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H. Vink investigated the functional properties of the endothelial glycocalyx. In work with B. R. Duling, the researcher compared the domains occupied by different components of blood within mammalian capillaries.[ref]
The 1996 experiments combined bright-field observations of blood cells with fluorescence microscopy of circulating macromolecules in hamster muscle. The study also included a light-and-dye perturbation, testing the relationship between the observed surface layer and the space accessible to flowing components.[ref]
Identification of distinct luminal domains for macromolecules, erythrocytes, and leukocytes within mammalian capillaries by H. Vink and B. R. Duling. Methods and indexed primary abstract: microscopy modalities and light-dye treatment
An illuminating measurement question is “accessible to what?” A boundary inferred from a fluorescent tracer need not coincide with the vessel wall or with the path occupied by a blood cell. Comparing components makes the probe's physical interaction with the surface part of the interpretation, rather than assuming that every measured width denotes the same anatomical opening.
B. R. Duling investigated the microcirculation, including how blood components occupy the internal space of capillaries. A 1996 study with H. Vink compared anatomical capillary dimensions with the domains available to flowing blood cells and macromolecules.[ref]
The comparison addressed the endothelial glycocalyx, a surface layer at the blood-facing side of the endothelium. A space bounded by the vessel wall need not be equally accessible to every circulating component. Fluorescence microscopy and observations of moving blood cells provided different views of that same microvascular space.[ref]
Identification of distinct luminal domains for macromolecules, erythrocytes, and leukocytes within mammalian capillaries by H. Vink and B. R. Duling. Abstract and study design: surface coat and component-specific luminal domains
T. R. Kumar is the researcher who led a 1997 study of the function of follicle-stimulating hormone in mouse reproduction. The study used a gene knockout affecting the hormone-specific follicle-stimulating hormone beta subunit, producing mice deficient in the active hormone.[ref]
Follicle stimulating hormone is required for ovarian follicle maturation but not male fertility by T. R. Kumar and others. Byline and Abstract: targeted FSH-beta deficiency
The outcomes differed between sexes. Females were infertile because ovarian follicle development stopped before formation of an antral cavity. Males retained reproductive capability despite having reduced testis size. The experiment therefore distinguished a requirement for normal organ development from an absolute requirement for the measured reproductive endpoint.[ref]
Follicle stimulating hormone is required for ovarian follicle maturation but not male fertility by T. R. Kumar and others. Abstract: female preantral arrest and male fertility despite reduced testicular size
For example, observing an altered organ size and observing failure to produce offspring answer different questions. The same perturbation can affect both endpoints to different degrees. These mouse results established a specific experimentally tested distinction; they do not by themselves determine the outcome of every reduction in follicle-stimulating hormone in another species.
Mia Phillipson is a researcher in physiology and inflammation. In a 2006 collaborative study, Mia Phillipson and colleagues used intravital microscopy to follow neutrophils inside inflamed mouse venules. The movies showed that after cell adhesion to the endothelium, neutrophils often crawled along the inner surface before leaving the blood vessel.[ref]
Intraluminal crawling of neutrophils to emigration sites: a molecularly distinct process from adhesion in the recruitment cascade by Mia Phillipson and others. Abstract and Results: real-time and time-lapse microscopy; Journal of Experimental Medicine 203, 2569–2575, 2006
The team compared mice lacking different integrins, the adhesion-related proteins LFA-1 and Mac-1. Loss of LFA-1 strongly reduced initial cell adhesion. Loss of Mac-1 allowed cell adhesion but severely reduced subsequent crawling and delayed passage out of the blood vessel. Watching successive steps revealed distinct functions that a single count of attached neutrophils would have missed. The experiment therefore separates arrival, crawling and exit as experimentally distinguishable stages of the inflammatory response.[ref]
Intraluminal crawling of neutrophils to emigration sites: a molecularly distinct process from adhesion in the recruitment cascade by Mia Phillipson and others. Abstract: contrasting LFA-1 and Mac-1 knockout phenotypes and delayed transmigration
Mark A. Knepper is a researcher in kidney physiology who uses systems biology to investigate the regulation of water transport. A central example is how vasopressin changes the distribution of aquaporin-2 between the plasma membrane and the interior of collecting duct cells. His 2010 research report describes combining mass spectrometry, measurements of gene expression, mathematical modeling and physiological experiments to investigate this regulation.[ref]
Solute And Water Transport In Renal Epithelia by Mark A. Knepper. NIH RePORTER project 1ZIAHL001285-24, fiscal year 2010; Abstract
The timing gives the mechanism its interest. On a scale of seconds to minutes, membrane trafficking can move existing aquaporin-2 into the plasma membrane, changing the route available for water movement. That is a different regulatory step from making additional aquaporin-2 through altered gene expression. Measuring how much channel protein exists and where it is located therefore answers different questions.[ref]
Solute And Water Transport In Renal Epithelia by Mark A. Knepper. Abstract: rapid redistribution between membrane and cytoplasm
Mark A. Knepper also wrote a scientific remembrance of Maurice B. Burg, explaining how experiments on isolated renal tubules opened individual transport mechanisms to direct investigation.[ref]
Maurice B. Burg (1931–2022), discoverer of kidney transport mechanisms by Mark A. Knepper. Opening and discussion of the isolated-perfused-tubule method; PNAS 119, e2209749119, 2022
C. Desjardins is a coauthor with B. R. Duling of a 1990 experiment investigating the endothelial glycocalyx and red blood cell distribution in capillaries. They perfused individual capillaries with heparinase and measured tube hematocrit, the fraction of the local vessel volume occupied by red blood cells. The measured fraction increased at least twofold without a significant change in red blood cell velocity.[ref]
Heparinase treatment suggests a role for the endothelial cell glycocalyx in regulation of capillary hematocrit by C. Desjardins and B. R. Duling. Abstract: in-situ enzyme microperfusion and tube hematocrit; American Journal of Physiology 258, H647–H654, 1990
The controls make the inference useful. Vehicle alone and heat-denatured heparinase did not produce the same effect, arguing against simple perfusion or the mere presence of added protein as explanations. Measuring both tube hematocrit and velocity also distinguishes more red blood cells occupying a segment from faster movement through it. The results supported a role for components of the inner capillary surface in cell distribution, without directly measuring every structural feature of the endothelial glycocalyx.[ref]
Samuel J. Sober is a researcher in motor learning and the control of skilled movement. His laboratory combines recordings from neurons and muscles, behavioral experiments and computational analysis to investigate how the nervous system produces and adjusts movement. These approaches connect an animal's observable performance with candidate mechanisms for controlling it.[ref]
Research overview of the Sober Lab. Lab-authored research overview: recordings, behavioral manipulations and sensory feedback
With Michael S. Brainard, Samuel J. Sober tested whether adult birds continually correct vocal errors. A microphone captured Bengalese finch song and processing equipment altered its pitch before playing it through headphones. Compensatory changes in the birds' pitch showed adjustment to a measurable error in auditory feedback. Unlike deafening alone, this manipulation supplied an error that a change in behavior could reduce.[ref]
Adult birdsong is actively maintained by error correction by Samuel J. Sober and Michael S. Brainard. Introduction and Figure 1: correctable feedback perturbations; Nature Neuroscience 12, 927–931, 2009
Michael S. Brainard is a researcher in neuroscience who studies how experience shapes sensorimotor learning. His work uses songbirds to connect measured behavior with the activity of the nervous system. Song offers a particularly useful task because a young bird first hears a tutor and then uses auditory feedback to refine its own performance.[ref]
Research profile of Michael Brainard at UCSF. Research summary: sensory and sensorimotor stages of song learning
In a 2009 study with Samuel J. Sober, adult Bengalese finches heard electronically shifted pitch through custom headphones. The birds changed their own pitch in the opposite direction and returned toward baseline when normal auditory feedback resumed. Thus an apparently stable adult skill could be actively maintained by feedback control, rather than being an unchanging motor program.[ref]
Adult birdsong is actively maintained by error correction by Samuel J. Sober and Michael S. Brainard. Abstract and Figure 1: feedback perturbation and compensation
Michael S. Brainard, institutional portrait from the UCSF Neuroscience Graduate Program.
V. Ruotsalainen is the first author of a 1999 study identifying the location of nephrin within the glomerular filtration barrier. The team used antibodies to detect nephrin in kidney tissue. Immunofluorescence placed the signal around the filtering capillaries, while immunogold labeling with electron microscopy located it at the slit diaphragm between neighboring podocyte projections.[ref]
Nephrin is specifically located at the slit diaphragm of glomerular podocytes by V. Ruotsalainen and others. Abstract and immunolocalization results; PNAS 96, 7962–7967, 1999
The different scales matter. A fluorescent band near a filtering surface does not by itself specify which tiny junction contains a protein; electron microscopy resolves the slit diaphragm within that region. Coupled with prior evidence that mutations in the nephrin gene cause severe urinary protein loss, the localization supported a structural role in the filtration apparatus. The proposed zipper-like arrangement of nephrin molecules was an explanatory model, distinct from the directly observed labeling pattern.[ref]
Nephrin is specifically located at the slit diaphragm of glomerular podocytes by V. Ruotsalainen and others. Abstract and Discussion: slit localization, congenital nephrotic syndrome and proposed zipper-like assembly
Diane Rebourcet is a researcher in reproductive biology whose experimental work examines interactions between cells in the testis. In a 2014 collaborative study, Diane Rebourcet and colleagues investigated whether adult Sertoli cells support other testicular functions as well as developing reproductive cells. They engineered mice so that Sertoli cells expressed a receptor making them susceptible to a selectively administered toxin.[ref]
Selective cell ablation was followed by loss of reproductive cells and a roughly 75 percent decline in adult Leydig cell numbers. Removing one population and observing another gives stronger evidence for a functional dependency than simply finding both populations together. The result shows that adult Sertoli cells help maintain the Leydig cell population in this mouse model; it does not, by itself, distinguish direct cell contact from an indirect signal or establish a human treatment.[ref]
Sertoli cells maintain Leydig cell number and peritubular myoid cell activity in the adult mouse testis by Diane Rebourcet and others. Abstract and Results: Sertoli-cell loss, Leydig-cell counts and retained tubular architecture
A. Lambert is the first author of a 2000 study improving measurements of follicle-stimulating hormone effects on aromatase in human granulosa-lutein cells. These cells, collected during in-vitro fertilization procedures, convert testosterone to estradiol through aromatase. The study addressed a measurement problem: hormone output during a long incubation depends both on the amount of active enzyme and on how much substrate remains.[ref]
Improved FSH sensitisation and aromatase assay in human granulosa-lutein cells by A. Lambert and others. Abstract: human follicular aspirates and interpretation of prolonged testosterone exposure
The researchers separated the stages. They first preincubated the granulosa-lutein cells, stimulated them with follicle-stimulating hormone for 24 hours, washed them, and then supplied testosterone for a two-hour assay. The short challenge limited substrate depletion and isolated the later measurement from the earlier stimulation. After preincubation, the observed stimulation was three- to fourteen-fold over basal activity, depending on the preparation. This illustrates why an enzyme assay needs control of both biological regulation and reaction conditions.[ref]
Improved FSH sensitisation and aromatase assay in human granulosa-lutein cells by A. Lambert and others. Abstract: 0/24/48-hour preincubation, 24-hour stimulation and two-hour testosterone challenge
T. M. Redmond is the first author of a 1998 study establishing an essential role for RPE65 in the mouse visual cycle. The team compared mice lacking RPE65 with control animals using electroretinography and biochemical measurements of vitamin A derivatives. The mutant mice lacked normal rod cell responses and rhodopsin, despite retaining the opsin component of the light-sensitive protein.[ref]
This separates two possible explanations of failed light detection. A rod cell may contain opsin yet fail to assemble working rhodopsin if the required light-absorbing retinal is unavailable. The mutant mice accumulated one group of vitamin A derivatives while lacking the normal 11-cis products, linking the physiological defect to disrupted visual cycle chemistry. The experiment demonstrated a requirement for RPE65 in this pathway; deleting a gene alone does not identify every reaction performed by its protein.[ref]
Rpe65 is necessary for production of 11-cis-vitamin A in the retinal visual cycle by T. M. Redmond and others. Abstract: retained opsin, accumulated all-trans-retinyl esters and absent 11-cis-retinyl esters
Krzysztof Palczewski is a researcher in the molecular basis of vision. In a 2000 collaborative study, he helped determine the X-ray crystallography structure of rhodopsin at 2.8 angstrom resolution. Rhodopsin is a light-sensitive G protein-coupled receptor; the structure showed its seven membrane-spanning alpha helices and the buried binding environment of retinal.[ref]
Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor by Krzysztof Palczewski and others. Page 739, Abstract and structure determination; Science 289, 739–745, 2000
The structure connected architecture with a signaling problem: how can a light-driven change near retinal influence the intracellular surface that activates a G protein? Locating the binding pocket, connecting loops and contacts between alpha helices constrained possible mechanisms. The measured inactive-state structure supplied a starting configuration for testing those mechanisms; it did not by itself record the complete time-dependent activation process.[ref]
Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor by Krzysztof Palczewski and others. Abstract and Figures 2–3: retinal environment, transmembrane organization and cytoplasmic interactions
Anthony G. Robson is a researcher in visual electrophysiology and the first author of the 2022 standard for full-field clinical electroretinography. The document specifies stimulus conditions, recording methods and reporting practices for measuring the retina's summed response to diffuse flashes of light. A shared protocol makes recordings from different laboratories more comparable.[ref]
ISCEV Standard for full-field clinical electroretinography (2022 update) by Anthony G. Robson and others. Abstract and author affiliations; Documenta Ophthalmologica 144, 165–177, 2022
The controlled background state is part of the measurement. Responses recorded after dark adaptation and under light adaptation probe different combinations of retinal activity; changing the adaptation condition can change a waveform even when the underlying tissue is unchanged. Specifying adaptation, flash conditions and electrodes therefore helps distinguish a physiological difference from a procedural difference. The standard addresses generalized retinal function; a summed response does not directly locate every abnormality within an individual retinal cell.[ref]
ISCEV Standard for full-field clinical electroretinography (2022 update) by Anthony G. Robson and others. Standard protocols: preparation, dark- and light-adapted responses, recording and reporting
Richard A. Stockton collaborated with Malcolm M. Slaughter on the physiology underlying electroretinography. Their 1989 study recorded light-evoked electrical responses together with extracellular potassium changes in amphibian retinas. These paired measurements allowed the researchers to compare a summed field response with an ionic response during selective suppression of retinal pathways.[ref]
B-wave of the electroretinogram. A reflection of ON bipolar cell activity by Richard A. Stockton and Malcolm M. Slaughter. Abstract: simultaneous intraretinal field and extracellular potassium measurements
Loss of ON retinal bipolar cell responses removed both the electroretinogram b-wave and corresponding light-on potassium changes. The result linked different measurable consequences of the same pathway, rather than treating the recorded wave as a direct view of one isolated neuron.[ref]
Malcolm M. Slaughter worked with Richard A. Stockton to identify the cellular origin of the electroretinogram b-wave. Their 1989 experiments used selective pharmacological suppression in amphibian retinas. Suppressing ON retinal bipolar cells abolished the electroretinogram b-wave, while suppressing other retinal pathways could leave it intact.[ref]
B-wave of the electroretinogram. A reflection of ON bipolar cell activity by Richard A. Stockton and Malcolm M. Slaughter. Abstract: selective ON-pathway suppression and comparison with OFF-pathway interventions
A component of a whole-tissue electrical recording cannot be assigned to a cell type just because the two occur together. Selectively disrupting one pathway while testing another made the proposed cellular explanation more discriminating.[ref]
B-wave of the electroretinogram. A reflection of ON bipolar cell activity by Richard A. Stockton and Malcolm M. Slaughter. Abstract and pharmacological experiments; Journal of General Physiology 93, 101–122, 1989
G. Gamba is the first author of a 1994 study identifying two related salt-transport proteins in the mammalian kidney. The team cloned the corresponding DNA sequences and tested the expressed proteins in Xenopus laevis oocytes. One transported sodium, potassium and chloride; the other transported sodium and chloride without the same potassium requirement.[ref]
Molecular cloning, primary structure, and characterization of two members of the mammalian electroneutral sodium-(potassium)-chloride cotransporter family expressed in kidney by G. Gamba and others. Abstract: cloned cDNAs and functional expression; Journal of Biological Chemistry 269, 17713–17722, 1994
The transporters also differed in their responses to inhibitors, including bumetanide. Combining sequence comparison, transport assays and localization within the kidney established a family resemblance without assuming identical function. This is an important experimental distinction: a similar protein primary structure suggests a relationship, while controlled measurements of ion movement test what each membrane transport protein actually does.[ref]
Molecular cloning, primary structure, and characterization of two members of the mammalian electroneutral sodium-(potassium)-chloride cotransporter family expressed in kidney by G. Gamba and others. Abstract: sequence similarity, differing ion requirements and inhibitor sensitivity, and intrarenal expression
Barry M. Brenner was a researcher in kidney physiology who helped make the physical forces driving glomerular filtration directly accessible to experiment. In 1971, Barry M. Brenner and collaborators studied rats whose glomeruli lay at the exposed surface of the kidney. This anatomical feature let them place pressure-measuring micropipettes inside glomerular capillaries, rather than infer their pressure only from upstream arterial measurements.[ref]
The Dynamics of Glomerular Ultrafiltration in the Rat by Barry M. Brenner and others. Byline and Abstract: surface-glomerulus Wistar rats and servo-nulling micropipette transducers
The team combined hydrostatic pressure measurements with oncotic pressure estimates and measurements of filtration by individual nephrons. These quantities describe different parts of the mechanism: a pressure difference can drive water across the glomerular filtration barrier, while the concentration of retained plasma proteins opposes that movement. Raising pressure in the receiving compartment can therefore reduce filtration without changing arterial pressure. Connecting these separately measurable quantities made the experiment a test of a physical explanation of kidney function.[ref]
The Dynamics of Glomerular Ultrafiltration in the Rat by Barry M. Brenner and others. Abstract: proximal-tubular pressures, plasma colloid-osmotic pressures and single-nephron filtration; qualitative conclusions only, in view of the linked October 1971 correction
J. Tapanainen is the first author of a 1991 study of steroid production in cultured human granulosa-lutein cells. The team compared 48-hour cultures with and without human chorionic gonadotropin or follicle-stimulating hormone, measuring several steroids and assaying aromatase activity separately.[ref]
Regulation of steroid and steroid sulfate production and aromatase activity in cultured human granulosa-luteal cells by J. Tapanainen and others. Abstract: culture design and measured endpoints
Both hormones increased pregnenolone and progesterone production substantially, while changes in several other steroid products were small. This illustrates why one hormone measurement cannot summarize a whole biochemical pathway: different reaction steps can impose different constraints. Separate measurements of products and enzyme activity make the proposed regulation experimentally testable, while the cultured-cell result remains distinct from a complete account of ovarian function in an animal.[ref]
Regulation of steroid and steroid sulfate production and aromatase activity in cultured human granulosa-luteal cells by J. Tapanainen and others. Abstract: differential steroid responses and aromatase regulation; Journal of Steroid Biochemistry and Molecular Biology 39, 19–25, 1991
Evren C. Tumer is a researcher whose work with Michael S. Brainard tested how small variations in a practiced skill can support further motor learning. Their 2007 study examined adult Bengalese finch song, which is highly repeatable but still varies slightly between performances. They asked whether this variation was merely unavoidable noise or could provide alternatives from which learning selects.[ref]
Performance variability enables adaptive plasticity of crystallized adult birdsong by Evren C. Tumer and Michael S. Brainard. Abstract and author byline; Nature 450, 1240–1244, 2007
A computerized system measured the pitch of selected song elements and delivered an auditory disruption for only some of the naturally occurring variations. The birds shifted pitch to avoid the disruption, with changes restricted to the targeted features. The experiment therefore linked a measurable action, its outcome and a later change in performance. It showed that a stable adult skill can contain useful variation on which adaptive motor learning operates.[ref]
Performance variability enables adaptive plasticity of crystallized adult birdsong by Evren C. Tumer and Michael S. Brainard. Abstract and Figures 1–4: contingent feedback, targeted changes and timing controls
Pinned article: Introduction to the OurBigBook Project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
Intro to OurBigBook
. Source. We have two killer features:
- topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculusArticles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.Figure 1. Screenshot of the "Derivative" topic page. View it live at: ourbigbook.com/go/topic/derivativeVideo 2. OurBigBook Web topics demo. Source. - local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 2. You can publish local OurBigBook lightweight markup files to either OurBigBook.com or as a static website.Figure 3. Visual Studio Code extension installation.Figure 5. . You can also edit articles on the Web editor without installing anything locally. Video 3. Edit locally and publish demo. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension. - Infinitely deep tables of contents:
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact






