MaxSynBio: Avenues Towards Creating Cells from the Bottom Up

A large German research consortium mainly within the Max Planck Society (“MaxSynBio”) was formed to investigate living systems from a fundamental perspective. The research program of MaxSynBio relies solely on the bottom‐up approach to synthetic biology. MaxSynBio focuses on the detailed analysis and understanding of essential processes of life through modular reconstitution in minimal synthetic systems. The ultimate goal is to construct a basic living unit entirely from non‐living components. The fundamental insights gained from the activities in MaxSynBio could eventually be utilized for establishing a new generation of biotechnological processes, which would be based on synthetic cell constructs that replace the natural cells currently used in conventional biotechnology.     

Determination of the LOQ in real-time PCR by receiver operating characteristic curve analysis: application to qPCR assays for Fusarium verticillioides and F. proliferatum

Real-time PCR (qPCR) is the principal technique for the quantification of pathogen biomass in host tissue, yet no generic methods exist for the determination of the limit of quantification (LOQ) and the limit of detection (LOD) in qPCR. We suggest using the Youden index in the context of the receiver operating characteristic (ROC) curve analysis for this purpose. The LOQ was defined as the amount of target DNA that maximizes the sum of sensitivity and specificity. The LOD was defined as the lowest amount of target DNA that was amplified with a false-negative rate below a given threshold. We applied this concept to qPCR assays for Fusarium verticillioides and Fusarium proliferatum DNA in maize kernels. Spiked matrix and field samples characterized by melting curve analysis of PCR products were used as the source of true positives and true negatives. On the basis of the analysis of sensitivity and specificity of the assays, we estimated the LOQ values as 0.11 pg of DNA for spiked matrix and 0.62 pg of DNA for field samples for F. verticillioides. The LOQ values for F. proliferatum were 0.03 pg for spiked matrix and 0.24 pg for field samples. The mean LOQ values correspond to approximately eight genomes for F. verticillioides and three genomes for F. proliferatum. We demonstrated that the ROC analysis concept, developed for qualitative diagnostics, can be used for the determination of performance parameters of quantitative PCR.     

Synthesis of substituted 1,1′-diaminoferrocenes from cyclo-2-pentene imines

Condensation of anilines and primary aliphatic amines with 3,4-diphenylcyclo-2-pentenone leads to the corresponding diphenylcyclopentene imines in good yields of 72-90%. Deprotonation of these aminocyclopentadiene tautomers and reaction with FeCl₂ leads to the synthesis of the respective 1,1′-diamino-3,3′,4,4′-tetraphenylferrocenes. Yields increase from 33% to 65% with a decrease in the steric bulk of the amine substituent. The observation that a successful conversion requires two equivalents of base is conceived on the basis of the discussed reaction mechanism. The molecular structure of 1,1′-dianilino-3,3′,4,4′-tetraphenylferrocene (3a), which was determined by single crystal X-ray analysis reveals a trans coordination of the two amine moieties with respect to the central Cp-Fe-Cp axis of the ferrocenyl backbone.     

pH‐Dependent Coordination of AgI Ions by Histidine: Experiment,Theory, and a Model for SilE

Artificial implants and biomaterials lack the natural defense system of our body and, thus, have to be protected from bacterial adhesion and biofilm formation. In addition to the increasing number of implanted objects, the resistance of bacteria is also an important problem. Silver ions are well‐known for their antimicrobial properties, yet not a lot is known about their mode of action. Silver is expected to interact on many levels, thus the development of silver resistance is very difficult. Nevertheless, some bacteria are able to resist silver, even at higher concentrations. One such defense mechanism of bacteria against heavy‐metal intoxication includes an efflux system. SilE, a periplasmic silver‐binding protein that is involved in this defense mechanism, has been shown to possess numerous histidine functions, which strongly bind to silver atoms, as demonstrated by ourselves previously. Herein, we address the question of how histidine binds to silver ions as a function of pH value. This property is important because the local proton concentration in cells varies. Thus, we solved the crystal structures of histidine–silver complexes at different pH values and also investigated the influence of the amino‐acid configuration. These results were completed by DFT calculations on the binding strength and packing effects and led to the development of a model for the mode of action of SilE.     

Microscale imaging of the preservation state of 5,000-year-old archaeological bones by synchrotron infrared microspectroscopy

Archaeological bone materials record characteristic markers of life in prehistoric times (dating, climate, environment, diet, human migration) in their isotopic and chemical composition in addition to palaeontological, archaeozoological, anthropological and palaeogenetic information. Thus, the discovery and conservation of archaeological bone materials is of great importance to get access to this information. However, archaeological materials are altered by different postmortem processes and it appears necessary to estimate if the archaeological information is still reliable or if it has been modified during burial. As archaeological bone materials present a high structural hierarchy at the micro- and nanoscale, changes induced by diagenetic phenomena have to be observed at these scales. One method for revealing post mortem changes of the bone structure and composition at the microscale is synchrotron radiation micro-FTIR imaging (SR micro-FTIR). Thus, thin sections of about 5,000-year-old archaeological bones have been analysed in transmission mode at the IRIS beamline (BESSY II, HZB Berlin) to determine markers of the state of bone preservation at the microscale. The archaeological bone material comes from station 19 of the Neolithic site of the Chalain Lake. By using SR micro-FTIR it was possible to image characteristic bone structures, e.g. osteons (the constitutive histological unit of cortical bone), using the absorption band ratios corresponding to different chemical bone constituents (collagen content and quality, phosphate crystallinity, carbonate content). These data allow us to precisely evaluate the state of preservation of a 5,000-year-old bone at the histological level.

Using an electrical potential to reversibly switch surfaces between two states for dynamically controlling cell adhesion

Smart surfaces presenting both antifouling molecules with a charged functional group at their distal end, and molecules that are terminated by RGD peptides for cell adhesion, were fabricated and characterized (see picture). By applying potentials of +300 or -300?mV, the surfaces could be dynamically switched to make the peptide accessible or inaccessible to cells.     

Generation and characterisation of the phenoxyl-radical containing Cu(ii) complex [Cu(triaz)(2)](+) (triaz(-) = O,N chelating triazole-phenolate)

The new copper complex [Cu(triaz)(2)] (Htriaz = 2,4-di-(tert-butyl)-6-(5-chloro-2H-benzo[d][1,2,3]triazol-2-yl)phenol) was investigated in detail by single crystal XRD, EPR-, UV/Vis-absorption-, CV-, and spectroelectrochemistry. The oxidised species [Cu(triaz)(2)](+) was characterised by UV/Vis spectroelectrochemistry and contains a phenoxyl-radical bound to Cu(ii). This quite stable species was chemically generated by two different methods: aerial oxidation of a Cu(i) precursor in the presence of Htriaz (and base) or from [Cu(triaz)(2)] by adding a Cu(ii) salt (disproportionation). The efficiency for the latter reaction has been studied by UV/Vis spectroscopy, XAS and catalytic test reactions (oxidation of benzyl alcohol).     

{(MesGa)3[GaP(H)Mes](PMes)4}, Ein phosphorsubstituiertes Ga?P-Heterocuban

{(MesGa)₃[GaP(H)Mes](PMes)₄}, a Phosphorus-substituted Ga? P-Heterocubane A mixture of MesGaCl₂/GaCl₃ (ratio 3:1) reacts with 5 equivalents of MesPLi₂ in THF at ?78°C to the title compound {(MesGa)₃[GaP(H)Mes](PMes)₄} ( 1 ) by use of the “dilution principle”. 1 can be obtained in 30% yield. Recrystallization of 1 from DME and toluene, respectively, gives 1 · 0.5 DME and 1 · toluene. 1 was characterized by NMR-, IR-, and MS-techniques. According to the X-ray structure determination of 1 · toluene, 1 has a heterocubane structure, one corner of which is substituted with an P(H)Mes group.