pinecone/core-2020-05-10-deduplication huggingface dataset:
Synthesis, NMR structural characterization and molecular modeling of substituted thiosemicarbazones and semicarbazones using DFT calculations to prove the syn/anti isomer formation

Thiosemicarbazones possessing electron-donating and electron-withdrawing groups were prepared, and their spectral characteristics determined. In all cases, the spectra showed that one isomer was formed, allowing further functionalization to molecules of biological interest. We provide NMR data for some of the thiosemicarbazones and semicarbazones. We also provide evidence that for 2-pyridyl thiosemicarbazone, the syn isomer slowly converts into the anti isomer in dimethyl sulfoxide solvent with first-order kinetics. Molecular modeling and density functional theory calculations confirmed these observations
Sterols associated with small unilamellar vesicles (SUVs): intrinsic mobility role for 1H NMR detection.

International audienceSmall unilamellar vesicles (SUVs) of phospholipids are often used as a membrane model system for studying the interaction of molecules. When using NMR under the standard liquid-state conditions, SUV phospholipid proton spectra can be recorded, exhibiting sharp signals. This is not only because of the fast vesicular tumbling but also because of the combination of this tumbling with the individual motion of the lipids inside the bilayer. This appears evident because addition of cholesterol is responsible of broader resonances because of the slowing down of the lipid motion. On the other hand, no (1)H signal is detected for cholesterol in the bilayer. This lack of detection of the inserted molecules explains why generally SUVs are not considered as a good model for NMR studies under the standard liquid-state conditions. Here, we use two other sterols in order to demonstrate that an increase of the molecular mobility inside the bilayer could allow the detection of their proton resonances. For desmosterol and lanosterol, which show higher mobility inside the bilayer, with increasing lateral diffusion rates, (1)H sterol signals are detected in contrast to cholesterol. For the fast diffusing lanosterol, no significant improvement in detection is observed using deuterated lipids, demonstrating that homonuclear dipolar coupling is fully averaged out. Furthermore, in the case of low mobility such as for cholesterol, the use of a fast magic angle spinning probe is shown to be efficient to recover the full proton spectrum
Size-exclusion chromatographic NMR of polymer mixtures

The use of chromatographic stationary phases or solvent modifiers to modulate diffusion properties in NMR experiments is now well established. Their use can be to improve resolution in the diffusion domain or to provide an insight into analyte–modifier interactions and, hence, the chromatography process. Here, we extend previous work using size-exclusion chromatographic sta- tionary phases to the investigation of polymer mixtures. We demonstrate that similar diffusion modulation behaviour is observed with a size-exclusion chromatographic stationary phase that can be understood in terms of size-exclusion behaviour
Effects of ions on water structure: a low-field (1) H T1 NMR relaxometry approach

Aqueous salt solutions play an important role in nature because of their effects on environmental biogeochemical processes and on structural properties of biomolecules. Upon dissolution, salts split in ions that are solvated. Water in hydration shells is subjected to molecular motions that can be monitored by (1) H T1 NMR relaxometry. This technique allowed the evaluation of the nature of the interactions between water and ions via variable temperature experiments. Examination of relaxometry properties of aqueous solutions at variable salt concentrations allowed acknowledgement of the role played by ions in either structuring or destructuring water aggregates. A mathematical model has been applied on six environmentally relevant salts: NaCl, KCl, CaCl2 , CaCO3 , NaNO3 , and NH4 NO3 . It was linear only for the concentration dependence of KCl-R1 . This model accorded with the one reported in literature where it has been considered valid only for diluted solutions. However, in the present study, the range of linearity for KCl was extended up to the saturation point. The model was modified for NaCl, CaCl2 , and CaCO3 by using it as an exponential form in order to account for the nonlinearity of the R1 -versus-concentration curves. Nonlinearity was explained by the nonnegligible ion-ion interactions occurring as concentration was increased. Finally, further modification was needed to account for the asymmetric distribution of water around nitrate (in NaNO3 and NH4 NO3 ) and ammonium (in NH4 NO3 ). This study is preliminary to the comprehension of the diffusion mechanisms of ions in water solutions at the equilibrium condition with solid surfaces such as soils and biochar-amended soils. Copyright © 2014 John Wiley & Sons, Ltd
HOBS methods for enhancing resolution and sensitivity in small DNA oligonucleotide NMR studies

1H NMR spectra from biopolymers give chemical shifts classified according to proton type and often suffer from signal degeneracy. Data from nucleic acids are particularly prone to this failing. Recent developments in proton broad-band decoupling techniques with the promise of enhanced resolution at full sensitivity have allowed us to investigate the application of homo-nuclear band-selective (HOBS) decoupling to the study of small synthetic DNA molecules and to compare these with results from classical and Pure Shift techniques. Improved signal resolution at full sensitivity in both HOBS-1D 1H and HOBS-2D [1H, 1H] NOESY NMR data are reported for three example small DNA molecules. Comparisons of 1H T1 and integrals of signals from HOBS-1D 1H and HOBS-2D [1H, 1H] NOESY NMR data with those of standard data collection methods are also reported. The results show that homo-nuclear HOBS-NOESY data are useful for data assignment purposes and have some merit for quantification purposes. In general we show that resolution and sensitivity enhancement of 1H NMR data for small DNA samples may be achieved without recourse to higher magnetic field strengths at full sensitivity in a band-selected manner
Water dynamics in different biochar fractions

Biochar is a carbonaceous porous material deliberately applied to soil to improve its fertility. The mechanisms through which biochar acts on fertility are still poorly understood. The effect of biochar texture size on water dynamics was investigated here in order to provide information to address future research on nutrient mobility towards plant roots as biochar is applied as soil amendment. A poplar biochar has been stainless steel fractionated in three different textured fractions (1.0-2.0mm, 0.3-1.0mm and <0.3mm, respectively). Water-saturated fractions were analyzed by fast field cycling (FFC) NMR relaxometry. Results proved that 3D exchange between bound and bulk water predominantly occurred in the coarsest fraction. However, as porosity decreased, water motion was mainly associated to a restricted 2D diffusion among the surface-site pores and the bulk-site ones. The X-ray μ-CT imaging analyses on the dry fractions revealed the lowest surface/volume ratio for the coarsest fraction, thereby corroborating the 3D water exchange mechanism hypothesized by FFC NMR relaxometry. However, multi-micrometer porosity was evidenced in all the samples. The latter finding suggested that the 3D exchange mechanism cannot even be neglected in the finest fraction as previously excluded only on the basis of NMR relaxometry results. X-ray μ-CT imaging showed heterogeneous distribution of inorganic materials inside all the fractions. The mineral components may contribute to the water relaxation mechanisms by FFC NMR relaxometry. Further studies are needed to understand the role of the inorganic particles on water dynamics
The use of residual dipolar coupling for conformational analysis of structurally related natural products

The authors would like to acknowledge the EPSRC for funding.Determining the conformational preferences of molecules in solution remains a considerable challenge. Recently, the use of residual dipolar coupling (RDC) analysis has emerged as a key method to address this. Whilst to date the majority of the applications have focused on biomolecules including proteins and DNA, the use of RDCs for studying small molecules is gaining popularity. Having said that, the method continues to develop and here we describe an early case study of the quantification of conformer populations in small molecules using RDC analysis. Having been inspired to study conformational preferences by unexpected differences in the NMR spectra and the reactivity of related natural products, we showed that the use of more established techniques was unsatisfactory in explaining the experimental observations. The use of RDCs provided an improved understanding which, following use of methods to quantify conformer populations using RDCs, culminated in a rationalisation of the contrasting diastereoselectivities observed in a ketone reduction reactionPostprintPeer reviewe
Evaluation of the surface affinity of water in three biochars using fast field cycling NMR relaxometry

Many soil functions depend on the interaction of water with soil. The affinity of water for soils can be altered by applying soilamendments like stone meal, manure, or biochar (a carbonaceous material obtained by pyrolysis of biomasses). In fact, the addi-tion of hydrophobic biochar to soil may increase soil repellency, reduce water-adsorbing capacity, inhibit microbial activity, altersoil filter, buffer, storage, and transformation functions. For this reason, it is of paramount importance to monitor water affinity forbiochar surface (also referred to as ‘wettability’) in order to better address its applications in soil systems. In this study, we proposethe use of fast field cycling NMR relaxometry technique with the application of a new mathematical model for data interpretation,as a valid alternative to the traditional contact angle (CA) measurements for biochar wettability evaluation. Either NMR or CA re-sults revealed the same wettability trend for the biochars studied here. The advantage of NMR relaxometry over CA measurementslies in the possibility to obtain at the microscopic level a variety of different information in only one shot. In fact, while CA providesonly wettability evaluation, NMR relaxometry also allows achievement of the mechanisms for water molecular dynamics onbiochar surface, thereby leading to the possibility to understand better, in future research, the role of biochar in increasing soilquality and plant nutrition
A microcontroller system for the automation of transient effect determination of the spin-lattice relaxation time using continuous wave NMR

A simple transient effect method for the determination of the spin-lattice relaxation time using continuous wave NMR (TEDSpiL) with a marginal oscillator was recently reported (doi:10.1002/mrc.4594). Such a system measures a parameter, called Tx, that is related to T1 and allows T1 to be determined with the aid of calibration samples. For such a system, the process of making the Tx measurement does not require variable parameters and so is ideal for implementing in microcontroller code. In this article, we demonstrate that TEDSpiL may be automated using two microcontrollers from the Teensy family to make a low power and portable system
Compressed NMR : combining compressive sampling and pure shift NMR techniques.

Historically, the resolution of multidimensional nuclear magnetic resonance (NMR) has been orders of magnitude lower than the intrinsic resolution that NMR spectrometers are capable of producing. The slowness of Nyquist sampling as well as the existence of signals as multiplets instead of singlets have been two of the main reasons for this underperformance. Fortunately, two compressive techniques have appeared that can overcome these limitations. Compressive sensing, also known as compressed sampling (CS), avoids the first limitation by exploiting the compressibility of typical NMR spectra, thus allowing sampling at sub‐Nyquist rates, and pure shift techniques eliminate the second issue “compressing” multiplets into singlets. This paper explores the possibilities and challenges presented by this combination (compressed NMR). First, a description of the CS framework is given, followed by a description of the importance of combining it with the right pure shift experiment. Second, examples of compressed NMR spectra and how they can be combined with covariance methods will be shown
Eigenstate versus Zeeman-based approaches to the solid-effect

The solid effect is one of the simplest and most effective mechanisms for
Dynamic Nuclear Polarization. It involves the exchange of polarization between
one electron and one nuclear spin coupled via the hyperfine interaction. Even
for such a small spin system, the theoretical understanding is complicated by
the contact with the lattice and the microwave irradiation. Both being weak,
they can be treated within perturbation theory. In this work, we analyze the
two most popular perturbation schemes: the Zeeman and the eigenstate-based
approaches which differ in the way the hyperfine interaction is treated. For
both schemes, we derive from first principles an effective Liouville equation
which describes the density matrix of the spin system; we then study
numerically the behavior of the nuclear polarization for several values of the
hyperfine coupling. In general, we obtain that the Zeeman-based approach
underestimates the value of the nuclear polarization. By performing a
projection onto the diagonal part of the spin-system density matrix, we are
able to understand the origin of the discrepancy, which is due to the presence
of parasite leakage transitions appearing whenever the Zeeman basis is
employed.Comment: 9 pages, 4 figures, 7 pages of supplementary materia
Reorganization of mouse sperm lipid rafts by capacitation

One of the hallmarks of mammalian sperm capacitation is the loss of cholesterol from the plasma membrane. Cholesterol has been associated with the formation of detergent insoluble membrane microdomains in many cell types, and sperm from several mammalian species have been shown to contain detergent‐resistant membranes (DRMs). The change in cholesterol composition of the sperm plasma membrane during capacitation raises the question of whether the contents of DRMs are altered during this process. In this study, we investigated changes in protein composition of DRMs isolated from uncapacitated or capacitated mouse sperm. TX‐100 insoluble membranes were fractionated by sucrose flotation gradient centrifugation and analyzed by Western and lectin blotting, and capacitation‐related differences in protein composition were identified. Following capacitation, the detergent insoluble fractions moved to lighter positions on the sucrose gradients, reflecting a global change in density or composition. We identified several individual proteins that either became enriched or depleted in DRM fractions following capacitation. These data suggest that the physiological changes in sperm motility, ability to penetrate the zona pellucida (ZP), ZP responsiveness, and other capacitation‐dependent changes, may be due in part to a functional reorganization of plasma membrane microdomains. Mol. Reprod. Dev. 73: 1541–1549, 2006. © 2006 Wiley‐Liss, Inc
Heads or tails? Structural events and molecular mechanisms that promote mammalian sperm acrosomal exocytosis and motility

Sperm structure has evolved to be very compact and compartmentalized to enable the motor (the flagellum) to transport the nuclear cargo (the head) to the egg. Furthermore, sperm do not exhibit progressive motility and are not capable of undergoing acrosomal exocytosis immediately following their release into the lumen of the seminiferous tubules, the site of spermatogenesis in the testis. These cells require maturation in the epididymis and female reproductive tract before they become competent for fertilization. Here we review aspects of the structural and molecular mechanisms that promote forward motility, hyperactivated motility, and acrosomal exocytosis. As a result, we favor a model articulated by others that the flagellum senses external signals and communicates with the head by second messengers to affect sperm functions such as acrosomal exocytosis. We hope this conceptual framework will serve to stimulate thinking and experimental investigations concerning the various steps of activating a sperm from a quiescent state to a gamete that is fully competent and committed to fertilization. The three themes of compartmentalization, competence, and commitment are key to an understanding of the molecular mechanisms of sperm activation. Comprehending these processes will have a considerable impact on the management of fertility problems, the development of contraceptive methods, and, potentially, elucidation of analogous processes in other cell systems.Fil: Buffone, Mariano Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental (i); Argentina. University of Pennsylvania; Estados UnidosFil: Ijiri, Takashi W.. University of Pennsylvania; Estados UnidosFil: Cao, Wenlei. University of Pennsylvania; Estados UnidosFil: Merdiushev, Tanya. University of Pennsylvania; Estados UnidosFil: Aghajanian, Haig K.. University of Pennsylvania; Estados UnidosFil: Gerton, George L.. University of Pennsylvania; Estados Unido
The effect of peri-conception hyperglycaemia and the involvement of the hexosamine biosynthesis pathway in mediating oocyte and embryo developmental competence

The environment that the oocyte is exposed to during the peri-conception period can have a significant impact on oocyte developmental competence (the ability of the oocyte to support fertilisation and subsequent embryo development) and the long-term health of the resulting offspring. This is particularly true for maternal hyperglycaemia. While maternal hyperglycaemia during early pregnancy through term development has been extensively studied, the effects on the oocyte itself, and the underlying mechanisms, remain largely unknown. There is increasing evidence, however, for the role of the fuel-sensing hexosamine biosynthesis pathway in mediating the effects of hyperglycaemia in many different cell types. In this review, we will focus on the reproductive consequences of maternal hyperglycaemia during the peri-conceptual period and the role of the hexosamine pathway in mediating these processes.Laura A. Frank, Melanie L. Sutton-McDowall, Robert B. Gilchrist, and Jeremy G. Thompso
Pre-maturation with cAMP modulators in conjunction with EGF-like peptides during in vitro maturation enhances mouse oocyte developmental competence

Recent studies have independently shown that cyclic adenosine 3'5'-monophosphate (cAMP) modulation prior to in vitro maturation (IVM) and epidermal growth factor (EGF)-like peptide supplementation during IVM improve subsequent oocyte developmental outcomes. This study investigated the effects of an IVM system that incorporates these two concepts. Cumulus-oocyte complexes (COCs) were collected from pre-pubertal mice either 46 hr post-equine chorionic gonadotropin (eCG) (IVM) or post-eCG + post-human chorionic gonadotropin (hCG) stimulation (in vivo maturation; IVV). IVM COCs were treated with the cAMP modulators forskolin and IBMX for 1, 2, or 4 hr (pre-IVM phase) prior to IVM. COCs then underwent IVM with the EGF-like peptides amphiregulin or epiregulin, or with the common IVM stimulants follicle-stimulating hormone (FSH) or EGF. A pre-IVM phase increased the size of the subsequent blastocysts' inner-cell-mass compared to standard IVM, regardless of IVM treatment (P < 0.05). Unlike FSH or EGF, amphiregulin or epiregulin significantly increased blastocyst quality (trophectoderm and total cell numbers) and/or yield (P < 0.01) compared to standard IVM, and were the only treatments that produced blastocysts comparable to IVV-derived blastocysts. Forskolin acutely up-regulated EGF-like peptide mRNA expression after a 2-hr pre-IVM phase (P < 0.001), although EGF receptor and ERK1/2 activities were not significantly different than control. IVV-like levels of EGF-like peptide mRNA expression during IVM were maintained only by supplementing with EGF-like peptides and EGF, since expression levels induced by FSH were significantly lower in vitro than during IVV. However, EGF receptor and ERK1/2 phosphorylation levels were not significantly different across treatment groups. In conclusion, a pre-IVM phase in conjunction with IVM in the presence of EGF-like peptides endows high oocyte developmental competence, as evidenced by increased embryo yield and/or quality relative to FSH and EGF.D. Richani, X. Wang, H. Zeng, J.E.J. Smitz, J.G. Thompson, and R.B. Gilchris
Oxytocin regulates the expression of aquaporin 5 in the late-pregnant rat uterus

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Aquaporins (AQPs) are integral membrane channels responsible for the transport of water across a cell membrane. Based on reports that AQPs are present and\ud
accumulate in the female reproductive tract late in pregnancy, our aim was to study the expression of AQP isoforms (AQP1, 2, 3, 5, 8, and 9) at the end of pregnancy in rat in order to determine if they play a role in parturition. Reverse-transcriptase PCR revealed that specific Aqp mRNAs were detectable in the myometrium of nonpregnant and late-pregnancy (Days 18, 20, 21, and 22 of pregnancy) rat uteri. The expression of Aqp5 mRNA and protein were most pronounced on Days 18-21, and were dramatically decreased on Day 22 of pregnancy. In contrast, a significant increase was found in the level of Aqp5 transcript in whole-blood samples on the last day of pregnancy. The effect of oxytocin on myometrial Aqp5 expression in an organ bath was also investigated. The level of Aqp5 mRNA significantly decreased 5 min after oxytocin (10-8 M) administration, similarly to its profile on the day of delivery; this effect was sensitive to the oxytocin antagonist atosiban. The vasopressin analog desmopressin (3.7x10-8 M), on the other hand, did not alter the expression of Aqp5, but did increased the amount of Aqp2 mRNA, an effect that was atosiban-resistant. These results lead us to propose that oxytocin selectively influences the expression of Aqp5 at the end of pregnancy, and may participate in events that lead to parturition in the rat. The sudden increase of AQP5 in the blood on the last dayof pregnancymayserve as a marker that indicates the initiation of delivery
Meiotic wave adds extra asymmetry to the development of female chicken gonads

Development of female gonads in the chicken is asymmetric. This asymmetry affects gene expression, morphology, and germ cell development; consequently only the left ovary develops into a functional organ, whereas the right ovary remains vestigial. In males, on the other hand, both gonads develop into functional testes. Here, we revisited the development of asymmetric traits in female (and male) chicken gonads between Hamburger Hamilton stage 16 (HH16) and hatching. At HH16, primordial germ cells migrated preferentially to the left gonad, accumulating in the left coelomic hinge between the gut mesentery and developing gonad in both males and females. Using the meiotic markers SYCP3 and phosphorylated H2AFX, we identified a previously undescribed, pronounced asymmetryc meiotic progression in the germ cells located in the central, lateral, and extreme cortical regions of the left female gonad from HH38 until hatching. Moreover, we observed that-in contrast to the current view-medullary germ cells are not apoptotic, but remain arrested in pre-leptotene until hatching. In addition to the systematic analysis of the asymmetric distribution of germ cells in female chicken gonads, we propose an updated model suggesting that the localization of germ cells-in the left or right gonad; in the cortex or medulla of the left gonad; and in the central part or the extremities of the left cortex-has direct consequences for their development and participation in adult reproduction