Nonuniform concerted evolution and chloroplast capture: heterogeneity of observed introgression patterns in three molecular data partition phylogenies of Asian Mitella (saxifragaceae)

Interspecific hybridization is one of the major factors leading to phylogenetic incongruence among loci, but the knowledge is still limited about the potential of each locus to introgress between species. By directly sequencing three DNA regions: chloroplast DNAs (matK gene and trnL-F noncoding region), the nuclear ribosomal external transcribed spacer (ETS) region, and internal transcribed spacer (ITS) regions, we construct three phylogenetic trees of Asian species of Mitella (Saxifragaceae), a genus of perennials in which natural hybrids are commonly observed. Within this genus, there is a significant topological conflict between chloroplast and nuclear phylogenies and also between the ETS and the ITS, which can be attributed to frequent hybridization within the lineage. Chloroplast DNAs show the most extensive introgression pattern, ITS regions show a moderate pattern, and the ETS region shows no evidence of introgression. Nonuniform concerted evolution best explains the difference in the introgression patterns between the ETS region and ITS regions, as the sequence heterogeneity of the ITS region within an individual genome is estimated to be twice that of an ETS in this lineage. Significant gene conversion patterns between two hybridizing taxa were observed in contiguous arrays of cloned ETS-ITS sequences, further confirming that only ITS regions have introgressed bidirectionally. The relatively slow concerted evolution in the ITS regions probably allows the coexistence of multiple alleles within a genome, whereas the strong concerted evolution in the ETS region rapidly eliminates heterogeneous alleles derived from other species, resulting in species delimitations highly concordant with those based on morphology. This finding indicates that the use of multiple molecular tools has the potential to reveal detailed organismal evolution processes involving interspecific hybridization, as an individual locus varies greatly in its potential to introgress between species.     

Tissue distribution of Ca2+-dependent activator protein for secretion family members CAPS1 and CAPS2 in mice.

The family of Ca2+-dependent activator proteins for secretion (CAPS) is involved in dense-core vesicle exocytosis. CAPS1/CADPS1 and CAPS2/CADPS2 have been identified in mammals. CAPS1 regulates catecholamine release from neuroendocrine cells, whereas CAPS2 is involved in the release of brain-derived neurotrophic factor and neurotrophin-3 from cerebellar granule cells. CAPS1 and CAPS2 are predominantly expressed in brain. Here we show the immunohistochemical localization of the CAPS family proteins in various mouse tissues. In the pituitary gland, CAPS1 and CAPS2 were localized to the pars nervosa and the pars intermedia, respectively. In non-neural tissues, CAPS1 was observed in the islets of Langerhans, minor cell types of the spleen and stomach, and medullary cells of the adrenal gland, whereas CAPS2 was present in bronchial epithelial cells, thyroid parafollicular cells, chief cells of the stomach, ductal epithelium of the salivary gland, kidney proximal tubules, and minor cell types of the thymus, spleen, and colon. These results suggest that secretion from distinct cell types in various tissues involves either or both members of the CAPS family.     

Design and synthesis of new potent dipeptidyl peptidase IV inhibitors with enhanced ex vivo duration

A series of 5beta-methylprolyl-2-cyanopyrrolidine analogs were synthesized and evaluated as DPP-IV inhibitors, and the duration of their ex vivo activity was assessed. Comparison of their potency and duration of action was done among three different species. The mode of binding was investigated, and the effect on the plasma glucose level was evaluated. Structure-activity relationships are also presented.     

Requirement for three distinct lymphokines for the induction of cytotoxic T lymphocytes from thymocytes

The induction of cytotoxic T lymphocytes (CTL) from CTL precursors requires a combination of antigen and lymphokine signals. To investigate lymphokine requirements for CTL generation, we used an assay in which helper T cell and accessory cell-depleted spleen cells or whole thymocytes were cultured with lectin (Con A) and lymphokines. This culture was followed by assessment of lectin-dependent cytolysis. High concentrations of recombinant interleukin 2 (R-IL 2) (100 U/ml) alone were not sufficient for lectin-mediated CTL induction from thymocytes, whereas 20 to 100 U/ml of R-IL 2 alone could induce a significant lectin-mediated CTL response from accessory cell-depleted spleen cells. Using thymocytes as responders, we found purified or recombinant interferon-gamma (IFN-gamma) did not cause cytolytic activity either in the absence of or in the presence of R-IL 2. However, supernatant from Con A-stimulated rat spleen cells (rat Con A SN) in combination with R-IL 2 could induce cytolytic activity, suggesting that several factors are required for CTL induction. Con A SN was fractionated by gel filtration and the fractions were tested for ability to induce CTL. In the presence of a low level of R-IL 2 (5 U/ml), fractions with a Mr of approximately 31,000 could induce CTL, and this activity was referred to as CTL differentiation factor (CDF). The peak fractions containing CDF activity did not have detectable IL 1, IL 2, IFN-gamma, or CSF activity. However, by add-back experiments and the use of blocking antibodies, a monoclonal antibody against the IL 2 receptor or antibodies against murine IFN-gamma, we demonstrated that CTL induction from mature thymocytes (L3T4-, Lyt-2+) requires CDF activity in addition to IL 2 and IFN-gamma.     

Phospholipase D family member 4, a transmembrane glycoprotein with no phospholipase D activity, expression in spleen and early postnatal microglia

Background

Phospholipase D (PLD) catalyzes conversion of phosphatidylcholine into choline and phosphatidic acid, leading to a variety of intracellular signal transduction events. Two classical PLDs, PLD1 and PLD2, contain phosphatidylinositide-binding PX and PH domains and two conserved His-x-Lys-(x)₄-Asp (HKD) motifs, which are critical for PLD activity. PLD4 officially belongs to the PLD family, because it possesses two HKD motifs. However, it lacks PX and PH domains and has a putative transmembrane domain instead. Nevertheless, little is known regarding expression, structure, and function of PLD4.

Methodology/Principal Findings

PLD4 was analyzed in terms of expression, structure, and function. Expression was analyzed in developing mouse brains and non-neuronal tissues using microarray, in situ hybridization, immunohistochemistry, and immunocytochemistry. Structure was evaluated using bioinformatics analysis of protein domains, biochemical analyses of transmembrane property, and enzymatic deglycosylation. PLD activity was examined by choline release and transphosphatidylation assays. Results demonstrated low to modest, but characteristic, PLD4 mRNA expression in a subset of cells preferentially localized around white matter regions, including the corpus callosum and cerebellar white matter, during the first postnatal week. These PLD4 mRNA-expressing cells were identified as Iba1-positive microglia. In non-neuronal tissues, PLD4 mRNA expression was widespread, but predominantly distributed in the spleen. Intense PLD4 expression was detected around the marginal zone of the splenic red pulp, and splenic PLD4 protein recovered from subcellular membrane fractions was highly N-glycosylated. PLD4 was heterologously expressed in cell lines and localized in the endoplasmic reticulum and Golgi apparatus. Moreover, heterologously expressed PLD4 proteins did not exhibit PLD enzymatic activity.

Conclusions/Significance

Results showed that PLD4 is a non-PLD, HKD motif-carrying, transmembrane glycoprotein localized in the endoplasmic reticulum and Golgi apparatus. The spatiotemporally restricted expression patterns suggested that PLD4 might play a role in common function(s) among microglia during early postnatal brain development and splenic marginal zone cells.     

Uncovering the roles of PINK1 and parkin in mitophagy

Parkinson disease (PD) is the second most prevalent neurodegenerative disorder, and thus elucidation of the pathogenic mechanism and establishment of a fundamental cure is essential in terms of public welfare. Fortunately, our understanding of the pathogenesis of two types of recessive familial PDs—early-onset familial PD caused by dysfunction of the PTEN-induced putative kinase 1 (PINK1) gene and autosomal recessive juvenile Parkinsonism (ARJP) caused by a mutation in the Parkin gene—has evolved and continues to expand.Key words: PINK1, parkin, ubiquitin, mitochondria, autophagy, mitophagy, membrane potential, quality controlSince the cloning of PINK1 and Parkin, numerous papers have been published about the corresponding gene products, but the mechanism by which dysfunction of PINK1 and/or Parkin causes PD remain unclear. Parkin encodes a ubiquitin ligase E3, a substrate recognition member of the ubiquitination pathway, whereas PINK1 encodes a mitochondria-targeted serine-threonine kinase that contributes to the maintenance of mitochondrial integrity. Based on their molecular functions, it is clear that Parkin-mediated ubiquitination and PINK1 phosphorylation are key events in disease pathogenesis. The underlying mechanism, however, is not as well defined and claims of pathogenicity, until recently, remained controversial. Although Parkin''s E3 activity was clearly demonstrated in vitro, we were unable to show a clear E3 activity of Parkin in cell/in vivo. In addition, despite a predicted mitochondrial localization signal for PINK1, we were unable to detect PINK1 on mitochondria by either immunoblotting or immunocytochemistry. More confusingly, overexpression of nontagged PINK1 mainly localized to the cytoplasm under steady state conditions.Work by Dr. Youle''s group at the National Institutes of Health in 2008, however, offered new insights. They reported that Parkin associated with depolarized mitochondria and that Parkin-marked mitochondria were subsequently cleared by autophagy. Soon after their publication, we also examined the function of Parkin and PINK1 following a decrease in mitochondrial membrane potential. Our findings, described below (Fig. 1), have contributed to the development of a mechanism explaining pathogenicity.Open in a separate windowFigure 1Model of mitochondrial quality control mediated by PINK1 and Parkin. Under steady-state conditions, the mature 60 kDa PINK1 is constantly cleaved by an unknown protease to a 50 kDa intermediate form that is subsequently degraded, presumably by the proteasome (upper part). The protein, however, is stabilized on depolarized mitochondria because the initial processing event is inhibited by a decrease in mitochondrial membrane potential (lower part). Accumulated PINK1 recruits cytosolic Parkin onto depolarized mitochondria resulting in activation of its E3 activity. Parkin then ubiquitinates a mitochondrial substrate(s). As a consequence, damaged mitochondria are degraded via mitophagy. Ub, ubiquitin.(1) We sought to determine the subcellular localization of endogenous PINK1, and realized that endogenous PINK1 is barely detectable under steady-state conditions. However, a decrease in mitochondrial membrane-potential following treatment with the mitochondrial uncoupler carbonyl cyanide m-chlorophenylhydrazone (CCCP) results in the gradual accumulation of endogenous PINK1 on mitochondria. Importantly, when CCCP is washed out, the accumulated endogenous PINK1 rapidly disappears (within 30 min) both in the presence and absence of cycloheximide. These results support the hypothesis that PINK1 is constantly transported to the mitochondria, but is rapidly degraded in a membrane potential-dependent manner (see below for details). We speculate that PINK1 is stabilized by a decrease in mitochondrial membrane potential and as a result accumulates on depolarized mitochondria.(2) We examined the potential role of PINK1 in the mitochondrial recruitment of Parkin. In control MEFs (PINK1^+/+), Parkin is selectively recruited to the mitochondria following CCCP treatment, and subsequently results in the selective disappearance of the mitochondria via autophagy (called mitophagy). In sharp contrast, Parkin is not translocated to the mitochondria in PINK1 knockout (PINK1^−/−) MEFs following CCCP treatment, and subsequent mitochondrial degradation is also completely impeded. These results suggest that PINK1 is “a Parkin-recruitment factor” that recruits Parkin from the cytoplasm to damaged mitochondria in a membrane potential-dependent manner for mitophagy.(3) We monitored the E3 activity of Parkin using an artificial pseudo-substrate fused to Parkin in cells. Parkin''s E3 activity was repressed under steady-state conditions; however, we find that Parkin ubiquitinates the pseudo-substrate when it is retrieved to the depolarized mitochondria, suggesting that activation of the latent Parkin E3 activity is likewise dependent on a decrease in mitochondrial membrane potential.(4) PINK1 normally exists as either a long (approximately 60 kDa) or a short (approximately 50 kDa) protein. Because the canonical mitochondrial targeting signal (matrix targeting signal) is cleaved after import into the mitochondria, the long form has been designated as the precursor and the short form as the mature PINK1. However, our subcellular localization study of endogenous PINK1 following CCCP treatment shows that the long form is recovered in the mitochondrial fraction, suggesting that it is not the pre-import precursor form. Moreover, by monitoring the degradation process of PINK1 following recovery of membrane potential, we realized that the short form of PINK1 transiently appears soon after CCCP is washed out and then later disappears, suggesting that the processed form of PINK1 is an intermediate in membrane-potential-dependent degradation. In conclusion, these results imply that PINK1 cleavage does not reflect a canonical maturation process accompanying mitochondrial import as initially thought, but rather represents constitutive degradation in healthy mitochondria by a two-step mechanism; i.e., first limited processing and subsequent complete degradation probably via the proteasome.(5) PINK1 accumulation by decrease of membrane potential and subsequent recruitment of Parkin onto mitochondria are presumably etiologically important because they are impeded for the most part by disease-linked mutations of PINK1 or Parkin.These results, together with reports by other groups, strongly suggest that recessive familial PD is caused by dysfunction of quality control for depolarized mitochondria.At present, we do not know whether the aforementioned pathogenic mechanism of recessive familial PD can be generalized to prevalent sporadic PD. However, the clinical symptoms of recessive familial PD caused by dysfunction of PINK1 or Parkin resembles that of idiopathic PD except early-onset pathogenesis, and thus it is plausible that there is a common pathogenic mechanism. We accordingly believe that our results provide solid insight into the molecular mechanisms of PD pathogenesis, not only for familial forms caused by Parkin and PINK1 mutations, but also the major sporadic form of PD.To fully understand the molecular mechanism of PINK1-Parkin-mediated mitophagy, further details need to be addressed including: identifying the protease(s) that processes PINK1 in a mitochondrial membrane-potential dependent manner and that presumably monitors mitochondrial integrity; identifying a physiological substrate(s) of PINK1; determining the molecular mechanism underlying Parkin activation; and identifying the protein(s) linking Parkin-mediated ubiquitination to mitophagy. A detailed mechanism of the aforementioned events will be the focus of future research, however, we feel our conclusion that PINK1 and Parkin function in the removal of depolarized mitochondria is evident and hope that our studies will provide a solid foundation for further studies.     

A nationwide attempt to standardize growth hormone assays

The Growth Hormone (GH) and Its Related Factors Study Committee of the Foundation for Growth Science, Japan, has been conducting a quality control study for 15 years to improve the equality of diagnosis of GH deficiency. It found that the greatest differences in measured GH values were due to the different potencies of the kit standards, which were primarily adjusted to WHO standards for human GH of pituitary origin. With the collaboration of kit makers and the Study Group of Hypothalamo-Pituitary Disorders of the Ministry of Health, Labor and Welfare, all GH kits in Japan have begun using the same recombinant human GH standard since April 2005. As a result the diagnostic cut-off peak GH has changed from 10 to 6 ng/ml.     

Inactivation of Escherichia coli Endotoxin by Soft Hydrothermal Processing

Bacterial endotoxins, also known as lipopolysaccharides, are a fever-producing by-product of gram-negative bacteria commonly known as pyrogens. It is essential to remove endotoxins from parenteral preparations since they have multiple injurious biological activities. Because of their strong heat resistance (e.g., requiring dry-heat sterilization at 250°C for 30 min) and the formation of various supramolecular aggregates, depyrogenation is more difficult than sterilization. We report here that soft hydrothermal processing, which has many advantages in safety and cost efficiency, is sufficient to assure complete depyrogenation by the inactivation of endotoxins. The endotoxin concentration in a sample was measured by using a chromogenic limulus method with an endotoxin-specific limulus reagent. The endotoxin concentration was calculated from a standard curve obtained using a serial dilution of a standard solution. We show that endotoxins were completely inactivated by soft hydrothermal processing at 130°C for 60 min or at 140°C for 30 min in the presence of a high steam saturation ratio or with a flow system. Moreover, it is easy to remove endotoxins from water by soft hydrothermal processing similarly at 130°C for 60 min or at 140°C for 30 min, without any requirement for ultrafiltration, nonselective adsorption with a hydrophobic adsorbent, or an anion exchanger. These findings indicate that soft hydrothermal processing, applied in the presence of a high steam saturation ratio or with a flow system, can inactivate endotoxins and may be useful for the depyrogenation of parenterals, including end products and medical devices that cannot be exposed to the high temperatures of dry heat treatments.Endotoxins are lipopolysaccharides (LPS) that are derived from the cell membranes of gram-negative bacteria and are continuously released into the environment. The release of LPS occurs not only upon cell death but also during growth and division. In the pharmaceutical industry, it is essential to remove endotoxins from parenteral preparations since they have multiple injurious biological activities, including pyrogenicity, lethality, Schwartzman reactivity, adjuvant activity, and macrophage activation (2, 9, 12, 13, 25, 32). Endotoxins are very stable molecules that are capable of resisting extreme temperatures and pH values (3, 16, 17, 29, 30, 34, 38). An endotoxin monomer has a molar mass of 10 to 20 kDa and forms supramolecular aggregates in aqueous solutions (22, 39) due to its amphipathic structure, which makes depyrogenation more difficult than sterilization. Endotoxins are not efficiently inactivated with the regular heat sterilization procedures recommended by the Japanese Pharmacopoeia. These procedures are steam heat treatment at 121°C for 20 min or dry-heat treatment for at least 1 h at 180°C. It is well accepted that only dry-heat treatment is efficient in destroying endotoxins (3, 16, 29, 30) and that endotoxins can be inactivated when exposed to a temperature of 250°C for more than 30 min or 180°C for more than 3 h (14, 36). In the production of parenterals, it is necessary to both depyrogenate the final products and carry out sterilization to avoid bacterial contamination.Several studies have examined dry-heat treatment, which is a very efficient means to degrade endotoxins (6, 20, 21, 26, 41, 42). However, its application is restricted to steel and glass implements that can tolerate high temperatures of >250°C. For sterilization, dry heat treatment tends to be used only with thermostable materials that cannot be sterilized by steam heat treatment (autoclaving). Alternative depyrogenation processes include the application of activated carbon (35), oxidation (15), and acidic or alkaline reagents (27), but steam heat treatment would be an attractive option if it were sufficiently effective. However, the data on the inactivation of endotoxins by steam heat treatment are insufficient and contradictory. It has been reported that endotoxins were not efficiently inactivated by steam heat treatment at 121°C (19, 45). However, Ogawa et al. (31) recently reported that steam heat treatment was efficient in inactivating low concentrations of endotoxin, and that Escherichia coli LPS are unstable in aqueous solutions even at relatively low temperatures such as 70°C (see also reference 40). As mentioned above, these reports have shown that although studies have been carried out on the use of steam heat for depyrogenation, there is little agreement on its efficiency.The U.S. Pharmacopoeia (USP) recommends depyrogenation by dry-heat treatment at temperatures above 220°C for as long as is necessary to achieve a ≥3-log reduction in the activity of endotoxin, if the value is ≥1,000 endotoxin units (EU)/ml (11, 44). Due to the serious risks associated with endotoxins, the U.S. Food and Drug Administration (FDA) has set guidelines for medical devices and parenterals. The protocol to test for endotoxin contamination of medical devices recommends immersion of the device in endotoxin-free water for at least 1 h at room temperature, followed by testing of this extract/eluate for endotoxin. Current FDA limits are such that eluates from medical devices may not exceed 0.5 EU/ml, or 0.06 EU/ml if the device comes into contact with cerebrospinal fluid (43). The term EU describes the biological activity of endotoxins. For example, 100 pg of the standard endotoxin EC-5, 200 pg of EC-2, and 120 pg of endotoxin from E. coli O111:B4 all have an activity of 1 EU (17, 23).Steam heat treatment is comparatively easy to apply and control. If steam heat treatment could reliably inactivate endotoxins, it could be applied with sterilization, reducing labor, time, and expenditure. However, to our knowledge, few studies have addressed steam heat inactivation to determine the chemical and physical reactions that occur during the hydrothermal process, nor have any studies examined the relationship between the steam saturation ratio and the inactivation of endotoxins. Moreover, to date no study has been conducted on steam heat activation of endotoxins with reference to the chemical and physical parameters of the hydrothermal process.We have developed a groundbreaking method to thermoinactivate endotoxins by means of a soft hydrothermal process, in which the steam saturation ratio can be controlled. The steam saturation ratio is calculated as follows: steam saturation ratio (%) = [steam density (kg/m³)/saturated steam density (kg/m³)] × 100.The soft hydrothermal process lies in the part of the liquid phase of water with a high steam saturation ratio that is characterized by a higher ionic product (k_w) than that of ordinary water. The ionic product is a key parameter in promoting ionic reactions and can be related to hydrolysis. The ionic product of water is 1.0 × 10⁻¹⁴ (mol/liter)² at room temperature and increases with increasing temperature and pressure. A high ionic product favors the solubility of highly polar and ionic compounds, creating the possibility of accelerating the hydrolysis reaction process of organic compounds. Thus, water can play the role of both an acidic and an alkaline catalyst in the hydrothermal process (Fig. ​(Fig.1)1) (1, 37, 46). However, the soft hydrothermal process lies in the high-density water molecular area of the steam-gas biphasic field (Fig. ​(Fig.1)1) and is characterized by a lower dielectric constant (ɛ) than that of ordinary water. This process opens the possibility of promoting the affinity of water for nonpolar or low-polarity compounds, such as lipophilic organic compounds (46). We previously reported that most of the predominant aromatic hydrocarbons were removed from softwood bedding that had been treated by soft hydrothermal processing (24, 28).Open in a separate windowFIG. 1.Reaction field in the pressure-temperature relationship of water. The curve represents the saturated vapor pressure curve. The fields show where the pressure-temperature relationships are conducive to a variety of hydrothermal processing conditions, in which water has a large impact as a reaction medium. Because high-density water has a large dielectric constant and ionic product, it is an effective reaction medium for advancing ionic reactions, whereas water (in the form of steam) on the lower-pressure side of the saturated vapor pressure curve shows a good ability to form materials by covalent bonding. Small changes in the density of water can result in changes in the chemical affinity, which has the potential to advance a range of ionic and radical reactions.The purpose of the present study was to evaluate the thermoinactivation of endotoxins by the soft hydrothermal process, by controlling the steam saturation ratio, temperature, and time of treatment. There have been reports that endotoxins were thermoinactivated by steam heat treatment at 121°C in the presence of a nonionic surfactant and at over 135°C in its absence (4, 5, 10), but the minimum temperature for the inactivation of endotoxin remained unknown. This report provides the answer to this question.