The effect of oak tannin (Quercus robur) and hops (Humulus lupulus) on dietary nitrogen efficiency, methane emission, and milk fatty acid composition of dairy cows fed a low-protein diet including linseed.

The objective of this study was to test the effects of inclusion of hop pellets (HP) and oak tannin extracts (OT) alone or in combination on N efficiency, methane (CH4) emission, and milk production and composition in 2 experiments with dairy cows fed low-N rations supplemented with linseed. In both experiments, 6 lactating Holstein cows were assigned to 3 dietary treatments in a 3 × 3 duplicated Latin square design (21-d periods). Cows were fed a total mixed ration at a restricted level to meet their nutrient requirements. In experiment 1, 169 g dry matter (DM) of OT or 56 g DM of HP was included separately in the control diet (C1). In experiment 2, the additives were included together (OT-HP) in the control diet (C2) similar to C1. Diet C2 was compared with a control without linseed (C0). In experiment 1, the supplementation of the control diet with OT decreased urinary N excretion by 12%. In experiment 2, the combination of OT and HP decreased urinary N by 7%. Oak tannin extracts and HP alone or in combination did not influence the daily enteric CH4 production of cows. Cows fed diet C0 produced 17% more enteric CH4 daily than those fed diet C2. Intake of diet C2, which contained 6.7% extruded linseed on a DM basis (experiment 2), decreased the sum of 6:0 to 14:0 fatty acids (-16%) and palmitic acid (-26%) and increased the stearic acid (+50%), oleic acid (+36%), vaccenic acid (trans-11 18:1; +285%), rumenic acid (cis-9,trans-11 18:2; +235%), and α-linolenic acid (+100%) in milk fat. The supplementation of diet C2 with the OT-HP mixture further improved the milk's fatty acid composition. Intake of the OT alone increased α-linolenic acid by 17.7% (experiment 1). The results of this study show that at the economically acceptable dose we tested, hops had no effect on urinary N excretion, CH4 emission, milk production, and milk composition. By contrast, supplementation of diets with oak tannin extract can be considered for reducing urinary N excretion. The combination of oak tannin and hops had no more effect than oak tannin alone except on the milk fatty acid profile, which was favorably influenced from a nutritional point of view.

Efficacy of Lemon Myrtle Essential Oil as a Bio-Fungicide in Inhibiting Citrus Green Mould.

The effectiveness of lemon myrtle (LM) (Backhousia citriodora) essential oil (EO) was investigated to combat Penicillium digitatum by in vitro agar diffusion and vapour assay and in artificially infected oranges. The main constituent of LM EO was revealed as citral when analysed in gas chromatography-mass spectrometry. Pure citral was also included in the experiment for comparison. The in vitro fungal growth was significantly inhibited by LM EO at 1, 2, 3, 4 and 5 µL per disc while complete growth inhibition by both the pure citral and LM EO occurred at 4 and 5 µL per disc. Inoculated fruits treated by dipping in 1000 µL L-1 LM EO solutions for 5, 10, 15, 30 and 120 s showed significantly lower fungal wounds compared to control. While longer dipping times led to some rind injuries, fruits with a 5 and 10 s dip were found free from any injury. The evaluation after dipping and storage confirmed that the fruits maintained the sensory attributes and were not compromised by the incorporation of the essential oil. The results of this study indicate that LM EO can be a promising alternative to synthetic fungicides for preserving the quality of citrus fruits during storage.

Quality Control Procedures for Genome-Wide Association Studies.

Genome-wide association studies (GWAS) are being conducted at an unprecedented rate in population-based cohorts and have increased our understanding of the pathophysiology of many complex diseases. Regardless of the context, the practical utility of this information ultimately depends upon the quality of the data used for statistical analyses. Quality control (QC) procedures for GWAS are constantly evolving. Here, we enumerate some of the challenges in QC of genotyped GWAS data and describe the approaches involving genotype imputation of a sample dataset along with post-imputation quality assurance, thereby minimizing potential bias and error in GWAS results. We discuss common issues associated with QC of the GWAS data (genotyped and imputed), including data file formats, software packages for data manipulation and analysis, sex chromosome anomalies, sample identity, sample relatedness, population substructure, batch effects, and marker quality. We provide detailed guidelines along with a sample dataset to suggest current best practices and discuss areas of ongoing and future research. © 2022 Wiley Periodicals LLC.

Temperature-induced switch to the pathogenic yeast form of Histoplasma capsulatum requires Ryp1, a conserved transcriptional regulator.

Histoplasma capsulatum, a fungal pathogen of humans, switches from a filamentous spore-forming mold in the soil to a pathogenic budding-yeast form in the human host. This morphologic switch, which is exhibited by H. capsulatum and a group of evolutionarily related fungal pathogens, is regulated by temperature. Using insertional mutagenesis, we identified a gene, RYP1 (required for yeast phase growth), which is required for yeast-form growth at 37 degrees C. ryp1 mutants are constitutively filamentous irrespective of temperature. Ryp1 is a member of a family of fungal proteins that includes Wor1, a master transcriptional regulator of the white-opaque transition required for mating in Candida albicans. Ryp1 associates with its own upstream regulatory region, consistent with a direct role in transcriptional control, and both the protein and its transcript accumulate to high levels in wild-type yeast-phase cells. Microarray analysis demonstrated that Ryp1 is required for the expression of the vast majority of yeast-specific genes, including two genes linked to virulence. Thus, Ryp1 appears to be a critical transcriptional regulator of a temperature-regulated morphologic switch in H. capsulatum.

Effectiveness of extruded rapeseed associated with an alfalfa protein concentrate in enhancing the bovine milk fatty acid composition.

Linseed and rapeseed, good sources of 18:3 n-3 and cis9-18:1, respectively, have been shown to improve the bovine milk fatty acid (FA) profile. However, rapeseed, unlike linseed, has little effect on the concentration of 18:3 n-3 in milk fat. Alfalfa protein concentrate (APC), besides being a valuable protein source for milk production, contains lipids rich in 18:3 n-3. Therefore, this experiment aimed at (1) evaluating the transfer efficiency of unsaturated FA (UFA), especially 18:3 n-3, of APC to bovine milk fat, and (2) evaluating whether extruded rapeseed (ER) associated with APC is as effective as extruded linseed (EL) in enhancing the bovine milk fat composition. Six lactating Holstein cows were used in a replicated 2 × 2 Latin square design with 2 iso-energy, iso-nitrogen and iso-FA corn silage-based diets (EL and ER-APC) and two 21-d periods. Extruded linseed, as main UFA source, was included in the first diet, whereas ER, as main UFA source, and APC, as supplemental 18:3 n-3, were included in the second diet. Diets were distributed as a restricted total mixed ration. Compared with the EL diet, the ER-APC diet, where ER was associated with APC, increased milk concentration of 18:3 n-3 (1.18 vs. 1.31% of FA) and cis9-18:1 (18.35 vs. 20.01% of FA). The apparent transfer efficiency of 18:3 n-3 from diet to milk was almost twice as much for the ER-APC diet than for the EL diet (7.4 vs. 3.8% of intake). Extruded linseed accounted for 84% of 18:3 n-3 provided in the EL diet, whereas ER and APC accounted for 33 and 38% of 18:3 n-3 provided in the ER-APC diet, respectively. Because both EL and ER underwent extrusion in similar conditions, these results suggest that 18:3 n-3 of EL in the EL diet and ER in the ER-APC diet were subjected to more extensive ruminal biohydrogenation than 18:3 n-3 of APC in the ER-APC diet. This experiment shows that corn silage-based diets supplemented with ER as the main UFA source, associated with APC as supplemental 18:3 n-3, are as effective as corn silage-based diets supplemented with EL as the main UFA source, in increasing bovine milk UFA and 18:3 n-3 contents. Furthermore, at similar levels of dietary incorporation, this experiment shows that the ruminal bypass of 18:3 n-3 is higher for APC compared with EL.

Dissociable neural correlates of uncertainty underlie different exploration strategies.

Most real-world decisions involve a delicate balance between exploring unfamiliar alternatives and committing to the best known option. Previous work has shown that humans rely on different forms of uncertainty to negotiate this "explore-exploit" trade-off, yet the neural basis of the underlying computations remains unclear. Using fMRI (n = 31), we find that relative uncertainty is represented in right rostrolateral prefrontal cortex and drives directed exploration, while total uncertainty is represented in right dorsolateral prefrontal cortex and drives random exploration. The decision value signal combining relative and total uncertainty to compute choice is reflected in motor cortex activity. The variance of this signal scales with total uncertainty, consistent with a sampling mechanism for random exploration. Overall, these results are consistent with a hybrid computational architecture in which different uncertainty computations are performed separately and then combined by downstream decision circuits to compute choice.

Protein Molecular Dynamics Simulations with Approximate QM: What Can We Learn?

Classical force fields are essential for computer simulations of proteins and are typically parameterized to reproduce secondary and tertiary structure of isolated proteins. However, while protein-protein interactions are ubiquitous in nature, they are not considered in parameterization efforts and are far less understood than isolated proteins. A better characterization of intermolecular interactions is widely recognized as a key to revolutionizing drug and therapeutic developments with high-throughput computational screening. Urgently needed is a critical assessment of the performance of modern protein force fields against first-principles electronic structure methods and experiments. In a daring step toward this goal, we here describe a comparison of peptide folding dynamics as predicted by a molecular mechanics force field on the one hand and by an approximate electronic structure quantum mechanical (QM) method based on density-functional tight-binding (DFTB) on the other. We further compare the dynamics from straightforward DFTB simulations with a near-linear scaling version of DFTB for massively parallel computation based on the fragment molecular orbital (FMO-DFTB) method. We illustrate differences between the phenomenology of the folding dynamics from these three methods for a small model peptide, as well as charge polarization and dynamic fluctuations, point out possible correlations and implications for force field developers, and discuss the lessons learned that might become applicable to future predictive high-throughput computer screening for personalized neoantigen cancer therapy.

A new strain group of common carp: The genetic differences and admixture events between Cyprinus carpio breeds.

Common carp (Cyprinus carpio) has an outstanding economic importance in freshwater aquaculture due to its high adaptive capacity to both food and environment. In fact, it is the third most farmed fish species worldwide according to the Food and Agriculture Organization. More than four million tons of common carp are produced annually in aquaculture, and more than a hundred thousand tons are caught from the wild. Historically, the common carp was also the first fish species to be domesticated in ancient China, and now, there is a huge variety of domestic carp strains worldwide. In the present study, we used double digestion restriction site-associated DNA sequencing to genotype several European common carp strains and showed that they are divided into two distinct groups. One of them includes central European common carp strains as well as Ponto-Caspian wild common carp populations, whereas the other group contains several common carp strains that originated in the Soviet Union, mostly as cold-resistant strains. We believe that breeding with wild Amur carp and subsequent selection of the hybrids for resistance to adverse environmental conditions was the attribute of the second group. We assessed the contribution of wild Amur carp inheritance to the common carp strains and discovered discriminating genes, which differed in allele frequencies between groups. Taken together, our results improve our current understanding of the genetic variability of common carp, namely the structure of natural and artificial carp populations, and the contribution of wild carp traits to domestic strains.

CDK phosphorylation of a novel NLS-NES module distributed between two subunits of the Mcm2-7 complex prevents chromosomal rereplication.

Cyclin-dependent kinases (CDKs) use multiple mechanisms to block reassembly of prereplicative complexes (pre-RCs) at replication origins to prevent inappropriate rereplication. In Saccharomyces cerevisiae, one of these mechanisms promotes the net nuclear export of a pre-RC component, the Mcm2-7 complex, during S, G2, and M phases. Here we identify two partial nuclear localization signals (NLSs) on Mcm2 and Mcm3 that are each necessary, but not sufficient, for nuclear localization of the Mcm2-7 complex. When brought together in cis, however, the two partial signals constitute a potent NLS, sufficient for robust nuclear localization when fused to an otherwise cytoplasmic protein. We also identify a Crm1-dependent nuclear export signal (NES) adjacent to the Mcm3 NLS. Remarkably, the Mcm2-Mcm3 NLS and the Mcm3 NES are sufficient to form a transport module that recapitulates the cell cycle-regulated localization of the entire Mcm2-7 complex. Moreover, we show that CDK regulation promotes net export by phosphorylation of the Mcm3 portion of this module and that nuclear export of the Mcm2-7 complex is sufficient to disrupt replication initiation. We speculate that the distribution of partial transport signals among distinct subunits of a complex may enhance the specificity of protein localization and raises the possibility that previously undetected distributed transport signals are used by other multiprotein complexes.

1,25-Dihydroxyvitamin D3 and its analogues inhibit acute myelogenous leukemia progenitor proliferation by suppressing interleukin-1beta production.

We hypothesized that 1,25-dihydroxyvitamin D3 (1,25D3) and its analogues may inhibit acute myelogenous leukemia (AML) proliferation by interrupting IL-1beta-mediated growth-stimulatory signals. The incubation of the IL-1beta- responsive AML cell line OCIM2 with 10 nM 1,25D3 reduced growth 80% in liquid culture, and a 100-1000-fold lower concentration of 20-epi analogues (MC1288 and MC1301) was sufficient to achieve similar growth inhibition. The growth inhibition was associated with a rapid but transient downregulation of IL-1beta and IL-1beta-converting enzyme (ICE) mRNAs in 1,25D3- and 20-epi analogue- treated cells, and the 20-epi analogue was more effective than 1,25D3 in repressing ICE expression. An examination of long-term changes in the levels of mature IL-1beta and its precursor revealed that 24-h incubation of OCIM2 with either 1,25D3 or its 20-epi analogues abolished the production of mature IL-1beta. The effect of 1,25D3 and its analogues on growth of fresh bone marrow cells from seven AML patients was tested by a clonogenic assay. Growth inhibition of 60% was reached in only one of seven 1,25D3-treated samples, but all seven samples were inhibited 60-90% by the 20-epi analogue MC1301. Growth inhibition by 1,25D3 and the analogue was reversible by addition of IL-1beta. These results suggest that 1,25D3 and its 20-epi analogues interrupt IL-1beta autocrine growth regulation by inhibiting IL-1beta production and processing but not the response to IL-1beta.

Targeting psychologic stress signaling pathways in Alzheimer's disease.

Alzheimer's Disease (AD) is the most prevalent progressive neurodegenerative disease; to date, no AD therapy has proven effective in delaying or preventing the disease course. In the search for novel therapeutic targets in AD, it has been shown that increased chronic psychologic stress is associated with AD risk. Subsequently, biologic pathways underlying psychologic stress have been identified and shown to be able to exacerbate AD relevant pathologies. In this review, we summarize the literature relevant to the association between psychologic stress and AD, focusing on studies investigating the effects of stress paradigms on transgenic mouse models of Amyloid-ß (Aß) and tau pathologies. In recent years, a substantial amount of research has been done investigating a key stress-response mediator, corticotropin-releasing hormone (CRH), and its interactions with AD relevant processes. We highlight attempts to target the CRH signaling pathway as a therapeutic intervention in these transgenic mouse models and discuss how targeting this pathway is a promising avenue for further investigation.

Analysis of the Expression of Repetitive DNA Elements in Osteosarcoma.

Osteosarcoma (OS) is a rare malignant bone tumor. It affects mostly young persons and has poor outcome with the present treatment. No improvement was observed since the introduction of chemotherapy. The better understanding of osteosarcoma development could indicate better management strategy. Repetitive DNA elements were found to play a role in cancer mechanism especially in epithelial tumors but not yet analyzed in osteosarcoma. We conducted the study to analyse the expression profile of repetitive elements (RE) in osteosarcoma. Methods: Fresh bone paired (tumor and normal bone) samples were obtained from excised parts of tumors of 18 patients with osteosarcoma. We performed sequencing of RNA extracted from 36 samples (18 tumor tissues and 18 normal bone for controls), mapped raw reads to the human genome and identified the REs. EdgeR package was used to analyse the difference in expression of REs between osteosarcoma and normal bone. Results: 82 REs were found differentially expressed (FDR < 0.05) between osteosarcoma and normal bone. Out of all significantly changed REs, 35 were upregulated and 47 were downregulated. HERVs (THE1C-int, LTR5, MER57F and MER87B) and satellite elements (HSATII, ALR-alpha) were the most significantly differential expressed elements between osteosarcoma and normal tissues. These results suggest significant impact of REs in the osteosarcoma. The role of REs should be further studied to understand the mechanism they have in the genesis of osteosarcoma.

Biosynthesis of tetrahydrobiopterin: a sensitive assay of 6-pyruvoyltetrahydropterin synthase using [2'-3H]dihydroneopterin 3'-triphosphate as substrate.

Pyruvoyltetrahydropterin synthase catalyzes the release of tritiated water from [2'-3H]dihydroneopterin 3'-triphosphate. The tritiated water formed during the enzymatic reaction is separated from substrate by adsorption of the latter to activated charcoal. The sensitivity and specificity of the assay allows the determination of the enzyme in crude cell extract.

Caspase 2 and caspase 3 as predictors of complete remission and survival in adults with acute lymphoblastic leukemia.

Dysregulation of apoptosis is an important mechanism in leukemogenesis. Caspases are cysteine proteases that play a major role in the activation of apoptotic pathways and chemotherapy-induced cell death. High levels of inactive, uncleaved caspase 2 and caspase 3 have recently been associated with poor survival in patients with acute myelogenous leukemia. We hypothesized a similarly significant role for caspase 2 and caspase 3 in patients with acute lymphoblastic leukemia. We determined levels of uncleaved caspase 2 and caspase 3 by quantitative Western blot analysis in peripheral blood samples of 45 adults with newly diagnosed ALL. We evaluated patient prognostic variables and caspase levels using multivariate logistic and Cox regression models to determine their impact on complete remission rate and overall survival probability. Levels of caspase 2 and, to a lesser degree, caspase 3 were highly associated with cytogenetic abnormalities, with lower levels in the diploid group (P = 0.016 and P = 0.10, respectively). No association between either caspase level and the percentage of bone marrow blasts was found. A high level of caspase 3 (>0.37 as determined graphically) was significantly associated with achieving complete remission (CR; P = 0.006). A multivariate logistic regression analysis including age, WBC count, percentage of peripheral and marrow blasts, hemoglobin, albumin, lactate dehydrogenase, bilirubin, and creatinine determined that a high level of caspase 3 was the most significant predictor of CR (P = 0.025, adjusted), with albumin the only other significant variable (P = 0.031). Caspase 2 levels were not associated with probability of CR. In a multivariate Cox model for survival, however, levels of caspase 2 above 0.37 were associated with a lower survival probability than were levels below that threshold (P = 0.064). High levels of caspase 3 may have a significant effect on achieving CR. Because of the limited power (n = 45) of our study, the significance of caspase 2 and caspase 3 on overall survival remains to be validated by further investigations.

Z-138: a new mature B-cell acute lymphoblastic leukemia cell line from a patient with transformed chronic lymphocytic leukemia.

We describe a new mature B-cell acute lymphoblastic leukemia (ALL) cell line designated Z-138 that was derived from a patient with chronic lymphocytic leukemia (CLL) whose disease underwent transformation to a rare, aggressive form of mature B-cell ALL. This cell line has an L3 morphology, ultrastructural characteristics of lymphoblasts, B-lineage surface markers and an immunoglobulin heavy-chain gene rearrangement identical to the rearrangement observed in the patient's blasts from whom the cell line was derived. Z-138 cells produce granulocyte-macrophage colony-stimulating factor (GM-CSF) and high levels of granulocyte-CSF (G-CSF), but they do not exhibit a proliferative response to either cytokine. Both the patient's lymphoblasts and Z-138 cells exhibited cytogenetic abnormalities including t(8;14), t(14;18) and a chromosome 11 abnormality similar to the t(11;14) of the parental cells, resulting in marked overexpression of cyclin D1 (BCL-1 (PRAD1)) mRNA in Z-138 cells. Since these karyotypic anomalies have been associated with low grade (t(14;18)), intermediate grade (t(11;14)) and high grade (t(8;14)) lymphomas, their development may be involved in the unusual aggressive transformation of this patient's CLL.

Thrombopoietin stimulates myelodysplastic syndrome granulocyte-macrophage and erythroid progenitor proliferation.

Thrombopoietin (TPO) has been successfully used to stimulate megakaryocyte progenitor proliferation and platelet production both in vitro and in vivo. We and other investigators have found that TPO also stimulates normal marrow colony-forming unit granulocyte-macrophage (CFU-GM) and burst-forming unit-erythroid (BFU-E) growth. In contrast to its effect on normal marrow precursors, TPO stimulates acute myelogenous leukemia (AML) progenitor proliferation in only 25% of the cases. Because the hematopoietic cells in Myelodysplastic syndrome (MDS) originate from both the normal and leukemic clones, we hypothesized that TPO may be a useful therapeutic agent for MDS. To test this hypothesis, we used fresh marrow samples taken from 14 MDS patients. We found that in the presence of fetal calf serum (FCS) and erythropoietin (EPO) TPO (5 to 40 ng/ml) MDS CFU-GM and BFU-E colony-forming cell proliferation were stimulated in a dose-dependent fashion by up to 103% and 93% respectively. This effect was similar to the stimulation obtained with optimal concentrations of granulocyte colony-stimulating factor (G-CSF), granulocyte-macrophage CSF (GM-CSF), or interleukin-3 (IL-3). Furthermore, TPO increased the colony-stimulatory effects of G-CSF, GM-CSF, IL-3, and stem cell factor (SCF) on MDS marrow cells. However, depletion of either T lymphocytes or adherent cells abrogated the effect of TPO, suggesting that the effect is not a direct one but is mediated through interaction with cytokines produced by accessory cells. Taken together, our data suggest that the therapeutic role of TPO in the management of MDS warrants further investigation.

Improved cross peak detection in two-dimensional proton NMR spectra using excitation sculpting.

In two-dimensional homonuclear experiments, reliable detection of very small cross peaks is sometimes hampered by t1-noise from larger diagonal peaks which have the same F2 frequency. This t1-noise can be selectively removed by recording partial 2D spectra using the double pulsed field gradient spin echo (DPFGSE). Resonances not selected by the DPFGSE do not contribute any t1-noise to the resulting spectrum. The absence of t1-noise from the diagonal peaks render the small cross peaks at the same F2 frequency observable. The success of this technique is shown by partial 2D NOESY and TOCSY spectra.

Observation of long-range small-molecule NOEs using a neoteric sensitivity enhancement scheme.

A new method to increase the sensitivity of the 1D transient NOE experiment for molecules in the positive NOE regime is presented. This method, the reverse NOE, simply replaces the conventional relaxation delay between scans. Transient positive NOE enhancements from all other spins are used to accelerate the recovery of the target resonance toward its equilibrium intensity. In favorable cases, the intensity of the target peak at the start of an experiment can actually be increased beyond its equilibrium value. There is also a sensitivity enhancement in the rapid pulsing regime, where recovery is always incomplete. This sensitivity enhancement is illustrated with the one-dimensional double pulsed field gradient spin echo NOE experiment to observe a "fourth-order" NOE. Sensitivity gains of 30% are demonstrated.

Reference deconvolution, phase correction, and line listing of NMR spectra by the 1D filter diagonalization method.

We describe a new way to attack the problem of identifying and quantifying the number of NMR transitions in a given NMR spectrum. The goal is to reduce the spectrum to a tabular line list of peak positions, widths, amplitudes, and phases, and to have this line list be of high fidelity. In this context "high fidelity" means that each true NMR transition is represented by a single entry, with no spurious entries and no missed peaks. A high fidelity line list allows the measurement of chemical shifts and coupling constants with good accuracy and precision and is the ultimate in data compression. There are two parts to the problem. The first is to overcome common imperfections: the non-Lorentzian lineshapes that can arise whenever the magnetic field inhomogeneity is less than perfect, and nonzero time delays that cause frequency-dependent phase errors. The second is to fit the spectral features to a model of Lorentzian lines. We use the recently developed filter diagonalization method (FDM) to accomplish the reference deconvolution, the phase correction, and the fitting, and show good progress toward the goal of obtaining a high fidelity line list.