Topological diversity in copper aromatic meta-dicarboxylate coordination polymers with bis(pyridylformyl)piperazine coligands

Hydrothermal synthesis has afforded divalent copper coordination polymers containing bis(4-pyridylformyl)piperazine (4-bpfp) tethers and aromatic meta-dicarboxylate ligands. {[Cu(ip)(4-bpfp)]·2H₂O}_n (1, ip = isophthalate) possesses a (4, 4) rectangular grid structure with an unusual ABCD stacking pattern along a 4₁ screw axis. Sterically bulky substituents in the 5-position of the isophthalate ligands reduced the coordination polymer dimensionality, with [Cu₂(tBuip)₂(4-bpfp)(H₂O)₂]_n (2, tBuip = 5-tert-butylisophthalate) and {[Cu(MeOip)(HMeOip)₂(4-bpfp)]·3H₂O}_n (3, MeOip = 5-methoxyisophthalate) displaying 1D polymeric ladder and chain motifs, respectively. Compound 3 possesses a rare twofold interpenetrated binodal supramolecular hms net with (6³)(6⁹8) topology. Longer meta-disposed acetate pendant arms induced a doubly interpenetrated 3D primitive cubic topology in {[Cu₂(1,3-phda)₂(H₂O)₂(4-bpfp)]}_n (4, 1,3-phda = 1,3-phenylenediacetate), which possesses antiferromagnetically coupled {Cu₂O₂} kernels (J = −6.14(8) cm⁻¹).     

Zinc maleate and fumarate coordination polymers containing hydrogen-bonding capable organodiimines featuring ligand dependent in situcis-trans isomerization

Solution phase reaction at ambient temperature of zinc nitrate, maleic acid and 4,4′-dipyridylamine (dpa) afforded {[Zn₂(maleate)₂(dpa)₂]·5H₂O}_n (1), which displayed parallel (4,4)-grid like coordination polymer layers interdigitated into double layer slab motifs via hydrogen bonding. A similar reaction employing bis(4-pyridylmethyl)piperazine (bpmp) caused in situcis-trans isomerization of maleic acid to fumarate, and generation of [Zn(fumarate)(bpmp)(H₂O)₂]_n (2). Compound 2 also manifested (4,4)-grid coordination polymer layers similar to those in 1; however, the larger apertures in 2 permit 2d + 2d → 3D mutually inclined interpenetration. Thermogravimetric and luminescence studies are also reported for 1 and 2.     

In situ hydrothermal syntheses, crystal structures and luminescent properties of two novel zinc(II) coordination polymers based on tetrapyridyl ligand

Two novel Zn(II) coordination polymers, [Zn(2-pytpy)(fum)]_n·nH₂O (1) and [Zn₆(4-pytpy)₃(mal)₄]_n·5n(H₂O) (2), (2-pytpy = 4′-(4-pyridyl)-2,2′:6′,2″-terpyridine, 4-pytpy = 4′-(4-pyridyl)-4,2′:6′,4″-terpyridine, H₂fum = fumaric acid and H₂mal = malic acid) have been hydrothermally synthesized and structurally characterized. Notably, in situ ligand reactions occur in the formation of complexes 1 and 2, in which maleic acid is converted into fumaric acid and malic acid, respectively. Complex 1 is a 1D infinite chain structure, which is extended into a supramolecular layer by intermolecular π…π stacking interactions. Complex 2 is a 3D network structure, in which the bidentate-bridging 4-pytpy ligands link the layers based on the tetranuclear Zn(II) subunits to form the (4,10)-connected network. The luminescent properties of 1 and 2 have been investigated with emission spectra and UV-Vis diffuse reflectance spectra in the solid state. Additionally, these two complexes possess great thermal stabilities.     

Zinc and cadmium flexible-arm ortho-dicarboxylate bis(pyridyl)piperazine coordination polymers with rare two- and three-dimensional topologies

Hydrothermal reaction of a d¹⁰ configuration divalent metal precursor with flexible-arm aromatic ortho-dicarboxylates and a bis(pyridyl)piperazine-type neutral co-ligand has generated four coordination polymers, some with rare topologies. {[Cd(hmph)(4-bpmp)_1.5]·4H₂O}_n (1, hmph = homophthalate, 4-bpmp = bis(4-pyridylmethyl)piperazine) manifests a new 3-fold interpenetrated uninodal 5-connected 3-D net with a very simple 4⁴6⁶ topology, different from the usual sqp 5-connected topology. [Cd₂(hmph)₂(4-bpfp)]_n (2, 4-bpfp = bis(4-pyridylformyl)piperazine) displays a rare 4,5-connected binodal tcs net with (4⁴6²)(4⁴6⁶) topology. [Zn₂(1,2-phda)₂(4-bpmp)(H₂O)₂]_n (3, 1,2-phda = 1,2-phenylenediacetate) possesses an uncommon 3,4-connected binodal 2-D layer with (4²6)(4²6³8) (V₂O₅ prototype) topology. [Zn₂(hmph)₂(4-bpfp)]_n (4) has a decorated (4,4) grid topology with embedded [Zn₂(OCO)₄] paddlewheel clusters. All materials exhibit ligand-centered fluorescent behavior. Thermal degradation behavior of the 3-D network materials is reported.     

Development of rRNA and rDNA-targeted probes for fluorescence in situ hybridization to detect Heterosigma akashiwo (Raphidophyceae)

Heterosigma akashiwo (Hada) is a fragile, fish-killing alga. Efforts to understand and prevent blooms due to this harmful species to mitigate the impact on aquaculture require the development of methods for rapid and precise identification and quantification, so that adequate warning of a harmful algal bloom may be given. Here, we report the development and application of rRNA and rDNA-targeted oligonucleotide probes for fluorescence in situ hybridization (FISH) to aid in the detection and enumeration of H. akashiwo. The designed probes were species specific, showing no cross-reactivity with four common HAB causative species: Prorocentrum micans Ehrenberg, P. minimum (Pavillard) Schiller, Alexandrium tarmarense (Lebour) Balech, and Skeletonema costatum (Greville) Cleve, or with four other microalgae, including Gymnodinium sp. Stein, Platy-monas cordiformis (Karter) Korsch, Skeletonema sp.1 Greville and Skeletonema sp.2. The rRNA-targeted probe hybridized to cytoplasmic rRNA, showing strong green fluorescence throughout the whole cell, while cells labeled by rDNA-targeted probe exhibited exclusively fluorescent nucleus. The detection protocols were optimized and could be completed within an hour. For rRNA and rDNA probes, about a corresponding 80% and 70% of targeted cells could be identified and quantified during the whole growth circle, despite the inapparent variability in the average probe reactivity. The established FISH was proved promising for specific, rapid, precise, and quantitative detection of H. akashiwo.     

Aromatic N-oxide bridged copper(II) coordination polymers: Synthesis, characterization and magnetic properties

The complexes [Cu₂(o-NO₂-C₆H₄COO)₄(PNO)₂] (1), [Cu₂(C₆H₅COO)₄(2,2′-BPNO)]_n (2), [Cu₂(C₆H₅COO)₄(4,4′-BPNO)]_n (3), [Cu(p-OH-C₆H₄COO)₂(4,4′-BPNO)₂·H₂O]_n (4), (where PNO = pyridine N-oxide, 2,2′-BPNO = 2,2′-bipyridyl-N,N′-dioxide, 4,4′-BPNO = 4,4′-bipyridyl-N,N′-dioxide) are prepared and characterized and their magnetic properties are studied as a function of temperature. Complex 1 is a discrete dinuclear complex while complexes 2-4 are polymeric of which 2 and 3 have paddle wheel repeating units. Magnetic susceptibility measurements from polycrystalline samples of 1-4 revealed strong antiferromagnetic interactions within the {Cu₂}⁴⁺ paddle wheel units and no discernible interactions between the units. The complex 5, [Cu(NicoNO)₂·2H₂O]_n·4nH₂O, in which the bridging ligand to the adjacent copper(II) ions is nicotinate N-oxide (NicoNO) the transmitted interaction is very weakly antiferromagnetic.     

Davallia (Polypodiales: Davalliaceae) macrofossils from Early Miocene Otago (New Zealand) with in situ spores

Fossil fern fronds referable to the extant fern genus Davallia (Polypodiales: Davalliaceae) bearing sporangia with in situ spores are described from the Early Miocene Foulden Maar diatomite deposit, Otago, New Zealand. The fronds are the first published Southern Hemisphere macrofossil record for the family and provide valuable palaeoclimate data supporting warm conditions in Early Miocene New Zealand. The matching of Davallia fronds to the form spore taxon Polypodiisporites radiatus shows that the genus has had a long, apparently continuous history throughout late Cenozoic New Zealand.     

基因组原位杂交鉴定牛筋草AA基因组在穇子染色体上的分布及探针长度优化方法

采用基因组原位杂交(Genomic in situ hybridization,GISH)方法研究了牛筋草(Eleusine indica)AA基因组在穇子(E.coracana)染色体上的分布,并探讨了AA、BB基因组的同源关系。用超声波破碎法进行预剪切,以缺口平移法标记的牛筋草总DNA为探针,BB基因组的E.floccifolia(Forssk.)Spreng.总DNA为封阻,与AABB基因组穇子的中期染色体进行杂交。结果表明,牛筋草AA基因组分布在穇子的18条染色体上。不加封阻或加过量封阻均不能鉴别AA基因组,说明AA和BB基因组间的分化程度不大,双方共享的重复序列较多。牛筋草与E.floccifolia总DNA分别用超声波破碎2 min和3 min后,可得到峰值为300-750 bp的DNA片段,这说明不同物种的超声波破碎时间需要调整,以获得合适长度的探针。     

Phylogenetic characterization and in situ detection of bacterial communities associated with seahorses (Hippocampus guttulatus) in captivity

Although there are several studies describing bacteria associated with marine fish, the bacterial composition associated with seahorses has not been extensively investigated since these studies have been restricted to the identification of bacterial pathogens. In this study, the phylogenetic affiliation of seahorse-associated bacteria was assessed by 16S rRNA gene sequencing of cloned DNA fragments. Fluorescence in situ hybridization (FISH) was used to confirm the presence of the predominant groups indicated by 16S rRNA analysis. Both methods revealed that Vibrionaceae was the dominant population in Artemia sp. (live prey) and intestinal content of the seahorses, while Rhodobacteraceae was dominant in water samples from the aquaculture system and cutaneous mucus of the seahorses. To our knowledge, this is the first time that bacterial communities associated with healthy seahorses in captivity have been described.     

Visualization of initial bacterial colonization on dentine and enamel in situ

Bacterial colonization of dentine is of high relevance in cariology, endodontology and periodontology. The aim of the present in situ study was to establish recent methods for visualization and quantification of initial bacterial adherence to dentine in comparison to enamel. For this purpose, bovine enamel and dentine slabs were fixed on buccal sites of individual upper jaw splints worn by 6 subjects for 30 min, 120 min and 360 min, respectively. Adherent bacteria on the slabs were visualized and quantified with DAPI-staining (4′,6-diamidino-2-phenylindole) and fluorescence in situ hybridization (FISH) of streptococci and eubacteria using the CLSM (confocal laser scanning microscopy) as well as an epifluorescence microscope. In addition, the number of colony forming units was quantified after desorption. Representative samples were processed for SEM (scanning electron microscopy) and TEM (transmission electron microscopy). All methods clearly indicated that a significantly higher number of bacteria adhered to dentine than to enamel. Furthermore, the amount of bacteria on the dentine increased with increasing oral exposure time, but remained rather constant on the enamel. The CLSM allowed visualization of bacteria in the dentinal tubules. Bacteria were found preferentially at the openings of the dentine tubules, but were distributed randomly on the enamel.In conclusion, the adopted methods are suitable for visualization and quantification of bacterial adhesion to dentine. Even the initial bacterial colonization of dentine is much more pronounced than bacterial adherence to the enamel.     

Entamoeba histolytica, heterologous expression and in situ immunolocalization of ornithine decarboxylase (EhODC)

Previous studies from this laboratory have dealt with the purification and biochemical characterization of ornithine decarboxylase (ODC) from Entamoeba histolytica. Enzyme compartmentalization has been described as a major mechanism in the regulation of polyamine metabolism. However, the subcellular location of ODC in the human parasite has remained unresolved. To examine this issue, we cloned the full-length gene (Ehodc) encoding for the parasite enzyme, whose open reading frame encodes for a peptide of 412 amino acids with an estimated molecular mass of 46 kDa that exhibits similarity to other ODCs. Heterologous overexpression of the gene allowed us to purify the recombinant protein (rEhODC) by metal affinity chromatography. The purified polypeptide was used to raise heteroclonal antibodies that were utilized to localize the enzyme in situ by immunofluorescence and confocal microscopy. EhODC was observed to be associated with the plasma membrane, in vesicles close to the plasma membrane and in the EhkOs organelle.     

Double salts of copper(I) chloride incorporated hydroxylpyrimidine and tetrazole ligands

Hydrothermal reaction of copper(II) chloride with 2-hydroxypyrimidine generated double salt of [Cu₂Cl(μ₄-pymo)] (1) (Hpymo = hydroxylpyrimidine) while hydrothermal treatment of CuCl₂, NaN₃ and acetonitrile resulted in double salt of [Cu₂(mtta)Cl] (2) (Hmtta = 5-methyltetrazole) in which in situ [2 + 3] cycloaddition reactions of acetonitrile with azide formed mtta ligand. X-ray single crystal structural analyses revealed that 1 shows a two-dimensional layer formed by fusion of one-dimensional structural motifs. The two-dimensional layers in 1 are held together by C-H?Cl hydrogen bonds to form three-dimensional supramolecular array. Compound 2 has a three-dimensional framework constructed from ribbons and [Cu₈Cl₄]⁴⁺ units. Uncommon coordination modes of μ₄-1,2κO:3κN:4κN′ pymo and μ₄-Cl (Cl at the apex of a Cu₄Cl square pyramid) in 1 and μ₄-η¹:η¹:η¹:η¹ mtta in 2 were also observed. The short Cu(I)?Cu(I) distances were found in 1 and 2, indicating the existence of Cu(I)?Cu(I) interactions.     

Chiral and achiral layered divalent metal aromatic ortho-dicarboxylate coordination polymers with bis(4-pyridylmethyl)piperazine ligands: Luminescent behavior and magnetic properties

Four divalent metal coordination polymers containing bis(4-pyridylmethyl)piperazine (4-bpmp) and the ortho-dicarboxylate ligands phthalate (pht) or 4-methylphthalate (mpht) have been prepared by solvent diffusion or hydrothermal methods. {[Cu₂(pht)₂(H4-bpmp)₂(H₂O)₂](NO₃)₂·H₂O}_n (1) and {[Cu₂(pht)₂(H4-bpmp)₂(H₂O)₂](SO₄)·2H₂O}_n (2) possess chiral cationic layer motifs formed by the junction of [Cu(H₂O)(pht)]_n chains by tethering curled-conformation H4-bpmp⁺ ligands. {[Co(pht)(H₂O)(4-bpmp)]·5.5H₂O}_n (3) displays a (4,4) grid constructed from anti-syn carboxylate-bridged {Co₂(H₂O)₂(pht)₂} dimeric clusters linked by open-conformation 4-bpmp ligands. {[Cd₂(mpht)₂(H₂O)₂(4-bpmp)(H4-bpmp)]ClO₄·4H₂O}_n (4) manifests cationic layered motifs based on neutral [Cd₂(H₂O)₂(mpht)₂] dinuclear units with {CdOC₄O}₂ 12-membered circuits, linked by open-conformation 4-bpmp and H4-bpmp⁺ ligands. Variable-temperature magnetic data indicate likely concomitant zero-field splitting and ferromagnetic coupling in 3. Violet light emission is observed when 4 is subjected to ultraviolet irradiation.     

Syntheses and structures of bis(2,6-xylyl-nacnac) copper(I) complexes

The copper(I) complexes {(bis-2,6-dimethylphenyl-penta-2,3-diiminato)Cu}₂(μ-toluene), 3 has been prepared and its reactivity against Lewis bases and nitrous oxide investigated. Complex 3 crystallizes as a toluene-bridged dimer and forms mono- and dinuclear benzene adducts in C₆D₆ solution. It does not coordinate excess THF, but reacts quantitatively with 1 equiv. of acetonitrile. Reaction with 2,6-xylyl isonitrile yields (bis-2,6-dimethylphenyl-penta-2,3-diiminato)Cu(2,6-xylyl isonitrile), 5, (ν_CN = 2123 cm⁻¹), which was characterized by an X-ray diffraction study. Complex 3 does not react with nitrous oxide in either C₆D₆ solution (5 days 50 °C) or in diethyl ether (13 days at ambient temperature).     

Gold-FISH: A new approach for the in situ detection of single microbial cells combining fluorescence and scanning electron microscopy

A novel fluorescence in situ hybridisation (FISH) method is presented that allows the combination of epifluorescence and scanning electron microscopy (SEM) to identify single microbial cells. First, the rRNA of whole cells is hybridised with horseradish peroxidase-labelled oligonucleotide probes and this is followed by catalysed reporter deposition (CARD) of biotinylated tyramides. This facilitates an amplification of binding sites for streptavidin conjugates covalently labelled with both fluorophores and nanogold particles. The deposition of Alexa Fluor 488 fluoro-nanogold–streptavidin conjugates was confirmed via epifluorescence microscopy and cells could be quantified in a similar way to standard CARD–FISH approaches. To detect cells by SEM, an autometallographic enhancement of the nanogold particles was essential, and allowed the in situ localisation of the target organisms at resolutions beyond light microscopy. Energy dispersive X-ray spectroscopy (EDS) was used to verify the effects of CARD and autometallography on gold deposition in target cells.     

Biotransformation of glycerol to 3-hydroxypropionaldehyde: Improved production by in situ complexation with bisulfite in a fed-batch mode and separation on anion exchanger

3-Hydroxypropionaldehyde (3HPA) is an important C3 chemical that can be produced from renewable glycerol by resting whole cells of Lactobacillus reuteri. However the process efficiency is limited due to substrate inhibition, product-mediated loss of enzyme activity and cell viability, and also formation of by-products. Complex formation of 3HPA with sodium bisulfite and subsequent binding to Amberlite IRA-400 was investigated as a means of in situ product recovery and for overcoming inhibition. The adsorption capacity and -isotherm of the resin were evaluated using the Langmuir model. The resin exhibited maximum capacity of 2.92 mmol complex/g when equilibrated with 45 mL solution containing an equilibrium mixture of 2.74 mmol 3HPA-bisulfite complex and 2.01 mmol free 3HPA. The dynamic binding capacity based on the breakthrough curve of 3HPA and its complex on passing a solution with 2.49 mmol complex and 1.65 mmol free 3HPA was 2.01 mmol/g resin. The bound 3HPA was desorbed from the resin using 0.20 M NaCl with a high purity as a mixture of complexed- and free 3HPA at a ratio of 0.77 mol/mol. Fed-batch biotransformation of glycerol (818.85 mmol) with in situ 3HPA complexation and separation on the bisulfite-functionalized resin resulted in an improved process with consumption of 481.36 mmol glycerol yielding 325.54 mmol 3HPA at a rate of 17.13 mmol/h and a yield of 68 mol%. Also, the cell activity was maintained for at least 28 h.     

Localization of strawberry (Fragaria x ananassa) and Methylobacterium extorquens genes of strawberry flavor biosynthesis in strawberry tissue by in situ hybridization

Strawberry flavor is one of the most popular fruit flavors worldwide, with numerous applications in the food industry. In addition, the biosynthetic origin of the most important strawberry flavor components, such as 2,5-dimethyl-4-hydroxy-2H-furan-3-one (DMHF), is a challenging research area. DMHF's precursor, 2-hydroxy-propanal (or lactaldehyde), is biosynthesized by the endophytic bacterium Methylobacterium extorquens (M. extorquens). In particular, the alcohol dehydrogenase (ADH) enzymes of M. extorquens are involved in the biogenesis of DMHF precursors since they have the capacity to oxidize the strawberry-derived 1,2-propanediol to lactaldehyde. In this study, the expression of the endophytic ADH and the plant DMHF biosynthesis genes was examined in the tissues of raw and ripe strawberry receptacles by in situ hybridization. The presence of endophytic bacteria was studied in the same tissues by probes targeting bacterial 16S ribosomal ribonucleic acid. Hybridization signals of probes specific for endophytic ADH and plant DMHF biosynthesis genes, as well as bacteria-specific probes, were detected in the same locations. The probes were localized near the plasma membranes or intercellular spaces of cortical and vascular tissues of the receptacle, and intracellularly in the tissues of achenes. By localizing the expression of the endophytic methanol ADH and plant DMHF biosynthesis genes to the same tissues, we have reinforced our original hypothesis that an intimate symbiotic relationship between strawberry and endophytic cells exists and leads to the biosynthesis of DMHF.     

Predator-prey interactions from in situ time-lapse observations of a sublittoral mussel bed in the Gulf of Trieste (Northern Adriatic)

Hexaplex trunculus (Linnaeus, 1758) is one of the most abundant and widespread muricid gastropods in the Northern Adriatic Sea, but relatively little is known about the feeding ecology of this predator. We examined the activity of H. trunculus on a sublittoral mussel bed at 24 m depth through in situ time-lapse observations and bulk samples. The camera photographed a 0.25 m² section of the mussel bed at 6-min intervals for ~ 23 h. Photos were examined frame-by-frame for gastropod movement and activities, especially interactions between H. trunculus and Mytilus galloprovincialis (Lamarck, 1819). Our survey indicates high activity-levels of H. trunculus on the sea floor: all gastropods made minor movements, most made major movements, and most left the field of view during the study-interval. On average, individuals remained stationary for only 7.3 h. Two predation attempts on Mytilus involving conspecific competition were documented, and one Hexaplex was consuming a mussel at the onset of the deployment. Additionally, 487 M. galloprovincialis from four diver-taken 0.25 m² quadrates were measured and examined for traces of marginal chipping and drilling predation. Mytilus from surface samples ranged from 11.1 mm to 95.5 mm in length, and one of the four samples had a significantly different average shell length from the others. 114 H. trunculus were collected and measured. Hexaplex ranged from 22.1 mm to 86.1 mm and the mean shell length did not differ among samples, though they were overwhelmingly medium and large. Predation frequency (the ratio of successfully preyed upon bivalves to the total number of bivalves sampled) is high at the studied site (> 55%), and large gastropods preferred a chipping mode of predation to drilling, supporting earlier laboratory studies showing a preference for M. galloprovincialis and this predation strategy. Prey effectiveness (the ratio of failed predatory attacks to total predatory attacks) is also high (63.8%), and no evidence of a size refuge was found. Feeding in H. trunculus is highly facultative, calling for caution when using drill holes to estimate predation intensities; whenever possible, traces of multiple predation modes should be considered.     

Dinuclear alkoxo-bridged copper(II) coordination polymers: Syntheses, structural and magnetic properties

The alkoxo-bridged dinuclear copper(II) complexes [Cu₂(ap)₂(NO₂)₂] (1), [Cu₂(ap)₂(C₆H₅COO)₂] (2) and [Cu₂(ap)₂μ-1,3-C₆H₄(COO)₂(dmso)₂]·dmso (3) (ap = 3-aminopropanolato and dmso = dimethyl sulfoxide) have been synthesized via self-assembly from copper(II) perchlorate, 3-aminopropanol as main chelating ligand and nitrite and isophthalate anions as spacers and benzoate anion as auxiliary ligand. Complexes 1 and 3 crystallize as 2D and 1D coordination polymers, respectively, and their structures consist of dinuclear [Cu₂(ap)₂]²⁺ units connected with nitrite and isophthalate ligands. The adjacent dinuclear units of 2 and 1D polymers of 3 are further connected by hydrogen bonds resulting in the formation of 2D layers. The variable temperature crystallographic measurements of 1 at 100, 173 and 293 K indicate the static Jahn-Teller distortion with librational disorder in the nitrite group. Experimental magnetic studies showed that complexes 1-3 exhibit strong antiferromagnetic couplings. The values of the magnetic exchange coupling constant for 1-3 are well reproduced by the theoretical calculations.     

Cobalt, nickel, copper and cadmium coordination polymers containing the bis(1,2,4-triazolyl)methane ligand

Co(II), Ni(II), Cu(II) and Cd(II) coordination polymers containing the flexible ditopic bis(1,2,4-triazol-1-yl)methane ligand (Btm) have been prepared by reaction of equimolar quantities of the corresponding cobalt, nickel, copper and cadmium salts in EtOH solution. Structure solution and refinement of polycrystalline materials were performed by powder diffraction technique (XRPD), using conventional laboratory data. The results show that architecturally different coordination polymers were obtained depending on the counter-ion employed. The XRPD results show also that non-covalent interactions are driving forces for the occurrence of different structures.