Comparative microarray data analysis for the expression of genes in the pathway of glioma

Our present work focuses on the set of genes, which are involved in primary brain tumors - the glioma pathway. These gliomas are mostly malignant (cancerous) in nature and are difficult to be cured and that's why they attract the attention of all the workers. To understand the relative functionality of these genes, we analyzed the expression pattern of all genes, using gene expression data, at genomic level, and then to check their universality in all other cancers, we compared their expression levels and patterns in all other types of cancers by using gene expression graphs, and observed their expression levels in all these cancers, whether they are over or under expressed. We found that every gene has its own unique expression pattern and level and on that basis it can be classified. We also found that oncogenes and tumor suppressor genes that were involved in the glioma pathway were showing similar expression patterns in other cancers too but their expression level is low.     

Antigiardial drugs

Giardia intestinalis is a world-wide cause of intestinal infection. Treatment of this debilitating disease is usually accomplished using one of several drugs. Metronidazole is the treatment of choice, but benzimidazoles are now being used more frequently. Other treatments include quinacrine, paromomycin and furazolidone. Even though these drugs are all used to treat the same disease, their modes of action differ in all cases. However, resistance is increasing and new alternatives are being sought. New wave antigiardials all appear to have their roots in natural herbal remedies. This mini-review looks at the current treatments available, their efficacy, side effects and different modes of action and addresses a possible way forward using natural products.     

Functions of DEAD-box proteins in bacteria: Current knowledge and pending questions

DEAD-box proteins are RNA-dependent ATPases that are widespread in all three kingdoms of life. They are thought to rearrange the structures of RNA or ribonucleoprotein complexes but their exact mechanism of action is rarely known. Whereas in yeast most DEAD-box proteins are essential, no example of an essential bacterial DEAD-box protein has been reported so far; at most, their absence results in cold-sensitive growth. Moreover, whereas yeast DEAD-box proteins are implicated in virtually all reactions involving RNA, in E. coli (the bacterium where DEAD-box proteins have been mostly studied) their role is limited to ribosome biogenesis, mRNA degradation, and possibly translation initiation. Plausible reasons for these differences are discussed here.     

A Nonlinear Model of the Behavior of Simple Cells in Visual Cortex

Despite their structured receptive fields (RFs) and the strong linear components in their responses, most simple cells in mammalian visual cortex exhibit nonlinear behaviors. Besides the contrast-response function, nonlinearities are evident in various types of failure at superposition tasks, in the disagreement between direction indices computed from drifting and counterphase flickering gratings, in various forms of response suppression (including end- and side-stopping, spatial-frequency-specific inhibition and cross-orientation inhibition), in the advance of phase with increasing contrast, and in phase-insensitive and frequency-doubled responses to counterphase flickering gratings. These behaviors suggest that nonlinearities are involved in the operation of simple cells, but current models fail to explain them. A quantitative model is presented here that purports to describe basic and common principles of operation for all visual cortical cells. Simple cells are described as receiving afferents from multiple subunits that differ in their individual RFs and temporal impulse responses (TIRs). Subunits are independent and perform a spatial integration across their RFs followed by halfwave rectification and temporal convolution with their TIRs. This parallel operation yields a set of temporal functions representing each subunit's contribution to the membrane potential of the host cell, whose final form is given by the weighted sum of all subunits' contributions. By varying the number of subunits and their particular characteristics, different instances of the model are obtained each of which displays a different set of behaviors. Extensive simulation results are presented that illustrate how all of the reported nonlinear behaviors of simple cells arise from these multi-subunit organizations.     

Epithelia and integration in sponges

An epithelium is important for integrity, homeostasis, communication and co-ordination, and its development must have been a fundamental step in the evolution of modern metazoan body plans. Sponges are metazoans that are often said to lack a true epithelium. We assess the properties of epithelia, and review the history of studies on sponge epithelia, focusing on their homology to bilaterian epithelia, their ultrastructure, and on their ability to seal. Electron micrographs show that adherens-type junctions are present in sponges but they can appear much slighter than equivalent junctions in other metazoans. Fine septae are seen in junctions of all sponge groups, but distinct septate junctions are only known from Calcarea. Similarly, all sponges can have collagenous sheets underlying their epithelia, but only homoscleromorphs are established to have a distinct basal lamina. The presence of most, but not all, gene families known to be involved in epithelial development and function also suggests that sponge epithelia function like, and are homologous to, bilaterian epithelia. However, physiological evidence that sponge epithelia regulate their internal environment is so far lacking. Given that up to six differentiated epithelia can be recognized in sponges, distinct physiological roles are expected. Recognition that sponges have epithelia challenges the perception that sponges are only loose associations of cells, and helps to relate the biology and physiology of the body plan of the adult sponge to the biology of other metazoans.     

若干北方落叶树木叶片养分的内外迁移：Ⅰ.浓度和含量的变化

研究了北方 1 2个落叶树种单位面积叶干重、叶片灰分、有机物质和 7个元素的浓度和含量在落叶前后的变化 ,同一元素不同树种间及同一树种不同元素间有着不同的变化模式 .单位面积叶干重、叶片有机物质浓度和含量在落叶后均表现下降的趋势 ;所有树种叶片灰分浓度和大部分树种的灰分含量 (除刺槐、胡颓子、核桃楸外 )均有增加 ;落叶时 N、P、K的单位叶面积含量均可减少约 1 / 3～ 2 / 3;Mg含量的减少在胡颓子、核桃楸、春榆、蒙古栎、日本落叶松等 5个树种中发生 ,其余树种表现增加 ;落叶中 Fe含量除胡颓子下降外 ,其余均表现升高 ;落叶中 Ca、Si浓度和含量在所有分析树种中均表现增加趋势     

Uniquely Localized Intra-Molecular Amino Acid Concentrations at the Glycolytic Enzyme Catalytic/Active Centers of Archaea, Bacteria and Eukaryota are Associated with Their Proposed Temporal Appearances on Earth

The distributions of amino acids at most-conserved sites nearest catalytic/active centers (C/AC) in 4,645 sequences of ten enzymes of the glycolytic Embden-Meyerhof-Parnas pathway in Archaea, Bacteria and Eukaryota are similar to the proposed temporal order of their appearance on Earth. Glycine, isoleucine, leucine, valine, glutamic acid and possibly lysine often described as prebiotic, i.e., existing or occurring before the emergence of life, were localized in positional and conservational defined aggregations in all enzymes of all Domains. The distributions of all 20 biologic amino acids in most-conserved sites nearest their C/ACs were quite different either from distributions in sites less-conserved and further from their C/ACs or from all amino acids regardless of their position or conservation. The major concentrations of glycine, e.g., perhaps the earliest prebiotic amino acid, occupies ≈16 % of all the most-conserved sites within a volume of ≈7–8 Å radius from their C/ACs and decreases linearly towards the molecule’s peripheries. Spatially localized major concentrations of isoleucine, leucine and valine are in the mid-conserved and mid-distant sites from their C/ACs in protein interiors. Lysine and glutamic acid comprise ≈25–30 % of all amino acids within an irregular volume bounded by ≈24–28 Å radii from their C/ACs at the most-distant least-conserved sites. The unreported characteristics of these amino acids: their spatially and conservationally identified concentrations in Archaea, Bacteria and Eukaryota, suggest some common structural organization of glycolytic enzymes that may be relevant to their evolution and that of other proteins. We discuss our data in relation to enzyme evolution, their reported prebiotic putative temporal appearances on Earth, abundances, biological “cost”, neighbor-sequence preferences or “ordering” and some thermodynamic parameters.     

Expression of floral MADS-box genes in basal angiosperms: implications for the evolution of floral regulators

The ABC model of floral organ identity is based on studies of Arabidopsis and Antirrhinum, both of which are highly derived eudicots. Most of the genes required for the ABC functions in Arabidopsis and Antirrhinum are members of the MADS-box gene family, and their orthologs are present in all major angiosperm lineages. Although the eudicots comprise 75% of all angiosperms, most of the diversity in arrangement and number of floral parts is actually found among basal angiosperm lineages, for which little is known about the genes that control floral development. To investigate the conservation and divergence of expression patterns of floral MADS-box genes in basal angiosperms relative to eudicot model systems, we isolated several floral MADS-box genes and examined their expression patterns in representative species, including Amborella (Amborellaceae), Nuphar (Nymphaeaceae) and Illicium (Austrobaileyales), the successive sister groups to all other extant angiosperms, plus Magnolia and Asimina, members of the large magnoliid clade. Our results from multiple methods (relative-quantitative RT-PCR, real-time PCR and RNA in situ hybridization) revealed that expression patterns of floral MADS-box genes in basal angiosperms are broader than those of their counterparts in eudicots and monocots. In particular, (i) AP1 homologs are generally expressed in all floral organs and leaves, (ii) AP3/PI homologs are generally expressed in all floral organs and (iii) AG homologs are expressed in stamens and carpels of most basal angiosperms, in agreement with the expectations of the ABC model; however, an AG homolog is also expressed in the tepals of Illicium. The broader range of strong expression of AP3/PI homologs is inferred to be the ancestral pattern for all angiosperms and is also consistent with the gradual morphological intergradations often observed between adjacent floral organs in basal angiosperms.     

Intracellular distribution and origin of sterols in Calendula officinalis leaves

In Calendula officinalis leaves 66% of all steryl forms are present in the ‘microsomal fraction’ (IV), 24% in the mitochondrial and Golgi membranes (III), 5% in the ‘chloroplast’ (II), 4% in the ‘cell wall and membrane’ (I) fraction and 1%. in the cytosol. Free sterols, their esters, glycosides and acylated glycosides are present in varying proportions in all cellular subtractions. Mevalonate-[2¹⁴C] labelling of sterols derived from various steryl forms showed that free sterols and all their derivatives, i.e. steryl esters and glucosides, are formed in fraction IV and are then translocated to other organelles. Fraction III is the main site of glycosylation of transported sterols as well as of acylation of steryl glycosides.     

Why sports injuries clinics?

Sport for all" means sports injuries for all. Facilities for their treatment are inadequate in the United Kingdom. An analysis of 1750 cases indicated that many injuries are specific to sporting activity and that the problem of their treatment cannot effectively be solved by the organization of special clinics for sportsmen based on existing services. There is a case for establishing regional or area clinics manned by appropriately trained, recognized, and committed specialists.     

On market forces and human evolution

This paper studies how an institution such as markets affects the evolution of mankind. My key point is that the forces of natural selection are made weaker because trade allows people to specialize in those activities where they are strong, and to offset their weaknesses by purchasing adequate goods on the market. Absent trade, people must allocate their time among all the activities necessary for their fitness. A productivity advantage in any given dimension will increase survival probability, so that in the long run natural selection makes sure that population is entirely made of individuals with the strongest alleles at all loci. Under trade, there exist long-run equilibria where weaker individuals are able to achieve the same survival potential as the fittest, by specializing in activities where they are not at a disadvantage, and purchasing goods that are substitute for activities for which they are weak.     

The Plasma Membrane of Myxosporidian Valve Cells: Freeze Fracture Data

Freeze fracturing of Myxosporidian spores reveals the occurrence of a continuous layer of transmembrane particles all over the surface area of the valve cells which form the spore envelope. These particles are densely packed all over the P face membrane. Due to their polygonal outline, their diameter (6-7 nm) and their central core, they resemble the particles forming the connections of gap junctions which metabolically couple the neighboring cells in animal tissues. In the present report, the role of the transmembrane particles is still hypothetical. However, they might represent a membrane structural specialization of the spores which are submitted to osmotic variations of the fluid external medium. Furthermore similar transmembrane particles are observed at the level of the septate junction which seals the valve cells. In this occurrence, they are arranged in a series of 40 double rows parallel to the suture of the spore envelope. These findings support the view that Myxosporidia are Metazoa and raise the problem of their origin.     

Measuring the discrepancy between fecundity and lifetime reproductive success in a pollinating fig wasp

Lifetime reproductive success in female insects is often egg‐ or time‐limited. For instance in pro‐ovigenic species, when oviposition sites are abundant, females may quickly become devoid of eggs. Conversely, in the absence of suitable oviposition sites, females may die before laying all of their eggs. In pollinating fig wasps (Hymenoptera: Agaonidae), each species has an obligate mutualism with its host fig tree species [Ficus spp. (Moraceae)]. These pro‐ovigenic wasps oviposit in individual ovaries within the inflorescences of monoecious Ficus (syconia, or ‘figs’), which contain many flowers. Each female flower can thus become a seed or be converted into a wasp gall. The mystery is that the wasps never oviposit in all fig ovaries, even when a fig contains enough wasp females with enough eggs to do so. The failure of all wasps to translate all of their eggs into offspring clearly contributes to mutualism persistence, but the underlying causal mechanisms are unclear. We found in an undescribed Brazilian Pegoscapus wasp population that the lifetime reproductive success of lone foundresses was relatively unaffected by constraints on oviposition. The number of offspring produced by lone foundresses experimentally introduced into receptive figs was generally lower than the numbers of eggs carried, despite the fact that the wasps were able to lay all or most of their eggs. Because we excluded any effects of intraspecific competitors and parasitic non‐pollinating wasps, our data suggest that some pollinators produce few offspring because some of their eggs or larvae are unviable or are victims of plant defences.     

Morphology and ultrastructure of orbicules in the subfamily Ixoroideae (Rubiaceae)

Orbicules were studied in 43 species belonging to 32 genera of the five tribes of the Ixoroideae (Rubiaceae). The orbicules were investigated with scanning electron microscopy (SEM), light microscopy (LM), and transmission electron microscopy (TEM). Orbicules are present in all species investigated of the tribes Pavetteae, Octotropideae and Coffeeae. In the tribes Gardenieae and Aulacocalyceae orbicules were found in some species, while they were absent in others. 15 species out of 11 genera lack orbicules. Three orbicule types (III, V, and VI) could be distinguished, mainly on the basis of general morphological and ultrastructural variations. Orbicules that belong to type III (0.50-1.29μm) have perforations in their wall, a regular or irregular shape and two or three electron transparent cores. This orbicule type, exclusively found in all Pavetteae species investigated, can be divided into two subtypes. Orbicules of subtype IIIa are present in all genera related to Ixora, and orbicules of subtype IIIb in those genera related to Tarenna. Orbicules of type V (0.97-1.86μm) are present in Himalrandia tetrasperma (Aulacocalyceae), and in all Octotropideae genera investigated, except Feretia. Complexes of more than three individual orbicules characterize this type. They are irregularly shaped and have many perforations as well as sporopollenin granules on the orbicule wall. In all species investigated of tribe Coffeeae, type VI orbicules (0.56-1.60μm) are present. These orbicules are characterized by their embedded position towards the tapetal membrane, their aggregated form and by the presence of perforations as well as sporopollenin granules on their orbicule wall. In the tribe Gardenieae different types of orbicule were found (V, VI and orbicules that cannot be classified in our typology). Our results suggest that orbicule characters in the Ixoroideae may be systematically useful on tribal level.     

Redox‐Regulation. Ein Netzwerk zur flexiblen Adaptation von Stoffwechsel und Entwicklung bei Pflanzen

Plants are dependent upon environmental factors for their photoautotrophic growth; but they are frequently exposed to suboptimal conditions due to their sessile life form. They are capable to adapt to a variety of conditions, since even plants of the same genotype exhibit a phenotypical plasticity by change of their “reaction norm”. All the informations are integrated, transduced via a highly flexible network, and realized. The reactions take place at all levels of regulation and comprise fast biophysical and biochemical processes (second and minute range) as well as slow reactions that are visible after hours (gene expression) or only after several days (growth). Redox processes are of importance in all these mechanisms. Deviation from redox‐homeostasis on the one hand serves as a signal, on the other hand it is necessary that larger imbalances are buffered to avoid damage.     

What are mycoplasmas: the relationship of tempo and mode in bacterial evolution

In phenotype the mycoplasmas are very different from ordinary bacteria. However, genotypically (i.e., phylogenetically) they are not. On the basis of ribosomal RNA homologies the mycoplasmas belong with the clostridia, and indeed have specific clostridial relatives. Mycoplasmas are, however, unlike almost all other bacteria in the evolutionary characteristics of their ribosomal RNAs. These RNAs contain relatively few of the highly conserved oligonucleotide sequences characteristic of normal eubacterial ribosomal RNAs. This is interpreted to be a reflection of an elevated mutation rate in mycoplasma lines of descent. A general consequence of this would be that the variation associated with a mycoplasma population is augmented both in number and kind, which in turn would lead to an unusual evolutionary course, one unique in all respects. Mycoplasmas, then, are actually tachytelic bacteria. The unusual evolutionary characteristics of their ribosomal RNAs are the imprints of their rapid evolution.     

Immunoregulation of cellular lifespan: physiologic autoantibodies and their peptide antigens.

Physiologic autoantibodies are part of our normal immune repertoire where they function to maintain homeostasis by performing physiologic functions. The role of physiologic autoantibodies in removing senescent and damaged cells is probably the best example of a physiologic autoantibody, complete with well established function. IgG autoantibodies bind to altered band 3 anion exchanger protein on senescent cells and trigger their removal by macrophages. Band 3 isoforms are found in all cells, tissues, and membranes, and in all species examined. In this paper, we discuss the innate immune response to band 3 membrane proteins and their regulation of cellular lifespan. The role of physiologic autoantibodies and their peptide antigens in health and disease, apoptosis, and their therapeutic potential is discussed focusing on the examples of senescence and malaria.     

Microsatellite analysis of relationships among North American plums (Prunus sect. Prunocerasus, Rosaceae)

Fifteen microsatellite primer pairs developed in sweet cherry and peach were used to explore genetic relationships among North American plums (Prunus section Prunocerasus). In all, 186 putative alleles were detected with a mean value of 12.4 per locus. The Jaccard coefficient of similarity was calculated between all pairs of accessions and their genetic similarities represented by a UPGMA dendrogram. Despite the apparent closeness among native American plums as evidenced by their ability to hybridize freely and their very similar ITS and trnL-trnF nucleotide sequences, all pairs of accessions among the North American plums shared fewer than half of their alleles. Some of the relationships suggested by the UPGMA dendrogram are congruent with current taxonomic hypotheses, but others are difficult to interpret. Further resolution of relationships among American plums will require molecular markers more variable than ITS yet less variable than microsatellites.     

Transposable element origins of epigenetic gene regulation

Transposable elements (TEs) are massively abundant and unstable in all plant genomes, but are mostly silent because of epigenetic suppression. Because all known epigenetic pathways act on all TEs, it is likely that the specialized epigenetic regulation of regular host genes (RHGs) was co-opted from this ubiquitous need for the silencing of TEs and viruses. With their internally repetitive and rearranging structures, and the acquisition of fragments of RHGs, the expression of TEs commonly makes antisense RNAs for both TE genes and RHGs. These antisense RNAs, particularly from heterochromatic reservoirs of 'zombie' TEs that are rearranged to form variously internally repetitive structures, may be advantageous because their induction will help rapidly suppress active TEs of the same family. RHG fragments within rapidly rearranging TEs may also provide the raw material for the ongoing generation of miRNA genes. TE gene expression is regulated by both environmental and developmental signals, and insertions can place nearby RHGs under the regulation (both standard and epigenetic) of the TE. The ubiquity of TEs, their frequent preferential association with RHGs, and their ability to be programmed by epigenetic signals all indicate that RGHs have nearly unlimited access to novel regulatory cassettes to assist plant adaptation.     

The plasma membrane of myxosporidian valve cells: freeze fracture data

Freeze fracturing of Myxosporidian spores reveals the occurrence of a continuous layer of transmembrane particles all over the surface area of the valve cells which form the spore envelope. These particles are densely packed all over the P face membrane. Due to their polygonal outline, their diameter (6-7 nm) and their central core, they resemble the particles forming the connections of gap junctions which metabolically couple the neighboring cells in animal tissues. In the present report, the role of the transmembrane particles is still hypothetical. However, they might represent a membrane structural specialization of the spores which are submitted to osmotic variations of the fluid external medium. Furthermore similar transmembrane particles are observed at the level of the septate junction which seals the valve cells. In this occurrence, they are arranged in a series of 40 double rows parallel to the suture of the spore envelope. These findings support the view that Myxosporidia are Metazoa and raise the problem of their origin.