Systematic embryology of the Scilla siberica alliance (Hyacinthaceae)

Eleven species of the Scilla siberica alliance, a well defined monophyletic group within the "genus by tradition" Scilla , have been investigated embryologically with special reference to embryo sac and endosperm development. Data are now available for 15 out of 20 known species. In most species embryo sacs develop according to the bisporic Allium-type, only in Scilla rosenii according to the tetrasporic Drusa-type. Endosperm development is either nuclear or helobial (in 10 and 4 species respectively, unknown in 1). The taxonomic significance of these traits is evaluated after character polarisation by out-group comparison. Among the out-group taxa, S. persica may be considered as the sister group of the S. siberica alliance because only these two groups have an Allium-type embryo sac, a synapomorphy derived from the plesiomorphic Polygonurn-type. The Drusa-type in S. rosenii is an autapomorphy for that species and evolved from an Allium-type embryo sac. S. rosenii is distinct from its sister species S. koenigii , previously thought to be conspecific. Nuclear endosperm is considered to be plesiomorphic rather than apomorphic within the S. siberica alliance, with respect to its occurrence in the presumed sister group and other outgroup taxa (S. hohenackeri group, S. bifolia alliance), but some doubt remains because of a helobial endosperm occurring in the out-group taxon S. messeniaca . The distribution of other synapomorphies within the S. siberica alliance suggests that a helobial endosperm evolved as a synapomorphy for S. bithynica, S. melaina and S. mischtschenkoana , but as a parallel trait in S. leepii . Species status for S. leepii is supported.     

Characterization of heterochromatin in different species of the Scilla siberica group (Liliaceae) by in situ hybridization of satellite DNAs and fluorochrome banding

Satellite DNAs have been isolated from the monocotyledonous plants Scilla siberica, S. amoena, S. ingridae (all are highly GC-rich), and S. mischtschenkoana by using the Ag⁺ –Cs₂SO₄ density centrifugation technique. Hybridization in situ has been performed with ₃H-cRNA to these satellite DNAs in all four species. In each species, the endogenous satellite DNA is located mainly in intercalary and major heterochromatin bands associated with terminal regions and nucleolar organizer regions (NORs) but not in centromeric regions. Patterns observed after cross-species hybridization show a high degree of satellite DNA homology between S. siberica, S. amoena, and S. ingridae. By contrast, satellite DNA of S. mischtschenkoana consists largely of different, non homologous DNA sequences, with two exceptions: (i) the NORs of all four species contain similar satellite sequences, and (ii) a strong homology exists between the satellite DNA of S. mischtschenkoana and centromeric DNA of S. siberica but not with those of S. amoena and S. ingridae. — Heterochromatin has also been characterized by the AT-specific fluorochromes quinacrine (Q) and DAPI and the GC-specific agent chromomycin A₃ (CMA₃), in combination with two counterstaining techniques. While CMA₃-fluorescence is largely in agreement with data on base composition and location of the specific satellite DNAs, the results with Q and DAPI are conflicting. Prolonged fixation has been found to change the fluorescence character in certain instances, indicating that other factors than the base sequence of the DNA also play a role in fluorochrome staining of chromosomes. The results are discussed in relation to the taxonomy and phylogeny of the four species.     

In situ analysis of centromeric satellite DNA segregating inMus species crosses

In situ hybridization of biotin-labeled mouse major satellite DNA clone pMR196 was applied toMus domesticus andMus spretus chromosomes (Chr). The same karyotypes were counterstained with distamycin A-DAPI to identify AT-rich heterochromatin. Chromosomes from the laboratory mouse, C57BL/6Ros (BL/6;M. domesticus) were uniformly labeled at the centromere except for the Y, while chromosomes from the divergentMus speciesM. spretus showed little or no hybridization. Differences betweenMus species in copy number of the major satellite DNA sequence were used to identify chromosomes ofM. domesticus andM. spretus in their F₁ hybrids and to discriminatedomesticus andspretus centromeres in backross progeny. The distribution pattern of heterochromatic regions demonstrated by distamycin A-DAPI counterstaining was comparable with that of in situ hybridization with pMR196, suggesting that A-T rich heterochromatin inM. domesticus is mainly constructed by the pMR196-related sequence. The in situ technique was used to examine segregation ofdomesticus centromeres in backcross progeny obtained by mating F₁ hybrid females withM. domesticus orM. spretus males. The segregation of centromeres did not deviate from the expected among the backcross progeny from C57BL/6Ros males, whereas chromosomes withM. domesticus centromeres were prone to appear in the progeny from backcross matings byM. spretus males.     

The impact of StuI digestion in situ on FISH to human chromosomes with satellite DNA probes

Human metaphase chromosomes were digested with StuI and subsequently hybridized in situ using chromosome 9 alphoid DNA and classical satellite III DNA as probes. The data obtained suggest that it is not possible to establish a general rule regarding the cytological effects induced by restriction enzymes in particular chromosome regions and that a number of factors, such as DNA sequences, DNA-protein interaction and enzyme structure, play a role in determining such effects.     

In situ methane enrichment in anaerobic digestion

A major cost consideration in the use of anaerobic digestion to convert biomass and waste to utility-grade gas is the expense of separating CO(2) from the product gas. Anaerobic digestion has a number of inherent properties that can be exploited to increase the methane content of the gas directly produced by the digester, the most important of which is the high solubility of CO(2)(40-60 times that of methane) in water under digestion conditions. The methane enrichment concept examined in this study involved the recirculation of a liquid stream from the digester through a CO(2) desorption process and the return of the liquid stream back to the digester for absorption of additional CO(2) produced by the conversion of organic materials. A steady-state equilibrium model predicted that a digester gas methane content exceeding 94% could be achieved with this scheme using modest recirculation rates provided a desorption process could be designed to achieve a 60+% CO(2) removal efficiency in the degassing of the liquid recycle stream. Using fixed-film laboratory digesters operated on synthetic feedstocks, the technique of methane enrichment was tested under pressurized and unpressurized conditions. A 93 + 2% methane gas stream was produced from a volatile-acid-fed bench-scale digester simulating the methanogenic stage of two-phase digestion under conditions of (1) a pH swing achieved without caustic addition that allowed digestion at pH 7. 5 and air stripping at pH 6. 5-7. 0, (2) digester pressurization to 30 psig, and (3) a recycle rate of 0. 33 L/L reactor/day. Significant but lower levels of methane enrichment were achieved with the single-stage digester at the low experimental recycle rate. However, the narrow range among all experiments of CO(2) desorption efficiencies achieved in air stripping the recycle stream (35-60% CO(2) removal) suggests that comparable methane enrichment-may be achieved with unpressurized single-stage digestion using greater recycle rates. A materials balance analysis of data from an unpressurized, single-stage digester employing no chemical addition and using laboratory degassing efficiencies indicated that 94% methane could be produced at recycle rates of less than 1. 4 L/L reactor/day with a methane loss of less than 2%.     

Sau3A in situ digestion of human chromosome 3 pericentrometric heterochromatin. I. Differential digestion of alpha-satellite and satellite 1 DNA sequences.

In situ digestion with the restriction endonuclease (RE) Sau3A (Sau3A REISD) uncovers a polymorphism for the pericentromeric heterochromatin of human chromosome 3, which can be positively stained (3+) or not (3-), and has proven useful to differentiate donor and recipient cells after sex-matched bone marrow transplantation and to analyze the so-called hemopoietic chimerism. The aim of the present investigation was to obtain insight into the molecular basis of such polymorphism to optimize its use for chimerism quantification using methodological approaches other than REISD. To this end, fluorescence in situ hybridization (FISH) assays using probes for the satellite DNA sequences that mainly constitute chromosome 3 pericentromeric heterochromatin (alpha-satellite and satellite 1 DNA) were performed on control and Sau3A-digested chromosomes. The results obtained suggest that chromosome 3 alpha-satellite DNA is digested in all individuals studied, irrespective of the karyotype obtained by Sau3A REISD (3++, 3+-, 3--), and thus it does not seem to be involved in the polymorphism uncovered by Sau3A on this chromosome. Satellite 1 DNA is not digested in any case, and shows a polymorphism for its domain size, which correlates with the polymorphism uncovered by Sau3A in such a way that 3+ chromosomes show a large domain (3L) and 3- chromosomes show a small domain (3S). It seems, therefore, that the cause of the polymorphism uncovered by Sau3A on the pericentromeric region of chromosome 3 is a difference in the size of the satellite 1 DNA domain. Small satellite 1 DNA domains fall under the resolution level of REISD technique and are identified as 3-.     

Changes in DNA content and chromosomal size during cell culture and plant regeneration of Scilla siberica: selective chromatin diminution in response to environmental conditions

The chromosomal complement and DNA content of cells of the monocotyledonous plant Scilla siberica were studied at various stages of growth, such as callus outgrowths from bulb tissue (bulb callus), callus grown from single protoplasts prepared from bulb callus (protoplast callus), regenerated plants kept for 2–4 years on agar medium and under constant climatic conditions, and regenerated plants grown first for 2 years on agar and then for 1 year in the garden. During callus culture, several different forms of chromatin loss were observed: (1) chromosome elimination early during cell culture, resulting in cells which were mostly diploid but still had large chromosomes similar to those of the original triploid plants (type 1 cells); from these cells no plants could be regenerated. (2) Dramatic reduction in heterochromatin containing the satellite DNA and, apparently subsequently, also of many other chromatin moieties, resulting in the formation of small chromosomes; frequent polyploidization in these cells, resulting in a variable number of chromosomes per cell (preferentially 30–40, in ca. 70% of the cells; type 2 cells). (3) Appearance of a large number of very small (< 1 m) Feulgenpositive chromatin particles (minute chromosomes; often arranged in metaphase-like arrays, suggesting that they were effectively distributed during mitosis). Such cells could survive and divide under cell culture conditions but did not regenerate plants (type 3 cells). In bulb calli, all three cell types were found whereas in protoplast calli only cells of type 2 and 3 were seen. Type 2 and 3 cells had lost, despite their frequent polyploidization, about 80% of their initial nuclear DNA content and an even higher proportion (>95%) of the satellite sequences. Southern DNA blot analysis revealed that sequences hybridizing with certain protein-coding genes such as that for chalcone synthase were also drastically reduced in copy number whereas the proportion of rDNA was even somewhat increased. In plants regenerated from type 2 cells of protoplast calli, which were aneuploid at near-pentaploidy to hexaploidy, further conspicuous changes in chromosomal and DNA content were not observed, as long as they were kept on agar medium and under constant climatic conditions. However, when such plants were grown in the garden for at least 1 year, the satellite DNA as well as the sequences hybridizing with the chalcone synthase gene were disproportionately increased to 30%–40% of their normal proportion, whereas the total DNA had increased by only approximately 15%. The chromosome numbers remained near-pentaploid to hexaploid as in the cell cultures from which these plants had been regenerated. These phenomena of selective loss and regain of chromatin in response to environmental conditions (cell culture, regenerated plants on agar, regenerated plants grown outdoors) are discussed in relation to other forms of chromatin loss, including developmentally controlled chromatin diminution in certain animals.     

Heterochromatin and DNA replication in Scilla sibirica

A cold-induced undercontraction of certain chromosome segments is found in Scilla sibirica after treatment at −12 °C. The regions showing heterochromatic properties in the classical sense are late-replicating and identical with the segments that are undercontracted after cold treatment.     

In situ hybridization with fluoresceinated DNA.

We have used fluorescein-11-dUTP in a nick-translation format to produce fluoresceinated human nucleic acid probes. After in situ hybridization of fluoresceinated DNAs to human metaphase chromosomes, the detection sensitivity was found to be 50-100 kb. The feasibility and the increase in detection sensitivity of microscopic imaging of in situ hybridized, fluoresceinated DNA with an integrating solid state camera for rapid cosmid mapping is illustrated. Combination of fluoresceinated DNA with biotinated and digoxigeninated DNAs allowed easy performance of triple fluorescence in situ hybridization. The potential of these techniques for DNA mapping, cytogenetics and biological dosimetry is briefly discussed.     

In situ localization of PCR-amplified DNA and cDNA

Combining the high sensitivity of PCR with the cell localizing ability ofin situ hybridization allows for the reproducible detection of low copy targets in intact cells. This article describes several key variables that include fixation, protease digestion, the hot start maneuver, stringency, and, for RNA analysis, DNase digestion that are important to successfulin situ PCR. Also stressed is the importance of performing and interpreting controls with each experiment. Important controls include omission of key components, use of samples known either to contain or lack the target of interest and, most importantly, the in-built controls invariably present in the heterogeneous component of any given tissue type.     

The anatomical,morphological features,and biological activity of Scilla siberica subsp. armena (Grossh.) Mordak (Asparagaceae)

Protoplasma - Scilla siberica subsp. armena is known as Siberian Squill which is naturally distributed in Lebanon-Syria, Transcaucasus, and Turkey. It is a perennial bulbous plant with a short...     

Oligonucleotide-priming methods for the chromosome-specific labelling of alpha satellite DNA in situ

It is demonstrated that either general staining of the centromeric regions of all primate chromosomes, or selective staining of the centromeric region of specific chromosomes, may be obtained in preparations of metaphase chromosomes by probing specifically for different regions within the alpha satellite DNA monomer. In order to exploit observed patterns of sequence variation within the monomer for this purpose, we have developed two new DNA analysis methods. In PRimed IN Situ labelling (PRINS), synthetic oligonucleotides derived from subsections of the monomer are hybridized to the chromosomes. The oligonucleotides then serve as primers for the in situ incorporation of biotin-labelled nucleotides catalysed by Klenow polymerase. Incorporated biotin is visualized with fluorescein isothiocyanate-labelled avidin (FITC-avidin). In Primed Amplification Labelling (PAL), biotin-labelled hybridization probes are produced in a polymerase chain reaction (PCR, Saiki et al. 1985), in which two synthetic oligonucleotide primers anneal within the same monomer. With the right choice of primers libraries of labelled probes derived from most monomers present as templates are produced. If DNA from a specific chromosome is used as template, then the resulting probe mixture gives stronger and more chromosome-specific signals in in situ hybridization experiments than does a cloned alpha satellite DNA probe derived from the same chromosome. The results obtained indicate that the alpha-repeat monomer is composed of regions with different degrees of chromosome specificity.     

Characterization of human heterochromatin by in situ hybridization with satellite DNA clones

Biotinylated DNA from two satellite-related, repetitive DNA clones, pHuR 98 and pHuR 195 (specific for chromosomes 9 and 16, respectively), and from a Y-specific clone, pY-3.4A, were hybridized to human metaphase chromosomes using fluoresceinated avidin to detect binding. The chromosomes were simultaneously counterstained with distamycin-DAPI to identify the AT-rich heterochromatin of chromosomes 1, 9, 15, 16, and the Y chromosome. With this method, clear results were obtained under both normal and low stringency conditions, allowing hybridization between molecules sharing 80-85% and 60-65% identity, respectively. Thus, additional sites related to the probes could be identified. A close relationship was shown between the heterochromatin of chromosomes 1 and 16, both hybridizing with clone pHuR 195 under low stringency. Hybridization with clone pHuR 98 was highly specific for chromosome 9, even under low stringency. A relationship between chromosomes 9, 15, and the Y chromosome, however, was shown by hybridization with clone pY-3.4A. The chromosomal distribution of the three repetitive DNA clones used in this study, and data from the literature, are in accordance with the distribution of the heterochromatin types characterized by staining with different fluorescent dyes and dye combinations. Furthermore, our sequence data for clones pHuR 98 and pHuR 195 may explain the fluorescent properties on which the cytogenetic classification of the heterochromatin is based.     

In situ proteolytic digestion of inclusion body polypeptides occurs as a cascade process

Misfolded proteins undergo a preferent degradation ruled by the housekeeping bacterial proteolytic system, but upon precipitation as inclusion bodies their stability dramatically increases. The susceptibility of aggregated polypeptides to proteolytic attack remains essentially unexplored in bacteria and also in eukaryotic cells. We have studied here the in vitro proteolysis of beta-galactosidase fusion proteins by trypsin treatment of purified inclusion bodies. A cascade digestion process similar to that occurring in vivo has been observed in the insoluble fraction of the digestion reaction. This suggests that major protease target sites are not either lost or newly generated by protein precipitation and that the digestion occurs in situ probably on solvent-exposed surfaces of inclusion bodies. In addition, the sequence of the proteolytic attack is influenced by protein determinants other than amino acid sequence, the early digestion steps having a dramatic influence on the further cleavage susceptibility of the intermediate degradation fragments. These observations indicate unexpected conformational changes of inclusion body proteins during their site-limited digestion, that could promote protein release from aggregates, thus partially accounting for the plasticity of in vivo protein precipitation and solubilization in bacteria.     

In situ digestion of Drosophila virilis polytene chromosomes by AluI and HaeIII restriction endonucleases

Polytene chromosomes of Drosophila virilis were treated with AluI and HaeIII restriction endonucleases. Both enzymes were capable of extensively digesting chromosomal DNA, with the exception of some regions that contain repetitive DNAs. Moreover, a comparison was made between our data and the data already obtained with the same enzymes in D. melanogaster. On this basis, AluI digestion showed that the 5S RNA genes of D. virilis and D. melanogaster have different base composition, while digestion with HaeIII revealed resistance of the histone genes in D. virilis, contrary to what was previously found in D. melanogaster.     

DNA composition in South American camelids I. Characterization and in situ hybridization of satellite DNA fractions

The DNA composition and the in situ hybridization of satellite fractions were analysed in the New World camelids llama, alpaca, guanaco and vicuña. In the four camelid forms, it was possible to identify a similar main band DNA and five satellite fractions (I–V) with G+C base contents ranging from 32% to 66%. Satellites II–V from llama were in situ reannealed on chromosomes from the four camelid forms. The results obtained were: (a) the four satellites hybridized with regions of C-banding (centromeric regions of all chromosomes and short arms of some autosomes); (b) in general, homologous hybridizations (llama DNA versus llama chromosomes) were more efficient than heterologous reassociations; there were however three exceptions to this rule (vicuña and alpaca satellite fraction II, chromosome group B; vicuña fraction V, chromosome groups A and B); (c) X chromosomes from the four camelids had satellites III–V but lacked satellite II, (d) no satellite fraction was detected on chromosome Y. The analysis of the in situ hybridization patterns allowed to conclude that most or all C-banded chromosome regions comprise several satellite DNA fractions. It is, moreover, proposed that there is an ample interspecies variation in the number of chromosomes that cross-react with a given satellite fraction. Our data give further support to the close genomic kinship of New World camelids.     

In situ localization of mRNA with T-T dimerized DNA probes

When a particular antigen is immunohistochemically localized at a given site, it is difficult to differentiate whether the antigen was produced at the site or immigrated to the site from elsewhere. If the antigen, e.g. hormone, is synthesized at the site, it indicates that the site is the effector cell and if the antigen is not synthesized at the site, it indicates that the site is the affector cell. Hence this differentiation is essential in order to establish physiological function of the antigen. One way to illustrate in situ synthesis of the antigen is to demonstrate the presence of messenger RNA (mRNA) which encodes the amino acid sequence of the antigen. To localize a particular mRNA at the lavel of cells, recently in situ hybridization techniques are utilized. As a non-radioactive marker for in situ hybridization. We introduced and utilize thymine-thymine dimers. When DNA is irradiated with ultraviolet light, thymine-thymine (T-T) dimer is formed between adjacent thymines. Since the T-T dimer is a well recognized antigen, after hybridization of T-T dimerized DNA with cellular mRNA, the sites of T-T dimer was recognized by routine immunohistochemistry. When the T-T dimerized probe is used, the resolution is high and intracellular sites of the target may be recognized both at the light and electron microscopic levels, and the sensitivity may be elevated by immunohistochemical and enzyme-histochemical procedural modifications.     

Radiation-induced DNA breaks in different human satellite DNA sequence areas,analyzed by DNA breakage detection-fluorescence in situ hybridization

Human blood leukocytes were exposed to X rays to analyze the initial level of DNA breakage induced within different satellite DNA sequence areas and telomeres, using the DNA breakage detection-FISH procedure. The satellite DNA families analyzed comprised alphoid sequences, satellite 1, and 5-bp classical satellite DNA sequences from chromosome 1 (D1Z1 locus), from chromosome 9 (D9Z3 locus), and from the Y chromosome (DYZ1 locus). Since the control hybridization signal was quite different in each of the DNA targets, the relative increase in whole fluorescence intensity with respect to unirradiated controls was the parameter used for comparison. Irradiation of nucleoids obtained after protein removal demonstrated that the alkaline unwinding solution generates around half the amount of signal when breaks are present in the 5-bp classical DNA satellites as when the same numbers of breaks are present the genome overall, whereas the signal is slightly stronger when the breaks are within the alphoids or satellite 1 sequences. After correction for differences in sensitivity to the alkaline unwinding-renaturation, DNA housed in chromatin corresponding to 5-bp classical satellites proved to be more sensitive to breakage than the overall genome, whereas DNA in the chromatin corresponding to alphoids or satellite 1 showed a sensitivity similar to that of the whole genome. The minimum detectable dose was 0.1 Gy for the whole genome, 0.2 Gy for alphoids and satellite 1, and 0.4 Gy for the 5-bp classical satellites. Telomeric DNA sequences appeared to be maximally labeled in unirradiated cells. Thus telomeric ends behave like DNA breaks, constituting a source of background in alkaline unwinding assays.     

In situ ammonia production as a sanitation agent during anaerobic digestion at mesophilic temperature

Aim: To measure the sanitizing effect of mesophilic (37°C) anaerobic digestion in high ammonia concentrations produced in situ. Methods and Results: Indicator organisms and salmonella were transferred to small‐scale anaerobic batch cultures and D‐values were calculated. Batch cultures were started with material from two biogas processes operating at high (46 mmol l^?1) and low (1·6 mmol l^?1) ammonia concentration. D‐values were shortened from c. 3 days to <1 day for the bacteria. MS2 had the same D‐value (1·3 days) independent of ammonia concentration whereas ΦX174 and 28B were faster inactivated in the control (1·1 and 7·9 days) than in the high ammonia (8·9 and 39 days) batch cultures. Conclusion: Running biogas processes at high levels of ammonia shortens the time to meet EU regulation concerning reduction of salmonella and enterococci (5 log). Unless a minimum retention time of 2 days, post‐treatment digestion is needed to achieve sufficient sanitation in continuous biogas processes. Significance and Impact of the Study: Running mesophilic biogas processes at high ammonia level produces residue with a high fertilizer value. With some stipulations concerning management parameters, such processes provide a method of bacterial sanitation without preceding pasteurization of the incoming organic waste.