From 8f5703bba52b3f965cfd1d700cd232e6cd5fb696 Mon Sep 17 00:00:00 2001
From: Arina Filatova <a.filatova@student.maastrichtuniversity.nl>
Date: Sun, 29 Sep 2024 15:40:08 +0000
Subject: [PATCH] fix pathways 2

---
 docs/.vuepress/components/IterativeCycle.vue | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/docs/.vuepress/components/IterativeCycle.vue b/docs/.vuepress/components/IterativeCycle.vue
index 17bfb16..6a9c6e2 100644
--- a/docs/.vuepress/components/IterativeCycle.vue
+++ b/docs/.vuepress/components/IterativeCycle.vue
@@ -58,17 +58,18 @@ export default {
                   title: 'Design',
                   description: `
                     <p>Designing DNA fragments for the Gibson assembly.</p>
-                    <p>**Nitrate Reduction Pathways**<br> Nitrates can be removed from water through several bacterial metabolic processes. The most prevalent pathway is denitrification, in which NO₃⁻ is sequentially reduced to NO₂⁻ and then to N₂, which is released into the atmosphere (Zhao et al., 2018). Other important nitrate reduction pathways include dissimilatory NO₃⁻ reduction to NH₄⁺ (DNRA) and NO₃⁻ assimilation (Moreno-Vivián et al., 1999).
+                    <p>**Nitrate Reduction Pathways**</p><br> 
+                    <p>Nitrates can be removed from water through several bacterial metabolic processes. The most prevalent pathway is denitrification, in which NO₃⁻ is sequentially reduced to NO₂⁻ and then to N₂, which is released into the atmosphere (Zhao et al., 2018). Other important nitrate reduction pathways include dissimilatory NO₃⁻ reduction to NH₄⁺ (DNRA) and NO₃⁻ assimilation (Moreno-Vivián et al., 1999).</p>
 
-                    DNRA, typically utilised by bacteria in anaerobic conditions for the purposes of energy conservation, involves converting NO₃⁻ into NH₄⁺ in a two-step reaction via the NO₂⁻ intermediate (Herrmann & Taubert, 2022). While DNRA retains nitrogen in its bioavailable form (NH₄⁺), it does not directly incorporate it into organic compounds. Thus, both denitrification and DNRA result in the loss of available nitrogen—either as atmospheric nitrogen in the case of denitrification or as NH₄⁺ that is not assimilated into biomass in the case of DNRA.
+                    <p>DNRA, typically utilised by bacteria in anaerobic conditions for the purposes of energy conservation, involves converting NO₃⁻ into NH₄⁺ in a two-step reaction via the NO₂⁻ intermediate (Herrmann & Taubert, 2022). While DNRA retains nitrogen in its bioavailable form (NH₄⁺), it does not directly incorporate it into organic compounds. Thus, both denitrification and DNRA result in the loss of available nitrogen—either as atmospheric nitrogen in the case of denitrification or as NH₄⁺ that is not assimilated into biomass in the case of DNRA.</p>
 
-                    In contrast, the assimilatory NO₃⁻ pathway leads to the incorporation of nitrogen into organic compounds, such as amino acids, conserving it within the organism (Moreno-Vivián & Flores, 2007; Jiang & Jiao, 2015). These amino acids can then be used to produce single-cell proteins (SCPs). The assimilatory pathway not only retains nitrogen but also contributes to the production of microbial biomass, thus providing a more efficient means of nitrogen utilisation.
+                    <p>In contrast, the assimilatory NO₃⁻ pathway leads to the incorporation of nitrogen into organic compounds, such as amino acids, conserving it within the organism (Moreno-Vivián & Flores, 2007; Jiang & Jiao, 2015). These amino acids can then be used to produce single-cell proteins (SCPs). The assimilatory pathway not only retains nitrogen but also contributes to the production of microbial biomass, thus providing a more efficient means of nitrogen utilisation.</p>
 
-                    The assimilatory pathway in bacteria comprises several steps. First, NO₃⁻ is captured and internalised from the extracellular environment to the intracellular space. This step is mediated by a NO₃⁻-transporter, which is most commonly an ATP-binding cassette (ABC)-type transporter located in the cytoplasmic membrane (Moreno-Vivián & Flores, 2007). The transporter consists of three subunits: a periplasmic protein that binds NO₃⁻ with high affinity (even at low extracellular concentrations of NO₃⁻), a transmembrane protein that facilitates the transport of NO₃⁻ across the membrane, and a cytoplasmic ATPase anchored to the membrane, which hydrolyses ATP to provide energy for the process (Lin & Stewart, 1997; Moreno-Vivián & Flores, 2007).
+                    <p>The assimilatory pathway in bacteria comprises several steps. First, NO₃⁻ is captured and internalised from the extracellular environment to the intracellular space. This step is mediated by a NO₃⁻-transporter, which is most commonly an ATP-binding cassette (ABC)-type transporter located in the cytoplasmic membrane (Moreno-Vivián & Flores, 2007). The transporter consists of three subunits: a periplasmic protein that binds NO₃⁻ with high affinity (even at low extracellular concentrations of NO₃⁻), a transmembrane protein that facilitates the transport of NO₃⁻ across the membrane, and a cytoplasmic ATPase anchored to the membrane, which hydrolyses ATP to provide energy for the process (Lin & Stewart, 1997; Moreno-Vivián & Flores, 2007).</p>
 
-                    Once NO₃⁻ is internalised, it is then reduced to NO₂⁻ by assimilatory nitrate reductase (Nas). This enzyme is NADH-dependent and has two subunits: a large catalytic subunit, which contains the essential active site for the reduction of NO₃⁻, and a small NADH oxidoreductase subunit, which facilitates the transfer of electrons to the active site (Lin & Stewart, 1997; Moreno-Vivián & Flores, 2007). In the following step, NO₂⁻ is further reduced to NH₄⁺ by the monomeric nitrite reductase (Nir). Afterwards, the produced NH₄⁺ is incorporated into amino acids, specifically glutamine and glutamate, through the GS-GOGAT and GDH pathways (Moreno-Vivián & Flores, 2007; van Heeswijk et al., 2013).
+                    <p>Once NO₃⁻ is internalised, it is then reduced to NO₂⁻ by assimilatory nitrate reductase (Nas). This enzyme is NADH-dependent and has two subunits: a large catalytic subunit, which contains the essential active site for the reduction of NO₃⁻, and a small NADH oxidoreductase subunit, which facilitates the transfer of electrons to the active site (Lin & Stewart, 1997; Moreno-Vivián & Flores, 2007). In the following step, NO₂⁻ is further reduced to NH₄⁺ by the monomeric nitrite reductase (Nir). Afterwards, the produced NH₄⁺ is incorporated into amino acids, specifically glutamine and glutamate, through the GS-GOGAT and GDH pathways (Moreno-Vivián & Flores, 2007; van Heeswijk et al., 2013).</p>
 
-                    The GS-GOGAT pathway consists of two key steps. First, the enzyme glutamine synthetase (GS) catalyses an ATP-dependent reaction that converts glutamate to glutamine by incorporating an ammonium ion. Following this, glutamate synthase (GOGAT) transfers the amide group from glutamine to 2-oxoglutarate, resulting in the production of two glutamate molecules. In contrast, the GDH pathway employs a more direct approach. The enzyme glutamate dehydrogenase (GDH) catalyses the incorporation of an ammonium ion (NH₄⁺) directly into 2-oxoglutarate, forming glutamate in a single step. The resulting amino acids, glutamate and glutamine, undergo further transamidation and transamination, yielding various amino acids, which then serve as building blocks for the biosynthesis of proteins during translation (van Heeswijk et al., 2013).</p>
+                    <p>The GS-GOGAT pathway consists of two key steps. First, the enzyme glutamine synthetase (GS) catalyses an ATP-dependent reaction that converts glutamate to glutamine by incorporating an ammonium ion. Following this, glutamate synthase (GOGAT) transfers the amide group from glutamine to 2-oxoglutarate, resulting in the production of two glutamate molecules. In contrast, the GDH pathway employs a more direct approach. The enzyme glutamate dehydrogenase (GDH) catalyses the incorporation of an ammonium ion (NH₄⁺) directly into 2-oxoglutarate, forming glutamate in a single step. The resulting amino acids, glutamate and glutamine, undergo further transamidation and transamination, yielding various amino acids, which then serve as building blocks for the biosynthesis of proteins during translation (van Heeswijk et al., 2013).</p>
                   `
                 },
                 {
-- 
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