Influence of substrate/inoculum ratio, inoculum source and ammonia inhibition on anaerobic digestion of poultry waste.

Poultry wastes are rich in organic matter, allowing their use as substrates for biogas production by anaerobic digestion (AD). The major difficulty in the anaerobic digestion of this protein-rich waste is ammonia inhibition. Different results of biochemical methane potential (BMP) were obtained after the mesophilic anaerobic digestion of different avian waste in batch mode.

Multi-Step Biomass Fractionation of Grape Seeds from Pomace, a Zero-Waste Approach.

Grape seeds are the wineries' main by-products, and their disposal causes ecological and environmental problems. In this study seeds from the pomace waste of autochthonous grape varieties from Lebanon, Obeidi (white variety) and Asswad Karech (red variety) were used for a multi-step biomass fractionation. For the first step, a lipid extraction was performed, and the obtained yield was 12.

Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface.

Following our previous work ( 2021, 12, 4889-4907), we study the structural dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of microsecond adaptive sampling molecular dynamics simulations (50 μs) using the AMOEBA polarizable force field (PFF). This interface is structured by a complex H-bond network that is stable only at physiological pH. Structural correlations analysis between its residues and the catalytic site confirms the presence of a buried allosteric site.

Quantum-Chemistry Based Design of Halobenzene Derivatives With Augmented Affinities for the HIV-1 Viral G/C Base-Pair.

The HIV-1 integrase (IN) is a major target for the design of novel anti-HIV inhibitors. Among these, three inhibitors which embody a halobenzene ring derivative (HR) in their structures are presently used in clinics. High-resolution X-ray crystallography of the complexes of the IN-viral DNA transient complex bound to each of the three inhibitors showed in all cases the HR ring to interact within a confined zone of the viral DNA, limited to the highly conserved 5'CpA 3'/5'TpG 3' step.

Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations.

Using polarizable (AMOEBA) and nonpolarizable (CHARMM) force fields, we compare the relative free energy stability of two extreme conformations of the HIV-1 nucleocapsid protein NCp7 that had been previously experimentally advocated to prevail in solution. Using accelerated sampling techniques, we show that they differ in stability by no more than 0.75-1.

Influence of pretreatment conditions on lignocellulosic fractions and methane production from grape pomace.

The lignocellulosic structure of grape pomace requires the use of pretreatments facilitating microbial decomposition of the matter and enhancing methane production. In this study, the effects of various pretreatments (freezing, alkaline treatment using NaOH and NH, acid treatment using HCl, ultrasounds and pulsed electric fields) were examined in batch mode. The highest methane production (0.

Anaerobic digestion of grape pomace: Effect of the hydraulic retention time on process performance and fibers degradability.

To optimize the anaerobic digestion of grape pomace under mesophilic conditions, continuous digesters were operated at different hydraulic retention times (HRT) (30, 20, 15 and 10 days) equivalent to organic loading rates (OLR) of 2.5, 3.7, 5.

Calibration of 1,2,4-Triazole-3-Thione, an Original Zn-Binding Group of Metallo-β-Lactamase Inhibitors. Validation of a Polarizable MM/MD Potential by Quantum Chemistry.

In the context of the SIBFA polarizable molecular mechanics/dynamics (PMM/PMD) procedure, we report the calibration and a series of validation tests for the 1,2,4-triazole-3-thione (TZT) heterocycle. TZT acts as the chelating group of inhibitors of dizinc metallo-β-lactamases (MBL), an emerging class of Zn-dependent bacterial enzymes, which by cleaving the β-lactam bond of most β-lactam antibiotics are responsible for the acquired resistance of bacteria to these drugs. Such a study is indispensable prior to performing PMD simulations of complexes of TZT-based inhibitors with MBL's, on account of the anchoring role of TZT in the dizinc MBL recognition site.

Importance of explicit smeared lone-pairs in anisotropic polarizable molecular mechanics. Torture track angular tests for exchange-repulsion and charge transfer contributions.

A correct representation of the short-range contributions such as exchange-repulsion (E ) and charge-transfer (E ) is essential for the soundness of separable, anisotropic polarizable molecular mechanics potentials. Within the context of the SIBFA procedure, this is aimed at by explicit representations of lone pairs in their expressions. It is necessary to account for their anisotropic behaviors upon performing not only in-plane, but also out-of-plane, variations of a probe molecule or cation interacting with a target molecule or molecular fragment.

The inhibition process of HIV-1 integrase by diketoacids molecules: Understanding the factors governing the better efficiency of dolutegravir.

The Human Immunodeficiency Virus-1 integrase is responsible for the covalent insertion of a newly synthesized double-stranded viral DNA into the host cells, and is an emerging target for antivirus drug design. Raltegravir (RAL) and elvitegravir (EVG) are the first two integrase strand transfer inhibitors used in therapy. However, treated patients eventually develop detrimental resistance mutations.

A Comparative Study of the Phenolic and Technological Maturities of Red Grapes Grown in Lebanon.

Grape harvest date is determined according to the technological and phenolic maturities. These parameters were calculated for different red grape (Vitis vinifera L.) varieties (Cabernet Sauvignon, Merlot, Syrah, Cabernet Franc) over four years (2008, 2009, 2010, and 2011) (642 samples).

A targeted DNA substrate mechanism for the inhibition of HIV-1 integrase by inhibitors with antiretroviral activity.

We recently reported that viral DNA could be the primary target of raltegravir (RAL), an efficient anti-HIV-1 drug, which acts by inhibiting integrase. To elucidate this mechanism, we conducted a comparative analysis of RAL and TB11, a diketoacid abandoned as an anti-HIV-1 drug for its weak efficiency and marked toxicity, and tested the effects of the catalytic cofactor Mg(2+) (5 mm) on drug-binding properties. We used circular dichroism and fluorescence to determine drug affinities for viral DNA long terminal repeats (LTRs) and peptides derived from the integrase active site and DNA retardation assays to assess drug intercalation into DNA base pairs.

Anaerobic digestion of grape pomace: Biochemical characterization of the fractions and methane production in batch and continuous digesters.

In this study, we have estimated the biogas and methane production from grape pomace (variety Cabernet Franc). The physical and chemical characteristics of the raw material were determined, and the structural polysaccharides were identified and analyzed by the Van Soest method. Batch anaerobic digestions were carried out to assess the methane production of the grape pomace, pulp and seeds.

Could the "Janus-like" properties of the halobenzene CX bond (X=Cl, Br) be leveraged to enhance molecular recognition?

The CX bond in halobenzenes (XCl, Br) exhibits a dual character, being electron-deficient along the CX direction, and electron-rich on its flanks. We sought to amplify both features by resorting to electron-withdrawing and electron-donating substituents, respectively. This was done by quantum chemistry (QC) computations in the recognition sites of three protein targets: farnesyl transferase, coagulation factor Xa, and the HIV-1 integrase.

Effect of the drying process on the intensification of phenolic compounds recovery from grape pomace using accelerated solvent extraction.

In light of their environmental and economic interests, food byproducts have been increasingly exploited and valorized for their richness in dietary fibers and antioxidants. Phenolic compounds are antioxidant bioactive molecules highly present in grape byproducts. Herein, the accelerated solvent extraction (ASE) of phenolic compounds from wet and dried grape pomace, at 45 °C, was conducted and the highest phenolic compounds yield (PCY) for wet (16.

Substituent-modulated affinities of halobenzene derivatives to the HIV-1 integrase recognition site. Analyses of the interaction energies by parallel quantum chemical and polarizable molecular mechanics.

The C-X bond of halobenzenes (X = Cl, Br) has a dual character, its electron density being depleted in its prolongation and built-up on its sides. We have recently considered three protein or nucleic acid recognition sites of halobenzenes and quantified the energy gains that either electron-attracting substituents or electron-donating ones contribute due to such a character (El Hage et al., paper in revision).

Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds?

Halogenated compounds are gaining an increasing importance in medicinal chemistry and materials science. Ab initio quantum chemistry (QC) has unraveled the existence of a "sigma hole" along the C-X (X = F, Cl, Br, I) bond, namely, a depletion of electronic density prolonging the bond, concomitant with a build-up on its sides, both of which are enhanced along the F < Cl < Br < I series. We have evaluated whether these features were intrinsically built-in in an anisotropic, polarizable molecular mechanics (APMM) procedure such as SIBFA (sum of interactions between fragments ab initio computed).

Unprocessed viral DNA could be the primary target of the HIV-1 integrase inhibitor raltegravir.

Integration of HIV DNA into host chromosome requires a 3'-processing (3'-P) and a strand transfer (ST) reactions catalyzed by virus integrase (IN). Raltegravir (RAL), commonly used in AIDS therapy, belongs to the family of IN ST inhibitors (INSTIs) acting on IN-viral DNA complexes (intasomes). However, studies show that RAL fails to bind IN alone, but nothing has been reported on the behaviour of RAL toward free viral DNA.

Specificity of LTR DNA recognition by a peptide mimicking the HIV-1 integrase {alpha}4 helix.

HIV-1 integrase integrates retroviral DNA through 3'-processing and strand transfer reactions in the presence of a divalent cation (Mg(2+) or Mn(2+)). The alpha4 helix exposed at the catalytic core surface is essential to the specific recognition of viral DNA. To define group determinants of recognition, we used a model composed of a peptide analogue of the alpha4 helix, oligonucleotides mimicking processed and unprocessed U5 LTR end and 5 mM Mg(2+).

An unusual helix turn helix motif in the catalytic core of HIV-1 integrase binds viral DNA and LEDGF.

Background: Integrase (IN) of the type 1 human immunodeficiency virus (HIV-1) catalyzes the integration of viral DNA into host cellular DNA. We identified a bi-helix motif (residues 149-186) in the crystal structure of the catalytic core (CC) of the IN-Phe185Lys variant that consists of the alpha(4) and alpha(5) helices connected by a 3 to 5-residue turn. The motif is embedded in a large array of interactions that stabilize the monomer and the dimer.