animals are also sometimes included.
............................Stygofauna can live within freshwater aquifers and within the pore spaces of limestone, calcrete or laterite, but are also found in marine caves and wells along coasts.
STYGOPHILE :...An aquatic Troglophile. Stygophiles (cave loving surface fauna) increase their population densities in organically enriched caves, and increase predation on the less robust stygobites.
STYGOXENE :...An aquatic Trogloxene.
THIGMOTACTISM :...Movement of an entire cell or organism in response to a direct tactile stimulus; also called "stereotactism".  [lit. a "cave lover".]
TROGLOBITE :...A cavernicole which shows morphological features (such as loss of eyes and surface pigment) which suggest that it has undergone a long history of cave habitation.
...........................[lit. a "cave dweller".]. An animal that lives in a cave and is unable to live outside of it. Troglobites usually have troglomorphic adaptions.
TROGLOMORPHY :...Adaptation to the Cave Environment. Troglomorphy is the process of becoming adapted to the special conditions of caves. The animals do this by :-
...................................-..Loss of pigmentation: [pigmentation is necessary as a protection against sunlight, especially the ultraviolet wavelengths. In caves this protection is obsolete.]
...................................-..Loss or atrophicaton of eyes and learning to navigate blind: [In caves the possibility to find ones way is esential. Possible alternatives are sound, tactile and smell.]
...................................-..The development of longer appendages such as legs, antennae etc.
TROGLOPHILE :...A cavernicole which is known to complete its whole life-cycle in non-cave habitats as well as in caves.
TROGLOXENE :...A cavernicole which spends only part of its life cycle in caves and returns periodically to the epigean domain for food. For example, these are creatures that use the cave for hibernation, or roost in the caves at night or during the day, but they need to go outside the cave for their food.
VENTRAL :...Pertaining or belonging to the underside (belly or abdomen), or that part turned towards the ground. [opposite = Dorsal]. 


Section 5b....TERMS USED IN THE TAXONOMIC CLASSIFICATION SYSTEM OF FAUNA :
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PHYLUM :   A taxonomic division of the animal kingdom, directly above a CLASS in size.
SUB-PHYLUM :
CLASS :   A taxonomic category ranking below a PHYLUM (animals) or a DIVISION (plants) and above an ORDER.
ORDER :   A taxonomic category of plants and animals ranking above the FAMILY and below the CLASS.
FAMILY :   A taxonomic category ranking below an ORDER and above a GENUS.
GENUS :   A taxonomic category ranking below a FAMILY and above a SPECIES, used in taxonomic nomenclature followed by a Latin adjective or epithet to form the name of a SPECIES.
SPECIES :   A fundamental category of taxonomic classification, ranking after GENUS and consisting of organisms capable of interbreeding.
SUB-SPECIES :

AMPHIBIA :   A CLASS of various cold-blooded, smooth-skinned, vertebrate organisms, such as frogs, toads and salamanders, characteristically hatching as aquatic larvae that breathe by means of gills and metamorphosing to an adult form having air-breathing lungs.
AMPHIPODA :  An ORDER of numerous small crustaceans.
ANNELIDA :   A PHYLUM, which includes the earthworms, leeches and other worms having cylindrical, segmented bodies.
ARTHROPODA :   A PHYLUM of numerous invertebrate organisms, which includes the insects, crustaceans, arachnids, millipedes and centipedes, all possessing a horny, segmented, external covering and jointed limbs.
ATYIDAE :   A FAMILY of crustaceans.
CHIROPTERA :   An ORDER of flying mammals, including Bats.
CHORDATA :   A PHYLUM containing numerous animals, which includes all vertebrates and certain marine and aquatic animals having a notochord.
COPEPODA :   A SUB-CLASS of numerous small marine and freshwater crustaceans, characteristically with "oar-like" or "paddle-shaped" legs. 
DECAPODA :   An ORDER of Crustaceans such as crabs, lobsters and shrimps, characteristically having 10 walking legs, in 5 pairs, each pair joined to a segment of the thorax.
CRUSTACEA :   A CLASS of various, though predominantly aquatic arthropods, including lobsters, crabs, shrimps and woodlice, having a characteristically segmented body, a chitinous exoskeleton and paired jointed limbs.
ISOPODA :   An ORDER of numerous crustaceans, which includes the woodlice and gribbles.
MAMMALIA :  A CLASS of vertebrate animals, distinguished by self-regulating body temperature, separation of oxygenated and de-oxygenated blood in the heart and, in the females, milk-producing mammae.
OSTRACODA :  An ORDER of various minute, chiefly freshwater crustaceans, having a bivalved carapace.
PISCES :  A taxonomic group that includes the cartilaginous and bony fishes.
POLYCHAETA :   A CLASS of marine worms, including the lugworms, bristleworms and ragworms, having paired, flattened, bristle-tipped organs of locomotion.
PROTEIDAE :   A FAMILY of Amphibians.
SERPULIDAE :   A FAMILY of Polychaete worms, especially of the GENUS Serpula, that live in specially secreted calcareous tubes attached to stone.
SYNCARIDA :   An ORDER of crustaceans.
URODELA :   An ORDER of Amphibia characterised by a long body and a tail and includes newts and salamanders.
VERTEBRATA :   A SUB-PHYLUM and primary division of the PHYLUM Chordata, which includes the fishes, amphibians, reptiles, birds and mammals, all of which are characterised by a segmented bony or cartilaginous spinal column.
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