The functions of Deoxyribonuclease II in immunity and development

Apoptosis, which is usually accompanied by DNA degradation, is important not only for the homeostasis of metazoans but also for mammalian development. If DNA is not properly degraded in these processes, it can cause diverse diseases, such as anemia, cataracts, and some autoimmune diseases. A large effort has been made to identify these nucleases that are responsible for these effects. In contrast to Deoxyribonuclease I (DNase I), Deoxyribonuclease II (DNase II) has been less well characterized in these processes. Additionally, enzymes of DNase II family in Trichinella spiralis, which is an intracellular parasitic nematode, are also considered involved in the development of the nematode. We have compiled information from studies on DNase II from various organisms and found some nonclassic features in these enzymes of T. spiralis. Here we have reviewed the characterization and functions of DNase II in these processes and predicted the functions of these enzymes in T. spiralis during host invasion and development.     

Uniform designation for genes of the Calvin-Benson-Bassham reductive pentose phosphate pathway of bacteria

Structural and regulatory genes encoding enzymes and proteins of the reductive pentose phosphate pathway have been isolated from a number of bacteria recently. In the phototroph Rhodobacter sphaeroides, and in two chemoautotrophic bacteria, Alcaligenes eutrophus and Xanthobacter flavus, these genes have been found in distinct operons. However, in these three organisms and in other bacteria where certain of these genes have been discovered, a uniform nomenclature to designate these genes has been lacking. This report represents an effort to provide uniformity to the designation of these genes from all bacteria.     

The strength of selection on ultraconserved elements in the human genome

Ultraconserved elements are stretches of consecutive nucleotides that are perfectly conserved in multiple mammalian genomes. Although these sequences are identical in the reference human, mouse, and rat genomes, we identified numerous polymorphisms within these regions in the human population. To determine whether polymorphisms in ultraconserved elements affect fitness, we genotyped unrelated human DNA samples at loci within these sequences. For all single-nucleotide polymorphisms tested in ultraconserved regions, individuals homozygous for derived alleles (alleles that differ from the rodent reference genomes) were present, viable, and healthy. The distribution of allele frequencies in these samples argues against strong, ongoing selection as the force maintaining the conservation of these sequences. We then used two methods to determine the minimum level of selection required to generate these sequences. Despite the lack of fixed differences in these sequences between humans and rodents, the average level of selection on ultraconserved elements is less than that on essential genes. The strength of selection associated with ultraconserved elements suggests that mutations in these regions may have subtle phenotypic consequences that are not easily detected in the laboratory.     

Quantification of noncyclooxygenase derived prostanoids as a marker of oxidative stress

Recently, we discovered there is a unique class of prostaglandin F2-like compounds that are formed in vitro from arachidonoyl-containing lipids in plasma by a free radical-catalyzed mechanism. More recent studies have elucidated that these prostanoids are also produced in vivo in humans by a similar noncyclooxygenase mechanism. Levels of these PGF2 compounds detected by a mass spectrometric assay in normal human plasma and urine range from approximately 5-50 pg/mL and 500-3000 pg/mg creatinine, respectively. Circulating levels of the compounds were shown to increase by as much as 200-fold in animal models of free radical-induced lipid peroxidation. These results suggest that quantification of these prostanoids may provide a new approach to assess oxidative stress in vivo in humans. Potential advantages of this approach are that the mass spectrometric assay has a high degree of sensitivity, accuracy, and specificity and the assay can be used to quantitate these compounds in a variety of biological fluids. In addition, quantification of these compounds is of interest because these compounds possess biological activity. Disadvantages of the assay are the potential of ex vivo formation of these compounds in biological fluids containing lipids and, further, these compounds must be differentiated from PGF2 compounds that are formed via the cyclooxygenase enzyme. In addition, because the levels of these compounds in normal human plasma and urine are relatively high, assaying these compounds in circulating plasma and urine may be somewhat insensitive for the detection of increased production at isolated sites of oxidant injury within the body, in which case sampling near localized sites of their formation may be required.(ABSTRACT TRUNCATED AT 250 WORDS)     

Biologically active MK-801 and SKF-10,047 binding sites distinct from those in rat brain are expressed on human lung cancer cells.

We have shown previously that cultured human lung cancer cells of different histologic types express multiple opioid receptors that can regulate their growth. In this report, we show that these cells also express specific, saturable, and high-affinity binding sites (Kd approximately 1 nM) for the non-opioid phencyclidine (PCP), [(+)-5-methyl-10,11-dihydro-5H-dibenzo[a,b]cyclohepten-5,10-imine hydrogen maleate] (MK-801) and sigma N-allylnormetazocine (SKF-10,047) receptor ligands. Characterization of these binding sites showed them to be protein in nature and sensitive to the guanine nucleotide GTP. Pharmacological studies showed that (+) MK-801 and (+) SKF-10,047 competed with each other for their binding sites and also for the methadone binding site present in these cells. However, the mu and delta opioid ligands did not compete for (+) MK-801 and (+) SKF-10,047 binding sites. In addition, these binding sites on lung cancer cells appear to be distinct from the N-methyl D-aspartate/PCP receptor ionophore complex reported to be present in rat brain. MK-801 and SKF-10,047, at nM concentrations, were found to inhibit the growth of these cells in culture within a few hours of exposure, and this effect was irreversible after 24 h. The growth effects of these ligands could not be reversed by the opioid antagonist naloxone, suggesting involvement of nonopioid type receptors in the actions of these ligands. The abundant expression of biologically active MK-801 and SKF-10 047 binding sites in these cell lines, distinct from those in rat brain, suggests that these cell lines may prove to be a valuable source for further characterization and purification of these binding sites.     

G2 and spindle assembly checkpoint adaptation, and tetraploidy arrest: implications for intrinsic and chemically induced genomic instability

While checkpoints that act in S-phase are essential to the maintenance of genomic stability, these checkpoints do not act alone. Additionally, G2 DNA damage checkpoints, the spindle assembly checkpoint, and a post-mitotic G1 tetraploidy checkpoint act subsequent to DNA replication to ensure genetic fidelity in cell division. In this review, we will examine how these checkpoints cooperate in the maintenance of genomic stability in response to either DNA damage or cytoskeletal disruption. Since the G2 and spindle assembly checkpoints are subject to adaptation, we will discuss how the G1 tetraploidy checkpoint acts in concert with these checkpoints to mediate stable arrest. We will also probe the relationship of these checkpoints by exploring common features of their regulation. Finally, the consequences of malfunction of these checkpoints for both intrinsic and chemically induced genomic instability will be examined. Among these consequences are aneuploidization, extranumerary centrosomes, and micronucleation.     

Significant variation for fitness impacts of ETS loci in hybrids between populations of Tigriopus californicus

The connections between the genes that cause hybrid incompatibilities and the physiological processes disrupted in hybrids by these incompatibilities are not well understood. The interactions between proteins in the electron transport system (ETS) in the copepod, Tigriopus californicus, have emerged as a potential model system to explore such connections. In this study, the effects on hybrid fitness of 3 different nuclear loci encoding proteins of the ETS are examined in hybrid copepods obtained from crosses of genetically divergent populations of this species. The potential interactions between these genes and mitochondrial-encoded proteins of the ETS are also explored; these interactions have been shown to have diverged functionally between these populations in other studies. Large deviations from Mendelian inheritance are found in genotypic ratios at each of the 3 loci in adults but not in nauplii, demonstrating genotype-based selection during development. The length of developmental time of hybrids appears to influence the pattern of deviations in these loci, likely in conjunction with levels of competition in these crosses. The major finding of this study is that in repeated crosses, the nature of deviations at these ETS loci shows dramatic differences suggesting that slight perturbations in initial conditions can dramatically shift the patterns of selection at these ETS loci in interpopulation hybrids.     

Microenvironmental factors and the binding of glycolytic enzymes to contractile filaments.

1. In reviewing the microenvironmental factors involved in the binding of the glycolytic enzymes to contractile filaments, consideration has been given to the significance of molecular crowding in maintaining these interactions under cellular conditions, and the influence of hormones, metabolites, pH and enzyme modifications on these phenomena. 2. Overall, these data serve to emphasize the biological reality of these associations, and their micro-organizational adaptations during physiological activities.     

Amyloid-Like Fibril Formation by Tachykinin Neuropeptides and Its Relevance to Amyloid β-Protein Aggregation and Toxicity

Protein aggregation and amyloid formation are associated with both pathological conditions in humans such as Alzheimer's disease and native functions such as peptide hormone storage in the pituitary secretory granules in mammals. Here, we studied amyloid fibrils formation by three neuropeptides namely physalaemin, kassinin and substance P of tachykinin family using biophysical techniques including circular dichroism, thioflavin T, congo red binding and microscopy. All these neuropeptides under study have significant sequence similarity with Aβ(25-35) that is known to form neurotoxic amyloids. We found that all these peptides formed amyloid-like fibrils in vitro in the presence of heparin, and these amyloids were found to be nontoxic in neuronal cells. However, the extent of amyloid formation, structural transition, and morphology were different depending on the primary sequences of peptide. When Aβ(25-35) and Aβ40 were incubated with each of these neuropeptides in 1:1 ratio, a drastic increase in amyloid growths were observed compared to that of individual peptides suggesting that co-aggregation of Aβ and these neuropeptides. The electron micrographs of these co-aggregates were dissimilar when compared with individual peptide fibrils further supporting the possible incorporation of these neuropeptides in Aβ amyloid fibrils. Further, the fibrils of these neuropeptides can seed the fibrils formation of Aβ40 and reduced the toxicity of preformed Aβ fibrils. The present study of amyloid formation by tachykinin neuropeptides is not only providing an understanding of the mechanism of amyloid fibril formation in general, but also offering plausible explanation that why these neuropeptide might reduce the cytotoxicity associated with Alzheimer's disease related amyloids.     

Precious essences: female secretions promote sperm storage in Drosophila

Sperm that females receive during mating are stored in special places in the females' reproductive tracts. These storage sites serve to support and retain the sperm, maintaining the sperms' motility and, in mammals, permitting final sperm-maturation. The molecules that attract sperm to these sites and mediate what happens to them there have remained elusive. New research, using elegant genetic tools in Drosophila, shows that secretory cells associated with a sperm storage organ are important in sperm-supportive functions. When females lack function of these cells, they do not store sperm, or the sperm that they do store lose motility. Intriguingly, these effects influence gametes beyond the secretory cells' immediate vicinity. Loss of these cells eliminates the motility of sperm stored elsewhere in the reproductive tract and prevents the movement of eggs through the tract to exit the female. As a result of the latter problem, fertilized eggs hatch inside female flies that lack these secretory cells: instead of laying eggs, these females can "give birth" to live offspring. Because the cellular source of these gamete-regulating substances is now known, future studies can identify the specific molecules and mechanisms by which a female attracts sperm into storage and regulates the movement of sperm and eggs within her reproductive tract. It will be fascinating to determine how these molecules and mechanisms maintain gametes in active and viable forms and how evolution can modulate this to result in diverse reproductive strategies. Identification of these molecules also has potential practical implications for strategies to regulate the reproduction of insects of medical or agricultural importance.     

Adaptation of organisms to extreme conditions of deep-sea hydrothermal vents

The deep-sea hydrothermal vents are located along the volcanic ridges and are characterized by extreme conditions such as unique physical properties (temperature, pression), chemical toxicity, and absence of photosynthesis. However, life exists in these particular environments. The primary producers of energy and organic molecules in these biotopes are chimiolithoautotrophic bacteria. Many animals species live in intimate and complex symbiosis with these sulfo-oxidizing and methanogene bacteria. These symbioses imply a strategy of nutrition and a specific metabolic organization involving numerous interactions and metabolic exchanges, between partners. The organisms of these ecosystems have developed different adaptive strategies. In these environments many microorganisms are adapted to high temperatures. Moreover to survive in these environments, living organisms have developed various strategies to protect themselves against toxic molecules such as H2S and heavy metals.     

Common conformational effects of p53 mutations

The tumor suppressor gene p53 has been identified as the most frequent target of genetic alterations in human cancers. Most of these mutations occur in highly conserved regions in the DNA-binding core domain of the p53 protein, suggesting that the amino acid residues in these regions are critical for maintaining normal p53 structure and function. We previously used molecular dynamics calculations to demonstrate that several amino acid substitutions in these regions that are induced by environmental carcinogens and found in human tumors produce certain common conformational changes in the mutant proteins that differ substantially from the wild-type structure. In order to determine whether these conformational changes are consistent for other p53 mutants, we have now used molecular dynamics to determine the structure of the DNA-binding core domain of seven other environmentally induced, cancer-related p53 mutants, namely His 175, Asp 245, Asn 245, Trp 248, Met 249, Ser 278, and Lys 286. The results indicate that all of these mutants differ substantially from the wild-type structure in certain discrete regions and that some of these conformational changes are similar for these mutants as well as those determined previously. The changes are also consistent with experimental evidence for alterations in structure in p53 mutants determined by epitope detectability using monoclonal antibodies directed against these regions of predicted conformational change.     

Focus: Zoonotic Disease: Ending the Neglect of Treatable Bacterial Zoonoses Responsible for Non-Malaria Fevers

Bacterial zoonotic diseases such as leptospirosis, Q fever, melioidosis, spotted fever group rickettsioses, and brucellosis are increasingly recognized causes of non-malaria acute fevers. However, though readily treatable with antibiotics, these diseases are commonly misdiagnosed resulting in poor outcomes in patients. There is a considerable deficit in the understanding of basic aspects of the epidemiology of these neglected diseases and diagnostic tests for these zoonotic bacterial pathogens are not always available in resource-poor settings. Raising awareness about these emerging bacterial zoonoses is directly beneficial to the patients by allowing a test-and-treat approach and is essential to control these life-threatening diseases.     

Integrating large-scale genotype and phenotype data

With the completion of the Human Genome Project, a new emphasis is focusing on the sequence variation and the resulting phenotype. The number of data available from genomic studies addressing this relationship is rapidly growing. In order to analyze these data as a whole, they need to be integrated, aggregated and annotated in a timely manner. The Pharmacogenetics and Pharmacogenomics Knowledge Base PharmGKB; () assembles and disseminates these data and their associated metadata that are needed for unambiguous identification and replication. Assembling these data in a timely manner is challenging, and the scalability of these data produce major challenges for a knowledge base such as PharmGKB. However, it is only through rapid global meta-annotation of these data that we will understand the relationship between specific genotype(s) and the related phenotype. PharmGKB has confronted these challenges, and these experiences and solutions can benefit all genome communities.     

Compensatory mutations, antibiotic resistance and the population genetics of adaptive evolution in bacteria

In the absence of the selecting drugs, chromosomal mutations for resistance to antibiotics and other chemotheraputic agents commonly engender a cost in the fitness of microorganisms. Recent in vivo and in vitro experimental studies of the adaptation to these "costs of resistance" in Escherichia coli, HIV, and Salmonella typhimurium found that evolution in the absence of these drugs commonly results in the ascent of mutations that ameliorate these costs, rather than higher-fitness, drug-sensitive revertants. To ascertain the conditions under which this compensatory evolution, rather than reversion, will occur, we did computer simulations, in vitro experiments, and DNA sequencing studies with low-fitness rpsL (streptomycin-resistant) mutants of E. coli with and without mutations that compensate for the fitness costs of these ribosomal protein mutations. The results of our investigation support the hypothesis that in these experiments, the ascent of intermediate-fitness compensatory mutants, rather than high-fitness revertants, can be attributed to higher rates of compensatory mutations relative to that of reversion and to the numerical bottlenecks associated with serial passage. We argue that these bottlenecks are intrinsic to the population dynamics of parasitic and commensal microbes and discuss the implications of these results to the problem of drug resistance and adaptive evolution in parasitic and commmensal microorganisms in general.     

A duplex retina and the electroretinogram in the nocturnal Perodicticus potto.

The presence of cones in potto's retina has been proved beyond doubt although they are very restricted in number (1 cone for 300 rods). Morphologically, speaking there is no point in calling these cones "rudimentary" except for their slender outer segment. There are red sensitive elements in that retina at wavelengths beyond the spectral sensitivity of visual purple and it is tempting to assume that these elements are cones. The ERG evoked from these elements by red light differs from that in response to white and blue light. They dark-adapt faster than the receptors sensitive to blue and white flashes. However in some of their properties, for example fusion frequency, these cones behave like rods in other species. As these few cones seem to activate the bipolar cells nearly as effectively as the numerous rods, it is suggested that these cones may be responsible for day vision in the potto.     

山茶科核果茶属、石笔木属和拟核果茶属的分类学位置

从形态学、胚胎学、孢粉学和解剖学４方面探讨了核果茶属（ＰｙｒｅｎａｒｉａＢｌ．）、石笔木属（ＴｕｌｃｈｅｒｉａＤｕｎｎ）和拟核果茶属（ＰａｒａｐｙｒｅｎａｒｉａＨ．Ｔ．Ｃｈａｎｇ）的分类学问题,３属在形态上的主要差异具有连续性而难以断开,大小孢子和雌雄配子体的发生过程高度相似,均具有皱波状至皱网状的花粉外壁纹饰和大头茶型（Ｇｏｒｄｏｎｉａｅｅｏｕｓ－Ｔｙｐｅ）气孔器,几方面的资料提示,核果茶属、石笔术属和拟核果茶属是一个不可分割的自然类群,从而以新的证据支持或主张将上述３属合并成１属。     

Conceptual and methodological issues in the genetics of mouse agonistic behavior

Currently, 36 genes have been reported to affect offensive behavior in male mice. Potentially, these genes could be used to analyze the mechanism of this behavior. But there are methodological flies in this conceptual ointment. The studies with these genes varied in the genetic background, the maternal environments, the postweaning housing, the strain or type of opponent, and the type of test. The effects of each of these on the genetics of offense are reviewed with examples. It is concluded that between-study variation in these environmental or experiential circumstances may make it difficult to impossible to relate the effect of one genetic variant to another and to use these to identify and relate the pathways for gene effects on offensive behaviors. For this reason, standardization of these conditions is recommended.     

New Biology of Pheochromocytoma and Paraganglioma

Pheochromocytomas and paragangliomas continue to be defined by significant morbidity and mortality despite their several recent advances in diagnosis, localization, and management. These adverse outcomes are largely related to mass effect as well as catecholamine-induced hypertension, tachyarrhythmias and consequent target organ damage, acute coronary syndromes, and strokes (ischemic and hemorrhagic stroke). Thus, a proper understanding of the physiology and pathophysiology of these tumors and recent advances are essential to affording optimal care. These major developments largely include a redefinition of metastatic behavior, a novel clinical categorization of these tumors into 3 genetic clusters, and an enhanced understanding of catecholamine metabolism and consequent specific biochemical phenotypes. Current advances in imaging of these tumors are shifting the paradigm from poorly specific anatomical modalities to more precise characterization of these tumors using the advent and development of functional imaging modalities. Furthermore, recent advances have revealed new molecular events in these tumors that are linked to their genetic landscape and, therefore, provide new therapeutic platforms. A few of these prospective therapies translated into new clinical trials, especially for patients with metastatic or inoperable tumors. Finally, outcomes are ever-improving as patients are cared for at centers with cumulative experience and well-established multidisciplinary tumor boards. In parallel, these centers have supported national and international collaborative efforts and worldwide clinical trials. These concerted efforts have led to improved guidelines collaboratively developed by healthcare professionals with a growing expertise in these tumors and consequently improving detection, prevention, and identification of genetic susceptibility genes in these patients.