The response of the skin of swine to increasing single exposures of 250-KVP X-rays

When the skin of the shoulder ("A" field) and lower back ("C" field) is irradiated through 10-cm-diameter fields with 250-kVp x-rays, having a HVL of 0.87 mm copper, a dose range is reached between approximately 1600 rads and 3000 rads in which a moist reaction is or is not formed. If a moist reaction is formed, it either heals completely, partially, or not at all. The evolution, time course, and dose dependence of the moist reaction that occurs following irradiation has been determined. The moist reaction is found at 17.5 +/- 0.6 days in the "A" field, and 20.8 +/-0.8 days in the "C" field. The reaction evolves to involve from 5 % to 100% of the field by 24.9 +/- 0.5 days in the "A" field and by 28.5 +/- 1.0 days in the "C" field. Healing is complete by 36.0 +/-1.0 days in the "A" field and by 38.0 +/- 1.3 days in the "C" field. The area of the field involved with a moist reaction at the time of maximal involvement is dose-dependent. The area of the field involved with a moist reaction at the time of complete healing is also dose-dependent. The dose at which 50 % of the fields were not healed was 2273 +/-103 rads in the "A" field, 2578 +/-141 rads in the "C" fields, and 2437 +/- 89 rads in the "A" and "C" fields. The values in the "C" field are significantly different from those in the "A" field except for the dose at which 50 % of the fields were not healed and the time at which the field was maximally healed.     

Role of JNK1-dependent Bcl-2 Phosphorylation in Ceramide-induced Macroautophagy

Macroautophagy is a vacuolar lysosomal catabolic pathway that is stimulated during periods of nutrient starvation to preserve cell integrity. Ceramide is a bioactive sphingolipid associated with a large range of cell processes. Here we show that short-chain ceramides (C₂-ceramide and C₆-ceramide) and stimulation of the de novo ceramide synthesis by tamoxifen induce the dissociation of the complex formed between the autophagy protein Beclin 1 and the anti-apoptotic protein Bcl-2. This dissociation is required for macroautophagy to be induced either in response to ceramide or to starvation. Three potential phosphorylation sites, Thr⁶⁹, Ser⁷⁰, and Ser⁸⁷, located in the non-structural N-terminal loop of Bcl-2, play major roles in the dissociation of Bcl-2 from Beclin 1. We further show that activation of c-Jun N-terminal protein kinase 1 by ceramide is required both to phosphorylate Bcl-2 and to stimulate macroautophagy. These findings reveal a new aspect of sphingolipid signaling in up-regulating a major cell process involved in cell adaptation to stress.Macroautophagy (referred to below as “autophagy”) is a vacuolar, lysosomal degradation pathway for cytoplasmic constituents that is conserved in eukaryotic cells (1–3). Autophagy is initiated by the formation of a multimembrane-bound autophagosome that engulfs cytoplasmic proteins and organelles. The last stage in the process results in fusion with the lysosomal compartments, where the autophagic cargo undergoes degradation. Basal autophagy is important in controlling the quality of the cytoplasm by removing damaged organelles and protein aggregates. Inhibition of basal autophagy in the brain is deleterious, and leads to neurodegeneration in mouse models (4, 5). Stimulation of autophagy during periods of nutrient starvation is a physiological response present at birth and has been shown to provide energy in various tissues of newborn pups (6). In cultured cells, starvation-induced autophagy is an autonomous cell survival mechanism, which provides nutrients to maintain a metabolic rate and level of ATP compatible with cell survival (7). In addition, starvation-induced autophagy blocks the induction of apoptosis (8). In other contexts, such as drug treatment and a hypoxic environment, autophagy has also been shown to be cytoprotective in cancer cells (9, 10). However, autophagy is also part of cell death pathways in certain situations (11). Autophagy can be a player in apoptosis-independent type-2 cell death (type-1 cell death is apoptosis), also known as autophagic cell death. This situation has been shown to occur when the apoptotic machinery is crippled in mammalian cells (12, 13). Autophagy can also be part of the apoptotic program, for instance in tumor necrosis factor-α-induced cell death when NF-κB is inhibited (14), or in human immunodeficiency virus envelope-mediated cell death in bystander naive CD4 T cells (15). Moreover autophagy has recently been shown to be required for the externalization of phosphatidylserine, the eat-me signal for phagocytic cells, at the surface of apoptotic cells (16).The complex relationship between autophagy and apoptosis reflects the intertwined regulation of these processes (17, 18). Many signaling pathways involved in the regulation of autophagy also regulate apoptosis. This intertwining has recently been shown to occur at the level of the molecular machinery of autophagy. In fact the anti-apoptotic protein Bcl-2 has been shown to inhibit starvation-induced autophagy by interacting with the autophagy protein Beclin 1 (19). Beclin 1 is one of the Atg proteins conserved from yeast to humans (it is the mammalian orthologue of yeast Atg6) and is involved in autophagosome formation (20). Beclin 1 is a platform protein that interacts with several different partners, including hVps34 (class III phosphatidylinositol 3-kinase), which is responsible for the synthesis of phosphatidylinositol 3-phosphate. The production of this lipid is important for events associated with the nucleation of the isolation membrane before it elongates and closes to form autophagosomes in response to other Atg proteins, including the Atg12 and LC3² (microtubule-associated protein light chain 3 is the mammalian orthologue of the yeast Atg8) ubiquitin-like conjugation systems (3, 21). Various partners associated with the Beclin 1 complex modulate the activity of hVps34. For instance, Bcl-2 inhibits the activity of this enzyme, whereas UVRAG, Ambra-1, and Bif-1 all up-regulate it (22, 23).In view of the intertwining between autophagy and apoptosis, it is noteworthy that Beclin 1 belongs to the BH3-only family of proteins (24–26). However, and unlike most of the proteins in this family, Beclin 1 is not able to trigger apoptosis when its expression is forced in cells (27). A BH3-mimetic drug, ABT-737, is able to dissociate the Beclin 1-Bcl-2 complex, and to trigger autophagy by mirroring the effect of starvation (25).The sphingolipids constitute a family of bioactive lipids (28–32) of which several members, such as ceramide and sphingosine 1-phosphate, are signaling molecules. These molecules constitute a “sphingolipid rheostat” that determines the fate of the cell, because in many settings ceramide is pro-apoptotic and sphingosine 1-phosphate mitigates this apoptotic effect (31, 32). However, ceramide is also engaged in a wide variety of other cell processes, such as the formation of exosomes (33), differentiation, cell proliferation, and senescence (34). Recently we showed that both ceramide and sphingosine 1-phosphate are able to stimulate autophagy (35, 36). It has also been shown that ceramide triggers autophagy in a large panel of mammalian cells (37–39). However, elucidation of the mechanism by which ceramide stimulates autophagy is still in its infancy. We have previously demonstrated that ceramide induces autophagy in breast and colon cancer cells by inhibiting the Class I phosphatidylinositol 3-phosphate/mTOR signaling pathway, which plays a central role in inhibiting autophagy (36). Inhibition of mTOR is another hallmark of starvation-induced autophagy (17). This finding led us to investigate the effect of ceramide on the Beclin 1-Bcl-2 complex. The results presented here show that ceramide is more potent than starvation in dissociating the Beclin 1-Bcl-2 complex (see Ref. 40). This dissociation is dependent on three phosphorylation sites (Thr⁶⁹, Ser⁷⁰, and Ser⁸⁷) located in a non-structural loop of Bcl-2. Ceramide induces the c-Jun N-terminal kinase 1-dependent phosphorylation of Bcl-2. Expression of a dominant negative form of JNK1 blocks Bcl-2 phosphorylation, and thus the induction of autophagy by ceramide. These findings help to explain how autophagy is regulated by a major lipid second messenger.     

Again on language of biology]

Some time ago I proposed in an Editorial in this journal some considerations on the language of biology. I concluded that, to realize an autonomy of such a language (and therefore of biology), we have to develop a valid language for biology. In such a context, it seemed to me that the term "metaphors" referred to the concepts concerning the information carried by genetic code, was a reasonable one. However, Barbieri's article in this issue of Rivista di Biologia / Biology Forum calls for a reply. Of course, we do not know very much in this field, even if we have some evidence that a sequence of bases on a DNA is not determined only by chance. In any case we can exclude that nature in this occasion has "invented" a code. Nature doesn't "invent" anything: it only follows its rules, that we name "laws of nature". Barbieri quotes the Morse code, but forgets to say that such a code is "conventional" in the sense that it is valid only because it is the result of an "agreement" between Morse and the users of that code. There is nothing more unnatural than a "code": with whom nature should actually have to "reach an agreement"? As a matter of fact, we interpret as "information" what happens by law of nature. Also Barbieri's thesis that genes and proteins are molecular artifacts, assembled by external agents, whereas generally molecules are determined by their bonds, i.e. by internal factors, is a disputable one. It is examined how much an external structure plays a role in ordinary chemical reactions. The "information" of physics is not a semantic information. For such information we can refer to history of literature, telegraphic offices, genetics or biochemistry.     

Clinical ethics and nursing: "yes" to caring, but "no" to a female ethics of care

According to a contemporary school of thought there is a specific female approach to ethics which is based not on abstract "male" ethical principles or rules, but on "care". Nurses have taken a keen interest in these female approaches to ethics. Drawing on the views expounded by Carol Gilligan and Nel Noddings, nurses claim that a female "ethics of care" better captures their moral experiences than a traditional male "ethics of justice". This paper argues that "care" is best understood in a dispositional sense, that is, as sensitivity and responsiveness to the particularities of a situation and the needs of "concrete" others. While "care", in this sense, is necessary for ethics, it is not sufficient. Ethics needs "justice" as well as "care". If women and nurses excessively devalue principles and norms, they will be left without the theoretical tools to condemn some actions or practices, and to defend others. They will, like generations of nurses before them, be condemned to silence.     

CLINICAL ETHICS AND NURSING: "YES" TO CARING, BUT "NO" TO A FEMALE ETHICS OF CARE

According to a contemporary school of thought there is a specific female approach to ethics which is based not on abstract "male" ethical principles or rules, but on "care". Nurses have taken a keen interest in these female approaches to ethics. Drawing on the views expounded by Carol Gilligan and Nel Noddings, nurses claim that a female "ethics of care" better captures their moral experiences than a traditional male "ethics of justice". This paper argues that "care" is best understood in a dispositional sense, that is, as sensitivity and responsiveness to the particularities of a situation and the needs of "concrete" others. While "care", in this sense, is necessary for ethics, it is not sufficient. Ethics needs "justice" as well as "care". If women and nurses excessively devalue principles and norms, they will be left without the theoretical tools to condemn some actions or practices, and to defend others. They will, like generations of nurses before them, be condemned to silence.     

Mineralization by Inhibitor Exclusion: THE CALCIFICATION OF COLLAGEN WITH FETUIN

One of our goals is to understand the mechanisms that deposit mineral within collagen fibrils, and as a first step we recently determined the size exclusion characteristics of the fibril. This study revealed that apatite crystals up to 12 unit cells in size can access the water within the fibril, whereas molecules larger than a 40-kDa protein are excluded. Based on these observations, we proposed a novel mechanism for fibril mineralization: that macromolecular inhibitors of apatite growth favor fibril mineralization by selectively inhibiting crystal growth in the solution outside of the fibril. To test this mechanism, we developed a system in which crystal formation is driven by homogeneous nucleation at high calcium phosphate concentration and the only macromolecule in solution is fetuin, a 48-kDa inhibitor of apatite growth. Our experiments with this system demonstrated that fetuin determines the location of mineral growth; in the presence of fetuin mineral grows exclusively within the fibril, whereas in its absence mineral grows in solution outside the fibril. Additional experiments showed that fetuin is also able to localize calcification to the interior of synthetic matrices that have size exclusion characteristics similar to those of collagen and that it does so by selectively inhibiting mineral growth outside of these matrices. We termed this new calcification mechanism “mineralization by inhibitor exclusion,” the selective mineralization of a matrix using a macromolecular inhibitor of mineral growth that is excluded from that matrix. Future studies will be needed to evaluate the possible role of this mechanism in bone mineralization.The type I collagen fibril plays several critical roles in bone mineralization. The mineral in bone is located primarily within the fibril (1–6), and during mineralization the fibril is formed first and then water within the fibril is replaced with mineral (7, 8). The collagen fibril therefore provides the aqueous compartment in which mineral grows. We have recently shown that the physical structure of the collagen fibril plays an important additional role in mineralization, that of a gatekeeper allowing molecules smaller than a 6-kDa protein to freely access the water within the fibril while preventing molecules larger than a 40-kDa protein from entering the fibril (9).Molecules too large to enter the collagen fibril can have important effects on mineralization within the fibril. We have suggested that large inhibitors of apatite growth can paradoxically favor mineralization within the fibril by selectively preventing apatite growth in the solution outside of the fibril (9). We have also proposed that large nucleators of apatite formation may generate small crystals outside the collagen fibril and that some of these crystals can subsequently diffuse into the fibril and grow (9). Because the size exclusion characteristics of the fibril allow rapid penetration of molecules the size of a 6-kDa protein, apatite crystals up to 12 unit cells in size should in principle be able to freely access all of the water within the fibril (9).We subsequently tested these hypotheses for the role of large molecules in fibril mineralization by determining the impact of removing fetuin on the serum-driven calcification of collagen fibrils (10). Fetuin is the most abundant serum inhibitor of apatite crystal growth (11, 12), and with a molecular weight of 48 kDa fetuin is too large to penetrate the collagen fibril (9). Fetuin is also termed fetuin-A (to distinguish it from a recently discovered homologue, fetuin-B (13)) and is sometimes called α2-HS glycoprotein in humans. Our working hypothesis was that fetuin is required for the serum-driven calcification of a collagen fibril and that its role is to favor calcification within the collagen fibril by selectively preventing apatite crystal growth in the solution outside the fibril.The results of this study demonstrate that removing fetuin from serum eliminates the ability of serum to induce the calcification of a type I collagen matrix and that adding purified fetuin to fetuin-depleted serum restores this activity (14). This study further shows that a massive mineral precipitate forms during the incubation of fetuin-depleted serum but not during the incubation of serum containing fetuin (14). These observations are consistent with the hypothesis that a large serum nucleator generates apatite crystals in the solution outside of the collagen fibril, some of which penetrate into the aqueous interior of the fibril (14). Because fetuin can trap only those nuclei that it can access, the crystal nuclei that penetrate the fibril grow far more rapidly than those nuclei trapped by fetuin outside of the fibril, and the collagen fibril therefore selectively calcifies.The goal of the present experiments was to further understand the role of fetuin in the calcification of type I collagen fibrils. To accomplish this goal, we developed a system in which crystal formation is driven by homogeneous nucleation at high calcium phosphate concentrations and the only macromolecule in the solution is fetuin. This system allowed us to probe the impact of fetuin and only fetuin on the location and extent of collagen calcification. Because fetuin is the subject of this study, it is useful to review briefly its occurrence and calcification-inhibitory activity. Fetuin is a 48-kDa glycoprotein that is synthesized in the liver and is found at high concentrations in mammalian serum (15, 16) and bone (17–22). The serum fetuin concentration in adult mammals ranges from 0.5 to 1.5 mg/ml, whereas the serum fetuin concentration in the fetus and neonate is typically far higher (16). Fetuin is also one of the most abundant noncollagenous proteins found in bone (17–22), with a concentration of about 1 mg fetuin/g bone in rat (21), bovine (17), and human (19, 23) bone. Despite the abundance of fetuin in bone, however, it has not been possible to demonstrate the synthesis of fetuin in calcified tissues, and it is therefore presently thought that the fetuin found in bone arises from hepatic synthesis via serum (20, 22). This view is supported by the observation that fetuin binds strongly to apatite, the mineral phase of bone, and is selectively concentrated from serum onto apatite (18).In vitro studies have demonstrated that fetuin is an important inhibitor of apatite growth and precipitation in serum containing increased levels of calcium and phosphate (12) and that targeted deletion of the fetuin gene reduces the ability of serum to arrest apatite formation by over 70% (11). More recent studies have shown that a fetuin-mineral complex is formed in the course of the fetuin-mediated inhibition of apatite growth and precipitation in serum containing increased calcium and phosphate (24, 25). Purified fetuin also potently inhibits the growth of apatite crystals from supersaturated solutions of calcium phosphate (12, 24). In solutions in which a decline in calcium occurs within minutes because of the spontaneous formation of apatite crystals, the presence of added fetuin sustains elevated calcium levels for at least 24 h (24).     

Mechanism of neurofibrillary degeneration in Alzheimer's disease

Neurofibrillary degeneration associated with the formation of intraneuronal neurofibrillary tangles of paired helical filaments (PHF) and 2.1 nm τ filaments is one of the most characteristic brain lesions of Alzheimer's disease. The major polypeptides of PHF are the microtubule associated protein, τ. τ, in PHF is present in abnormally phosphorylated forms. In addition to the PHF, the abnormal τ is present in soluble non-PHF form in the alzheimer's disease brain. The level of τ in Alzheimer's disease neocortex is severalfold higher than in aged control brain, and this increase is in the form of the abnormally phosphorylated protein. The abnormally phosphorylated τ does not promote the assembly of tubulin into microtubules in vitro, and it inhibits the normal τ-stimulated microtubule assembly. After in vitro dephosphorylation both PHF and non-PHF abnormal τ stimulate the assembly of tubulin into microtubules. The activities of phosphoseryl/phosphothreonyl protein phosphatase 2A and nonreceptor phosphotyrosyl phosphatase(s) are decreased in AD brain. It is suggested that

1. A defect(s) in the protein phosphorylation/dephosphorylation system is one of the early events in the neurofibrillary pathology in AD;
2. A decrease in protein phosphatase, activities, at least in part, allows the hyperphosphorylation of τ; and
3. Abnormal phosphorylation and polymerization of τ into PHF most probably lead to a breakdown of the microtubule system and consequently to neuronal degeneration.

     

A Novel Mechanism for SUMO System Control: Regulated Ulp1 Nucleolar Sequestration

The small ubiquitin-related modifiers (SUMOs) are evolutionarily conserved polypeptides that are covalently conjugated to protein targets to modulate their subcellular localization, half-life, or activity. Steady-state SUMO conjugation levels increase in response to many different types of environmental stresses, but how the SUMO system is regulated in response to these insults is not well understood. Here, we characterize a novel mode of SUMO system control: in response to elevated alcohol levels, the Saccharomyces cerevisiae SUMO protease Ulp1 is disengaged from its usual location at the nuclear pore complex (NPC) and sequestered in the nucleolus. We further show that the Ulp1 region previously demonstrated to interact with the karyopherins Kap95 and Kap60 (amino acids 150 to 340) is necessary and sufficient for nucleolar targeting and that enforced sequestration of Ulp1 in the nucleolus significantly increases steady-state SUMO conjugate levels, even in the absence of alcohol. We have thus characterized a novel mechanism of SUMO system control in which the balance between SUMO-conjugating and -deconjugating activities at the NPC is altered in response to stress via relocalization of a SUMO-deconjugating enzyme.The small ubiquitin-related modifiers (SUMOs) are a family of evolutionarily conserved polypeptides that are conjugated to protein targets via the concerted action of SUMO-specific E1 (activation), E2 (conjugation), and E3 (ligase) enzymes to effect changes in subcellular localization, half-life, or target activity. A family of SUMO-specific proteases act to remove the modifier from conjugates (8, 20). The SUMO system has been implicated in a variety of critical cellular functions, such as DNA repair and replication, RNA metabolism, and stress responses (8, 16, 20). Importantly, the SUMO system is highly dynamic and the SUMO pathway enzymes appear to work together to precisely control SUMO conjugate levels in the cell (8, 16, 20). However, how the SUMO system itself is regulated is poorly understood.Localization of the SUMO pathway enzymes may play an important role in SUMO system function (21). For example, the budding yeast SUMO protease Ulp1 is tethered to the nuclear face of the nuclear pore complex (NPC) via an unconventional interaction with the karyopherin Kap121 and the heterodimeric Kap95/Kap60 complex (12, 13, 23). However, this SUMO protease is not maintained exclusively at the NPC but appears to be mobile, effecting desumoylation at diverse subcellular locations: e.g., during mitosis, Saccharomyces cerevisiae Ulp1 is recruited to the septin ring to desumoylate septins (15), Schizosaccharomyces pombe Ulp1 localization is regulated throughout the cell cycle (31), and a mammalian Ulp1 homolog, SENP2, is shuttled between the nucleus and the cytoplasm (7). Consistent with these observations, SUMO conjugate levels are significantly altered in yeast strains expressing mislocalized Ulp1 (13, 37).Dramatic changes in SUMO conjugate populations have been noted in response to many different types of stresses in yeasts, mammals, and plants (9, 17, 27, 32, 38). For example, in S. cerevisiae, significantly increased steady-state SUMO conjugate levels are observed in response to elevated concentrations of ethanol (38). To better understand how the SUMO system is regulated in response to stress, we utilized alcohol as a model of a physiologically relevant stressor in yeast. Here, we demonstrate that alcohol stress results in a rapid, reversible nucleolar sequestration of Ulp1 and that enforced localization of Ulp1 in the nucleolus leads to a dramatic increase in steady-state SUMO conjugate levels. This is the first demonstration of regulated modulation of the intracellular localization of a SUMO enzyme in response to stress and thus represents a novel mechanism for SUMO system control.     

Functional Characterization of a Silicon Transporter Gene Implicated in Silicon Distribution in Barley

Silicon (Si) is a beneficial element for plant growth. In barley (Hordeum vulgare), Si uptake by the roots is mainly mediated by a Si channel, Low Silicon1 (HvLsi1), and an efflux transporter, HvLsi2. However, transporters involved in the distribution of Si in the shoots have not been identified. Here, we report the functional characterization of a homolog of HvLsi1, HvLsi6. HvLsi6 showed permeability for Si and localized to the plasma membrane. At the vegetative growth stage, HvLsi6 was expressed in both the roots and shoots. The expression level was unaffected by Si supply. In the roots, HvLsi6 was localized in epidermis and cortex cells of the tips, while in the leaf blades and sheaths, HvLsi6 was only localized at parenchyma cells of vascular bundles. At the reproductive growth stage, high expression of HvLsi6 was also found in the nodes. HvLsi6 in node I was polarly located at the transfer cells surrounding the enlarged vascular bundles toward the numerous xylem vessels. These results suggest that HvLsi6 is involved in Si uptake in the root tips, xylem unloading of Si in leaf blade and sheath, and intervascular transfer of Si in the nodes. Furthermore, HvLsi2 was found to be localized at the parenchyma cell layer adjacent to the transfer cells with opposite polarity of HvLsi6, suggesting that the coupling of HvLsi6 and HvLsi2 is involved in the intervascular transfer of Si at the nodes. Si translocated via the enlarged vascular bundles is unloaded to the transfer cells by HvLsi6, followed by HvLsi2 to reload Si to the diffuse vascular bundles, which are connected to the upper part of the plant, especially the panicles, the ultimate Si sink.Silicon (Si) is a beneficial element for plant growth. It enhances the resistance of plants to various biotic and abiotic stresses (Epstein, 1999; Ma and Takahashi, 2002; Ma and Yamaji, 2006). For example, Si reduces the epidemics of both leaf and panicle blast in rice (Oryza sativa; Datnoff and Rodrigues, 2005) and decreases the incidence of powdery mildew in cucumber (Cucumis sativus), barley (Hordeum vulgare), and wheat (Triticum aestivum; Fauteux et al., 2005). Si also suppresses insect pests such as stem borer (Chilo suppressalis), brown planthopper (Nilaparvata lugens), and rice green leafhopper (Nephotettix cincticeps; Savant et al., 1997). Resistance to the damage by wild rabbit in wheat is also enhanced by an increased amount of Si in leaf tissue (Cotterill et al., 2007). Si is also able to alleviate lodging, drought, and low- and high-temperature stresses (Ma, 2004). The beneficial effects of Si under phosphate deficiency, phosphate excess, and manganese and salt toxicity stresses have been observed in many plants (Ma and Takahashi, 2002). Usually, the more Si that accumulates in the shoots, the greater its effect in enhancing the plant’s response. This is because most effects of Si are expressed through the formation of silica gel, which is deposited on leaves, stems, and other organs of plants (Ma and Yamaji, 2006). Therefore, for the plant to benefit from Si, a high accumulation is required. However, Si accumulation greatly varies with plant species, and this difference has been attributed to the ability of plants to take up Si.Transporters responsible for Si uptake by roots have been identified in several plant species, including barley, maize (Zea mays), pumpkin (Cucurbita moschata), rice, wheat (Ma et al., 2011), and most recently in horsetail (Equisetum arvense; EaNIP3s [for Nod26-like major intrinsic protein3]; Grégoire et al., 2012). Two different types of transporter, Si-permeable channel and efflux transporter, are involved in the Si-uptake process. Low Silicon1 (Lsi1) belongs to a NIP subfamily of aquaporin-like proteins and functions as a Si-permeable channel. Lsi1 in rice is localized in the distal side of root exodermis and endodermis (Ma et al., 2006), but Lsi1 in barley, maize, and pumpkin is localized in the epidermis and cortex (Chiba et al., 2009; Mitani et al., 2009b, 2011). On the other hand, Lsi2 functions as an efflux Si transporter and belongs to a putative anion transporter family without any similarity to Lsi1. Lsi2 in rice is also localized at the root exodermis and endodermis as Lsi1, but it is polarly localized at the proximal side (Ma et al., 2007). By contrast, Lsi2 in barley and maize is localized only to the endodermis of roots. Furthermore, these transporters do not show polar localization in barley and maize (Mitani et al., 2009a). Therefore, Si uptake mediated by Lsi1 and Lsi2 shows different pathways between rice and other plant species (Ma et al., 2011).Following uptake by the roots through Lsi1 and Lsi2, Si is translocated to the aboveground part and distributed in different tissues. Lsi6, a homolog of Lsi1, is involved in xylem unloading of Si in rice (Yamaji et al., 2008). Lsi6 is localized on the adaxial side of the xylem parenchyma cells in the leaf sheaths and leaf blades. Knockout of Lsi6 resulted in altered distribution of Si in the leaf cells. Furthermore, at the reproductive growth stage of rice, Lsi6 is also highly expressed at the nodes (Yamaji and Ma, 2009). At node I below the panicle, Lsi6 is mainly localized at the xylem transfer cells with polarity facing toward the xylem vessel (Yamaji and Ma, 2009). Knockout of Lsi6 decreased Si accumulation in the panicle but increased Si accumulation in the flag leaf. These findings indicate that Lsi6 is also required for the intervascular transfer of Si in rice, transferring Si from the enlarged vascular bundles coming from the roots to the diffuse vascular bundles connected to the panicle.Barley is a Si-accumulating species, although the accumulation extent is lower than that of rice. Transporters responsible for Si uptake in barley roots have been identified (Chiba et al., 2009; Mitani et al., 2009a); however, transporters for Si distribution in aboveground plant tissues are unknown. In this study, we functionally characterized a rice Lsi6 homolog gene in barley, HvLsi6, in terms of transport activity and expression pattern, as well as cellular and subcellular localizations. We found that HvLsi6 is probably involved in Si uptake in the root tip, xylem unloading in the leaf, and intervascular transfer of Si at the nodes in barley. We further found that HvLsi2 was also expressed in the nodes and involved in the intervascular transfer by coupling with HvLsi6.     

Genetico-demographic patterns of the prevalence of various forms of endogenous psychoses

Prevalence rates (PRs) for EFP (schizophrenic, schizoaffective and affective psychoses), with allowance for proband sex and age-of-onset data were studied in a subdivided population from the North-East of the European Region of the USSR. The population includes three subpopulations: a small old religious semi-isolate of Russians ("Rs"), aboriginal Komi people ("Ks")--an ethnic community of Ugro-Finnish lineage, and a mixed group of migrants ("Ms") from various regions of the USSR. The latter is mainly an urban population, while the "Rs" and "Ks" are, on the whole, rural populations. The total PR for EFP was found to be 0.97% for the "Rs", 0.63% for the "Ks" and 0.35% for the "Ms", whereas PRs-0.85-1.15% in other parts of the USSR, mainly for "panmixed" populations in large towns. The lower PRs for EFP in the "Ms" is caused by a backmigration flow involving certain groups of patients; consequently, the mean liability for "Ms" offsprings (as a whole) should also be lower. On the other hand, the lower PRs for EFP in the "Ks" is caused by underpresentation of clinically mild cases of the mental disease (mainly, pseudoneurotic schizophrenia), especially among female patients, probably due to that the so affected persons are sufficiently adapted to the cultural traditions of this rural population. It was shown that in the "Rs" the total PR for "nuclear" and paranoid schizophrenia is 0.68% versus 0.25% in a "panmixed" population. The increase is most likely caused by the high inbreeding level in the "Rs" semi-isolate, and if this is correct, we may suppose that at least one or two recessive genes are involved in the liability to the most heavy forms of schizophrenia. On the other hand, in the "Ms" (as in other "panmixed" populations) positive assortative mating among hereditary-predisposed persons is a more significant factor influencing family transmission of EFP, since the correlation between probands and their spouses is rpp = 0.31 (p less than 0.001) in the "Ms", as compared to rpp = 0.19 (p less than 0.1) in the "Rs". Thus, our general conclusion is that neither the place of inhabitance nor the life mode are the causal factors for EFP, but rather some genetic factors, more accurately, certain sets of specific genes.     

Quantification of the Impact of Feature Selection on the Variance of Cross-Validation Error Estimation

Given the relatively small number of microarrays typically used in gene-expression-based classification, all of the data must be used to train a classifier and therefore the same training data is used for error estimation. The key issue regarding the quality of an error estimator in the context of small samples is its accuracy, and this is most directly analyzed via the deviation distribution of the estimator, this being the distribution of the difference between the estimated and true errors. Past studies indicate that given a prior set of features, cross-validation does not perform as well in this regard as some other training-data-based error estimators. The purpose of this study is to quantify the degree to which feature selection increases the variation of the deviation distribution in addition to the variation in the absence of feature selection. To this end, we propose the coefficient of relative increase in deviation dispersion (CRIDD), which gives the relative increase in the deviation-distribution variance using feature selection as opposed to using an optimal feature set without feature selection. The contribution of feature selection to the variance of the deviation distribution can be significant, contributing to over half of the variance in many of the cases studied. We consider linear-discriminant analysis, 3-nearest-neighbor, and linear support vector machines for classification; sequential forward selection, sequential forward floating selection, and the -test for feature selection; and -fold and leave-one-out cross-validation for error estimation. We apply these to three feature-label models and patient data from a breast cancer study. In sum, the cross-validation deviation distribution is significantly flatter when there is feature selection, compared with the case when cross-validation is performed on a given feature set. This is reflected by the observed positive values of the CRIDD, which is defined to quantify the contribution of feature selection towards the deviation variance.[1,2,3,4,5,6,7,8,9,10,11,12,13]     

Source-sink landscape theory and its ecological significance

Exploring the relatiouships between landscape pattern and ecological processes is the key topic of landscape ecology,for which,a large number of indices as well as landscape pattern analysis model were developed.However,one problem faced by landscape ecologists is that it is hard to link the landscape indices with a specific ecological process.Linking landscape pattern and ecological processes has become a challenge for landscape ecologists."Source" and "sink" are common concepts used in air pollution research,by which the movement direction and pattern of different pollutants in air can be clearly identified.In fact,for any ecological process,the research can be considered as a balance between the source and the sink in space.Thus,the concepts of "source" and "sink" could be implemented to the research of landscape pattern and ecological processes.In this paper,a theory of sourcesink landscape was proposed,which include:(1) In the research of landscape pattern and ecological process,all landscape types can be divided into two groups,"source"landscape and "sink" landscape."Source" landscape contributes positively to the ecological process,while "sink" landscape is unhelpful to the ecological process.(2) Both landscapes are recognized with regard to the specific ecological process."Source" landscape in a target ecological process may change into a "sink"landscape as in another ecological process.Therefore,the ecological process should be determined before "source"or "sink" landscape were defined.(3) The key point to distinguish "source" landscape from "sink" landscape is to quantify the effect of landscape on ecological process.The positive effect is made by "source" landscape,and the negative effect by "sink" landscape.(4) For the same ecological process,the contribution of "source" landscapes may vary,and it is the same to the "sink"landscapes.It is required to determine the weight of each landscape type on ecological processes.(5) The sourcesink principle can be applied to non-point source pollution control,biologic diversity protection,urban heat island effect mitigation,etc.However,the landscape evaluation models need to be calibrated respectively,because different ecological processes correspond with different source-sink landscapes and evaluation models for the different study areas.This theory is helpful to further study landscape pattern and ecological process,and offers a basis for new landscape index design.     

Refined crystal structures of "aged" and "non-aged" organophosphoryl conjugates of gamma-chymotrypsin

"Aged" organophosphoryl conjugates of serine hydrolases differ from the corresponding "non-aged" conjugates in their striking resistance to nucleophilic reactivation. The refined X-ray structures of "aged" and "non-aged" organophosphoryl conjugates of gamma-chymotrypsin were compared in order to understand the molecular basis for this resistance of "aged" conjugates. "Aged" and "non-aged" crystalline organophosphoryl-gamma-chymotrypsin conjugates were obtained by prolonged soaking of native gamma-chymotrypsin crystals with appropriate organophosphates. Thus, a representative "non-aged" conjugate, diethylphosphoryl-gamma-chymotrypsin, was obtained by soaking native crystals with paraoxon (diethyl-p-nitrophenyl phosphate), and a closely related "aged" conjugate, monoisopropyl-gamma-chymotrypsin, was obtained by soaking with diisopropylphosphorofluoridate. In both crystalline conjugates, the refined structures clearly reveal a high occupancy of the active site by the appropriate organophosphoryl moiety within covalent bonding distance of Ser195 O gamma. Whereas in the "non-aged" conjugate both ethyl groups can be visualized clearly, in the putative "aged" conjugate, as expected, only one isopropyl group is present. There is virtually no difference between the "aged" and "non-aged" conjugates either with respect to the conformation of the polypeptide backbone as a whole or with respect to the positioning of the side-chains within the active site. In the "aged" conjugate, however, close proximity (2.6 A) of the negatively charged phosphate oxygen atom of the dealkylated organophosphoryl group to His57 N epsilon 2 indicates the presence of a salt bridge between these two moieties. In contrast, in the "non-aged" conjugate the DEP moiety retains its two alkyl groups; thus, lacking a negative oxygen atom, it does not enter into such a charge-charge interaction and its nearest oxygen atom is 3.6 A away from His57 N epsilon 2. It is suggested that steric constraints imposed by the salt bridge in the "aged" conjugate lie at the basis of its resistance to reactivation.     

Generation of Single-Copy Transposon Insertions in Clostridium perfringens by Electroporation of Phage Mu DNA Transposition Complexes

Transposon mutagenesis is a tool that is widely used for the identification of genes involved in the virulence of bacteria. Until now, transposon mutagenesis in Clostridium perfringens has been restricted to the use of Tn916-based methods with laboratory reference strains. This system yields primarily multiple transposon insertions in a single genome, thus compromising its use for the identification of virulence genes. The current study describes a new protocol for transposon mutagenesis in C. perfringens, which is based on the bacteriophage Mu transposition system. The protocol was successfully used to generate a single-insertion mutant library both for a laboratory strain and for a field isolate. Thus, it can be used as a tool in large-scale screening to identify virulence genes of C. perfringens.Clostridium perfringens is a gram-positive, anaerobic bacterium that forms heat-resistant spores. It is widespread in the soil and commonly found in the gastrointestinal tract of mammals. It has been implicated in several medical conditions in humans, ranging from mild food poisoning to necrotic enteritis and gas gangrene. C. perfringens strains also cause a variety of important diseases in domestic animals, including several enteric syndromes, such as enterotoxemia in cattle, sheep, and pigs, necrotic enteritis in poultry, and typhocolitis in equines (17, 40).Understanding the pathogenesis of these infections is of crucial importance for the development of new tools for the prevention and control of C. perfringens-related diseases. Genetic modification is a valuable approach to identify new virulence factors and to study their role in the pathogenesis of C. perfringens.Since the 1980s, several tools for manipulation of C. perfringens at the molecular level have been developed (1, 5, 28, 35, 38). Among these tools, transposon mutagenesis is a method that is widely used for identification of virulence genes. Until now, the only reproducible method for transposon mutagenesis in C. perfringens was based on Tn916, a tetracycline resistance-encoding conjugative transposon originally isolated from Enterococcus faecalis (10, 11, 13). Tn916 has been used extensively for transposon mutagenesis due to its broad host range and has been proven to be valuable for the identification of genes in C. perfringens (3, 7, 22). Nevertheless, this method has major disadvantages; multiple Tn916 insertion events occur with an incidence of 65% to 75%, severely complicating identification of genes responsible for phenotype changes (3, 7, 19). Furthermore, Tn916 is still active after insertion, resulting in unstable mutants (6, 39, 42). To our knowledge, generation of Tn916-derived transposon mutants in C. perfringens field strains has never been described.Although a variety of transposon mutagenesis methods are available for gram-positive bacteria (4, 37, 41, 43), the inherent species nonspecificity, as well as the lack of mobility of the integrated transposon, makes the bacteriophage Mu-based transposon delivery system a system of choice for a variety of species (16, 26, 46). The Mu transposition approach includes in vitro assembly of a complex between the transposon DNA and the transposase enzyme, the transpososome, followed by delivery of the transpososome into the recipient cells. Once inside a cell, the Mu transpososome becomes activated in the presence of divalent cations, resulting in genomic integration of the delivered transposon. The bacteriophage Mu transposition system is also functional in vitro (15, 32, 33), in contrast to the Tn916 mutagenesis strategy, which is restricted to transposon mobilization in vivo following conjugation or electroporation. Under the optimal in vitro conditions, the Mu transposition reaction requires only the MuA transposase, a mini-Mu transposon, and target DNA as macromolecular components (15).In this study, a novel protocol is described for transposon mutagenesis in C. perfringens that exploits the bacteriophage Mu transposition system. To our knowledge, this report is the first report describing a mutagenesis method generating single-insertion transposon mutants in laboratory and field isolates of C. perfringens. This method is important for the identification of C. perfringens virulence factors involved in the numerous diseases caused by this bacterium.