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WHAT I SEE IN MY PRESCRIPTION

While we would love for election season to be over right about now, we've gotta admit that the resulting political memes have been top-notch. The internet has been loving this particular dank meme, which shows Speaker of the House Nancy Pelosi ripping up Donald Trump's State of the Union speech.

DOGE trades at premium on Upbit and Bithumb relative to Binance. - The price differential is still noticeably lower than the previous bull market peaks. Today is just that day as Koreans seem to be jumping into the DOGE market, driving prices higher and creating a noticeable premium on local…

GCMGames via Eneba has Xbox Game Pass Ultimate: 3 Month Subscription (Digital Delivery - Stackable) on sale for around $26.99 when you follow the instructions below:

Deal Instructions:

• Go to product page
• Click on Buy Now.
• Click on "Got discount code?" under "Total Price" and apply discount code XGPUUS
• Proceed to checkout.
• Total price after service/payment fees should be around $26.99

Note: Codes are stackable, you can stack up to three years.

By Keegan Kelly Published: November 11th, 2024

This is, without doubt, the stupidest coffee device I have ever bought. But I have bought it.

The post A Spring Trip to Lake Baikal appeared first on English Russia.

The conference has been scheduled for Oct. 9-11, 2025. All Princeton alumni are invited back to campus for the gathering. 

Vistors to the North Coast 500 are being asked to sign a pledge amin concerns of speeding drivers

For those who seek the thrill of adventure and the rush of adrenaline, the Smoky Mountains present a vast playground of untamed wilderness and exhilarating activities. This majestic region is not just for the serene soul seeking peace in nature but also for the adventure lovers who crave excitement and challenge. From the rugged trails to the rapid waters, the Smokies offer a diverse array of experiences that cater to every kind of thrill-seeker. Let’s delve into ten thrilling activities that promise to ignite your adventurous spirit in the heart of the Smokies. 1. Hiking to Alum Cave Bluffs The journey to Alum Cave Bluffs is one of the most rewarding adventures the Smokies have to offer. This 4.6-mile hike is not just a physical challenge; it’s a passage through the varying moods of the mountains. As you ascend through the dense forest, you’ll encounter unique geological features, like Arch Rock, and the sweeping views from Inspiration Point. The trail culminates at Alum Cave Bluff, offering spectacular vistas. It’s an immersive experience that combines physical exertion with the tranquil beauty of the natural surroundings. 2. Jeep Ride Adventures For those who prefer their adventures on wheels, a Jeep ride through the Smoky Mountains provides an exhilarating way to explore the rugged landscapes. The winding mountain roads and off-road trails offer a thrilling ride with panoramic views that are simply unmatched. For Jeep owners, the experience can be further enhanced by customizing their vehicles with accessories from local outfitters like Smoky Mountain Off-Road Outfitters. Adding specialized Jeep badges not only personalizes your ride but also commemorates your adventure in the Smokies, making each journey as unique as the trails you choose to explore. 3. Whitewater Rafting on the Pigeon River Whitewater rafting on the Pigeon River is an adrenaline-packed activity that draws adventure-seekers from all over. The river features sections suitable for all levels, from the gentle flows ideal for beginners to the challenging Class III and IV rapids that test even the most experienced rafters. This exhilarating experience not only offers a thrilling ride through the rapids but also provides a unique perspective of the Smokies’ natural beauty, all from the heart of the river. 4. Ziplining Through the Canopy Ziplining offers a bird’s-eye view of the Smokies’ breathtaking landscapes, making it a must-try for anyone seeking adventure. Gliding through the canopy, adventurers can experience the forest in a way that’s impossible to do so from the ground. The sensation of flying above the trees, with the wind in your face and the valley below, is both exhilarating and serene. Zipline tours in the Smokies cater to a range of ages and thrill levels, ensuring that everyone can enjoy the rush of soaring through the air. 5. Mountain Biking on the Trails Mountain biking in the Smokies offers an off-road adventure that combines physical challenge with the natural beauty of the mountains. The region boasts a variety of trails, from gentle forest paths to rugged mountain tracks that require skill and endurance. Biking through these landscapes offers a unique way to explore the wilderness, with the added thrill of navigating the terrain at speed. It’s an activity that appeals to both seasoned bikers and those looking to try something new and exciting. 6. Rock Climbing and Bouldering The rugged terrain of the Smoky Mountains offers prime spots for rock climbing and bouldering, providing both beginners and seasoned climbers with the perfect setting to test their skills. The region’s natural rock formations offer a variety of climbs, from short, challenging boulders to towering cliff faces that demand endurance and technique. Climbing in the Smokies is not just about getting an adrenaline rush; it’s an opportunity to connect with the raw beauty of the mountains, offering a sense of achievement and exhilaration that is unmatched. 7. Horseback Riding Through the Forest Horseback riding through the Smoky Mountains offers a unique blend of adventure and tranquility. It’s an opportunity to explore the dense forests and rolling hills at a leisurely pace, allowing for a deeper connection with the natural surroundings. Riding trails meander through the heart of the Smokies, offering riders stunning views and the chance to encounter wildlife in their natural habitat. Whether you’re an experienced rider or trying it for the first time, horseback riding is a wonderful way to experience the Smokies’ serene beauty. 8. Fishing in Mountain Streams Fishing in the pristine mountain streams of the Smokies is an adventure that combines the thrill of the catch with the peace of being surrounded by nature. The clear, cool waters are home to a variety of fish, including trout, providing both challenge and reward for anglers. Fishing in the Smokies is not just about the sport; it’s an immersive experience that allows you to slow down and appreciate the subtle beauty of the mountain landscapes. Whether you’re fly fishing or using traditional methods, the streams of the Smokies offer a serene yet adventurous escape. 9. Exploring Caves and Caverns Delving into the caves and caverns of the Smoky Mountains is an adventure that takes you beneath the surface of the earth into a world of ancient rock formations, hidden chambers, and underground streams. Cave exploration in the Smokies allows adventurers to experience the thrill of discovery and the awe of natural wonders that have formed over millions of years. The cool, dark environments of these caves provide a stark contrast to the lush, vibrant landscapes above, offering a unique and thrilling exploration experience. 10. Camping Under the Stars Camping in the Smoky Mountains is the ultimate adventure for those who wish to immerse themselves fully in the natural beauty of the region. Whether you’re setting up camp in a designated campground or venturing into the backcountry, camping allows you to connect with the wilderness in a profound way. Sleeping under the stars, waking up to the sounds of nature, and living off the land are experiences that not only challenge but also rejuvenate the spirit. Camping here offers a blend of adventure, tranquility, and a deep connection with the natural world. Conclusion: More Than A Rush! The Smoky Mountains are a treasure trove of adventures, offering a plethora of activities for those who seek the thrill of the outdoors. The best part is that these adventures not only provide an adrenaline rush but also allow you to connect with nature in an intimate and memorable way. Whether you’re a seasoned adventurer or looking to step out of your comfort zone, the Smokies invite you to explore, challenge yourself, and create unforgettable memories amidst their majestic landscapes.

The post An Adventure Lover’s Guide For a Trip to The Smokies appeared first on Geeky Traveller.

A selection of pictures on the theme of 'road trip'.

Dart Charge bailiffs have collected nearly £112m since 2019, it emerges.

The itinerary on my 13-day Norwegian cruise was too packed. Spending only two of the 13 days at sea left me exhausted, even as a seasoned cruiser.

If you’re an entrepreneur nurturing your own company to a full-blown success, you are always looking for insights and ideas to take your business to the next level, right? But you’re probably super busy as well, and don’t always have the time to figure out where you should be looking for those insights.

If you run an eCommerce website, you may prefer to use a graphic as the call-to-action button for your subscription-style products or services. Below you can find a number of different subscription buttons suitable for use on a website’s landing page or the product page. Want some Buy Now button or Add to Cart button […]

The post Subscription Button Graphics for eCommerce Websites appeared first on Tips and Tricks HQ.

Iif you're a new owner or just bought your first travel trailer, these are the must-have travel trailer accessories that may not have occurred to you.

The post Travel Trailer Accessories You Absolutely Need (Read This BEFORE Your First Trip) appeared first on Vagabondish.

Plan a trip to Rome, and you’ll wish you were there for weeks! From the Colosseum to the Vatican Museums, there’s a lot in the Eternal City to check off your bucket list.  But if you can tear yourself away from Rome’s top attractions, there are plenty of excellent day trips from Rome. Rome is […]

The post 18 Fun Day Trips from Rome appeared first on Adventurous Kate.

I’ve been to Las Vegas a handful of times for conferences and weekend trips. I don’t gamble, but I’d do some other Vegas-y things — graze the buffets, go to shows and nightclubs, and lounge around the pool. With the exception of the pools (I love the city’s extravagant pools), I was never a big fan of the […]

The article Getting Off the Las Vegas Strip originated at EverInTransit.com

Mitochondria are specialized compartments that produce requisite ATP to fuel cellular functions and serve as centers of metabolite processing, cellular signaling, and apoptosis. To accomplish these roles, mitochondria rely on the genetic information in their small genome (mitochondrial DNA) and the nucleus. A growing appreciation for mitochondria's role in a myriad of human diseases, including inherited genetic disorders, degenerative diseases, inflammation, and cancer, has fueled the study of biochemical mechanisms that control mitochondrial function. The mitochondrial transcriptional machinery is different from nuclear machinery. The in vitro re-constituted transcriptional complexes of Saccharomyces cerevisiae (yeast) and humans, aided with high-resolution structures and biochemical characterizations, have provided a deeper understanding of the mechanism and regulation of mitochondrial DNA transcription. In this review, we will discuss recent advances in the structure and mechanism of mitochondrial transcription initiation. We will follow up with recent discoveries and formative findings regarding the regulatory events that control mitochondrial DNA transcription, focusing on those involved in cross-talk between the mitochondria and nucleus.

Timothy J. Griffin
Apr 1, 2002; 1:323-333
Research

Linn Fagerberg
Feb 1, 2014; 13:397-406
Research

HIV Type 1 (HIV-1) and simian immunodeficiency virus (SIV) display differential replication kinetics in macrophages. This is because high expression levels of the active host deoxynucleotide triphosphohydrolase sterile α motif domain and histidine-aspartate domain–containing protein 1 (SAMHD1) deplete intracellular dNTPs, which restrict HIV-1 reverse transcription, and result in a restrictive infection in this myeloid cell type. Some SIVs overcome SAMHD1 restriction using viral protein X (Vpx), a viral accessory protein that induces proteasomal degradation of SAMHD1, increasing cellular dNTP concentrations and enabling efficient proviral DNA synthesis. We previously reported that SAMHD1-noncounteracting lentiviruses may have evolved to harbor RT proteins that efficiently polymerize DNA, even at low dNTP concentrations, to circumvent SAMHD1 restriction. Here we investigated whether RTs from SIVmac239 virus lacking a Vpx protein evolve during in vivo infection to more efficiently synthesize DNA at the low dNTP concentrations found in macrophages. Sequence analysis of RTs cloned from Vpx (+) and Vpx (−) SIVmac239–infected animals revealed that Vpx (−) RTs contained more extensive mutations than Vpx (+) RTs. Although the amino acid substitutions were dispersed indiscriminately across the protein, steady-state and pre-steady-state analysis demonstrated that selected SIVmac239 Vpx (−) RTs are characterized by higher catalytic efficiency and incorporation efficiency values than RTs cloned from SIVmac239 Vpx (+) infections. Overall, this study supports the possibility that the loss of Vpx may generate in vivo SIVmac239 RT variants that can counteract the limited availability of dNTP substrate in macrophages.

Hepatocyte nuclear factor-1β (HNF-1β) is a tissue-specific transcription factor that is required for normal kidney development and renal epithelial differentiation. Mutations of HNF-1β produce congenital kidney abnormalities and inherited renal tubulopathies. Here, we show that ablation of HNF-1β in mIMCD3 renal epithelial cells results in activation of β-catenin and increased expression of lymphoid enhancer–binding factor 1 (LEF1), a downstream effector in the canonical Wnt signaling pathway. Increased expression and nuclear localization of LEF1 are also observed in cystic kidneys from Hnf1b mutant mice. Expression of dominant-negative mutant HNF-1β in mIMCD3 cells produces hyperresponsiveness to exogenous Wnt ligands, which is inhibited by siRNA-mediated knockdown of Lef1. WT HNF-1β binds to two evolutionarily conserved sites located 94 and 30 kb from the mouse Lef1 promoter. Ablation of HNF-1β decreases H3K27 trimethylation repressive marks and increases β-catenin occupancy at a site 4 kb upstream to Lef1. Mechanistically, WT HNF-1β recruits the polycomb-repressive complex 2 that catalyzes H3K27 trimethylation. Deletion of the β-catenin–binding domain of LEF1 in HNF-1β–deficient cells abolishes the increase in Lef1 transcription and decreases the expression of downstream Wnt target genes. The canonical Wnt target gene, Axin2, is also a direct transcriptional target of HNF-1β through binding to negative regulatory elements in the gene promoter. These findings demonstrate that HNF-1β regulates canonical Wnt target genes through long-range effects on histone methylation at Wnt enhancers and reveal a new mode of active transcriptional repression by HNF-1β.

Distinct cell types emerge from embryonic stem cells through a precise and coordinated execution of gene expression programs during lineage commitment. This is established by the action of lineage specific transcription factors along with chromatin complexes. Numerous studies have focused on epigenetic factors that affect embryonic stem cells (ESC) self-renewal and pluripotency. However, the contribution of chromatin to lineage decisions at the exit from pluripotency has not been as extensively studied. Using a pooled epigenetic shRNA screen strategy, we identified chromatin-related factors critical for differentiation toward mesodermal and endodermal lineages. Here we reveal a critical role for the chromatin protein, ARID4B. Arid4b-deficient mESCs are similar to WT mESCs in the expression of pluripotency factors and their self-renewal. However, ARID4B loss results in defects in up-regulation of the meso/endodermal gene expression program. It was previously shown that Arid4b resides in a complex with SIN3A and HDACS 1 and 2. We identified a physical and functional interaction of ARID4B with HDAC1 rather than HDAC2, suggesting functionally distinct Sin3a subcomplexes might regulate cell fate decisions Finally, we observed that ARID4B deficiency leads to increased H3K27me3 and a reduced H3K27Ac level in key developmental gene loci, whereas a subset of genomic regions gain H3K27Ac marks. Our results demonstrate that epigenetic control through ARID4B plays a key role in the execution of lineage-specific gene expression programs at pluripotency exit.

Thoracic great vessels such as the aorta and subclavian arteries are formed through dynamic remodeling of embryonic pharyngeal arch arteries (PAAs). Previous work has shown that loss of a basic helix-loop-helix transcription factor Hey1 in mice causes abnormal fourth PAA development and lethal great vessel anomalies resembling congenital malformations in humans. However, how Hey1 mediates vascular formation remains unclear. In this study, we revealed that Hey1 in vascular endothelial cells, but not in smooth muscle cells, played essential roles for PAA development and great vessel morphogenesis in mouse embryos. Tek-Cre–mediated Hey1 deletion in endothelial cells affected endothelial tube formation and smooth muscle differentiation in embryonic fourth PAAs and resulted in interruption of the aortic arch and other great vessel malformations. Cell specificity and signal responsiveness of Hey1 expression were controlled through multiple cis-regulatory regions. We found two distal genomic regions that had enhancer activity in endothelial cells and in the pharyngeal epithelium and somites, respectively. The novel endothelial enhancer was conserved across species and was specific to large-caliber arteries. Its transcriptional activity was regulated by Notch signaling in vitro and in vivo, but not by ALK1 signaling and other transcription factors implicated in endothelial cell specificity. The distal endothelial enhancer was not essential for basal Hey1 expression in mouse embryos but may likely serve for Notch-dependent transcriptional control in endothelial cells together with the proximal regulatory region. These findings help in understanding the significance and regulation of endothelial Hey1 as a mediator of multiple signaling pathways in embryonic vascular formation.

Investigations of bacterial resistance strategies can aid in the development of new antimicrobial drugs as a countermeasure to the increasing worldwide prevalence of bacterial antibiotic resistance. One such strategy involves the TipA class of transcription factors, which constitute minimal autoregulated multidrug resistance (MDR) systems against diverse antibiotics. However, we have insufficient information regarding how antibiotic binding induces transcriptional activation to design molecules that could interfere with this process. To learn more, we determined the crystal structure of SkgA from Caulobacter crescentus as a representative TipA protein. We identified an unexpected spatial orientation and location of the antibiotic-binding TipAS effector domain in the apo state. We observed that the α6–α7 region of the TipAS domain, which is canonically responsible for forming the lid of antibiotic-binding cleft to tightly enclose the bound antibiotic, is involved in the dimeric interface and stabilized via interaction with the DNA-binding domain in the apo state. Further structural and biochemical analyses demonstrated that the unliganded TipAS domain sterically hinders promoter DNA binding but undergoes a remarkable conformational shift upon antibiotic binding to release this autoinhibition via a switch of its α6–α7 region. Hence, the promoters for MDR genes including tipA and RNA polymerases become available for transcription, enabling efficient antibiotic resistance. These insights into the molecular mechanism of activation of TipA proteins advance our understanding of TipA proteins, as well as bacterial MDR systems, and may provide important clues to block bacterial resistance.

15 July 2020

Cellular energy demands are met by uptake and metabolism of nutrients like glucose. The principal transcriptional regulator for adapting glycolytic flux and downstream pathways like de novo lipogenesis to glucose availability in many cell types is carbohydrate response element–binding protein (ChREBP). ChREBP is activated by glucose metabolites and post-translational modifications, inducing nuclear accumulation and regulation of target genes. Here we report that ChREBP is modified by proline hydroxylation at several residues. Proline hydroxylation targets both ectopically expressed ChREBP in cells and endogenous ChREBP in mouse liver. Functionally, we found that specific hydroxylated prolines were dispensable for protein stability but required for the adequate activation of ChREBP upon exposure to high glucose. Accordingly, ChREBP target gene expression was rescued by re-expressing WT but not ChREBP that lacks hydroxylated prolines in ChREBP-deleted hepatocytes. Thus, proline hydroxylation of ChREBP is a novel post-translational modification that may allow for therapeutic interference in metabolic diseases.

Mouse embryonic stem cells (mESCs) display unique mechanical properties, including low cellular stiffness in contrast to differentiated cells, which are stiffer. We have previously shown that mESCs lacking the clathrin heavy chain (Cltc), an essential component for clathrin-mediated endocytosis (CME), display a loss of pluripotency and an enhanced expression of differentiation markers. However, it is not known whether physical properties such as cellular stiffness also change upon loss of Cltc, similar to what is seen in differentiated cells, and if so, how these altered properties specifically impact pluripotency. Using atomic force microscopy (AFM), we demonstrate that mESCs lacking Cltc display higher Young's modulus, indicative of greater cellular stiffness, compared with WT mESCs. The increase in stiffness was accompanied by the presence of actin stress fibers and accumulation of the inactive, phosphorylated, actin-binding protein cofilin. Treatment of Cltc knockdown mESCs with actin polymerization inhibitors resulted in a decrease in the Young's modulus to values similar to those obtained with WT mESCs. However, a rescue in the expression profile of pluripotency factors was not obtained. Additionally, whereas WT mouse embryonic fibroblasts could be reprogrammed to a state of pluripotency, this was inhibited in the absence of Cltc. This indicates that the presence of active CME is essential for the pluripotency of embryonic stem cells. Additionally, whereas physical properties may serve as a simple readout of the cellular state, they may not always faithfully recapitulate the underlying molecular fate.

The Wnt/β-catenin pathway is one of the major pathways that regulates embryonic development, adult homeostasis, and stem cell self-renewal. In this pathway, transcription factors T-cell factor and lymphoid enhancer factor (TCF/LEF) serve as a key switch to repress or activate Wnt target gene transcription by recruiting repressor molecules or interacting with the β-catenin effector, respectively. It has become evident that the protein stability of the TCF/LEF family members may play a critical role in controlling the activity of the Wnt/β-catenin signaling pathway. However, factors that regulate the stability of TCF/LEFs remain largely unknown. Here, we report that pVHL binding protein 1 (VBP1) regulates the Wnt/β-catenin signaling pathway by controlling the stability of TCF/LEFs. Surprisingly, we found that either overexpression or knockdown of VBP1 decreased Wnt/β-catenin signaling activity in both cultured cells and zebrafish embryos. Mechanistically, VBP1 directly binds to all four TCF/LEF family members and von Hippel-Lindau tumor-suppressor protein (pVHL). Either overexpression or knockdown of VBP1 increases the association between TCF/LEFs and pVHL and then decreases the protein levels of TCF/LEFs via proteasomal degradation. Together, our results provide mechanistic insights into the roles of VBP1 in controlling TCF/LEFs protein stability and regulating Wnt/β-catenin signaling pathway activity.

Mitochondrial dysfunction is associated with a variety of human diseases including neurodegeneration, diabetes, nonalcohol fatty liver disease (NAFLD), and cancer, but its underlying causes are incompletely understood. Using the human hepatic cell line HepG2 as a model, we show here that endoplasmic reticulum-associated degradation (ERAD), an ER protein quality control process, is critically required for mitochondrial function in mammalian cells. Pharmacological inhibition or genetic ablation of key proteins involved in ERAD increased cell death under both basal conditions and in response to proinflammatory cytokines, a situation frequently found in NAFLD. Decreased viability of ERAD-deficient HepG2 cells was traced to impaired mitochondrial functions including reduced ATP production, enhanced reactive oxygen species (ROS) accumulation, and increased mitochondrial outer membrane permeability. Transcriptome profiling revealed widespread down-regulation of genes underpinning mitochondrial functions, and up-regulation of genes associated with tumor growth and aggression. These results highlight a critical role for ERAD in maintaining mitochondrial functional and structural integrity and raise the possibility of improving cellular and organismal mitochondrial function via enhancing cellular ERAD capacity.

AMP-activated protein kinase (AMPK) is a key regulator of energy metabolism that phosphorylates a wide range of proteins to maintain cellular homeostasis. AMPK consists of three subunits: α, β, and γ. AMPKα and β are encoded by two genes, the γ subunit by three genes, all of which are expressed in a tissue-specific manner. It is not fully understood, whether individual isoforms have different functions. Using RNA-Seq technology, we provide evidence that the loss of AMPKβ1 and AMPKβ2 lead to different gene expression profiles in human induced pluripotent stem cells (hiPSCs), indicating isoform-specific function. The knockout of AMPKβ2 was associated with a higher number of differentially regulated genes than the deletion of AMPKβ1, suggesting that AMPKβ2 has a more comprehensive impact on the transcriptome. Bioinformatics analysis identified cell differentiation as one biological function being specifically associated with AMPKβ2. Correspondingly, the two isoforms differentially affected lineage decision toward a cardiac cell fate. Although the lack of PRKAB1 impacted differentiation into cardiomyocytes only at late stages of cardiac maturation, the availability of PRKAB2 was indispensable for mesoderm specification as shown by gene expression analysis and histochemical staining for cardiac lineage markers such as cTnT, GATA4, and NKX2.5. Ultimately, the lack of AMPKβ1 impairs, whereas deficiency of AMPKβ2 abrogates differentiation into cardiomyocytes. Finally, we demonstrate that AMPK affects cellular physiology by engaging in the regulation of hiPSC transcription in an isoform-specific manner, providing the basis for further investigations elucidating the role of dedicated AMPK subunits in the modulation of gene expression.

Acute lung injury (ALI), is a rapidly progressing heterogenous pulmonary disorder that possesses a high risk of mortality. Accumulating evidence has implicated the activation of the p65 subunit of NF-κB [NF-κB(p65)] activation in the pathological process of ALI. microRNAs (miRNAs), a group of small RNA molecules, have emerged as major governors due to their post-transcriptional regulation of gene expression in a wide array of pathological processes, including ALI. The dysregulation of miRNAs and NF-κB activation has been implicated in human diseases. In the current study, we set out to decipher the convergence of miR-99b and p65 NF-κB activation in ALI pathology. We measured the release of pro-inflammatory cytokines (IL-1β, IL-6, and TNFα) in bronchoalveolar lavage fluid using ELISA. MH-S cells were cultured and their viability were detected with cell counting kit 8 (CCK8) assays. The results showed that miR-99b was up-regulated, while PRDM1 was down-regulated in a lipopolysaccharide (LPS)-induced murine model of ALI. Mechanistic investigations showed that NF-κB(p65) was enriched at the miR-99b promoter region, and further promoted its transcriptional activity. Furthermore, miR-99b targeted PRDM1 by binding to its 3'UTR, causing its down-regulation. This in-creased lung injury, as evidenced by increased wet/dry ratio of mouse lung, myeloperoxidase activity and pro-inflammatory cytokine secretion, and enhanced infiltration of inflammatory cells in lung tissues. Together, our findings indicate that NF-κB(p65) promotion of miR-99b can aggravate ALI in mice by down-regulating the expression of PRDM1.

Paramphistomosis, caused by the rumen fluke, Calicophoron daubneyi, is a parasitic infection of ruminant livestock which has seen a rapid rise in prevalence throughout Western Europe in recent years. Following ingestion of metacercariae (parasite cysts) by the mammalian host, newly-excysted juveniles (NEJs) emerge and invade the duodenal submucosa which causes significant pathology in heavy infections. The immature larvae then migrate upwards, along the gastrointestinal tract, and enter the rumen where they mature and begin to produce eggs. Despite their emergence, and sporadic outbreaks of acute disease, we know little about the molecular mechanisms used by C. daubneyi to establish infection, acquire nutrients and to avoid the host immune response. Here, transcriptome analysis of four intra-mammalian life-cycle stages, integrated with secretome analysis of the NEJ and adult parasites (responsible for acute and chronic disease respectively), revealed how the expression and secretion of selected families of virulence factors and immunomodulators are regulated in accordance with fluke development and migration. Our data show that whilst a family of cathepsins B with varying S2 sub-site residues (indicating distinct substrate specificities) are differentially secreted by NEJs and adult flukes, cathepsins L and F are secreted in low abundance by NEJs only. We found that C. daubneyi has an expanded family of aspartic peptidases, which is up-regulated in adult worms, although they are underrepresented in the secretome. The most abundant proteins in adult fluke secretions were helminth defence molecules (HDMs) that likely establish an immune environment permissive to fluke survival and/or neutralise pathogen-associated molecular patterns (PAMPs) such as bacterial lipopolysaccharide in the microbiome-rich rumen. The distinct collection of molecules secreted by C. daubneyi allowed the development of the first coproantigen-based ELISA for paramphistomosis which, importantly, did not recognise antigens from other helminths commonly found as co-infections with rumen fluke.

In nucleotide excision repair, bulky DNA lesions such as UV-induced cyclobutane pyrimidine dimers are removed from the genome by concerted dual incisions bracketing the lesion, followed by gap filling and ligation. So far, two dual-incision patterns have been discovered: the prokaryotic type, which removes the damage in 11–13-nucleotide-long oligomers, and the eukaryotic type, which removes the damage in 24–32-nucleotide-long oligomers. However, a recent study reported that the UvrC protein of Mycobacterium tuberculosis removes damage in a manner analogous to yeast and humans in a 25-mer oligonucleotide arising from incisions at 15 nt from the 3´ end and 9 nt from the 5´ end flanking the damage. To test this model, we used the in vivo excision assay and the excision repair sequencing genome-wide repair mapping method developed in our laboratory to determine the repair pattern and genome-wide repair map of Mycobacterium smegmatis. We find that M. smegmatis, which possesses homologs of the Escherichia coli uvrA, uvrB, and uvrC genes, removes cyclobutane pyrimidine dimers from the genome in a manner identical to the prokaryotic pattern by incising 7 nt 5´ and 3 or 4 nt 3´ to the photoproduct, and performs transcription-coupled repair in a manner similar to E. coli.