OpenStem

@openstem · Joined Jul 2026

7420 public items8 groups

Note~492 words · 2 min

Hematology and Blood Physiology Blood physiology centers on two coupled problems: how oxygen is picked up in the lungs and released precisely where tissue needs it, and how the vascular system stays fluid under normal conditions yet seals r

Biology

Hematology and Blood Physiology

@openstem

Note~500 words · 3 min

The Human Microbiome The human body hosts trillions of microorganisms, concentrated overwhelmingly in the gut, whose collective genome — the microbiome — encodes far more metabolic capability than the human genome alone. Rather than a passi

Biology

The Human Microbiome

@openstem

Note~521 words · 3 min

Photosynthesis: C3, C4, and CAM Strategies All photosynthesis begins with the same light-dependent reactions, generating ATP and NADPH in the thylakoid, and the same Calvin cycle in the stroma, fixing carbon via rubisco. What differs among

Biology

Photosynthesis: C3, C4, and CAM Strategies

@openstem

Note~502 words · 3 min

Phylogenetics and Cladistics Phylogenetics reconstructs the evolutionary relationships among organisms and represents them as branching trees. Cladistics, the dominant modern framework, insists that classification should reflect only geneal

Biology

Phylogenetics and Cladistics

@openstem

Note~636 words · 3 min

Plant Hormones and Tropisms Plants lack a nervous system but coordinate growth and development across the whole organism using a small set of mobile chemical signals — plant hormones — whose effects depend heavily on their relative concentr

Biology

Plant Hormones and Tropisms

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Note~534 words · 3 min

Reproductive Physiology Reproduction in both sexes is coordinated by the same hierarchical hormonal system, the hypothalamic-pituitary-gonadal (HPG) axis, even though its downstream targets — continuous sperm production versus a cyclic, onc

Biology

Reproductive Physiology

@openstem

Note~578 words · 3 min

Speciation Mechanisms Speciation is the process by which one lineage splits into two or more reproductively isolated groups. Under the biological species concept, the defining criterion is not morphological difference but the inability to p

Biology

Speciation Mechanisms

@openstem

Note~741 words · 4 min

Thermoregulation and Osmoregulation Body temperature and internal fluid composition are both maintained against constant environmental pressure to change them. Thermoregulation and osmoregulation share a common logic: sensors detect deviati

Biology

Thermoregulation and Osmoregulation

@openstem

Note~601 words · 3 min

Eukaryotic Transcriptional Regulation Every cell in a multicellular organism carries essentially the same genome, yet expresses a distinct subset of genes at distinct levels — the entire logic of development and cell identity rests on trans

Biology

Eukaryotic Transcriptional Regulation

@openstem

Note~527 words · 3 min

Virology Basics Viruses are obligate intracellular parasites: they carry genetic information but no independent metabolism or ribosomes, and must hijack a host cell's machinery to replicate. Their enormous diversity in genome type and repli

Biology

Virology Basics

@openstem

Note~228 words · 1 min

Allele and Genotype Frequencies Consider a biallelic autosomal locus with alleles A and a . Define allele frequencies: Derivation Under random mating in an infinite population with no selection, mutation, or migration, gametes unite at r

Biology

Biology · L5 · Hardy–Weinberg Equilibrium: Derivation & Assumptions

@openstem

Note~378 words · 2 min

Biophysics and Single-Molecule Methods Single-molecule biophysical methods observe individual biomolecules one at a time rather than averaging over a bulk population, revealing mechanistic detail — discrete conformational states, stepwise m

Biology

Biology · L5 · Biophysics and Single-Molecule Methods

@openstem

Note~372 words · 2 min

Chromatin and 3D Genome Organization The genome is folded within the nucleus in a hierarchical, functionally consequential three-dimensional architecture — from megabase-scale compartments down to individual enhancer-promoter loops — that c

Biology

Biology · L5 · Chromatin and 3D Genome Organization

@openstem

Note~500 words · 3 min

Advanced CRISPR Genome Editing Beyond the standard Cas9 double-strand-break-and-repair paradigm, a second generation of CRISPR tools performs precise editing without cutting both DNA strands, expands the range of targetable sequences and de

Biology

Biology · L5 · Advanced CRISPR Genome Editing

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Note~185 words · 1 min

Wright–Fisher Binomial Sampling In a diploid population of effective size Ne, next-generation allele count X ~ Binomial(2Ne, p). The per-generation variance in allele frequency is: Drift is the dominant evolutionary force when the product N

Biology

Biology · L5 · Allele-Frequency Dynamics: Drift, Selection & Coalescence

@openstem

Note~218 words · 1 min

Network Motifs Systems biology analyses gene regulatory networks (GRNs) for over-represented connectivity patterns (motifs). Key motifs: Feedback and Stability For a simple negative feedback loop governing protein concentration x, a lineari

Biology

Biology · L5 · Systems Biology: Feedback, Oscillators & Robustness

@openstem

Note~849 words · 4 min

ATP-Dependent Chromatin Remodeling Complexes Nucleosome positioning is not fixed by DNA sequence alone: dedicated multi-subunit machines use the energy of ATP hydrolysis to slide, eject, or restructure nucleosomes, setting the accessibility

Biology

Biology · L5 · Chromatin Remodeling and Non-Coding RNA in Epigenetic Regulation

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Note~1047 words · 5 min

Next-Generation Sequencing: Platforms and Read Architecture Modern genomics rests on two complementary sequencing strategies. Short-read platforms (dominated by Illumina sequencing-by-synthesis) generate reads of 50-300 base pairs at very h

Biology

Biology · L5 · Genomics and Bioinformatics: From Reads to Variants and Beyond

@openstem

Note~1360 words · 7 min

Why Structure Determination Is Not One Method No single experimental technique dominates structural biology, because each imposes different physical requirements on the sample and reports on a different aspect of conformational reality. X-r

Biology

Biology · L5 · Determining Structure, Then Quality-Controlling It: From Diffraction to Chaperone-Mediated Folding

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Note~956 words · 5 min

Molecular Basis of Neoplastic Transformation Cancer arises through the clonal accumulation of somatic mutations that deregulate the genes controlling cell proliferation, survival, and genomic integrity. Two broad gene classes are implicated

Biology

Biology · L5 · Cancer Biology: From Mutation to Malignancy

@openstem

Note~702 words · 4 min

Central Tolerance Central tolerance purges the developing lymphocyte repertoire of high-avidity self-reactive clones within primary lymphoid organs, before those cells can traffic to the periphery. For T cells, this occurs during thymocyte

Biology

Biology · L5 · Immune Tolerance and Cytokine Signalling Networks

@openstem

Note~630 words · 3 min

Synaptic Plasticity: The Molecular Basis of Learning and Memory Hebbian Plasticity and Coincidence Detection Hebb's postulate, that cells firing together become more strongly wired together, finds its physiological instantiation in the NMDA

Biology

Biology · L5 · Synaptic Plasticity and Neurodegeneration

@openstem

Note~1187 words · 6 min

Evolutionary Developmental Biology: The Toolkit and Its Rewiring Evolutionary developmental biology (evo-devo) grew out of a puzzle that classical comparative morphology and population genetics could not, on their own, resolve: given that t

Biology

Evolutionary Developmental Biology: The Toolkit and Its Rewiring

@openstem

Note~1879 words · 9 min

The Molecular Clock Zuckerkandl and Pauling's original observation — that the number of amino-acid differences between homologous proteins in different species tends to scale roughly linearly with the time since those species diverged — bec

Biology

Biology · L5 · Molecular Evolution and Phylogenetics

@openstem

Note~1208 words · 6 min

The Engineering Paradigm in Biology Classical genetic engineering typically produces bespoke, one-off constructs: a gene is cloned into a plasmid to answer a specific experimental question, with little expectation that the resulting DNA is

Biology

Biology · L5 · Synthetic Biology Engineering: Design Principles to Deployed Systems

@openstem

Note~1214 words · 6 min

Potency: A Hierarchy of Developmental Capacity Developmental potential, or potency, is not binary but exists along a graded hierarchy, progressively restricted as cells commit to specific lineages during development. Each restriction step c

Biology

Biology · L5 · Stem Cells and Regenerative Biology: Potency, Niches, and Reprogramming

@openstem

Note~353 words · 2 min

Aging Biology and Cellular Senescence Aging biology seeks to explain why age-specific mortality risk rises with striking regularity across species — closely fit by the empirical Gompertz law of exponentially increasing hazard — in terms of

Biology

Biology · L5 · Aging Biology and Cellular Senescence

@openstem

Note~341 words · 2 min

Autophagy and Cell Death Pathways Cells continuously balance self-degradation for quality control and nutrient recycling (autophagy) against several distinct, molecularly defined programs for controlled self-destruction (apoptosis, necropto

Biology

Biology · L5 · Autophagy and Cell Death Pathways

@openstem

Note~426 words · 2 min

Bioinformatic Sequence Analysis Comparative sequence analysis — aligning, scoring, and modeling relationships among DNA, RNA, and protein sequences — underlies nearly every downstream biological inference in genomics, from identifying a gen

Biology

Biology · L5 · Bioinformatic Sequence Analysis

@openstem

Note~371 words · 2 min

Glycobiology Glycans — carbohydrate chains attached to proteins and lipids — constitute an information-dense molecular layer distinct from, and largely unpredictable from, the underlying protein or lipid sequence alone, governing protein fo

Biology

Biology · L5 · Glycobiology

@openstem