ANKRD1 is a mesenchymal-specific driver of cancer-associated fibroblast activation bridging androgen receptor loss to AP-1 activation

There are significant commonalities among several pathologies involving fibroblasts, ranging from auto-immune diseases to fibrosis and cancer. Early steps in cancer development and progression are closely linked to fibroblast senescence and transformation into tumor-promoting cancer-associated fibroblasts (CAFs), suppressed by the androgen receptor (AR). Here, we identify ANKRD1 as a mesenchymal-specific transcriptional coregulator under direct AR negative control in human dermal fibroblasts (HDFs) and a key driver of CAF conversion, independent of cellular senescence. ANKRD1 expression in CAFs is associated with poor survival in HNSCC, lung, and cervical SCC patients, and controls a specific gene expression program of myofibroblast CAFs (my-CAFs). ANKRD1 binds to the regulatory region of my-CAF effector genes in concert with AP-1 transcription factors, and promotes c-JUN and FOS association. Targeting ANKRD1 disrupts AP-1 complex formation, reverses CAF activation, and blocks the pro-tumorigenic properties of CAFs in an orthotopic skin cancer model. ANKRD1 thus represents a target for fibroblast-directed therapy in cancer and potentially beyond.

DNA methylation sites in early adulthood characterised by pubertal timing and development: a twin study

BACKGROUND

Puberty is a highly heritable and variable trait, with environmental factors having a role in its eventual timing and development. Early and late pubertal onset are both associated with various diseases developing later in life, and epigenetic characterisation of pubertal timing and development could lead to important insights. Blood DNA methylation, reacting to both genotype and environment, has been associated with puberty; however, such studies are relatively scarce. We investigated peripheral blood DNA methylation profiles (using Illumina 450 K and EPIC platforms) of 1539 young adult Finnish twins associated with pubertal development scale (PDS) at ages 12 and 14 as well as pubertal age (PA).

RESULTS

Fixed effect meta-analysis of the two platforms on 347,521 CpGs in common identified 58 CpG sites associated (p < 1 × 10-5) with either PDS or PA. All four CpGs associated with PA and 45 CpGs associated with PDS were sex-specific. Thirteen CpGs had a high heritability (h2: 0.51-0.98), while one CpG site (mapped to GET4) had a high shared environmental component accounting for 68% of the overall variance in methylation at the site. Utilising twin discordance analysis, we found 6 CpG sites (5 associated with PDS and 1 with PA) that had an environmentally driven association with puberty. Furthermore, genes with PDS- or PA-associated CpGs were consistently linked to various developmental processes and diseases such as breast, prostate and ovarian cancer, while methylation quantitative trait loci of associated CpG sites were enriched in immune pathways developing during puberty.

CONCLUSIONS

By identifying puberty-associated DNA methylation sites and examining the effects of sex, environment and genetics, we shed light on the intricate interplay between environment and genetics in the context of puberty. Through our comprehensive analysis, we not only deepen the understanding of the significance of both genetic and environmental factors in the complex processes of puberty and its timing, but also gain insights into potential links with disease risks.

Probabilistic graphlets capture biological function in probabilistic molecular networks

MOTIVATION

Molecular interactions have been successfully modeled and analyzed as networks, where nodes represent molecules and edges represent the interactions between them. These networks revealed that molecules with similar local network structure also have similar biological functions. The most sensitive measures of network structure are based on graphlets. However, graphlet-based methods thus far are only applicable to unweighted networks, whereas real-world molecular networks may have weighted edges that can represent the probability of an interaction occurring in the cell. This information is commonly discarded when applying thresholds to generate unweighted networks, which may lead to information loss.

RESULTS

We introduce probabilistic graphlets as a tool for analyzing the local wiring patterns of probabilistic networks. To assess their performance compared to unweighted graphlets, we generate synthetic networks based on different well-known random network models and edge probability distributions and demonstrate that probabilistic graphlets outperform their unweighted counterparts in distinguishing network structures. Then we model different real-world molecular interaction networks as weighted graphs with probabilities as weights on edges and we analyze them with our new weighted graphlets-based methods. We show that due to their probabilistic nature, probabilistic graphlet-based methods more robustly capture biological information in these data, while simultaneously showing a higher sensitivity to identify condition-specific functions compared to their unweighted graphlet-based method counterparts.

AVAILABILITYAND IMPLEMENTATION

Our implementation of probabilistic graphlets is available at https://github.com/Serdobe/Probabilistic_Graphlets.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Effects of Dry Chilling on the Microflora on Beef Carcasses at a Canadian Beef Packing Plant

The aim of this study was to determine the course of effects on the microflora on beef carcasses of a commercial dry chilling process in which carcasses were dry chilled for 3 days. Groups of 25 carcasses selected at random were sampled when the chilling process commenced and after the carcasses were chilled for 1, 2, 4, 6, 8, 24, and 67 h for determination of the numbers of aerobes, coliforms, and Escherichia coli. The temperatures of the surfaces and the thickest part of the hip (deep leg) of carcasses, as well as the ambient air conditions, including air temperature, velocity, and relative humidity (RH), were monitored throughout the chilling process. The chiller was operated at 0°C with an off-coil RH of 88%. The air velocity was 1.65 m/s when the chiller was loaded. The initial RH levels of the air in the vicinity of carcasses varied with the locations of carcasses in the chiller and decreased rapidly during the first hour of chilling. The average times for shoulder surfaces, rump surfaces, and the deep leg of carcasses to reach 7°C were 13.6 ± 3.1, 16.0 ± 2.4 and 32.4 ± 3.2 h, respectively. The numbers of aerobes, coliforms, and E. coli on carcasses before chilling were 5.33 ± 0.42, 1.95 ± 0.77, 1.42 ± 0.78 log CFU/4,000 cm(2), respectively. The number of aerobes on carcasses was reduced by 1 log unit each in the first hour of chilling and in the subsequent 23 h of chilling. There was no significant difference (P > 0.05) between the numbers of aerobes recovered from carcasses after 24 and 67 h of chilling. The total numbers (log CFU/100,000 cm(2)) on carcasses before chilling and after the first hour of chilling were 3.86 and 2.24 for coliforms and 3.30 and 2.04 for E. coli. The subsequent 23 h of chilling reduced the numbers of both groups of organisms by a further log unit. No coliforms or E. coli were recovered after 67 h of chilling. The findings show that the chilling regime investigated in this study resulted in significant reductions of all three groups of indicator organisms.

Efficacy of laparoscopically assisted high ligation of patent processus vaginalis in children

INTRODUCTION

Laparoscopic hernia repairs have been proven to be efficient and safe for children, despite the slightly higher recurrence rate compared with the classic surgical repair. They have the advantage of easy and precise identification of the type of defect and its correction, both in ipsilateral and contralateral sides.

OBJECTIVES

The objectives of this study were to evaluate the efficacy, safety and outcome of the laparoscopically assisted piecemeal high ligation of a patent processus vaginalis (PPV) in children.

METHODS

A total of 40 children were enrolled into this prospective study; they were aged ≥ 6 months and had an inguinal hernia. The peritoneal cavity, including the contralateral side, was inspected for the possibility of bilateral hernias using a 3-mm 30° telescope. Another 3-mm port was introduced through the same infra-umbilical incision. The hernia was manually reduced or with the aid of a working infra-umbilical grasper. A prolene or vicryl 2/0 or 3/0 suture on a curved semicircle round-bodied taper-ended 25-30 mm needle was introduced through a very small inguinal skin-crease incision. It was passed through the abdominal wall layers to the peritoneum and was manipulated by the laparoscopic grasper to pick up the peritoneum in piecemeal all around the internal ring. The needle was then pushed to the outside near to the entrance site, thus forming a semicircle around the internal ring. The suture was then tied and the knot was subcutaneously buried. The primary outcome of the procedure was the incidence of intraoperative diagnosis and surgical repair of contralateral hernias in pre-operatively diagnosed unilateral cases. The secondary outcomes were defined as the incidence of complications and hernia recurrence.

DISCUSSION

The exploratory laparoscopy found contralateral patent processus vaginalis (CPPV) with a detection rate of 28.1%. Chan et al., Esposito et al., Toufique et al. and Niyogi et al. reported similar figures for laparoscopic contralateral hernia detection rates of 28%, 39%, 39.7% and 29.2%, respectively. The limitations of this study were the small sample size, plus the risk factors and clinical significance for CPPV.

CONCLUSION

Laparascopically assisted piecemeal closure of the internal inguinal ring in children is a safe and effective procedure. It helps in detecting a contralateral hernia without prolonging the operative time.

Unusual compositions of microflora of vacuum-packaged beef primal cuts of very long storage life

Vacuum-packaged top butt cuts from a beef packing plant that does not use any carcass decontaminating interventions were assessed for their organoleptic and microbiological properties during storage at 2 or -1.5°C. Cuts stored at 2°C were acceptable after storage for 140 days but were unacceptable after 160 days because of persistent sour, acid odors. Odors of cuts stored at -1.5°C for 160 days were acceptable. The numbers of aerobes on cuts increased from <1 log CFU/cm(2) to 7 or 6 log CFU/cm(2) for cuts stored at 2 or -1.5°C, respectively. The numbers of Enterobacteriaceae increased from <-1 log CFU/cm(2) to 5 or 3 log CFU/cm(2) for cuts stored at 2 or -1.5°C, respectively. Bacteria recovered from initial microflora were, mainly, strictly aerobic organisms. Bacteria recovered from cuts stored for 160 days were mainly Carnobacterium spp. that grew on an acetate-containing agar generally selective for lactic acid bacteria other than Carnobacterium. C. divergens and C. maltaromaticum were recovered from cuts stored at 2°C, but C. maltaromaticum was the only species of Carnobacterium recovered from cuts stored at -1.5°C. No lactic acid bacteria of genera that usually predominate in the spoilage microflora of vacuum-packaged beef at late storage times were recovered from the spoilage microflora. The findings indicate that carnobacteria, initially present at very small numbers, grew exponentially to persistently dominate the spoilage microflora of vacuum-packaged beef cuts of unusually long storage life.

Effects of selected cooking procedures on the survival of Escherichia coli O157:H7 in inoculated steaks cooked on a hot plate or gas barbecue grill

Beef steaks (2 cm thick) were each inoculated at three sites in the central plane with Escherichia coli O157:H7 at 5.9 ± 0.3 log CFU per site. Temperatures at steak centers were monitored during cooking on a hot plate or the grill of a gas barbeque. Steaks were cooked in groups of five using the same procedures and cooking each steak to the same temperature, and surviving E. coli O157:H7 at each site was enumerated. When steaks cooked on the hot plate were turned over every 2 or 4 min during cooking to between 56 and 62°C, no E. coli O157:H7 was recovered from steaks cooked to ≥58 or 62°C, respectively. When steaks were cooked to ≤71°C and turned over once during cooking, E. coli O157:H7 was recovered from steaks in groups turned over after ≤8 min but not from steaks turned over after 10 or 12 min. E. coli O157:H7 was recovered in similar numbers from steaks that were not held or were held for 3 min after cooking when steaks were turned over once after 4 or 6 min during cooking. When steaks were cooked on the grill with the barbeque lid open and turned over every 2 or 4 min during cooking to 63 or 56°C, E. coli O157:H7 was recovered from only those steaks turned over at 4-min intervals and cooked to 56°C. E. coli O157:H7 was recovered from some steaks turned over once during cooking on the grill and held or not held after cooking to 63°C. E. coli O157:H7 was not recovered from steaks turned over after 4 min during cooking to 60°C on the grill with the barbeque lid closed or when the lid was closed after 6 min. Apparently, the microbiological safety of mechanically tenderized steaks can be assured by turning steaks over at intervals of about 2 min during cooking to ≥60°C in an open skillet or on a barbecue grill. When steaks are turned over only once during cooking to ≥60°C, microbiological safety may be assured by covering the skillet or grill with a lid during at least the final minutes of cooking.

Enhanced control of microbiological contamination of product at a large beef packing plant

Swab samples were obtained from groups of 25 carcasses at various stages of processing at a large beef packing plant. The log mean number of aerobes recovered from carcasses after skinning was 2.2 log CFU/cm(2). Spraying the uneviscerated carcasses with 5% lactic acid reduced the numbers of aerobes by about 1 log unit; but subsequent carcass dressing operations, a second treatment with 5% lactic acid, pasteurizing, and carcass cooling had no substantial effect upon the number of aerobes on carcasses. The total numbers of coliforms or Escherichia coli cells recovered from skinned carcasses were <2 log CFU/2,500 cm(2). The numbers were reduced by the washing of uneviscerated carcasses but increased after evisceration operations. The numbers were reduced by spraying with lactic acid and pasteurizing, with no coliforms or E. coli being recovered from pasteurized carcass sides. No coliforms or E. coli cells were recovered from the forequarters of cooled carcass sides, but E. coli cells were recovered from the hindquarters of 1 of 50 cooled carcass sides, at 1.4 log CFU/1,000 cm(2). The numbers of aerobes on conveyor belts in the carcass breaking facility were similar to the numbers on cooled carcass, but the numbers of aerobes on cuts and trimmings and the number of coliforms and E. coli cells on the products and belts were higher than the numbers on carcasses. The findings indicate that most cooled carcasses produced at the plant carry E. coli at numbers <1 CFU/10,000 cm(2) but that product can be contaminated with small numbers of E. coli (<1 CFU/100 cm(2)) during carcass breaking.

Fat reduction in comminuted meat products-effects of beef fat, regular and pre-emulsified canola oil

The effects of fat reduction (25.0%, 17.5%, and 10.0%) and substituting beef fat with canola oil or pre-emulsified canola oil (using soy protein isolate, sodium caseinate or whey protein isolate) on cooking loss, texture and color of comminuted meat products were investigated. Reducing fat from 25 to 10% increased cooking loss and decreased hardness. Canola oil or pre-emulsified treatments showed a positive effect on improving yield and restoring textural parameters. Using sodium caseinate to pre-emulsify the oil resulted in the highest hardness value. Cohesiveness was affected by fat type and level. The color of reduced fat meat batters was darker for all, except the beef fat treatments. Using canola oil or pre-emulsified oil resulted in a significant reduction in redness. The results show that pre-emulsification can offset some of the changes in reduced fat meat products when more water is used to substitute for the fat and that pre-emulsification can also help to produce a more stable meat matrix.

Skeletal muscle reinnervation by reduced axonal numbers results in whole muscle force deficits

Patients sustaining a peripheral nerve injury will frequently experience residual muscle weakness after muscle reinnervation, even if the nerve repair is performed under optimal circumstances to allow rapid muscle reinnervation. The mechanisms responsible for this contractile dysfunction remain unclear. It is hypothesized that after peripheral nerve injury and repair, a reduced number of axons are available for skeletal muscle reinnervation that results in whole muscle force and specific force deficits. A rat model of peroneal nerve injury and repair was designed so that the number of axons available for reinnervation could be systematically reduced. In adult rats, the peroneal nerve to the extensor digitorum longus muscle was either left intact (sham group, n = 8) or divided and repaired with either 50 percent (R50 group, n = 7) or 100 percent (R100 group, n = 8) of the axons in the proximal stump included in the repair. Four months after surgery, maximal tetanic isometric force was measured and specific force was calculated for each animal. Mean tetanic isometric force for extensor digitorum longus muscles from R50 rats (2765.7 +/- 767.6 mN) was significantly lower than sham (4082.8 +/- 196.5 mN) and R100 (3729.0 +/-370.2 mN) rats (p < 0.003). Mean specific force calculations revealed significant deficits in both the R100 (242.1 +/- 30 kN/m2) and R50 (190.6 +/- 51.8 kN/m2) rats compared with the sham animals (295.9 +/- 14 kN/m2) (p < 0.0005). These data support our hypothesis that after peripheral nerve injury and repair, reinnervation of skeletal muscle by a reduced number of axons results in a reduction in tetanic isometric force and specific force. The greater relative reduction in specific force compared with absolute force production after partial nerve repair may indicate that a population of residual denervated muscle fibers is responsible for this deficit.

Acetaminophen plasma level after oral administration in liver cirrhotic patients suffering from schistosomal infection

Hepatosplenic schistosomal infection is a common parasitic liver disease in Egypt, resulting in the formation of granuloma followed by fibrosis which leads to the chronic liver disease. Plasma level of acetaminophen (AAP) and its glucuronide and sulfate metabolites after oral administration at a dose of 1 g was determined in liver-cirrhotic younger (9 - 25 years old) and elderly patients (45 - 65 years old) suffering from schistosomal infection. These levels of AAP and its metabolites in patient groups were compared with those in corresponding healthy subject groups. Examinations for participants in the present study by physicians indicated the more severe cirrhosis in elderly patients compared to younger patients and the formation of collateral circulation and the renal insufficiency in elderly patients. The elimination of AAP from plasma was significantly prolonged in both younger and elderly patient groups. In elderly patients plasma concentration of AAP in early stage (before the time to reach Cmax) was significantly higher, indicating the partial avoidance of first-pass metabolism due to the formation of hepatic shunt pathway. Plasma concentration of AAP-glucuronide was greatly decreased in both patient groups, whereas no significant difference in the plasma concentration of AAP-sulfate compared to those in corresponding healthy subject groups. These results will suggest that with repeated dosing of AAP special care must be taken in schistosomal patients since the elimination of AAP from plasma is remarkably reduced.

Management of facial contour deformities with deepithelialized lateral intercostal free flap

Ten cases suffering from facial contour deformities caused by loss of subcutaneous tissue are presented. Three cases had hemifacial microsomia, 3 had postmaxillectomy collapsed cheek, while the remaining 4 patients had Romberg's disease. All cases were treated by the insertion of a deepithelialized, revascularized lateral intercostal flap. The flaps used had dimensions ranging from 9 cm x 6 cm to 12 cm x 14 cm. The vascular pedicle of the flap is the lateral cutaneous branch of one of the lower four posterior intercostal bundles (usually the tenth or the eleventh). The flap is designed to have the pedicle in its center, thus allowing defattening of the edges at the primary surgery and minimizing the need for secondary debulking. Nine flaps were successful and one failed. All successful flaps gave a permanent and satisfactory correction of the deformity. The difficulties and advantages of the flap are presented.

Paper chromatographic determination of chlortetracycline

Chlortetracycline was successfully separated from its degradation products and from other tetracyclines on a paper chromatogram previously impregnated with a mixture of edetate disodium and urea solution in pH 5.0 McIlvaine buffer. Chlortetracycline separation from its degradation products and from both tetracycline and oxytetracycline was attributed primarily to the complexation of these antibiotics with urea and edetate on the chromatogram. The separated spots were located under UV light, and their Rf values were calculated. Chlortetracycline recovery from the paper chromatogram was satisfactory (98.3 +/- 0.002%). The developed method was successfully applied to the determination of chlortetracycline in various dosage forms. In addition, the method was adequate for monitoring chlortetracycline hydrochyloride stability in aqueous solutions.