bluuebunny/crossref_metadata_2025 huggingface dataset:
Retrotransposable elements on the W chromosome of the silkworm, Bombyx mori
Authors: Abe H. , Mita K. , Yasukochi Y. , Oshiki T. , Shimada T.
Published: July 2005

The sex chromosomes of the silkworm, Bombyxmori, are designated ZW(XY) for females and ZZ(XX) for males. The W chromosome of B. mori does not recombine with the Z chromosome and autosomes and no genes for morphological characters have been mapped to the W chromosome as yet. Furthermore, femaleness is determined by the presence of a single W chromosome, regardless of the number of autosomes or Z chromosomes. To understand these interesting features of the W chromosome, it is necessary to analyze the W chromosome at the molecular biology level. Initially to isolate DNA sequences specific for the W chromosome as randomly amplified polymorphic DNA (RAPD) markers, we compared the genomic DNAs between males and females by PCR with arbitrary 10-mer primers. To the present, we have identified 12 W-specific RAPD markers, and with the exception of one RAPD marker, all of the deduced amino acid sequences of these W-specific RAPD markers show similarity to previously reported amino acid sequences of retrotransposable elements from various organisms. After constructing a genomic DNA lambda phage library of B. mori we obtained two lambda phage clones, one containing the W-Kabuki RAPD sequence and one containing the W-Samurai RAPD sequence and found that these DNA sequences comprised nested structures of many retrotransposable elements. To further analyze the W chromosome, we obtained 14 W-specific bacterial artificial chromosome (BAC) clones from three BAC libraries and subjected these clones to shotgun sequencing. The resulting assembly of sequences did not produce a single contiguous sequence due to the presence of many retrotransposable elements. Therefore, we coupled PCR with shotgun sequencing. Through these analyses, we found that many long terminal repeat (LTR) and non-LTR retrotransposons, retroposons, DNA transposons and their derivatives, have accumulated on the W chromosome as strata. These results strongly indicate that retrotransposable elements are the main structural component of the W chromosome.
HeT-A and TART, two Drosophila retrotransposons with a bona fide role in chromosome structure for more than 60 million years
Authors: Casacuberta E. , Pardue M.-L.
Published: July 2005

Drosophila telomeres have been maintained by retrotransposition for at least 60 MY, which predates the separation of extant species of this genus. Studies of D. melanogaster, D. yakuba, and D. virilis show that, in Drosophila, telomeres are composed of two non-LTR retrotransposons, HeT-A and TART. Far from being static, HeT-A and TART evolve faster than Drosophila euchromatic genes. In spite of their high rate of sequence change, HeT-A and TART maintain their basic structures and unusual individual features. The maintenance of their separate identities suggests that HeT-A and TART cooperate either in the process of retrotransposition onto the chromosome end, or in the formation of telomere chromatin by transposed DNA copies. The telomeric retrotransposons and the Drosophila genome constitute an example of a robust symbiotic relationship between mobile elements and the genome.
Fixed and unstable I-related transposable elements in heterochromatin of Drosophila melanogaster
Authors: Junakovic N. , Fortunati D. , Soriano S.
Published: July 2005

Transposable elements are disproportionately abundant in the heterochromatin of Drosophila melanogaster. Among the forces contributing to this bias in genomic distribution, fixation due to positive selection has been put forward. We have studied I-related elements which are located in pericentromeric heterochromatin and are believed to have a role in the control of active I elements. Flies straight from the wild have been studied where fixed elements are expected to emerge clearly over the highly polymorphic background in the genomic distribution of transposable elements. The results show that some restriction fragments due to I-related elements are conserved in size and are present in all individuals tested, consistent with a selective pressure for a role. Other fragments are polymorphic in presence/absence and intensity in individuals from the wild but appear homogeneous in laboratory stocks. Although the significance of this type of instability is unclear, the finding that these polymorphic bands are recurrent in populations from distant geographical locations is also suggestive of a selective pressure for a role.
The structures of mouse and human L1 elements reflect their insertion mechanism
Authors: Martin S.L. , Li W-L.P. , Furano A.V. , Boissinot S.
Published: July 2005

L1 is an abundant, interspersed repeated DNA element of mammalian genomes. It has achieved its high copy number via retrotransposition. Like other non-LTR retrotransposons, L1 insertion into chromosomal DNA apparently occurs by target-site primed reverse transcription, or TPRT. L1 retrotransposition often generates elements with 5′ truncations that are flanked by a duplication of the genomic target site (TSD). It is typically assumed that the 5′ truncated elements are the consequence of poor processivity of the L1 reverse transcriptase. However, we find that the majority of young L1 elements from both the human and mouse genomes are truncated at sequences that can basepair with the target site. Thus, to whatever extent truncation is a consequence of poor processivity, we suggest that truncation is likely to occur when target site sequence can basepair with L1 sequence. This finding supports a model for insertion that occurs by two sequential TPRT reactions, the second of which relies upon the homology between the target site and L1. Because perfect heteroduplex formation is not required for all insertions, a dynamic relationship between the primer, template and enzyme during reverse transcription is inferred. 5′ truncation may be a successful evolutionary strategy that is exploited by L1 as a means to escape host suppression of transposition.
Reverse transcriptase and integrase of the Saccharomyces cerevisiae Ty1 element
Authors: Wilhelm F.-X. , Wilhelm M. , Gabriel A.
Published: July 2005

Integrase (IN) and reverse transcriptase (RT) play a central role in transposition of retroelements. The mechanism of integration by IN and the steps of the replication process mediated by RT are briefly described here. Recently, active recombinant forms of Ty1 IN and RT have been obtained. This has allowed a more detailed understanding of their biochemical and structural properties and has made possible combined in vitro and in vivo analyses of their functions. A focus of this review is to discuss some of the results obtained thus far with these two recombinant proteins and to propose future directions.
Transfer RNA gene-targeted integration: an adaptation of retrotransposable elements to survive in the compact Dictyostelium discoideum genome
Authors: Winckler T. , Szafranski K. , Glöckner G.
Published: July 2005

Almost every organism carries along a multitude of molecular parasites known as transposable elements (TEs). TEs influence their host genomes in many ways by expanding genome size and complexity, rearranging genomic DNA, mutagenizing host genes, and altering transcription levels of nearby genes. The eukaryotic microorganism Dictyostelium discoideum is attractive for the study of fundamental biological phenomena such as intercellular communication, formation of multicellularity, cell differentiation, and morphogenesis. D. discoideum has a highly compacted, haploid genome with less than 1 kb of genomic DNA separating coding regions. Nevertheless, the D. discoideum genome is loaded with 10% of TEs that managed to settle and survive in this inhospitable environment. In depth analysis of D. discoideum genome project data has provided intriguing insights into the evolutionary challenges that mobile elements face when they invade compact genomes. Two different mechanisms are used by D. discoideum TEs to avoid disruption of host genes upon retrotransposition. Several TEs have invented the specific targeting of tRNA gene-flanking regions as a means to avoid integration into coding regions. These elements have been dispersed on all chromosomes, closely following the distribution of tRNA genes. By contrast, TEs that lack bona fide integration specificities show a strong bias to nested integration, thus forming large TE clusters at certain chromosomal loci that are hardly resolved by bioinformatics approaches. We summarize our current view of D. discoideum TEs and present new data from the analysis of the complete sequences of D. discoideum chromosomes 1 and 2, which comprise more than one third of the total genome.
Competition between R1 and R2 transposable elements in the 28S rRNA genes of insects
Authors: Ye J. , Pérez-González C.E. , Eickbush D.G. , Eickbush T.H.
Published: July 2005

R1 and R2 are non-LTR retrotransposons that insert in the 28S rRNA genes of arthropods. R1 elements insert into a site that is 74 bp downstream of the R2 insertion site, thus the presence of an R2 in the same 28S gene may inhibit the expression of R1. Consistent with such a suggestion, the R1 elements of Drosophila melanogaster have a strong bias against inserting into 28S genes already containing an R2 element. R2 elements, on the other hand, are only 2–3 fold inhibited from inserting into a 28S gene already containing an R1. D. melanogaster R1 elements are unusual in that they generate a 23-bp deletion of the target site upstream of the insertion. Using in vitro assays developed to study R2 integration, we show that the presence of R1 sequences 51 bp downstream of the R2 insertion site changes the nucleosomal structure that can be formed by the R2 target site. The R2 endonuclease is inhibited from cleaving these altered nucleosomes. We suggest that R1 elements have been selected to make this large deletion of the 28S gene to block the insertion of an upstream R2 element. These findings are consistent with the model that R1 and R2 are in competition for the limited number of insertion sites available within their host’s genome.
Human retroelements may introduce intragenic polyadenylation signals
Authors: Roy-Engel A.M. , El-Sawy M. , Farooq L. , Odom G.L. , Perepelitsa-Belancio V. , Bruch H. , Oyeniran O.O. , Deininger P.L.
Published: July 2005

In the human genome, the insertion of LINE-1 and Alu elements can affect genes by sequence disruption, and by the introduction of elements that modulate the gene’s expression. One of the modulating sequences retroelements may contribute is the canonical polyadenylation signal (pA), AATAAA. L1 elements include these within their own sequence and AATAAA sequences are commonly created in the A-rich tails of both SINEs and LINEs. Computational analysis of 34 genes randomly retrieved from the human genome draft sequence reveals an orientation bias, reflected as a lower number of L1s and Alus containing the pA in the same orientation as the gene. Experimental studies of Alu-based pA sequences when placed in pol II or pol III transcripts suggest that the signal is very weak, or often not used at all. Because the pA signal is highly affected by the surrounding sequence, it is likely that the Alu constructs evaluated did not provide the required recognition signals to the polyadenylation machinery. Although the effect of pA signals contributed by Alus is individually weak, the observed reduction of “sense” oriented pA-containing L1 and Alu elements within genes reflects that even a modest influence causes a change in evolutionary pressure, sufficient to create the biased distribution.
SINE extinction preceded LINE extinction in sigmodontine rodents: implications for retrotranspositional dynamics and mechanisms
Authors: Rinehart T.A. , Grahn R.A. , Wichman H.A.
Published: July 2005

Short Interspersed Nuclear Elements, or SINEs, retrotranspose despite lacking protein-coding capability. It has been proposed that SINEs utilize enzymes produced in trans by Long Interspersed Nuclear Elements, or LINEs. Strong support for this hypothesis is found in LINE and SINE pairs that share sequence homology; however, LINEs and SINEs in primates and rodents are only linked by an insertion site motif. We have now profiled L1 LINE and B1 SINE activity in 24 rodent species including candidate taxa for the first documented L1 extinction. As expected, there was no evidence for recent activity of B1s in species that also lack L1 activity. However, B1 silencing appears to have preceded L1 extinction, since B1 activity is also lacking in the genus most closely related to those lacking active L1s despite the presence of active L1s in this genus. A second genus with active L1s but inactive B1s was also identified.
Comparative evolution history of SINEs in Arabidopsis thaliana and Brassica oleracea: evidence for a high rate of SINE loss
Authors: Lenoir A. , Pélissier T. , Bousquet-Antonelli C. , Deragon J.M.
Published: July 2005

Brassica oleracea and Arabidopsis thaliana belong to the Brassicaceae(Cruciferae) family and diverged 16 to 19 million years ago. Although the genome size of B. oleracea (∼600 million base pairs) is more than four times that of A. thaliana (∼130 million base pairs), their gene content is believed to be very similar with more than 85% sequence identity in the coding region. Therefore, this important difference in genome size is likely to reflect a different rate of non-coding DNA accumulation. Transposable elements (TEs) constitute a major fraction of non-coding DNA in plant species. A different rate in TE accumulation between two closely related species can result in significant genome size variations in a short evolutionary period. Short interspersed elements (SINEs) are non-autonomous retroposons that have invaded the genome of most eukaryote species. Several SINE families are present in B. oleracea and A. thaliana and we found that two of them (called RathE1 and RathE2) are present in both species. In this study, the tempo of evolution of RathE1 and RathE2 SINE families in both species was compared. We observed that most B. oleracea RathE2 SINEs are “young” (close to the consensus sequence) and abundant while elements from this family are more degenerated and much less abundant in A. thaliana. However, the situation is different for the RathE1 SINE family for which the youngest elements are found in A. thaliana. Surprisingly, no SINE was found to occupy the same (orthologous) genomic locus in both species suggesting that either these SINE families were not amplified at a significant rate in the common ancestor of the two species or that older elements were lost and only the recent (lineage-specific) insertions remain. To test this latter hypothesis, loci containing a recently inserted SINE in the A. thaliana col-0 ecotype were selected and characterized in several other A. thaliana ecotypes. In addition to the expected SINE containing allele and the pre-integrative allele (i.e. the “empty” allele), we observed in the different ecotypes, alleles with truncated portions of the SINE (up to the complete loss of the element) and of the immediate genomic flanking sequences. The absence of SINEs in orthologous positions between B. oleracea and A. thaliana and the presence in recently diverged A. thaliana ecotypes of alleles containing severely truncated SINEs suggest a very high rate of SINE loss in these species.
Classification and nomenclature of retrotransposable elements
Authors: Capy P.
Published: July 2005

The classification and nomenclature of retrotransposable elements is reviewed. A comparison is made between the initial classification summarized in Capy et al. (1997b), and the more recent proposal based on the classification of the viruses (Hull, 2001). Several problems, mainly relating to the position of elements belonging to the DIRS-like or Bel-like groups, are discussed. The first classification is now out of date, and must be revisited to take account of the discovery of new elements, however the second cannot be extended to the DNA elements. There is therefore, clear evidence of the need to adopt a general and a common classification.
Genome-wide experimental identification and functional analysis of human specific retroelements
Authors: Buzdin A. , Vinogradova T. , Lebedev Y. , Sverdlov E.
Published: July 2005

Retroelements (REs) actively reshape genomes through genomic rearrangements, creation of new genes and modulation of the regulatory machinery of existing genes, thus introducing genomic novelties which potentially may be subject to natural selection. Thousands of RE integrations, presumably distinguishing the human and chimpanzee genomes, might well be involved in modern human speciation. In this self-review we describe our recent results on genome-wide identification of human specific RE integrations and their transcriptional activity obtained with three new experimental techniques (TGDA, DiffIR and SDDIR) developed by us for such studies. A new mechanism of the formation of retroelements involving template switches during L1-mediated mRNA reverse transcription, revealed in this research, will also be described in the review.
SINEs and LINEs: symbionts of eukaryotic genomes with a common tail
Authors: Ohshima K. , Okada N.
Published: July 2005

Many SINEs and LINEs have been characterized to date, and examples of the SINE and LINE pair that have the same 3′ end sequence have also increased. We report the phylogenetic relationships of nearly all known LINEs from which SINEs are derived, including a new example of a SINE/LINE pair identified in the salmon genome. We also use several biological examples to discuss the impact and significance of SINEs and LINEs in the evolution of vertebrate genomes.
Penelope-like elements – a new class of retroelements: distribution, function and possible evolutionary significance
Authors: Evgen’ev M.B. , Arkhipova I.R.
Published: July 2005

Here we describe a new class of retroelements termed PLE (Penelope-like elements). The only transpositionally active representative of this lineage found so far has been isolated from Drosophila virilis. This element, Penelope, is responsible for the hybrid dysgenesis syndrome in this species, characterized by simultaneous mobilization of several unrelated TE families in the progeny of dysgenic crosses. Several lines of evidence favor the hypothesis of recent Penelope invasion into D. virilis. Moreover, when D. virilisPenelope was introduced by P element-mediated transformation into the genome of D. melanogaster, it underwent extensive amplification in the new host and induced several traits of the dysgenesis syndrome, including gonadal atrophy and numerous mutations. The single ORF encoded by PLE consists of two principal domains: reverse transcriptase (RT) and endonuclease (EN), which is similar to GIY-YIG intron-encoded endonucleases. With the appearance of a large number of PLEs in genome databases from diverse eukaryotes, including amoebae, fungi, cnidarians, rotifers, flatworms, roundworms, fish, amphibia, and reptilia, it becomes possible to resolve their phylogenetic relationships with other RT groups with a greater degree of confidence. On the basis of their peculiar structural features, distinct phylogenetic placement, and structure of transcripts, we conclude that PLE constitute a novel class of eukaryotic retroelements, different from non-LTR and LTR retrotransposons.
The Alu Yc1 subfamily: sorting the wheat from the chaff
Authors: Garber R.K. , Hedges D.J. , Herke S.W. , Hazard N.W. , Batzer M.A.
Published: July 2005

Members of the Alu Yc1 subfamily are distinguished from the older Alu Y subfamily by a signature G→A substitution at base 148 of their 281-bp consensus sequence. Members of the much older and larger Alu Y subfamily could have by chance accumulated this signature G→A substitution and be misclassified as belonging to the Alu Yc1 subfamily. Using a Mahanalobis classification method, it was estimated that the “authentic” Alu Yc1 subfamily consists of approximately 262 members in the human genome. PCR amplification and further analysis was successfully completed on 225 of the Yc1 Alu family members. One hundred and seventy-seven Yc1 Alu elements were determined to be monomorphic (fixed for presence) in a panel of diverse human genomes. Forty-eight of the Yc1 Alu elements were polymorphic for insertion presence/absence in diverse human genomes. The insertion polymorphism rate of 21% in the human genome is similar to rates reported previously for other “young” Alu subfamilies. The polymorphic Yc1 Alu elements will be useful genetic loci for the study of human population genetics.
Group II intron retroelements: function and diversity
Authors: Robart A.R. , Zimmerly S.
Published: July 2005

Group II introns are a class of retroelements capable of carrying out both self-splicing and retromobility reactions. In recent years, the number of known group II introns has increased dramatically, particularly in bacteria, and the new information is altering our understanding of these intriguing elements. Here we review the basic properties of group II introns, and summarize the differences between the organellar and bacterial introns with regard to structures, insertion patterns and inferred behaviors. We also discuss the evolution of group II introns, as they are the putative ancestors of spliceosomal introns and possibly non-LTR retroelements, and may have played an important role in the development of eukaryote genomes.
Meckel’s Cartilage Differentiation Is Dependent on Hedgehog Signaling
Authors: Melnick Michael , Witcher Daniel , Bringas Jr. Pablo , Carlsson Peter , Jaskoll Tina
Published: July 2005

The hedgehog (Hh) signaling pathway has been shown to be essential for craniofacial development. Although mandibular arch derivatives are largely absent in Shh null mice, little is known about the role of Hh signaling during Meckel’s cartilage development per se. Mandible development is dependent on the morphogenesis of Meckel’s cartilage, which then serves as a template for subsequent skeletal differentiation. In this study, we examine the biological function of Hh signaling during Meckel’s cartilage development in vivo and in vitro. E13.5 Shh null mice present a small mesenchymal condensation in the region of a presumptive Meckel’s cartilage in the hypoplastic mandibular arch. By E15.5, the Shh mutant exhibits a mere remnant of the mandibular arch, without evidence of Meckel’s cartilage differentiation. Further, wild-type embryonic (E11 or E12) mandibular explants cultured for up to 5 days in the presence of cyclopamine, a steroidal alkaloid that specifically disrupts the Hh signaling pathway, exhibit a stage-dependent inhibition of Meckel’s cartilage chondroblast differentiation to mature chondrocytes. This phenotype can be rescued by exogenous FGF8, a downstream effector of Hh signaling. Taken together, our results indicate that the Hh signaling pathway is critical to Meckel’s cartilage ontogenesis and the rate of chondrogenesis, but not to initial primordium formation. The reliance on Hh signaling is stage dependent.
Structure of the Ovaries of the Nimba Otter Shrew, Micropotamogale lamottei, and the Madagascar Hedgehog Tenrec, Echinops telfairi
Authors: Enders A.C. , Carter A.M. , Künzle H. , Vogel P.
Published: July 2005

The otter shrews are members of the subfamily Potamogalinae within the family Tenrecidae. No description of the ovaries of any member of this subfamily has been published previously. The lesser hedgehog tenrec, Echinops telfairi, is a member of the subfamily Tenrecinae of the same family and, although its ovaries have not been described, other members of this subfamily have been shown to have ovaries with non-antral follicles. Examination of these two species illustrated that non-antral follicles were characteristic of the ovaries of both species, as was clefting and lobulation of the ovaries. Juvenile otter shrews range from those with only small follicles in the cortex to those with 300- to 400-µm follicles similar to those seen in non-pregnant and pregnant adults. As in other species, most of the growth of the oocyte occurred when follicles had one to two layers of granulosa cells. When larger follicles became atretic in the Nimba otter shrew, hypertrophy of the theca interna produced nodules of glandular interstitial tissue. In the tenrec, the hypertrophying theca interna cells in most large follicles appeared to undergo degeneration. Both species had some follicular fluid in the intercellular spaces between the more peripheral granulosa cells. It is suggested that this fluid could aid in separation of the cumulus from the remaining granulosa at ovulation. The protruding follicles in lobules and absence of a tunica albuginea might also facilitate ovulation of non-antral follicles. Ovaries with a thin-absent tunica albuginea and follicles with small-absent antra are widespread within both the Eulipotyphla and in the Afrosoricida, suggesting that such features may represent a primitive condition in ovarian development. Lobulated and deeply crypted ovaries are found in both groups but are not as common in the Eulipotyphla making inclusion of this feature as primitive more speculative.
Hypoxia Preconditioning in the Brain
Authors: Ran Ruiqiong , Xu Huichun , Lu Aigang , Bernaudin Myriam , Sharp Frank R.
Published: July 2005

Exposure to moderate hypoxia alone does not cause neuronal death as long as blood pressure and cerebral blood flow are maintained in mammals. In neonatal and adult mammals including rats and mice, carotid occlusion in combination with hypoxia produces neuronal death and brain infarction. However, preexposure to 8% oxygen for 3 h protects the brain and likely other organs of neonatal and adult rats against combined hypoxia-ischemia 24 h later. In this paper, the possible mechanisms of this so-called hypoxia-induced tolerance to ischemia is discussed. One mechanism likely involves hypoxia-inducible factor-1α (HIF-1α). HIF-1α is a transcription factor that – during hypoxia – binds with a second protein (HIF-1β) in the nucleus to promoter elements in hypoxia-responsive target genes. This causes upregulation of HIF target genes including VEGF, erythropoietin, iNOS, glucose transporter-1, glycolytic enzymes, and many other genes to protect the brain against ischemia 24 h later. In addition, non-HIF pathways including MTF-1, Egr-1 and others act directly or indirectly on other target genes to also promote hypoxia-induced preconditioning. Hypoxia preconditioning can be mimicked by iron chelators like desferrioxamine and transition metals like cobalt chloride that inhibit prolyl hydroxylases, increase HIF-1α levels in the brain, and produce protection of the brain against combined hypoxia-ischemia 24 h later. This hypoxia preconditioning has potential clinical usefulness in protecting high-risk newborns or to provide protection prior to surgery.
Morphogenesis of the Dentate Gyrus: What We Are Learning from Mouse Mutants
Authors: Li Guangnan , Pleasure Samuel J.
Published: July 2005

The dentate gyrus is one of two locations with continuing neurogenesis in adult mammals. While the function of adult neurogenesis is unknown, it is believed that it is involved in learning and memory. For adult neurogenesis to occur, the dentate gyrus must maintain the appropriate precursor cell niche in the subgranular zone, which is likely to be dependent on the developmental mechanisms at play in forming the dentate gyrus. In this review, we graft a molecular framework onto the known neuroanatomic developmental plan by considering the phenotypes of several mouse mutants that have well characterized dentate gyrus developmental abnormalities. This effort reveals that there are at least six distinct developmental steps that need to occur in the formation of the dentate gyrus, which can be associated with specific gene defects: (1) defining the dentate neuroepithelium; (2) forming the primary radial glial scaffolding; (3) radial migration of granule neurons to form the primordial granule cell layer; (4) establishing the precursor pool in the hilus; (5) radial transformation of the tertiary matrix, and (6) differentiation of dentate granule cells. From this analysis, it is clear that some molecular pathways control multiple steps in the development of the dentate gyrus. For example the Wnt pathway (steps 1, 2, 4) and the chemokine receptor CXCR4 (steps 3, 4) are involved in multiple developmental steps, while the neuronal differentiation gene NeuroD (step 6) and the integrin signaling pathway (step 5) are involved only in discrete stages of the dentate gyrus morphogenesis.
A New Model for Determining the Influence of Age and Sex on Functional Recovery following Hypoxic-Ischemic Brain Damage
Authors: Yager Jerome Y. , Wright Sandra , Armstrong Edward A. , Jahraus Cleo M. , Saucier Deborah M.
Published: July 2005

Stroke is a disorder affecting the lives of all age groups, and particularly those at the opposite ends of the age spectrum. It is generally believed that the immature brain is more resistant to damage resulting from a hypoxic/ischemic injury, and that it is also more ‘plastic’ in terms of its ability to recover. Evidence from our laboratory, and a host of others, has indicated, however, that the developing brain may in fact be more sensitive to injury resulting from hypoxia-ischemia. The question remains, however, whether the immature brain has a greater capacity for recovery. In order to determine the relative capability for functional recovery between age groups, a stroke model of comparable injury is required. This paper describes a new rodent model of ischemic injury allowing for comparisons of behavioral recovery spanning the spectrum of ages between newborn and the elderly. Endothelin-1, a potent vasoconstrictor, was stereotactically injected into the brains of 10-, 63-, and 180-day-old Wistar rats, immediately adjacent to the middle cerebral artery. Regionally, the cortex, caudate, and thalamus were most significantly affected, with sparing of the hippocampus. Pathologic assessment indicated a similar degree of injury across age groups affecting the territorial distribution of the middle cerebral artery, with a predominance of damage in the anterior sections of the cortex and caudate (p < 0.05), compared to the posterior sections including the cortex and thalamus. There were no regional differences in the extent of damage between age groups. Interestingly, however, there were significant differences between males and females regarding the overall extent of brain damage (p < 0.05), with males showing greater damage than females. In addition, there were significant regional differences in the extent of damage between males and females, particularly regarding cortical damage (p < 0.05), both anteriorly and posteriorly, and the caudate anteriorly (p < 0.05). Our findings provide an important new model for comparison of brain damage among the entire spectrum of ages affected by stroke. Importantly, this will allow for further investigations regarding both functional recovery and gender difference comparisons. This may have important ramifications for the development of therapeutic interventions that are age and gender specific.
Gray Matter Oligodendrocyte Progenitors and Neurons Die Caspase-3 Mediated Deaths Subsequent to Mild Perinatal Hypoxic/Ischemic Insults
Authors: Rothstein Raymond P. , Levison Steven W.
Published: July 2005

With significant improvements in neonatal care, fewer infants sustain severe injury as a consequence of hypoxia/ischemia (H/I). However, the majority of experimental studies have inflicted moderate to severe injuries, or they have assessed damage to the caudal forebrain; therefore, to better understand how a mild H/I episode affects the structures and cells of the rostral forebrain, we assessed the relative vulnerabilities of cells in the neocortex, striatum, corpus callosum, choroid plexus and subventricular zone (SVZ). To inflict mild H/I injury, the right common carotid artery was ligated followed by 1 h of hypoxia (8% O2) at 37°C. Regional vulnerabilities were assessed using TUNEL, active caspase-3 and hematoxylin and eosin staining at 24 and 48 h of recovery. Scattered columns of cell death were observed in the neocortex with deep-layer neurons more vulnerable than more superficial neurons. The majority of these dying neurons appeared to be dying apoptotic rather than necrotic deaths. In addition, approximately 1/3 of the apoptotic cells in the neocortex were O4+ oligodendrocyte progenitors. We also observed a decrease in NG2 staining within the affected regions of the forebrain. By contrast, active caspase-3+/S-100β+ astrocytes were not observed. Neurons and O4+ oligodendrocyte progenitors also died apoptotic deaths within the striatum. The lining cells of the choroid plexus also sustained damage. Elevated numbers of apoptotic cells were observed in the most lateral region of the SVZ and some of these dying cells were O4+. The most novel finding of this study, that oligodendrocyte progenitors in the gray matter are damaged and eliminated as a consequence of perinatal H/I, provides new insights into the histopathology and neurological deficits observed in infants who sustain mild H/I brain injuries.
Patterns of Excitotoxin-Induced Brain Lesions in the Newborn Rabbit: A Neuropathological and MRI Correlation
Authors: Sfaello Ignacio , Daire Jean-Luc , Husson Isabelle , Kosofsky Barry , Sebag Guy , Gressens Pierre
Published: July 2005

There is pressing need to employ new advances in structural MR brain imaging to better diagnose brain damage in newborn infants. Timely application of such technology will enable improved therapeutic interventions. Diffusion-weighted sequences are a sensitive marker of very early neuronal injury, the spatial pattern of which provides critical information regarding the underlying pathophysiology. We have modified our murine model of excitotoxic neonatal brain injury to the rabbit, an animal whose brain is larger and where the neuroanatomic organization of the subcortical white matter more closely resembles that of the human. Utilizing this rabbit model, we undertook an MRI/histopathologic correlation. We found that as with the mouse, there is a spatiotemporal selectivity to the pattern of brain injury, and that the period from postnatal day (P) 7 to P9 in rabbits corresponds to the time of maximum vulnerability of the brain to excitotoxic white matter damage, which neuropathologically simulates periventricular leukomalacia (PVL). We additionally noted that diffusion-weighted imaging provided the most sensitive means of detecting such lesions and that this method was sensitive to structural maturational changes accompanying the normal cortical ontogeny. Taken together, our findings suggest that this rabbit model of perinatal excitotoxic brain injury will be a valuable addition to experimental approaches to further our understanding of perinatal brain damage, that diffusion-weighted imaging will be an invaluable adjunct to the diagnosis of such injury, and that therapeutic strategies aimed at interrupting the evolution of PVL should include targeting the pathophysiologic cascade induced by excitotoxic neonatal brain injury.
Overexpression of Glutathione Peroxidase Protects Immature Murine Neurons from Oxidative Stress
Authors: McLean Claire W. , Mirochnitchenko Oleg , Claus Catherine P. , Noble-Haeusslein Linda J. , Ferriero Donna M.
Published: July 2005

Neuronal enzyme systems involved in free radical detoxification are developmentally regulated such that intracellular glutathione peroxidase (GPx-1) activity is low in the newborn mouse brain. We hypothesized that neurons expressing a higher level of GPx-1 will be more resistant to hydrogen peroxide (H2O2) exposure. We show a dose-dependent protection against H2O2 in primary neuronal cultures from fetuses overexpressing human GPx-1 compared to wild types of the same genetic background. Exogenous antioxidants completely protected neurons, even at extremely high H2O2 concentrations and regardless of the genotype. Specific depletion of glutathione with buthionine sulfoximine increased cell death in transgenic cultures exposed to 200 µM H2O2, reducing protection afforded by increased GPx-1 activity. Increased GPx-1 expression in immature cortical neurons confers protection from oxidative stress, but availability of reducing equivalents determines susceptibility to oxidative cell death.
Non-Protein-Bound Iron in Brain Interstitium of Newborn Pigs after Hypoxia
Authors: Sävman Karin , Nilsson Ulf A. , Thoresen Marianne , Kjellmer Ingemar
Published: July 2005

Oxidative damage is implied in perinatal hypoxic-ischemic brain injury, most importantly in white matter. Nonprotein-bound iron (NPBI) catalyzes the formation of toxic hydroxyl radicals. We measured the extracellular level of NPBI through microdialysis in the cortex, striatum, and periventricular white matter before, during and after severe hypoxia in newborn pigs. NPBI was analyzed by a new spectrophotometric method in which ferrous iron is chelated by bathophenanthroline. NPBI was present in all brain areas under baseline conditions and increased in white matter from 0.97 (0.69) to 2.75 (1.85) µmol/l (not corrected for recovery rate) during early reoxygenation. NPBI may contribute to oxidative injury after perinatal hypoxic insults.
Brief Induced Hypothermia Improves Outcome after Asphyxial Cardiopulmonary Arrest in Juvenile Rats
Authors: Fink Ericka L. , Marco Christina D. , Donovan Holly A. , Alexander Henry , Dixon C. Edward , Jenkins Larry W. , Stange Christopher J. , Kochanek Patrick M. , Clark Robert S.B.
Published: July 2005

The American Heart Association has endorsed the use of mild hypothermia for adults after cardiopulmonary arrest. However, there are no contemporary trials testing hypothermia in children after cardiopulmonary arrest and extrapolation from adult studies is problematic given differences in brain development and primary etiology (asphyxia in children vs. ventricular arrhythmia in adults). Accordingly, we tested the effects of mild postresuscitative hypothermia on functional and histopathological outcome after asphyxial cardiac arrest in juvenile rats. Postnatal day 17 rats were subjected to 8 min of asphyxia-induced cardiac arrest followed by resuscitation. Rats were randomized to normothermic (37°C), hypothermic (32°C), or unregulated temperature groups (n = 7–8/group) to begin after return of spontaneous circulation for a duration of 1 h. Brain temperature in the unregulated group dropped to 34.0 ± 0.4°C at 1 h. The hypothermic group had improved motor function assessed using beam balance and inclined plane tests vs. the normothermic group. The depth of hypothermia was associated with increased CA1 hippocampal neuron survival at 5 weeks. Neurodegeneration in the CA1 hippocampus assessed using Fluoro-Jade B labeling at 5 weeks was not detected in the 32°C group, whereas 2/7 and 4/7 rats in the 34 and 37°C groups, respectively, showed neurodegeneration. Brief treatment with moderate induced hypothermia improved functional outcome and prevented long-term neurodegeneration in a model that mimics the clinical and histopathological scenario of pediatric cardiac arrest. Similar to adults, infants and children may benefit from induced hypothermia after cardiopulmonary arrest, warranting further study.
Melatonin Provides Neuroprotection in the Late-Gestation Fetal Sheep Brain in Response to Umbilical Cord Occlusion
Authors: Miller Suzanne L. , Yan Edwin B. , Castillo-Meléndez Margie , Jenkin Graham , Walker David W.
Published: July 2005

Oxygen free radicals, including the highly toxic hydroxyl radical (·OH), initiate lipid peroxidation and DNA/RNA fragmentation and damage cells. The pineal hormone melatonin is an antioxidant and powerful scavenger of ·OH. We hypothesized that maternally administered melatonin could reduce ·OH formation, lipid peroxidation, and DNA/RNA damage in the fetal brain in response to asphyxia. In 15 fetal sheep, extracellular ·OH was measured by microdialysis in white and gray matter of the parasagittal cortex. In 10 fetuses, asphyxia was induced by umbilical cord occlusion for 10 min using an inflatable cuff – the ewes of these fetuses received either intravenous melatonin (1 mg bolus, then 1 mg/h for 2 h; n = 5) or vehicle (1% ethanol in saline; n = 5), and results were compared to fetuses with sham cord occlusion and vehicle-infused ewes (n = 5). Hypoxemia, acidemia, hypertension and bradycardia produced by cord occlusion was similar in the melatonin- and vehicle-treated groups. In the vehicle-treated group, cord occlusion resulted in a significant increase in ·OH in gray matter at 8–9.5 h after occlusion (p < 0.05); in contrast, there was no ·OH change in the melatonin-treated group. After cord occlusion, lipid peroxidation (4-hydroxynonenal immunoreactivity) found throughout the brain of vehicle-infused ewes was significantly less in the melatonin-infused group. Melatonin had no significant effect on the distribution of DNA/RNA fragmentation, as shown by 8-hydroxydeoxyguanosine immunoreactivity. Thus, brief asphyxia results in significant and delayed entry of ·OH into the extracellular space of cortical gray matter in the fetal sheep brain, and melatonin given to the mother at the time of the insult abrogates this increase. Melatonin, in reducing O2 free radical production, may be an effective neuroprotective treatment for the fetus.
Differential Effects of Hypoxia-Ischemia on Phosphorylation of the N-Methyl-D-Aspartate Receptor in One- and Three-Week-Old Rats
Authors: Vij Shilpa , Vannucci S.J. , Gurd James W.
Published: July 2005

The effects of transient cerebral hypoxia-ischemia (HI) on phosphorylation of the NR1 subunit of the N-methyl-D-aspartate (NMDA) receptor were investigated in 7 (P7)- and 21 (P21)-day-old rats. Unilateral HI was induced by ligation of the right common carotid artery and exposure to 8% O2/92% N2 for 120 (P7) or 90 (P21) min. Phosphorylation by protein kinase A (PKA; S897) and PKC (S896 and S890) was depressed in the ipsilateral hemisphere relative to both naïve controls and the contralateral hemisphere immediately following HI at both ages. At P7, but not P21, reperfusion resulted in an initial recovery to control phosphorylation levels at all 3 sites followed by a secondary decline. At both ages, pS896 was less than control values after 24 h of recovery, whereas pS890 had returned to control levels by this time. pS897 recovered to control levels by 24 h in P21 animals but not in P7 animals. Differential effects of HI on phosphorylation of the NMDA receptor at P7 and P21 may contribute to age-related changes in sensitivity to HI.
Subventricular Zone Proliferation after α-Amino-3-Hydroxy-5-Methyl-4-Isoxazolepropionic Acid Receptor-Mediated Neonatal Brain Injury
Authors: Xu G. , Ong J. , Liu Y.-Q. , Silverstein F.S. , Barks J.D.E.
Published: July 2005

The mammalian forebrain subventricular zone (SVZ) contains stem cells capable of generating new neurons and glia. Recent studies indicate that acute brain injury is a potent stimulus for SVZ stem cell proliferation. To better understand mechanisms of the SVZ response to neonatal brain injury, we used a model that focuses on a unique mechanism of vulnerability of the immature CNS, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor-mediated excitotoxicity. We previously demonstrated that intracerebroventricular injection of the glutamate analog AMPA in rats at postnatal day 7 (P7) caused bilateral periventricular gray and white matter injury. We hypothesized that excitotoxic injury would stimulate cellular proliferation in the SVZ; we used the AMPA intracerebroventricular injection model to test this hypothesis. P7 rat pups received either left or right intracerebroventricular injections of S-AMPA (2.5 nmol). Normal and PBS-injected littermates were included as controls. On P8 or P14, serial coronal sections through the SVZ were collected; an immunohistochemical assay was performed with an antibody to the cell proliferation marker Ki-67. Bilateral Ki-67+ cells/SVZ were quantitated stereologically using the optical disector method. The median number of Ki-67+ cells/SVZ was increased in the SVZ of AMPA-injected rats relative to normal controls on both P8 and P14. To evaluate neurogenesis, we assayed the expression of doublecortin, a microtubular protein expressed only by immature neurons. From P8 to P14, there was a marked increase in doublecortin immunoreactive cells in the AMPA-injected SVZ. Many Ki-67+ nuclei were immediately surrounded by doublecortin staining. This study indicates that there is a proliferative response in the immature SVZ after an excitotoxic stimulus. Our findings suggest that some of these newly generated cells differentiate as immature neurons. This model may provide information about the mechanisms that regulate SVZ responses to neonatal brain injury.
Study of Tobacco Habits and Alterations in Enzymatic Antioxidant System in Oral Cancer
Authors: Patel Beena P. , Rawal Upendra M. , Shah Pankaj M. , Prajapati Jayesh A. , Rawal Rakesh M. , Dave Tina K. , Patel Prabhudas S.
Published: July 2005

Aim and Objective: Tobacco is a major etiological factor for oral cancer development, accounting 30–40% of all cancer cases in India. Tobacco consumption generates free radicals and causes oxidative damages. In order to counteract these lethal effects, normal living cells have multiple antioxidant defense systems in a cascade manner. Thus, it seems that studying biological parameters, like antioxidant enzyme system, may be helpful in risk assessment and early diagnosis of oral cancer. Therefore, we analyzed erythrocytic and tissue antioxidant enzyme activities in terms of glutathione-S-transferase (GST), glutathione reductase (GR), superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and plasma thiol levels. Materials and Methods: Study included healthy controls with no habit of tobacco (NHT, n = 25), controls with habit of tobacco (WHT, n = 31) and oral cancer patients (n = 52). All the parameters were analyzed with highly sensitive and specific spectrophotometric methods. Results: Erythrocytic SOD and plasma thiol levels were significantly lower (p = 0.03), while GPx and CAT levels were higher (p = 0.017) in WHT as compared to NHT. No significant changes in GST and GR levels were observed between NHT and WHT. GST, GR, SOD and CAT activities were significantly higher (p = 0.05, p < 0.001, p = 0.003 and p < 0.001, respectively) while GPx and thiol levels were lower (p = 0.035 and p < 0.001, respectively) in oral cancer as compared to WHT. Odds ratio for erythrocytic GR, SOD, CAT and plasma thiol showed significantly higher risk of oral cancer development in WHT. Mean levels of SOD and CAT were increased, while GPx and thiol were decreased with the increase in habit duration in oral cancer. GST, GR and SOD activities were significantly higher (p = 0.0001, p = 0.005 and p = 0.005, respectively), while, CAT and thiol levels were lower (p = 0.0001 and p = 0.015, respectively) in malignant tissues as compared to adjacent normal tissues. Conclusion: The data revealed that evaluation of antioxidant enzyme activities and thiol levels in WHT can be helpful to identify individuals at a higher risk of oral cancer development