Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning

Different protocols based on Illumina high-throughput DNA sequencing and denaturing gradient gel electrophoresis (DGGE)-cloning were developed and applied for investigating hot spring related samples. The study was focused on three target genes: archaeal and bacterial 16S rRNA and mcrA of methanogenic microflora. Shorter read lengths of the currently most popular technology of sequencing by Illumina do not allow analysis of the complete 16S rRNA region, or of longer gene fragments, as was the case of Sanger sequencing. Here, we demonstrate that there is no need for special indexed or tailed primer sets dedicated to short variable regions of 16S rRNA since the presented approach allows the analysis of complete bacterial 16S rRNA amplicons (V1–V9) and longer archaeal 16S rRNA and mcrA sequences. Sample augmented with transposon is represented by a set of approximately 300 bp long fragments that can be easily sequenced by Illumina MiSeq. Furthermore, a low proportion of chimeric sequences was observed. DGGE-cloning based strategies were performed combining semi-nested PCR, DGGE and clone library construction. Comparing both investigation methods, a certain degree of complementarity was observed confirming that the DGGE-cloning approach is not obsolete. Novel protocols were created for several types of laboratories, utilizing the traditional DGGE technique or using the most modern Illumina sequencing.     

Identification of pericytes in the central nervous system by silver staining of the basal lamina

Vibratome sections obtained from perfusion-fixed rat brains were stained by means of silver impregnation and physical development according to Gallyas (1970). Small pieces of the cerebral cortex were postfixed with buffered osmium tetroxide solution and processed for electron microscopy to examine the localization of the silver deposit at the cellular level. The cell surfaces of pericytes and smooth muscle cells were completely outlined by silver grains. Endothelial cells and perivascular astrocytes, however, showed an asymmetric distribution of the silver deposit, i.e., the deposit was restricted to the abluminal endothelial surface and to the astrocytic membrane adjacent to the vessel wall, respectively. The method allowed a clear-cut distinction between perikarya of endothelial cells and pericytes as well as glial cells in perivascular position, even at the light-microscopic level.     

Influence of Bacterial Lysate Quality on Growth of Two Bacterioplankton Species

All physico-chemical parameters that affect bacterial growth rate will also affect bacterial molecular composition, which in turn influences the chemical composition of bacterial lysate and its turnover rate in the ecosystem. To produce qualitatively different lysates, Vibrio sp. cells were grown under different pH, salt, or temperature conditions in rich growth media and then washed and lysed by autoclaving. Both the absolute concentrations and the ratios between elements in the lysates varied with different growth conditions, implying differences in lysate quality. Either Pseudoalteromonas sp. or Vibrio sp. was grown on the lysates at non-limiting lysate concentrations. Different lysates supported growth rates of Pseudoalteromonas sp. in the range from 0.25 to 1.53 h⁻¹. On the other hand, growth rates of Vibrio sp. grown on its own lysates were around 0.4 h⁻¹ and were not dependent on lysate quality. Two orders of magnitude decrease in Zn concentration in Vibrio sp. cells grown on different lysates as compared to cells grown on rich growth medium suggested that Zn might be a factor limiting growth. In the simple microbial loop studied, the initial difference in lysate quality was preserved in Pseudoalteromonas sp., whereas Vibrio sp. decreased the initial differences in lysate quality, thereby neutralizing the primary effect of environmental conditions on carbon turnover.     

Identification of Chinese cabbage sentrin as a suppressor of Bax-induced cell death in yeast

Studies into the cell death program termed apoptosis have resulted in new information regarding how cells control and execute their own demise, including insights into the mechanism by which death-preventing factors can inhibit Bax-induced caspase activation. We investigated high temperature stress-induced cell death in Brassica rapa. Using a yeast functional screening from a Brassica rapa cDNA library, the BH5-127 EST clone encoding an apoptotic suppressor peptide was identified. However, a phylogenic tree showed that BH5-127 clusters within a clade containing SUMO-1 (Small Ubiquitin-like Modifier- 1). BH5-127 was confirmed similar to have function to SUMO-1 as Fas suppression. Expression of BH5-127 showed that substantial suppression of cell death survived on SD-galactose-Leu--Ura- medium. The results suggest that BrSE (Brassica rapa Sentrin EST, BH5-127) is one of the important regulatory proteins in programming cell death, especially in the seedling stage of Chinese cabbage.     

Are right- and left-handedness relevant as general categories in a non-industrialized country?

Whether right- and left-handedness are defined as a function of individual tasks or represent general categories across tasks has been long debated. However, the literature on handedness primarily concerns industrialized societies in which manual work has been extensively automated, and the majority of individuals in those countries do not use their arms and hands intensively for highly specialized tasks on an everyday basis. Thus, the question remains whether results from those countries regarding handedness are transferable to countries where the majority of individuals are still exploiting their lateralized skills. Here, we sampled 506 individuals from 143 locations on the islands of Flores and Adonara, Indonesia, to assess their hand preference for and hand performance on several tasks in order to evaluate, in a non-industrialized country, the level of manual specialization and the relevance of right- or left-handedness as general categories. Generalized-declared handedness was consistent with task-declared handedness across 10 specific tasks and with a measure of strength and a measure of skilfulness, suggesting that general handedness is a valid concept. This hand specialization for tasks is discussed in the context of intense and daily tool use in this agricultural society.     

Seasonal changes in the dietary compositions of rusa deer in Pangandaran Nature Reserve,West Java,Indonesia

Information regarding the food habits of tropical cervids is limited. We studied the food habits of rusa deer (Rusa timorensis), a tropical cervid in the Pangandaran Nature Reserve, West Java, Indonesia. The faecal composition of the rusa deer collected over a year was analysed using microscopy of plant fragments. The results showed marked seasonal changes: in the rainy season, the rusa deer mainly fed on Cynodon dactylon, a lawn-like grass, which accounted for approximately 50% of the faecal composition. During the dry season, C. dactylon in the faeces decreased to approximately 20%, while the composition of fruits increased, suggesting that food conditions for the deer were better in this season. This pattern differs from that of temperate cervids which can feed on abundant plant leaves during summer but are forced to consume low-quality foods such as bark and dead leaves during winter.     

Post-embryonic nerve-associated precursors to adult pigment cells: genetic requirements and dynamics of morphogenesis and differentiation

The pigment cells of vertebrates serve a variety of functions and generate a stunning variety of patterns. These cells are also implicated in human pathologies including melanoma. Whereas the events of pigment cell development have been studied extensively in the embryo, much less is known about morphogenesis and differentiation of these cells during post-embryonic stages. Previous studies of zebrafish revealed genetically distinct populations of embryonic and adult melanophores, the ectotherm homologue of amniote melanocytes. Here, we use molecular markers, vital labeling, time-lapse imaging, mutational analyses, and transgenesis to identify peripheral nerves as a niche for precursors to adult melanophores that subsequently migrate to the skin to form the adult pigment pattern. We further identify genetic requirements for establishing, maintaining, and recruiting precursors to the adult melanophore lineage and demonstrate novel compensatory behaviors during pattern regulation in mutant backgrounds. Finally, we show that distinct populations of latent precursors having differential regenerative capabilities persist into the adult. These findings provide a foundation for future studies of post-embryonic pigment cell precursors in development, evolution, and neoplasia.     

Responses of Mature and Aged Sympathetic Neurons to Laminin and NGF: An in Vitro Study

Whilst the potent effects of NGF and laminin on developing neurons are well documented, relatively little is known about the effects of, or altered availability of or altered responsiveness to, these substances on the growth of adult neurons. We have therefore examined this question using explant cultures of sympathetic neurons from the superior cervical ganglion (SCG) of mature and aged rats. Explants were grown on substrata containing different doses of laminin, either with or without added NGF in culture medium containing FCS. Individually, laminin and NGF had relatively small effects on neurite outgrowth and length, which tended to be reduced in old neurons. In contrast, laminin in the presence of exogenous NGF exerted a powerful effect on nerve growth which was substantially greater than the sum of the effects of the individual factors. This synergy was evident in all experimental groups and was greatest in old explants at high doses of laminin, where growth was comparable to that of mature neurons. The dose-response curve of old neurons to laminin in the presence of added NGF indicated reduced responsiveness. These results suggest that variations in the availability of laminin and/or exogenous NGF, together with altered patterns of neuronal responsiveness, may contribute to impaired neuronal plasticity in old age.