Extreme rainstorms drive exceptional organic carbon export from forested humid-tropical rivers in Puerto Rico.

Extreme rainfall events in the humid-tropical Luquillo Mountains, Puerto Rico export the bulk of suspended sediment and particulate organic carbon. Using 25 years of river carbon and suspended sediment data, which targeted hurricanes and other large rainstorms, we estimated biogenic particulate organic carbon yields of 65 ± 16 tC km-2 yr-1 for the Icacos and 17.7 ± 5.1 tC km-2 yr-1 for the Mameyes rivers. These granitic and volcaniclastic catchments function as substantial atmospheric carbon-dioxide sinks, largely through export of river biogenic particulate organic carbon during extreme rainstorms. Compared to other regions, these high biogenic particulate organic carbon yields are accompanied by lower suspended sediment yields. Accordingly, particulate organic carbon export from these catchments is underpredicted by previous yield relationships, which are derived mainly from catchments with easily erodible sedimentary rocks. Therefore, rivers that drain petrogenic-carbon-poor bedrock require separate accounting to estimate their contributions to the geological carbon cycle.

Water and solute mass balance of five small, relatively undisturbed watersheds in the U.S.

Geochemical mass balances were computed for water years 1992-1997 (October 1991 through September 1997) for the five watersheds of the U.S. Geological Survey Water, Energy, and Biogeochemical Budgets (WEBB) Program to determine the primary regional controls on yields of the major dissolved inorganic solutes. The sites, which vary markedly with respect to climate, geology, physiography, and ecology, are: Allequash Creek, Wisconsin (low-relief, humid continental forest); Andrews Creek, Colorado (cold alpine, taiga/tundra, and subalpine boreal forest); Río Icacos, Puerto Rico (lower montane, wet tropical forest); Panola Mountain, Georgia (humid subtropical piedmont forest); and Sleepers River, Vermont (humid northern hardwood forest). Streamwater output fluxes were determined by constructing empirical multivariate concentration models including discharge and seasonal components. Input fluxes were computed from weekly wet-only or bulk precipitation sampling. Despite uncertainties in input fluxes arising from poorly defined elevation gradients, lack of dry-deposition and occult-deposition measurements, and uncertain sea-salt contributions, the following was concluded: (1) for solutes derived primarily from rock weathering (Ca, Mg, Na, K, and H(4)SiO(4)), net fluxes (outputs in streamflow minus inputs in deposition) varied by two orders of magnitude, which is attributed to a large gradient in rock weathering rates controlled by climate and geologic parent material; (2) the net flux of atmospherically derived solutes (NH(4), NO(3), SO(4), and Cl) was similar among sites, with SO(4) being the most variable and NH(4) and NO(3) generally retained (except for NO(3) at Andrews); and (3) relations among monthly solute fluxes and differences among solute concentration model parameters yielded additional insights into comparative biogeochemical processes at the sites.

Consistent land- and atmosphere-based U.S. carbon sink estimates.

For the period 1980-89, we estimate a carbon sink in the coterminous United States between 0.30 and 0.58 petagrams of carbon per year (petagrams of carbon = 10(15) grams of carbon). The net carbon flux from the atmosphere to the land was higher, 0.37 to 0.71 petagrams of carbon per year, because a net flux of 0.07 to 0.13 petagrams of carbon per year was exported by rivers and commerce and returned to the atmosphere elsewhere. These land-based estimates are larger than those from previous studies (0.08 to 0.35 petagrams of carbon per year) because of the inclusion of additional processes and revised estimates of some component fluxes. Although component estimates are uncertain, about one-half of the total is outside the forest sector. We also estimated the sink using atmospheric models and the atmospheric concentration of carbon dioxide (the tracer-transport inversion method). The range of results from the atmosphere-based inversions contains the land-based estimates. Atmosphere- and land-based estimates are thus consistent, within the large ranges of uncertainty for both methods. Atmosphere-based results for 1980-89 are similar to those for 1985-89 and 1990-94, indicating a relatively stable U.S. sink throughout the period.

A multicenter investigation with D-FISH BCR/ABL1 probes.

Twenty-eight laboratories evaluated a new fluorescence in situ hybridization (FISH) strategy for chronic myeloid leukemia. In a three-part study, bcr/abl1 D-FISH probes were used to study bone marrow specimens. First, laboratories familiarized themselves with the strategy by applying it to known normal and abnormal specimens. Then, collectively the laboratories studied 20 normal and 20 abnormal specimens blindly and measured workload. Finally, each laboratory and two experts studied six serial dilutions with 98-0% abnormal nuclei. Using the reported normal cutoff of < 1% abnormal nuclei, participants reported no false-negative cases and 15 false-positive cases (1-6.6% abnormal nuclei). Results provided by participants for serial dilutions approximated the expected percentages of abnormal nuclei, but those from the experts exhibited greater precision. The clinical sensitivity, precision, nomenclature, workload, recommendations for training, and quality assurance in methods using D-FISH in clinical practice are discussed.

A multicenter investigation with interphase fluorescence in situ hybridization using X- and Y-chromosome probes.

Twenty-six laboratories used X and Y chromosome probes and the same procedures to process and examine 15,600 metaphases and 49,400 interphases from Phaseolus vulgaris-leucoagglutinin (PHA)-stimulated lymphocytes. In Part I, each laboratory scored 50 metaphases and 200 interphases from a normal male and a normal female from its own practice. In Part II, each laboratory scored 50 metaphases and 200 interphases on slides prepared by a central laboratory from a normal male and a normal female and three mixtures of cells from the male and female. In Part III, each laboratory scored 50 metaphases (in samples of 5, 10, 15, and 20) and 100 interphases (in samples of 5, 10, 15, 20, and 50) on new, coded slides of the same specimens used in Part II. Metaphases from male specimens were scored as 98-99% XY with no XX cells, and 97-98% of interphases were scored as XY with 0.04% XX cells. Metaphases from female specimens were scored as 96-97% XX with 0.03% XY cells, and 94-96% of interphases were scored as XX with 0.05% XY cells. Considering the data as a model for any probe used with fluorescence in situ hybridization (FISH), a statistical approach assessing the impact of analytical sensitivity on the numbers of observations required to assay for potential mosaicisms and chimerisms is discussed. The workload associated with processing slides and scoring 50 metaphases and 200 interphases using FISH averaged 27.1 and 28.6 minutes, respectively. This study indicates that multiple laboratories can test/develop guidelines for the rapid, efficacious, and cost-effective integration of FISH into clinical service.

Characterization of neo-centromeres in marker chromosomes lacking detectable alpha-satellite DNA.

Recent studies have implicated alpha-satellite DNA as an integral part of the centromere, important for the normal segregation of human chromosomes. To explore the relationship between the normal functioning centromere and alpha-satellite DNA, we have studied eight accessory marker chromosomes in which fluorescence in-situ hybridization could detect neither pancentromeric nor chromosome-specific alpha-satellite DNA. These accessory marker chromosomes were present in the majority of or all cells analyzed and appeared mitotically stable, thereby indicating the presence of a functional centromere. FISH analysis with both chromosome-specific libraries and single-copy YACs, together with microsatellite DNA studies, allowed unequivocal identification of both the origin and structure of these chromosomes. All but one of the marker chromosomes were linear mirror image duplications, and they were present along with either two additional normal chromosomes or with one normal and one deleted chromosome. Indirect immunofluorescence analysis revealed that the centromere protein CENP-B was not present on these markers; however, both CENP-C and CENP-E were present at a position defining a 'neo-centromere'. These studies provide insight into a newly defined class of marker chromosomes that lack detectable alpha-satellite DNA. At least for such marker chromosomes, alpha-satellite DNA at levels detectable by FISH appears unnecessary for chromosome segregation or for the association of CENP-C and CENP-E at a functional centromere.

Sex chromosome markers: characterization using fluorescence in situ hybridization and review of the literature.

Fluorescence in situ hybridization (FISH) using biotin labeled X- and Y-chromosome DNA probes was utilized in the analysis of 23 sex chromosome-derived markers. Specimens were obtained through prenatal diagnosis, because of a presumptive diagnosis of Ullrich-Turner syndrome, mental retardation, and minor anomalies or ambiguous genitalia; three were spontaneous abortuses. Twelve markers were derived from the X chromosome and eleven from the Y chromosome; this demonstrates successfully the value and necessity of FISH utilizing DNA probes in the identification of sex chromosome markers. Both fresh and older slides, some of which had been previously G-banded, were used in these determinations. We have also reviewed the literature on sex chromosome markers identified using FISH.

Toward quality assurance for metaphase FISH: a multicenter experience.

Although fluorescent in situ hybridization (FISH) is rapidly becoming a part of clinical cytogenetics, no organization sponsors multicenter determinations of the efficacy of probes. We report on 23 laboratories that volunteered to provide slides and to use a probe for small nuclear ribonucleoprotein polypeptide N (SNRPN) and a control locus. Experiences with FISH for these laboratories during 1994 ranged from 0 to 645 utilizations (median = 84) involving blood, amniotic fluid, and bone marrow. In an initial study of hybridization efficiency, the median percentage of metaphases from normal individuals showing two SNRPN and two control signals for slides prepared at each site was 97.0 (range = 74-100); for slides prepared by a central laboratory, it was 97.8 (range = 81.6-100). In a subsequent blind study, each laboratory attempted to score 5 metaphases from each of 23 specimens [8 with del(15)(q11.2-->q12) and 15 with normal #15 chromosomes]. Of 529 challenges, the correct SNRPN pattern was found in 5 of 5 metaphases in 457 (86%) and in 4 of 5 in 33 (6%). Ambiguous, incomplete, or no results were reported for 32 (6%) challenges. Seven (1%) diagnostic errors were made, including 6 false positives and 1 false negative: 1 laboratory made 3 errors, 1 made 2, and 2 made 1 each. Most errors and inconsistencies seemed due to inexperience with FISH. The working time to process and analyze slides singly averaged 49.5 min; slides processed in batches of 4 and analyzed singly required 36.9 min. We conclude that proficiency testing for FISH by using an extensive array of challenges is possible and that multiple centers can collaborate to test probes and to evaluate costs.

Toward quality assurance for metaphase FISH: a multi-center experience.

Although fluorescent in situ hybridization (FISH) is rapidly becoming a part of clinical cytogenetics, no organization sponsors multi-center determinations of the efficacy of probes. We report on 23 laboratories that volunteered to provide slides and to use a probe for SNRPN and a control locus. Experiences with FISH for these laboratories during 1994 ranged from 0 to 645 utilizations (median = 84) involving blood, amniotic fluid and bone marrow. In an initial study of hybridization efficiency, the median percentage of metaphases from normal individuals showing two SNRPN and 2 control signals for slides prepared at each site was 97.0 (range = 74-100); for slides prepared by a central laboratory, it was 97.8 (range = 81.6-100). In a subsequent blind study, each laboratory attempted to score 5 metaphases from each of 23 specimens [8 with del(15) (q11.2-->q12) and 15 with normal 15 chromosomes]. Of 529 challenges, the correct SNRPN pattern was found in 5 of 5 metaphases in 457 (86%) and in 4 of 5 in 33 (6%). Ambiguous, incomplete or no results were reported for 32 (6%) challenges. Seven (1%) diagnostic errors were made including 6 false positives and 1 false negative: 1 laboratory made 3 errors, 1 made 2, and 2 made 1 each. Most errors and inconsistencies seemed due to inexperience with FISH. The working time to process and analyze slides singly averaged 49.5 minutes; slides processed in batches of 4 and analyzed singly required 36.9 minutes. We conclude that proficiency testing for FISH using an extensive array of challenges is possible and that multiple centers can collaborate to test probes and to evaluate costs.

Uniparental isodisomy 13 in a normal female due to transmission of a maternal t(13q13q).

Chromosomes from a normal 23-year-old, primigravid woman were examined at 10 weeks of gestation because of her mother's history: 8 miscarriages and two liveborn infants (the proposita and a brother who died at 3 days with multiple anomalies). Karyotypes of the proposita and her normal mother were 45,XX,t(13q13q). No evidence of mosaicism was encountered. When the proposita inherited the t(13q13q), she received two copies of 13q from her mother. Moreover, she and her mother shared the same homozygous pattern of alleles from 7 highly polymorphic microsatellite repeats localized along 13q. No evidence of paternal markers from 13 was detected, although biparental inheritance was demonstrated with DNA markers from chromosomes 2 and 17. Cytogenetic and molecular findings indicated that the proposita's chromosomal complement included mUPD 13q. The proposita's normal phenotype suggested that no maternally imprinted genes map to 13q.

Partial X chromosome trisomy with functional disomy of Xp due to failure of X inactivation.

A 5-month-old girl with mild phenotypic abnormalities, developmental delay, and seizures was found to have the de novo karyotype 46,XX,-13,+der(13)t(X;13)(p21.2;p11.1). The partial trisomy of Xp21.2-->pter was confirmed with fluorescence in situ hybridization, using an X chromosome painting probe and several cosmid and YAC probes for Xp sequences. Replication banding showed that one of the structurally normal X chromosomes was late-replicating, but that the Xp segment of the der(13) was early-replicating in all cells examined. Since segments of the X chromosome separated from the X inactivation center in Xq13.2 cannot undergo X inactivation, the result is functional disomy of distal Xp. As the loss of short arm material from chromosome 13 is not considered to be clinically significant, the genomic imbalance of Xp expressed in this patient most likely accounts for her abnormal phenotype.

Dynamics of soil carbon during deglaciation of the laurentide ice sheet.

Deglaciation of the Laurentide Ice Sheet in North America was accompanied by sequestration of organic carbon in newly exposed soils. The greatest rate of land exposure occurred around 12,000 to 8,000 years ago, and the greatest increase in the rate of carbon sequestration by soils occurred from 8,000 to 4,000 years ago. Sequestration of carbon in deglaciated peat lands continues today, and a steady state has not been reached. The natural rate of carbon sequestration in soils, however, is small relative to the rate of anthropogenic carbon dioxide production.

Two anonymous DNA segments distinguish the Wilms' tumor and aniridia loci.

The association of Wilms' tumor with aniridia (the WAGR complex) in children with 11p13 chromosomal abnormalities has been established, but the paucity of molecular probes in 11p13 has hampered identification of the responsible genes. Two new anonymous DNA segments have been identified that map to the WAGR region of 11p13. Both DNA probes identify a cytologically undetectable deletion associated with a balanced chromosome translocation inherited by a patient with familial aniridia, but not Wilms' tumor. The same two DNA segments are also included in the distal p13-p14.1 deletion of another patient, who has aniridia, Wilms' tumor, and hypogonadism, but they are not included in the p12-p13 deletion of a third patient, who does not have aniridia but has had a Wilms' tumor. The discovery of this aniridia deletion and these two DNA segments that physically separate the Wilms' tumor and aniridia loci should facilitate identification of the genes in the WAGR locus, beginning with the aniridia gene.

Dideoxy sequencing of double-stranded DNA from poly(A)-extended 3'-ends.

A simple method has been developed for sequencing double-stranded DNA by the chain termination method. The DNA to be sequenced is cut with a restriction enzyme that leaves a 3'-overhang which is extended by terminal deoxynucleotidyltransferase with limiting amounts of dATP. The sequencing reaction is then primed with an oligo(dT) primer which has a base pair "anchor" complementary to the overhang generated by the restriction enzyme. The method presented here eliminates the need for subcloning of the DNA or sequencing by chemical modification. Furthermore, sequences of more than 300 nucleotides are obtained from any 3'-overhanging restriction end.

Lymphocyte proliferation in a 31-week premature neonate with 69, XXX chromosomal constitution.

The clinical syndrome of triploidy has only recently been described with its phenotypic characteristics emerging from a series of descriptive case reports. This paper describes the mitogen induced lymphocyte proliferative responses of a 31-week gestation neonate. Similar data, collected simultaneously, from 27 healthy 30-32-week gestation neonates is also reported for comparison. Since the capability of lymphocytes to become activated is dependent on and indicative of the host's ability to develop a cellular immune reaction, these data indicate no diminution in cell mediated immunity by this polyploid individual.

Dissociation of a t(12;21) resulting in a normal cell line in two trisomic 21 sons of a nonmosaic t(12;21) father?

A normal cell line arising from a translocation, t(12;21), possibly by dissociation, was observed in two brothers in early life. Each was conceived as trisomic 21 by their 45,XY,-12,-21,+t(12;21) father, who was phenotypically normal. Each brother showed morphologic manifestations of trisomy 21 syndrome, and each was mildly mentally retarded. Dermatoglyphic indices were not diagnostic of trisomy 21 syndrome. At 4 months the younger brother had a 50:50 proportion of trisomic:normal blood cells which became 25:75 of trisomic 21:normal at 36 months. The older brother had a 25:75 proportion of trisomic 21:normal when first studied at 41/2 years. A similar t(12;21) has not previously been reported. The occurrence of an apparently normal cell line arising spontaneously is unique.

New deletion syndrome: 1q43.

A male infant showed dysmorphology of the head and face, neck, extremities, and genitalia, as well as growth and mental retardation. His G-banded karyotype was 46,XY,--1+der(1),t(1;16)(q43;q24)mat. Combined with five previously reported cases involving similar terminal deletions beginning at 1q42 or 43, we show that the homology of phenotypic characteristics permits identification of a new deletion syndrome, the first involving chromosome 1.

Partial monosomy 7q syndrome due to distal interstitial deletion.

A female infant was ascertained at 10 weeks because of failure to thrive and a peculiar cry and was found to have few morphologic variants. Her karyotype was 46,XX,del(7)(q3105::q3405). The parental karyotypes were normal. At one year she manifested physical retardation and development delay and required surgery for gastroesophageal incompetence. The phenotypic characteristics of this patient and those of six previously reported cases of 7q medial or distal interstitial deletion include many anomalies. Morphologic abnormalities of the head, ears, eyes, mouth, chest, hands, feet, and nerves combined with characteristics of birth weight, growth, and development define a detectable syndrome. An unusual cry may help in the recognition of this new syndrome.