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Biology subjects

Kaur, M.

Publications and source records attributed to Kaur, M..

At least 19 recordsLinked to original sources

Reciprocal control of the stomach and intestine by viscerosensory neurons in caudal brainstem

Digestion requires precisely timed transit of food through the gastrointestinal tract. Here we show that emptying of food from the stomach occurs in discrete pulses, separated by pauses that allow the proximal duodenum to clear before the next bolus arrives. By combining X-ray fluoroscopy of the gut with calcium imaging of the brainstem, we identify a population of neurons defined by expression of neuropeptide FF (NPFF) that tracks these duodenal dynamics. Stimulation of NPFF neurons induces a coordinated response that inhibits gastric emptying and accelerates intestinal transit, thereby clearing the proximal intestine for the next bolus of food. These neurons also bidirectionally control food intake through cholinergic signaling in the gut. These findings reveal a mechanism by which brainstem transforms the sensory detection of nutrients in the duodenum into the opposing control of the stomach and intestine. They also establish an experimental approach for dissecting gut-brain signaling in behaving animals.

neuroscience↗

MCT1 activity defines an aggressive metabolic phenotype and therapeutic target in non-small cell lung cancer

Lactate uptake through monocarboxylate transporter 1 (MCT1) is associated with aggressive disease in non-small cell lung cancer (NSCLC), but how lactate transport supports tumor metabolism remains incompletely understood. Integrating stable isotope tracing, metabolomics, and transcriptomics across patient tumors, animal models, and cultured cells, we show that elevated lactate utilization and SLC16A1 expression correlate with worse clinical outcomes in NSCLC. Although MCT1 inhibition with AZD3965 does not significantly impair tumor growth as a monotherapy, it depletes purine-associated metabolite pools, alters redox balance, and induces a conserved transcriptional response involving MYC target dysregulation and suppression of nucleotide metabolism genes. Addition of exogenous hypoxanthine, or expression of the E. coli-derived NADH-producing enzyme soluble transhydrogenase, partially rescues the effects of MCT1 inhibition. Importantly, this metabolically compromised state sensitizes NSCLC to nucleotide-targeting chemotherapies, including pemetrexed. These findings reveal that MCT1 mediated lactate uptake sustains nucleotide homeostasis in NSCLC, and that its inhibition exposes a context-dependent vulnerability that can be leveraged to enhance chemotherapy efficacy.

cancer biology↗

Genetically-encoded discovery and development of peptide-macrocycle imaging agents for PD-L1

The unique cell surface composition of tumor cells forms the molecular basis for many targeting and cell-based therapies. Here, we describe the development of novel peptide-based targeting agents for programmed death ligand 1 (PD-L1). Molecular imaging by peptide agents, coupled with therapeutic intervention using the same modality, represents a critical advancement in cancer management. Whole-body PET imaging of PD-L1 expression offers a superior alternative to traditional immuno-histochemistry, making PD-L1 radiodiagnostic imaging a highly sought-after modality. PD-L1 targeting modalities developed for clinical imaging to date can be divided into antibodies, protein domains, and small macrocyclic peptides with fewer than 20 amino acids. The latter modalities can address many challenges seen in antibody-based targeting vectors. All potent PD-L1 targeting peptide modalities reported to date rely extensively on non-canonical amino acids (ncAAs). Here, we report a comprehensive structure-activity relationship (SAR) analysis of a family of macrocycles discovered from an Sx2Cx8Cx2 phage-display library composed entirely of natural amino acids (x represents 19 natural amino acids excluding Cys). Using >10,000 variants in ''focused'' phage-display libraries, we optimized these macrocycles to achieve single-digit-nanomolar potency in protein- and cell-based assays. En route to this optimization, the activity of 216 synthetic macrocycles towards PD-L1 was measured in five distinct assays; two leads have been evaluated by imaging in tumor xenografts in mice, and the X-ray structure of one advanced lead in complex with PD-L1 has been determined at 2.78 [A] resolution. This publication demonstrates the development potential of PD-L1-targeting macrocycles that do not require extensive incorporation of ncAAs and the democratization of discovery by mapping the optimization path to single-digit-nanomolar assets for targeted radiopharmaceuticals via canonical phage-display technology.

pharmacology and toxicology↗

Understanding the physiological alterations of Vibrio cholerae upon exposure to L-ascorbic acid

The scourge of cholera remains a major global public health threat. It affects up to 4 million people worldwide and causes tens of thousands of deaths each year. The disease is experiencing a concerning resurgence in many parts of Africa, the Middle East, and Asia. To effectively tackle cholera and circumvent rising antimicrobial resistance, targeted biological and preventive approaches, complementing traditional rehydration, are urgently needed. In this regard, our group has demonstrated the efficacy of L-ascorbic acid in controlling the growth and pathogenesis of Vibrio cholerae in vitro. The present work further provides a mechanistic elucidation of the L-ascorbic acid-mediated physiological changes in V. cholerae and also bolsters such a non-antibiotic approach to control cholera.

microbiology↗

Functional segregation of body-brain signals in the area postrema

Nausea arises from activation of specialized neurons in the area postrema (AP)1-8. The AP also mediates much of the satiety produced by GLP1R agonists9-12, suggesting a broader role in non-aversive physiology, yet the functions of AP cell types are not well understood. Here, we have used optical recordings in behaving mice to systematically define the natural regulation of an array of AP neurons, including the cell types that are principal targets of widely-used weight loss drugs. We discover that neurons expressing GFRAL, the receptor for the sickness-related hormone GDF15, are unexpectedly activated when mice consume food rich in fat. This fat-specific GFRAL neuron activation is required for fat satiation but does not involve GDF15 or canonical gut-brain pathways. Instead, "anti-nausea" neurons expressing GIPR, which directly inhibit GFRAL neurons, are selectively activated by sugar, enabling macronutrient-specific gating of GFRAL responses. In addition, we show that CALCR neurons link intestinal hyperosmolality to the suppression of feeding, whereas PRLHR neurons respond to changes in blood volume and pressure. These findings reveal a broad role for AP cell types in sensing and responding to physiologic signals unrelated to nausea. They also reveal that GFRAL and GIPR neurons, which are key targets of the weight-loss drug tirzepatide, have a natural function in sensing ingestion of fat and sugar, respectively.

neuroscience↗

CRADLE: A Clinically Robust, Anatomy-Aware Post-Processing Framework for Infant GMA Landmark Tracking in 2D Videos

Accurate pose estimation is central to automated infant General Movements Assessment during the fidgety period, when subtle limb movements, particularly at distal joints inform neurodevelopmental risks. Robust 2D pose tracking from handheld videos remains challenging in real-world settings, where occlusion, rapid motions, and visually ambiguous smaller joints frequently compromise anatomical accuracy. We present CRADLE, a clinically motivated, anatomy-aware post-processing pipeline designed to refine infant 2D movement trajectories across 24-anatomocal landmarks detected by our DeepLabCut-trained model. CRADLE integrates segment-length constraints, velocity-based anomaly detection, anatomically constrained interpolation, and Kalman filtering to correct both large localization failures and subtle persistent joint misplacements without relying primarily on confidence scores. Evaluations against conventional Confidence-Thresholding using Mean Absolute Error (MAE), {Delta}MAE, average Percentage of Correct Keypoints, and net keypoint correction rate showed consistently reduced or preserved error while maintaining accurate trajectories, with the strongest gains achieved at clinically important distal joints. Mean improvements reached up to 5 pixels for some smaller distal landmarks, large-magnitude corrections occurred more often than with Confidence-Thresholding, and well-localised joints remained largely unaffected. Positive net correction rates across metacarpophalangeal and metatarsophalangeal distal-landmarks further confirmed a favourable correction-degradation balance. By improving pose trajectory quality, CRADLE enhances the reliability of downstream movement analysis.

bioengineering↗

Vacidobactin A: An anti-Pseudomonas aeruginosa siderophore

Multidrug-resistant (MDR) Pseudomonas aeruginosa poses a significant clinical challenge due to its poorly permeable outer membrane, efflux systems, biofilm formation, and rapid acquisition of resistance genes. The lack of new treatments for P. aeruginosa infections underscores the necessity for innovative therapeutic solutions. Iron uptake is essential for bacterial survival, making it a promising target for the development of new antimicrobials. Iron-chelating siderophores are vital for bacterial iron acquisition, important agents for direct antimicrobial action, adjuvants to enhance the effectiveness of currently available antibiotics, and components of prodrugs that facilitate the transport of covalently linked antibiotics into the cell. Here, we report the anti-pseudomonal activity of vacidobactin A, a siderophore produced by the soil bacterium Variovorax paradoxus, identified through a screen of natural product extracts targeting a clinical MDR strain of P. aeruginosa. Vacidobactin A inhibits P. aeruginosa growth by limiting iron availability, particularly in strains that do not produce pyoverdine, their native siderophore. Expression of a TonB-dependent transporter sourced from the vacidobactin producer in a P. aeruginosa pyoverdine and pyochelin-null mutant restored its ability to acquire iron and grow in the presence of vacidobactin. Additionally, vacidobactin A synergized with thiostrepton, which hijacks pyoverdine receptors to enter the cell and inhibit protein synthesis. This study supports the therapeutic potential of targeting P. aeruginosa iron acquisition pathways and leveraging siderophores as adjuvants to enhance the efficacy of existing antimicrobials. These findings, along with recent advancements in siderophore-based research and combination therapies, offer innovative strategies to combat antibiotic-resistant infections. IMPORTANCEMultidrug-resistant Pseudomonas aeruginosa is a critical priority pathogen for which new therapeutic strategies are urgently needed. Iron acquisition is essential for P. aeruginosa survival and virulence, yet remains underexploited as a drug target. Here, we demonstrate that vacidobactin A, a siderophore produced by Variovorax paradoxus, suppresses P. aeruginosa growth by limiting iron availability, particularly in strains deficient in pyoverdine production. We further show that vacidobactin A enhances the activity of thiostrepton, an antibiotic that exploits siderophore uptake pathways. These findings highlight iron competition as a source of anti-pseudomonal agents and support the development of siderophore-based therapeutics and adjuvant strategies. Targeting iron acquisition networks offers a mechanistically distinct approach to combat antibiotic resistance and expands the repertoire of vulnerabilities that can be leveraged against this highly drug-resistant pathogen.

microbiology↗

Fine-tuning STEAP1 protein expression and purification to preserve its conformation and function

Six-transmembrane Epithelial Antigen of the Prostate 1 (STEAP1) has emerged as a promising therapeutic target for prostate cancer. We have optimized the expression and purification conditions of human STEAP1 to maximize the production of its homotrimeric form, which is crucial for metal ion reduction and maintaining cellular redox balance. Proteins obtained from these optimized conditions were complexed with both heme and flavin-adenine dinucleotide (FAD), two cofactors that are fundamental to STEAP functionality, suggesting native folding and interactions of the protein. In addition, we compared the impact of stable and transient expression systems on the protein quality of STEAP1. We found that stable expression promoted heme incorporation, improved expression homogeneity, and ensured correct protein orientation on cell surfaces. Our findings present effective strategies for optimizing the recombinant production of STEAP1, with potential applicability to other STEAP family proteins to facilitate therapeutic discovery.

biochemistry↗

European taurine vs Indian indicine cattle: a comparative genomic study reveals regions of differentiation during evolution and selection during crossbreeding

Cattle are broadly classified into two subspecies: Bos taurus, adapted to temperate climates, and Bos indicus, adapted to tropical environments. Indicine cattle show better heat tolerance and stronger disease resistance, whereas taurine cattle are known for higher milk yield and better meat quality. Improving milk yield while maintaining resistance to heat stress and infectious diseases is an important objective in cattle breeding. Marker-assisted selection is an effective approach for improving economically important traits, highlighting the need to understand genetic differences between taurine and indicine cattle. However, genome-wide comparisons between European taurine and Indian indicine cattle remain limited. To address this gap, whole-genome sequencing of 48 Indian indicine cattle was performed and combined with publicly available data. This enabled a comparative genomic analysis of 74 Indian indicine and 83 European taurine individuals to identify genes involved in heat tolerance and immune response. Genome-wide analyses using Fst and XP-CLR identified 4,343 and 1,457 differentiated genes, respectively, with 826 genes common to both methods. These genes were mainly associated with immune response, protein stability, and cytoskeletal structure. Strong selection signals were observed in three heat shock protein genes (DNAJC11, DNAJC5, and DNAJB11) and 229 immune-related genes. To examine the inheritance of these genes through crossbreeding, a haplotype-resolved genome assembly was generated for the Indian crossbreed Sunandini, which showed predominantly taurine ancestry (69.13-96.04%), with a smaller indicine contribution (1.22-1.87%). Several genes related to heat tolerance and immune response were inherited exclusively from indicine cattle, highlighting their importance for environmental adaptation and future breeding programs.

genomics↗

Blown-Arc plasma: A safe treatment with potential to boost wheat seed germination without phytotoxicity.

ContextCold plasma is an ionised gas composed of reactive nitrogen and oxygen species, with demonstrated potential for improving wheat seed vigour. AimTo assess wheat seed vigour and grain quality after Blown-Arc plasma treatment. MethodsWheat seeds were treated with Blown-Arc plasma for 60 or 180 s from a distance of 21 cm in a closed environment to assess in vitro germination, seed quality, seedling emergence, and crop yield in the field. Key ResultsSeeds treated with Blown-Arc plasma showed significantly faster initial in vitro germination (day 4), although total germination by day 8 was similar to untreated controls. In the field, the treated seed showed no significant difference in seedling emergence in 2020, but in 2021 seed treated for 180 s produced a significantly lower number of seedlings, possibly due to differences in the soil microbial environment. The wheat grown from 180 s Blown-Arc plasma-treated seed produced more heads per plant; however, overall yield was unchanged. The treatment had no adverse effect on grain quality parameters, all remaining within acceptable Australian standards. ConclusionsBlown-Arc plasma did not alter seedling emergence, yield, or grain quality properties of the crop produced from treated wheat seeds. ImplicationsBlown-arc plasma is a safe treatment that can potentially increase wheat seed germination without affecting grain quality or yield. Faster germination of seeds when sown under adequate moisture may promote healthy root systems and plant growth. Further research is needed to determine how these benefits translate under variable field conditions in Australian wheat-growing regions.

plant biology↗

Plasma plasmalogen levels and risk of lymph node positive breast cancer

Lymph node involvement is a key predictor of poor breast cancer prognosis. Systemic lipid alterations can contribute to cancer cell survival in lymph nodes, but their relevance in humans remains unclear. Here, we combine human epidemiologic analyses from the Nurses Health Study 2 and complementary mechanistic studies in mouse models to investigate how systemic lipid profiles relate to lymph node positive breast cancer. We show that in pre-diagnostic human plasma (n=511), lower levels of phosphatidylethanolamine (PE) and phosphatidylcholine (PC)-enriched plasmalogens are associated with increased risk of lymph node positivity, with stronger associations in samples collected closer to diagnosis. Consistent with the human data, lower levels of PE and PC-enriched plasma plasmalogens are found in mice with nodal involvement. Furthermore, in mice, dietary PUFA depletion reduces lipid oxidation in breast cancer cells in lymph nodes and promotes their survival and metastatic spread. These findings suggest that reduced levels of PE and PC-plasmalogens and decreased PUFA availability creates a lipid environment that enables breast cancer lymph node involvement.

cancer biology↗

RBProximity-CLIP Enables Subcellular Mapping of RNA-Binding Protein Interactions at Nucleotide Resolution

RNA-binding proteins (RBPs) enable post-transcriptional gene regulation (PTGR) through specific interactions with RNA molecules, influencing processes ranging from nuclear processing and export to cytoplasmic localization, translation, storage and degradation. A key determinant of PTGR processes is the subcellular compartmentalization of RBPs, which dictates RNA targets they can access and the regulation performed in that environment. To characterize RBP-RNA interactions at subcellular resolution, we developed RBProximity-CLIP. RBProximity-CLIP enables compartment-specific isolation and profiling of individual RBP-RNA interactions by combining APEX2-based proximity labeling and 4-thiouridine-enhanced RNA-protein crosslinking, with sequential RBP- and biotin-affinity purifications. Using this approach, we profiled the RNA targets of three RBPs, AGO2, YBX1, and ELAVL1, across the cytoplasmic, nuclear, and nucleolar compartments, revealing nucleus-specific miRNA-mediated AGO2 targets, as well as subsets of YBX1 and ELAVL1 targets that differ by compartment, yet share identical binding motifs. RBProximity-CLIP enables specific and sensitive detection of compartment-specific RBP-RNA interactomes, thereby providing new insight into spatial gene regulation by RBPs.

cell biology↗

Nanoscale PI(4,5)P2 partitioning driven by FGF2 oligomerization triggers membrane pore formation

Fibroblast Growth Factor 2 (FGF2) is a potent tumor cell survival factor. Unlike most secreted proteins, FGF2 lacks a signal peptide and is exported by an unconventional secretory pathway, bypassing the ER/Golgi system. A key event of this unusual secretory mechanism is FGF2 recruitment at the inner plasma membrane leaflet mediated by the phosphoinositide PI(4,5)P2. This interaction induces FGF2 oligomerization which, in turn triggers the formation of a transient lipidic membrane pore with a toroidal structure. FGF2 oligomers populating such membrane pores are captured and disassembled at the outer plasma membrane leaflet through interactions with heparan sulfate chains of the cell surface proteoglycan GPC1, resulting in full translocation of FGF2 across the plasma membrane. Once FGF2 appears on cell surfaces, it engages in signaling complexes initiating autocrine or paracrine signaling. Here, using a multidisciplinary and multiscale approach, we show that FGF2 self-assembles into oligomers that induce lateral PI(4,5)P2 partitioning and membrane remodeling. This process depends on PI(4,5)P2 reaching a critical local threshold concentration that, due to its non-bilayer properties destabilizes the bilayer, facilitating pore formation and FGF2 translocation across the plasma membrane. Our findings highlight a fundamental principle of how protein oligomerization can induce lateral partitioning of membrane lipids that in turn leads to a drastic membrane remodeling event: the transformation of the lipid bilayer into a toroidal membrane pore. The underlying mechanism is likely to be applicable to a wide range of membrane lipid interacting proteins that induce membrane remodeling in other cellular processes.

biochemistry↗

PRESTIGE-ST: Patch Resolution and Encoder STrategies for Inference of Gene Expression from Spatial Transcriptomics

Spatial Transcriptomics (ST) integrates histology with spatially resolved gene expression, offering rich insights into tissue architecture and function. However, its clinical and large-scale deployment is hindered by high costs, technical complexity, and limited accessibility. To address this, computational pathology methods have emerged to predict gene expression directly from histology images, typically framing the task as a multi-output regression problem mapping image patches to gene expression profiles. While several Convolutional Neural Network (CNN) models have been proposed, little is known about how performance is influenced by (a) the number of trainable parameters and (b) the patch size used for prediction. Moreover, existing studies rely primarily on quantitative metrics and overlook biological relevance of predictions. In this study, we systematically evaluated multiple convolution based models (including a Vision Transformer (ViT) model) with different patch sizes on the Xenium based Autoimmune Machine Learning Challenge (AMLC) dataset. We assessed model performance on both globally expressed genes and subsets enriched for immune or disease associated pathways. Our findings reveal that compact CNNs trained on larger patches outperform deeper models, offering superior accuracy in predicting gene expression, especially for biologically important genes. These insights provide practical guidance for designing efficient and biologically meaningful models in the emerging field of image-based gene expression prediction. CCS CONCEPTSComputing methodologies [->] Computer vision; Neural networks; * Applied computing [->] Computational genomics; Imaging.

pathology↗

Gut microbes mediate the synergistic effects of dietary cholesterol and saturated fat in driving fibrosing MASH

Metabolic dysfunction-associated steatotic liver disease (MASLD) affects approximately one-third of the global population and can progress to metabolic dysfunction-associated steatohepatitis (MASH) with fibrosis, increasing risk of cirrhosis, hepatocellular carcinoma, and mortality. Gut microbes driven by diets high in saturated fat, simple sugar, and cholesterol contribute to disease progression, yet underlying mechanisms remain undefined. We explored the independent and synergistic effects of dietary saturated fat and cholesterol on MASH development using specific pathogen-free (SPF) and germ-free (GF) mice. We demonstrate that 1) both dietary cholesterol and saturated fat are required to induce fibrosing MASH in SPF mice, whereas GF mice are protected, 2) saturated fat and cholesterol individually alter gut microbial membership, potentially via altered bile acid metabolism, while their combination promotes a distinct composition, including an increase in Parasutterella spp. which correlates with hepatic fibrosis, and 3) diluted cecal contents from SPF, but not GF, mice fed high-fat, high-cholesterol diets are enriched in deoxycholic acid and activate human hepatic stellate cells in vitro, suggesting a mechanistic link between dietary lipid-induced microbiota and liver fibrogenesis. These findings reveal how specific Western dietary components shape the gut microbiota and contribute to hepatic liver fibrosis via stellate activation, offering potential targets for therapeutic intervention in MASLD/MASH.

physiology↗

Plasma membrane transbilayer asymmetry of PI(4,5)P2 drives unconventional secretion of Fibroblast Growth Factor 2

Unconventional secretion of Fibroblast Growth Factor 2 (FGF2) is based upon direct self-translocation across the plasma membrane, a process that involves the transient formation of a lipidic membrane pore. The opening of this pore is triggered by PI(4,5)P2-dependent oligomerization of FGF2 at the inner plasma membrane leaflet. Subsequently, FGF2 oligomers populating the pore are captured by membrane-proximal heparan sulfate chains of Glypican-1 (GPC1), resulting in translocation of FGF2 to cell surfaces. PI(4,5)P2 is a highly negatively charged membrane lipid that is exclusively localized at the inner plasma membrane leaflet. Therefore, local accumulation of PI(4,5)P2 triggered by FGF2 oligomerization at the inner plasma membrane leaflet produces a steep and spatially restricted electrochemical gradient across the plasma membrane. Furthermore, PI(4,5)P2 has a wedge-like shape, turning it into a non-bilayer lipid that destabilizes membranes at high local concentrations. Here we demonstrate that an asymmetric distribution of PI(4,5)P2 across the leaflets of synthetic lipid bilayers accelerates the opening of FGF2-induced membrane pores. Consistently, we find unconventional secretion of FGF2 from cells to be inhibited under conditions compromising the native transbilayer asymmetry of PI(4,5)P2 of plasma membranes. We propose the asymmetric distribution of PI(4,5)P2 to lower the free energy required to transform the lipid bilayer into a lipidic membrane pore. Furthermore, in the proximity of FGF2 membrane translocation sites, PI(4,5)P2 in the outer plasma membrane leaflet could potentially repel negatively charged heparan sulfates chains compromising the function of GPC1 in FGF2 translocation into the extracellular space. Thus, transbilayer asymmetry of PI(4,5)P2 is a key parameter enabling fast kinetics of FGF2 membrane translocation into the extracellular space.

biochemistry↗

Theta oscillations dictate the evolution of memories across periods of sleep or wakefulness

How does the brain select which experiences to consolidate into long-term memory? Numerous neurobiological frameworks suggest that certain memories are "tagged" at learning for consolidation during later sleep. However, experimental evidence of such a tagging mechanism in the human brain is lacking. Using electroencephalography in humans, we reliably differentiate brain states for memories that are tagged at learning for consolidation across sleep or wakefulness. The tagging of memories for consolidation across sleep (but not wakefulness) was linked to 3-8Hz theta rhythms during learning. The magnitude of this tagging-related theta response predicted the coupling of slow oscillations to sleep spindles during post-learning sleep (an established neural correlate of sleep-dependent memory processing). In turn, slow oscillation-spindle coupling was associated with better memory performance at the post-sleep test. These findings provide new insights into the neural mechanisms through which our brains determine which information is retained for the future.

neuroscience↗

Structure of Blm10:13S proteasome intermediate reveals parallel assembly pathways for the proteasome core particle

Proteasomes are formed by chaperone-assisted assembly of core particles (CPs) and regulatory particles (RPs). The CP chaperone dimer Pba1/Pba2 binds early to proteasome subunits, and is thought to be replaced by Blm10 to form Blm10:CP, which promotes ATP-independent degradation of disordered proteins. Here, we present evidence of distinct parallel assembly pathways for CP by solving five cryo-EM structures including a Blm10:13S pre-assembly intermediate. Our data conflict with the current model of Blm10 and Pba1/Pba2 sequential activity in a single assembly pathway, as we find their CP binding is mutually exclusive and both are present on early and late assembly intermediates. CP affinity for Pba1/Pba2 is reduced during maturation, promoting Pba1/Pba2 release. We find Blm10 undergoes no such affinity switch, suggesting this pathway predominantly yields mature Blm10-bound CP. Altogether, our findings conflict with the current paradigm of sequential CP binding to instead indicate parallel assembly pathways by Pba1/Pba2 and Blm10.

biochemistry↗