In vitro plantlet formation by organogenesis in E. camaldulensis and by somatic embryogenesis in Eucalyptus citriodora

Adventitious shoots were formed through callus on leaf explants of Eucalyptus camaldulensis Dehnh. (River red gum) taken from shoot cultures of mature trees. Callus formed in dark on a medium containing 1 g/l casein hydrolysate, 3 mg/l 1-naphthaleneacetic acid, 0.1 mg/l 6-benzyladenine and 50 g/l sucrose. Shoot initiation occurred in 4 weeks on calli shifted to light on a regeneration medium containing 10% coconut milk, 0.5 mg/l 6-benzyladenine and 20 g/l sucrose. Rooting occured in dark on a liquid medium containing 4 mg/l 1-naphthaleneacetic acid. Zygotic embryos of Eucalyptus citriodora Hook f. (Lemon scented gum) cultured in dark on a medium containing 3 mg/l 1-naphthaleneacetic acid and 50 g/l sucrose formed somatic embryoids which grew to normal plantlets on the same regeneration medium used for organogenesis.Abbreviations BAP 6-benzyladenine - CH Casein hydrolysate - CM Coconut Milk - NAA 1-naphthaleneacetic acid NCL Communication no. 4162     

Using Integrative Modeling Platform to compute,validate, and archive a model of a protein complex structure

Biology is advanced by producing structural models of biological systems, such as protein complexes. Some systems are recalcitrant to traditional structure determination methods. In such cases, it may still be possible to produce useful models by integrative structure determination that depends on simultaneous use of multiple types of data. An ensemble of models that are sufficiently consistent with the data is produced by a structural sampling method guided by a data‐dependent scoring function. The variation in the ensemble of models quantified the uncertainty of the structure, generally resulting from the uncertainty in the input information and actual structural heterogeneity in the samples used to produce the data. Here, we describe how to generate, assess, and interpret ensembles of integrative structural models using our open source Integrative Modeling Platform program ( https://integrativemodeling.org ).     

Some conditions apply: Systems for studying Plasmodium falciparum protein function

Malaria, caused by infection with Plasmodium parasites, remains a significant global health concern. For decades, genetic intractability and limited tools hindered our ability to study essential proteins and pathways in Plasmodium falciparum, the parasite associated with the most severe malaria cases. However, recent years have seen major leaps forward in the ability to genetically manipulate P. falciparum parasites and conditionally control protein expression/function. The conditional knockdown systems used in P. falciparum target all 3 components of the central dogma, allowing researchers to conditionally control gene expression, translation, and protein function. Here, we review some of the common knockdown systems that have been adapted or developed for use in P. falciparum. Much of the work done using conditional knockdown approaches has been performed in asexual, blood-stage parasites, but we also highlight their uses in other parts of the life cycle and discuss new ways of applying these systems outside of the intraerythrocytic stages. With the use of these tools, the field’s understanding of parasite biology is ever increasing, and promising new pathways for antimalarial drug development are being discovered.     

Synthesis of Zidovudine Derivatives with Anti-HIV-1 and Antibacterial Activities

Twelve novel zidovudine derivatives were prepared by modifying 5 ′-hydroxyl group of sugar moiety (1–8) and 5-methyl group of thymidine nucleus (9–12) and characterized spectrally. The compounds were evaluated for anti-HIV-1, antitubercular and antibacterial activities. Compound (3-azido-tetrahydro-5- (3,4-dihydro-5-methyl-2,4-dioxopyrimidin- 1 (2H)-yl) furan-2-yl)methyl 7- (4- (2-phenylacetoyloxy) -3,5- dimethylpiperazin-1-yl) -5- (2-phenylacetoyloxyamino) -1-cyclopropyl-6,8-difluoro-1,4-dihydro-4-oxoquinoline-3-carboxylate (5) was found to be the most potent anti-HIV-1 agent with EC₅₀ of 0.0012 μM against HIV-1_IIIB and CC₅₀ of 34.05 μM against MT-4 with selectivity index of 28,375. Compound 5 inhibited Mycobacterium tuberculosis with MIC of 1.72 μM and inhibited four pathogenic bacteria with MIC of less than 1 μM.     

Improving ranking of models for protein complexes with side chain modeling and atomic potentials

An atomically detailed potential for docking pairs of proteins is derived using mathematical programming. A refinement algorithm that builds atomically detailed models of the complex and combines coarse grained and atomic scoring is introduced. The refinement step consists of remodeling the interface side chains of the top scoring decoys from rigid docking followed by a short energy minimization. The refined models are then re‐ranked using a combination of coarse grained and atomic potentials. The docking algorithm including the refinement and re‐ranking, is compared favorably to other leading docking packages like ZDOCK, Cluspro, and PATCHDOCK, on the ZLAB 3.0 Benchmark and a test set of 30 novel complexes. A detailed analysis shows that coarse grained potentials perform better than atomic potentials for realistic unbound docking (where the exact structures of the individual bound proteins are unknown), probably because atomic potentials are more sensitive to local errors. Nevertheless, the atomic potential captures a different signal from the residue potential and as a result a combination of the two scores provides a significantly better prediction than each of the approaches alone. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Thermoluminescence and photoluminescence studies on γ‐ray‐irradiated Ce3+,Tb3+‐doped potassium chloride single crystals

Single crystals of KCl doped with Ce³⁺,Tb³⁺ were grown using the Bridgeman–Stockbarger technique. Thermoluminescence (TL), optical absorption, photoluminescence (PL), photo‐stimulated luminescence (PSL), and thermal‐stimulated luminescence (TSL) properties were studied after γ‐ray irradiation at room temperature. The glow curve of the γ‐ray‐irradiated crystal exhibits three peaks at 420, 470 and 525 K. F‐Light bleaching (560 nm) leads to a drastic change in the TL glow curve. The optical absorption measurements indicate that F‐ and V‐centres are formed in the crystal during γ‐ray irradiation. It was attempted to incorporate a broad band of cerium activator into the narrow band of terbium in the KCl host without a reduction in the emission intensity. Cerium co‐doped KCl:Tb crystals showed broad band emission due to the d–f transition of cerium and a reduction in the intensity of the emission peak due to ⁵D₃–⁷F_j (j = 3, 4) transition of terbium, when excited at 330 nm. These results support that energy transfer occurs from cerium to terbium in the KCl host. Co‐doping Ce³⁺ ions greatly intensified the excitation peak at 339 nm for the emission at 400 nm of Tb³⁺. The emission due to Tb³⁺ ions was confirmed by PSL and TSL spectra. Copyright © 2015 John Wiley & Sons, Ltd.     

Chemical sensing of DNT by engineered olfactory yeast strain

With the increasing threat of environmental toxicants including biological and chemical warfare agents, fabricating innovative biomimetic systems to detect these harmful agents is critically important. With the broad objective of developing such a biosensor, here we report the construction of a Saccharomyces cerevisiae strain containing the primary components of the mammalian olfactory signaling pathway. In this engineered yeast strain, WIF-1alpha, olfactory receptor signaling is coupled to green fluorescent protein expression. Using this 'olfactory yeast', we screened for olfactory receptors that could report the presence of the odorant 2,4-dinitrotoluene, an explosive residue mimic. With this approach, we have identified the novel rat olfactory receptor Olfr226, which is closely related to the mouse olfactory receptors Olfr2 and MOR226-1, as a 2,4-dinitrotoluene-responsive receptor.     

Metabolism of 1alpha,25-dihydroxyvitamin D(3) and its C-3 epimer 1alpha,25-dihydroxy-3-epi-vitamin D(3) in neonatal human keratinocytes

We previously reported that 1alpha,25-dihydroxyvitamin D(3) [1alpha,25(OH)(2)D(3)] is metabolized into 1alpha,25-dihydroxy-3-epi-vitamin D(3) [1alpha,25(OH)(2)-3-epi-D(3)] in primary cultures of neonatal human keratinocytes. We now report that 1alpha,25(OH)(2)-3-epi-D(3) itself is further metabolized in human keratinocytes into several polar metabolites. One of the polar metabolite was unequivocally identified as 1alpha,23,25-trihydroxy-3-epi-vitamin D(3) by mass spectrometry and its sensitivity to sodium periodate. Three of the polar metabolites were identified as 1alpha,24,25-trihydroxy-3-epi-vitamin D(3), 1alpha,25-dihydroxy-24-oxo-3-epi-vitamin D(3) and 1alpha,23,25-trihydroxy-24-oxo-3-epi-vitamin D(3) by comigration with authentic standards on both straight and reverse phase HPLC systems. In addition to the polar metabolites, 1alpha,25(OH)(2)-3-epi-D(3) was also metabolized into two less polar metabolites. A possible structure of either 1alphaOH-3-epi-D(3)-20,25-cyclic ether or 1alphaOH-3-epi-D(3)-24,25-epoxide was assigned to one of the less polar metabolites through mass spectrometry. Thus, we indicate for the first time that 1alpha,25(OH)(2)-3-epi-D(3) is metabolized in neonatal human keratinocytes not only via the same C-24 and C-23 oxidation pathways like its parent, 1alpha,25(OH)(2)D(3); but also is metabolized into a less polar metabolite via a pathway that is unique to 1alpha,25(OH)(2)-3-epi-D(3).     

Voxel Based Morphometry Alterations in Mal de Debarquement Syndrome

Background

Mal de debarquement syndrome (MdDS) is a disorder of chronic self-motion perception that occurs though entrainment to rhythmic background motion, such as from sea voyage, and involves the perception of low-frequency rocking that can last for months or years. The neural basis of this persistent sensory perception abnormality is not well understood.

Methods

We investigated grey matter volume differences underlying persistent MdDS by performing voxel-based morphometry on whole brain and pre-specified ROIs in 28 individuals with MdDS and comparing them to 18 age, sex, and handedness matched controls.

Results

MdDS participants exhibited greater grey matter volume in the left inferior parietal lobule, right inferior occipital gyrus (area V3v), right temporal pole, bilateral cerebellar hemispheric lobules VIII/IX and left lobule VIIa/VIIb. Grey matter volumes were lower in bilateral inferior frontal, orbitofrontal, pregenual anterior cingulate cortex (pgACC) and left superior medial gyri (t = 3.0, p<0.005_uncorr). In ROI analyses, there were no volume differences in the middle occipital gyrus (region of V5/MT) or parietal operculum 2 (region of the parietoinsular vestibular cortex). Illness duration was positively related to grey matter volume in bilateral inferior frontal gyrus/anterior insula (IFG/AI), right posterior insula, superior parietal lobule, left middle occipital gyrus (V5/MT), bilateral postcentral gyrus, anterior cerebellum, and left cerebellar hemisphere and vermian lobule IX. In contrast, illness duration was negatively related to volume in pgACC, posterior middle cingulate gyrus (MCC), left middle frontal gyrus (dorsolateral prefrontal cortex-DLPFC), and right cerebellar hemispheric lobule VIIIb (t = 3.0, p<0.005_uncorr). The most significant differences were decreased volume in the pgACC and increased volume in the left IFG/AI with longer illness duration (qFDR_corr <0.05). Concurrent medication use did not correlate with these findings or have a relationship with duration of illness. MdDS participants showed positive correlations between grey matter volume in pgACC and bilateral cerebellar lobules VIII/IX, which was not seen in controls.

Conclusions

Individuals with MdDS show brain volume differences from healthy controls as well as duration of illness dependent volume changes in (a) visual-vestibular processing areas (IPL, SPL, V3, V5/MT), (b) default mode network structures (cerebellar IX, IPL, ACC), (c) salience network structures (ACC and IFG/AI) (d) somatosensory network structures (postcentral gyrus, MCC, anterior cerebellum, cerebellar lobule VIII), and (e) a structure within the central executive network (DLPFC). The identification of these associations may enhance future investigations into how exposure to oscillating environments can modulate brain function and affect motion perception as well cognitive and affective control.