Identification of messenger RNA for human type II collagen

The fluorescence polarization of acridine orange-stained, oriented lambda phages was measured. The parameters of DNA packing within the phage head cos2 theta and cos4 theta were calculated (theta, angle between the direction of a small segment of DNA and the phage axis). It is shown that simple models of lambda phage DNA tertiary structure are not consistent with calculated values. A new model is proposed.     

An amino acid code to define a protein's tertiary packing surface

One difficult aspect of the protein‐folding problem is characterizing the nonspecific interactions that define packing in protein tertiary structure. To better understand tertiary structure, this work extends the knob‐socket model by classifying the interactions of a single knob residue packed into a set of contiguous sockets, or a pocket made up of 4 or more residues. The knob‐socket construct allows for a symbolic two‐dimensional mapping of pockets. The two‐dimensional mapping of pockets provides a simple method to investigate the variety of pocket shapes to understand the geometry of protein tertiary surfaces. The diversity of pocket geometries can be organized into groups of pockets that share a common core, which suggests that some interactions in pockets are ancillary to packing. Further analysis of pocket geometries displays a preferred configuration that is right‐handed in α‐helices and left‐handed in β‐sheets. The amino acid composition of pockets illustrates the importance of nonpolar amino acids in packing as well as position specificity. As expected, all pocket shapes prefer to pack with hydrophobic knobs; however, knobs are not selective for the pockets they pack. Investigating side‐chain rotamer preferences for certain pocket shapes uncovers no strong correlations. These findings allow a simple vocabulary based on knobs and sockets to describe protein tertiary packing that supports improved analysis, design, and prediction of protein structure. Proteins 2016; 84:201–216. © 2015 Wiley Periodicals, Inc.     

Minimizing Venous Thromboembolism in Feminizing Hormone Therapy: Applying Lessons From Cisgender Women and Previous Data

ObjectiveTo review he impact of estrogen-containing feminizing hormone regimens on transgender individuals’ risk for VTE.MethodsWe evaluated VTE risk by screening 1170 relevant studies published from 1994 to 2020, focusing on meta-analysis data.ResultsThe type of oral estrogen, route of administration, patient demographics, and comorbidities may affect the risk of VTE. Venous thrombosis is the most common vascular complication associated with HT.ConclusionConjugated equine estrogens and 17-β estradiol appear to be safer than oral ethinyl estradiol. Transdermal estrogen formulations appear to be the least thrombogenic estrogens. Estrogens used concomitantly with progestins increase the risk of VTE compared to estrogens alone.To date, there are no data to demonstrate the benefit of holding HT prior to vaginoplasty or other gender affirming surgeries. For most young, healthy transgender women, there is little risk of VTE with HT, while older patients with risk factors should be discussed case by case.     

The adenosine wedge: A new structural motif in ribosomal RNA

Here, we present a new recurrent RNA arrangement, the so-called adenosine wedge (A-wedge), which is found in three places of the ribosomal RNA in both ribosomal subunits. The arrangement has a hierarchical structure, consisting of elements previously described as recurrent motifs, namely, the along-groove packing motif, the A-minor and the hook-turn. Within the A-wedge, these elements are involved in different types of cause–effect relationships, providing together for the particular tertiary structure of the motif.     

On the stereochemistry of 2,3-dihydroxy fatty acids. The single crystal structure of potassium d-erythro-2,3-dihydroxyoctadecanoate

The erythro-2,3-dihydroxyoctadecanoic acid studied is a synthetic homologue of a natural occurring constituent of sphingolipids. The potassium salt of the acid crystallizes in the monoclinic space group P2, with the unit cell dimension: $\text{a = 5.39, b = 7.06, c = 26.26}\text{A}\text{?}\text{and}\text{β = 94.9°}$. The crystal structure was solved by direct methods and was refined to R = 0.062. The absolute configuration of the compound was determined by means of anomalous scattering effects, showing that the natural fatty acid has d-erythro configuration. The compound packs tail to tail in an unusual bilayer arrangement. The hydrocarbon chains have an extreme tilt of 60° and opposite inclination in the two halves of the bilayer. Laterally the hydrocarbon chains are arranged according to the monoclinic M∥ packing mode. The carbon chain makes a perpendicular bent at carbon atom 2. This places the 2-hydroxyl group in a preferred co-planar conformation towards the carboxylate group and at hydrogen bond distance to one of the carboxylate oxygens. The carboxylate group and the two hydroxyl groups are co-ordinated to K⁺ ions and together account for a large molecular cross-ection of 38 Ų. Monolayer studies show that the acid forms a phase with this spacious molecular area also in contact with water. On compression above 10 mN m^?1 transition to a more condensed state ($\text{S = 27}\text{A}\text{?}{}^2$) takes place accompanied by marked changes of the surface potential.     

Longhorn beetles and predatory clerid beetles attracted to a blend of longhorn beetle pheromone compounds in a Central European oak forest (Coleoptera: Cerambycidae,Cleridae)

1. A blend of longhorn beetle pheromones was tested as a generic attractant in a Central European oak forest. Overall, 20 cerambycid species totalling 1250 specimens were captured using two trap types.
2. More adults of Phymatodes testaceus and Leiopus nebulosus nebulosus were attracted to pheromone-baited traps compared to solvent controls. Significant numbers of four other species were caught by panel traps but not funnel traps. For the cerambycine Pyrrhidium sanguineum, significantly more beetles were caught in treatment traps than controls. For the cerambycine Anaglyptus mysticus, lepturines Cortodera humeralis and Rhagium sycophanta, the numbers of beetles caught in treatment or control traps were similar, indicating no attraction to the lure blend. Adults of a predatory clerid beetle Clerus mutillarius were caught in significantly larger numbers by both baited trap types in comparison to controls, totalling 1514 specimens.
3. Antennae of both sexes of C. mutillarius showed responses to 3-hydroxyhexan-2-one and 2-methylbutan-1-ol, and males also responded to syn-2,3-hexanediol.
4. Strong attraction of C. mutillarius suggests eavesdropping on the pheromones of cerambycids and that such attractant baits, without traps, might be used to manipulate the local population density of predators in a push-pull biological control program.

     

Life cycle assessment of electrical and thermal energy systems for commercial buildings

Background, Aim and Scope The objective of this life cycle assessment (LCA) study is to develop LCA models for energy systems in order to assess the potential environmental impacts that might result from meeting energy demands in buildings. The scope of the study includes LCA models of the average electricity generation mix in the USA, a natural gas combined cycle (NGCC) power plant, a solid oxide fuel cell (SOFC) cogeneration system; a microturbine (MT) cogeneration system; an internal combustion engine (ICE) cogeneration system; and a gas boiler. Methods LCA is used to model energy systems and obtain the life cycle environmental indicators that might result when these systems are used to generate a unit energy output. The intended use of the LCA analysis is to investigate the operational characteristics of these systems while considering their potential environmental impacts to improve building design using a mixed integer linear programming (MILP) optimization model. Results The environmental impact categories chosen to assess the performance of the energy systems are global warming potential (GWP), acidification potential (AP), tropospheric ozone precursor potential (TOPP), and primary energy consumption (PE). These factors are obtained for the average electricity generation mix, the NGCC, the gas boiler, as well as for the cogeneration systems at different part load operation. The contribution of the major emissions to the emission factors is discussed. Discussion The analysis of the life cycle impact categories indicates that the electrical to thermal energy production ratio has a direct influence on the value of the life cycle PE consumption factors. Energy systems with high electrical to thermal ratios (such as the SOFC cogeneration systems and the NGCC power plant) have low PE consumption factors, whereas those with low electrical to thermal ratios (such as the MT cogeneration system) have high PE consumption factors. In the case of GWP, the values of the life cycle GWP obtained from the energy systems do not only depend on the efficiencies of the systems but also on the origins of emissions contributing to GWP. When evaluating the life cycle AP and TOPP, the types of fuel as well as the combustion characteristics of the energy systems are the main factors that influence the values of AP and TOPP. Conclusions An LCA study is performed to eraluate the life cycle emission factors of energy systems that can be used to meet the energy demand of buildings. Cogeneration systems produce utilizable thermal energy when used to meet a certain electrical demand which can make them an attractive alternative to conventional systems. The life cycle GWP, AP, TOPP and PE consumption factors are obtained for utility systems as well as cogeneration systems at different part load operation levels for the production of one kWh of energy output. Recommendations and Perspectives Although the emission factors vary for the different energy systems, they are not the only factors that influence the selection of the optimal system for building operations. The total efficiencies of the system play a significant part in the selection of the desirable technology. Other factors, such as the demand characteristics of a particular building, influence the selection of energy systems. The emission factors obtained from this LCA study are used as coefficients of decision variables in the formulation of an MILP to optimize the selection of energy systems based on environmental criteria by taking into consideration the system efficiencies, emission characteristics, part load operation, and building energy demands. Therefore, the emission factors should not be regarded as the only criteria for choosing the technology that could result in lower environmental impacts, but rather one of several factors that determine the selection of the optimum energy system. ESS-Submission Editor: Arpad Horvath (horvath@ce.berkeley.edu)     

Synergistic cytotoxicity of perifosine and ABT-737 to colon cancer cells

An acidic environment and hypoxia within the tumour are hallmarks of cancer that contribute to cell resistance to therapy. Deregulation of the PI3K/Akt pathway is common in colon cancer. Numerous Akt-targeted therapies are being developed, the activity of Akt-inhibitors is, however, strongly pH-dependent. Combination therapy thus represents an opportunity to increase their efficacy. In this study, the cytotoxicity of the Akt inhibitor perifosine and the Bcl-2/Bcl-xL inhibitor ABT-737 was tested in colon cancer HT-29 and HCT-116 cells cultured in monolayer or in the form of spheroids. The efficacy of single drugs and their combination was analysed in different tumour-specific environments including acidosis and hypoxia using a series of viability assays. Changes in protein content and distribution were determined by immunoblotting and a “peeling analysis” of immunohistochemical signals. While the cytotoxicity of single agents was influenced by the tumour-specific microenvironment, perifosine and ABT-737 in combination synergistically induced apoptosis in cells cultured in both 2D and 3D independently on pH and oxygen level. Thus, the combined therapy of perifosine and ABT-737 could be considered as a potential treatment strategy for colon cancer.     

Neoadjuvant PD-1 blockade plus chemotherapy versus chemotherapy alone in locally advanced stage II-III gastric cancer: A single-centre retrospective study

BackgroundPD-1 blockade has been shown to have promising efficacy and acceptable safety profiles in advanced and metastatic gastric cancer; however, the efficacy and safety of neoadjuvant PD-1 blockade-based immunotherapy plus chemotherapy in locally advanced gastric cancer (LAGC) remain uncertain.MethodsWe performed a retrospective review of patients with LAGC who received neoadjuvant treatment followed by D2 radical resection at the Affiliated Hospital of Qingdao University from 2019 to 2021. The primary aim was to investigate the difference in pathological response rates between neoadjuvant PD-1 immunotherapy plus chemotherapy and neoadjuvant chemotherapy alone. Multivariable models for pathological complete response (pCR) were constructed to investigate the factors that facilitate pCR. Trial registration: QYFYWZLL27406.ResultsA total of 77 patients were included in the analysis, among whom 34 (44.2%) received neoadjuvant PD-1 blockade immunotherapy plus chemotherapy. A higher pCR rate was observed in the neoadjuvant PD-1 blockade immunotherapy plus chemotherapy group (8 of 34, 23.5% vs. 2 of 43, 4.7%, P=0.019). Multivariate logistic regression analysis of pCR revealed neoadjuvant PD-1 blockade plus chemotherapy regimen promoted pCR (OR 12.95, P=0.016). Regarding safety, 76.5% (26 of 34) of patients in the PD-1 blockade plus chemotherapy group and 76.7% (33 of 43) of patients in the chemotherapy group experienced treatment-related adverse events (TRAEs), and grade 3 or worse adverse events were 29.4% (10 of 34) and 34.9% (15 of 43), respectively.ConclusionNeoadjuvant PD-1 blockade plus chemotherapy induced a higher pCR rate than neoadjuvant chemotherapy, and the combined therapy was tolerable in LAGC patients.     

Optimization of a genome-wide disordered lentivector-based short hairpin RNA library

To obtain a whole genome library that suppresses the total diversity of human mRNAs, lentiviral vector constructs and a short hairpin RNA (shRNA) expression cassette were optimized. The optimization of the vector increased the virus titer in preparations by 15–20 times. A simple shRNA structure with a 21-bp stem proved to be the most effective. Lentivector-based shRNA expression constructs were obtained by using puro ^R, copGFP, or H-2K ^k as a selectable marker. The efficiency of the optimized library was demonstrated when screening for shRNAs reactivating the tumor suppressor p53 in HeLa cells. Cells carried a reporter construct ensuring p53-responsive synthesis of a fluorescent protein, which allowed selection of cells with reactivated p53 by flow cytometry.