Hovenkamp's ostracized vicariance analysis: testing new methods of historical biogeography

All methods currently employed in cladistic biogeography usually give contrasting results and are theoretically disputed. In two overlooked papers, Hovenkamp (1997, 2001 ) strongly criticized methods currently used by biogeographers and proposed two other methods. However, his criticisms have remained unanswered and his methods rarely applied. I used three different data sets to show the superiority of Hovenkamp's methods. Both methods proposed by Hovenkamp do not suffer from the unrealistic assumptions that underlie other methods commonly used in cladistic biogeography. The method proposed in 2001 is more powerful than the previous method published in 1997, because it does not use a priori assumptions about the areas involved. However, the method proposed in 1997 may be a valid alternative for large data sets.
© The Willi Hennig Society 2007.     

Extreme hydrologic banding in a large-river Floodplain, California, U.S.A.

Where tributaries meet, certain conditions of flow and topography often result in incomplete mixing and the formation of spatially and temporally persistent plumes or bands. Yolo Bypass, the primary floodplain of the lower Sacramento River (California, USA), provides an extreme example of this effect. Inspection of recent and historical aerial photographs revealed that the four major tributaries of Yolo Bypass typically do not substantially mix laterally within the floodplain. The phenomenon is notable in the number of tributaries involved (4), the distance over which the bands remain distinct (>61 km), and the persistence of the bands despite channel constrictions and long cross-wind fetch. This effect demonstrates the importance of lateral variability during floodplain flow events, including transport and distribution of chemical constituents, and habitat for fish and other organisms that use floodplains as migration corridors and rearing areas. Handling editor: S. M. Thomaz     

Rha1, a new mutant of Arabidopsis disturbed in root slanting,gravitropism and auxin physiology

A new Arabidopsis mutant is characterized (rha1) that shows, in the roots, reduced right-handed slanting, reduced gravitropism and resistance to 2,4-D, TIBA, NPA and ethylene. It also shows reduced length in the shoot and root, reduced number of lateral roots and shorter siliques. The gene was cloned through TAIL-PCR and resulted in a HSF. Because none of the known gravitropic and auxinic mutants result from damage in a HSF, rha1 seems to belong to a new class of this group of mutants. Quantitative PCR analysis showed that the expression of the gene is increased by heat and cold shock, and by presence of 2,4-D in the media. Study of the expression through the GUS reporter gene revealed increased expression in clinostated and gravistimulated plants, but only in adult tissues, and not in the apical meristems of shoots and roots.Key words: auxin, ethylene, slanting, gravitropism, HSFsArabidopsis primary roots, and especially those from some ecotypes (Ws, Landsberg), when grown on an agar dish, tilted on the vertical, show a wavy pattern, and a clear slanting towards a direction that has been considered the right-hand.^1–4 In the case of the mutant rha1, the right-handed slanting is notably reduced, its primary roots growing partly to the right-hand, partly straight down and partly to the left-hand, even though a slight preference for the right-hand is apparent.In addition, its roots show resistance to the inhibitory action of the auxin 2,4-D, ethylene (ACC), and the auxin transport inhibitors TIBA and NPA. These characteristics qualify the mutant as an auxinic one, and therefore a connection between the reduced slanting and the auxinic disturbances could be imagined. It is not known, however, what controls the slanting process itself, even though it appears as the consequence of a chiral circumnutational process. As reported,⁴ it seems the result of a chiral circumnutation with preference for the right-hand, transformed in a lateral slanting movement, because of the impact of the helix with the hard agar surface. This process results in the formation of waves, when the circumnutation helix impactig the agar reverses direction at every half turn, or the formation of large loops and strict loops (coils) when there is no reversion. The latter case seems to be a consequence of the fact that gravity is no longer “felt”. This has been previously noted in some mutants, or sometimes in old roots.rha1 is not the only mutant known to show reduction or increase of slanting, because other mutants were reported by Rutherford and Masson,³ and subsequent publications from the same group. Almost all show an increase of slant, with the exception of rhd3 and its alleles that show a complete suppression of the process.⁵ The mutated gene in rha1 was cloned through TAIL-PCR and shown to be a HSF. No other auxinic mutant, among those for which the gene was cloned, is known to be mutated in a HSF.HSFs, that are characteristically involved in the activation of the HSPs (heat shock proteins), which protect the cells from damage arising from high temperature and other stresses, have been shown to be involved also in different processes.^6,7 Hence, also in the case of rha1, we can well imagine other different functions, beside that of counteracting the heat shock. In particular, since the connection with auxin regulated processes is evident, we can suppose that the action could be on the PP2A phosphatase, as in the case of the rcn1 mutant, or of the human HSF2. The RCN1 protein corresponds to one unit of the PP2A,⁸ and the HSF2⁹ has been shown to substitute itself for the C subunit and alter the function of the phosphatase (Fig. 1). Experiments directed to see if a heat shock can modify the slanting of the roots in the wild-type and rha1, gave negative results, even though these experiments will need to be repeated under more widely ranging conditions. These results seem to indicate that the mechanism which induces asymmetric growth in roots is complex, and it is not controlled by a single gene.Open in a separate windowFigure 1Model proposed for the regulation of the PP2A activity by the RHA1 protein. (modified after Hong and Sarge, 1999).On the other hand, another puzzling characteristic of rha1 is the fact that its roots are resistant only to the auxin 2,4-D, and not to NAA and IAA. Differences in the response of the primary roots to different auxins have already been reported, and it was suggested that the response to NAA should be different, because this substance can penetrate passively the cell membranes.¹⁰ In the case of rha1, however, it seems that IAA can also penetrate the cells passively. This is in line with the chemiosmotic hypothesis,¹¹ but seems in contrast with the previous supposition. The resistance to ethylene, however, could indicate that the reduced inhibitory effect of 2,4-D is a consequence of the ethylene production induced by the synthetic auxin. On the other hand, the resistance to the auxin transport inhibitors TIBA and NPA, cannot be explained so easily. Possibly, in the mutant rha1, there is a reduced level of receptors for the considered substances.Using semiquantitative PCR analysis it was shown that rha1 retains the function of a HSF, the gene being clearly upregulated by heat and cold stress, and also by 2,4-D, but not by rotation on a clinostat or gravistimulation. The upregulation of the expression by 2,4-D was confirmed by a study of GUS expression in a transformed rha1, and with this technique the effects of gravity and simulated microgravity appeared clearly stimulatory too. No GUS expression however was apparent in the shoot and root meristems, and consequently we propose that the gene does not influence the first part of the graviresponse, but possibly the general transport of auxin through the plant.Thus, the mutant seems to be disturbed in root gravitropism, as well as in responses to the auxines and circumnutation. However not in the general circumnutation process, but in its chiral aspect, which is the cause of the slanting to the right-hand. Gravitropism, circumnutation and auxin physiology, thus, seem to be in some way connected in a complex integrated process, that, hopefully, will be gradually revealed in all its different aspects, through the future efforts of plant scientists.     

α-Ketoglutarate abrogates the nuclear localization of HIF-1α in aluminum-exposed hepatocytes

Aluminum (Al), a known environmental pollutant, has been linked to numerous pathologies such as Alzheimer's disease and anaemia. In this study, we show that α-ketoglutarate (KG) mitigates the Al-mediated nuclear accumulation of hypoxia inducible factor-1α (HIF-1α) in cultured human hepatocytes (HepG2). The nuclear localization of HIF-1α appeared to be triggered by the Al-induced perturbation of prolyl hydroxylase 2 (PHD2). This enzyme was markedly diminished in the Al-challenged hepatocytes. The fate of PHD2 and HIF-1α was intricately linked to the mitochondrial dysfunction observed during Al stress. BN-PAGE, immunoblot, and HPLC revealed that the loss of α-ketoglutarate dehydrogenase (KGDH) and succinate dehydrogenase (SDH) activities were coupled to the accumulation of succinate. However, the treatment of the Al-stressed cells with KG recovered the activity and expression of KGDH, SDH, and PHD2 with a concomitant decrease in the levels of HIF-1α in the nucleus. Taken together, these data indicate that the homeostasis of KG plays a pivotal role in aerobic and anaerobic respiration.     

The Cosmic Silence experiment: on the putative adaptive role of environmental ionizing radiation

Previously we reported that yeast and Chinese hamster V79 cells cultured under reduced levels of background environmental ionizing radiation show enhanced susceptibility to damage caused by acute doses of genotoxic agents. Reduction of environmental radiation dose rate was achieved by setting up an underground laboratory at Laboratori Nazionali del Gran Sasso, central Italy. We now report on the extension of our studies to a human cell line. Human lymphoblastoid TK6 cells were maintained under identical in vitro culture conditions for six continuous months, at different environmental ionizing radiation levels. Compared to “reference” environmental radiation conditions, we found that cells cultured in the underground laboratories were more sensitive to acute exposures to radiation, as measured both at the level of DNA damage and oxidative metabolism. Our results are compatible with the hypothesis that ultra-low dose rate ionizing radiation, i.e. environmental radiation, may act as a conditioning agent in the radiation-induced adaptive response.     

Tuning towards tomorrow? Common nightingales Luscinia megarhynchos change and increase their song repertoires from the first to the second breeding season

In many oscines, song repertoire size correlates with male quality and female mate choice, and can vary with age. In a cross-sectional field study in common nightingales Luscinia megarhynchos , one y old birds had substantially smaller repertoires than did older ones. In laboratory experiments males can acquire new song types during this period. This longitudinal field study therefore investigates whether individual nightingales increase their repertoires from the first to the second breeding season. We report a striking repertoire turnover, with an average overall increase of 24% of the first season's repertoire, resulting from added and dropped song types (54% and 30%, respectively). The number of added song types correlated positively with the size of the first season's repertoire. These results are consistent with the notion that repertoire size in nightingales correlates with male quality, although the overlap between repertoire sizes of first and second season birds makes it impossible to discriminate age based solely on repertoire size. Comparing the number of song types an individual sang in both seasons ('permanent song types') revealed a lower overlap than reported for subsequent seasons. The frequencies with which these were sung in the first season were less predictive of how often they were sung in the second season than was the case between later years. This drastic repertoire turnover from the first to the second season may be a selective process in response to the local song types, constrained by genetic makeup and shaped by early experience.     

The proteoglycan region of the tumor-associated carbonic anhydrase isoform IX acts as anintrinsic buffer optimizing CO2 hydration at acidic pH values characteristic of solid tumors

The enzymatic activities of carbonic anhydrase (CA, EC 4.2.1.1) isozymes CA I, II, IX (catalytic domain (cdCA IX) and catalytic domain plus proteoglycan, flCA IX), XII and XIV were investigated as a function of pH for the CO₂ hydration to bicarbonate and a proton. The cytosolic isoforms CA I and II as well as the catalytic domain of CA IX, together with the transmembrane isoforms CA XII and XIV showed sigmoid pH dependencies of k_cat/K_M, with a pK_a of 6.90–7.10, showing thus optimal catalytic efficiency around pH 7. The full length CA IX had a similar shape of the pH dependency curve but with a pK_a of 6.49, having thus maximal catalytic activity at pH values around 6.5, typical of hypoxic solid tumors in which CA IX is overexpressed. The proteoglycan domain of CA IX (present only in this transmembrane isoform) may thus act as an intrinsic buffer promoting efficient CO₂ hydration at acidic pH values found in hypoxic tumors.