Structural and Energetic Properties of Amino Acids and Peptides Benchmarked by Accurate Theoretical and Experimental Data.

Structural, energetic, and spectroscopic data derived in this work aim at the setup of an "experimentally validated" database for amino acids and polypeptides conformers. First, the "cheap" composite scheme (ChS, CCSD(T)/(CBS+CV)MP2) is tested for evaluation of conformational energies of all eight stable conformers of glycine, by comparing to the more accurate CCSD(T)/CBS+CV computations (Phys. Chem. Chem. Phys. 2013, 15, 10094-10111 and J Mol. Model. 2020, 26, 129). The recently proposed jun-ChS (J. Chem. Theory and Comput. 2020, 16, 988-1006), employing the jun-cc-pVnZ basis set family for CCSD(T) computations and CBS extrapolation, yields conformational energies accurate to 0.2 kJ·mol-1, at reduced computational cost with respect to aug-ChS employing aug-cc-pVnZ basis sets. The jun-ChS composite scheme is further applied to derive conformational energies for three dipeptide analogues Ac-Gly-NH2, Ac-Ala-NH2, and Gly-Gly. Finally, dipeptide conformational energies and semiexperimental equilibrium rotational constants along with the CCSD(T)/(CBS+CV)MP2 structural parameters (J. Phys. Chem. Lett. 2014, 5, 534-540) stand as the reference for benchmarking of selected density functional methodologies. The double-hybrid functionals B2-PLYP-D3(BJ) and DSD-PBEP86, perform best for structural and energetic characterization of all dipeptide analogues. From hybrid functionals CAM-B3LYP-D3(BJ) and ωB97X-D3(BJ) represent promising methods applicable for larger peptide-based systems for which computations with double-hybrid functionals are not feasible.

Truncating PICK1 Variant Identified in Azoospermia Affected Mitochondrial Dysfunction in Knockout Mice.

OBJECTIVE: The protein interacting with C kinase 1 (PICK1) plays a critical role in vesicle trafficking, and its deficiency in sperm cells results in abnormal vesicle trafficking from Golgi to acrosome, which eventually disrupts acrosome formation and leads to male infertility. METHODS: An azoospermia sample was filtered, and the laboratory detection and clinical phenotype indicated typical azoospermia in the patient. We sequenced all of the exons in the PICK1 gene and found that there was a novel homozygous variant in the PICK1 gene, c.364delA (p.Lys122SerfsX8), and this protein structure truncating variant seriously affected the biological function. Then we constructed a PICK1 knockout mouse model using clustered regularly interspaced short palindromic repeat cutting technology (CRISPRc). RESULTS: The sperm from PICK1 knockout mice showed acrosome and nucleus abnormalities, as well as dysfunctional mitochondrial sheath formation. Both the total sperm and motility sperm counts were decreased in the PICK1 knockout mice compared to wild-type mice. Moreover, the mitochondrial dysfunction was verified in the mice. These defects in the male PICK1 knockout mice may have eventually led to complete infertility. CONCLUSION: The c.364delA novel variant in the PICK1 gene associated with clinical infertility, and pathogenic variants in the PICK1 may cause azoospermia or asthenospermia by impairing mitochondrial function in both mice and humans.

A study of the genus Limnophora Robineau-Desvoidy (Diptera: Muscidae), with descriptions of six new species from China.

This paper provides the characters of genus Limnophora (Diptera: Muscidae) and a key to the Chinese species of Limnophora, six new species collected from Hainan Island of China, namely, L. brevispatula, n. sp., L. cothurnosurstyla, n. sp., L. dyadocerca, n. sp., L. longitarsis, n. sp., L. nuditibia, n. sp. and L. ypocerca, n. sp. are diagnosed, described and illustrated, a new record species in China, namely, L. argentifrons ( Shinonaga et Kano, 1977 ), is also included.

CYP4F2-Catalyzed Metabolism of Arachidonic Acid Promotes Stromal Cell-Mediated Immunosuppression in Non-Small Cell Lung Cancer.

SIGNIFICANCE: The identification of a role for CYP4F2-dependent metabolism in driving immune evasion in non-small cell lung cancer reveals a strategy to improve the efficacy of immunotherapy by inhibiting CYP4F2. See related article by Van Ginderachter, p. 3882.

Thinning or Opening: A Randomized Sibling-Embryo Pilot Trial on the Efficacy of Two Laser-Assisted Hatching Modes During the Extended Culture of Highly Fragmented Cleavage Embryos.

A randomized sibling-embryo pilot trial investigated whether two ways of laser-assisted hatching result in different blastulation and clinical outcomes after extended in vitro culture process of highly fragmented day-3 cleavage embryos. From 92 couples, a total of 315 highly fragmented day-3 embryos (the fragmentation >25%) were recruited and randomized into laser-assisted zona thinning (LAT, n=157) and opening (LAO, n=158) groups, and then underwent a blastocyst culture in vitro. The main endpoint measurements including blastocyst formation and grading as well as the clinical pregnancy after blastocyst transfer were obtained during the treatment procedure of in vitro fertilization and embryo transfer, and then analyzed with generalized estimating equation (GEE) and/or time-to blastocyst analysis models. A total of 166 day-3 embryos developed into blastocyst stage (52.70%), of which 97 were viable blastocysts (30.79%), and 42 top-quality ones (13.33%). LAT did not have any inferior or superior to LAO in the endpoints of either total, viable, top-quality or hatched blastocyst formation, with the ORs (95%CI) from GEE model as 0.89 (0.55-1.45), 0.71 (0.42-1.21), 1.12 (0.56-2.25) and 0.68 (0.42-1.12) respectively for LAT treatment. And the time-to-blastocyst analysis showed a similar result. Additionally, no difference in clinical outcomes after blastocyst transfer was found between the two groups. The author concluded that when applying the LAHs during the extended culture of highly fragmented embryos, both LAT and LAO can generate a promising clinical outcome, and the LAT operation be equivalent to the LAO. Future well-designed, multiple-center, larger-sample investigations are required to ascertain above conclusion.

Toward accurate prediction of amino acid derivatives structure and energetics from DFT: glycine conformers and their interconversions.

This work provides the accurate reference data for structural and energetic properties relevant for computational studies of amino acids and polypeptides. Glycine due to its small size allows for detailed theoretical explorations of its whole conformational space. The reference energies are computed at the CCSD(T)/CBS+CV level on the best estimated geometries of all local minima and the transition states. For the minima, we complete the set of reference structures reported in Phys. Chem. Chem. Phys., 2013, 15, 10094, by determining the CCSD(T)/(CBS+CV)MP2 quality geometries for the two highest energy conformers VIIp/tcc and VIIIn/gtc. These data stand as the reference to asses reliability and accuracy of less expensive computational models, with particular focus on dispersion-corrected hybrid and double-hybrid DFT approaches, considering several basis sets of double- and triple-ζ quality. Based on results for minima the B2LYP-D3(BJ)/aug-cc-pVTZ level is set as the reference for transition states geometries. Considering accuracy of both single point energies and structural parameters B2PLYP(-D3BJ) and DSDPBEP86 in conjunction with aug-cc-pVTZ basis set can be recommended for reference studies of amino-acids and small poly-peptides, while B3LYP(-D3(BJ)) shown to be the most robust from considered hybrid DFT approaches. Graphical abstract TOC: Benchmarking DFT for amino acid analogues: highly accurate characterization of energies and structures from full glycine conformational space.

Role of SPECT/CT in diagnosis of hepatic hemangiomas.

AIM: To investigate the role of SPECT/CT in the diagnosis of hepatic hemangiomas whose anatomical positions are not ideal, situated adjacent to the heart, the inferior cava, hepatic vessels or abdominal aorta, etc. METHODS: The hepatic perfusion, blood pool, and fusion imaging were carried out using SPECT/CT in 54 patients, who were suspected for hepatic hemangiomas. When the anatomical positions were not ideal, the diagnosis was difficult by SPECT only. So the information of computed tomography (CT) was applied to help in diagnosing. The results were recorded as hemangiomas or not. RESULTS: Of the 54 patients, 31 patients were diagnosed as suffering from hepatic hemangiomas. The anatomical positions of eight patients' hepatic hemangiomas (25.81%) were not ideal. Among these lesions of the eight patients, three patients' hepatic lesions were located near to the abdominal aorta, one to the heart, and four to the inferior cava. In addition, six abnormal radioactivity accumulation regions, adjacent to the heart and inferior cava, with the help of CT, were confirmed to be the imaging of inferior cava other than hepatic hemangiomas. CONCLUSION: When the anatomical positions of hepatic hemangiomas are not good enough for diagnosis, the fusion imaging of SPECT/CT is a simple and efficient method for differential diagnosis.

Expression of Shelterin component POT1 is associated with decreased telomere length and immunity condition in humans with severe aplastic anemia.

Abnormal telomere attrition has been found to be closely related to patients with SAA in recent years. To identify the incidence of telomere attrition in SAA patients and investigate the relationship of telomere length with clinical parameters, SAA patients (n=27) and healthy controls (n=15) were enrolled in this study. Telomere length of PWBCs was significantly shorter in SAA patients than in controls. Analysis of gene expression of Shelterin complex revealed markedly low levels of POT1 expression in SAA groups relative to controls. No differences in the gene expression of the other Shelterin components-TRF1, TRF2, TIN2, TPP1, and RAP1-were identified. Addition of IFN-γ to culture media induced a similar fall in POT1 expression in bone marrow cells to that observed in cells cultured in the presence of SAA serum, suggesting IFN-γ is the agent responsible for this effect of SAA serum. Furthermore, ATR, phosphorylated ATR, and phosphorylated ATM/ATR substrate were all found similarly increased in bone marrow cells exposed to SAA serum, TNF-α, or IFN-γ. In summary, SAA patients have short telomeres and decreased POT1 expression. TNF-α and IFN-γ are found at high concentrations in SAA patients and may be the effectors that trigger apoptosis through POT1 and ATR.