Retrotransposon insertions in rice gene pairs associated with reduced conservation of gene pairs in grass genomes

Small-scale changes in gene order and orientation are common in plant genomes, even across relatively short evolutionary distances. We investigated the association of retrotransposons in and near rice gene pairs with gene pair conservation, inversion, rearrangement, and deletion in sorghum, maize, and Brachypodium. Copia and Gypsy LTR-retrotransposon insertions were found to be primarily associated with reduced frequency of gene pair conservation and an increase in both gene pair rearrangement and gene deletions. SINEs are associated with gene pair rearrangement, while LINEs are associated with gene deletions. Despite being more frequently associated with retrotransposons than convergent and tandem pairs, divergent gene pairs showed the least effects from that association. In contrast, convergent pairs were least frequently associated with retrotransposons yet showed the greatest effects. Insertions between genes were associated with the greatest effects on gene pair arrangement, while insertions flanking gene pairs had significant effects only on divergent pairs.     

Proteins associated with rabbit reticulocyte mRNA caps during translation as investigated by photocrosslinking.

This laboratory previously detected by UV crosslinking a number of proteins associated with cytoplasmic mRNA in mammalian cells, and the data suggested that they are involved in translation. To find out which proteins are associated with caps we made use of reticulocyte mRNA specifically labeled in the cap with 32P together with a cell-free translation system and UV crosslinking. Approximately 8 bands corresponding to proteins crosslinked to the cap itself have been detected by polyacrylamide gel electrophoresis after UV crosslinking and digestion with RNases or tobacco pyrophosphatase. All but one were specific for methylated caps. One was similar in size and partial peptide map to a cap-binding protein, CBP I, previously identified in other laboratories, and most of the others corresponded to proteins previously known to be associated with mRNA but not known to be associated with caps. The results suggest that most mRNA-associated proteins are associated with caps or poly(A). Also, the number of cap-associated proteins may be greater than previously suspected.     

Associations between chronotype,sleep disturbances and seasonality with fatigue and inflammatory bowel disease symptoms

Growing number of studies suggests link between circadian rhythms and inflammatory bowel diseases (IBD) manifestation. We hypothesize that: 1) IBD are associated with increased eveningness and sleep disturbances; 2) eveningness and sleep disturbances are related to more severe IBD symptoms. In total, 129 participants were enrolled to this study, divided into three groups: 34 Crohn’s disease (CD) patients, 38 ulcerative colitis (UC) patients and 57 healthy controls (HC) group. They all fulfilled a questionnaire, consisting of the Composite Scale of Morningness (CSM), Seasonal Pattern Assessment Questionnaire (SPAQ), Pittsburgh Sleep Quality Index, Inflammatory Bowel Disease Questionnaire (IBDQ) and Multidimensional Fatigue Inventory (MFI). Multiple regression models controlled for age and sex revealed that in CD group higher eveningness measured with CSM was associated with higher general fatigue, physical fatigue, mental fatigue and reduced motivation measured by MFI. Lower CSM morning affect is associated with greater general fatigue, physical fatigue and more reduced activity. Greater seasonality scores are associated with increased physical fatigue and more reduced activity and motivation. Lower sleep quality measured with PSQI is associated with higher physical fatigue and more reduced activity. Correlational analysis revealed that higher seasonality and lower sleep quality are associated with increased systemic and bowel symptoms and decreased emotional and social functions measured with IBDQ. In UC group, eveningness is associated with greater general fatigue, physical fatigue and more reduced activity. Higher CSM morning affect is associated with decreased general fatigue, physical fatigue and less reduced activity. Higher CSM circadian preference scores are associated with decreased general and physical fatigue, and less reduced activity. Increased seasonality is associated with more physical fatigue. Lower sleep quality is associated with greater general and physical fatigue. To our best knowledge this is the first study evaluating associations between chronotype and sleep disturbances with IBD symptoms. We have found that chronotype preferences, whose role in IBD has been until now overlooked, may be one of the important factors contributing to fatigue in this clinical group.     

Small Heat Shock Proteins and Distal Hereditary Neuropathies

Classification of small heat shock proteins (sHsp) is presented and processes regulated by sHsp are described. Symptoms of hereditary distal neuropathy are described and the genes whose mutations are associated with development of this congenital disease are listed. The literature data and our own results concerning physicochemical properties of HspB1 mutants associated with Charcot–Marie–Tooth disease are analyzed. Mutations of HspB1, associated with hereditary motor neuron disease, can be accompanied by change of the size of HspB1 oligomers, by decreased stability under unfavorable conditions, by changes in the interaction with protein partners, and as a rule by decrease of chaperone-like activity. The largest part of these mutations is accompanied by change of oligomer stability (that can be either increased or decreased) or by change of intermonomer interaction inside an oligomer. Data on point mutation of HspB3 associated with axonal neuropathy are presented. Data concerning point mutations of Lys141 of HspB8 and those associated with hereditary neuropathy and different forms of Charcot–Marie–Tooth disease are analyzed. It is supposed that point mutations of sHsp associated with distal neuropathies lead either to loss of function (for instance, decrease of chaperone-like activity) or to gain of harmful functions (for instance, increase of interaction with certain protein partners).     

Protein-based HDL subspecies: Rationale and association with cardiovascular disease,diabetes, stroke,and dementia

HDL-cholesterol is associated with reduced risk of cardiovascular disease, and is used in clinical practice for risk stratification. HDL is composed of many protein-defined subspecies that each comprises just a few percent of the total, some associated with lower and some with higher risk of CVD. HDL that contains apoC3 or apoE are subspecies that have opposing actions on HDL reverse cholesterol transport and opposing associations with risk of future CVD, apoC3 adverse and apoE beneficial. In addition to coronary heart disease, HDL that contains apoC3 is associated with risk of future type 2 diabetes and insulin resistance; ischemic stroke and cerebral infarction; dementia and the deposition of beta-amyloid in the brain. HDL that contains apoE and apoE itself are associated with lower risk of dementia. Other HDL subspecies that contain complement C3, alpha-2 macroglobulin, plasminogen, or haptoglobin are associated with higher future risk of coronary heart disease, whereas others such as HDL that contains apoC1 are associated with lower risk. At this time, these findings provide improved understanding of the multifaceted HDL system to better determine risk and targeting of therapy for the most prevalent chronic lifestyle diseases in our society.     

Song structure,behaviour, and sequence of song types in a population of village indigobirds, Vidua chalybeata

Different song types are associated with certain behaviours including intrasexual aggression, mating, and initiation of song bouts. All song types are used in territorial advertisement. Songs associated with sexual and aggressive behaviours are similar in structure; female mate choice may have driven sexual selection in favour of the more aggressive males. Song sequence is non-random with repetition of all song types and alternation of some, and songs with similar messages are often associated in sequence. Predictions from alternative models were tested, but the significance of the large song repertoire in this species is largely explained by the message content of the different song types.     

Polysome-associated proteins in herpes simplex virus-infected cells

In the cytoplasm of eucaryotic cells, mRNA is associated with proteins. These mRNA-protein complexes, termed messenger ribonucleoprotein (mRNP) particles, are divided into two functional classes. The first class contains free (non-ribosome-associated) mRNPs which have been termed informosomes by others. The second class of mRNPs, those associated with polysomes, are actively engaged in protein synthesis and are termed polysomal mRNPs. The experiments described in this paper examined the proteins associated with polyribosomes in uninfected and herpes simplex virus type 1-infected cells. The data indicate that after infection with herpes simplex virus type 1, specific changes occur in the proteins which normally are found associated with these polysomal mRNPs. These changes include both the appearance of new and possibly virus-specific proteins and the loss of normal host-specific proteins. The relationship of these changes to the patterns of protein synthesis in these cells is also discussed.     

Polymorphisms in the glucocorticoid receptor gene that modulate glucocorticoid sensitivity are associated with rheumatoid arthritis

Introduction  

The glucocorticoid receptor (GR) plays an important regulatory role in the immune system. Four polymorphisms in the GR gene are associated with differences in glucocorticoid (GC) sensitivity; the minor alleles of the polymorphisms N363 S and BclI are associated with relative hypersensitivity to GCs, while those of the polymorphisms ER22/23EK and 9β are associated with relative GC resistance. Because differences in GC sensitivity may influence immune effector functions, we examined whether these polymorphisms are associated with the susceptibility to develop Rheumatoid Arthritis (RA) and RA disease severity.     

东北旱田土壤中Anabaena伴生细菌的分离与鉴定

[背景]鱼腥藻(Anabaena)在农田土壤中广泛分布,具有固碳和固氮功能。明确伴生细菌与蓝细菌的关系,对提高农田土壤中Anabaena的功能具有重要意义。[目的]从东北不同旱田土壤中分离Anabaena sp.PCC7120的伴生细菌,初步鉴定伴生细菌的分类归属,推测伴生细菌的功能,为明确旱田土壤蓝细菌与伴生细菌的关系提供数据支撑。[方法]采用平板分离、PCR-DGGE、克隆测序技术测定并分析不同旱田土壤中伴生细菌的16S rRNA基因序列,确定伴生细菌的分类地位。[结果]PCR-DGGE图谱显示东北旱田14个土样中分离获得Anabaena sp.PCC7120伴生细菌数量和种类不同;PCR-克隆测序获得伴生细菌的16S rRNA基因序列37条,可鉴定到种水平的菌株36条,主要归为鞘氨醇盒菌属(Sphingopyxis)、贪噬菌属(Variovorax)、黄杆菌属(Flavobacterium)和红球菌属(Rhodococcus)等,推测这些伴生细菌具有适应寡营养、富集微量元素、清除毒素等功效。[结论]东北旱田不同土壤中Anabaena sp.PCC7120伴生细菌种类和数量各异,这...     

Glycosylation and rheumatic disease

Rheumatoid arthritis (RA) and other rheumatic diseases are associated with a significant defect in the galactosyltransferase enzyme that results in a profound change in the galactosylation of immunoglobulin G. This change has been demonstrated to be integrally associated with pathogenic mechanisms associated with inflammation in RA. It is not thought that these changes are unique to RA, but it is thought that there may be subtle changes in the disruption of glycosylation homeostasis causing a unique sugar change to be associated with a number of other rheumatic diseases. This is referred to as 'sugar printing the rheumatic diseases' and may be a concept useful both diagnostically and therapeutically.     

The function of proteins that interact with mRNA

Specific proteins are associated with mRNA in the cytoplasm of eukaryotic cells. The complement of associated proteins depends upon whether the mRNA is an integral component of the polysomal complex being translated, or, alternatively, whether it is part of the non-translated free mRNP fraction. By subjecting cells to ultraviolet irradiation in vivo to cross-link proteins to mRNA, mRNP proteins have been shown to be associated with specific regions of the mRNA molecule. Examination of mRNP complexes containing a unique mRNA has suggested that not all mRNA contain the same family of associated RNA binding proteins. The function of mRNA associated proteins may include a role in providing stability for mRNA, and/or in modulating translation. With the recent demonstrations that both free and polysomal mRNPs are associated with the cytoskeletal framework, specific mRNP proteins may play a role in determining the subcellular localization of specific mRNPs.     

Sexual dimorphism in birds: why are there so many different forms of dimorphism?

Variation in the extent of sexual dimorphism among bird species is traditionally attributed to differences in social mating system. However, there are many different forms of dimorphism among birds, and not all of them show an obvious correlation with social mating system. For example, recent work has shown that many highly polygamous species are, in fact, monomorphic, whereas many putatively monogamous species are dimorphic. In this paper we break up sexual dimorphism into subcomponents and then use comparative analyses to examine the pattern of covariation between these subcomponents and various aspects of sexual, social, and parental behaviour. Our first finding is that size dimorphism and plumage-colour dimorphism do not show the same pattern of covariation. Differences in size dimorphism are associated with variation in social mating system and sex differences in parental care, whereas differences in plumage-colour dimorphism are associated with variation in the frequency of extra-bond paternity. These results suggest that size dimorphism is associated with the sort of intrasexual competition described by traditional classifications of social mating system, whereas plumage-colour dimorphism is associated with cryptic female choice. However, when we break up plumage-colour dimorphism according to whether it is due to melanins, carotenoids or structural colours, we find that each category of plumage-colour dimorphism shows a different pattern of covariation. The correlation between overall plumage-colour dimorphism and the rate of extra-bond paternity is due to structural colours, whereas melanin-based dimorphism is associated with sex differences in parental care. The former result is particularly interesting given that new work suggests structural colours are associated with active sexual displays and the reflection of ultraviolet light.     

Peripheral Nerve Injury Is Associated with Chronic,Reversible Changes in Global DNA Methylation in the Mouse Prefrontal Cortex

Changes in brain structure and cortical function are associated with many chronic pain conditions including low back pain and fibromyalgia. The magnitude of these changes correlates with the duration and/or the intensity of chronic pain. Most studies report changes in common areas involved in pain modulation, including the prefrontal cortex (PFC), and pain-related pathological changes in the PFC can be reversed with effective treatment. While the mechanisms underlying these changes are unknown, they must be dynamically regulated. Epigenetic modulation of gene expression in response to experience and environment is reversible and dynamic. Epigenetic modulation by DNA methylation is associated with abnormal behavior and pathological gene expression in the central nervous system. DNA methylation might also be involved in mediating the pathologies associated with chronic pain in the brain. We therefore tested a) whether alterations in DNA methylation are found in the brain long after chronic neuropathic pain is induced in the periphery using the spared nerve injury modal and b) whether these injury-associated changes are reversible by interventions that reverse the pathologies associated with chronic pain. Six months following peripheral nerve injury, abnormal sensory thresholds and increased anxiety were accompanied by decreased global methylation in the PFC and the amygdala but not in the visual cortex or the thalamus. Environmental enrichment attenuated nerve injury-induced hypersensitivity and reversed the changes in global PFC methylation. Furthermore, global PFC methylation correlated with mechanical and thermal sensitivity in neuropathic mice. In summary, induction of chronic pain by peripheral nerve injury is associated with epigenetic changes in the brain. These changes are detected long after the original injury, at a long distance from the site of injury and are reversible with environmental manipulation. Changes in brain structure and cortical function that are associated with chronic pain conditions may therefore be mediated by epigenetic mechanisms.     

Embryonic development of a peripheral nervous system: nerve tract associated cells and pioneer neurons in the antenna of the grasshopper Schistocerca gregaria

The grasshopper antenna is an articulated appendage associated with the deutocerebral segment of the head. In the early embryo, the meristal annuli of the antenna represent segment borders and are also the site of differentiation of pioneer cells which found the dorsal and ventral peripheral nerve tracts to the brain. We report here on another set of cells which appear earlier than the pioneers during development and are later found arrayed along these tracts at the border of epithelium and lumen. These so-called nerve tract associated cells differ morphologically from pioneers in that they are bipolar, have shorter processes, and are not segmentally organized in the antenna. Nerve tract associated cells do not express horseradish peroxidase and so are not classical neurons. They do not express antigens such as repo and annulin which are associated with glia cells in the nervous system. Nerve tract associated cells do, however, express the mesodermal/mesectodermal cell surface marker Mes-3 and putatively derive from the antennal coelom and then migrate to the epithelium/lumen border. Intracellular recordings show that such nerve tract associated cells have resting potentials similar to those of pioneer cells and can be dye coupled to the pioneers. Similar cell types are present in the maxilla, a serially homologous appendage on the head. The nerve tract associated cells are organized into a cellular scaffold which we speculate may be relevant to the navigation of pioneer and sensory axons in the early embryonic antennal nervous system.     

Cylindrical organelles associated with microtubules during sperm elongation in a mealybug.

Spermiogenesis in the mealybug Pseudococcus obscurus involves the elongation of a cytoplasmic papilla from the surface of a spermatid. Longitudinally oriented fibers and microtubules, with diameters of 250 A and a non-9+2 arrangement, are associated with this process. Fibers alone are found in early stages of papilla emergence and in the basal region of the elongated papilla. They appear to be continuous with the microtubules in the more distal region of an elongated papilla. Disk-shaped, circular, and rectangular profiles are associated with the basal ends of the fibers. Probably the fibers are microtubular "anlagen" and the associated structures may be microtubular "organizing centers".     

Cell cycle-dependent binding of HMGN proteins to chromatin

Throughout the cell cycle, the histones remain associated with DNA, but the repertoire of proteins associated with the chromatin fiber continuously changes. The chromatin interaction of HMGNs, a family of nucleosome binding proteins that modulates the structure and activity of chromatin, during the cell cycle is controversial. Immunofluorescence studies demonstrated that HMGNs are not associated with chromatin, whereas live cell imaging indicated that they are present in mitotic chromosomes.     

The small heat shock proteins αB-crystallin and Hsp27 suppress SOD1 aggregation in vitro

Amyotrophic lateral sclerosis is a devastating neurodegenerative disease. The mechanism that underlies amyotrophic lateral sclerosis (ALS) pathology remains unclear, but protein inclusions are associated with all forms of the disease. Apart from pathogenic proteins, such as TDP-43 and SOD1, other proteins are associated with ALS inclusions including small heat shock proteins. However, whether small heat shock proteins have a direct effect on SOD1 aggregation remains unknown. In this study, we have examined the ability of small heat shock proteins αB-crystallin and Hsp27 to inhibit the aggregation of SOD1 in vitro. We show that these chaperone proteins suppress the increase in thioflavin T fluorescence associated with SOD1 aggregation, primarily through inhibiting aggregate growth, not the lag phase in which nuclei are formed. αB-crystallin forms high molecular mass complexes with SOD1 and binds directly to SOD1 aggregates. Our data are consistent with an overload of proteostasis systems being associated with pathology in ALS.     

Factors affecting the distribution of the mole (Talpa europaea) in Snowdonia (North Wales)

Moles are widespread in the uplands of Snowdonia, North Wales, and their distribution has been studied in relation to soil physical and chemical characteristics. Moles are significantly associated with freely drained mineral soils of pH greater than about 4.0. They are not present in soils with a very stony matrix which would preclude the construction of an effective tunnel system. Data are presented showing that moles are associated with sites showing a high return of sheep dung and the reason for this may be an increase in arthropod populations associated with decaying dung. The sites sampled which were not selected with this study in mind show that no factors other than soil characteristics need be invoked to explain the present distribution of moles.