Why do lower order branches show greater shoot growth than higher order branches? Considering space availability as a factor affecting shoot growth

Many woody plants show hierarchical shoot growth: annual shoot length decreased with increasing branching order. We hypothesize that plants showing hierarchical shoot growth improve the efficiency in terms of space acquisition and use per invested shoot length. This hypothesis was tested by using a simple geometric simulation model of branch development. In this study, the effective shoot length (EL), the shoot length produced within a growth season without any overlap from other shoots, was used as the index of space availability. We compared EL among shoots on different branching orders of a “simulated” branch system. The EL decreased with an increasing branching order. The results suggested that space availability decreased with increasing branching orders. The results also showed that simulated plants with the hierarchical shoot growth showed higher efficiency in terms of space acquisition per investment than those with the non-hierarchical shoot growth. We concluded that the difference in space availability between the branching orders could be an important ultimate factor causing hierarchical shoot growth.     

Effects of experimental season of prescribed fire and nutrient addition on structure and function of previously grazed grassland

Aims Understanding the drivers of grassland structure and function following livestock removal will inform grassland restoration and management. Here, we investigated the effects of fire and nutrient addition on structure and function in a subtropical semi-native grassland recently released from grazing in south-central Florida. We examined responses of soil nutrients, plant tissue nutrients, biomass of live, standing dead and litter, and plant species composition to experimental annual prescribed fire applied during different seasons (wet season vs. dry season), and nutrient additions (N, P and N + P) over 9 years.Methods Experimental plots were set up in a randomized block split-plot design, with season of prescribed fire as the main treatment and nutrient addition as the subplot treatment. Species cover data were collected annually from 2002 to 2011 and plant tissue and plant biomass data were collected in 2002–2006 and 2011. Soil nutrients were analyzed in 2004, 2006 and 2011.Important findings Soil total phosphorus (P) levels increased substantially with P addition but were not influenced by prescribed fire. Addition of P and N led to increased P and N concentrations in live plant tissues, but prescribed fire reduced N in live tissue. Levels of tissue N were higher in all plots at the beginning of the experiment, an effect that was likely due to grazing activity prior to removal of livestock. Plant tissue N steadily declined over time in all plots, with annually burned plots declining faster than unburned plots. Prescribed fire was an important driver of standing dead and litter biomass and was important for maintaining grass biomass and percent cover. Nutrient addition was also important: the addition of both N and P was associated with greater live biomass and woody forbs. Removal of grazing, lack of prescribed fire, and addition of N + P led to a reduction of grass biomass and a large increase in biomass of a woody forb. Annual prescribed fire promoted N loss from the system by reducing standing dead and litter, but maintained desirable biomass of grasses.     

Brox, a novel farnesylated Bro1 domain-containing protein that associates with charged multivesicular body protein 4 (CHMP4)

Human Brox is a newly identified 46 kDa protein that has a Bro1 domain-like sequence and a C-terminal thioester-linkage site of isoprenoid lipid (CAAX motif) (C standing for cysteine, A for generally aliphatic amino acid, and X for any amino acid). Mammalian Alix and its yeast ortholog, Bro1, are known to associate with charged multivesicular body protein 4 (CHMP4), a component of endosomal sorting complex required for transport III, via their Bro1 domains and to play roles in sorting of ubiquitinated cargoes. We investigated whether Brox has an authentic Bro1 domain on the basis of its capacity for interacting with CHMP4s. Both Strep Tactin binding sequence (Strep)-tagged wild-type Brox (Strep-Brox(WT)) and Strep-tagged farnesylation-defective mutant (Cys-->Ser mutation; Strep-Brox(C408S)) pulled down FLAG-tagged CHMP4b that was coexpressed in HEK293 cells. Treatment of cells with a farnesyltransferase inhibitor, FTI-277, caused an electrophoretic mobility shift of Strep-Brox(WT), and the mobility coincided with that of Strep-Brox(C408S). The inhibitor also caused a mobility shift of endogenous Brox detected by western blotting using polyclonal antibodies to Brox, suggesting farnesylation of Brox in vivo. Fluorescence microscopic analyses revealed that Strep-Brox(WT) exhibited accumulation in the perinuclear area and caused a punctate pattern of FLAG-CHMP4b that was constitutively expressed in HEK293 cells. On the other hand, Strep-Brox(C408S) showed a diffuse pattern throughout the cell, including the nucleus, and did not cause accumulation of FLAG-CHMP4b. Fluorescent signals of monomeric green fluorescent protein (mGFP)-fused Brox(WT) merged partly with those of Golgi markers and with those of abnormal endosomes induced by overexpression of a dominant negative mutant of AAA type ATPase SKD1/Vps4B in HeLa cells, but such colocalization was less efficient for mGFP-Brox(C408S). These results suggest a physiological significance of farnesylation of Brox in its subcellular distribution and efficient interaction with CHMP4s in vivo.     

Thermal unfolding mechanism of lipocalin-type prostaglandin D synthase

Lipocalin-type prostaglandin (PG) D synthase (L-PGDS) is a dual-functioning protein in the lipocalin family, acting as a PGD(2)-synthesizing enzyme and as an extracellular transporter for small lipophilic molecules. We earlier reported that denaturant-induced unfolding of L-PGDS follows a four-state pathway, including an activity-enhanced state and an inactive intermediate state. In this study, we investigated the thermal unfolding mechanism of L-PGDS by using differential scanning calorimetry (DSC) and CD spectroscopy. DSC measurements revealed that the thermal unfolding of L-PGDS was a completely reversible process at pH 4.0. The DSC curves showed no concentration dependency, demonstrating that the thermal unfolding of L-PGDS involved neither intermolecular interaction nor aggregation. On the basis of a simple two-state unfolding mechanism, the ratio of van't Hoff enthalpy (DeltaH(vH)) to calorimetric enthalpy (DeltaH(cal)) was below 1, indicating the presence of an intermediate state (I) between the native state (N) and unfolded state (U). Then, statistical thermodynamic analyses of a three-state unfolding process were performed. The heat capacity curves fit well with a three-state process; and the estimated transition temperature (T(m)) and enthalpy change (DeltaH(cal)) of the N<-->I and I<-->U transitions were 48.2 degrees C and 190 kJ.mol(-1), and 60.3 degrees C and 144 kJ.mol(-1), respectively. Correspondingly, the thermal unfolding monitored by CD spectroscopy at 200, 235 and 290 nm revealed that L-PGDS unfolded through the intermediate state, where its main chain retained the characteristic beta-sheet structure without side-chain interactions.     

Effects of CO2-bath immersion (100 ppm) on thermoregulatory responses in humans

The effects of CO₂ (100 ppm) bathing were investigated. It was found that the chest blood flow, chest sweat rate and tympanic temperature were significantly greater during the immersion in CO₂ bathing than in freshwater bathing (P<0.05). Thus, CO₂ bathing at 100 ppm could produce cutaneous vasodilatation in the immersed skin, affecting thermoregulation.     

Diversity and similarity of microbial communities in petroleum crude oils produced in Asia

To understand microbial communities in petroleum crude oils, we precipitated DNA using high concentrations of 2,2,4-trimethylpentane (isooctane) and purified. Samples of DNA from five crude oils, (Middle East, 3; China, 1; and Japan, 1) were characterized based upon their 16S rRNA gene sequences after PCR amplification and the construction of clone libraries. We detected 48 eubacterial species, one cyanobacterium, and one archaeon in total. The microbial constituents were diverse in the DNA samples. Most of the bacteria affiliated with the sequences of the three oils from the Middle East comprised similar mesophilic species. Acinetobacter, Propionibacterium, Sphingobium and a Bacillales were common. In contrast, the bacterial communities in Japanese and Chinese samples were unique. Thermophilic Petrotoga-like bacteria (11%) and several anaerobic-thermophilic Clostridia- and Synergistetes-like bacteria (20%) were detected in the Chinese sample. Different thermophiles (12%) and Clostridia (2%) were detected in the Japanese sample.     

Characterization of two different endo-alpha-N-acetylgalactosaminidases from probiotic and pathogenic enterobacteria, Bifidobacterium longum and Clostridium perfringens

Endo-alpha-N-acetylgalactosaminidase (endo-alpha-GalNAc-ase) catalyzes the hydrolysis of the O-glycosidic bond between alpha-GalNAc at the reducing end of mucin-type sugar chains and serine/threonine of proteins to release oligosaccharides. Previously, we identified the gene engBF encoding endo-alpha-GalNAc-ase from Bifidobacterium longum, which specifically released the disaccharide Gal beta 1-3GalNAc (Fujita K, Oura F, Nagamine N, Katayama T, Hiratake J, Sakata K, Kumagai H, Yamamoto K. 2005. Identification and molecular cloning of a novel glycoside hydrolase family of core 1 type O-glycan-specific endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum. J Biol Chem. 280:37415-37422). Here we cloned a similar gene named engCP from Clostridium perfringens, a pathogenic enterobacterium, and characterized the gene product EngCP. Detailed analyses on substrate specificities of EngCP and EngBF using a series of p-nitrophenyl-alpha-glycosides chemically synthesized by the di-tert-butylsilylene-directed method revealed that both enzymes released Hex/HexNAc beta 1-3GalNAc (Hex = Gal or Glc). EngCP could also release the core 2 trisaccharide Gal beta 1-3(GlcNAc beta 1-6)GalNAc, core 8 disaccharide Gal alpha 1-3GalNAc, and monosaccharide GalNAc. Our results suggest that EngCP possesses broader substrate specificity than EngBF. Actions of the two enzymes on native glycoproteins and cell surface glycoproteins were also investigated.     

Novel echinocandin antifungals. Part 1: novel side-chain analogs of the natural product FR901379

A series of novel acylated analogs of the novel water-soluble echinocandin FR901379 have been prepared and evaluated for antifungal and hemolytic activity. A relationship between antifungal activity and lipophilicity of the acyl side chain, expressed as ClogP was demonstrated, and an analog (3c) with 5.5- to 8-fold superior in vivo activity relative to the previously disclosed 4-(n-octyloxy)benzoyl side chain analog, FR131535 obtained.     

The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins

Double-stranded RNA induces RNA silencing and is cleaved into21–24 nt small RNA duplexes by Dicer enzyme. A strandof Dicer-generated small RNA duplex (called the guide strand)is then selected by a thermodynamic mechanism to associate withArgonaute (AGO) protein. This AGO–small RNA complex functionsto cleave mRNA, repress translation or modify chromatin structurein a sequence-specific manner. Although a model plant, Arabidopsisthaliana, contains 10 AGO genes, their roles and molecular mechanismsremain obscure. In this study, we analyzed the roles of ArabidopsisAGO2 and AGO5. Interestingly, the 5' nucleotide of small RNAsthat associated with AGO2 was mainly adenine (85.7%) and thatwith AGO5 was mainly cytosine (83.5%). Small RNAs that wereabundantly cloned from the AGO2 immunoprecipitation fraction(miR163-LL, which is derived from the Lower Left of mature miR163in pre-miR163, and miR390) and from the AGO5 immunoprecipitationfraction (miR163-UL, which is derived from the Upper Left ofmature miR163 in pre-miR163, and miR390^*) are derived from thesingle small RNA duplexes, miR163-LL/miR163-UL and miR390/miR390^*.Each strand of the miR163-LL/miR163-UL duplex is selectivelysorted to associate with AGO2 or AGO5 in a 5' nucleotide-dependentmanner rather than in a thermodynamic stability-dependent manner.Furthermore, we showed that both AGO2 and AGO5 have the abilityto bind cucumber mosaic virus-derived small RNAs. These resultsclearly indicate that the mechanism selecting the guide strandis different among AGO proteins and that multiple AGO genesare involved in anti-virus defense in plants.     

Temperature-dependent changes of cell shape during heterophyllous leaf formation in <Emphasis Type="Italic">Ludwigia </Emphasis><Emphasis Type="Italic">arcuata</Emphasis> (Onagraceae)

Although elongation of epidermal cells in submerged leaves is thought to be a common feature of heterophyllous aquatic plants, such elongation has not been observed in Ludwigia arcuata Walt. (Onagraceae). In this study we found that reduced culture temperature induced the elongation of epidermal cells of submerged leaves in L. arcuata. Since such submerged leaves also showed a reduction in the number of epidermal cells aligned across the leaf transverse axis, these data indicate that heterophyllous leaf formation in L. arcuata is partially temperature sensitive, i.e., the elongation of epidermal cells was temperature sensitive while the reduction in the number of epidermal cells did not show such temperature sensitivity. To clarify the mechanisms that cause such temperature sensitivity, we examined the effects of ethylene, which induced the formation of submerged-type leaves on aerial shoots at the relatively high culture-temperature of 28 degrees C. At 23 degrees C, ethylene induced both cell elongation and reduction in the number of epidermal cells across the leaf transverse axis, while cell elongation was not observed at 28 degrees C. Moreover, both submergence and ethylene treatment induced a change in the arrangement of cortical microtubules (MTs) in epidermal cells of developing leaves at 23 degrees C. Such changes in the arrangement of MTs was not induced at 28 degrees C. Factors involved in the temperature-sensitive response to ethylene would be critical for temperature-sensitive heterophyllous leaf formation in L. arcuata.