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1.
Foot Ankle Int ; : 10711007241227880, 2024 Jun 08.
Article in English | MEDLINE | ID: mdl-38850062

ABSTRACT

BACKGROUND: Primary arthrodesis of Lisfranc fracture-dislocations is a reliable treatment option, yet concerns remain about nonunion. Nitinol staple use has recently proliferated in midfoot arthrodesis. The purpose of this study is to examine the union rate of primary arthrodesis of acute Lisfranc fracture-dislocations treated with nitinol staples compared with traditional plate-and-screw fixation. The secondary objective is to assess the difference in operative times and reoperation rates. METHODS: Midfoot fracture-dislocations treated with primary arthrodesis by 7 foot and ankle orthopaedic surgeons were reviewed. Of 160 eligible patients, 121 patients (305 joints) met the required 4-month minimum radiographic follow-up. Radiographic outcomes were analyzed at the individual joint level. Each joint was classified as either staples alone (45 patients, 154 joints), staples plus plates and screws (hybrid) (45 patients, 40 joints), or plates and screws alone (31 patients, 111 joints). The primary outcome was arthrodesis union at each joint fused. RESULTS: Nonunion was more common (9.0%, 10/111) among joints fixed with plate and screws than with hybrid (2.5%, 1/40) or staples only (1.3%, 2/154) (P = .0085). Multivariable regression demonstrated that autograft use was independent associated with union (P = .0035) and plate-and-screw only fixation was an independent risk factor for nonunion (P = .0407). Median operating room and tourniquet times were shorter for hybrid (92 and 83 minutes) and staple only (67 and 63 minutes) constructs compared to plate-and-screw only fixation (105 and 95 minutes) (P ≤ .0001 and .0003). There was no difference in reoperation rates among patients with different fixation types. CONCLUSION: We found that use of nitinol compression staple and bone autograft in primary arthrodesis of Lisfranc and midfoot fracture-dislocations was associated with both improved union rates and shorter tourniquet and operative times compared to traditional plate-and-screw fixation techniques. LEVEL OF EVIDENCE: Level III, therapeutic.

2.
PLoS Genet ; 19(9): e1010945, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37747878

ABSTRACT

Facultative heterochromatin controls development and differentiation in many eukaryotes. In metazoans, plants, and many filamentous fungi, facultative heterochromatin is characterized by transcriptional repression and enrichment with nucleosomes that are trimethylated at histone H3 lysine 27 (H3K27me3). While loss of H3K27me3 results in derepression of transcriptional gene silencing in many species, additional up- and downstream layers of regulation are necessary to mediate control of transcription in chromosome regions enriched with H3K27me3. Here, we investigated the effects of one histone mark on histone H4, namely H4K20me3, in the fungus Zymoseptoria tritici, a globally important pathogen of wheat. Deletion of kmt5, the gene encoding the sole methyltransferase responsible for H4K20 methylation, resulted in global derepression of transcription, especially in regions of facultative heterochromatin. Derepression in the absence of H4K20me3 not only affected known genes but also a large number of novel, previously undetected transcripts generated from regions of facultative heterochromatin on accessory chromosomes. Transcriptional activation in kmt5 deletion strains was accompanied by a complete loss of Ash1-mediated H3K36me3 and chromatin reorganization affecting H3K27me3 and H3K4me2 distribution in regions of facultative heterochromatin. Strains with H4K20L, M or Q mutations in the single histone H4 gene of Z. tritici recapitulated these chromatin changes, suggesting that H4K20me3 is important for Ash1-mediated H3K36me3. The ∆kmt5 mutants we obtained were more sensitive to genotoxic stressors than wild type and both, ∆kmt5 and ∆ash1, showed greatly increased rates of accessory chromosome loss. Taken together, our results provide insights into an unsuspected mechanism involved in the assembly and maintenance of facultative heterochromatin.


Subject(s)
Heterochromatin , Histones , Heterochromatin/genetics , Histones/genetics , Histones/metabolism , Chromatin , Nucleosomes , Methylation
3.
Sci Total Environ ; 861: 160455, 2023 Feb 25.
Article in English | MEDLINE | ID: mdl-36435237

ABSTRACT

Soil and bedrock weathering and phosphate (P) fertilizers may both contribute to the uranium (U) load of rivers in agricultural regions, but controls over their relative influence are not well known. This study investigates the U sources to rivers in Ohio, United States, part of the Eastern Corn Belt in the Mississippi River watershed. We present a regional picture of seasonal U sources to rivers based on four analyses: 1) a spatial analysis of legacy soil and water data, 2) new measurements of U and carbonate weathering products from rivers at 50 locations across the state collected seasonally over two years, 3) a weekly time series with additional 234U/238U (n = 5) and 87Sr/86Sr (n = 5) measurements from an agricultural river, and 4) a mass-balance approach to U addition to the landscape based on reported P fertilizer use. Uranium concentrations in surface waters collected statewide ranged 0.1-21 nM (n = 132), with significantly higher concentrations in the glaciated agricultural portion of the state (mean = 7.3 nM; n = 105) than the non-glaciated portion (mean = 2.0 nM; n = 24). Concentrations in the glaciated region were highest during the spring and summer and decreased during baseflow. In the time-series, concentrations were ~7 nM during baseflow and ~14 nM during intermediate seasonal discharge conditions, indicating a second more surficial endmember source of U in addition to bedrock weathering that is well correlated with other carbonate weathering products. Systematic increases in 87Sr/86Sr and decreases in 234U/238U with increasing discharge confirm a changing source of carbonate and U weathering and a third surficial endmember during high discharge events. Our mass balance approach and geochemical analysis suggest that elevated U concentrations are the result of carbonate weathering deep in the soil column during elevated seasonal flow. Further work on U dynamics in agricultural rivers is required to understand mechanism controlling seasonal changes in U concentrations and 234U/238U in downstream rivers and U flux.


Subject(s)
Fertilizers , Uranium , Fertilizers/analysis , Seasons , Uranium/analysis , Zea mays , Phosphates/analysis , Carbonates/analysis , Soil , Environmental Monitoring
4.
Foot Ankle Orthop ; 7(3): 24730114221117150, 2022 Jul.
Article in English | MEDLINE | ID: mdl-36046550

ABSTRACT

Background: Ankle arthroplasty has emerged as a viable alternative to ankle arthrodesis due in large part to recent advancements in both surgical technique and implant design. This study seeks to document trends of arthroplasty and arthrodesis for ankle osteoarthritis in New York State from 2009-2018 in order to determine if patient demographics play a role in procedure selection and to ascertain the utilization of each procedure and rates of complications. Methods: Patients 40 years and older from 2009-2018 were identified using International Classification of Diseases, Ninth and Tenth Revisions (ICD-9 and ICD-10), Clinical Modification (CM) diagnosis and procedure codes for ankle osteoarthritis, ankle arthrodesis, and ankle arthroplasty in the New York statewide planning and research cooperative system database. A trend analysis for both inpatient and outpatient procedures was performed to evaluate the changing trends in utilization of ankle arthrodesis and ankle arthroplasty over time. A multivariable logistic regression was used to assess the odds of receiving ankle arthrodesis relative to ankle arthroplasty. Complications were compared between inpatient ankle arthrodesis and arthroplasty using multivariable Cox proportional hazards regression. Results: A total of 3735 cases were included. Ankle arthrodesis increased by 25%, whereas arthroplasty increased by 757%. African American race, federal insurance, workers compensation, presence of comorbidities, and higher social deprivation were associated with increased odds of having an ankle arthrodesis vs an ankle arthroplasty. Compared with ankle arthroplasty, ankle arthrodesis was associated with increased rates of readmission, surgical site infection, acute renal failure, cellulitis, urinary tract infection, and deep vein thrombosis. Conclusion: Ankle arthroplasty volume has grown substantially without a decrease in ankle arthrodesis volume, suggesting that ankle arthroplasty may be selectively used for a different population of patients than ankle arthrodesis patients. Despite the increased growth of ankle arthroplasty, certain patient demographics including patients from minority populations, federal insurance, and from areas of high social deprivation have higher odds of receiving arthrodesis. Level of Evidence: Level III, retrospective cohort.

5.
R I Med J (2013) ; 104(10): 26-30, 2021 Dec 01.
Article in English | MEDLINE | ID: mdl-34846379

ABSTRACT

Weekend warriors are recreational athletes who compress their physical activity into 1-2 weekly exercise sessions. The characteristic combination of general deconditioning and excessive activity can predispose these individuals to a multitude of foot and ankle injuries. The purpose of this review is to highlight the etiology and management of common foot and ankle injuries in recreational athletes.


Subject(s)
Ankle Injuries , Athletic Injuries , Foot Injuries , Ankle Injuries/therapy , Athletes , Athletic Injuries/therapy , Exercise , Foot Injuries/therapy , Humans
6.
Orthop J Sports Med ; 9(8): 23259671211022245, 2021 Aug.
Article in English | MEDLINE | ID: mdl-34423057

ABSTRACT

BACKGROUND: Comminuted inferior pole patellar fractures can be treated in numerous ways. To date, there have been no studies comparing the biomechanical properties of transosseous tunnels versus suture anchor fixation for partial patellectomy and tendon advancement of inferior pole patellar fractures. HYPOTHESIS: Suture anchor repair will result in less gapping at the repair site. We also hypothesize no difference in load to failure between the groups. STUDY DESIGN: Controlled laboratory study. METHODS: Ten cadaveric knee extensor mechanisms (5 matched pairs; patella and patellar tendon) were used to simulate a fracture of the extra-articular distal pole of the patella. The distal simulated fracture fragment was excised, and the patellar tendon was advanced and repaired with either transosseous bone tunnels through the patella or 2 single-loaded suture anchors preloaded with 1 suture per anchor. Load to failure and elongation from cycles 1 to 250 between 20 and 100 N of force were measured, and modes of failure were recorded. Statistical analysis was performed using a paired 2-tailed Student t test. RESULTS: The suture anchor group had less gapping during cyclic loading as compared with the transosseous tunnel group (mean ± SD, 6.83 ± 2.23 vs 13.30 ± 5.74 mm; P = .047). There was no statistical difference in the load to failure between the groups. The most common mode of failure was at the suture-anchor interface in the suture anchor group (4 of 5) and at the knot proximally on the patella in the transosseous tunnel group (4 of 5). CONCLUSION: Suture anchors yielded similar strength profiles and less tendon gapping with cyclic loading when compared with transosseous tunnels in the treatment of comminuted distal pole of the patellar fractures managed with partial patellectomy and patellar tendon advancement. CLINICAL RELEVANCE: Suture anchors may offer robust repair and earlier range of motion in the treatment of fractures of the distal pole of the patella. Clinical randomized controlled trials would help clinicians better understand the difference in repair techniques and confirm the translational efficacy in clinical practice.

7.
Proc Biol Sci ; 288(1954): 20210974, 2021 07 14.
Article in English | MEDLINE | ID: mdl-34256001

ABSTRACT

The ability to rapidly detect and respond to wildlife morbidity and mortality events is critical for reducing threats to wildlife populations. Surveillance systems that use pre-diagnostic clinical data can contribute to the early detection of wildlife morbidities caused by a multitude of threats, including disease and anthropogenic disturbances. Here, we demonstrate proof of concept for use of a wildlife disease surveillance system, the 'Wildlife Morbidity and Mortality Event Alert System', that integrates pre-diagnostic clinical data in near real-time from a network of wildlife rehabilitation organizations, for early and enhanced detection of unusual wildlife morbidity and mortality events. The system classifies clinical pre-diagnostic data into relevant clinical classifications based on a natural language processing algorithm, generating alerts when more than the expected number of cases is recorded across the rehabilitation network. We demonstrated the effectiveness and efficiency of the system in alerting to events associated with both common and emerging diseases. Tapping into this readily available unconventional general surveillance data stream offers added value to existing wildlife disease surveillance programmes through a relatively efficient, low-cost strategy for the early detection of threats.


Subject(s)
Animals, Wild , Animals , Morbidity
9.
J Am Acad Orthop Surg ; 28(16): 678-683, 2020 Aug 15.
Article in English | MEDLINE | ID: mdl-32769723

ABSTRACT

INTRODUCTION: The incidence of geriatric ankle fractures is rising. With the substantial variation in the physiologic and functional status within this age group, our null hypothesis was that mortality and complications of open reduction and internal fixation (ORIF) between patients who are aged 65 to 79 are equivalent to ORIF in patients who are aged 80 to 89. METHODS: Patients with ankle fracture were identified using the International Classification of Diseases, Ninth Revision, Clinical Modification diagnosis codes. Patients treated with ORIF were identified using the Current Procedural Terminology codes. Patients were divided into two age cohorts: 65 to 79 years of age and 80 to 89 years of age. The primary outcome studied was 30-day mortality. Secondary outcomes included 30-day readmission, revision surgery, surgical site infection, sepsis, wound dehiscence, pulmonary embolism, deep vein thrombosis, blood transfusion, urinary tract infection, pneumonia, stroke, myocardial infarction, renal insufficiency or failure, and length of hospital stay. RESULTS: Our cohort included 2,353 ankle fractures: 1,877 were among 65 to 79 years of age and 476 were among 80 or older. Thirty-day mortality was 3.2-fold higher in the 80 to 89 years of age group compared with the 65 to 79 years of age group (1.47% versus 0.48%, P = 0.019). However, after controlling for the ASA class, 80 to 89 years of age patients no longer had a significantly higher mortality (P = 0.0647). Similarly, revision surgery rate (3.36% versus 1.81%, P = 0.036), transfusion requirement (2.94% versus 1.49%, P = 0.033), urinary tract infection (1.89% versus 0.75%, P = 0.023), and hospital length of stay (4.9 versus 2.9 days, P < 0.0001) were all significantly higher in the 80 to 90 years of age group compared with the 65 to 79 years old group. However, after controlling for the ASA class, 80 to 89 years old patients no longer had a rate of complications in comparison to the 65 to 79 years old age group. DISCUSSION: After controlling for comorbidities (ie, the ASA class), no increased risk is observed for the 30-day mortality or complication rate between geriatric ankle fracture in the 65 to 79 years old and the 80 to 99 years old age groups. LEVEL OF EVIDENCE: Prognostic level III, retrospective study.


Subject(s)
Ankle Fractures/mortality , Ankle Fractures/surgery , Fracture Fixation, Internal/mortality , Open Fracture Reduction/mortality , Age Factors , Aged , Aged, 80 and over , Ankle Fractures/epidemiology , Cohort Studies , Female , Fracture Fixation, Internal/adverse effects , Humans , Male , Morbidity , Open Fracture Reduction/adverse effects , Patient Readmission/statistics & numerical data , Postoperative Complications/epidemiology , Postoperative Complications/etiology , Reoperation/statistics & numerical data , Retrospective Studies , Surgical Wound Infection/epidemiology
10.
Sci Rep ; 10(1): 10861, 2020 07 02.
Article in English | MEDLINE | ID: mdl-32616777

ABSTRACT

Recent empirical studies have documented the importance of tropical mountainous rivers on global silicate weathering and suspended sediment transport. Such field studies are typically based on limited temporal data, leaving uncertainty in the strength of observed relationships with controlling parameters over the long term. A deficiency of long-term data also prevents determination of the impact that multi-year or decadal climate patterns, such as the El Niño Southern Oscillation (ENSO), might have on weathering fluxes. Here we analyze an 18-year hydrochemical dataset for eight sub-basins of the Panama Canal Watershed of high-temporal frequency collected between 1998 and 2015 to address these knowledge gaps. We identified a strongly positive covariance of both cation (Ca2+, Mg2+, K+, Na+) and suspended sediment yields with precipitation and extent of forest cover, whereas we observed negative relationships with temperature and mosaic landcover. We also confirmed a statistical relationship between seasonality, ENSO, and river discharge, with significantly higher values occurring during La Niña events. These findings emphasize the importance that long-term datasets have on identifying short-term influences on chemical and physical weathering rates, especially, in ENSO-influenced regions.

11.
J Pediatr Orthop ; 40(6): 310-313, 2020 Jul.
Article in English | MEDLINE | ID: mdl-32501928

ABSTRACT

INTRODUCTION: Given the rapidly increasing population of Spanish-speaking patients in the United States, medical providers must have the capability to effectively communicate both with pediatric patients and their caregivers. The purpose of this study was to query the Spanish language proficiency of pediatric orthopaedic surgeons, assess the educational resources available to Spanish-speaking patients and their families, and identify the barriers to care at academic pediatric orthopaedic centers. METHODS: The Web sites of medical centers within the United States that have pediatric orthopaedic surgery fellowships recognized by the Pediatric Orthopaedic Society of North America (POSNA) were accessed. Web sites were investigated for a health library as well as the availability of interpreter services. Profiles of attending surgeons within each Pediatric Orthopaedic Department were evaluated for evidence of Spanish proficiency as well as educational qualifications. Centers were contacted by phone to determine if the resources and physicians who could converse in Spanish were different than what was readily available online and if automated instructions in Spanish or a person who could converse in Spanish were available. RESULTS: Forty-six centers with 44 fellowship programs were identified. The profiles of 12 of 334 (3.6%) surgeons who completed pediatric orthopaedic fellowships indicated Spanish proficiency. Seventeen physicians (5.1%) were identified as proficient in Spanish after phone calls. Thirty-eight pediatric orthopaedic centers (82.6%) noted interpreter service availability online, although services varied from around-the-clock availability of live interpreters to interpreter phones. When contacted by phone, 45 of 46 centers (97.8%) confirmed the availability of any interpreter service for both inpatient and outpatient settings. Sixteen centers (34.8%) had online information on orthopaedic conditions or surgical care translated into Spanish. Twenty centers (43.5%) did not have automated phone messages in Spanish or live operators that spoke Spanish. CONCLUSIONS: There is a scarcity of surgical providers in pediatric orthopaedic centers proficient in Spanish, demonstrating a large discrepancy with the growing Hispanic population. Interpreter services are widely available, although there is variability in the services provided. Considerable barriers exist to Spanish-speaking patients who attempt to access care by phone or online.


Subject(s)
Communication Barriers , Culturally Competent Care , Fellowships and Scholarships/methods , Orthopedic Surgeons , Orthopedics , Child , Culturally Competent Care/methods , Culturally Competent Care/organization & administration , Female , Hispanic or Latino , Humans , Male , Needs Assessment , Orthopedic Surgeons/education , Orthopedic Surgeons/standards , Orthopedics/methods , Orthopedics/organization & administration , Translating , United States
12.
J Pediatr Orthop ; 40(1): e14-e18, 2020 Jan.
Article in English | MEDLINE | ID: mdl-30973474

ABSTRACT

BACKGROUND: Recent studies indicate that formal postreduction radiographs may be unnecessary for closed, isolated pediatric wrist, and forearm when mini C-arm fluoroscopy is used for reduction. Our institution changed the Emergency Department (ED) management protocol to reflect this by allowing orthopaedic providers to determine if fluoroscopy was acceptable to assess fracture reduction. We hypothesized that using fluoroscopy as definitive postreduction imaging would decrease total encounter time, without an increase in the rate of rereduction or surgery. METHODS: Patients with closed, isolated distal radius/distal ulna (DR/DU) or both bone forearm (BBFA) fractures that required sedation and reduction under mini C-arm fluoroscopy at our Level 1 pediatric ED were reviewed for 6 months both before and after this policy change. Before, all patients had formal postreduction radiographs; after, the decision was left to the orthopaedic physician. Timestamp data were collected, as was the need for rereduction or surgery. In addition to descriptive statistics, between-group differences were analyzed with the Student t test, χ test, and multivariable regression as appropriate. RESULTS: A total of 243 patients (119 before, 124 after) had 165 DR/DU and 78 BBFA fractures. Demographic data were similar before and after. After protocol implementation, univariable analysis (Student t test) showed that sedation times were longer, while total ED time and the time from sedation beginning to discharge were similar. The proportion of patients requiring rereduction or surgery were similar.After multivariable regression, "fluoroscopy as definitive imaging" was the only independent determinant of the time intervals compared with using conventional radiography. Sedation was an average of 13.8 minutes longer (P<0.001), while the interval from sedation beginning to discharge was 15.8 minutes shorter (P=0.007), and total ED time was 33.0 minutes shorter (P=0.018). Fluoroscopy as definitive imaging was not a predictor of surgery (odds ratio=0.63, P=0.520), although having a BBFA increased the likelihood (odds ratio=4.50, P=0.008). CONCLUSIONS: Implementing a protocol in which the provider could use mini C-arm fluoroscopy for definitive postreduction imaging did not result in increased rates remanipulation or need for surgery. Regression analysis further demonstrated time savings associated with foregoing conventional radiographs. LEVEL OF EVIDENCE: Level III-therapeutic.


Subject(s)
Closed Fracture Reduction , Conscious Sedation , Fluoroscopy , Length of Stay , Radius Fractures/diagnostic imaging , Ulna Fractures/diagnostic imaging , Child , Emergency Service, Hospital , Female , Forearm , Humans , Male , Radiography , Radius Fractures/surgery , Time Factors , Ulna Fractures/surgery , Wrist
14.
ISME J ; 14(3): 659-675, 2020 03.
Article in English | MEDLINE | ID: mdl-31754206

ABSTRACT

Assigning a functional role to a microorganism has historically relied on cultivation of isolates or detection of environmental genome-based biomarkers using a posteriori knowledge of function. However, the emerging field of function-driven single-cell genomics aims to expand this paradigm by identifying and capturing individual microbes based on their in situ functions or traits. To identify and characterize yet uncultivated microbial taxa involved in cellulose degradation, we developed and benchmarked a function-driven single-cell screen, which we applied to a microbial community inhabiting the Great Boiling Spring (GBS) Geothermal Field, northwest Nevada. Our approach involved recruiting microbes to fluorescently labeled cellulose particles, and then isolating single microbe-bound particles via fluorescence-activated cell sorting. The microbial community profiles prior to sorting were determined via bulk sample 16S rRNA gene amplicon sequencing. The flow-sorted cellulose-bound microbes were subjected to whole genome amplification and shotgun sequencing, followed by phylogenetic placement. Next, putative cellulase genes were identified, expressed and tested for activity against derivatives of cellulose and xylose. Alongside typical cellulose degraders, including members of the Actinobacteria, Bacteroidetes, and Chloroflexi, we found divergent cellulases encoded in the genome of a recently described candidate phylum from the rare biosphere, Goldbacteria, and validated their cellulase activity. As this genome represents a species-level organism with novel and phylogenetically distinct cellulolytic activity, we propose the name Candidatus 'Cellulosimonas argentiregionis'. We expect that this function-driven single-cell approach can be extended to a broad range of substrates, linking microbial taxonomy directly to in situ function.


Subject(s)
Bacteria/metabolism , Cellulose/metabolism , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Cellulase/genetics , Cellulase/metabolism , Environmental Microbiology , Genome, Bacterial , Genomics , Metagenomics , Phylogeny , RNA, Ribosomal, 16S/genetics
15.
Orthop Rev (Pavia) ; 11(1): 7883, 2019 Feb 26.
Article in English | MEDLINE | ID: mdl-30996841

ABSTRACT

Fluoroscopy poses an occupational hazard to orthopedic surgeons. The purpose of this study was to examine resident and faculty understanding of radiation safety and to determine whether or not a radiation safety intervention would improve radiation safety knowledge. An anonymous survey was developed to assess attitudes and knowledge regarding radiation safety and exposure. It was distributed to faculty and residents at an academic orthopedic program before and after a radiation safety lecture. Pre- and post-lecture survey results were compared. 19 residents and 22 faculty members completed the pre-lecture survey while 11 residents and 17 faculty members completed the post-lecture survey. Pre-lecture survey scores were 48.3% for residents and 49.5% for faculty; post-lecture survey scores were 52.7% and 46.1% respectively. Differences between pre and post-survey scores were not significant. This study revealed low baseline radiation safety knowledge scores for both orthopedic residents and faculty. As evidence by our results, a single radiation safety information lecture did not significantly impact radiation knowledge. Radiation safety training should have a formal role in orthopedic surgery academic curricula.

16.
Nat Methods ; 14(11): 1045-1054, 2017 Oct 31.
Article in English | MEDLINE | ID: mdl-29088131

ABSTRACT

Over the past decade, it has become nearly routine to sequence genomes of individual microbial cells directly isolated from environmental samples ranging from deep-sea hydrothermal vents to insect guts, providing a powerful complement to shotgun metagenomics in microbial community studies. In this review, we address the technical aspects and challenges of single-cell genome sequencing and discuss some of the scientific endeavors that it has enabled. Specifically, we highlight newly added leaves and branches in the genomic tree of bacterial and archaeal life and illustrate the unique and exciting advantages that single-cell genomics offers over metagenomics, both now and in the near future.


Subject(s)
Single-Cell Analysis , Metagenomics , Microbiota/genetics , Phylogeny , Polymerase Chain Reaction , Sequence Analysis, DNA
17.
Biotechnol Biofuels ; 10: 178, 2017.
Article in English | MEDLINE | ID: mdl-28702083

ABSTRACT

BACKGROUND: Rhodopseudomonas palustris is a versatile microbe that encounters an innate redox imbalance while growing photoheterotrophically with reduced substrates. The resulting excess in reducing equivalents, together with ATP from photosynthesis, could be utilized to drive a wide range of bioconversions. The objective of this study was to genetically modify R. palustris to provide a pathway to reduce n-butyrate into n-butanol for maintaining redox balance. RESULTS: Here, we constructed and expressed a plasmid-based pathway for n-butanol production from Clostridium acetobutylicum ATCC 824 in R. palustris. We maintained the environmental conditions in such a way that this pathway functioned as the obligate route to re-oxidize excess reducing equivalents, resulting in an innate selection pressure. The engineered strain of R. palustris grew under otherwise restrictive redox conditions and achieved concentrations of 1.5 mM n-butanol at a production rate of 0.03 g L-1 day-1 and a selectivity (i.e., products compared to the consumed substrate) of close to 40%. Since the theoretical maximum selectivity is 45%, the engineered strain converted close to its maximum selectivity. CONCLUSIONS: The innate redox imbalance of R. palustris can be used to drive the reduction of n-butyrate into n-butanol after expression of a plasmid-based enzyme from a butanol-producing Clostridium strain.

18.
FEMS Microbiol Rev ; 41(4): 538-548, 2017 07 01.
Article in English | MEDLINE | ID: mdl-28591840

ABSTRACT

Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology. Function-driven single-cell genomics provides a solution by using a function-based screen to subsample complex microbial communities in a targeted manner for the isolation and genome sequencing of single cells. This enables single-cell sequencing to be focused on cells with specific phenotypic or metabolic characteristics of interest. Recovered genomes are conclusively implicated for both encoding and exhibiting the feature of interest, improving downstream annotation and revealing activity levels within that environment. This emerging approach has already improved our understanding of microbial community functioning and facilitated the experimental analysis of uncharacterized gene product space. Here we provide a comprehensive review of strategies that have been applied for function-driven single-cell genomics and the future directions we envision.


Subject(s)
Genomics , Microbiological Techniques/trends , Single-Cell Analysis
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