Structurally diverse low molecular weight activators of the mammalian pre-mRNA 3′ cleavage reaction

The 3′ end formation of mammalian pre-mRNA contributes to gene expression regulation by setting the downstream boundary of the 3′ untranslated region, which in many genes carries regulatory sequences. A large number of protein cleavage factors participate in this pre-mRNA processing step, but chemical tools to manipulate this process are lacking. Guided by a hypothesis that a PPM1 family phosphatase negatively regulates the 3′ cleavage reaction, we have found a variety of new small molecule activators of the in vitro reconstituted pre-mRNA 3′ cleavage reaction. New activators include a cyclic peptide PPM1D inhibitor, a dipeptide with modifications common to histone tails, abscisic acid and an improved l-arginine β-naphthylamide analog. The minimal concentration required for in vitro cleavage has been improved from 200 μM to the 200 nM–100 μM range. These compounds provide unexpected leads in the search for small molecule tools able to affect pre-mRNA 3′ end formation.     

Photolytic discoloration of azo dye incorporated organoiron polymer

Organoiron polymers with azo dyes pendant to the backbone incurred loss of color upon irradiation with UV light (λ = 300 nm) in acetonitrile solution. The loss of color is attributed to the interaction of the cleaved iron moiety with the azo chromophore. Similarly, addition of small amounts (⩽1 mM) of both Fe(II) and Fe(III) to the organic polymer analogue yielded comparable discoloration rates upon irradiation. The iron cation forms a complex with the azo chromophore group in the polymer, and subsequently leads to the photodegradation of the azo dye. At higher initial polymer concentrations, minimal discoloration was observed due to the light attenuation effect of the deeply colored solutions. In the presence of small amounts of water, the iron cation is inhibited from partaking in complex formation and no polymer discoloration was observed. For the organic polymer analogue, the presence of water did not show significant change over its absence upon irradiation. The discoloration of the polymer relies solely on its interaction with the iron cation present in solution, and does not require addition of any catalyst or reagent. This process might be developed into a pragmatic and viable method for the treatment of specifically designed colored materials using only UV light.     

Sensitivity and resistance of soil fertility indicators to land-use changes: New concept and examples from conversion of Indonesian rainforest to plantations

Tropical forest conversion to agricultural land leads to a strong decrease of soil organic carbon (SOC) stocks. While the decrease of the soil C sequestration function is easy to measure, the impacts of SOC losses on soil fertility remain unclear. Especially the assessment of the sensitivity of other fertility indicators as related to ecosystem services suffers from a lack of clear methodology. We developed a new approach to assess the sensitivity of soil fertility indicators and tested it on biological and chemical soil properties affected by rainforest conversion to plantations. The approach is based on (non-)linear regressions between SOC losses and fertility indicators normalized to their level in a natural ecosystem. Biotic indicators (basal respiration, microbial biomass, acid phosphatase), labile SOC pools (dissolved organic carbon and light fraction) and nutrients (total N and available P) were measured in Ah horizons from rainforests, jungle rubber, rubber (Hevea brasiliensis) and oil palm (Elaeis guineensis) plantations located on Sumatra. The negative impact of land-use changes on all measured indicators increased in the following sequence: forest < jungle rubber < rubber < oil palm. The basal respiration, microbial biomass and nutrients were resistant to SOC losses, whereas the light fraction was lost stronger than SOC. Microbial C use efficiency was independent on land use. The resistance of C availability for microorganisms to SOC losses suggests that a decrease of SOC quality was partly compensated by litter input and a relative enrichment by nutrients. However, the relationship between the basal respiration and SOC was non-linear; i.e. negative impact on microbial activity strongly increased with SOC losses. Therefore, a small decrease of C content under oil palm compared to rubber plantations yielded a strong drop in microbial activity. Consequently, management practices mitigating SOC losses in oil palm plantations would strongly increase soil fertility and ecosystem stability. We conclude that the new approach enables quantitatively assessing the sensitivity and resistance of diverse soil functions to land-use changes and can thus be used to assess resilience of agroecosystems with various use intensities.     

Oxindole-based intraocular pressure reducing agents

The study represents the new findings at the crossroads of chemistry and medicine, particularly between medicinal and organic chemistry and ophthalmology. In this work we describe how the chemical reactivity of indolinone scaffold may be used to create small molecule ligands with strong biological response comparable with and larger than that of endogenous hormone. The synthesis of oxindole-based melatonin and 5-methoxycarbonylamino-N-acetyltryptamine (5-MCA-NAT) analogues was proposed and their ability to influence intraocular pressure (IOP) was studied in vivo. Time-dependent study revealed the prolonged effect (more than 6 h) of the lead-compound. This effect in combination with high IOP reducing effect (41 ± 6%) in low concentrations of the active compound (0.1 wt%) and with high water solubility represents a great potential of low-cost oxindole derivatives as potent antiglaucoma agents.     

Synthesis of potent chemical inhibitors of dynamin GTPase

Dynamin is a key regulatory protein in clathrin mediated endocytosis. Compared to genetic or immunological tools, small chemical dynamin inhibitors such as dynasore have the potential to study the dynamic nature of endocytic events in cells. Dynasore inhibits dynamin GTPase activity and transferrin uptake at IC₅₀ ～15 μM but use in some biological applications requires more potent inhibitor than dynasore. Here, we chemically modified the side chains of dynasore and found that two derivatives, DD-6 and DD-11 more potently inhibited transferrin uptake (IC₅₀: 4.00 μM for DD-6, 2.63 μM for DD-11) and dynamin GTPase activity (IC₅₀: 5.1 μM for DD-6, 3.6 μM for DD-11) than dynasore. The effect was reversible and they were washed more rapidly out than dynasore. TIRF microscopy showed that they stabilize the clathrin coats on the membrane. Our results indicated that new dynasore derivatives are more potent inhibitor of dynamin, displaying promise as leads for the development of more effective analogues for broader biological applications.     

Defining RNA motif–aminoglycoside interactions via two-dimensional combinatorial screening and structure–activity relationships through sequencing

RNA is an extremely important target for the development of chemical probes of function or small molecule therapeutics. Aminoglycosides are the most well studied class of small molecules to target RNA. However, the RNA motifs outside of the bacterial rRNA A-site that are likely to be bound by these compounds in biological systems is largely unknown. If such information were known, it could allow for aminoglycosides to be exploited to target other RNAs and, in addition, could provide invaluable insights into potential bystander targets of these clinically used drugs. We utilized two-dimensional combinatorial screening (2DCS), a library-versus-library screening approach, to select the motifs displayed in a 3 × 3 nucleotide internal loop library and in a 6-nucleotide hairpin library that bind with high affinity and selectivity to six aminoglycoside derivatives. The selected RNA motifs were then analyzed using structure–activity relationships through sequencing (StARTS), a statistical approach that defines the privileged RNA motif space that binds a small molecule. StARTS allowed for the facile annotation of the selected RNA motif–aminoglycoside interactions in terms of affinity and selectivity. The interactions selected by 2DCS generally have nanomolar affinities, which is higher affinity than the binding of aminoglycosides to a mimic of their therapeutic target, the bacterial rRNA A-site.     

Influence of the fish pond aquaculture effluent discharge on abiotic environmental factors of selected rivers in Northwest Poland

Pollution of rivers caused by human activity is a widely discussed problem, however there is not much attention paid to the changes of water quality that result from the inflow of effluent discharged from fish breeding ponds. The paper presents results of studies on changes of the abiotic parameters (hydrochemical and hydrological) of water observed in the yearly cycle between 2004 and 2008 in selected rivers of Northwest Poland. It was proved that the fastest reaction on the inflow of the effluent discharged from the fish ponds was reflected in changes of biogenic and organic compounds in the river water. The largest, i.e. threefold (rivers Krapiel and Tywa) or even fourfold (rivers Rurzyca and Stepnica) increase in nutrients and organic matter was recorded during the pond effluent discharge into the rivers. At that time values of the organic matter ranged from 8.9 to 18.3 mgO₂/dm³ (BOD₅), the nitrogen compounds from 16.868 to 26.930 mgN/dm³, while the phosphorus from 1.928 to 6.353 mgP/dm³. Interestingly, an additional dry mass of seston was recorded no earlier than the activity of the harmful element had been stopped and the river had resumed to the “initial” state (i.e. before the effluent discharge); that period varied from one to two months, depending on the river characteristics. The highest values of the dry seston mass (580.9 mg/dm³) was recorded in river Krapiel in November 2006. It seems that in spite of remarkable influence on values of individual physical and chemical indices of the river water quality, the effluent discharge from the fish ponds is not a factor hampering the self-purification processes of the rivers.     

Effect of soluble and particulate organic compounds on microfauna the community in subsurface flow constructed wetlands

The effect of particulate and soluble organic load on experimental subsurface flow constructed wetlands was evaluated by means of changes in the microfauna community. Two experimental constructed wetlands with a length of 0.93 m, a width of 0.59 m and a wetted depth of 0.3 m were monitored for a period of 5 months with both physical–chemical and biological analyses carried out on a weekly basis. The results obtained suggest that there are no relevant differences in terms of pollutant removal efficiency when particulate or soluble organic matter is supplied. However, the microfauna composition appears to be highly dependent on the source of organic matter supplied. Specifically, when the wetland was supplied with particulate matter, the ciliates represented more than the 60% of the total microfauna abundance at the initial section of the system, whereas when it was supplied with soluble matter, the heterotrophic microflagellates represented more than the 95%. Furthermore, the increase in particulate organic load doubled the ciliate abundance in the system, whereas the increase in soluble organic load caused a hundred fold decrease of microflagellate abundance.     

Pharmacophore-guided lead optimization: The rational design of a non-zinc coordinating,sub-micromolar inhibitor of the botulinum neurotoxin serotype a metalloprotease

Botulinum neurotoxins, responsible for the neuroparalytic syndrome botulism, are the deadliest of known biological toxins. The work described in this study was based on a three-zone pharmacophore model for botulinum neurotoxin serotype A light chain inhibition. Specifically, the pharmacophore defined a separation between the overlaps of several different, non-zinc(II)-coordinating small molecule chemotypes, enabling the design and synthesis of a new structural hybrid possessing a K_i = 600 nM (±100 nM).     

A low power DC/DC booster circuit designed for microbial fuel cells

A DC/DC booster circuit was fabricated and tested for use with microbial fuel cells (MFCs) to increase the typical operational voltage (100–300 mV) to a maximum power of >3 V. In steady state, the low power DC/DC voltage booster circuit was sustainable, i.e., powered by the MFCs alone, but required an external power source to start (but not needed to maintain) the oscillator. The operating principle and function of each part of the circuit is described. A procedure for determining the optimal set of values for each component in the circuit was established. The performance of the circuit was demonstrated using three Shewanella oneidensis MR-1 based MFCs connected in parallel. The power consumption of the booster circuit was less than 20 μW, which was less than the output from the three MFCs. After the output capacitor was charged to 5 V, the booster circuit can be powered by the MFCs alone. Under normal operation, the MFCs were able to power the booster circuit and a light emitting diode.     

Protective effect of chemical stimulation of cerebellar fastigial nucleus on stress gastric mucosal injury in rats

AimsWe investigated the protective effects of chemical stimulation of cerebellar fastigial nucleus (FN) on stress gastric mucosal injury (SGMI) and its possible neuro-regulatory mechanisms in rats.Main methodsChemical stimulation, electrical stimulation, chemical ablation, electrolytic lesion, and microinjection were used to investigate the effects of FN simulation on SGMI. The model of SGMI was established by restraint and water (21 ± 1 °C)-immersion (RWI) for 3 h in rats. The gastric mucosal injury index indicated the severity of gastric mucosal injuries.Key findingsWe showed that microinjection of L-glutamic acid into the FN or electrical stimulation of the FN markedly attenuated SGMI. Either chemical lesion of the FN or electrical ablation of the decussation of superior cerebellar peduncle (DSCP) obviously aggravated SGMI. The protective effect of FN stimulation on SGMI was reversed after chemical ablation of the lateral hypothalamic area (LHA). The protective effect of FN was prevented by pretreatment with the glutamic acid decarboxylase antagonist, 3-MPA into the FN or GABA_A receptor antagonist, bicuculline into the LHA. The protective effect of FN was abolished by pretreatment with sympathectomy. The discharge frequency of greater splanchnic nerve (GSN) was decreased and gastric mucosal blood flow (GMBF) was increased after chemical stimulation of FN. These results indicate that the FN participates in regulation of SGMI, and is a specific area in the CNS for exerting protective effects on the SGMI. The DSCP, LHA and peripheral sympathetic nerve may be involved in this process.SignificanceOur findings might provide a new and improved understanding of the cerebellar function and an effective treatment strategy for stress gastric mucosal injury.     

Changes in sEMG parameters among trunk and thigh muscles during a fatiguing bilateral isometric multi-joint task in trained and untrained subjects

This study aimed to explore changes in the electrical activity distribution among synergist muscles involved in the maintenance of this bilateral multi-joint task. It also tested relations between changes in surface electromyographic (sEMG) parameters with endurance time. Eighteen subjects, trained and untrained in hiking, performed a submaximal (50% of maximal contraction) isometric hiking test until exhaustion. The electrical activity of main superficial muscles implicated in this posture was recorded bilaterally. Trained subjects sustained the hiking position for 315 ± 82 s, versus 225 ± 68 s for untrained subjects. Patterns of electrical activity and mean power frequency (MPF) were different between populations. MPF shift in abdominal muscles was higher than in other synergists for both groups. Although typical changes in sEMG parameters were observed, few relations with endurance time were found, and for untrained subjects only. Changes in the relative contribution among synergists were observed, mainly for trained subjects. It is hypothesized that the task (a complex multi-joint posture involving numerous joints and muscles) may allow some variability in the contribution of synergist muscles during fatigue especially for the trained group. This probably explains the absence of relationship between endurance time and sEMG changes for trained subjects.     

Factors influencing chemical quality of composted poultry waste

The need for organic recycling is justified in the case of poultry waste because after ensuring hygienization there is a chance of obtaining a compost with substantial fertilizer value. Organic recycling of slaughter waste has its justification in sustainable development and retardation of resources. In the research being described, composting of hydrated poultry slaughterhouse waste with maize straw was carried out. Combinations with fodder yeast and postcellulose lime were also introduced in order to modify chemical and physicochemical properties of the mixtures. The experiment was carried out within 110 days in 1.2 × 1.0 × 0.8 m laboratory reactors. Temperature of the biomass was recorded during composting, and the biomass was actively aerated through a perforated bottom.Composting of substrates selected in such a way caused losses of some elements in gaseous form, an increase in concentration of other elements, and changes in relationships between elements. The ability to select substrates influences compost quality. This ability is determined by chemical indicators. Among other things, compost evaluation based on carbon to nitrogen ratio shows the intensity of the composting process and possible nitrogen losses. The addition of slaughter waste to maize straw reduced the content of individual fractions of carbon in the composts, whereas the addition of postcellulose lime intensified that process. The addition of fodder yeast significantly increased the phosphorus content in the compost. Since iron compounds were used in the processing of poultry carcasses, composts that were based on this material had an elevated iron content. The applied postcellulose lime significantly increased the copper, zinc, chromium, nickel, and lead contents. Proper selection of substrates for composting of hydrated poultry slaughterhouse waste allows to obtain a compost with chemical properties that create favorable conditions for natural application of that compost. Addition of large quantities of postcellulose lime to the composting process leads to obtaining an organic-mineral substratum for cultivation or to obtaining an agent that improves soil properties.     

Visible light-induced nitric oxide release from a novel nitrobenzene derivative cross-conjugated with a coumarin fluorophore

Nitric oxide (NO) is a well-known free-radical molecule which is endogenously biosynthesised and shows various functions in mammals. To investigate NO functions, photocontrollable NO donors, compounds which release NO in response to light, are expected to be potentially useful. However, most of the conventional NO donors require harmful ultra-violet light for NO release. In this study, two dimethylnitrobenzene derivatives conjugated with coumarins were designed, synthesized and evaluated as photocontrollable NO donors. The optical properties and efficiency of photo-induced NO release were dependent upon the nature of the conjugation system. One of these compounds, Bhc-DNB (1), showed spatiotemporally well-controlled NO release in cultured cells upon exposure to light in the less-cytotoxic visible wavelength range (400–430 nm).     

The rate of Qx→Qy relaxation in bacteriochlorophylls of reaction centers from Rhodobacter sphaeroides determined by kinetics of the ultrafast carotenoid bandshift

Transient absorption changes induced by excitation of isolated reaction centers (RCs) from Rhodobacter sphaeroides with 600 nm laser pulses of 20 fs (full width at half maximum) were monitored in the wavelength region of 420–560 nm. The spectral features of the spectrum obtained are characteristic for an electrochromic band shift of the single carotenoid (Car) molecule spheroidene, which is an integral constituent of these RCs. This effect is assigned to an electrochromic bandshift of Car due to the local electric field of the dipole moment formed by electronic excitation of bacteriochlorophyll (BChl) molecule(s) in the neighborhood of Car. Based on the known distances between the pigments, the monomeric BChl (B_B) in the inactive B-branch is inferred to dominate this effect. The excitation of B_B at 600 nm leads to a transition into the S₂ state (Q_x band), which is followed by rapid internal conversion to the S₁ state (Q_y band), thus leading to a change of strength and orientation of the dipole moment, i.e., of the electric field acting on the Car molecule. Therefore, the time course of the electrochromic bandshift reflects the rate of the internal conversion from S₂ to S₁ of B_B. The evaluation of the kinetics leads to a value of 30 fs for this relaxation process. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.     

An ultraviolet light sensitive target in nitrate reductase of Escherichia coli K-12

Ultraviolet light was shown to inactivate purified nitrate reductase in the presence of reduced benzyl viologen. Loss of activity was not complete, reaching 60 to 70%. Photolysis was maximum at 345 nm. The differential spectrum between native and irradiated enzyme exhibited absorption bands at 216, 275, 314 and 365 nm. The photosensitive electron carrier could be extracted by organic solvents. It had the following absorption bands: 225, 275 and 285 nm. It was reduced by Nile blue A but not by methylene blue. The precise nature of this light sensitive molecule could not be determined although the results support the idea that this chromophore might be a naphthoquinone.     

Discovery of pyrazolo[1,5-a]pyrimidine-3-carbonitrile derivatives as a new class of histone lysine demethylase 4D (KDM4D) inhibitors

Herein we report the discovery of a series of new small molecule inhibitors of histone lysine demethylase 4D (KDM4D). Molecular docking was first performed to screen for new KDM4D inhibitors from various chemical databases. Two hit compounds were retrieved. Further structural optimization and structure-activity relationship (SAR) analysis were carried out to the more selective one, compound 2, which led to the discovery of several new KDM4D inhibitors. Among them, compound 10r is the most potent one with an IC₅₀ value of 0.41 ± 0.03 μM against KDM4D. Overall, compound 10r could be taken as a good lead compound for further studies.     

Formation of poly(ε-caprolactone) scaffolds loaded with small molecules by integrated processes

Cell stimulation by bioactive molecules has become an important tool in tissue engineering. The homogeneous incorporation of such molecules within the bulk of a polymer-based scaffold compared to surface coating is considered advantageous for most applications and minimizes a burst effect. An efficient way of bulk loading is the incorporation of these molecules during the scaffold formation process. In this paper, two different integrated processes for the preparation of scaffolds from poly(ε-caprolactone) (PCL) loaded with a small molecule are investigated. Both formation and loading of the scaffold is carried out in a single-step process. Sudan Red G was selected as a model compound for lipophilic small molecules. A freeze drying and pressure quench (PQ) formation process was selected, and the influence of the small molecule on the formation processes and on the morphology of the obtained scaffold was evaluated and compared. It could be shown for both processes that the formation of loaded scaffolds is possible, and that the small molecule has a very high impact on the foam morphology. In case of the freeze-drying (FD) method, only a load of 1 wt% Sudan Red G was incorporated within the bulk and showed no influence on the foam morphology. In the case of PQ foaming, an incorporation of 43 wt% Sudan Red G was achieved (although tiny crystal needles of the small molecule were found on the surface) and a strong effect on the foam morphology was found. This paper presents an efficient method of incorporating small molecules by integrated processes.     

Dosimetric shield evaluation with tungsten sheet in 4, 6, and 9 MeV electron beams

In electron radiotherapy, shielding material is required to attenuate beam and scatter. A newly introduced shielding material, tungsten functional paper (TFP), has been anticipated to become a very useful device that is lead-free, light, flexible, and easily processed, containing very fine tungsten powder at as much as 80% by weight. The purpose of this study was to investigate the dosimetric changes due to TFP shielding for electron beams. TFP (thickness 0–15 mm) was placed on water or a water-equivalent phantom. Percentage depth ionization and transmission were measured for 4, 6, and 9 MeV electron beams. Off-center ratio was also measured using film dosimetry at depth of dose maximum under similar conditions. Then, beam profiles and transmission with two shielding materials, TFP and lead, were evaluated. Reductions of 95% by using TFP at 0.5 cm depth occurred at 4, 9, and 15 mm with 4, 6, and 9 MeV electron beams, respectively. It is found that the dose tend to increase at the field edge shaped with TFP, which might be influenced by the thickness. TFP has several unique features and is very promising as a useful tool for radiation protection for electron beams, among others.     

2,3 Butanediol production in an obligate photoautotrophic cyanobacterium in dark conditions via diverse sugar consumption

Cyanobacteria are under investigation as a means to utilize light energy to directly recycle CO₂ into chemical compounds currently derived from petroleum. Any large-scale photosynthetic production scheme must rely on natural sunlight for energy, thereby limiting production time to only lighted hours during the day. Here, an obligate photoautotrophic cyanobacterium was engineered for enhanced production of 2,3-butanediol (23BD) in continuous light, 12 h:12 h light-dark diurnal, and continuous dark conditions via supplementation with glucose or xylose. This study achieved 23BD production under diurnal conditions comparable to production under continuous light conditions. The maximum 23BD titer was 3.0 g L⁻¹ in 10 d. Also achieving chemical production under dark conditions, this work enhances the feasibility of using cyanobacteria as industrial chemical-producing microbes.