Strategies to repair lost sensory connections to the spinal cord

Failure of injured axons to regenerate in the central nervous system (CNS) is the main obstacle for repair of stroke and traumatic injuries to the spinal cord and sensory roots. This regeneration failure is high-lighted at the dorsal root transitional zone (DRTZ), the boundary between the peripheral (PNS) and central nervous system where sensory axons enter the spinal cord. Injured sensory axons regenerate in the PNS compartment of the dorsal root but are halted as soon as they reach the DRTZ. The failure of regenerating dorsal root axons to re-enter the mature spinal cord is a reflection of the generally nonpermissive nature of the CNS environment, in contrast to the regeneration supportive properties of the PNS. The dorsal root injury paradigm is therefore an attractive model for studying mechanisms underlying CNS regeneration failure in general and how to overcome the hostile CNS environment. Here we review the main lines that have been pursued to achieve growth of injured dorsal root axons into the spinal cord: (i) modifying the inhibitory nature of the DRTZ by breaking down or blocking the effect of growth repelling molecules, (ii) stimulate elongation of injured dorsal root axons by a prior conditioning lesion or administration of specific growth factors, (iii) implantation of olfactory ensheathing cells to provide a growth supportive cellular terrain at the DRTZ, and (iv) replacing the regeneration deficient adult dorsal root ganglion neurons with embryonic neurons or neural stem cells.     

Entobdella soleae--pointers to the future

The biology of the monogenean skin parasite Entobdella soleae and its relationship with its host, the common sole (Solea solea), are probably better known than those of any other monogeneans. The author describes his early involvement with this parasite and the special features of parasite and host that make this relationship so suitable for parasitological studies. Aspects of the biology of E. soleae that have been investigated are briefly mentioned, but most of the paper is concerned with areas of the parasite's biology that remain a challenge to determine. Unresolved areas are as follows: (1) the identity of the factor (or factors) in host skin mucus that stimulates hatching of the parasite's eggs; (2) whether or not the larvae of the parasite are attracted to their host; (3) the nature of factors controlling the contrasting behaviour of adult parasites on the upper and lower surfaces of the host; (4) how nutrients are supplied to the remote regions of the haptor; (5) whether the host has any control via its immune system over parasite invasion success and survival; (6) how the parasite copes with the migratory habits of some sole populations, assuming that such populations are infested with the parasite. The intimacy of this parasite/host relationship is its most remarkable feature, the reflection of which, not surprisingly, is the greatly restricted host range of the parasite. E. soleae has been reported from only three host species, all highly specialised bottom-dwelling members of Solea. It is all the more surprising that relatives of E. soleae, such as Neobenedenia melleni, retain the ability to parasitise an enormous range of hosts. How this versatility is achieved remains to be seen.     

Negative factor from SIV binds to the catalytic subunit of the V-ATPase to internalize CD4 and to increase viral infectivity

The accessory protein negative factor (Nef) from human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) is required for optimal viral infectivity and the progression to acquired immunodeficiency syndrome (AIDS). Nef interacts with the endocytic machinery, resulting in the down-regulation of cluster of differentiation antigen 4 (CD4) and major histocompatibility complex class I (MHCI) molecules on the surface of infected cells. Mutations in the C-terminal flexible loop of Nef result in a lower rate of internalization by this viral protein. However, no loop-dependent binding of Nef to adaptor protein-2 (AP-2), which is the adaptor protein complex that is required for the internalization of proteins from the plasma membrane, could be demonstrated. In this study we investigated the relevance of different motifs in Nef from SIV(mac239) for its internalization, CD4 down-regulation, binding to components of the trafficking machinery, and viral infectivity. Our data suggest that the binding of Nef to the catalytic subunit H of the vacuolar membrane ATPase (V-ATPase) facilitates its internalization. This binding depends on the integrity of the whole flexible loop. Subsequent studies on Nef mutant viruses revealed that the flexible loop is essential for optimal viral infectivity. Therefore, our data demonstrate how Nef contacts the endocytic machinery in the absence of its direct binding to AP-2 and suggest an important role for subunit H of the V-ATPase in viral infectivity.     

Improvement to the air-injection technique to estimate xylem vulnerability to cavitation

Several techniques have been developed to quantify the degree of embolism of the xylem using hydraulic conductance. Although there have been several improvements to these techniques, their reliability is still questionable and many technical pitfalls persist. We are proposing here a manometric approach to improve the accuracy of xylem cavitation measurement by the original air-injection technique which uses twigs exposed to pressurized air to cause cavitation. The measured parameter is air bubble production (P _b) caused by xylem cavitation in birch (Betula pendula Roth) twigs from which the percent increase in bubble production is calculated to quantify xylem cavitation. Data produced by three different methods (bench-drying, air-injection, and manometric approach) are compared. Xylem vulnerability curves (VCs) constructed by the reference and reliable bench-drying technique and the manometric approach show similar sigmoid “S” shape, but a small anomaly appeared in the VC constructed by the original air-injection technique. The xylem pressure inducing 50% of embolism (P ₅₀) was the same with the three techniques. Furthermore, there was a strong positive correlation between the estimators of xylem cavitation measured by the three different methods. For its reliability, precision and ease we recommend the manometric technique as an improved version of the original hydraulic air-injection method.     

Phosphoinositide binding to the substrate regulates susceptibility to proteolysis by calpain

Calpain-mediated proteolysis regulates cytoskeletal dynamics and is altered during aging and the progression of numerous diseases or pathological conditions. Although several cytoskeletal proteins have been identified as substrates, how localized calpain activity is regulated and the mechanisms controlling substrate recognition are not clear. In this study, we report that phosphoinositide binding regulates the susceptibility of the cytoskeletal adhesion protein alpha-actinin to proteolysis by calpains 1 and 2. At first, alpha-actinin did not appear to be a substrate for calpain 2; however, phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P(3)) binding to alpha-actinin resulted in nearly complete proteolysis of the full-length protein, producing stable breakdown products. Calpain 1 was able to cleave alpha-actinin in the absence of phosphoinositide binding; however, PtdIns(3,4,5)P(3) binding increased the rate of proteolysis, and phosphatidylinositol 4,5-diphosphate (PtdIns(4,5)P(2)) binding significantly inhibited cleavage. Phosphoinositide binding appeared to regulate calpain proteolysis of alpha-actinin by modulating the exposure of a highly sensitive cleavage site within the calponin homology 2 domain. In U87MG glioblastoma cells, which contain elevated levels of PtdIns(3,4,5)P(3), alpha-actinin colocalized with calpain within dynamic actin cytoskeletal structures. Furthermore, proteolysis of alpha-actinin producing stable breakdown products was observed in U87MG cells treated with calcium ionophore to activate the calcium-dependent calpains. Additional evidence of PtdIns(3,4,5)P(3)-mediated calpain proteolysis of alpha-actinin was observed in rat embryonic fibroblasts. These results suggest that PtdIns(3,4,5)P(3) binding is a critical determinant for alpha-actinin proteolysis by calpain. In conclusion, phosphoinositide binding to the substrate is a potential mechanism for regulating susceptibility to proteolysis by calpain.     

A contribution to the generalization of the Gompertz function

SCHARF (1976) discusses various growth models. For the Gompertz function the differential equation (Formula: see text) is used. In words: the difference between relative growth rate and relative growth acceleration is constant. On the other hand, according to WENK (1973), the differential equation (Formula: see text) applies to the Gompertz function. It can be shown mathematically that (Formula: see text) applies in general. From Eq. (2) one obtains without trouble (Formula: see text). Therefore, the property leading to the Gompertz function may be defined as follows; the logarithmic derivation of the relative growth rate is constant. Eq. (2) is applicable only in special cases. It can be extended by assuming that c is not constant, but a function of time. In this way, a great number of growth functions can be found, which have to be regarded as model-based extensions of the Gompertz function.     

Contribution of the FtsQ transmembrane segment to localization to the cell division site

The Escherichia coli cell division protein FtsQ is a central component of the divisome. FtsQ is a bitopic membrane protein with a large C-terminal periplasmic domain. In this work we investigated the role of the transmembrane segment (TMS) that anchors FtsQ in the cytoplasmic membrane. A set of TMS mutants was made and analyzed for the ability to complement an ftsQ mutant. Study of the various steps involved in FtsQ biogenesis revealed that one mutant (L29/32R;V38P) failed to functionally insert into the membrane, whereas another mutant (L29/32R) was correctly assembled and interacted with FtsB and FtsL but failed to localize efficiently to the cell division site. Our results indicate that the FtsQ TMS plays a role in FtsQ localization to the division site.     

Identification of nonprotein ligands to the metal ions bound to glutamine synthetase

Electron paramagnetic resonance (EPR) was used to study the environment of Mn2+ bound to the tight (n1) metal ion binding site of glutamine synthetase in the presence of analogues of the tetrahedral adduct, L-methionine (S)-sulfoximine [Met(O)(NH)-S] and L-methionine (R)-sulfoximine [Met(O)(NH)-R]. The Mn2+ EPR spectrum in the presence of Met(O)(NH)-S is identical with the previously published spectrum obtained from a mixture of isomers [Met(O)(NH)-RS] [Villafranca, J. J., Ash, D. E., & Wedler, F. C. (1976) Biochemistry 15, 544] and is characteristic of a highly octahedral metal ion environment with a small zero field splitting. The presence of Met(O)(NH)-R produces an EPR spectrum that appears characteristic of a more distorted metal ion environment, with a larger zero field splitting. These data demonstrate that the two isomers interact differently with the enzyme-bound Mn2+. Broadening of the Mn2+ EPR spectrum in the presence of Met(O)(NH) is observed in 17O-enriched water due to superhyperfine coupling of water to the metal ion. Deconvolution of the spectrum demonstrates the presence of at least a single water molecule in the inner coordination sphere of the metal ion. Superhyperfine coupling due to the 14N nucleus of the imine nitrogen of the sulfoximine moiety of Met(O)(NH)-S but not of Met(O)(NH)-R has been detected by electron spin-echo envelope modulation spectroscopy. Two intense peaks are evident in the presence of Met(O)(NH)-S with frequencies at 1.7 and 3.3 MHz. These peaks are absent when [15N]imine-labeled Met(O)(NH) is used, indicating the presence of the sulfoximine nitrogen of Met(O)(NH)-S in the inner coordination sphere of the metal ion.(ABSTRACT TRUNCATED AT 250 WORDS)     

LOV to BLUF: flavoprotein contributions to the optogenetic toolkit

Optogenetics is an emerging field that combines optical and genetic approaches to non-invasively interfere with cellular events with exquisite spatiotemporal control. Although it arose originally from neuroscience, optogenetics is widely applicable to the study of many different biological systems and the range of applications arising from this technology continues to increase. Moreover, the repertoire of light-sensitive proteins used for devising new optogenetic tools is rapidly expanding. Light, Oxygen, or Voltage sensing (LOV) and Blue-Light-Utilizing flavin adenine dinucleotide (FAD) (BLUF) domains represent new contributors to the optogenetic toolkit. These small (100-140-amino acids) flavoprotein modules are derived from plant and bacterial photoreceptors that respond to UV-A/blue light. In recent years, considerable progress has been made in uncovering the photoactivation mechanisms of both LOV and BLUF domains. This knowledge has been applied in the design of synthetic photoswitches and fluorescent reporters with applications in cell biology and biotechnology. In this review, we summarize the photochemical properties of LOV and BLUF photosensors and highlight some of the recent advances in how these flavoproteins are being employed to artificially regulate and image a variety of biological processes.     

Human D-Tyr-tRNA(Tyr) deacylase contributes to the resistance of the cell to D-amino acids

DTD (D-Tyr-tRNA(Tyr) deacylase) is known to be able to deacylate D-aminoacyl-tRNAs into free D-amino acids and tRNAs and therefore contributes to cellular resistance against D-amino acids in Escherichia coli and yeast. We have found that h-DTD (human DTD) is enriched in the nuclear envelope region of mammalian cells. Treatment of HeLa cells with D-Tyr resulted in nuclear accumulation of tRNA(Tyr). D-Tyr treatment and h-DTD silencing caused tRNA(Tyr) downregulation. Furthermore, inhibition of protein synthesis by D-Tyr treatment and h-DTD silencing were also observed. D-Tyr, D-Asp and D-Ser treatment inhibited mammalian cell viability in a dose-dependent manner; overexpression of h-DTD decreased the inhibition rate, while h-DTD-silenced cells became more sensitive to the D-amino acid treatment. Our results suggest that h-DTD may play an important role in cellular resistance against D-amino acids by deacylating D-aminoacyl tRNAs at the nuclear pore. We have also found that m-DTD (mouse DTD) is specifically enriched in central nervous system neurons, its nuclear envelope localization indicates that D-aminoacyl-tRNA editing may be vital for the survival of neurons under high concentration of D-amino acids.     

It takes two to tango to the melanosome

The role of clathrin adaptor proteins in sorting cargo in the biosynthetic and recycling routes is an area of intense research. In this issue, Delevoye et al. (2009. J. Cell Biol. doi:10.1083/jcb.200907122) show that a close interaction between the clathrin adaptor AP-1 and a kinesin motor KIF13A is essential for delivering melanogenic enzymes from recycling endosomes to nascent melanosomes and for organelle biogenesis.Melanosomes, along with platelet-dense granules and lung type II alveolar cell lamellar bodies, are lysosome-related organelles (LROs), compartments that originate from endosomes but are distinct from and usually coexist with lysosomes (Fig. 1). The most characteristic features of melanosomes are their ability to synthesize and store melanin and their presence in specialized pigmented cells such as skin melanocytes and iris and retinal pigment epithelial cells (Raposo and Marks, 2007; Wasmeier et al., 2008). In this issue, Delevoye et al. (see p. 247) report a melanogenic role for the clathrin adaptor AP-1 that involves interactions between the adaptor and the plus end kinesin motor KIF13A. An impressive set of data support a scenario in which the adaptor and the motor tightly interact, like in tango, to position donor recycling endosomes (REs) near nascent melanosomes at the cell periphery and to generate tubulovesicular intermediates that deliver newly synthesized pigmenting enzymes to melanosomes.Open in a separate windowFigure 1.Role of clathrin adaptor proteins in melanosome biogenesis. Post-Golgi trafficking routes of three melanosome cargoes (Pmel17, tyrosinase, and Tyrp1) in melanocytes are shown. Newly synthesized Pmel17 is transported to the limiting membrane and intraluminal vesicles of stage I melanosomes/early sorting endosomes via the plasma membrane. This process (depicted by a question mark) might involve clathrin and AP-2. From these EEA1-positive vacuolar endosomes, Pmel17 is sorted away from the late endosome/multivesicular body pathway into stage II melanosomes. Little is known as to how the enzymes essential for melanin synthesis, tyrosinase and Tyrp1, are sorted from the TGN to early REs, and it is likely that clathrin and its adaptors are involved in this process. Tyrosinase, which binds both AP-1 and -3, is transported to stage III melanosomes from tubular regions of REs, containing Tf/TfR and Rab11, by two distinct routes: one regulated by AP-3 and the other regulated by BLOC-1, BLOC-2, and perhaps AP-1. However, Tyrp1 binds only AP-1 and not AP-3, indicating a divergence of sorting mechanisms between tyrosinase and Tyrp1. Delevoye et al. (2009) now show that AP-1 interacts with the kinesin motor KIF13A to transport recycling endosomal domains to the melanocytic cell periphery. The close apposition of Tyrp1-containing tubules with melanosomes allows cargo transfer and biogenesis of stage III and IV melanosomes. Although Tf is found in these peripheral endosomal tubules, there appears to be a filtering mechanism that sorts it out before the tubules fuse with melanosomes. It is likely, although not yet confirmed, that BLOC-1 and -2 act in concert with AP-1 to transport Tyrp1. The tissue-specific Rabs, Rab32 and Rab38, might function in any or all of these pathways.Extensive studies have shown that melanosome biogenesis occurs in two waves that correspond to four morphologically distinct stages (Fig. 1; Marks and Seabra, 2001; Raposo and Marks, 2007). The first wave (stages I and II) is the formation of immature, pigment-free ellipsoidal melanosomes from vacuolar domains of early sorting endosomes. This process requires Pmel17, an integral membrane protein that likely reaches sorting endosomes by clathrin-dependent endocytosis from the plasma membrane. Upon proteolysis in the sorting endosomes/stage I melanosomes, Pmel17 forms intraluminal proteinaceous fibrils with characteristics of amyloid. The second wave starts with the post-Golgi transport of enzymes involved in melanin synthesis such as tyrosinase and tyrosinase-related protein 1 (Tyrp1) to nascent melanosomes. Melanin deposition occurs on Pmel17 fibrils and leads to the biogenesis of mature (stages III and IV) melanosomes. The clathrin adaptors AP-1 and -3 have partially redundant functions in sorting cargo proteins to melanosomes. Melanosomal cargo proteins have dileucine motifs that are recognized differentially by AP-1 and -3 in post-Golgi endosomes (Huizing et al., 2001; Theos et al., 2005). Nascent tyrosinase is found in distinct endosomal buds that contain either AP-3 or -1 in normal melanocytes and loss of AP-3 results only in a partial mislocalization of the enzyme. As these adaptors also mediate sorting from endosomes to other compartments, additional machinery, such as biogenesis of LRO complex 1 (BLOC-1), BLOC-2, and the tissue-specific small GTPases Rab32 and Rab38, regulate cargo delivery to melanosomes. Mutations in components of this melanosomal targeting machinery result in a variety of well-studied pigmentation defects in humans and animals such as Hermansky–Pudlak syndrome (Wei, 2006).Delevoye et al. (2009) show that knockdown of AP-1 in melanocytic MNT-1 cells decreases melanin content, demonstrating that AP-1 has a role in melanogenesis. Only late-stage (III/IV) melanosomes are decreased in number; unpigmented (stage I/II) melanosomes are unaffected, indicating that AP-1 functions selectively in the second wave of melanosome biogenesis. In AP-1–depleted cells, the melanosome cargo protein Tyrp1 is retained in vacuolar endosomes in a manner similar to that seen in BLOC-1–deficient melanocytes (Setty et al., 2007). Using immunofluorescence to monitor markers of various endosomal compartments, Delevoye et al. (2009) show that AP-1 performs its melanogenic function in early REs. Interestingly, additional data show that AP-1–containing REs have a peripheral distribution in MNT-1 cells, which is strikingly different from the perinuclear localization observed in other cells. Furthermore, siRNA-mediated knockdown of AP-1, but not of AP-3, relocates RE to a pericentriolar location.How might AP-1 influence endosome position? One possibility is by its association with the plus end–directed kinesin motor KIF13A (Fig. 1). Nakagawa et al. (2000) have previously shown that a subunit of AP-1 binds the C-terminal domain of KIF13A, mediating TGN to plasma membrane transport of the mannose 6-phosphate receptor. Indeed, Delevoye et al. (2009) show that KIF13A partially colocalizes with AP-1 in MNT-1 cells and coimmunoprecipitates with both AP-1 and Tyrp1. Furthermore, knockdown of KIF13A replicates the phenotype seen with AP-1 depletion: pericentriolar clustering of RE, accumulation of Tyrp1 in vacuolar endosomes, and reduction in mature melanosomes and melanin content. Delevoye et al. (2009) go on to show that the peripheral RE localization facilitates sorting of melanosomal proteins but decreases the efficiency of transferrin (Tf) receptor (TfR) recycling to the plasma membrane. They also show the converse; i.e., the pericentriolar localization of RE decreases the efficiency of melanosomal targeting and increases the efficiency of TfR recycling. Thus, the position of REs, determined by the interaction between a clathrin adaptor and a kinesin, is key for specific sorting functions of this organelle (like TfR recycling) and also regulates the biogenesis of another organelle (the melanosome). This is a novel and exciting finding and is an emerging theme in cell biology. It was recently reported that AP-1 interacts with another plus end–directed kinesin, KIF5, which helps transport endosomes to the cell periphery (Schmidt et al., 2009).The next question that Delevoye et al. (2009) approach is what is the nature of the carriers that transport melanosomal proteins from peripheral REs to immediately adjacent stage III/IV melanosomes? Live imaging experiments showed a dynamic network of Tf-containing RE tubules that extend and retract, making contact with melanosomes for at least 30 s. Double-tilt 3D electron tomography of thick (350–400 nm) sections of cells preserved by high pressure freezing and freeze substitution, a technique recently adapted to the study of melanosomes by Hurbain et al. (2008), revealed that some of these tubular elements are continuous with the melanosomal limiting membrane and that their lumens are often connected. Collectively, these results indicate that peripheral RE domains serve to deliver biosynthetic cargo to maturing melanosomes by the coordinated actions of AP-1 and KIF13A and that the mechanism involves tubular connections rather than vesicular transport (Fig. 1).The study by Delevoye et al. (2009) beautifully demonstrates the power of carefully chosen morphological and live imaging techniques, in combination with siRNA-mediated knockdown of molecules under study, to elucidate important details of cellular sorting processes. As always, several questions emerge from their results. Does this type of mechanism also operate in perinuclear REs, which were recently shown to cooperate with adjacent TGN in biosynthetic trafficking to the plasma membrane (Cancino et al., 2007; Gravotta et al., 2007)? Do newly synthesized melanosomal enzymes move from the TGN to REs using vesicular trafficking and clathrin adaptors or, rather, result from “maturation” of REs from the TGN? What is the role of clathrin in melanosome maturation? Are AP-1 and KIF13A essential for tubulogenesis from REs as the authors speculate? How are RE proteins (e.g., TfR) prevented from incorporating into melanosomes through the tubular connections? What is the mechanism that regulates docking and fusion of RE tubules with melanosomes? Likely, Rab32 and Rab38 participate in this process, as these proteins localize to tubulovesicular endosomal structures, and their loss causes mislocalization of tyrosinase and Tyrp1 (Wasmeier et al., 2006), but the SNAREs (if any) that participate in the mechanism are still unknown. Lastly, another intriguing aspect of this study is how adaptors sort proteins by differential recognition of dileucine motifs. Tyrp1 also has a dileucine motif that exclusively binds AP-1, but not AP-3, in melanocytic cells (Theos et al., 2005), whereas tyrosinase has dileucine motifs that bind AP-1 and -3, indicating that not all dileucine motifs are equal in the eyes of the adaptor.     

Methylmercury's chemistry: From the environment to the mammalian brain

Methylmercury is a neurotoxicant that is found in fish and rice. MeHg's toxicity is mediated by blockage of -SH and -SeH groups of proteins. However, the identification of MeHg's targets is elusive. Here we focus on the chemistry of MeHg in the abiotic and biotic environment. The toxicological chemistry of MeHg is complex in metazoans, but at the atomic level it can be explained by exchange reactions of MeHg bound to –S(e)H with another free –S(e)H group (R¹S(e)-HgMe + R²-S(e)H ↔ R¹S(e)H + R²-S(e)-HgMe). This reaction was first studied by professor Rabenstein and here it is referred as the “Rabenstein's Reaction”. The absorption, distribution, and excretion of MeHg in the environment and in the body of animals will be dictated by Rabenstein's reactions. The affinity of MeHg by thiol and selenol groups and the exchange of MeHg by Rabenstein's Reaction (which is a diffusion controlled reaction) dictates MeHg's neurotoxicity. However, it is important to emphasize that the MeHg exchange reaction velocity with different types of thiol- and selenol-containing proteins will also depend on protein-specific structural and thermodynamical factors. New experimental approaches and detailed studies about the Rabenstein's reaction between MeHg with low molecular mass thiol (LMM-SH) molecules (cysteine, GSH, acetyl-CoA, lipoate, homocysteine) with abundant high molecular mass thiol (HMM-SH) molecules (albumin, hemoglobin) and HMM-SeH (GPxs, Selenoprotein P, TrxR1-3) are needed. The study of MeHg migration from –S(e)-Hg- bonds to free –S(e)H groups (Rabenstein's Reaction) in pure chemical systems and neural cells (with special emphasis to the LMM-SH and HMM-S(e)H molecules cited above) will be critical to developing realistic constants to be used in silico models that will predict the distribution of MeHg in humans.     

Mitochondrial density contributes to the immune response of macrophages to lipopolysaccharide via the MAPK pathway

We investigated the role of mitochondrial reactive oxygen species (ROS) in the response of macrophages to lipopolysaccharide (LPS) using RAW 264.7 cells and their ρ(o) cells lacking mitochondria. Mitochondrial density, respiratory activity and related proteins in ρ(o) cells were significantly lower than those in RAW cells. LPS rapidly stimulated mitochondrial ROS prior to cytokine secretion, such as TNF-α and IL-6, from RAW 264.7 cells by activating the MAPK pathway, while the response was attenuated in ρ(o) cells. Exposure of ρ(o) cells to H(2)O(2) partially restored the secretion of cytokines induced by LPS. These results suggest that mitochondrial density and/or the respiratory state contribute to intracellular oxidative stress, which is responsible for the stimulation of LPS-induced MAPK signaling to enhance cytokine release from macrophages.     

Contributions to the debate on water transport

The useful criticisms of my theory of water transport by Comstock (American Journal of Botany 86: 1077-1081) and by Stiller and Sperry (American Journal of Botany 86: 1082-1086) are acknowledged and reviewed. I make the following responses. (1) Tensile stresses to contain tissue pressure are kept within modest limits by the organization of vascular tissues into cylindrical bundles with small ratios of radius/boundary thickness. (2) The balance of pressures within tissues of a nontranspiring leaf is best understood by treating it as a single compartment containing several pressure-generating engines whose resultant is the pressure throughout the compartment. An error in the published notional balances for a transpiring leaf is corrected. (3) The argument against a valve in the transpiring leaf, which allows water out but not in, is not convincing. (4) The "robust and extremely consistent" cohesion theory gains this status by neglecting large bodies of experimental fact, once well known to plant physiologists. (5) The demonstration that living cells are not involved in the refilling of embolisms in birch stems is welcomed as an important advance. However, the major questions remain unresolved. (6) Proof is still needed that embolisms in vessels are not refilled by the collapse of gas bubbles under small positive pressures during conductance measurement. (7) The survival of unbroken water threads in vessels under centrifugal stress has still not been demonstrated. (8) Both questions 6 and 7 can be easily answered by direct observation of gas/liquid volumes in frozen stems in the cryo-scanning electron microscope.     

Ringing changes to the 'bell-shaped curve'

The 'bell-shaped' curve relating cytosolic Ca(2+) concentration to IP(3) receptor activation is considered important in the generation of the complex Ca(2+) signals seen inside many cells. But recent findings suggest this bimodal relationship is not always evident and may not apply to some IP(3) receptor isoforms.     

Four ways to define the growing season

What is addressed as growing season in terrestrial ecosystems is one of the main determinants of annual plant biomass production globally. However, there is no well-defined concept behind. Here, we show different facets of what might be termed growing season, each with a distinct meaning: (1) the time period during which a plant or a part of it actually grows and produces new tissue, irrespective of net carbon gain (growing season sensu stricto). (2) The period defined by developmental, that is, phenological markers (phenological season). (3) The period during which vegetation as a whole achieves its annual net primary production (NPP) or a net ecosystem production (NEP), expressed as net carbon gain (productive season) and (4) the period during which plants could potentially grow based on meteorological criteria (meteorological season). We hypothesize that the duration of such a ‘window of opportunity’ is a strong predictor for NPP at a global scale, especially for forests. These different definitions have implications for the understanding and modelling of plant growth and biomass production. The common view that variation in phenology is a proxy for variation in productivity is misleading, often resulting in unfounded statements on potential consequences of climatic warming such as carbon sequestration.     

Letter to the Editor

Regarding Paper “Sample size determination in clinical trials with multiple co‐primary endpoints including mixed continuous and binary variables” by T. Sozu , T. Sugimoto , and T. Hamasaki Biometrical Journal (2012) 54 (5): 716–729 Article: http://dx.doi.org/10.1002/bimj.201100221 Authors' Reply: http://dx.doi.org/10.1002/bimj.201300032 This paper recently introduced a methodology for calculating the sample size in clinical trials with multiple mixed binary and continuous co‐primary endpoints modeled by the so‐called conditional grouped continuous model (CGCM). The purpose of this note is to clarify certain aspects of the methodology and propose an alternative approach based on latent means tests for the binary endpoints. We demonstrate that our approach is more powerful, yielding smaller sample sizes at powers comparable to those used in the paper.     

Introduction to the Rosetta Special Collection

The Rosetta macromolecular modeling software is a versatile, rapidly developing set of tools that are now being routinely utilized to address state-of-the-art research challenges in academia and industrial research settings. A Rosetta Conference (RosettaCon) describing updates to the Rosetta source code is held annually. Every two years, a Rosetta Conference (RosettaCon) special collection describing the results presented at the annual conference by participating RosettaCommons labs is published by the Public Library of Science (PLOS). This is the introduction to the third RosettaCon 2014 Special Collection published by PLOS.     

Osteometric dimensions of metacarpal bones with respect to the professional exposure to vibration

The comparative analysis of the osteometric dimensions of metacarpal bones in three groups of males (aged from 23 to 63 years) differing with respect to the presence of the professionally connected long-term exposure to the vibration is performed. The sample encompasses forest workers employed in wood industry (exposed to heavy physical work and to the daily use of hand-held vibrating tools) from two regions of Croatia: Podravina (n = 192) and Gorski Kotar (n = 115). The control group is formed using the random sample (selected according to age criterion) of phenotypically healthy male inhabitants of rural communities of Eastern Adriatic islands and peninsula (n = 200). Additionally, the influence of the level of calcium in diet, as a regional nutritional characteristic of particular regions of Croatia, is also considered. The regression of the percent cortical area (PCA) of the second left metacarpal bone and age showed that significant decrease of PCA in older age can be observed only in males from Eastern Adriatic (the control group), while that is not so in either group of males professionally exposed to vibration. Authors conclude that the analysis of the osteometric dimensions performed on males professionally daily exposed to vibration missed to provide evidence to support the hypothesis of long-term exposure to vibration as a risk for accelerated osteoporosis of metacarpal bones.