Environmental impacts and effects on greenhouse gas emissions in shrimp feed production system for aquaculture - A case study in India.

Attributional life cycle assessment study examines the environmental impact of raw materials, machinery, and unit operations. In the present work, an attributional life cycle assessment (LCA) was employed to assess the environmental and greenhouse gas impacts of a shrimp feed production system. A commercial shrimp feed mill in Tamil Nadu, India, provided inventory data for one-ton shrimp feed (functional unit) for a Cradle-to-Gate evaluation using environmental impact methodologies, specifically Impact 2002+ in SimaPro® (V9.3.0.3) software. The results showed that human health (0.003357 DALY), ecosystem quality (2720.518 PDF × m2 × yr), climate change (2031.696 kg CO2 eq), and resources (71019.42 MJ primary) were the most significantly impacted. The human health category was found to be the most prominent after normalization and weighting (0.47 pt), and strategies were suggested accordingly. The GWP20 and GWP100 measures for long-term climate change were calculated to be 8.7 and 7.33 kg CO2 eq, respectively. Cast iron used in machinery production (GWP 20-15.40%, GWP100-134.5%) and electricity use (GWP 20-6.13%, GWP 100-6.9%) accounted for sizable portions of the burden. Feed production is estimated to contribute 0.2% of global CO2 emissions within the proposed global context. These findings are significant regarding economically and environmentally sustainable shrimp feed production worldwide.

Temporal changes in sleep quality and knee function following primary total knee arthroplasty: a prospective study.

PURPOSE: Several patient-reported outcome measures (PROMs) have been used to assess improvement in the quality of life following total knee arthroplasty (TKA). However, there is paucity of studies evaluating the sleep quality and knee function following TKA. The primary aim of our study was to evaluate the sleep quality and knee function in primary TKA patients using the Pittsburgh Sleep Quality Index (PSQI) and Knee Society Score (KSS), respectively. The secondary aim was to assess the correlation between the two outcome measures over the course of first post-operative year following TKA. METHODS: One hundred sixty-eight patients (female-140/male-28) with mean age of 64.63 years (± 7.50) who underwent 168 primary unilateral TKA using a cemented posterior-stabilised implant without patella resurfacing between June 2018 and October 2018 were included in the study. Global PSQI and KSS were recorded pre-operatively and post-operatively weekly up to six weeks and at one year. Body mass index (BMI) and Charlson comorbidity index (CCI) were recorded during pre-operative assessment. RESULTS: Mean(± SD) BMI and CCI were 28.45(± 4.64) and 2.48(± 0.93), respectively. Pre-operative global PSQI of 1.98(± 0.97) increased to 13.48(± 3.36) in the first post-operative week (p < 0.001) and remained high during all the six weeks following TKA (p < 0.001), whereas at the first post-operative year, it reduced to 2.10(± 1.15) (p = 0.15). Pre-operative KSS of 52.00(± 9.98) increased to 71.67(± 6.58) and 85.49(± 4.67) at 6 weeks and the first post-operative year respectively (p < 0.001). Pre-operative global PSQI had moderate correlation with pre-operative KSS (r = 0.39) (p < 0.001). Strong correlation was noted between pre-operative global PSQI and six week post-operative KSS (r = 0.47) (p < 0.001). Low correlation was noted between pre-operative global PSQI and KSS at the first post-operative year (r = 0.10, p = 0.19) following TKA. Multiple regression analysis revealed age, CCI, and pre-operative range of motion as independent predictors of global PSQI. CONCLUSIONS: Patients undergoing TKA experience changes in sleep quality but report an overall improvement in knee function during the first post-operative year. Sleep quality has moderate to strong correlation with knee function in the early post-operative period beyond which there is a low correlation with knee function thereby suggesting a transient phenomenon. Hence patients undergoing TKA can be appropriately counselled regarding the variation in sleep quality in the post-operative period and reassured accordingly.

Ultraparamagnetic Cells Formed through Intracellular Oxidation and Chelation of Paramagnetic Iron.

Making cells magnetic is a long-standing goal of chemical biology, aiming to enable the separation of cells from complex biological samples and their visualization in vivo using magnetic resonance imaging (MRI). Previous efforts towards this goal, focused on engineering cells to biomineralize superparamagnetic or ferromagnetic iron oxides, have been largely unsuccessful due to the stringent required chemical conditions. Here, we introduce an alternative approach to making cells magnetic, focused on biochemically maximizing cellular paramagnetism. We show that a novel genetic construct combining the functions of ferroxidation and iron chelation enables engineered bacterial cells to accumulate iron in "ultraparamagnetic" macromolecular complexes, allowing these cells to be trapped with magnetic fields and imaged with MRI in vitro and in vivo. We characterize the properties of these cells and complexes using magnetometry, nuclear magnetic resonance, biochemical assays, and computational modeling to elucidate the unique mechanisms and capabilities of this paramagnetic concept.

Neuropathy Dermatitis: An Underdocumented Complication Following Total Knee Arthroplasty.

Background: Midline surgical incision used in Total Knee Arthroplasty (TKA) is associated with iatrogenic injury to the infrapatellar branch of the saphenous nerve, which leads to neuropathic dermatitis around the healed surgical scar. There are very few studies with a limited number of cases that have reported this complication. We evaluated the incidence of neuropathic dermatitis and its implication for the functional outcome in TKA patients. Methodology: Patients who underwent primary TKA between 1 January 2010 and 31 August 2019 and presented in follow-up with sensory disturbances and skin lesions adjacent to the surgical incision were evaluated in this study. Results: A total of 3318 patients with 4282 TKAs were included, of which 188 patients presented with the clinical picture of neuropathic dermatitis. There were 136 females and 52 males with a mean age of 67.13 years (range 37-92 years). The mean duration from surgery to the appearance of skin lesions was 4.4 months (range 2-6 months), and they resolved at a mean duration of 7.67 (range 6-12) weeks. In our study, we found an incidence of 5.52%. All these patients had a stable and well-functioning knee at the time of presentation of the lesion with a mean Knee Society Score (KSS) of 92 (range 84-96). Conclusion: In our study, we found the incidence of neuropathic dermatitis to be 5.52%, without any long-term implication on the functional outcome of operated knees. For a self-limiting complication of midline knee incision of TKA, it either resolves on its own or requires a short duration of topical steroid application.

BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences.

The design choices underlying machine-learning (ML) models present important barriers to entry for many biologists who aim to incorporate ML in their research. Automated machine-learning (AutoML) algorithms can address many challenges that come with applying ML to the life sciences. However, these algorithms are rarely used in systems and synthetic biology studies because they typically do not explicitly handle biological sequences (e.g., nucleotide, amino acid, or glycan sequences) and cannot be easily compared with other AutoML algorithms. Here, we present BioAutoMATED, an AutoML platform for biological sequence analysis that integrates multiple AutoML methods into a unified framework. Users are automatically provided with relevant techniques for analyzing, interpreting, and designing biological sequences. BioAutoMATED predicts gene regulation, peptide-drug interactions, and glycan annotation, and designs optimized synthetic biology components, revealing salient sequence characteristics. By automating sequence modeling, BioAutoMATED allows life scientists to incorporate ML more readily into their work.

Real-Time, Multiplexed SHERLOCK for in Vitro Diagnostics.

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need for simple, low-cost, and scalable diagnostics that can be widely deployed for rapid testing. Clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics have emerged as a promising technology, but its implementation in clinical laboratories has been limited by the requirement of a separate amplification step prior to CRISPR-associated (Cas) enzyme-based detection. This article reports the discovery of two novel Cas12 enzymes (SLK9 and SLK5-2) that exhibit enzymatic activity at 60°C, which, when combined with loop-mediated isothermal amplification (LAMP), enable a real-time, single-step nucleic acid detection method [real-time SHERLOCK (real-time SLK)]. Real-time SLK was demonstrated to provide accurate results comparable to those from real-time quantitative RT-PCR in clinical samples, with 100% positive and 100% negative percent agreement. The method is further demonstrated to be compatible with direct testing (real-time SLK Direct) of samples from anterior nasal swabs, without the need for standard nucleic acid extraction. Lastly, SLK9 was combined with either Alicyclobacillus acidoterrestris AacCas12b or with SLK5-2 to generate a real-time, multiplexed CRISPR-based diagnostic assay for the simultaneous detection of SARS-CoV-2 and a human-based control in a single reaction, with sensitivity down to 5 copies/µL and a time to result of under 30 minutes.

Detection of viral RNAs at ambient temperature via reporter proteins produced through the target-splinted ligation of DNA probes.

Nucleic acid assays are not typically deployable in point-of-care settings because they require costly and sophisticated equipment for the control of the reaction temperature and for the detection of the signal. Here we report an instrument-free assay for the accurate and multiplexed detection of nucleic acids at ambient temperature. The assay, which we named INSPECTR (for internal splint-pairing expression-cassette translation reaction), leverages the target-specific splinted ligation of DNA probes to generate expression cassettes that can be flexibly designed for the cell-free synthesis of reporter proteins, with enzymatic reporters allowing for a linear detection range spanning four orders of magnitude and peptide reporters (which can be mapped to unique targets) enabling highly multiplexed visual detection. We used INSPECTR to detect a panel of five respiratory viral targets in a single reaction via a lateral-flow readout and ~4,000 copies of viral RNA via additional ambient-temperature rolling circle amplification of the expression cassette. Leveraging synthetic biology to simplify workflows for nucleic acid diagnostics may facilitate their broader applicability at the point of care.

RNA-responsive elements for eukaryotic translational control.

The ability to control translation of endogenous or exogenous RNAs in eukaryotic cells would facilitate a variety of biotechnological applications. Current strategies are limited by low fold changes in transgene output and the size of trigger RNAs (trRNAs). Here we introduce eukaryotic toehold switches (eToeholds) as modular riboregulators. eToeholds contain internal ribosome entry site sequences and form inhibitory loops in the absence of a specific trRNA. When the trRNA is present, eToeholds anneal to it, disrupting the inhibitory loops and allowing translation. Through optimization of RNA annealing, we achieved up to 16-fold induction of transgene expression in mammalian cells. We demonstrate that eToeholds can discriminate among viral infection status, presence or absence of gene expression and cell types based on the presence of exogenous or endogenous RNA transcripts.

Spatial Control of Probiotic Bacteria in the Gastrointestinal Tract Assisted by Magnetic Particles.

Engineered probiotics have the potential to diagnose and treat a variety of gastrointestinal (GI) diseases. However, these exogenous bacterial agents have limited ability to effectively colonize specific regions of the GI tract due to a lack of external control over their localization and persistence. Magnetic fields are well suited to providing such control, since they freely penetrate biological tissues. However, they are difficult to apply with sufficient strength to directly manipulate magnetically labeled cells in deep tissue such as the GI tract. Here, it is demonstrated that a composite biomagnetic material consisting of microscale magnetic particles and probiotic bacteria, when orally administered and combined with an externally applied magnetic field, enables the trapping and retention of probiotic bacteria within the GI tract of mice. This technology improves the ability of these probiotic agents to accumulate at specific locations and stably colonize without antibiotic treatment. By enhancing the ability of GI-targeted probiotics to be at the right place at the right time, cellular localization assisted by magnetic particles (CLAMP) adds external physical control to an important emerging class of microbial theranostics.

Sequence-to-function deep learning frameworks for engineered riboregulators.

While synthetic biology has revolutionized our approaches to medicine, agriculture, and energy, the design of completely novel biological circuit components beyond naturally-derived templates remains challenging due to poorly understood design rules. Toehold switches, which are programmable nucleic acid sensors, face an analogous design bottleneck; our limited understanding of how sequence impacts functionality often necessitates expensive, time-consuming screens to identify effective switches. Here, we introduce Sequence-based Toehold Optimization and Redesign Model (STORM) and Nucleic-Acid Speech (NuSpeak), two orthogonal and synergistic deep learning architectures to characterize and optimize toeholds. Applying techniques from computer vision and natural language processing, we 'un-box' our models using convolutional filters, attention maps, and in silico mutagenesis. Through transfer-learning, we redesign sub-optimal toehold sensors, even with sparse training data, experimentally validating their improved performance. This work provides sequence-to-function deep learning frameworks for toehold selection and design, augmenting our ability to construct potent biological circuit components and precision diagnostics.

Improving the accuracy of tibial component placement during total knee replacement in varus knees with tibial bowing: A prospective randomised controlled study.

BACKGROUND: Lateral tibial bowing leads to varus placement of the tibial component during total knee replacement in varus knees. Lateralised tibial jig placement can improve the accuracy of the tibial cut. METHODS: A total of 227 patients (300 knees) undergoing total knee replacements were randomised into two groups. In the study group, the point of intersection of the distal tibial diaphyseal line at the tibial plateau drawn on long films was represented by zones. Knees with femoral bowing >5° (28%) were excluded. Tibial jig placement on the proximal tibia was lateralised according to the zones. In the control group, the mid-point of the tibial plateau was taken as a reference. Femoral and tibial bowing, postoperative limb alignment and component placement were assessed. RESULTS: Of the 216 knees that were studied, 106 were in the study group and 110 in the control group. Bowing ≥3° had a significant positive correlation with lateralisation of the proximal tibial reference (p < 0.001). The Incidence of tibial bowing ≥3° was 57.33%. The mean postoperative hip-knee-ankle (HKA) angle was 178.31 ±â€¯2.88° and 176.53 ±â€¯2.88° (p < 0.001), whereas the mean medial proximal tibial angle (MPTA) was 89.91 ±â€¯1.42° and 88.79 ±â€¯1.72° (p < 0.001) in the study and control groups, respectively. Considering bowed tibiae alone, HKA angle and MPTA in the study group were 178.08 ±â€¯2.81° and 89.72 ±â€¯1.39° compared with 175.88 ±â€¯2.87° and 88.38 ±â€¯1.38° in the control group (p < 0.001). CONCLUSION: There is a high incidence of tibial bowing in varus knees. Lateralised tibial jig placement improved tibial component placement and postoperative limb alignment in total knee arthroplasty in varus knees with tibial bowing.

Mapping the microscale origins of magnetic resonance image contrast with subcellular diamond magnetometry.

Magnetic resonance imaging (MRI) is a widely used biomedical imaging modality that derives much of its contrast from microscale magnetic field patterns in tissues. However, the connection between these patterns and the appearance of macroscale MR images has not been the subject of direct experimental study due to a lack of methods to map microscopic fields in biological samples. Here, we optically probe magnetic fields in mammalian cells and tissues with submicron resolution and nanotesla sensitivity using nitrogen-vacancy diamond magnetometry, and combine these measurements with simulations of nuclear spin precession to predict the corresponding MRI contrast. We demonstrate the utility of this technology in an in vitro model of macrophage iron uptake and histological samples from a mouse model of hepatic iron overload. In addition, we follow magnetic particle endocytosis in live cells. This approach bridges a fundamental gap between an MRI voxel and its microscopic constituents.

Biomolecular MRI reporters: Evolution of new mechanisms.

Magnetic resonance imaging (MRI) is a powerful technique for observing the function of specific cells and molecules inside living organisms. However, compared to optical microscopy, in which fluorescent protein reporters are available to visualize hundreds of cellular functions ranging from gene expression and chemical signaling to biomechanics, to date relatively few such reporters are available for MRI. Efforts to develop MRI-detectable biomolecules have mainly focused on proteins transporting paramagnetic metals for T1 and T2 relaxation enhancement or containing large numbers of exchangeable protons for chemical exchange saturation transfer. While these pioneering developments established several key uses of biomolecular MRI, such as imaging of gene expression and functional biosensing, they also revealed that low molecular sensitivity poses a major challenge for broader adoption in biology and medicine. Recently, new classes of biomolecular reporters have been developed based on alternative contrast mechanisms, including enhancement of spin diffusivity, interactions with hyperpolarized nuclei, and modulation of blood flow. These novel reporters promise to improve sensitivity and enable new forms of multiplexed and functional imaging.

FBAR syndapin 1 recognizes and stabilizes highly curved tubular membranes in a concentration dependent manner.

Syndapin 1 FBAR, a member of the Bin-amphiphysin-Rvs (BAR) domain protein family, is known to induce membrane curvature and is an essential component in biological processes like endocytosis and formation and growth of neurites. We quantify the curvature sensing of FBAR on reconstituted porcine brain lipid vesicles and show that it senses membrane curvature at low density whereas it induces and reinforces tube stiffness at higher density. FBAR strongly up-concentrates on the high curvature tubes pulled out of Giant Unilamellar lipid Vesicles (GUVs), this sorting behavior is strongly amplified at low protein densities. Interestingly, FBAR from syndapin 1 has a large affinity for tubular membranes with curvatures larger than its own intrinsic concave curvature. Finally, we studied the effect of FBAR on membrane relaxation kinetics with high temporal resolution and found that the protein increases relaxation time of the tube holding force in a density-dependent fashion.