Biotransformation of (RS)-tropic acid in suspension cultures of Coffea arabica,Datura innoxia,Eucalyptus perriniana and Nicotiana tabacum

Suspension cultures of Datura innoxia and Nicotiana tabacum are able to convert (RS)-tropic acid into its glucose esters (2RS)-3-hydroxy-2-phenylpropionyl β-d-glucopyranoside and (2RS)-2-O-(3-hydroxy-2-phenylpropionyl)-d-glucose whereas a cultures of Eucalyptus perriniana converts it into its glucoside (2RS)-3-O-β-d-glucopyranosyl-2-phenylpropionic acid in addition to glucose esters. Suspension cultures of Coffea arabica converts: (RS)-tropic acid into its glucose, sucrose and isotrehalose esters and a small amount of its glucoside; (RS)-2-(4-hydroxyphenyl)propionic acid into its glucose and sucrose esters and a small amount of its glucoside; and (RS)-ethyl 2-(4-hydroxyphenyl)propionate into its gentiobioside. The formation of sucrose esters and linkage of the aglycone to the C-6 position of glucose are characteristic of the biotransformation of carboxylic acids by suspension cultures of C. arabica. The suspension culture of C. arabica selectively converted (R)-tropic acid into its isotrehalose ester on administration of (RS)-tropic acid.     

Mycobacterium tuberculosis Rv3802c Encodes a Phospholipase/Thioesterase and Is Inhibited by the Antimycobacterial Agent Tetrahydrolipstatin

The cell wall of M. tuberculosis is central to its success as a pathogen. Mycolic acids are key components of this cell wall. The genes involved in joining the α and mero mycolates are located in a cluster, beginning with Rv3799c and extending at least until Rv3804c. The role of each enzyme encoded by these five genes is fairly well understood, except for Rv3802c. Rv3802 is one of seven putative cutinases encoded by the genome of M. tuberculosis. In phytopathogens, cutinases hydrolyze the waxy layer of plants, cutin. In a strictly mammalian pathogen, such as M. tuberculosis, it is likely that these proteins perform a different function. Of the seven, we chose to focus on Rv3802c because of its location in a mycolic acid synthesis gene cluster, its putative essentiality, its ubiquitous presence in actinomycetes, and its conservation in the minimal genome of Mycobacterium leprae. We expressed Rv3802 in Escherichia coli and purified the enzymatically active form. We probed its activities and inhibitors characterizing those relevant to its possible role in mycolic acid biosynthesis. In addition to its reported phospholipase A activity, Rv3802 has significant thioesterase activity, and it is inhibited by tetrahydrolipstatin (THL). THL is a described anti-tuberculous compound with an unknown mechanism, but it reportedly targets cell wall synthesis. Taken together, these data circumstantially support a role for Rv3802 in mycolic acid synthesis and, as the cell wall is integral to M. tuberculosis pathogenesis, identification of a novel cell wall enzyme and its inhibition has therapeutic and diagnostic implications.     

From heritability to probability

Can a heritability value tell us something about the weight of genetic versus environmental causes that have acted in the development of a particular individual? Two possible questions arise. Q1: what portion of the phenotype of X is due to its genes and what portion to its environment? Q2: what portion of X’s phenotypic deviation from the mean is a result of its genetic deviation and what portion a result of its environmental deviation? An answer to Q1 provides the full information about X’s development, while an answer to Q2 leaves out a large portion unexplained—that portion which corresponds to the phenotypic mean. Q1 is unanswerable, but I show it is nevertheless legitimate under certain quantitative genetics models. With regard to Q2, opinions in the philosophical and biological literature differ as to its legitimacy. I argue that not only is it legitimate, but in particular, under a few simplifying assumptions, it allows for a quantitative probabilistic answer: for normally distributed quantitative traits with no G-E correlation or statistical G × E interaction, we can assess the probability that X’s genes had a greater effect than its environment on its deviation from the mean population value. This probability is expressed as a function the heritability and the individual’s phenotypic value; we can also provide a quantitative probabilistic answer to Q2 for an arbitrary individual where the probability is a function only of heritability.     

Ecology of aphidophagous ladybird Propylea species: A review

Herein, the ecology of genus Propylea, with special reference to its three species — viz. P. dissecta (Mulsant), P. japonica (Thunberg), and P. quatuordecimpunctata Linnaeus is reviewed, with an eye toward its position in natural habitats and amongst other ladybirds and its biocontrol potential. Although Propylea is not as polyphagous as other successful species, it evidences a preference for certain prey, specifically aphids and whiteflies. This genus is a good model for studies of mating, reproduction, sexual selection, etc. Propylea is usually an intraguild prey in the guilds containing ladybirds, such as Harmonia axyridis (Pallas) and Coccinella septempunctata L. It also appears that it retains some intrinsic advantages that aid in the sustenance and survival of the species. Owing to its smaller size and level of victimization in the guild, its biocontrol potential is questionable, but its size disadvantages are counter-balanced by its high intrinsic rate of increase, high predation, reproductive potential, and bioconversion efficiency, as well as the ease with which it can be reared in the laboratory. Further research will be necessary to ascertain clearly the biocontrol potential of Propylea.     

Ostéologie et affinités de Trematochampsa taqueti (Crocodylia,Mesosuchia) du Sénonien inférieur d'In Beceten (République du Niger)

Among the abundant remains of Mesosuchia that have been yielded by the early Senonian locality of In Beceten (Niger), the most numerous belong to the species Trematochampsa taquetiBuffetaut, 1974. The osteology of this species is described here. This medium-sized crocodilian, with a moderately elongated skull, is characterized, among other features, by its antorbital fenestra, its surangular-quadratojugal articulation, its slightly displaced post-orbital pillar, its teeth with wrinkled enamel, and its amphicoelous vertebrae. In its general outlook, this animal is rather reminiscent of the Goniopholidae, from the Upper Jurassic and the Cretaceous of Laurasia, but it is more primitive than them, and resemblances are probably due to convergence phenomena. The family Trematochampsidae is probably essentially Gondwanian, and could persist until the Senonian thanks to a certain isolation from Laurasia, where more progressive Crocodylia became predominant much earlier than in Africa and South America.     

Characterization of a homolog of DEAD-box RNA helicases in Toxoplasma gondii as a marker of cytoplasmic mRNP stress granules

Toxoplasma gondii is an obligate intracellular protozoan which infects one-third of the human population. Due to its high infection prevalence, Toxoplasma offers an ideal system for the study of host–parasite interaction. Similar to other eukaryotes, Toxoplasma maintains levels and localization of cytoplasmic mRNAs throughout its life cycle as part of a gene regulation network to meet all cellular and biochemical requirements. More recently, it was reported that the presence of cytoplasmic mRNA granules could contribute to the parasite pathogenesis and viability. Here we identified a novel Toxoplasma DEAD-box RNA helicase, referred to as Toxoplasma gondiiHomolog of DOZI (TgHoDI), because of its high homology (81%) to Plasmodium DOZI. TgHoDI is the functional ortholog of yeast DHH1, and its function was authenticated by complementation studies in Δdhh1 yeast strain. We demonstrated that TgHoDI is a marker of cytoplasmic RNA stress granules, which assemble when the parasites experience cellular stresses and translational arrest.     

Influence of planktonic and sessile Listeria monocytogenes on Caenorhabditis elegans

Listeria monocytogenes is the etiologic agent of listeriosis, a food-borne disease affecting humans and a variety of animals. In order to combat this pathogen, it is crucial to have an understanding of its natural interplay with the environment. For this reason, the free soil nematode Caenorhabditis elegans was focused upon because of its shared natural habitat with Listeria and its potential as a model organism for Listeria pathogenesis. Previous studies have generated some contradictory results on Listeria’s ability to kill C. elegans, making additional interaction studies such as this more attractive. In our study, we carried out a series of killing assays in a systematic manner using different Listeria strains under different growth conditions. In addition to studying the effects of planktonic cells, we examined the interaction between C. elegans and sessile listerial cells. Our findings suggest that, rather than causing infection and death, L. monocytogenes may extend the life span of C. elegans. This indicates that Listeria is not pathogenic to C. elegans. We also found that C. elegans can feed and ingest sessile cells, as well as carry the pathogen in its gut, implying that C. elegans could be a vehicle for L. monocytogenes spread in the environment.     

Mechanistic Basis of Plasmid-Specific DNA Binding of the F Plasmid Regulatory Protein,TraM

The conjugative transfer of bacterial F plasmids relies on TraM, a plasmid-encoded protein that recognizes multiple DNA sites to recruit the plasmid to the conjugative pore. In spite of the high degree of amino acid sequence conservation between TraM proteins, many of these proteins have markedly different DNA binding specificities that ensure the selective recruitment of a plasmid to its cognate pore. Here we present the structure of F TraM RHH (ribbon–helix–helix) domain bound to its sbmA site. The structure indicates that a pair of TraM tetramers cooperatively binds an underwound sbmA site containing 12 base pairs per turn. The sbmA is composed of 4 copies of a 5-base-pair motif, each of which is recognized by an RHH domain. The structure reveals that a single conservative amino acid difference in the RHH β-ribbon between F and pED208 TraM changes its specificity for its cognate 5-base-pair sequence motif. Specificity is also dictated by the positioning of 2-base-pair spacer elements within sbmA; in F sbmA, the spacers are positioned between motifs 1 and 2 and between motifs 3 and 4, whereas in pED208 sbmA, there is a single spacer between motifs 2 and 3. We also demonstrate that a pair of F TraM tetramers can cooperatively bind its sbmC site with an affinity similar to that of sbmA in spite of a lack of sequence similarity between these DNA elements. These results provide a basis for the prediction of the DNA binding properties of the family of TraM proteins.     

Effect of double bond geometry in sphingosine base on the antioxidant function of sphingomyelin

We previously showed that sphingomyelin (SM) inhibits peroxidation of phosphatidylcholine (PC) and cholesterol. Since SM uniquely has a trans unsaturation in its sphingosine base, we investigated whether this feature is important for its antioxidant function. Substitution of the natural trans Δ⁴-double bond with a cis double bond (cis-SM), however, increased SM’s ability to inhibit Cu²⁺-mediated 16:0-18:2 PC oxidation by up to eightfold. Dihydro-SM, which lacks the double bond, was equally effective as trans-SM. In contrast to its effect in the sphingosine base, the presence of a cis double bond in the N-acyl group of trans-SM was not protective. cis-SM also inhibited the oxidation of cholesterol by FeSO₄/ascorbate more efficiently than the trans isomer. The enhanced protective effect of cis-SM is selective for metal ion-promoted oxidation, and appears to arise from a decrease in the effective concentration of metal ions. These studies show that the trans double bond of SM is not essential for its antioxidant effects.     

The Promoter of the Immunoglobulin J Chain Gene Receives Its Authentic Enhancer Activity through the Abutting MEF2 and PU.1 Sites in a DNA-Looping Interaction

Immunoglobulin J chain (IgJ) promoter had previously been dissected in the context of a heterologous enhancer and/or promoter because its strength was weak and its authentic enhancer was not available at that time. Thus, it has been questioned whether the previous dissection of the IgJ promoter might also be relevant in the context of its authentic enhancer. Now that the authentic IgJ enhancer has been identified, redelineation of the IgJ promoter could be performed in the context of this authentic enhancer. In this redelineation, the previously identified MEF2 and PU.1 sites were shown to be critical for communicating with its authentic enhancer and thereby for receiving enhancer activity. In accordance with this finding, a DNA-looping interaction between the IgJ promoter and its enhancer was demonstrated using chromosome conformation capture assays not only in IgJ-expressing S194 plasma cells but also during interleukin-2-induced BCL1 B-cell terminal differentiation. Furthermore, MEF2 was shown to be reciprocally coimmunoprecipitated with E47, which had been identified to bind to the IgJ enhancer, suggesting that the DNA-looping interaction between the IgJ promoter and its enhancer might be mediated by these proteins. However, the previously identified USF and BSAP sites were shown to be not important for IgJ promoter activity in the context of its authentic enhancer. These findings were further supported by in vivo footprinting and/or chromatin immunoprecipitation assays, which showed the binding of MEF2 and PU.1—but not the binding of USF and BSAP—to the IgJ promoter.     

Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis

Polyploidization may precipitate dramatic changes to the genome, including chromosome rearrangements, gene loss, and changes in gene expression. In dioecious plants, the sex-determining mechanism may also be disrupted by polyploidization, with the potential evolution of hermaphroditism. However, while dioecy appears to have persisted through a ploidy transition in some species, it is unknown whether the newly formed polyploid maintained its sex-determining system uninterrupted, or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop a bioinformatic pipeline using RNA-sequencing data from natural populations to demonstrate that the allopolyploid plant Mercurialis canariensis directly inherited its sex-determining region from one of its diploid progenitor species, M. annua, and likely remained dioecious through the transition. The sex-determining region of M. canariensis is smaller than that of its diploid progenitor, suggesting that the non-recombining region of M. annua expanded subsequent to the polyploid origin of M. canariensis. Homeologous pairs show partial sexual subfunctionalization. We discuss the possibility that gene duplicates created by polyploidization might contribute to resolving sexual antagonism.     

Depletion of host cell riboflavin reduces Wolbachia levels in cultured mosquito cells

Wolbachia is an obligate intracellular alphaproteobacterium that occurs in arthropod and nematode hosts. Wolbachia presumably provides a fitness benefit to its hosts, but the basis for its retention and spread in host populations remains unclear. Wolbachia genomes retain biosynthetic pathways for some vitamins, and the possibility that these vitamins benefit host cells provides a potential means of selecting for Wolbachia-infected cell lines. To explore whether riboflavin produced by Wolbachia is available to its host cell, we established that growth of uninfected C7-10 mosquito cells decreases in riboflavin-depleted culture medium. A well-studied inhibitor of riboflavin uptake, lumiflavin, further inhibits growth of uninfected C7-10 cells with an LC₅₀ of approximately 12 μg/ml. Growth of C/wStr1 mosquito cells, infected with Wolbachia from the planthopper, Laodelphax striatellus, was enhanced in medium containing low levels of lumiflavin, but Wolbachia levels decreased. Lumiflavin-enhanced growth thus resembled the improved growth that accompanies treatment with antibiotics that deplete Wolbachia, rather than a metabolic advantage provided by the Wolbachia infection. We used the polymerase chain reaction to validate the decrease in Wolbachia abundance and evaluated our results in the context of a proteomic analysis in which we detected nearly 800 wStr proteins. Our data indicate that Wolbachia converts riboflavin to FMN and FAD for its own metabolic needs, and does not provide a source of riboflavin for its host cell.     

Genomic analysis of the aconidial and high-performance protein producer,industrially relevant Aspergillus niger SH2 strain

Aspergillus niger is usually regarded as a beneficial species widely used in biotechnological industry. Obtaining the genome sequence of the widely used aconidial A. niger SH2 strain is of great importance to understand its unusual production capability. In this study we assembled a high-quality genome sequence of A. niger SH2 with approximately 11,517 ORFs. Relatively high proportion of genes enriched for protein expression related FunCat items verify its efficient capacity in protein production. Furthermore, genome-wide comparative analysis between A. niger SH2 and CBS513.88 reveals insights into unique properties of A. niger SH2. A. niger SH2 lacks the gene related with the initiation of asexual sporulation (PrpA), leading to its distinct aconidial phenotype. Frame shift mutations and non-synonymous SNPs in genes of cell wall integrity signaling, β-1,3-glucan synthesis and chitin synthesis influence its cell wall development which is important for its hyphal fragmentation during industrial high-efficiency protein production.     

Species identification of the medicinal plant Tulipa edulis (Liliaceae) by DNA barcode marker

Tulipa edulis (Liliaceae) is the botanical origin of the traditional Chinese medicine (TCM) “Guangcigu”. Due to overexploitation that induced a decline in natural sources, many dried bulbs from other species of Tulipa have been used, adulterating the medicine in recent years. This practice may cause a series of inconsistent therapeutic effects and quality control problems in the herbal medicine industry. Hence, three DNA regions (matK, psbA-trnH and rbcL) were evaluated as barcodes for identifying T. edulis and its adulterants. All candidate DNA barcodes were successfully amplified from leaf samples. Based on the sequence divergences, rbcL and psbA-trnH can assign T. edulis and its adulterants to the correct genus, while matK can accurately differentiate T. edulis and its adulterants. Thus, at the DNA level, the matK intergenic region is a more suitable, accurate and applicable identification of T. edulis and its adulterants than rbcL and psbA-trnH.     

Characterization of the Bacterial Community of the Chemically Defended Hawaiian Sacoglossan Elysia rufescens

Sacoglossans are characterized by the ability to sequester functional chloroplasts from their algal diet through a process called kleptoplasty, enabling them to photosynthesize. The bacterial diversity associated with sacoglossans is not well understood. In this study, we coupled traditional cultivation-based methods with 454 pyrosequencing to examine the bacterial communities of the chemically defended Hawaiian sacoglossan Elysia rufescens and its secreted mucus. E. rufescens contains a defense molecule, kahalalide F, that is possibly of bacterial origin and is of interest because of its antifungal and anticancer properties. Our results showed that there is a diverse bacterial assemblage associated with E. rufescens and its mucus, with secreted mucus harboring higher bacterial richness than entire-E. rufescens samples. The most-abundant bacterial groups affiliated with E. rufescens and its mucus are Mycoplasma spp. and Vibrio spp., respectively. Our analyses revealed that the Vibrio spp. that were highly represented in the cultivable assemblage were also abundant in the culture-independent community. Epifluorescence microscopy and matrix-assisted laser desorption–ionization mass spectrometry (MALDI-MS) were utilized to detect the chemical defense molecule kahalalide F on a longitudinal section of the sacoglossan.     

Arthrostemma primaevum (Melastomataceae): A new species endemic to southeastern Mexico

Arthrostemma primaevum, a new species endemic to southeastern Mexico, is described, illustrated, and compared with its closest extant relative,A. ciliatum. The chromosome count ofn=15, reported here forA. primaevum, suggests thatA. ciliatum, withn=30, is a tetraploid derivative with a much broader geographic and elevational range. In addition to its distinctive unlobed staminal appendages and unique chromosome number,A. primaevum is notable for its shorter, urceolate hypanthium and seeds that have essentially smooth continuous semicircular ridges.