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Motivation: The inference of cellular compositions from bulk and spatial transcriptomics data increasingly complements data analyses. Multiple computational approaches were suggested and recently, machine learning techniques were developed to systematically improve estimates. Such approaches allow to infer additional, less abundant cell types. However, they rely on training data which do not capture the full biological diversity encountered in transcriptomics analyses; data can contain cellular contributions not seen in the training data and as such, analyses can be biased or blurred. Thus, computational approaches have to deal with unknown, hidden contributions. Moreover, most methods are based on cellular archetypes which serve as a reference; e.g. a generic T-cell profile is used to infer the proportion of T-cells. It is well known that cells adapt their molecular phenotype to the environment and that pre-specified cell archetypes can distort the inference of cellular compositions., Results: We propose Adaptive Digital Tissue Deconvolution (ADTD) to estimate cellular proportions of pre-selected cell types together with possibly unknown and hidden background contributions. Moreover, ADTD adapts prototypic reference profiles to the molecular environment of the cells, which further resolves cell-type specific gene regulation from bulk transcriptomics data. We verify this in simulation studies and demonstrate that ADTD improves existing approaches in estimating cellular compositions. In an application to bulk transcriptomics data from breast cancer patients, we demonstrate that ADTD provides insights into cell-type specific molecular differences between breast cancer subtypes., Availability and Implementation: A python implementation of ADTD and a tutorial are available at Gitlab and zenodo (doi:10.5281/zenodo.7548362)., (© The Author(s) 2024. Published by Oxford University Press.)

Fresh boar sperm were incubated with small unilamellar liposomes composed of either the total lipids extracted from head plasma membranes (HPM) of fresh boar sperm or selected lipids (SL) of five defined phospholipids with specific acyl chains. To optimize fusion, liposomes with 2 mol% octadecyl rhodamine fluorophore in Beltsville Thawing Solution +/- 1 mM CaCl(2) were incubated at 35 degrees C with 1;ts 10(7) or 10(8) spermatozoa/ml and monitored over 60 min, using flow cytometry and fluorescence microscopy. The HPM fused to both sperm concentrations faster than SL but was equivalent by 30 min (10(8) sperm/ml) or 60 min (10(7) sperm/ml; 57.5 +/- 3% and 67.1 +/- 8% sperm fused to HPM and SL, respectively) +/- Ca(2+). Neither HPM nor SL affected onset of capacitation or spontaneous or ionophore-induced acrosome reactions at 0 or 3 h (chlortetracycline and fluorescein isothiocyanate-Pisum sativum agglutinin; n = 3). During cooling and after cryopreservation (n = 4 ejaculates), SL but not HPM significantly improved sperm motility and viability (Sybr14/propidium iodide staining) +/- 20% egg yolk, but egg yolk alone was more effective than SL alone. Liposomes of complex composition can fuse to boar sperm without harming in vitro capacitation or acrosome reaction and reduce sperm chilling sensitivity.

Wide angle x-ray diffraction and fluorescence polarization were used to determine the structural properties of membranes from rat luteal cells. Examination of a plasma membrane fraction by x-ray diffraction revealed a significant increase in the gel phase melting temperature during luteal regression. The membrane fluidity of this fraction as well as that of a preparation of microsomes was also studied by fluorescence polarization. Using a fluorescent probe, membrane fluidity was observed to decrease during luteolysis. The temporal correlation between structural changes in the membrane and decreased progesterone secretion suggests that alterations in the physical properties of cellular membranes may be involved in the process of luteal cell regression.

Wide angle x-ray diffraction has been used to examine the phase behavior of microsomal membranes from regressing corpora lutea of prepubertal pseudopregnant rats. During periods of optimal progesterone secretion, all of the membrane lipid was in the liquid-crystalline phase at physiological temperature and, therefore, was fluid. However, mixtures of liquid-crystalline and gel phase lipid were observed under identical conditions in microsomal membrane preparations from animals undergoing spontaneous or prostaglandin F2 alpha-induced regression. This was accompanied by a parallel rise in the lipid phase transition temperature. In addition, the proportion of lipid in the gel phase increased with time after prostaglandin F2 alpha treatment. These results indicate that the mechanism of corpus luteum regression may involve phase changes in the phospholipid bilayer of cellular membranes. The resulting presence of gel phase lipid in the membrane matrices could contribute to the loss of tissue function.

Microsomal membranes prepared from bovine corpora lutea (CL) were examined by wide angle x-ray diffraction to determine if there were structural changes in the cellular membranes during regression. In samples prepared from CL removed at midcycle, all of the membrane lipid was in the liquid crystalline phase at body temperature. However, examination of microsomes prepared from regressing luteal tissue revealed a phase transition in which a portion of the lipid bilayer was in a gel phase at body temperature. Coincident with this physical change was a decline in CL function. These results indicate that there are structural changes that occur at the submicroscopic level in cellular membranes during luteal regression, which appear to be related to the loss in cellular function.

Wide angle x-ray diffraction has revealed that during corpus luteum regression there is a liquid-crystalline to gel phase transition in the phospholipid molecules of the cellular membranes. In the present study we have examined the lipid composition of these membranes and looked for evidence of membrane protein involvement in this change. Lipid analysis of smooth microsomal membranes prepared from rat corpora lutea revealed no significant change in the cholesterol to phospholipid ratio or in the ratio of unsaturated to saturated fatty acids with advancing luteolysis. In addition, there was no clear trend for these changes in the relative proportions of the major fatty acids. Liposomes were prepared from smooth microsomal fractions of regressing rat corpora lutea, and examination of these lipid vesicles by x-ray diffraction revealed that the temperature of the liquid-crystalline to gel phase transition was much lower (approximately 25-30 C) than that for the corresponding microsomes. These observations are consistent with the view that membrane proteins contribute to the ordering of lipid that results in a mixture of liquid-crystalline and gel phases in membranes from regressed corpora lutea.

The role of plasma lipoproteins and hypophyseal hormones in the maintenance of progesterone secretion by the rat corpus luteum was investigated. In the first experiment, rats were treated daily from days 1-6 of pregnancy with 5 mg/kg 4-aminopyrozolopyramidine (4APP), a blocker of hepatic lipoprotein secretion, or with 5 mg/kg 4APP and 1 or 2 mg ovine PRL or 0.1 ml 0.5% phosphoric acid (4APP vehicle). The administration of 4APP reduced serum cholesterol and progesterone levels on days 2-6 of pregnancy and ovarian progesterone on day 6. The reduced progesterone secretion had no effect on embryo implantation. PRL, in the doses used, was incapable of abrogating the effects of 4APP on circulating or ovarian progesterone levels. Ovaries and adrenals, but not kidneys, of pseudopregnant rats exhibited specific and saturable uptake of porcine high density lipoprotein (HDL). Time-course studies indicated that the uptake of HDL was rapid in ovaries compared to that in adrenals. Ovaries from rats not only exhibited uptake of porcine HDL, but also were capable of using it for progesterone synthesis. Immature rats were assigned to 7 groups of 16 rats each; 8 rats from each group received 4 mg/kg 4APP, and 8 received 4APP vehicle from day 1 of pseudopregnancy. Four groups underwent hypophysectomy on day 1 and received one of the following: 0.1 mg (30 IU/mg) ovine PRL, 0.1 mg ovine LH or 0.1 mg synthetic ACTH daily, or no replacement therapy. Three sham-hypophysectomized groups received 0.1 mg PRL or LH twice daily or no hormone treatment. On day 5 of pseudopregnancy, rats received intravascular HDL, as described above, and were killed 1 h later. Treatment with 4APP increased the adrenal uptake of HDL, but ovarian uptake was not different from that in the control group. Hypophysectomy reduced both adrenal and ovarian uptake of HDL. In adrenals only ACTH at the dose employed ameliorated reduction of HDL uptake induced by hypophysectomy, while in the ovaries, both PRL and LH reversed the effect of hypophysectomy. The effect of PRL on uptake was specific to [125I]HDL and did not alter [125I]albumin uptake. It is concluded that: 1) hypophysectomy reduces HDL uptake in the luteinized rat ovary; and 2) PRL and LH replacement therapy maintain ovarian uptake of HDL, suggesting a direct effect of these luteotropins on lipoprotein uptake.