Histones: a novel class of lipopolysaccharide-binding molecules

Unlike soluble and membrane forms of lipopolysaccharide (LPS)-binding proteins, intracellular LPS-binding molecules are poorly documented. We looked for such molecules in a murine lung epithelial cell line. Two proteins with LPS-binding activity were isolated and unambiguously identified as histones H2A.1 and H4 by mass spectrometry. Synthetic peptides representing partial structures indicated that the LPS binding site is located in the C-terminal moiety of the histones. Extending the study, we found that histones H1, H2A, H2B, H3, and H4 from calf thymus are all able to bind LPS. Bindings were specific, and affinities, determined by isothermal titration calorimetry, were (except for H4) higher than that of the LPS-binding antibiotic polymyxin B. In the presence of H2A the binding of LPS to the macrophage cell line RAW 264.7, and the LPS-induced production of TNF-alpha and nitric oxide by these cells, were markedly reduced. Histones may thus represent a new class of intracellular and extracellular LPS sensors.     

Crystal structure of human PNP complexed with guanine

Purine nucleoside phosphorylase (PNP) catalyzes the phosphorolysis of the N-ribosidic bonds of purine nucleosides and deoxynucleosides. PNP is a target for inhibitor development aiming at T-cell immune response modulation and has been submitted to extensive structure-based drug design. More recently, the 3-D structure of human PNP has been refined to 2.3A resolution, which allowed a redefinition of the residues involved in the substrate-binding sites and provided a more reliable model for structure-based design of inhibitors. This work reports crystallographic study of the complex of Human PNP:guanine (HsPNP:Gua) solved at 2.7A resolution using synchrotron radiation. Analysis of the structural differences among the HsPNP:Gua complex, PNP apoenzyme, and HsPNP:immucillin-H provides explanation for inhibitor binding, refines the purine-binding site, and can be used for future inhibitor design.     

Degree of social contact affects the emission of food calls in the common marmoset (Callithrix jacchus)

The aim of this study was to investigate whether the emission of food calls in common marmosets (Callithrix jacchus) is influenced by different social contexts. Food calls are emitted by this species only in the presence of preferred food. If these calls have any communicative function, it may be that individuals produce food calls in order to call family mates toward the food source. If this is the case, the number of calls produced should vary in accordance with the number of family mates present at the moment of the discovery of the food, i.e., the fewer family mates nearby, the more food calls are emitted. This hypothesis was tested with five pairs of common marmosets, by recording the number of food calls emitted in four experimental conditions: 1). isolation: completely isolated from the family mates; 2). visual isolation: separated by a wooden panel from the family mates; 3). visual contact: separated by a wire-mesh from the family mates; and 4). physical interaction: together with the family mates. The results show that the proportion of intervals during which food calls were produced by the pairs was significantly different in the four experimental conditions. It decreased from the isolation and visual isolation condition, through the visual contact condition, reaching the lowest value in the physical interaction condition. The variation observed in the proportion of intervals during which food calls were emitted, in relation to different social contexts, is an indication in favor of the communicative function of this vocalization.     

Expression of correctly processed human growth hormone in seeds of transgenic tobacco plants

Human growth hormone was expressed in transgenic tobacco seeds using the monocot tissue-specific promoter from sorghum -kafirin seed storage protein gene. During tobacco seed ripening, the expressed hormone was directed to the endoplasmic reticulum by a signal peptide from a Coix prolamin and was secreted into the apoplastic space, where it accounted for 0.16% of total soluble seed protein. The expressed hormone has the same amino acid sequence and receptor-binding properties as the native mature hormone.     

Influences of evergreen gymnosperm and deciduous angiosperm tree species on the functioning of temperate and boreal forests

It has been recognized for a long time that the overstorey composition of a forest partly determines its biological and physical–chemical functioning. Here, we review evidence of the influence of evergreen gymnosperm (EG) tree species and deciduous angiosperm (DA) tree species on the water balance, physical–chemical soil properties and biogeochemical cycling of carbon and nutrients. We used scientific publications based on experimental designs where all species grew on the same parent material and initial soil, and were similar in stage of stand development, former land use and current management. We present the current state of the art, define knowledge gaps, and briefly discuss how selection of tree species can be used to mitigate pollution or enhance accumulation of stable organic carbon in the soil. The presence of EGs generally induces a lower rate of precipitation input into the soil than DAs, resulting in drier soil conditions and lower water discharge. Soil temperature is generally not different, or slightly lower, under an EG canopy compared to a DA canopy. Chemical properties, such as soil pH, can also be significantly modified by taxonomic groups of tree species. Biomass production is usually similar or lower in DA stands than in stands of EGs. Aboveground production of dead organic matter appears to be of the same order of magnitude between tree species groups growing on the same site. Some DAs induce more rapid decomposition of litter than EGs because of the chemical properties of their tissues, higher soil moisture and favourable conditions for earthworms. Forest floors consequently tend to be thicker in EG forests compared to DA forests. Many factors, such as litter lignin content, influence litter decomposition and it is difficult to identify specific litter‐quality parameters that distinguish litter decomposition rates of EGs from DAs. Although it has been suggested that DAs can result in higher accumulation of soil carbon stocks, evidence from field studies does not show any obvious trend. Further research is required to clarify if accumulation of carbon in soils (i.e. forest floor + mineral soil) is different between the two types of trees. Production of belowground dead organic matter appears to be of similar magnitude in DA and EG forests, and root decomposition rate lower under EGs than DAs. However there are some discrepancies and still are insufficient data about belowground pools and processes that require further research. Relatively larger amounts of nutrients enter the soil–plant biogeochemical cycle under the influence of EGs than DAs, but recycling of nutrients appears to be slightly enhanced by DAs. Understanding the mechanisms underlying forest ecosystem functioning is essential to predicting the consequences of the expected tree species migration under global change. This knowledge can also be used as a mitigation tool regarding carbon sequestration or management of surface waters because the type of tree species affects forest growth, carbon, water and nutrient cycling.     

A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes

Background

Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality. Cassava is threatened by several pathogens, but the mechanisms of defense are far from being understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organization in the cassava genome.

Results

A high dense genetic map of cassava containing 2,141 SNPs has been constructed. Eighteen linkage groups were resolved with an overall size of 2,571 cM and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred eighty nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map with 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on physical map of the corresponding sequencing scaffolds, unambiguous genetic localization was possible for 569 IRPs.

Conclusions

This is the first study reported so far of an integrated high density genetic map using SNPs with integrated genetic and physical localization of newly annotated immunity related genes in cassava. These data build a solid basis for future studies to map and associate markers with single loci or quantitative trait loci for agronomical important traits. The enrichment of the physical map with novel scaffolds is in line with the efforts of the cassava genome sequencing consortium.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1397-4) contains supplementary material, which is available to authorized users.     

Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis

Molecular Biology Reports - A significant proportion of plant genomes is consists of transposable elements (TEs), especially LTR retrotransposons (LTR-RTs) which are known to drive genome...     

Entraining effects of variations in light spectral composition on the rest-activity rhythm of a nocturnal rodent

The ability to predict and adjust physiology and behavior to recurring environmental events has been necessary for survival on Earth. Recent discoveries revealed that not only changes in irradiance but also light spectral composition can stimulate the suprachiasmatic nucleus (SCN), ensuring the body’s synchronization to the environment. Therefore, using a lighting system that modulates spectral composition during the day using combined red-green-blue (RGB) lights, we evaluated the effect of variations in light spectral composition on the rest-activity rhythm of rodents. Male Wistar rats (n = 17) were gestated and raised under different lighting conditions and exposed to a long photoperiod (16 h light: 8 h dark). The difference between groups was the presence of variations in light spectral composition during the day (RGB-v) to simulate daily changes in natural light, or not (RGB-f). After weaning, spontaneous motor activity was recorded continuously for rhythm evaluation. Our results indicated that animals under RGB-v did not present a reactive peak of activity after the beginning of the light phase, suggesting that this group successfully detected the variations aimed at mimicking daily alterations of natural light. Furthermore, RGB-v animals exhibited an earlier activity acrophase in comparison to animals under RGB-f (RGB-v = 12:16 – “hh:mm”, RGB-f = 13:02; p < 0.001), which might have been due to the capability to predict the beginning of the dark phase when exposed to variations in light spectrum. However, this earlier activity acrophase can be also explained by the blue-light peak that occurred in RGB-v. The spectral and waveform analysis of daily patterns of motor activity revealed that rats in the RGB-v group were better entrained to a circadian rhythm throughout the experiment. RGB-v showed higher interdaily stability (IS) values (29.75 ± 6.5, n = 9) than did RGB-f (t₍₁₅₎ = 2.74, p = 0.015). Besides, the highest power content (PC) on the first harmonic (circadian) was reached earlier in the RGB-v group. The circadianity index (CI) of the whole period was higher in the RGB-v group (t₍₁₅₎ = 3.47, p = 0.003). Thus, we could consider that locomotor activity rhythm was entrained to the light-dark cycle in the RGB-v rats earlier compared to the RGB-f rats. Our results provide additional evidence for the effect of variations in light spectral composition on the rest-activity pattern of nocturnal rodents. This suggests that these animals might predict the arrival of the activity phase by its advanced acrophase when exposed to RGB-v, demonstrating a better synchronization to a 24-h rhythm.     

Temperature,incubation time and virulence of Cercospora coffeicola in the production of cercosporin

This study considers the influence of temperature, incubation time and virulence in the production of the toxin cercosporin by Cercospora coffeicola, the causal agent of brown eye spot in coffee. The area under the progress curve of cercosporin production (AUPCCP) was also evaluated. A pathogenicity test was performed in a group with 58 isolates of C. coffeicola, which allowed the selection of four isolates, two representing the highest (LFP 12 and LFP 59) and two the lowest (LFP 24 and LFP 43) severity groups. The four isolates were cultivated in potato dextrose agar (PDA) and incubated in growth chambers at different temperatures (15, 20, 25 and 30°C) for 20 days. The experiments were conducted in a randomized complete block design with four replications. The cercosporin production decreased in all tested isolates at 30°C, resulting in a lower AUPCCP. The higher values of cercosporin were obtained at 20 and 25°C between 8 and 12 days of incubation. The isolates that produced the highest and lowest cercosporin concentrations were LFP 12 and LFP 43, respectively. After 15 days of incubation, toxin production is practically null in all isolates independently of the incubation temperature. Thus, the hypothesis for quantification of cercosporin production as a variability parameter within the species is suggested.     

G6PD deficient alleles and haplotype analysis of human G6PD locus in São Tomé e Príncipe (West Africa)

A population sample from S?o Tomé e Príncipe (West Africa) was screened for the G6PD-deficient variants A- (376G/202A), Betica (376G/968C), and Santa Maria (376G/542T). G6PD locus haplotype diversity was also investigated using six intragenic RFLPs (FokI, PvuII, BspHI, PstI, BclI, NlaIII) and a (CTT)n microsatellite 18.61 kb within the G6PD locus. The estimated frequencies of the G6PD*B normal allele, the G6PD*A variant (376G), and the G6PD*A- allele were 0.698, 0.194, and 0.108, respectively. G6PD variants Betica and Santa Maria were not found. Similar levels of microsatellite diversity were found on variants G6PD*B and G6PD*A (H = 0.61 and 0.68, respectively), indicating a similar age for both alleles. All G6PD*A- alleles share the RFLP-microsatellite haplotype ++(-)+(-)+/195, the same haplotype described in nearly all the *A-alleles from sub-Saharan, Mexican Mestizo, and Portuguese populations, consistent with a single and recent origin of the G202A mutation on this *A haplotype.