Cryptic diversity within the choanoflagellate morphospecies complex Codosiga botrytis - Phylogeny and morphology of ancient and modern isolates

Choanoflagellates are closely related to metazoans and fungi according to recent phylogenetic studies; therefore the systematics of these organisms is of particular interest. The choanoflagellate morphospecies Codosiga botrytis is the first described choanoflagellate, and is one of the most frequently reported choanoflagellate species. In this study we present phylogenetic and morphological data on eight different strains of Codosiga botrytis. Among these there are five ancient strains; these cultures have been established from up to 43,000 years old cysts from Siberian permafrost. We found that based on the variable V4 region of the small subunit (SSU) of the rDNA, all the investigated freshwater isolates of Codosiga botrytis, together with Sphaeroeca volvox, form a cluster at the base of all other choanoflagellate species. Moreover, the morphospecies described classically as Codosiga botrytis contains at least four different genotypes separated by considerably high genetic distance. All these 'cryptic species' have identical general morphology and cell structure. Strains have a similar life cycle with several different life forms and large morphological plasticity. For the first time we were able to establish cultures from cryo-conserved cysts of choanoflagellates. The ancient strains did not differ significantly in partial SSU rDNA from the modern ones. Besides, no biogeographically pattern could be established. This fact and the low genetic distances of some strains from remote locations support the distribution of dormant stages via air.     

On the problem of ecological evolution in <Emphasis Type="Italic">Volvox</Emphasis>

A concept of evolution of ontogeny based on the original data on the comparative biology of Volvox development and published paleoclimatic data is presented. Previously, we have demonstrated that evolutionary reorganizations of asexual development in Volvox are related to the changes in the rate, diel rhythms, and light/dark control of cell divisions. Here, we propose that such rearrangements could take place during much of Cenozoic time (e.g., in Eocene and Miocene) as adaptations to short and warm winter day in high latitudes. This proposal is confirmed by experimental data on culturing Volvox species with different types of development under short photoperiod.     

A short form of the prolactin (PRL) receptor is able to rescue mammopoiesis in heterozygous PRL receptor mice

The heterozygous prolactin (PRL) receptor (PRLR +/-) mouse fails to develop a fully functional mammary gland at the end of the first pregnancy and shows markedly impaired lobuloalveolar development and milk secretion in young females. The PRLR is expressed ubiquitously, with various proportions of long and short isoforms in different tissues. Conflicting data have appeared on the putative role of the receptor short forms, with both agonist and antagonistic actions proposed. To assess whether the mouse PR-1 short isoform of the PRLR is potentially able to transduce a signal, we overexpressed it in heterozygous mice and investigated its effect on the rescue of mammary development. PRLR+/- mice were not able to develop a functional mammary gland, but restoration of mammary alveolar development and an increase in the expressions of casein and whey acidic protein genes were observed in transgenic PRLR+/- mice expressing the short form of the PRLR, leading to a complete rescue of mammary gland development and function in young females. These results demonstrate that PR-1, the short form of the PRLR, can improve mammary development in PRLR+/- mice, which compensates for the haploinsufficiency of the receptor long form; this effect is probably caused by accelerated proliferation and an activation of the PRLR signaling cascade, resulting in activation of target genes involved in mammary development and milk synthesis.     

Physiological variation in insects: large-scale patterns and their implications

In this paper we demonstrate how broad scale comparative physiology has an important role to play in informing a variety of assumptions made in macroecology. We do so by examining large-scale geographic variation in insect development, thermal tolerance and metabolic rate. From these studies, and those from the literature on insect water loss and thermoregulation, we show that there is often a bias to the geographic extent of available empirical data. Studies of cold hardiness are most usually undertaken at high latitudes, while investigations of upper thermal tolerances and water loss are most common in warm arid regions. Likewise, we demonstrate that much variation in insect physiological tolerances is partitioned at higher taxonomic levels, which has important implications for comparative physiology. Intriguingly, data on the full range of variables we review are available for only three species. We also show that, despite its importance, body size is regularly reported in only some kinds of investigations (metabolic rate, water loss rate), whereas in others (upper lethal temperature, cold hardiness, development) this variable is often ignored. In short, although large-scale comparative physiology can contribute considerable understanding to both physiology and ecology, there is much that remains to be done.     

Interactome data and databases: different types of protein interaction

In recent years, the biomolecular sciences have been driven forward by overwhelming advances in new biotechnological high-throughput experimental methods and bioinformatic genome-wide computational methods. Such breakthroughs are producing huge amounts of new data that need to be carefully analysed to obtain correct and useful scientific knowledge. One of the fields where this advance has become more intense is the study of the network of 'protein-protein interactions', i.e. the 'interactome'. In this short review we comment on the main data and databases produced in this field in last 5 years. We also present a rationalized scheme of biological definitions that will be useful for a better understanding and interpretation of 'what a protein-protein interaction is' and 'which types of protein-protein interactions are found in a living cell'. Finally, we comment on some assignments of interactome data to defined types of protein interaction and we present a new bioinformatic tool called APIN (Agile Protein Interaction Network browser), which is in development and will be applied to browsing protein interaction databases.     

Aggregation of crystallins induced by pulsed laser UV light (308 nm)

Here we compile and analyze the data on photoaggregation of a model protein carboanhydrase and the main eye lens proteins α-, β-, γ-crystallins under the action of pulsed UV irradiation from a Xe-Cl laser (308 nm) with broad variation of pulse energy density and repetition rate. The aggregation efficacy proves to be a nonlinear function of these parameters and protein concentration. A theoretical model is proposed that qualitatively explains the experimental data. It is shown that N-arm-truncated βA3-crystallin is more prone to UV-induced aggregation than the full-sized protein; such defects caused by mutation or aging may aggravate the development of lenticular opacity. Analyzed is the effect of some low-molecular compounds on the aggregation of β-crystallin and its mixture with α-crystallin. A combination of short peptides prepared on this basis markedly impedes crystallin aggregation and retards the development of UV-induced cataract in rats.     

A Microarray-Based Analysis Reveals that a Short Photoperiod Promotes Hair Growth in the Arbas Cashmere Goat

Many animals exhibit different behaviors in different seasons. The photoperiod can have effects on migration, breeding, fur growth, and other processes. The cyclic growth of the fur and feathers of some species of mammals and birds, respectively, is stimulated by the photoperiod as a result of hormone-dependent regulation of the nervous system. To further examine this phenomenon, we evaluated the Arbas Cashmere goat (Capra hircus), a species that is often used in this type of research. The goats were exposed to an experimentally controlled short photoperiod to study the regulation of cyclic cashmere growth. Exposure to a short photoperiod extended the anagen phase of the Cashmere goat hair follicle to increase cashmere production. Assessments of tissue sections indicated that the short photoperiod significantly induced cashmere growth. This conclusion was supported by a comparison of the differences in gene expression between the short photoperiod and natural conditions using gene chip technology. Using the gene chip data, we identified genes that showed altered expression under the short photoperiod compared to natural conditions, and these genes were found to be involved in the biological processes of hair follicle growth, structural composition of the hair follicle, and the morphogenesis of the surrounding skin appendages. Knowledge about differences in the expression of these genes as well as their functions and periodic regulation patterns increases our understanding of Cashmere goat hair follicle growth. This study also provides preliminary data that may be useful for the development of an artificial method to improve cashmere production by controlling the light cycle, which has practical significance for livestock breeding.     

Short LNA-modified oligonucleotide probes as efficient disruptors of DNA G-quadruplexes

G-quadruplexes (G4s) are well known non-canonical DNA secondary structures that can form in human cells. Most of the tools available to investigate G4-biology rely on small molecule ligands that stabilise these structures. However, the development of probes that disrupt G4s is equally important to study their biology. In this study, we investigated the disruption of G4s using Locked Nucleic Acids (LNA) as invader probes. We demonstrated that strategic positioning of LNA-modifications within short oligonucleotides (10 nts.) can significantly accelerate the rate of G4-disruption. Single-molecule experiments revealed that short LNA-probes can promote disruption of G4s with mechanical stability sufficient to stall polymerases. We corroborated this using a single-step extension assay, revealing that short LNA-probes can relieve replication dependent polymerase-stalling at G4 sites. We further demonstrated the potential of such LNA-based probes to study G4-biology in cells. By using a dual-luciferase assay, we found that short LNA probes can enhance the expression of c-KIT to levels similar to those observed when the c-KIT promoter is mutated to prevent the formation of the c-KIT1 G4. Collectively, our data suggest a potential use of rationally designed LNA-modified oligonucleotides as an accessible chemical-biology tool for disrupting individual G4s and interrogating their biological functions in cells.     

Psychosocial adaptation to short stature - an indication for growth hormone therapy?

Although growth hormone does not clearly improve final height in non-growth-hormone-deficient children with short stature, it leads to a temporary acceleration of growth velocity. It is an ongoing discussion whether this effect supports psychosocial adaptation to short stature and therefore could be an indication for growth hormone treatment in children with short stature without growth hormone deficiency. We have reviewed recent literature concerning psychosocial consequences of short stature. Together with own data we can demonstrate that short people regularly adapt well to their height and have a good self-esteem. On the other hand, we focus on the problem that most studies on this subject suffer from methodical problems. A growth-related questionnaire that evaluates subjective and objective perceptions of being short in patients and peers is not at hand. As a consequence, psychosocial problems due to short stature have not been exactly classified yet and therefore do not represent an indication for growth hormone therapy.     

Molecular analysis of the chromosome 11p region in renal cell carcinomas.

Comparative histological data suggest that papillary renal cell tumors in adults and Wilms' tumors in children develop from maturation-arrested cells of similar origin. Wilms' tumor is characterized by genetic changes at the chromosome 11p region. In the present study, we have analyzed 10 papillary and 10 non-papillary renal cell tumors and determined the allelic status of 6 loci on the short arm of chromosome 11. Only one papillary renal cell carcinoma among the 20 tumors showed a loss of constitutional heterozygosity for the chromosome 11p region. These data suggest that separate molecular events occur in the development of Wilms' tumor and papillary renal cell tumors, subsequent to the proliferation of maturation-arrested cells of the kidney.     

Short repetitive sequences in green algal mitochondrial genomes: potential roles in mitochondrial genome evolution

Current data on green algal mitochondrial genomes suggest an unexpected dichotomy within the group with respect to genome structure, organization, and sequence affiliations. The present study suggests that there is a correlation between this dichotomy on one hand and the differences in the abundance, base composition, and distribution of short repetitive sequences we observed among green algal mitochondrial genomes on the other. It is conceivable that the accumulation of GC- rich short repeated sequences in the Chlamydomonas-like but not Prototheca-like mitochondrial genomes might have triggered evolutionary events responsible for the distinct series of evolutionary changes undergone by the two green algal mitochondrial lineages. The similarity in base composition, nucleotide sequence, abundance, and mode of organization we observed between the short repetitive sequences present in Chlamydomonas-like mitochondrial genomes on one hand and fungal and vertebrate homologs on the other might extend to some of the roles that the short repetitive sequences have been shown to have in the latter. Potential involvements we propose for the short repetitive sequences in the evolution of Chlamydomonas-like mitochondrial genomes include fragmentation and scrambling of the ribosomal-RNA-coding regions, extensive gene rearrangements, coding-region deletions, surrogate origins of replication, and chromosomal linearization.      

Nano-structure of the laminin γ-1 short arm reveals an extended and curved multidomain assembly

Laminins are multidomain glycoproteins that play important roles in development and maintenance of the extracellular matrix via their numerous interactions with other proteins. Several receptors for the laminin short arms revealed their importance in network formation and intercellular signaling. However, both the detailed structure of the laminin γ-1 short arm and its organization within the complexes is poorly understood due to the complexity of the molecule and the lack of a high-resolution structure. The presented data provide the first subatomic resolution structure for the laminin γ-1 short arm in solution. This was achieved using an integrated approach that combined a number of complementary biophysical techniques such as small angle X-ray scattering (SAXS), analytical ultracentrifugation, dynamic light scattering and electron microscopy. As a result of this study, we have obtained a significantly improved model for the laminin γ-1 short arm that represents a major step forward in molecular understanding of laminin-mediated complex formations.     

NGC: lossless and lossy compression of aligned high-throughput sequencing data

A major challenge of current high-throughput sequencing experiments is not only the generation of the sequencing data itself but also their processing, storage and transmission. The enormous size of these data motivates the development of data compression algorithms usable for the implementation of the various storage policies that are applied to the produced intermediate and final result files. In this article, we present NGC, a tool for the compression of mapped short read data stored in the wide-spread SAM format. NGC enables lossless and lossy compression and introduces the following two novel ideas: first, we present a way to reduce the number of required code words by exploiting common features of reads mapped to the same genomic positions; second, we present a highly configurable way for the quantization of per-base quality values, which takes their influence on downstream analyses into account. NGC, evaluated with several real-world data sets, saves 33–66% of disc space using lossless and up to 98% disc space using lossy compression. By applying two popular variant and genotype prediction tools to the decompressed data, we could show that the lossy compression modes preserve >99% of all called variants while outperforming comparable methods in some configurations.     

The contributions of dsRNA structure to Dicer specificity and efficiency

Dicer processes long double-stranded RNA (dsRNA) and pre-microRNAs to generate the functional intermediates (short interfering RNAs and microRNAs) of the RNA interference pathway. Here we identify features of RNA structure that affect Dicer specificity and efficiency. The data presented show that various attributes of the 3' end structure, including overhang length and sequence composition, play a primary role in determining the position of Dicer cleavage in both dsRNA and unimolecular, short hairpin RNA (shRNA). We also demonstrate that siRNA end structure affects overall silencing functionality. Awareness of these new features of Dicer cleavage specificity as it is related to siRNA functionality provides a more detailed understanding of the RNAi mechanism and can shape the development of hairpins with enhanced functionality.     

Latency-Related Development of Functional Connections in Cultured Cortical Networks

To study plasticity, we cultured cortical networks on multielectrode arrays, enabling simultaneous recording from multiple neurons. We used conditional firing probabilities to describe functional network connections by their strength and latency. These are abstract representations of neuronal pathways and may arise from direct pathways between two neurons or from a common input. Functional connections based on direct pathways should reflect synaptic properties. Therefore, we searched for long-term potentiation (this mechanism occurs in vivo when presynaptic action potentials precede postsynaptic ones with interspike intervals up to ∼20 ms) in vitro. To investigate if the strength of functional connections showed a similar latency-related development, we selected periods of monotonously increasing or decreasing strength. We observed increased incidence of short latencies (5-30 ms) during strengthening, whereas these rarely occurred during weakening. Furthermore, we saw an increased incidence of 40-65 ms latencies during weakening. Conversely, functional connections tended to strengthen in periods with short latency, whereas strengthening was significantly less than average during long latency. Our data suggest that functional connections contain information about synaptic connections, that conditional firing probability analysis is sensitive enough to detect it and that a substantial fraction of all functional connections is based on direct pathways.     

法瑞学派的发展历史及其对当代植被生态学的影响

法瑞学派也称Braun-Blanquet学派, 盛行于欧洲大陆, 也是当今全球植被科学的一个重要学派。该文对这一学派的发展历史、植被科学理论和野外实践, 以及群落分类系统做了简要介绍。法瑞学派的发展可分为开创(1910-1943年)、发展(1945-1980年)、分化(1980-1990年)和融合(1990年至今)四个时期。法瑞学派重视野外实践, 强调植物群落内的相互关系和动态发展, 强调植物群落主要属性是物种组成, 以及特征种(或鉴别种)在群落分类和评价环境中的重要作用; 制定了一套详细的野外调查方法和样地归类的程序; 建立了以“群丛”为基本等级的一个自下而上、严谨的、正规的植被分类体系; 具有理论上的兼容性和技术上的开放性等优点。这些都为当代植被生态学的发展奠定了坚实的基础。同时, 法瑞学派在特征种界定、群丛定义、样地数据集成与转换、与生态外貌系统连接等方面存在一些尚需改进的地方。最后, 该文概述了法瑞学派在中国的发展历史与现状, 以及目前在中国植被研究中所能发挥的作用。     

Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression

The development of codon bias indices (CBIs) remains an active field of research due to their myriad applications in computational biology. Recently, the relative codon usage bias (RCBS) was introduced as a novel CBI able to estimate codon bias without using a reference set. The results of this new index when applied to Escherichia coli and Saccharomyces cerevisiae led the authors of the original publications to conclude that natural selection favours higher expression and enhanced codon usage optimization in short genes. Here, we show that this conclusion was flawed and based on the systematic oversight of an intrinsic bias for short sequences in the RCBS index and of biases in the small data sets used for validation in E. coli. Furthermore, we reveal that how the RCBS can be corrected to produce useful results and how its underlying principle, which we here term relative codon adaptation (RCA), can be made into a powerful reference-set-based index that directly takes into account the genomic base composition. Finally, we show that RCA outperforms the codon adaptation index (CAI) as a predictor of gene expression when operating on the CAI reference set and that this improvement is significantly larger when analysing genomes with high mutational bias.