diff --git a/src/components/pages/ArticlePage.tsx b/src/components/pages/ArticlePage.tsx index 2f381eb..6ac8282 100644 --- a/src/components/pages/ArticlePage.tsx +++ b/src/components/pages/ArticlePage.tsx @@ -7,6 +7,7 @@ import { articleContent } from '@/content/articles' import type { ArticleSlug } from '@/data/articles' import { getArticleBySlug } from '@/data/articles' import { site } from '@/data/site' +import { SpeciesHighlight } from '@/components/shared/SpeciesHighlight' interface ArticlePageProps { slug: ArticleSlug @@ -70,11 +71,11 @@ export function ArticlePage({ slug }: ArticlePageProps) {

- {article.title} +

- {article.subtitle} +
diff --git a/src/components/sections/WritingSection.tsx b/src/components/sections/WritingSection.tsx index e8c0f6b..ee29873 100644 --- a/src/components/sections/WritingSection.tsx +++ b/src/components/sections/WritingSection.tsx @@ -3,6 +3,7 @@ import Link from 'next/link' import { SectionHeader } from '@/components/shared/SectionHeader' +import { SpeciesHighlight } from '@/components/shared/SpeciesHighlight' import { articles } from '@/data/articles' import { type } from '@/lib/typography' @@ -27,9 +28,13 @@ export function WritingSection() { >
{article.tag}
-
{article.title}
+
+ +
-
{article.excerpt}
+
+ +
{article.chips.map((chip) => ( diff --git a/src/components/shared/SpeciesHighlight.tsx b/src/components/shared/SpeciesHighlight.tsx new file mode 100644 index 0000000..2d4744d --- /dev/null +++ b/src/components/shared/SpeciesHighlight.tsx @@ -0,0 +1,38 @@ +import type { ReactNode } from 'react' + +export const speciesClassName = 'text-[var(--accent)] italic' + +export function SpeciesEm({ children }: { children: ReactNode }) { + return {children} +} + +const speciesPattern = /(Picrophilus torridus|P\.\s*[Tt]orridus)/g + +function formatSpeciesMatch(match: string) { + return /^P\./i.test(match) ? 'P. torridus' : match +} + +export function SpeciesHighlight({ text }: { text: string }) { + const parts: ReactNode[] = [] + let lastIndex = 0 + + for (const match of text.matchAll(speciesPattern)) { + const index = match.index ?? 0 + + if (index > lastIndex) { + parts.push(text.slice(lastIndex, index)) + } + + parts.push( + {formatSpeciesMatch(match[0])}, + ) + + lastIndex = index + match[0].length + } + + if (lastIndex < text.length) { + parts.push(text.slice(lastIndex)) + } + + return <>{parts} +} diff --git a/src/content/articles/p-torridus-extremophile.tsx b/src/content/articles/p-torridus-extremophile.tsx index 9b0f887..aac9516 100644 --- a/src/content/articles/p-torridus-extremophile.tsx +++ b/src/content/articles/p-torridus-extremophile.tsx @@ -1,3 +1,5 @@ +import { SpeciesEm } from '@/components/shared/SpeciesHighlight' + export function PTorridusContent() { return ( <> @@ -10,8 +12,9 @@ export function PTorridusContent() {

What's interesting about the domain of life is that extremities exist. We have life forms that can survive in conditions at the ends of the ranges of the various conditions that - define the existence of life. One of these life forms is Picrophilus torridus (P. - Torridus) of phylum Euryarchaeota. P. Torridus, first extracted from moderately + define the existence of life. One of these life forms is{' '} + Picrophilus torridus (P. torridus) of phylum + Euryarchaeota. P. torridus, first extracted from moderately high-temperature hydrothermal areas in solfataric fields in Hokkaido, Japan, are known to grow in regions of pH around 0 and temperatures between 47 and 65 degrees Celsius.

@@ -21,20 +24,20 @@ export function PTorridusContent() {

- Thermoacidophile P. Torridus was discovered by Dr. Christa Schleper and her colleagues in - 1995 among the wet layers of coal in the acidic and geothermally heated fields of the - solfataras. P. Torridus is an aerobic life form, hence discovered in the oxygenous upper - layers of coal. The acid that gives the solfataric fields their acidic behavior is sulfuric - acid, produced from the oxidation of hydrogen sulfide. + Thermoacidophile P. torridus was discovered by Dr. Christa Schleper + and her colleagues in 1995 among the wet layers of coal in the acidic and geothermally heated + fields of the solfataras. P. torridus is an aerobic life form, hence + discovered in the oxygenous upper layers of coal. The acid that gives the solfataric fields + their acidic behavior is sulfuric acid, produced from the oxidation of hydrogen sulfide.

- The fact that P. Torridus, together with Picrophilus oshimae, could grow in these highly - acidic and hot environments makes it one of the most thermoacidophilic organisms known to - exist. Most organisms cannot grow in these conditions — low intracellular pH values denature - protein structures, leading to cell death through reactions between peptide linkages and - hydronium ions. High temperatures weaken the hydrogen bonding that gives proteins their - structure and functionality. + The fact that P. torridus, together with Picrophilus oshimae, could + grow in these highly acidic and hot environments makes it one of the most thermoacidophilic + organisms known to exist. Most organisms cannot grow in these conditions — low intracellular + pH values denature protein structures, leading to cell death through reactions between + peptide linkages and hydronium ions. High temperatures weaken the hydrogen bonding that gives + proteins their structure and functionality.

@@ -43,10 +46,10 @@ export function PTorridusContent() {

We've established that acidic and high-temperature environments are destructive to - proteins. But how does P. Torridus keep its proteins functional in such an environment? - Little is known about the complete mechanisms by which these organisms combat their - environment. However, P. Torridus maintains an intracellular pH of about 4-5 pH units above - the extracellular pH. + proteins. But how does P. torridus keep its proteins functional in + such an environment? Little is known about the complete mechanisms by which these organisms + combat their environment. However, P. torridus maintains an + intracellular pH of about 4-5 pH units above the extracellular pH.

This hypothesis is supported by the evident use of secondary cation transporters, especially - potassium ions, in the sequenced genome of P. Torridus. The genome also contains genes that - encode for enzymes that degrade organic acids — another pH correction mechanism. + potassium ions, in the sequenced genome of P. torridus. The genome also + contains genes that encode for enzymes that degrade organic acids — another pH correction + mechanism.

@@ -75,10 +79,11 @@ export function PTorridusContent() {

- We've explored how P. Torridus thrives in low pH regions, but how does it combat high - temperatures? The genome of P. Torridus offers insights. These microorganisms have the - smallest genome among all aerobic non-parasitic microorganisms, with one of the highest - coding densities compared to other extremophiles like Thermoplasma acidophilum. + We've explored how P. torridus thrives in low pH regions, but how + does it combat high temperatures? The genome of P. torridus offers + insights. These microorganisms have the smallest genome among all aerobic non-parasitic + microorganisms, with one of the highest coding densities compared to other extremophiles like + Thermoplasma acidophilum.

@@ -93,19 +98,19 @@ export function PTorridusContent() {

- The existence of P. Torridus is not by mere coincidence. This microorganism evolved under - the selective pressure of both low pH and high temperatures. The key features that resulted - from these pressures are the very small genome size and its high coding density. This can be - deduced by comparing P. Torridus with closely related extremophiles like Sulfolobus - solfataricus and Thermoplasma volcanii. + The existence of P. torridus is not by mere coincidence. This + microorganism evolved under the selective pressure of both low pH and high temperatures. The + key features that resulted from these pressures are the very small genome size and its high + coding density. This can be deduced by comparing P. torridus with + closely related extremophiles like Sulfolobus solfataricus and Thermoplasma volcanii.

The genome contains a large proportion of genes encoding protein transporters, particularly gradient-driven secondary transporters, suggesting adaptation to use the pH difference between the inner cell membrane and extracellular regions. We can conceptualize the - phenotype of P. Torridus by studying the selective pressures that led to its evolution: low - pH and high temperature. + phenotype of P. torridus by studying the selective pressures that led + to its evolution: low pH and high temperature.

@@ -113,9 +118,9 @@ export function PTorridusContent() {

- P. Torridus is an aerobic, non-parasitic, and thermoacidophilic microorganism that presents - one of the most extreme examples of life, stretching the boundaries where life was once - thought impossible. + P. torridus is an aerobic, non-parasitic, and thermoacidophilic + microorganism that presents one of the most extreme examples of life, stretching the + boundaries where life was once thought impossible.

@@ -128,8 +133,8 @@ export function PTorridusContent() { text: ( <> Angelov, A., & Liebl, W. (2006). Insights into extreme thermoacidophily based on - genome analysis of Picrophilus torridus and other thermoacidophilic archaea.{' '} - Journal of Biotechnology, 126(1), 3-10. + genome analysis of Picrophilus torridus and other + thermoacidophilic archaea. Journal of Biotechnology, 126(1), 3-10. ), href: 'https://doi.org/10.1016/j.jbiotec.2006.02.011', @@ -137,9 +142,9 @@ export function PTorridusContent() { { text: ( <> - Fütterer, O., et al. (2004). Genome sequence of Picrophilus torridus and its - implications for life around pH 0. Proceedings of the National Academy of - Sciences, 101(24), 9091-9096. + Fütterer, O., et al. (2004). Genome sequence of{' '} + Picrophilus torridus and its implications for life around pH + 0. Proceedings of the National Academy of Sciences, 101(24), 9091-9096. ), href: 'https://doi.org/10.1073/pnas.0401356101', @@ -157,10 +162,11 @@ export function PTorridusContent() { { text: ( <> - Schleper, C., et al. (1996). Picrophilus oshimae and Picrophilus torridus fam. nov., - gen. nov., sp. nov., two species of hyperacidophilic, thermophilic, heterotrophic, - aerobic archaea. International Journal of Systematic and Evolutionary - Microbiology, 46(3), 814-816. + Schleper, C., et al. (1996). Picrophilus oshimae and{' '} + Picrophilus torridus fam. nov., gen. nov., sp. nov., two + species of hyperacidophilic, thermophilic, heterotrophic, aerobic archaea.{' '} + International Journal of Systematic and Evolutionary Microbiology, 46(3), + 814-816. ), href: 'https://doi.org/10.1099/00207713-46-3-814', diff --git a/src/data/articles.ts b/src/data/articles.ts index 5b8694c..fc4e9e3 100644 --- a/src/data/articles.ts +++ b/src/data/articles.ts @@ -2,7 +2,7 @@ export const articles = [ { slug: 'p-torridus-extremophile', tag: 'Science · Biology', - title: 'Life at the Edge: How P. Torridus Survives at pH 0', + title: 'Life at the Edge: How P. torridus Survives at pH 0', date: 'Feb 2024', readTime: '6 min read', excerpt: