Differential expression analysis with global network adjustment

<p>Background: Large-scale chromosomal deletions or other non-specific perturbations of the transcriptome can alter the expression of hundreds or thousands of genes, and it is of biological interest to understand which genes are most profoundly affected. We present a method for predicting a gene’s expression as a function of other genes thereby accounting for the effect of transcriptional regulation that confounds the identification of genes differentially expressed relative to a regulatory network. The challenge in constructing such models is that the number of possible regulator transcripts within a global network is on the order of thousands, and the number of biological samples is typically on the order of 10. Nevertheless, there are large gene expression databases that can be used to construct networks that could be helpful in modeling transcriptional regulation in smaller experiments.</p> <p>Results: We demonstrate a type of penalized regression model that can be estimated from large gene expression databases, and then applied to smaller experiments. The ridge parameter is selected by minimizing the cross-validation error of the predictions in the independent out-sample. This tends to increase the model stability and leads to a much greater degree of parameter shrinkage, but the resulting biased estimation is mitigated by a second round of regression. Nevertheless, the proposed computationally efficient “over-shrinkage” method outperforms previously used LASSO-based techniques. In two independent datasets, we find that the median proportion of explained variability in expression is approximately 25%, and this results in a substantial increase in the signal-to-noise ratio allowing more powerful inferences on differential gene expression leading to biologically intuitive findings. We also show that a large proportion of gene dependencies are conditional on the biological state, which would be impossible with standard differential expression methods.</p> <p>Conclusions: By adjusting for the effects of the global network on individual genes, both the sensitivity and reliability of differential expression measures are greatly improved.</p&gt

Network Features of the Mammalian Circadian Clock

The mammalian circadian clock is a cell-autonomous system that drives oscillations in behavior and physiology in anticipation of daily environmental change. To assess the robustness of a human molecular clock, we systematically depleted known clock components and observed that circadian oscillations are maintained over a wide range of disruptions. We developed a novel strategy termed Gene Dosage Network Analysis (GDNA) in which small interfering RNA (siRNA)-induced dose-dependent changes in gene expression were used to build gene association networks consistent with known biochemical constraints. The use of multiple doses powered the analysis to uncover several novel network features of the circadian clock, including proportional responses and signal propagation through interacting genetic modules. We also observed several examples where a gene is up-regulated following knockdown of its paralog, suggesting the clock network utilizes active compensatory mechanisms rather than simple redundancy to confer robustness and maintain function. We propose that these network features act in concert as a genetic buffering system to maintain clock function in the face of genetic and environmental perturbation

Emergence of Noise-Induced Oscillations in the Central Circadian Pacemaker

Computational modeling and experimentation explain how intercellular coupling and intracellular noise can generate oscillations in a mammalian neuronal network even in the absence of cell-autonomous oscillators

Internal Ribosomal Entry Site-Mediated Translation Is Important for Rhythmic PERIOD1 Expression

The mouse PERIOD1 (mPER1) plays an important role in the maintenance of circadian rhythm. Translation of mPer1 is directed by both a cap-dependent process and cap-independent translation mediated by an internal ribosomal entry site (IRES) in the 5′ untranslated region (UTR). Here, we compared mPer1 IRES activity with other cellular IRESs. We also found critical region in mPer1 5′UTR for heterogeneous nuclear ribonucleoprotein Q (HNRNPQ) binding. Deletion of HNRNPQ binding region markedly decreased IRES activity and disrupted rhythmicity. A mathematical model also suggests that rhythmic IRES-dependent translation is a key process in mPER1 oscillation. The IRES-mediated translation of mPer1 will help define the post-transcriptional regulation of the core clock genes

Synaptic E3 Ligase SCRAPPER in Contextual Fear Conditioning: Extensive Behavioral Phenotyping of Scrapper Heterozygote and Overexpressing Mutant Mice

SCRAPPER, an F-box protein coded by FBXL20, is a subunit of SCF type E3 ubiquitin ligase. SCRAPPER localizes synapses and directly binds to Rab3-interacting molecule 1 (RIM1), an essential factor for synaptic vesicle release, thus it regulates neural transmission via RIM1 degradation. A defect in SCRAPPER leads to neurotransmission abnormalities, which could subsequently result in neurodegenerative phenotypes. Because it is likely that the alteration of neural transmission in Scrapper mutant mice affect their systemic condition, we have analyzed the behavioral phenotypes of mice with decreased or increased the amount of SCRAPPER. We carried out a series of behavioral test batteries for Scrapper mutant mice. Scrapper transgenic mice overexpressing SCRAPPER in the hippocampus did not show any significant difference in every test argued in this manuscript by comparison with wild-type mice. On the other hand, heterozygotes of Scrapper knockout [SCR (+/−)] mice showed significant difference in the contextual but not cued fear conditioning test. In addition, SCR (+/−) mice altered in some tests reflecting anxiety, which implies the loss of functions of SCRAPPER in the hippocampus. The behavioral phenotypes of Scrapper mutant mice suggest that molecular degradation conferred by SCRAPPER play important roles in hippocampal-dependent fear memory formation

Characteristics of biologicak activity of phospholipids in egg yolk

Jaja są źródłem cennych składników pokarmowych, charakteryzujących się dużym stopniem przyswajalności. Lipidy stanowią ok. 60 % suchej masy żółtka jaja i składają się w 62 % z triacylogliceroli, w 33 % z fosfolipidów, a cholesterolu jest w nich mniej niż 5 %. Profil kwasów tłuszczowych frakcji fosfolipidów wykazuje wyższy stopień nienasycenia niż frakcji triacylogliceroli. Ponadto fosfolipidy, które są składnikami błon komórkowych, wykazują pozytywny wpływ na układ sercowo-naczyniowy, obniżają poziom cholesterolu, zmniejszają syntezę triacylogliceroli, hamują agregację płytek i obniżają ciśnienie krwi. Spożycie fosfatydylocholiny wpływa na zwiększenie poziomu choliny w osoczu i w mózgu oraz na przyspieszenie neuronalnej syntezy acetylocholiny, będącej neuroprzekaźnikiem. Jednocześnie jaja projektowane, pozyskane od niosek żywionych mieszankami paszowymi wzbogaconymi m.in. w algi morskie i olej lniany, są również źródłem wielonienasyconych kwasów tłuszczowych, w skład których wchodzą kwasy z rodziny n-3 (ALA, EPA, DHA) i n-6 (LA, ARA).Eggs are a source of valuable nutrients that are characterized by a high degree of bioavailability. Lipids constitute ca. 60 % of the dry matter content in egg yolk and consist of 62 % of triglycerides, 33 % of phospholipids; the amount of cholesterol therein is less than 5 %. The profile of fatty acids in the phospholipid fraction shows a higher degree of unsaturation compared to the triacylglycerol fraction. In addition, phospholipids, which are components of cell membranes, have a positive effect on the cardiovascular system; they decrease the cholesterol level, reduce the synthesis of triacylglycerols, inhibit the platelet aggregation, and lower the blood pressure. The intake of phosphatidylcholine helps increase the level of choline in the plasma and brain as well as accelerate neuronal synthesis of acetylcholine, which is a neurotransmitter. Also, the designed eggs laid by hens fed fodder mixtures enriched with marine algae oil and linseed oil are a source of polyunsaturated fatty acids including n-3 fatty acids (ALA, EPA, DHA) and n-6 fatty acids (LA, ARA)

Fractionation of egg yolk to obtain preparations enriched in biologically active substances

Jaja są surowcem żywnościowym zawierającym wszystkie niezbędne substancje do rozwoju młodego organizmu. Wykorzystywane są w przemyśle żywnościowym, jak również w farmaceutycznym, kosmetycznym, chemicznym i paszowym ze względu na zawartość substancji biologicznie aktywnych m.in. immunoglobuliny (IgY), foswityny i fosfolipidów. W pracy podjęto próbę frakcjonowania żółtek jaj kurzych ukierunkowaną na pozyskanie frakcji bogatych w immunoglobulinę (IgY), foswitynę oraz w celu izolacji fosfolipidów. Surowiec stanowiły świeże jaja pozyskane od niosek linii Lohmann Brown, pochodzące z gospodarstwa specjalistycznego zarządzanego przez firmę TRONINA. Nioski utrzymywano w dwóch grupach i żywiono ad libitum. Grupie kontrolnej niosek podawano pełnoporcjową standardową mieszankę paszową oraz preparat o nazwie handlowej Biostrong 510, stanowiący mieszaninę olejków eterycznych i wysokowartościowych ekstraktów ziołowych w formie otoczkowanej. W grupie doświadczalnej pasza wzbogacona była w preparaty Humobentofet i Humokarbowit (zawierające kwasy omega 3), zmieszane w stosunku masowym 1 : 2. Zawartość IgY w plazmie jaj grupy kontrolnej utrzymywała się na poziomie ok. 3,6 mg/ml, natomiast plazma wyizolowana z żółtek jaj niosek żywionych paszą wzbogaconą zawierała ok. 1 mg/ml więcej tego białka. Zawartość foswityny z żółtek jaj pozyskanych zarówno od niosek żywionych paszą standardową, jak i wzbogaconą wyniosła ok. 4 %. Zawartość białka ogółem we frakcji foswitynowej była na podobnym poziomie ok. 60 %. Czystość frakcji fosfolipidowej pozyskanej w obydwóch wariantach żywieniowych, określonej jako ilość substancji nierozpuszczalnej w acetonie, wyniosła ok. 85 %. We frakcji tej zawartość fosfatydylocholiny (PC) wynosiła ok. 75 %, a fosfatydyloetanoloaminy (PE) ok. 24 %.Eggs are a raw food material containing all substances indispensable for the development of young organism. They are used in the food industry, as well as in the pharmaceutical, cosmetic, chemical, and feed industry owing to the content of biologically active substances, among other things, immunoglobulin (IgY), phosvitin, and phospholipids. In the research covered by this paper, it was attempted to fraction chicken egg yolk in order to receive fractions containing rich amounts of immunoglobulin (IgY) and phosvitin, and, also, to isolate phospholipids. The raw material constituted fresh eggs laid by Lohmann Brown hens received from a specialist farm managed by the "Tronina" company. The layers were held in two groups and fed ad libitum. The control group of layers received a standard, full-portion feed mix and a preparation called Biostrong 510 (commercial name), which was a mixture of essential oils and high-quality herbal extracts in the encapsulated form. In the experimental group, the feed was supplemented with Humokarbowit and Humobentofet preparations (containing omega-3 acids) mixed at a mass ratio of 1 : 2. The content of IgY in the egg plasma of the control group remained at a level of approximately 3.6 mg / ml, while the plasma isolated from the enriched egg yolk laid by the hens fed a supplemented feed contained about 1 mg / ml more of protein. The content of phosvitin in egg yolk of the eggs laid by the layers fed the standard and enriched feed amounted to about 4%. The total protein content in the phosvitin fraction was at a similar level of approximately 60 %. The pure phospholipid fraction, extracted from the egg yolk of hens fed two types of feed and defined as the amount of a substance insoluble in acetone, was roughly 85%. The content of phosphatidylcholine (PC) in this fraction was about 75 %, and of phosphatidylethanolamine (PE) – approximately 24 %