bluuebunny/crossref_metadata_2025 huggingface dataset:
112 A Meta-Analysis on the Effect of Guanidinoacetic Acid Supplementation on Growth Performance of Growing Pigs
Authors: Mendoza S Maria , Htoo John K K , Bauer Lukas
Published: April 2022

Guanidinoacetic acid (GAA) is produced in the kidney from arginine and glycine and transported to the liver for the synthesis of creatine. Dietary GAA supplementation can have arginine and energy-sparing effects. The objective of this meta-analysis was to assess the effect size of GAA in growing pigs based on available literature. Using internet search (until October 31, 2021), we identified 7 scientific publications. Only studies that 1) reported growth performance of growing pigs (7 to 107 kg BW), 2) had control without GAA supplementation, and 3) did not aim to demonstrate GAA sparing effects of energy or arginine were selected. From the 7 publications, 4 publications met the criteria, and 2 of the publications contained 2 studies, therefore, a total of 6 studies were included in the meta-analysis. The statistical analysis utilized a random effect model to estimate the mean effect size (MES) of the difference between control and GAA-supplemented pigs, the 95% confidence interval of MES, the probability of MES being different from zero, the probability of the studies to share a common effect size (heterogeneity), and no publication bias. The data were analyzed using SAS 9.4 using a SAS macro created by Rendina-Gobioff and Kromrey (2006). Summary statistics and average change in percentage are reported in Table 1. Pigs fed GAA-supplemented diets had greater (P < 0.001) final BW, ADG, and G:F, and the magnitude of the effect is considered to be large (>|0.8|). GAA did not influence (P = 0.976) ADFI. The presence of heterogeneity was observed in all the responses, suggesting that the effect size varies among studies. Publication bias was not found for any of the responses. Overall, supplementation of GAA increased BW, ADG, and G:F by 1.68, 3.95 and 7.01%, respectively, and the effect size varies, potentially due to the inclusion rate and duration of supplementation.
116 Effect of Zinc Oxide and Organic Zinc on Weanling Pig Performance
Authors: LaRosae Marissa N , Samuel Ryan S , Clizer David A
Published: April 2022

Pharmacological levels (> 2,000 ppm) of Zn from ZnO have been reported to enhance pig growth during the nursery phase. Alternatively, organic Zn sources added to nursery diets below pharmacological concentrations may provide similar growth performance benefits. Therefore, the objective of this study was to evaluate the effects of source and concentration of Zn on growth performance of weanling pigs. Newly weaned pigs (n = 1,144; 21 d of age; 5.8 ± 0.1 kg BW) were stocked at 26 pigs per pen of equal sex in 44 pens in a wean-to-finish commercial research barn. Pens within similar barn location were randomly assigned to receive 1 of 4 dietary treatments applied over 4 dietary phases (PH) in a factorial arrangement: 1) Control: complex commercial nursery diet with dietary Zn at nutritional requirement 2) Control plus ZnO providing Zn at 3,000 ppm in PH1-2, 1,500 ppm in PH3, and removal of ZnO in PH4; 3) Control plus an organic Zn providing Zn at 100 ppm in PH1-4; 4) Control plus a combination of both ZnO and organic Zn source at the same inclusion levels as dietary treatments 2 and 3. The addition of organic Zn increased (P < 0.01) ADFI from d 0 to 7 (175 vs. 149 g/d), but decreased (P < 0.01) G:F (0.763 vs. 0.902) and then improved (P < 0.01) G:F from d 7 to 14 (0.821 vs. 0.754). The addition of Zn from ZnO increased (P < 0.05) ADG (312 vs. 290 g/d) and ADFI (428 vs 401 g/d) for the initial 28 d and improved (P < 0.05) G:F (0.776 vs. 0.738) for the initial 21 d post-weaning, but not for the latter 14 d (28 to 42 d) of the nursery phase or overall (0 to 42 d). These results demonstrate that Zn above dietary requirement may improve early growth performance.
167 Effect of Reducing Dietary Crude Protein on Growth Performance of Fattening Pigs: A Meta-Analysis
Authors: Cappelaere Léa , Van Milgen Jaap , Syriopoulos Kostas , Simongiovanni Aude , Lambert William , Létourneau-Montminy Marie-Pierre
Published: April 2022

Reducing dietary crude protein (CP) is a nutritional strategy implemented to improve the sustainability of pig production. Its effect on growth performance has been broadly studied in fattening pigs but the literature is lacking a quantitative summary of the knowledge acquired. A meta-analysis was performed to assess the effects of reducing dietary CP on pig growth performance. Articles included in the meta-analysis studied effects of CP reduction, with at least 3 CP levels, on the growth performance of fattening pigs (20-115 kg) and were published from 1990 to 2019. The database contained 42 articles, which correspond to 67 trials. Diet composition was recalculated with INRA-AFZ (2004) tables. Trials using iso-digestible lysine and iso-net energy diets with constant or above requirements levels of essential amino acids (EAA, METEX NØØVISTAGO recommendations) were selected for the final analysis, with a 5% acceptance limit. The final selection contained 11 trials and 44 treatments. The general linear model procedure of MINITAB (2019) was used to build regression models, including a fixed trial effect. Dietary CP reduction tested ranged between 1.6 and 7.5 percentage points (%pt) and was performed by reducing soybean meal and increasing cereals inclusion in all trials except one using rapeseed meal. Reducing dietary CP did not significantly impacted feed intake, average daily gain or feed conversion ratio when EAA were adequately supplied. Nitrogen efficiency was improved by 2.7 %pt per %pt of CP reduction (P < 0.001). No statistical analysis could be performed on carcass composition data as there were only 6 trials remaining after selection for these parameters, but fatter carcasses were observed in half of the trials. This study highlighted that few CP reduction studies have been performed while controlling energy and EAA levels. There was no effect of reducing dietary CP on growth performance when those parameters were controlled but more research is needed on very low CP diets for fattening pigs.
225 Effect of Increasing Doses of Encapsulated Butyric Acid and Zinc on Beef Feedlot Steer Growth Performance, Dietary Net Energy Utilization, and Carcass Characteristics
Authors: Francis Forest L , Gubbels Erin , Hamilton Thomas G , Rusche Warren C , Lafleur Doug , Hergenreder Jerilyn , Smith Zachary K
Published: April 2022

The objective of this study was to determine the effects that increasing doses of encapsulated butyric acid and zinc (BPZ) have on beef feedlot steer growth performance, dietary net energy utilization, and carcass characteristics. Steers (n = 272; shrunk BW = 360 kg ± 74 kg) were assigned to dietary treatment [0 (CON), 1, 2, or 3 g BPZ/kg diet DM] in a randomized complete block design (RCBD) with pen (n = 32) as experimental unit. Cattle were fed until visually assessed to have 1.27 cm rib-fat and were shipped for harvest at a commercial beef abattoir. Carcass and liver health data was recorded. Feedlot performance data was calculated on a carcass-adjusted basis (HCW/0.625). Data were analyzed as a RCBD with fixed effects of BPZ inclusion level and block was considered a random effect; pre-planned contrasts for CON vs. BPZ, plus linear, and quadratic responses were tested. No differences (P ≥ 0.14) were observed for final BW, DMI, ADG, feed conversion efficiency, observed dietary NEm and NEg, observed-to-expected dietary NEm and NEg, HCW, REA, rib-fat thickness, marbling score, estimated EBF, or distribution of USDA YG 1, 3, 4, 5, and USDA quality grade among treatments. A tendency (P = 0.10) was observed for CON vs. BPZ for calculated YG. Tendencies were detected for USDA YG 2 carcass distribution (linear; P = 0.07) and for normal and abscessed liver prevalence (quadratic; P = 0.08). Dressed yield tended to be greater (P = 0.08) for BPZ vs. Con and increased with dose (linear; P = 0.05). Supplementation of BPZ in finishing cattle diets does not appreciably influence growth performance, but increases dressed yield. Data from this study suggests that the addition of BPZ to feedlot finishing diets for decreasing the prevalence of abscessed livers should be further investigated.
PSIII-4 Characterization of Digital Overgrowth in Sow Breeding Herds: A Case Study
Authors: Henningsen Derek , Moeller Grace A , Mainenti Marta , Michael Alyona , Johnson Anna K , Stalder Kenneth J
Published: April 2022

Digital overgrowth has been documented as one of the most common foot abnormalities observed in U.S. commercial sow breeding herds and often leads to lameness and culling. Previous research has reported that 8.2% of lactating sows had digital overgrowth. When examining a 3,500 gestating sows, at least 32% were scored with moderate or severe digital overgrowth. Digital overgrowth negatively impacts piglet pre-wean mortality, lower NBA, and lower weaning weights. In addition to the digital overgrowth, sows have increased risk for cracked hooves and other hoof lesions. The objective of this study was to characterize a true standard (mm) for digital overgrowth and to determine if varying toe cell structure contributes to toe overgrowth. Initially, 2 crossbred sows that visually exhibited digital overgrowth were evaluated into this case study. Sows were euthanized at the Iowa State Veterinary Diagnostic Laboratory. Sow toe measurements were collected from the tip of the toe to the coronary band that is anatomically located at the sagittal line. Medial and lateral toe measurements were recorded for each limb. The mean toe measurements were front right limb: lateral digit (LD; 40 mm), medial digit (MD; 40 mm); front left limb: LD (36.5 mm), MD (38.5 mm); hind right limb: LD (73.5 mm), MD (49 mm); hind left limb: LD (50.5 mm), MD (50 mm). Dew claw and histopathological evaluations are in progress.
PSIII-12 Identification and Classification of Novel Animal Associated Viruses from the Human Skin Virome of Pet Owners and Agricultural Workers
Authors: Graham Ema H , Herr Joshua R , Adamowicz Michael , Clarke Jennifer , Fernando Samodha C , Angeletti Peter
Published: April 2022

Viruses are the most abundant biological entity on earth. Despite this, viral diversity in current reference databases is poorly described. With limited number of studies investigating environmental viromes, our understanding of the virosphere composition and diversity is limited. Improvement in metagenomic sequencing methodologies has allowed for identification of novel genomic sequences, especially for new and emerging viral taxa, and improvement in existing ambiguous viral phylogenetic groupings. Here we describe a viral discovery-based study that evaluated viral metagenomes collected from the hands and scalps of 42 human subjects (n = 642) for identification of environmentally contracted DNA viruses. Due to direct interaction between humans and animals either through owning pets or through vocation, it is hypothesized that surveillance of the human skin virome will contain animal associated viruses contracted through environmental contact that can then potentially become zoonotic pathogens. To investigate this, viral genome assemblies from the metagenomes were bioinformatically predicted using model and reference-based tools. A gene and protein sequence variation and binning approach was then employed to resolve viral dark matter. Evaluation of animal associated viruses resulted in the identification of a feline papillomavirus from a subject who reportedly owned a cat. Phylogenetic analysis suggests this isolate is related to feline papillomavirus type 2 sharing approximately 75% sequence synteny thus making it a novel papillomavirus isolate. Additionally, a new grouping of porcine associated Cressdnaviricota viruses were identified through protein sequence similarity network clustering of conserved Rep genes and all other NCBI reported Rep gene sequences. This grouping contained both novel viral genomes collected from the human skin virome dataset and unclassified Cressdnaviruses all collected from porcine samples obtained from NCBI. Further phylogenetic analysis showed similarity to this novel cluster to that of porcine circovirus (PCV). This discovery and phylogenetic based investigation of novel viral genome assemblies demonstrates that animal associated viruses can be identified from the skin of humans and thus studying human viromes can provide information into the spread and emergence of novel viruses.
PSVI-14 Impact of Bacillus Subtilis and Bacillus Licheniformis on Weaning Weight and Subsequent Performance, Health and Immune Parameters When Challenged with PRRSV with and Without PRRS Vaccination
Authors: Bertram Mark J , Kitt Steve J , Kinsely Keith
Published: April 2022

A study was conducted examining the impact of feeding BioPlus 2B to PRRSV naïve sows during gestation and lactation on litter performance and on post-weaning performance when challenged with PRRSV in vaccinated and unvaccinated pigs. A total of 108 sows were allotted by parity and received a control diet (C) or BioPlus 2B (B2B) supplemented diet beginning a minimum of 31 d prior to farrowing through weaning. Pig weight was measured at birth and 17 d of age. At weaning, a subset of 200 pigs from each treatment were transported to a nursery and randomly allotted within dietary treatment on day 1 to a control (-V) or Ingelvac PRRS MLV vaccine (+V), establishing treatments of C+V, C-V, B2B+V, and B2B-V. On d 21, all pigs were intramuscularly challenged with a 1-18-2 PRRS virus. Growth rate and feed intake were monitored, serological and immune measures were recorded on d 21, 28, 35 and 42, post-weaning and on d 42 gross lung lesions were recorded. Pigs from sows receiving B2B tended (P < 0.10) to weigh more at 17 d of age and 21 d post-weaning (Table 1). Prior to challenge, there were no performance differences among treatments. Post challenge, there was a V x B2B interaction with C+V, B2B+V and B2B-V pigs having higher ADG and FG (P < .05) compared with C-V. On day 42, pigs fed B2B displayed improved lung lesion scores (P < 0.05) regardless of vaccine status. PRRSV viremia, measured by PCR and qPCR decreased more quickly when pigs consumed B2B (P < 0.05). Additionally, B2B modulated PRRSV specific T-cell interferon gamma production (P < 0.05). In conclusion, pigs consuming B2B from sows fedB2B were heavier at weaning and when subjected to a PRRSV challenge post-weaning, grew faster, were more efficient, and had reduced gross lung lesions, likely due to changes in immune function.
PSIII-10 Heat Stress Causes Persistent Multisystemic Dysfunction
Authors: Roths Melissa S , Rudolph Tori E , Freestone Alyssa , Baumgard Lance H , Selsby Joshua T
Published: April 2022

Heat stress (HS) causes multisystemic dysfunction and negatively impacts animal production. That the deleterious effects on production persist after HS abates raises the possibility of continuing injury and pathology that is not remediated by reestablishing euthermia. We hypothesized that a single bout of HS would cause immediate and persistent heart, liver, and kidney injury. To test this hypothesis, we collected blood from 3 month-old crossbred pigs (n = 12; 8 barrows, 4 gilts) under thermoneutral (TN; Pre) conditions (20.6 ± 0.2 ºC), following a 24 h HS (37.4 ± 0.2 ºC, 24hP), and 3 mo following HS (3mP). Skeletal muscle and cardiac muscle injury were apparent as creatine kinase (P < 0.05), myoglobin (P < 0.05), cardiac troponin I (cTnI; P < 0.05) and NT-proBNP (P < 0.05) were increased in 24hP compared with Pre, and elevations in NT-proBNP in 3mP raise the possibility of lasting cardiac injury. Additionally, cTnI and NT-proBNP were greater in gilts than barrows as a main effect of sex (P < 0.05). Increased creatinine, Mg, and blood urea nitrogen (BUN) in 24hP, and chronic elevations in creatinine, Cl, Mg, Na, Ca, bicarbonate, and BUN and reduced phosphorus and K (P < 0.05 < 0.1) in 3mP, indicate a single HS causes rapid and lasting impairments in renal function. Heat stress also increased aspartate aminotransferase (AST; P < 0.05) 24hP but decreased alkaline phosphatase (P < 0.05) and total bilirubin in 24hP (P < 0.1) and AST (P < 0.05) and total bilirubin in 3mP (P < 0.05). In total, these data suggest that HS causes both immediate and long-term cardiac, liver, and renal dysfunction and this appears to be influenced, at least in part, by biological sex.
PSI-3 Effects of Increasing Dietary Arginine Supply on Pig Growth Performance Following Weaning Stress
Authors: Perez-Palencia Jorge Y , Reiman Noah , Haydon Keith D , Levesque Crystal L
Published: April 2022

Intestinal health has important implications for pig overall health status and growth performance. In this regard, arginine participates in important regulatory functions associated with nutrient metabolism, cell proliferation, and immune response that contribute to the maintenance of a functional intestinal tract. However, Current nutritional practices for weaned pigs do not consider the critical regulatory roles of arginine related to pig gut health and function. The objective of this study was to determine growth response of weaned pigs fed increasing levels of L-Arginine during the first weeks after weaning. A total of 225 weaned pigs (BW 5.8 ± 0.9 kg) were used in a randomized complete block design and assigned to 1 of 5 dietary treatments, with 9 replicate pens of 5 pigs. A basal diet was formulated to meet current arginine requirements (0.66% - NRC, 2012) and L-arginine was supplemented at 0.3, 0.6, 0.9, and 1.2%. Experimental diets were provided in meal form during phases 1 and 2 of a 3-phase nursery feeding program: Phase 1 (d 0-d 7), Phase 2 (d 8-d 21), and Phase 3 (d 22-d 42). A common diet was provided during phase 3. Feed disappearance and body weight were measured at d 7, 14, 21, and 42 after weaning. Through the first 3 weeks after weaning, increasing dietary arginine supply linearly improved (P ≤ 0.05) body weight (8.25 - 11.20 kg), average daily gain (Figure 1), average daily feed intake (251.53 - 387.75 g), and gain to feed ratio (0.60 – 0.66) of pigs. These beneficial effects persisted throughout phase 3, where arginine supplementation resulted in a linear improvement in pig overall growth performance. In addition, increasing arginine supply reduced the percentage of pigs that lost weight during the first week post-weaning by 29%. Overall, weaned pigs require more dietary arginine for optimal nursery performance, which includes reducing fall back pigs.
Present status of germline findings in precision medicine for Japanese cancer patients: issues in the current system
Authors: Higashigawa Satomi , Matsubayashi Hiroyuki , Kiyozumi Yoshimi , Kado Nobuhiro , Nishimura Seiichiro , Oishi Takuma , Sugino Takashi , Fushiki Kunihiro , Shirasu Hiromichi , Yasui Hirofumi , Mamesaya Nobuaki , Fukuzaki Naomi , Kunitomo Kana , Horiuchi Yasue , Kenmotsu Hirotsugu , Serizawa Masakuni
Published: April 2022

Objective

Since 2019, precision cancer medicine has been covered by national insurance in Japan; however, to date, germline findings have not been fully reported. The aim of this study was to evaluate the current status and raise a problem of germline finding analysis and disclosure in Japanese precision cancer medicine.

Methods

Germline findings of 52 genes were examined in 296 cases with advanced cancer by a case series study.

Results

Six (2.0%) cases were examined by the Oncoguide™ NCC Oncopanel with germline testing, but no germline findings were reported. The remaining 290 (98.0%) cases were analyzed by FoundationOne® CDx (tumor-only testing), which recognized 404 pathogenic variants; those of BRCA1/2 were recognized in 16 (5.5%) tumors. Our institutional algorithm suggested 39 candidate germline findings in 34 cases, while the public algorithm listed at least 91 candidate germline findings. Four germline findings had been previously identified (BRCA1: 3 and ATM: 1). Nine of 30 cases with candidate germline findings excluding these known germline findings refused or deferred germline testing. Only 4 of 16 cases that received counseling underwent germline testing, and those 4 revealed 3 germline findings (BRCA2, CDK4 and RAD51C); in total, 8 (2.7%) germline findings were revealed. Reasons for refusing genetic counseling and/or germline testing included extra hospital visits, added expense for germline testing due to limited national insurance coverage, poor patient physical condition and no known family members associated with the possible germline finding.

Conclusions

In current Japanese precision cancer medicine, only a small fraction of the patients undergoes germline testing and demonstrated germline finding. The current results suggested a need for earlier indications for precision cancer medicine, broader insurance coverage and more efficient germline finding prediction algorithms, to increase the number of germline testings and to improve the following managements.
Cartilaginous defect of the lateral trochlea following suprapatellar nailing of an open tibial shaft fracture: a case report
Authors: Kuechly Henry A , Thomson Cameron G , Sabbagh Ramsey S , Shah Nihar S , Figueras Jorge H , Grawe Brian M
Published: April 2022

A 34-year-old female sustained a 1.8 cm full-thickness chondral defect of the right lateral trochlear surface as the result of intramedullary tibial nailing via a suprapatellar portal to treat a displaced right sided open comminuted spiral fracture of the distal tibial shaft. An osteochondral allograft was used to treat the chondral defect. Iatrogenic injury to intraarticular structures is a potential complication when inserting a tibial nail via a suprapatellar portal. Using proper technique with cannula systems and guide pins is essential to lowering the risk of damage to intraarticular structures.
Profiles of Recruits Entering Army Basic Training in New Zealand
Authors: Hall Narelle , Constantinou Maria , Brown Mark , Beck Belinda , Steele Michael , Rousseau Jacques , Kuys Suzanne
Published: April 2022

Introduction

A high incidence of musculoskeletal injuries is sustained by army recruits during basic training. Describing recruits’ personal, lifestyle, and physical performance characteristics at the entry to training can help identify existing intrinsic risk factors that may predispose some recruits to injury. Identifying modifiable and preventable intrinsic risk factors may contribute to lower recruit injury and associated burdens during the course of basic training. The aim of this study was to therefore describe the profile of New Zealand Army recruits upon entry to basic training using personal, lifestyle, and physical performance characteristics.

Methods

New Zealand Army male and female recruits from two intakes in the same year were invited to participate. Recruits’ data on personal (sex, age, height, and weight), lifestyle (self-reported responses to the Military Pre-training Questionnaire comprising physical and injury history, diet, alcohol, and smoking status) and physical performance characteristics (2.4-km timed run, weight-bearing dorsiflexion lunge test, and the Y Balance TestTM for lower limb dynamic stability) were collected and analyzed.

Results

Participants included 248 New Zealand Army recruits: 228 males (91.9%), 20 females (8.1%), average age of 20.3 ± 2.8 years. Findings indicated 30.9% of recruits reported injury in the 12 months prior to training commencing, with 44.8% of those injuries in the lower limbs. Pre-entry alcohol consumption was higher than recommended and 20.1% of recruits identified as current smokers. Recruits who passed the 2.4-km timed run included 53.8% of males and 28.6% of females. Weight-bearing dorsiflexion lunge test performance was within a normal range (right = 10.3 ± 3.3 cm), however limb asymmetry (>1.5 cm) was present with 30.9% of recruits. For the Y Balance TestTM for dynamic lower limb stability, 70% of female recruits had high posterolateral reach asymmetry (8.1 ± 6.0 cm), while normalized composite reach scores were low (right) for male (92.2 ± 8.1%) and female recruits (89.0 ± 7.5%).

Conclusions

New Zealand Army recruits entering basic training were predominantly active young males, reported few injuries in the previous year, had higher than recommended alcohol consumption and a minority were smokers. The majority of recruits had low aerobic fitness, average ankle dorsiflexion range, and low dynamic lower limb stability. While a number of adverse characteristics identified are potentially modifiable, more research is required to identify an association to musculoskeletal injury risk in New Zealand Army recruits. Describing the profile of recruits entering training, particularly recruits at risk of injury is one of the first steps in injury prevention.
Dynamo effect in unstirred self-gravitating turbulence
Authors: Brandenburg Axel , Ntormousi Evangelia
Published: April 2022

In many astrophysical environments, self-gravity can generate kinetic energy, which, in principle, is available for driving dynamo action. Using direct numerical simulations, we show that in unstirred self-gravitating subsonic turbulence with helicity and a magnetic Prandtl number of unity, there is a critical magnetic Reynolds number of about 25 above which the work done against the Lorentz force exceeds the Ohmic dissipation. The collapse itself drives predominantly irrotational motions that cannot be responsible for dynamo action. We find that, with a weak magnetic field, one-third of the work done by the gravitational force goes into compressional heating and the remaining two-thirds go first into kinetic energy of the turbulence before a fraction of it is converted further into magnetic and finally thermal energies. Close to the collapse, however, these fractions change toward 1/4 and 3/4 for compressional heating and kinetic energy, respectively. When the magnetic field is strong, the compressional heating fraction is unchanged. Out of the remaining kinetic energy, one quarter goes directly into magnetic energy via work against the Lorentz force. The fraction of vortical motions diminishes in favour of compressive motions that are almost exclusively driven by the Jeans instability. For an initially uniform magnetic field, field amplification at scales larger than those of the initial turbulence are driven by tangling.
Venom Gene Sequence Diversity and Expression Jointly Shape Diet Adaptation in Pitvipers
Authors: Mason Andrew J. , Holding Matthew L. , Rautsaw Rhett M. , Rokyta Darin R. , Parkinson Christopher L. , Gibbs H. Lisle
Published: April 2022

Understanding the joint roles of protein sequence variation and differential expression during adaptive evolution is a fundamental, yet largely unrealized goal of evolutionary biology. Here, we use phylogenetic path analysis to analyze a comprehensive venom-gland transcriptome dataset spanning three genera of pitvipers to identify the functional genetic basis of a key adaptation (venom complexity) linked to diet breadth (DB). The analysis of gene-family-specific patterns reveals that, for genes encoding two of the most important venom proteins (snake venom metalloproteases and snake venom serine proteases), there are direct, positive relationships between sequence diversity (SD), expression diversity (ED), and increased DB. Further analysis of gene-family diversification for these proteins showed no constraint on how individual lineages achieved toxin gene SD in terms of the patterns of paralog diversification. In contrast, another major venom protein family (PLA2s) showed no relationship between venom molecular diversity and DB. Additional analyses suggest that other molecular mechanisms—such as higher absolute levels of expression—are responsible for diet adaptation involving these venom proteins. Broadly, our findings argue that functional diversity generated through sequence and expression variations jointly determine adaptation in the key components of pitviper venoms, which mediate complex molecular interactions between the snakes and their prey.
Chemical biology and medicinal chemistry of RNA methyltransferases
Authors: Fischer Tim R , Meidner Laurenz , Schwickert Marvin , Weber Marlies , Zimmermann Robert A , Kersten Christian , Schirmeister Tanja , Helm Mark
Published: April 2022

RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.
Holliday junction resolution by At-HIGLE: an SLX1 lineage endonuclease from Arabidopsis thaliana with a novel in-built regulatory mechanism
Authors: Verma Prabha , Kumari Poonam , Negi Shreya , Yadav Gitanjali , Gaur Vineet
Published: April 2022

Holliday junction is the key homologous recombination intermediate, resolved by structure-selective endonucleases (SSEs). SLX1 is the most promiscuous SSE of the GIY-YIG nuclease superfamily. In fungi and animals, SLX1 nuclease activity relies on a non-enzymatic partner, SLX4, but no SLX1-SLX4 like complex has ever been characterized in plants. Plants exhibit specialized DNA repair and recombination machinery. Based on sequence similarity with the GIY-YIG nuclease domain of SLX1 proteins from fungi and animals, At-HIGLE was identified to be a possible SLX1 like nuclease from plants. Here, we elucidated the crystal structure of the At-HIGLE nuclease domain from Arabidopsis thaliana, establishing it as a member of the SLX1-lineage of the GIY-YIG superfamily with structural changes in DNA interacting regions. We show that At-HIGLE can process branched-DNA molecules without an SLX4 like protein. Unlike fungal SLX1, At-HIGLE exists as a catalytically active homodimer capable of generating two coordinated nicks during HJ resolution. Truncating the extended C-terminal region of At-HIGLE increases its catalytic activity, changes the nicking pattern, and monomerizes At-HIGLE. Overall, we elucidated the first structure of a plant SLX1-lineage protein, showed its HJ resolving activity independent of any regulatory protein, and identified an in-built novel regulatory mechanism engaging its C-terminal region.
3DLigandSite: structure-based prediction of protein–ligand binding sites
Authors: McGreig Jake E , Uri Hannah , Antczak Magdalena , Sternberg Michael J E , Michaelis Martin , Wass Mark N
Published: April 2022

3DLigandSite is a web tool for the prediction of ligand-binding sites in proteins. Here, we report a significant update since the first release of 3DLigandSite in 2010. The overall methodology remains the same, with candidate binding sites in proteins inferred using known binding sites in related protein structures as templates. However, the initial structural modelling step now uses the newly available structures from the AlphaFold database or alternatively Phyre2 when AlphaFold structures are not available. Further, a sequence-based search using HHSearch has been introduced to identify template structures with bound ligands that are used to infer the ligand-binding residues in the query protein. Finally, we introduced a machine learning element as the final prediction step, which improves the accuracy of predictions and provides a confidence score for each residue predicted to be part of a binding site. Validation of 3DLigandSite on a set of 6416 binding sites obtained 92% recall at 75% precision for non-metal binding sites and 52% recall at 75% precision for metal binding sites. 3DLigandSite is available at https://www.wass-michaelislab.org/3dligandsite. Users submit either a protein sequence or structure. Results are displayed in multiple formats including an interactive Mol* molecular visualization of the protein and the predicted binding sites.
The Importance of the C-Terminal Cys Pair of Phosphoribulokinase in Phototrophs in Thioredoxin-Dependent Regulation
Authors: Fukui Kazuha , Yoshida Keisuke , Yokochi Yuichi , Sekiguchi Takatoshi , Wakabayashi Ken-ichi , Hisabori Toru , Mihara Shoko
Published: April 2022

Phosphoribulokinase (PRK), one of the enzymes in the Calvin–Benson cycle, is a well-known target of thioredoxin (Trx), which regulates various enzyme activities by the reduction of disulfide bonds in a light-dependent manner. PRK has two Cys pairs conserved in the N-terminal and C-terminal regions, and the N-terminal one near the active site is thought to be responsible for the regulation. The flexible clamp loop located between the N-terminal two Cys residues has been deemed significant to Trx-mediated regulation. However, cyanobacterial PRK is also subject to Trx-dependent activation despite the lack of this clamp loop. We, therefore, compared Trx-mediated regulation of PRK from the cyanobacterium Anabaena sp. PCC 7120 (A.7120_PRK) and that from the land plant Arabidopsis thaliana (AtPRK). Interestingly, peptide mapping and site-directed mutagenesis analysis showed that Trx was more effective in changing the redox states of the C-terminal Cys pair in both A.7120_PRK and AtPRK. In addition, the effect of redox state change of the C-terminal Cys pair on PRK activity was different between A.7120_PRK and AtPRK. Trx-mediated redox regulation of the C-terminal Cys pair was also important for complex dissociation/formation with CP12 and glyceraldehyde 3-phosphate dehydrogenase. Furthermore, in vivo analysis of the redox states of PRK showed that only one disulfide bond is reduced in response to light. Based on the enzyme activity assay and the complex formation analysis, we concluded that Trx-mediated regulation of the C-terminal Cys pair of PRK is important for activity regulation in cyanobacteria and complex dissociation/formation in both organisms.
Digital image analysis of intraepithelial B-lymphocytes to assess lymphoepithelial lesions in salivary glands of Sjögren’s syndrome patients
Authors: van Ginkel Martha S , van der Sluis Tineke , Bulthuis Marian L C , Buikema Henk J , Haacke Erlin A , Arends Suzanne , Harder Stine , Spijkervet Fred K L , Bootsma Hendrika , Vissink Arjan , Kroese Frans G M , van der Vegt Bert
Published: April 2022

Objective

Salivary glands of primary SS (pSS) patients characteristically harbour periductal infiltrates, in which lymphoepithelial lesions (LELs) can develop. LELs are composed of hyperplastic ductal epithelium with infiltrating lymphocytes and may assist in the challenging diagnostic process of pSS. As manual identification of LELs remains difficult, we aimed to identify LELs by using an objective digital image analysis (DIA) algorithm that detects intraepithelial lymphocytes.

Methods

A virtual triple-staining technique developed for this study was used to count intraepithelial lymphocytes in consecutive slides stained for CD3 (T-lymphocytes), high-molecular-weight cytokeratin (hmwCK) (striated ducts) and CD20 (B-lymphocytes) in labial and parotid gland biopsies in a diagnostic cohort of 109 sicca patients. Patients were classified as having pSS or non-SS according to the ACR-EULAR classification criteria.

Results

T-lymphocytes were detected in almost all analysed ducts of pSS and non-SS sicca patients, whereas intraepithelial B-lymphocytes were present in 59–68% of labial and parotid gland biopsies of pSS patients, against only 2–3% of patients classified as non-SS. Intraepithelial B-lymphocytes were found in almost all striated ducts with hyperplasia (LELs). Remarkably, ∼25% of analysed striated ducts without hyperplasia of pSS patients also contained B-lymphocytes (precursor-LELs). Furthermore, presence of intraepithelial B-lymphocytes was associated with clinical parameters of pSS (i.e. serology).

Conclusion

The presence of intraepithelial B-lymphocytes in salivary gland biopsies of sicca patients is a clear indicator of pSS and can be used as an objective alternative to LEL scoring. Therefore, identification of B-lymphocyte–containing ducts should be added to the diagnostic histopathological work-up of patients suspected of pSS.
Survival analysis of mortality and development of lupus nephritis in patients with systemic lupus erythematosus up to 40 years of follow-up
Authors: Luo Weike , Farinha Filipa , Isenberg David A , Rahman Anisur
Published: April 2022

Objectives

Patients with SLE have increased mortality compared with age- and sex-matched controls. LN is a severe manifestation of SLE and an important cause of death. We carried out a retrospective survival analysis to investigate factors that could influence the risk of mortality and LN in a large multi-ethnic cohort of patients with SLE.

Methods

By careful review of medical records, we identified 496 patients with SLE for whom we had complete information regarding the period of observation and occurrence of death and nephritis. Patients were stratified into groups according to sex, ethnicity, age at start of follow-up and time period of diagnosis. Kaplan–Meier analysis was used to investigate differences between the groups.

Results

Of the 496 patients in the study, 91 (18.3%) died, 165 (33.3%) developed LN and 33 (6.7%) developed end-stage renal failure. There was no difference between men and women in either mortality or development of LN. Caucasian patients were significantly less likely to develop LN than other ethnic groups (P < 0.0001) but not less likely to die. Patients diagnosed before the median age of 28 years were significantly more likely to develop LN (P < 0.0001) but significantly less likely to die (P = 0.0039) during the period of observation. There has been a significant improvement in survival in patients diagnosed between 1978 and 1989 and those diagnosed between 2006 and 2011 (P = 0.019).

Conclusion

In our cohort, non-Caucasian ethnicity and younger age at diagnosis are associated with the risk of developing LN. There is evidence of improvement in survival of patients with SLE over time.
Impact of COVID-19 and COVID-19 vaccination on high-risk patients with antiphospholipid syndrome: a nationwide survey
Authors: Pengo Vittorio , Del Ross Teresa , Tonello Marta , Andreoli Laura , Tincani Angela , Gresele Paolo , Silvestri Elena , Simioni Paolo , Campello Elena , Hoxha Ariela , Falanga Anna , Ghirarduzzi Angelo , Denas Gentian ,   COVID-19 APS collaborators, Semeraro Paolo , Bertocchi Stefania , Paciullo Francesco , Veropalumbo Maria Rosaria
Published: April 2022

Objectives

Patients with APS and triple-positive for aPL are at high risk of recurrent events. As COVID-19 and COVID-19 vaccination may induce thrombotic complications, the objective of the study was to assess the course of COVID-19 and adverse events after vaccination in these patients.

Methods

This is a nationwide multicentre survey conducted in nine APS referral centres by means of a questionnaire. Included patients are thrombotic APS with triple-positive aPL confirmed 12 weeks apart. Reference specialist physicians used a four-graded scale of severity for COVID-19 [from 0 (asymptomatic) to 3 (hospitalization in intensive care unit)] and a six-graded scale for adverse reactions to vaccination [from 0 (transient local injection site sign/symptoms) to 5 (potentially life-threatening reactions)]. Outcomes were considered within a 30-day period.

Results

Out of 161 patients interviewed, 18 (11%) had COVID-19. All of them fully recovered without any progression to severe disease nor thromboembolic event. A total of 146 patients received the first (92%) and 129 (80%) the second dose of vaccine; side effects were minimal and, in most cases (83% after the first and 68% after the second vaccination) limited to a sore arm. Fifteen patients (9%) were unvaccinated. Most of them raised doubts on the need for vaccination, complained of poor safety and in general were reluctant about COVID-19 vaccination.

Conclusion

Patients with triple-positive thrombotic APS did not suffer from severe COVID-19 outcomes. Importantly, COVID-19 vaccination was well tolerated. These data may reassure patients and physicians and contribute to reducing hesitancy in unvaccinated patients.
Low-dose glucocorticoids withdrawn in systemic lupus erythematosus: a desirable and attainable goal
Authors: Ji Lanlan , Gao Dai , Hao Yanjie , Huang Hong , Wang Yu , Deng Xuerong , Geng Yan , Zhang Zhuoli
Published: April 2022

Objectives

To assess the risk of flare in systemic lupus erythematosus (SLE) patients after low-dose glucocorticoid (GC) discontinuation and to evaluate the risk factors of flare.

Methods

SLE patients who ever discontinued GCs were identified from the Peking University First Hospital SLE cohort. The disease flare profile after GC discontinuation was analysed. The flare rate was analysed using Kaplan–Meier analysis. Cox regression was used to determine the effects of variables on SLE flare. A prognostic nomogram using Cox proportional hazards regression modelling was developed.

Results

A total of 132 SLE patients were eligible for the final analysis. They were followed up for a median of 21.8 months (interquartile range 9.01–36.7). The cumulative probability of flare after GC discontinuation was 8.3% at 6 months, 16.8% at 1 years and 27.5% at 2 years. In multivariate Cox analysis, hypocomplementemia and serologically active clinically quiescent (SACQ) were independent risk factors of flare [hazard ratio (HR0 2.53 (95% CI 1.32, 4.88); HR 3.17 (95% CI 1.44, 6.97), respectively]. Age ≥40 years at GC withdrawal and hydroxychloroquine (HCQ) usage were independent protective factors of flare [HR 0.53 (95% CI 0.29, 0.99); HR 0.32 (95% CI 0.17, 0.62), respectively]. The protective effect of HCQ was dosage related. From the perspective of different tapering strategies embodied as the duration from prednisone 5 mg/day to complete discontinuation, a slower tapering strategy (12–24 months) significantly reduced the risk of flare compared with a faster tapering strategy (<3 months) [HR 0.30 (95% CI 0.11, 0.82), P = 0.019]. The prognostic nomogram including the aforementioned factors effectively predicted the 1 and 2 year probability of being flare-free.

Conclusion

Low-dose GC is feasibly discontinued in real-life settings. SACQ and younger age are potential risk factors of SLE flare, while HCQ use and slow GC tapering to withdrawal can reduce relapse. The visualized model we developed may help to predict the risk of flare among SLE patients who discontinued GC.
Case report and review of the literature: immune dysregulation in a large familial cohort due to a novel pathogenicRELAvariant
Authors: Lecerf Kelsey , Koboldt Daniel C , Kuehn Hye Sun , Jayaraman Vijayakumar , Lee Kristy , Mihalic Mosher Theresa , Yonkof Jennifer R , Mori Mari , Hickey Scott E , Franklin Samuel , Drew Joanne , Akoghlanian Shoghik , Sivaraman Vidya , Rosenzweig Sergio D , Wilson Richard K , Abraham Roshini S
Published: April 2022

Objective

To explore and define the molecular cause(s) of a multi-generational kindred affected by Bechet’s-like mucocutaneous ulcerations and immune dysregulation.

Methods

Whole genome sequencing and confirmatory Sanger sequencing were performed. Components of the NFκB pathway were quantified by immunoblotting, and function was assessed by cytokine production (IL-6, TNF-α, IL-1β) after lipopolysaccharide (LPS) stimulation. Detailed immunophenotyping of T-cell and B-cell subsets was performed in four patients from this cohort.

Results

A novel variant in the RELA gene, p. Tyr349LeufsTer13, was identified. This variant results in premature truncation of the protein before the serine (S) 536 residue, a key phosphorylation site, resulting in enhanced degradation of the p65 protein. Immunoblotting revealed significantly decreased phosphorylated [p]p65 and pIκBα. The decrease in [p]p65 may suggest reduced heterodimer formation between p50/p65 (NFκB1/RelA). Immunophenotyping revealed decreased naïve T cells, increased memory T cells, and expanded senescent T-cell populations in one patient (P1). P1 also had substantially higher IL-6 and TNF-α levels post-stimulation compared with the other three patients.

Conclusion

Family members with this novel RELA variant have a clinical phenotype similar to other reported RELA cases with predominant chronic mucocutaneous ulceration; however, the clinical phenotype broadens to include Behçet’s syndrome and IBD. Here we describe the clinical, immunological and genetic evaluation of a large kindred to further expand identification of patients with autosomal dominant RELA deficiency, facilitating earlier diagnosis and intervention. The functional impairment of the canonical NFκB pathway suggests that this variant is causal for the clinical phenotype in these patients.
Evaluation and validation of the prognostic value of anti-MDA5 IgG subclasses in dermatomyositis-associated interstitial lung disease
Authors: Xu Yue-Tong , Zhang Ya-Mei , Yang Hong-Xia , Ye Li-Fang , Chen Fang , Lu Xin , Wang Guo-Chun , Peng Qing-Lin
Published: April 2022

Objective

To investigate the association between the anti-melanoma differentiation associated gene 5 (MDA5) IgG subclasses and prognosis of patients with dermatomyositis (DM)-associated interstitial lung disease (ILD).

Methods

This retrospective study included 122 anti-MDA5 positive DM-ILD patients admitted from October 2017 to October 2020 as training cohort, and additional 68 patients from August 2014 to September 2017 as validation cohort. The levels of anti-MDA5 total IgG and IgG subclasses were measured using in-house enzyme-linked immunosorbent assays, and analysed in association with the patient prognosis.

Results

In the training cohort, the concentrations of anti-MDA5 IgG1 and IgG3 in non-survivors were significantly higher than in survivors (P < 0.05), whereas there were no significant differences in the IgG2 and IgG4 levels. Kaplan–Meier survival analysis revealed that the levels of anti-MDA5 total IgG, IgG1 and IgG3 were associated with mortality (P < 0.05). Multivariate analysis revealed anti-MDA5 IgG1 >13 U/ml and anti-MDA5 IgG3 >11 U/ml were independent risk factors for death of DM-ILD patients (P < 0.05). Anti-MDA5 IgG1 was confirmed as an independent risk factor in the validation cohort, while anti-MDA5 IgG3 was not. Anti-MDA5 IgG1 showed greater discriminable power for patient prognosis (Youden index 0.494) than anti-MDA5 total IgG, IgG3, or the combination of IgG1 and IgG3 (Youden index 0.356, 0.32 and 0.447, respectively).

Conclusion

Anti-MDA5 IgG1 and IgG3 are significantly associated with poor prognosis in DM-ILD patients, and anti-MDA5 IgG1 is more efficient as a prognostic biomarker in DM-ILD patients.