| 1. |
- Friedman, Ran
(författare)
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Proton Transfer on the Molecular Surface of Proteins and Model Systems
- 2009
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Ingår i: Israel Journal of Chemistry. - 0021-2148. ; 49:2, s. 149-153
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Tidskriftsartikel (refereegranskat)abstract
- Proton transfer (PT) reactions take place oil the molecular Surface of proteins, membranes, ionic polymers, and other molecules. The rates of the reactions can be followed experimentally, while the atomistic details can be elucidated by molecular modeling. This manuscript gives a brief overview of the use of computer simulations and molecular modeling, in conjuction with experiments, to study PT reactions oil the surface of solvated molecules. An integrative approach is discussed, where molecular dynamics simulations are performed with a protein, and quantum-mechanics-based calculations are performed oil a small molecule. The simulation results allow the identification of the necessary conditions that yield PT reactions oil the molecular surface. The reactions are efficient when they involve a donor and acceptor located a few A apart and under the influence of a negative electrostatic field. In proton-pumping proteins, it is possible to identify such conditions a priori and locate proton-attracting antenna domains without the need to mutate each potential donor and acceptor. Based on density functional theory calculations, the arrangement of water molecules that interconnect the donor and acceptor moieties is suggested as the rate-limiting step for proton transfer on the molecular surface.
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| 2. |
- Gross, Elisabeth, et al.
(författare)
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Allelochemical interactions among aquatic primary producers
- 2012. - 1
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Ingår i: Chemical Ecology in Aquatic Systems. - Oxford : Oxford University Press. - 9780199583102 ; , s. 196-209
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Bokkapitel (refereegranskat)abstract
- Allelopathy is the study of biochemically-driven organismic interactions among primary producers. One organism affects others by the release of allelochemicals that are transported to the target cells, and cause a negative (or positive) response. Most aquatic allelochemicals are amphiphilic, thus have a sufficient solubility in the water, and at the same time can bind to and penetrate lipophilic cell membranes. Allelopathic interactions are not static but are influenced by variable environmental stressors. Resource availability can both affect the production and release of allelochemicals by the producing organism, but also influence the susceptibility of the target cells. The biosynthesis and excretion of allelochemicals might involve costs for the producing organism, and these costs will only be balanced if a net gain, i.e. better resource availability such as space or nutrients or secondary benefits, e.g. predator deterrence, are achieved. Allelopathic effects against cooccurring organisms might lead to coevolutionary responses, i.e. a lower susceptibility of target cells or to more advanced allelochemicals. Target organisms from different habitats might be more susceptible, especially if they are not acquainted with the allelochemicals. The transfer of laboratory results on allelopathy to realistic field conditions is complex, and might in the long run benefit from advanced analytical and molecular methods identifying specific target cell responses in situ.
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| 3. |
- Härlin, Mikael, et al.
(författare)
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Cladistic analysis of the eureptantic nemerteans (Nemertea : Hoplonemertea)
- 1995
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Ingår i: Invertebrate taxonomy. - 0818-0164 .- 1445-4572. ; 9:6, s. 1211-1229
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Tidskriftsartikel (refereegranskat)abstract
- A phylogeny for the 34 species we consider well enough described in the suborder Eureptantia (phylum Nemertea) is inferred by cladistic analysis based on 38 morphological characters. The phylogenetic reconstruction indicates that many previously recognised genera and families are paraphyletic. These findings are discussed and compared with earlier classifications. We also present an identification key to the species based on the cladistic analysis.
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| 4. |
- Härlin, Mikael
(författare)
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Classification nomenclature
- 2004
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Ingår i: McGraw-Hill yearbook of science and technology. - 0076-2016. ; , s. 52-54
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 5. |
- Härlin, Mikael
(författare)
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Definitions and phylogenetic nomenclature
- 2005
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Ingår i: Proceedings of the California Academy of Sciences. ; , s. 216-224
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Konferensbidrag (refereegranskat)abstract
- Recent developments in biological nomenclature suggest advantages of phylogenetic alternatives to more traditional Linnaean approaches. My aim is to discuss some fundamental aspects underlying biological nomenclature in general and phylogenetic nomenclature in particular. A basic assumption, in both traditional and phylogenetic nomenclature, is that taxon names can and should be defined. From the ontological view of individuality I question this view and argue that taxon names only refer since no defining properties are involved for particular clades. Even if we accept the idea that a taxon is a natural kind with a historical essence, and thus has defining properties, I see problems of definitions from an epistemological and inferential point of view. Our conceptualization of phylogeny is dependent on our hypotheses. Therefore, definitions based on discarded hypotheses are problematic. Instead, each new and accepted hypothesis should form the basis of our conceptualization. Another theme in this paper is what should count as the same taxon under different hypotheses. Can a phylogenetic definition guarantee that a name always refers to the same taxon under different hypotheses? I argue that this is questionable. I conclude by suggesting that we need to rethink the role of definition, sameness, and stability in nomenclature. Rethinking these concepts, I believe, will shed some new light on biological nomenclature. My conclusions strongly favor a phylogenetic approach to nomenclature but also suggest that we, besides some practical problems, still have many interesting theoretical and philosophical aspects to take into account.
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| 6. |
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| 7. |
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| 8. |
- Härlin, Mikael
(författare)
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On the relationship between content, ancestor, and ancestry in phylogenetic nomenclature
- 2003
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Ingår i: Cladistics. - 0748-3007 .- 1096-0031. ; 19:2, s. 144-147
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Tidskriftsartikel (refereegranskat)abstract
- In this paper I draw attention to the concepts of content and ancestry in phylogenetic nomenclature. I argue that these concepts are tightly linked and that they cannot be separated as suggested by Bryant and Cantino [Biol. Rev. 77 (2002) 39] in their recent response to a critique of phylogenetic nomenclature. In addition, I argue that the basic assumption in phylogenetic nomenclature that a taxon-name always refers to the same ancestor or ancestry is questionable.
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| 9. |
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| 10. |
- Härlin, Mikael
(författare)
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Taxonomic names and phylogenetic trees
- 1998
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 27:4, s. 381-390
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Tidskriftsartikel (refereegranskat)abstract
- This paper addresses the issue of philosophy of names within the context of biological taxonomy, more specifically how names refer. By contrasting two philosophies of names, one that is based on the idea that names can be defined and one that they cannot be defined, I point out some advantages of the latter within phylogenetic systematics. Due to the changing nature of phylogenetic hypotheses, the former approach tends to rob taxonomy from its unique communicative value since a name that is defined refers to whatever fits the definition. This is particularly troublesome should the hypothesis of phylogenetic relationship change. I argue that, should we decide to accept a new phylogenetic hypothesis, it is also likely that our view of what to name may change. A system where names only refer acknowledge this, and accordingly leaves it open whether to keep a name (and accept the way it refers in the new hypothesis) or discard a name and introduce new names for the parts of the tree that we find scientifically interesting. One of the main differences between a phylogenetic system of definition (PSD) and a phylogenetic system of reference (PSR) is that the former is governed by laws of language while the latter by communicative needs of taxonomists. Thus, a PSR tends to give primacy to phylogenetic trees rather than phylogenetic definitions of names should our views of which phylogenetic hypothesis to accept change.
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