Dipodal Silanes Greatly Stabilize Glass Surface Functionalization for DNA Microarray Synthesis and High-Throughput Biological Assays

Glass is by far the most common substrate for biomolecular arrays, including high-throughput sequencing flow cells and microarrays. The native glass hydroxyl surface is modified by using silane chemistry to provide appropriate functional groups and reactivities for either in situ synthesis or surface immobilization of biologically or chemically synthesized biomolecules. These arrays, typically of oligonucleotides or peptides, are then subjected to long incubation times in warm aqueous buffers prior to fluorescence readout. Under these conditions, the siloxy bonds to the glass are susceptible to hydrolysis, resulting in significant loss of biomolecules and concomitant loss of signal from the assay. Here, we demonstrate that functionalization of glass surfaces with dipodal silanes results in greatly improved stability compared to equivalent functionalization with standard monopodal silanes. Using photolithographic in situ synthesis of DNA, we show that dipodal silanes are compatible with phosphoramidite chemistry and that hybridization performed on the resulting arrays provides greatly improved signal and signal-to-noise ratios compared with surfaces functionalized with monopodal silanes.

Global transcriptome profiling reveals root- and leaf-specific responses of barley (Hordeum vulgare L.) to H2O2

In cereal crops, such as barley (Hordeum vulgare L.), the ability to appropriately respond to environmental cues is an important factor for yield stability and thus for agricultural production. Reactive oxygen species (ROS), such as hydrogen peroxide (H2O2), are key components of signal transduction cascades involved in plant adaptation to changing environmental conditions. H2O2-mediated stress responses include the modulation of expression of stress-responsive genes required to cope with different abiotic and biotic stresses. Despite its importance, knowledge of the effects of H2O2 on the barley transcriptome is still scarce. In this study, we identified global transcriptomic changes induced after application of 10 mM H2O2 to five-day-old barley plants. In total, 1883 and 1001 differentially expressed genes (DEGs) were identified in roots and leaves, respectively. Most of these DEGs were organ-specific, with only 209 DEGs commonly regulated and 37 counter-regulated between both plant parts. A GO term analysis further confirmed that different processes were affected in roots and leaves. It revealed that DEGs in leaves mostly comprised genes associated with hormone signaling, response to H2O2 and abiotic stresses. This includes many transcriptions factors and small heat shock proteins. DEGs in roots mostly comprised genes linked to crucial aspects of H2O2 catabolism and oxidant detoxification, glutathione metabolism, as well as cell wall modulation. These categories include many peroxidases and glutathione transferases. As with leaves, the H2O2 response category in roots contains small heat shock proteins, however, mostly different members of this family were affected and they were all regulated in the opposite direction in the two plant parts. Validation of the expression of the selected commonly regulated DEGs by qRT-PCR was consistent with the RNA-seq data. The data obtained in this study provide an insight into the molecular mechanisms of oxidative stress responses in barley, which might also play a role upon other stresses that induce oxidative bursts.

Comparative analysis of stress-induced calcium signals in the crop species barley and the model plant Arabidopsis thaliana

BACKGROUND

Plants are continuously exposed to changing environmental conditions and biotic attacks that affect plant growth. In crops, the inability to respond appropriately to stress has strong detrimental effects on agricultural production and yield. Ca²⁺ signalling plays a fundamental role in the response of plants to most abiotic and biotic stresses. However, research on stimulus-specific Ca²⁺ signals has mostly been pursued in Arabidopsis thaliana, while in other species these events are little investigated .

RESULTS

In this study, we introduced the Ca²⁺ reporter-encoding gene APOAEQUORIN into the crop species barley (Hordeum vulgare). Measurements of the dynamic changes in [Ca²⁺]_cyt in response to various stimuli such as NaCl, mannitol, H₂O₂, and flagellin 22 (flg22) revealed the occurrence of dose- as well as tissue-dependent [Ca²⁺]_cyt transients. Moreover, the Ca²⁺ signatures were unique for each stimulus, suggesting the involvement of different Ca²⁺ signalling components in the corresponding stress response. Alongside, the barley Ca²⁺ signatures were compared to those produced by the phylogenetically distant model plant Arabidopsis. Notable differences in temporal kinetics and dose responses were observed, implying species-specific differences in stress response mechanisms. The plasma membrane Ca²⁺ channel blocker La³⁺ strongly inhibited the [Ca²⁺]_cyt response to all tested stimuli, indicating a critical role of extracellular Ca²⁺ in the induction of stress-associated Ca²⁺ signatures in barley. Moreover, by analysing spatio-temporal dynamics of the [Ca²⁺]_cyt transients along the developmental gradient of the barley leaf blade we demonstrate that different parts of the barley leaf show quantitative differences in [Ca²⁺]_cyt transients in response to NaCl and H₂O₂. There were only marginal differences in the response to flg22, indicative of developmental stage-dependent Ca²⁺ responses specifically to NaCl and H₂O₂.

CONCLUSION

This study reveals tissue-specific Ca²⁺ signals with stimulus-specific kinetics in the crop species barley, as well as quantitative differences along the barley leaf blade. A number of notable differences to the model plants Arabidopsis may be linked to different stimulus sensitivity. These transgenic barley reporter lines thus present a valuable tool to further analyse mechanisms of Ca²⁺ signalling in this crop and to gain insights into the variation of Ca²⁺-dependent stress responses between stress-susceptible and -resistant species.

Organellar calcium signaling in plants: An update

Calcium ion (Ca²⁺) is a versatile signaling transducer in all eukaryotic organisms. In plants, intracellular changes in free Ca²⁺ levels act as regulators in many growth and developmental processes. Ca²⁺ also mediates the cellular responses to environmental stimuli and thus plays an important role in providing stress tolerance to plants. Ca²⁺ signals are decoded by a tool kit of various families of Ca²⁺-binding proteins and their downstream targets, which mediate the transformation of the Ca²⁺ signal into appropriate cellular response. Early interest and research on Ca²⁺ signaling focused on its function in the cytosol, however it has become evident that this important regulatory pathway also exists in organelles such as nucleus, chloroplast, mitochondria, peroxisomes and the endomembrane system. In this review, we give an overview on the knowledge about organellar Ca²⁺ signaling with a focus on recent advances and developments.

Synthesis, DNA interactions and antibacterial PDT of Cu(II) complexes of phenanthroline based photosensitizers via singlet oxygen generation

Cu(II) complexes [Cu(mqt)(B)H2O]ClO4(1-3) of 2-thiol 4-methylquinoline and phenanthroline bases (B), viz 1,10-phenanthroline (phen in 1), Dipyrido[3,2-d:2',3'-f]quinoxaline (dpq in 2) and Dipyrido[3,2-a:2',3'-c]phenazine (dppz in 3) have been prepared and characterized by elemental analysis, IR, UV-Vis, magnetic moment values, EPR spectra and conductivity measurements. The spectral data reveal that all the complexes exhibit square-pyramidal geometry. The DNA-binding behaviors of the three complexes were investigated by absorption spectra, viscosity measurements and thermal denaturation studies. The DNA binding constants for complexes (1), (2) and (3) were determined to 2.2×10(3), 1.3×10(4) and 8.6×10(4)M(-1) respectively. The experimental results suggest that these complexes interact with DNA through groove-binding mode. The photo induced cleavage studies shows that the complexes possess photonuclease property against pUC19 DNA under UV-Visible irradiation via a mechanistic pathway involving formation of singlet oxygen as the reactive species. Antimicrobial photodynamic therapy was studied using photodynamic antimicrobial chemotherapy (PACT) assay against Escherichiacoli and all complexes exhibited significant reduction in bacterial growth on photoirradiation.

Novel complexes of Co(III) and Ni(II) containing peptide ligands: synthesis, DNA binding and photonuclease activity

The new cobalt(III) and nickel(II) complexes of the type [M(L)2(H2O)2](n)(+) (where M = Co(III) or Ni(II) ion, n = 3 for Co and 2 for Ni, L = peptides Fmoc. Ala-val-OH (F-AVOH), Fmoc-Phe-Leu-Ome (F-PLOMe) and Z-Ala-Phe-CONH2 (Z-APCONH2)) were synthesized and structurally characterized by FTIR, (1)H NMR, elemental analysis and electronic spectral data. An octahedral geometry has been proposed for all the synthesized Co(III) and Ni(II) metal complexes. The binding property of the complexes with CT-DNA was studied by absorption spectral analysis, followed by viscosity measurement and thermal denaturation studies. Detailed analysis revealed that the metal complexes intercalates into the DNA base stack as intercalator. The photo induced cleavage studies shows that the complexes possess photonuclease property against pUC19 DNA under UV-Visible irradiation.

Clinicohistopathological concordance in leprosy - a clinical, histopathological and bacteriological study of 100 cases

Leprosy is a treatable chronic infectious disease, prevalent in South Asian countries, especially India. Before labeling a patient as a case of leprosy and starting multidrug treatment for particular type, the clinical findings should be correlated and confirmed with histopathological examination and bacteriological index of skin biopsy. Skin biopsy is an important tool in diagnosing leprosy and determining the type of leprosy. In the present study, one hundred untreated clinically diagnosed cases of leprosy were studied according to Ridley-Jopling scale for confirmation of diagnosis and classification of leprosy. The study was done by routine H & E (Haematoxylin & Eosin) staining and Fite-Faraco's staining for acid-fast bacillus. The data pertaining to age, sex, clinical and histopathological classification of the type of leprosy were collected and analyzed. In analyzing the histopathology of a lesion, special attention was given to the following features, viz., invasion of the epidermis with or without erosion, involvement of the sub-epidermal zone, character and extent of granuloma, density of lymphocytic infiltrate epithelioid cells and other cellular elements, nerve involvement and the presence of Mycobacterium leprae. Histological diagnosis of leprosy was established in 98% of clinically diagnosed cases. Clinicohistopathological concordance was maximum in LL(93.75%) followed by BL(87.5%), TT(78.5%), BT(73.8%) and least in IL(27.78%). Overall, it was 60.23%. Indeterminate type of leprosy was diagnosed more on histologythan on clinical evaluation.

Significance of serum endotoxin and antiendotoxin antibody levels in predicting the severity of acute pancreatitis

PURPOSE

A close association between endotoxemia and acute pancreatitis has been reported, and attempts have been made to predict the severity of pancreatitis by estimating the levels of endotoxin. The present study was designed to correlate endotoxemia with the severity and complications of acute pancreatitis as graded by contrast-enhanced computed tomography and Blamey's criteria.

METHODS

We examined 20 patients with acute pancreatitis, using Blamey's criteria to assess the severity of pancreatitis. The endotoxin level was estimated by the Limulus Amoebocyte Lysate method and the antiendotoxin antibody level was assayed by the enzyme-linked immunoassay technique measuring combined levels of IgG and IgM.

RESULTS

Severe pancreatitis was confirmed in 9 of the 20 patients, 17 (85%) of whom were found to have endotoxemia. There was no correlation between the presence and level of endotoxemia and the severity of pancreatitis; however, antiendotoxin antibody titers were significantly lower in patients with severe disease ( P < 0.05), those who suffered of major complications ( P < 0.01), and those who died of the disease ( P < 0.01).

CONCLUSION

The findings of this study demonstrated that the presence of endotoxemia accompanied by a fall in antiendotoxin antibody titer predicts poor outcome in patients with acute pancreatitis.

Anomalous bile duct injury during laparoscopic cholecystectomy

We report a patient in whom the common hepatic duct drained into the gall bladder body and the cystic duct continued as the bile duct into the duodenum. The anomalous duct was inadvertently injured during laparoscopic cholecystectomy. The injury was repaired and end-to-end anastomosis of the hepatic and cystic ducts was done through a subcostal incision.

Expectant management of haemoperitoneum

Nonoperative management was successful in 81 of the 90 patients including two patients with penetrating injury. Nine patients were operated on after an initial period of observation, eight because of continued bleeding and one because of features of peritonitis. There were four deaths. These were due to multisystem injuries and not directly related to haemoperitoneum alone. Nonoperative management is a relatively safe and effective method in management of selected cases of haemoperitoneum.