Taxonomic indexing--extending the role of taxonomy

Taxonomic indexing refers to a new array of taxonomically intelligent network services that use nomenclatural principles and elements of expert taxonomic knowledge to manage information about organisms. Taxonomic indexing was introduced to help manage the increasing amounts of digital information about biology. It has been designed to form a near basal layer in a layered cyberinfrastructure that deals with biological information. Taxonomic Indexing accommodates the special problems of using names of organisms to index biological material. It links alternative names for the same entity (reconciliation), and distinguishes between uses of the same name for different entities (disambiguation), and names are placed within an indefinite number of hierarchical schemes. In order to access all information on all organisms, Taxonomic indexing must be able to call on a registry of all names in all forms for all organisms. NameBank has been developed to meet that need. Taxonomic indexing is an area of informatics that overlaps with taxonomy, is dependent on the expert input of taxonomists, and reveals the relevance of the discipline to a wide audience.

Incendies et peuplements à Pinus mugo Turra dans les Alpes occidentales (Val de Suse, Italie) durant la transition Tardiglaciaire–Holocène : une zone refuge évidente

In western Italian Alps, small distinct populations of Pinus mugo Turra raise some questions concerning its ecological status and dynamics in the occidental Alps. This note present new palaeobotanical data based on cone imprints of Pinus mugo, identified in travertine systems located in the Val di Susa and dated back to the Late Dryas (11506+/-66 BP) and the Early Holocene (10145+/-225 et 9475+/-670 BP). Heliophilous species and charcoal fragments were also identified, testifying to the oldness of wildfires in this region. The data support the hypothesis that this zone was a refuge area of this pine during the last glaciation. Here we discuss about the postglacial dynamics of the Pinus mugo in the occidental Alps.

The cribriform approach to the retrieval of palynological evidence from the turbinates of murder victims

As well as being the route for gaseous exchange, the nasal passages protect the lungs from debris and fine particulates inhaled during breathing. Foreign particles are trapped by mucus produced by membranes that line the upper respiratory tract. Even when a corpse has skeletonised, particles can be retrieved from the surface of nasal bones and may provide valuable evidence of events leading up to, and including the death of a murder victim. In this paper, we give a brief anatomical description of the parts of the nasal passages that yield most information, the methods for extraction of the evidence, and brief description of a case where such evidence has proved useful.

Hypericum pollen determines the presence of burglars at the scene of a crime: an example of forensic palynology

Two male intruders entered a house in which the sole female occupant slept having left the back door unlocked for the return of her live-in boyfriend. She awoke and saw strangers in her bedroom. The intruders ran off, one leaving a jacket behind on the kitchen floor. One of the intruders subsequently returned to recover his jacket, but in his rush to leave the house he brushed against a flowering Hypericum bush growing just outside the back door. A suspect was arrested later that day and charged with indecent assault on a female and burglary, but denied any involvement and refused to name any associate. A day following the offence the suspect's clothes were taken for forensic examination. Pollen analysis of selected parts of his clothing showed that his track pants contained 14% Hypericum pollen, denim jacket 24%, and polo shirt 27.5%. Traces of Hypericum pollen occurred on other items. Most of these pollen grains still had their cell contents preserved and were on the clothing in clumps consistent with having recently been collected by the clothing and not having been aerially dispersed. The pollen from the Hypericum bush was identical in colour, shape, development, and size range to the pollen from the clothing. The clothes had so much Hypericum pollen on them that they had to have been in direct and intimate contact with a flowering bush. Pollen evidence is by its nature circumstantial and often cannot be used on its own to convict, or more strictly to determine the truth. The suspect may have been in contact with Hypericum elsewhere, but detailed investigations indicated that this was unlikely. In 30 years of New Zealand forensic work Hypericum had only ever been found on clothing in trace amounts. This is but one way in which forensic palynology can assist law enforcement agencies to determine the history behind a criminal action, and demonstrates that forensic palynology should be considered as an integral part of any criminal investigation.

An unusual appearance of a common pollen type indicates the scene of the crime

Forensic palynology is a useful source of evidence in cases of violence committed in the open. A young girl was grabbed off the street, threatened and brutally raped. During the investigation the exact place of the rape became an issue. Growing around the scene identified by the victim were shrubs identified as Coprosma, a common New Zealand plant and one that produces abundant, easily wind-dispersed pollen. Abundant Coprosma pollen was found at the scene. The pollen were unusual in that the site was very damp, encouraging fungal growth, and fungal hyphae had penetrated the pores of many of the tricolporate pollen grains. Some grains had fungal spores inside. Coprosma pollen identical in preservational characteristics and morphology to those from the scene and containing fungal hyphae and spores were found in considerable numbers on the victim's clothes. This and rare Coprosma pollen grains and fungal remains recovered from vaginal swabs provided evidence that she had been at the scene where she claimed to have been raped. The diversity of pollen types recovered from the clothing in this case provides further evidence of the usefulness of clothing in picking up and retaining pollen from crime scenes and that obvious staining on clothes is not a pre-requisite for good pollen recovery. It also demonstrates the importance of collecting samples from different parts of the same garment in order to get a full picture of events since different parts of a garment can come into contact with different plants or different parts of the ground in a scuffle. It is also demonstrated that significant evidential material can be collected from the body, in this case from vaginal swabs from the victim. Forensic palynology should be considered in every case of violent assault, especially, but not exclusively, when having occurred in an open area subject to extensive pollen settlement.

A molecular identification system for grasses: a novel technology for forensic botany

Our present inability to rapidly, accurately and cost-effectively identify trace botanical evidence remains the major impediment to the routine application of forensic botany. Grasses are amongst the most likely plant species encountered as forensic trace evidence and have the potential to provide links between crime scenes and individuals or other vital crime scene information. We are designing a molecular DNA-based identification system for grasses consisting of several PCR assays that, like a traditional morphological taxonomic key, provide criteria that progressively identify an unknown grass sample to a given taxonomic rank. In a prior study of DNA sequences across 20 phylogenetically representative grass species, we identified a series of potentially informative indels in the grass mitochondrial genome. In this study we designed and tested five PCR assays spanning these indels and assessed the feasibility of these assays to aid identification of unknown grass samples. We confirmed that for our control set of 20 samples, on which the design of the PCR assays was based, the five primer combinations produced the expected results. Using these PCR assays in a 'blind test', we were able to identify 25 unknown grass samples with some restrictions. Species belonging to genera represented in our control set were all correctly identified to genus with one exception. Similarly, genera belonging to tribes in the control set were correctly identified to the tribal level. Finally, for those samples for which neither the tribal or genus specific PCR assays were designed, we could confidently exclude these samples from belonging to certain tribes and genera. The results confirmed the utility of the PCR assays and the feasibility of developing a robust full-scale usable grass identification system for forensic purposes.

Forensic botany: using plant evidence to aid in forensic death investigation

Forensic botany is still an under-utilized resource in forensic casework, although it has been used on occasion. It is an area of specialty science that could include traditional botanical classification of species, DNA, or materials evidence (trace and transfer evidence), crime mapping or geo-sourcing, all dependent on the specific case application under consideration. Critical to the evaluation of plant evidence is careful collection, documentation, and preservation for later scientific analysis. This article reviews proper procedures and recent cases where botanical evidence played a role in establishing either manner or time of death. Plant evidence can be useful for determining if a death was due to an accident, suicide, or homicide, or what time of year burial may have taken place. In addition, plant evidence can be used to determine if a crime scene is a primary or secondary scene and to locate missing bodies.

European plant science: a field of opportunities

Plants have a pivotal role in eco- and agricultural systems. Genomics is driving a rapid expansion of our understanding of how genes, individually and in networks, determine plant function. Technological developments in breeding and genomics are providing strategies to translate this knowledge into crop improvement. The possibilities range from improvement of existing crops and the systematic use of natural diversity through to the domestication of completely new species. As examples of possible goals, it is discussed how profiling of composition will integrate plant breeding and agronomic practice with emerging knowledge about nutrition and health, how improved and novel crops will contribute to the creation of new bio-based economies revolving around plant products, and how advances in our knowledge about plant-environment and plant-pathogen interactions will provide novel strategies to stabilize agricultural yield in a fluctuating environment and contribute to integrated approaches in which modern agriculture is carried out in concert with the environment. In addition, knowledge generated by plant science will be needed to monitor, understand, and cope with climate change and its impact on agriculture and ecosystems. Realization of these goals will require close interactions with related disciplines including agronomy and ecology. Further, it will be important to continue and deepen open support for research in the developing world.

Aloe Vera: A Valuable Ingredient for the Food, Pharmaceutical and Cosmetic Industries—A Review

Scientific investigations on Aloe vera have gained more attention over the last several decades due to its reputable medicinal properties. Some publications have appeared in reputable Scientific Journals that have made appreciable contributions to the discovery of the functions and utilizations of Aloe--"nature's gift." Chemical analysis reveals that Aloe vera contains various carbohydrate polymers, notably glucomannans, along with a range of other organic and inorganic components. Although many physiological properties of Aloe vera have been described, it still remains uncertain as to which of the component(s) is responsible for these physiological properties. Further research needs to be done to unravel the myth surrounding the biological activities and the functional properties of A. vera. Appropriate processing techniques should be employed during the stabilization of the gel in order to affect and extend its field of utilization.

Impetus for sowing and the beginning of agriculture: ground collecting of wild cereals

The Agricultural Revolution in Western Asia, which took place some 11,000 years ago, was a turning point in human history [Childe, V. G. (1952) New Light on the Most Ancient East (Routledge & Kegan Paul, London)]. In investigating the cultural processes that could have led from gathering to intentional cultivation, various authors have discussed and tested wild cereal harvesting techniques. Some argue that Near Eastern foragers gathered grains by means of sickle harvesting, uprooting, plucking (hand stripping), or beating into baskets [Hillman, G. C. & Davies, M. S. (1999) in Prehistory of Agriculture: New Experimental and Ethnographic Approaches, ed. Anderson, P. (The Institute of Archaeology, University of California, Los Angeles), pp. 70-102]. During systematic experiments, we found that archaeobotanical data from regional Neolithic sites support ground collection of grains by early hunter-gatherers. Ground collecting suits the natural shattering of wild species that ripen and drop grains at the beginning of summer. We show that continual collection off the ground from May to October would have provided surplus grains for deliberate sowing in more desirable fields, and facilitate the transition to intentional cultivation. Because ground gathering enabled collectors to observe that fallen seeds are responsible for the growth of new plants in late fall, they became aware of the profitability of sowing their surplus seeds for next year's food. Ground collecting of wild barley and wild wheat may comprise the missing link between seed collecting by hunter-gatherers and cereal harvesting by early farmers.

[Diversity of medicinal plant species grown in the greenhouse of Kaunas Botanical Garden of Vytautas Magnus University]

Collections of ornamental plants, as the object of the research, have been accumulated since 1924 in Kaunas Botanical Garden of Vytautas Magnus University. Plants are grown in six sections of the greenhouse following the geographic-climatic principle. It is also used for educational purposes in order to introduce students and public with plant world and the variety of its species. According to the data of taxonomical analysis made in 2002-2004 it was estimated that in the sections of the greenhouse there are grown 110 species of medicinal plants belonging to 83 genera, 56 families, 7 subclasses, 6 classes and to 3 divisions. The division Magnoliophyta is the largest of number of taxons: 2 classes, 7 subclasses, 50 families, 77 genus and 104 species. The number of plant species in 56 families of medicinal plants differs: the biggest (5-8 species) is in two families, the lowest (1-2 species)--in 41 and medium (3-4 species) in 13 families. Medicinal plants make 15% of all plant species grown in the greenhouse. According to the using these plants are: oil, aromatic, dye-stuff, ornamental, resiniferous, food, timber, melliferous, fibrous, spice, saponin, stimulating, tannin-bearing and technical.

Towering tribute to botany

One of the world's greatest plant collections has won a top heritage award at a time when it is highlighting with a tree-top walkway the need to study the forest canopy which is one of the most crucial but least understood habitats.

Rainforest composition and histories of human disturbance in Solomon Islands

On the basis of a Solomon Islands case study, we report that tropical rainforests hitherto perceived as untouched, pristine, virgin, etc., are actually sites of former settlement, extensive forest clearance, and irrigated/swidden agriculture. An unusually wide range of sources--rainforest ecology, forest classification and mapping, ethnobotany, land-use history, oral traditions, ethnographic and archaeological observations--supports our conclusions. These observations have bearings for contemporary perspectives on scenarios for rainforest regeneration after logging. They also force a revision of certain assumptions concerning Melanesian prehistory and historical demography, and indicate that interdisciplinary links between botany, archaeology and social anthropology are needed to achieve a better appreciation of rainforest dynamics.

The contribution of plant biology to the concept of virus (1886-1917)

Between 1860 and 1880 the so-called "theory of the infective germ", which stated in final way that every infectious disease was produced by a living pathogen agent, achieved great consent. The criteria of determining the presence of infectious pathogens (fungi, bacteria, protozoa) were established by "Koch's postulate", a set of experimental procedures conceived for isolating and determining single pathogens. In the last quarter of the 19th century became however evident that the agents of severe infectious diseases could not be identified through the "postulates". These agents could not be seen in light microscopy nor cultured in vitro but could pass through the thin pores of filters which hold back cellular micro-organisms. This last characteristic became a selective method to recognise these peculiar agents, from then named "filterable viruses". Most microbiologists considered the filterable viruses as living micro-organisms because of their extraordinary capacity of in vivo proliferation, and the impossibility of pointing out their structures was due to limits of the experimental techniques. Between the end of the 19th century and 1917, four plant biologists suggested that the filterable viruses were complex chemical substances rather than cellular microorganisms. Their contribution, not appreciated by the contemporary colleagues, laid the foundation of the modern concept of virus.

Exploring the city of Rubble: botanical fieldwork in bombed cities in Germany after World War II

In recent decades, the flora and fuana of cities have become the objects of the inter-disciplinary research field of urban ecology and related policies of urban nature conservation. Although the term "urban ecology" is quite recent, it is argued in this paper that the formation of urban nature as an object of ecological knowledge has a much longer history. For example, in Germany, after World War II, the large rubble areas that existed in all bombed cities soon became important research fields for botanists studying plant migration and vegetation development in the context of the city. This paper uses the case of these botanical research activities to shed light on the historical origins of ecological thinking about nature in the city. Drawing upon a socio-spatial approach to science and practice, the paper explores the interaction between the social and material order of the city and the formation of ecological knowledge. As will be shown, botanists studying the rubble areas created various representations (e.g., lists, statistical tabulations, maps) of urban space that contributed to the transformation of the cultural and political meaning of urban wastelands. At the same time, it will be argued, urban wastelands were practically appropriated as scientific workplaces in which these representations were locally crafted. What later became the science and politics of urban ecology is to a large extent the outcome of this mutual shaping of knowledge and urban space in the post-Second World War period.

[Neotropical plant morphology]

An analysis on plant morphology and the sources that are important to the morphologic interpretations is done. An additional analysis is presented on all published papers in this subject by the Revista de Biología Tropical since its foundation, as well as its contribution to the plant morphology development in the neotropics.