Mora: abundance aware metagenomic read re-assignment for disentangling similar strains.

BACKGROUND: Taxonomic classification of reads obtained by metagenomic sequencing is often a first step for understanding a microbial community, but correctly assigning sequencing reads to the strain or sub-species level has remained a challenging computational problem. RESULTS: We introduce Mora, a MetagenOmic read Re-Assignment algorithm capable of assigning short and long metagenomic reads with high precision, even at the strain level. Mora is able to accurately re-assign reads by first estimating abundances through an expectation-maximization algorithm and then utilizing abundance information to re-assign query reads. The key idea behind Mora is to maximize read re-assignment qualities while simultaneously minimizing the difference from estimated abundance levels, allowing Mora to avoid over assigning reads to the same genomes. On simulated diverse reads, this allows Mora to achieve F1 scores comparable to other algorithms while having less runtime. However, Mora significantly outshines other algorithms on very similar reads. We show that the high penalty of over assigning reads to a common reference genome allows Mora to accurately infer correct strains for real data in the form of E. coli reads. CONCLUSIONS: Mora is a fast and accurate read re-assignment algorithm that is modularized, allowing it to be incorporated into general metagenomics and genomics workflows. It is freely available at https://github.com/AfZheng126/MORA .

Advancing entity recognition in biomedicine via instruction tuning of large language models.

MOTIVATION: Large Language Models (LLMs) have the potential to revolutionize the field of Natural Language Processing, excelling not only in text generation and reasoning tasks but also in their ability for zero/few-shot learning, swiftly adapting to new tasks with minimal fine-tuning. LLMs have also demonstrated great promise in biomedical and healthcare applications. However, when it comes to Named Entity Recognition (NER), particularly within the biomedical domain, LLMs fall short of the effectiveness exhibited by fine-tuned domain-specific models. One key reason is that NER is typically conceptualized as a sequence labeling task, whereas LLMs are optimized for text generation and reasoning tasks. RESULTS: We developed an instruction-based learning paradigm that transforms biomedical NER from a sequence labeling task into a generation task. This paradigm is end-to-end and streamlines the training and evaluation process by automatically repurposing pre-existing biomedical NER datasets. We further developed BioNER-LLaMA using the proposed paradigm with LLaMA-7B as the foundational LLM. We conducted extensive testing on BioNER-LLaMA across three widely recognized biomedical NER datasets, consisting of entities related to diseases, chemicals, and genes. The results revealed that BioNER-LLaMA consistently achieved higher F1-scores ranging from 5% to 30% compared to the few-shot learning capabilities of GPT-4 on datasets with different biomedical entities. We show that a general-domain LLM can match the performance of rigorously fine-tuned PubMedBERT models and PMC-LLaMA, biomedical-specific language model. Our findings underscore the potential of our proposed paradigm in developing general-domain LLMs that can rival SOTA performances in multi-task, multi-domain scenarios in biomedical and health applications. AVAILABILITY AND IMPLEMENTATION: Datasets and other resources are available at https://github.com/BIDS-Xu-Lab/BioNER-LLaMA.

TOWARD AN IMAGING-CENTRIC DEFINITION OF NONPARANEOPLASTIC AUTOIMMUNE RETINOPATHY.

PURPOSE: To explore characteristic imaging features of nonparaneoplastic autoimmune retinopathy (npAIR) to augment diagnostic criteria. METHODS: This is a retrospective cohort study of patients with npAIR evaluated at the Emory Eye Center between 2013 and 2019. Multimodal fundus images were evaluated to characterize the evolution of the disease. RESULTS: Twenty-one eyes of 12 patients were classified as having npAIR. Five patients (42%) were female, with median (range) age of 59 years (45-85 years). Median baseline visual acuity was 20/30 (20/20 to hand motions). Disease was asymmetric in 11 patients (92%). Common imaging findings included absence of bone spicules (86% of affected eyes), presence of attenuated vessels (86%), and speckled hypoautofluorescence in perimacular and perivenular regions. Three eyes were noted to present early with subtle splotchy fundus autofluorescence abnormality, ultimately developing characteristic speckled perimacular hypoautofluorescence. On optical coherence tomography, 18 eyes (86%) had loss of outer retinal bands with relative foveal sparing and a tapered transition zone. CONCLUSION: Many eyes with npAIR exhibit a subacute, asymmetric, generalized photoreceptor degeneration featuring outer retinal atrophy with relative foveal sparing, retinal vascular attenuation, absence of bone spicules, and speckled hypoautofluorescence often in a perimacular and perivenular distribution. Findings of this study augment diagnostic criteria to improve specificity and accessibility of testing for npAIR.

Epigenetic drugs induce the potency of classic chemotherapy, suppress post-treatment re-growth of breast cancer, but preserve the wound healing ability of stem cells.

Epigenetic therapy augments neoadjuvant chemotherapy (NACT) in breast cancer and may aid post-surgical wound healing affected by NACT. Our study investigates: (1) The cytotoxicity of classic paclitaxel chemotherapy on triple negative breast cancer (TNBC) independently and in combination with epigenetic drugs. (2) The sustainable inhibition of breast cancer regrowth following paclitaxel and epigenetic therapies. (3) The effects of paclitaxel with and without epigenetic therapy on the post-treatment viability and wound healing potential of adipose stem cells (ASCs). Cytotoxicity assays were performed on TNBC and ASCs. Cells were treated and recovered in drug-free medium. Cell viability was measured via cell counts and MTT assays. W -ound healing was tested with scratch assays. The combination of epigenetic drugs shows increased toxicity against TNBC cells compared to standard chemotherapy alone. Moreover, the combination of paclitaxel with epigenetic treatments causes cancer toxicity that is sustainable to TNBC cells after the drugs' removal with minimal effect on ASCs wound healing ability. The use of epigenetic drugs in addition to standard chemotherapy is cytotoxic to TNBC cells and prevents post-treatment recovery of TNBC while maintaining ASC wound healing ability. This strategy may be useful in maximizing post-surgical wound healing following NACT in TNBC.

Scalp and serum profiling of frontal fibrosing alopecia reveals scalp immune and fibrosis dysregulation with no systemic involvement.

BACKGROUND: Frontal fibrosing alopecia (FFA) is a progressive, scarring alopecia of the frontotemporal scalp that poses a substantial burden on quality of life. Large-scale global profiling of FFA is lacking, preventing the development of effective therapeutics. OBJECTIVE: To characterize FFA compared to normal and alopecia areata using broad molecular profiling and to identify biomarkers linked to disease severity. METHODS: This cross-sectional study assessed 33,118 genes in scalp using RNA sequencing and 350 proteins in serum using OLINK high-throughput proteomics. Disease biomarkers were also correlated with clinical severity and a fibrosis gene set. RESULTS: Genes differentially expressed in lesional FFA included markers related to Th1 (IFNγ/CXCL9/CXCL10), T-cell activation (CD2/CD3/CCL19/ICOS), fibrosis (CXCR3/FGF14/FGF22/VIM/FN1), T-regulatory (FOXP3/TGFB1/TGFB3), and Janus kinase/JAK (JAK3/STAT1/STAT4) (Fold changes [FCH]>1.5, FDR<.05 for all). Only one protein, ADM, was differentially expressed in FFA serum compared to normal (FCH>1.3, FDR<.05). Significant correlations were found between scalp biomarkers (IL-36RN/IL-25) and FFA severity, as well as between JAK/STAT and fibrosis gene-sets (r>.6; P <.05). LIMITATIONS: This study was limited by a small sample size and predominantly female FFA patients. CONCLUSION: Our data characterize FFA as an inflammatory condition limited to scalp, involving Th1/JAK skewing, with associated fibrosis and elevated T-regulatory markers, suggesting the potential for disease reversibility with JAK/STAT inhibition.

Dimensions, Function and Applications of the Auricular Muscle in Facial Plastic Surgery.

PURPOSE: To determine the dimensions and function of the auricular muscle and to consider applications of this muscle in facial plastic surgery. METHODS: Nonpreserved fresh frozen human cadaver dissections from the (HOSPITAL-Blinded) Body Donation program were dissected. The length and width of the superior auricular muscle were measured. One surgeon performed all dissections and measurements. RESULTS: A total of seven left and five right hemifaces were studied. The average central height of the superior auricular muscle was 4.7 cm, and an average width was 5.0 cm. There was no significant difference between the average values of the left versus the right hemiface measurements. The muscle originated in the fibers of the galea and temporal fascia and inserted into the conchal cartilage in each specimen. Engaging the muscle in its line of action yielded slight elevation of the forehead and prevented movement of the galea along the vertex of the scalp. CONCLUSIONS: The auricular muscle acts as an occipitofrontalis stabilizer and a weak brow elevator. LEVEL OF EVIDENCE IV: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors - www.springer.com/00266 .

Locally Transplanted Adipose Stem Cells Reduce Anastomotic Leaks in Ischemic Colorectal Anastomoses: A Rat Model.

BACKGROUND: Anastomotic leakage remains a dreaded complication after colorectal surgery. Stem-cell-based therapies have been shown to increase angiogenesis and cell proliferation. OBJECTIVE: The purpose of this research was to investigate the use of adipose-derived stem cells on the healing of ischemic colonic anastomoses in a rat model. DESIGN: This is an animal research study using xenotransplantation. SETTINGS: Male Wistar rats (300-400 g, n = 48) were purchased from a licensed breeder. PATIENTS: Adipose stem cells were isolated from the subcutaneous fat of healthy human donors. INTERVENTIONS: The rats underwent laparotomy with creation of an ischemic colorectal anastomosis created by ligation of mesenteric vessels. The animals were divided into 3 groups: control group with an ischemic anastomosis, vehicle-only group in which the ischemic anastomosis was treated with an absorbable gelatin sponge, and a treatment group in which the ischemic anastomosis was treated with an absorbable gelatin sponge plus adipose stem cells. Animals were killed at postoperative days 3 and 7. MAIN OUTCOME MEASURES: Anastomotic leakage was defined as the finding of feculent peritonitis or perianastomotic abscess on necropsy. Rat mRNA expression was measured using real-time polymerase chain reaction. RESULTS: Adipose-derived stem cells significantly decreased anastomotic leakage when compared with control at both postoperative days 3 (25.0% vs 87.5%; p = 0.02) and 7 (25.0% vs 87.5%; p = 0.02). The use of an absorbable gelatin sponge alone had no effect on anastomotic leakage when compared with control and postoperative days 3 or 7. We found that stem cell-treated animals had a 5.9-fold and 7.4-fold increase in the expression of vascular endothelial growth factor when compared with control at 3 and 7 days; however, this difference was not statistically significant when compared with the absorbable gelatin sponge group. LIMITATIONS: This is a preclinical animal research study using xenotransplantation of cultured stem cells. CONCLUSIONS: Locally transplanted adipose stem cells enhance the healing of ischemic colorectal anastomoses and may be a novel strategy for reducing the risk of anastomotic leakage in colorectal surgery. See Video Abstract at http://links.lww.com/DCR/B203. EL TRANSPLANTE LOCAL DE CÉLULAS MADRE ADIPOSAS REDUCE LA FUGA ANASTOMÓTICA EN LAS SUTURAS COLORRECTALES ISQUÉMICAS: MODELO EN RATAS: Las fugas anastomóticas son una complicación pusilánime después de toda cirugía colorrectal. Se ha demostrado que el tratamiento con células madre aumenta la angiogénesis y la proliferación celular.Investigar el uso de células madre derivadas de tejido adiposo en la cicatrización de una anastomosis colónica isquémica basada en ratas como modelo.Estudio de investigación en animales utilizando xenotrasplantes.Adquisición de típicas ratas de laboratorio raza Wistar, todas machos (300-400 g, n = 48) de un criadero autorizado.Aislamiento de células madre de tipo adiposo del tejido celular subcutáneo en donantes humanos sanos.Las ratas se sometieron a laparotomía con la creación de una anastomosis colorrectal isquémica obtenida mediante ligadura controlada de los vasos mesentéricos correspondientes. Los animales se dividieron en tres grupos: grupo de control con anastomosis isquémica, grupo de vehículo único en el que la anastomosis isquémica se trató con una esponja de gelatina absorbible, y un grupo de tratamiento en el que la anastomosis isquémica se trató con una esponja de gelatina absorbible asociada a un vástago adiposo de células madre. Los animales fueron sacrificados el POD3 y el POD7.La fuga anastomótica fué definida como el hallazgo de peritonitis fecaloidea o absceso perianastomótico a la necropsia. La expresión de RNAm de las ratas se midió usando PCR en tiempo real.Las células madre derivadas de tejido adiposo disminuyeron significativamente la fuga anastomótica en comparación con el grupo control tanto en el POD3 (25% frente a 87.5%, p = 0.02) como en el POD7 (25% frente a 87.5%, p = 0.02). El uso de una esponja de gelatina absorbible sola, no tuvo efecto sobre la fuga anastomótica en comparación con los controles el POD3 o el POD7. Descubrimos que los animales tratados con células madre adiposas tenían un aumento de 5,9 y 7,4 veces en la expresión de VEGF en comparación con el control a los 3 y 7 días, respectivamente; sin embargo, esta diferencia no fue estadísticamente significativa en comparación con el grupo de esponja de gelatina absorbible.Este es un estudio preclínico de investigación en animales que utiliza xenotrasplantes de células madre adiposas cultivadas.Las células madre de tipo adiposo trasplantadas localmente mejoran la cicatrisación en casos de anastomosis colorrectales isquémicas, y podrían convertirse en una nueva estrategia para reducir el riesgo de fugas anastomóticas en casos de cirugía colorrectal. Consulte Video Resumen en http://links.lww.com/DCR/B203. (Traducción-Dr Xavier Delgadillo).

Surgical Options and Outcomes in the Treatment of Optic Pit Maculopathy: A Meta-analysis and Systematic Review.

PURPOSE: Optic pit maculopathy (OPM) is an uncommon cause of vision loss with no standard surgical treatment. Surgical treatment involves pars plana vitrectomy (PPV), often combined with adjunctive procedures. Large studies comparing outcomes of these approaches are lacking because of low disease incidence. Therefore, we conducted a meta-analysis of PPV without or with adjunctive procedures. DESIGN: Meta-analysis and systematic literature review. METHODS: We conducted a literature search to identify clinical studies and case series of surgically managed OPM. Inclusion criteria were: (1) more than 2 patients, (2) treatment with PPV, and (3) reporting of preoperative and postoperative visual acuity data. We excluded review articles and studies not available in English. Results were analyzed using a 1-way analysis of variance, Pearson's chi-square test, and simple linear regression. Publication bias was modeled using funnel plots. MAIN OUTCOME MEASURES: Visual acuity changes, resolution rate, resolution time, and change in OCT thickness. RESULTS: We identified 26 studies, encompassing 27 years and 342 patients. We identified 6 commonly reported techniques: PPV alone (92 patients), PPV plus juxtapapillary laser treatment (JPL; 146 patients), PPV plus internal limiting membrane peeling (ILMP; 50 patients), PPV plus both ILMP and JPL (16 patients), PPV plus inner retinal fenestration (18 patients), and PPV plus autologous platelet concentrate (22 patients). All groups demonstrated improved best-corrected visual acuity (BCVA; average, 0.46 logarithm of the minimum angle of resolution [logMAR]; 95% confidence interval [CI], 0.41-0.51 logMAR) compared with baseline, with no differences between groups (P = 0.11). The average OPM resolution rate was 70% among all groups (range, 56%-100%), and the average time to resolution was 8.4 months for all groups (95% CI, 7.2-9.6 months). Central macular thickness was reduced in all groups with no differences between groups (P = 0.15). Tamponade had no effect on outcomes. Linear regression analysis demonstrated significant correlations between preoperative BCVA and above outcome measures. Funnel plots demonstrated positive publication bias in PPV and PPV plus JPL groups. CONCLUSIONS: We did not identify any significant differences in outcomes among 6 different surgical techniques. This study is limited by its inclusion of primarily retrospective studies and positive publication bias.

Noninvasive Structural Imaging of a Retinal Cavernous Hemangioma Using SS-OCTA and Correlation to Previously Reported Histopathology.

Optical coherence tomography angiography (OCTA) is a novel imaging modality, and its role in the clinical evaluation of patients remains to be defined. In this report, the authors describe a case of a retinal cavernous hemangioma and show that OCTA of the lesion recapitulates many structural features first described in previous histopathologic studies, including aneurysmal architecture, septated blood flow, and epiretinal membrane. Thus, OCTA provides a new, noninvasive means of studying retinal cavernous hemangioma structure, a unique capability that may also be clinically relevant to the evaluation of other pathologic retinal vascular tumors, such as capillary and racemose hemangiomas. [Ophthalmic Surg Lasers Imaging Retina. 2019;50:e320-e323.].

Epigenetic therapy can inhibit growth of ovarian cancer cells and reverse chemoresistant properties acquired from metastatic omentum.

OBJECTIVE: To examine the cytotoxicity of epigenetic drugs independently and in combination with chemotherapy on ovarian cancer cells Caov-3, and to investigate their ability to acquire chemoresistance in omental microenvironments and whether epigenetic drugs can counteract this chemoresistance. METHODS: A pilot study was conducted in Cooper University Hospital, NJ, USA from August 1 to October 31, 2017, among women undergoing surgeries for uterine and ovarian cancer. Cytotoxicity assays using IC50 values of epigenetic drugs and paclitaxel and cisplatin were performed on Caov-3. Omental adipose-derived stem cells (OASCs) were isolated from omentum with/without metastases. Caov-3 was cultured with OASCs' conditioned medium and subjected to different drugs. Cell viability and secretome was measured using MTT and Elisa, respectively. RESULTS: Three women met the eligibility criteria and were included in the study. Epigenetic drugs alone or in combination with chemotherapy showed 85%-94% increased cytotoxicity against Caov-3 (P≤0.005). Metastatic OASCs conditioned medium showed up to 27-fold increase in tumorigenic factors and promoted chemoresistance (28%-35%; P < 0.050) against chemotherapy. Epigenetic therapy resulted in up to a 40-fold reversal in this chemoresistance. CONCLUSION: Epigenetic therapies could have an important role in treating a subgroup of ovarian cancer patients that demonstrate resistance to first-line chemotherapy.

Polyp Detection Rates among Body Mass Index Categories at First Screening Colonoscopy.

In the United States, obesity is an epidemic and colorectal cancer is the second deadliest cancer for men and women. A link between obesity and colorectal adenomas and carcinoma has been suggested but not proven. We sought out to determine if obesity was associated with increased rates of polyp formation. All patients undergoing a first screening colonoscopy by one of the participating endoscopists at Thomas Jefferson University Hospital from January 2012 to March 2015 were considered for the study. Their demographics, body mass index (BMI), and colonoscopy findings were recorded at the time of the procedure and prospectively maintained in our database. The final pathologic diagnosis was recorded for each participant as it became available. A total of 758 subjects were included. Of these, 22 per cent had a BMI <25 kg/m2, 29 per cent had a BMI between 25 and 29.9 kg/m2, and 49 per cent had a BMI of at least 30 kg/m2. Overall, 21.9 per cent of the participants were found to have at least one adenomatous polyp. The polyp detection rates were 24.4 per cent in the group with a BMI less than 25, 20.5 per cent in the overweight group, and 21.6 per cent in the obese group. Our study included 56 super obese individuals with a BMI ≥45 kg/m2. About 17.9 per cent of subjects in the super obese group had an adenomatous polyp. There were no differences in the incidence of adenomatous polyps between BMI categories in our study.

Dynamic monitoring of antimicrobial resistance using magnesium zinc oxide nanostructure-modified quartz crystal microbalance.

Antimicrobial resistance (AMR) is becoming a major global-health concern prompting an urgent need for highly-sensitive and rapid diagnostic technology. Traditional assays available for monitoring bacterial cultures are time-consuming and labor-intensive. We present a magnesium zinc oxide (MZO) nanostructure-modified quartz crystal microbalance (MZOnano-QCM) biosensor to dynamically monitor antimicrobial effects on E. coli and S. cerevisiae. MZO nanostructures were grown on the top electrode of a standard QCM using metal-organic chemical-vapor deposition (MOCVD). The MZO nanostructures are chosen for their multifunctionality, biocompatibility, and giant effective sensing surface. The MZO surface-wettability and morphology are controlled, offering high-sensitivity to various biological/biochemical species. MZO-nanostructures showed over 4-times greater cell viability over ZnO due to MZO releasing 4-times lower Zn2+ density in the cell medium than ZnO. The MZOnano-QCM was applied to detect the effects of ampicillin and tetracycline on sensitive and resistant strains of E.coli, as well as effects of amphotericin-B and miconazole on S. cerevisiae through the device's time-dependent frequency shift and motional resistance. The MZOnano-QCM showed 4-times more sensitivity over ZnOnano-QCM and over 10-times better than regular QCM. For comparison, the optical density at 600nm (OD600) method and the cell viability assay were employed as standard references to verify the detection results from MZOnano-QCM. In the case of S. cerevisiae, the OD600 method failed to distinguish between cytotoxic and cytostatic drug effects whereas the MZOnano-QCM was able to accurately detect the drug effects. The MZOnano-QCM biosensor provides a promising technology enabling dynamic and rapid diagnostics for antimicrobial drug development and AMR detection.

COMBINED VITRECTOMY AND INTRAVITREAL DEXAMETHASONE (OZURDEX) SUSTAINED-RELEASE IMPLANT.

PURPOSE: To evaluate the safety and efficacy of combining intravitreal dexamethasone implantation (Ozurdex) with pars plana vitrectomy (PPV). METHODS: A retrospective review was conducted on cases where Ozurdex injection was performed in the operating room in conjunction with pars plana vitrectomy. Our primary outcome measure was the presence of surgical complications in the perioperative and 3-month postoperative window. We also measured visual acuity, intraocular pressure (IOP), and macular edema at baseline, one, and 3 months after surgery. RESULTS: Fifteen eyes in 14 cases were reviewed. There were no complications intraoperatively or at 1-month postoperatively. Two patients (2 eyes) with prior retinal detachment developed proliferative vitreoretinopathy and redetachment at 3 months. Visual acuity improved in 7 of 15 eyes, and an average improvement of 2 lines was achieved for the entire cohort. There was no overall change in intraocular pressure although 1 patient developed an increase in intraocular pressure >5 mmHg. Five of 9 patients with baseline macular edema experienced improvement or resolution at 3 months. CONCLUSION: Intraoperative Ozurdex in combination with PPV may be safe and effective in treating macular edema caused by many different underlying diseases.

Laser-Induced Photic Injury Phenocopies Macular Dystrophy.

OBJECTIVE: To describe the phenotypes associated with laser-induced retinal damage in children. METHODS: Five patients with maculopathy and reduced visual acuity associated with laser pointer use were evaluated. Best-corrected visual acuity, retinal structure, and function were monitored with color fundus, infrared (IR), and red-free images, fundus autofluorescence (AF), spectral domain-optical coherence tomography (SD-OCT), and full-field electroretinography (ERG). RESULTS: All five laser pointer injury patients had retinal lesions resembling a macular dystrophy (one bilateral and four unilateral). These lesions were irregular in shape but all had a characteristic dendritic appearance with linear streaks radiating from the lesion. Photoreceptor damage was present in all patients, but serial OCT monitoring showed that subsequent photoreceptor recovery occurred over time in the eyes of at least four patients. One patient also had bilateral pigment epithelial detachments (PED). Both hyper- and hypoautofluorecence were observed in the laser damage area. CONCLUSIONS: In general, OCT and IR images are quite useful to diagnose laser damage, but AF is not as sensitive. Laser pointer damage in children can occasionally be misdiagnosed as a macular dystrophy disease, but the distinctive lesions and OCT features are helpful for differentiating laser damage from other conditions.

Precision Medicine: Genetic Repair of Retinitis Pigmentosa in Patient-Derived Stem Cells.

Induced pluripotent stem cells (iPSCs) generated from patient fibroblasts could potentially be used as a source of autologous cells for transplantation in retinal disease. Patient-derived iPSCs, however, would still harbor disease-causing mutations. To generate healthy patient-derived cells, mutations might be repaired with new gene-editing technology based on the bacterial system of clustered regularly interspersed short palindromic repeats (CRISPR)/Cas9, thereby yielding grafts that require no patient immunosuppression. We tested whether CRISPR/Cas9 could be used in patient-specific iPSCs to precisely repair an RPGR point mutation that causes X-linked retinitis pigmentosa (XLRP). Fibroblasts cultured from a skin-punch biopsy of an XLRP patient were transduced to produce iPSCs carrying the patient's c.3070G > T mutation. The iPSCs were transduced with CRISPR guide RNAs, Cas9 endonuclease, and a donor homology template. Despite the gene's repetitive and GC-rich sequences, 13% of RPGR gene copies showed mutation correction and conversion to the wild-type allele. This is the first report using CRISPR to correct a pathogenic mutation in iPSCs derived from a patient with photoreceptor degeneration. This important proof-of-concept finding supports the development of personalized iPSC-based transplantation therapies for retinal disease.

Personalized therapeutic strategies for patients with retinitis pigmentosa.

INTRODUCTION: Retinitis pigmentosa (RP) encompasses many different hereditary retinal degenerations that are caused by a vast array of different gene mutations and have highly variable disease presentations and severities. This heterogeneity poses a significant therapeutic challenge, although an answer may eventually be found through two recent innovations: induced pluripotent stem cells (iPSCs) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas genome editing. AREAS COVERED: This review discusses the wide-ranging applications of iPSCs and CRISPR-including disease modelling, diagnostics and therapeutics - with an ultimate view towards understanding how these two technologies can come together to address disease heterogeneity and orphan genes in a novel personalized medicine platform. An extensive literature search was conducted in PubMed and Google Scholar, with a particular focus on high-impact research published within the last 1 - 2 years and centered broadly on the subjects of retinal gene therapy, iPSC-derived outer retina cells, stem cell transplantation and CRISPR/Cas gene editing. EXPERT OPINION: For the retinal pigment epithelium, autologous transplantation of gene-corrected grafts derived from iPSCs may well be technically feasible in the near future. Photoreceptor transplantation faces more significant unresolved technical challenges but remains an achievable, if more distant, goal given the rapid pace of advancements in the field.

Characterization of G2P[4] rotavirus strains associated with increased detection in Australian states using the RotaTeq® vaccine during the 2010-2011 surveillance period.

The introduction of rotavirus vaccines Rotarix® and RotaTeq® into the Australian National Immunisation Program in July 2007 has resulted in a dramatic decrease in the burden of rotavirus disease. G2P[4] strains became the dominant genotype Australia-wide during the 2010-2011 surveillance period and for the first time since vaccine introduction, a higher proportion were isolated in jurisdictions using RotaTeq® vaccine compared to locations using Rotarix®. Phylogenetic analysis of the VP7 gene of 32 G2P[4] strains identified six genetic clusters, these distinct clusters were also observed in the VP4 gene for a subset of 12 strains. The whole genome was determined for a representative strain of clusters; A (RVA/Human-wt/AUS/SA066/2010/G2P[4]), B (RVA/Human-wt/AUS/WAPC703/2010/G2P[4]), C (RVA/Human-wt/AUS/MON008/2010/G2P[4]) and E (RVA/Human-wt/AUS/RCH041/2010/G2P[4]). All of the strains possessed the archetypal DS-1 like genome constellation G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Three of the strains, SA066, MON008 and WAPC703 clustered together and were distinct to RCH041 for all 11 genes. The VP7 genes of 31/32 of the strains characterized in this study possessed five conserved amino acid substitutions when compared to the G2 VP7 gene present in the RotaTeq® vaccine. Three of the substitutions were in the VP7 antigenic regions A and C, the substitutions A87T, D96N and S213D have been reported in the majority of G2P[4] strains circulating globally over the previous decade. These changes may have improved the ability of strains to circulate in settings of high vaccine use.

Anti-HIV activity of defective cyanovirin-N mutants is restored by dimerization.

Cyanovirin-N (CV-N) is a two-domain, cyanobacterial protein that inhibits human immunodeficiency virus (HIV) at nanomolar concentrations by binding to high mannose sugars on the HIV envelope glycoprotein gp120. The wild type protein can exist as a monomer or a domain-swapped dimer with the monomer and dimer containing two or four sugar binding sites, respectively, one on each domain. Here we demonstrate that monomeric, single binding site mutants are completely inactive and that a single site, whether located on domain A or B, is insufficient to impart the antiviral activity. Linking inactive, monomeric proteins in a head-to-head fashion by an intermolecular disulfide bond or by creating an exclusively domain-swapped dimer via a hinge residue deletion restored antiviral activity to levels similar to that of wild type CV-N. These findings demonstrate unequivocally that multisite binding by CV-N type lectins is necessary for viral inhibition.