Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations.

Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting one to three genomic sites per cell. We engineer an Acidaminococcus Cas12a (AsCas12a) variant, multiplexed transcriptional interference AsCas12a (multiAsCas12a), that incorporates R1226A, a mutation that stabilizes the ribonucleoprotein-DNA complex via DNA nicking. The multiAsCas12a-KRAB fusion improves CRISPRi activity over DNase-dead AsCas12a-KRAB fusions, often rescuing the activities of lentivirally delivered CRISPR RNAs (crRNA) that are inactive when used with the latter. multiAsCas12a-KRAB supports CRISPRi using 6-plex crRNA arrays in high-throughput pooled screens. Using multiAsCas12a-KRAB, we discover enhancer elements and dissect the combinatorial function of cis-regulatory elements in human cells. These results instantiate a group testing framework for efficiently surveying numerous combinations of chromatin perturbations for biological discovery and engineering.

Integration of a battery of biomarkers to evaluate the health status of field-collected frogs of Leptodactylus luctator living in ecosystems with different anthropogenic disturbances.

Amphibians are the most threatened group of vertebrates because they have certain biological and ecological characteristics that make them sensitive to environmental changes. The aim of this study was to evaluate the health status of field-collected adult frogs of Leptodactylus luctator (Amphibia, Anura) living in sites with different anthropogenic disturbances (florihorticulture, petrochemical industry and sewage discharges) and a reference site without any detectable influence of such activities. To this end, a battery of 21 biomarkers (hematological, biochemical and individual biomarkers) was studied using a multivariate approach that allows us to evaluate the relationship between them and provide information on their usefulness. The frogs at the florihorticulture, petrochemical and sewage discharges sites exhibited several biomarkers far from homeostasis. In addition, we identified 11 of 21 biomarkers that were useful indicators of the health status of the frogs and allowed discrimination between study sites in the following order: lymphocytes (98 %), neutrophils (45 %), hemoglobin (42 %), monocytes (41 %), fat body index (35 %), eosinophils (35 %), hepatosomatic index (33 %), mean corpuscular hemoglobin (32 %), thrombocytes (27 %), catalase in liver (26 %), and GST in liver (26 %). The results suggest that hematological biomarkers contribute the most to site separation, whereas biochemical biomarkers contribute the least. The integral interpretation of the results also allowed us to diagnose the different health status of L. luctator: The frogs from the petrochemical industry were the most negatively affected, followed by the frogs from the sewages discharges and finally the frogs from the florihorticulture and reference sites. This is the first field study with anurans in which so many biomarkers were examined.

Assessment of sulfonamide contamination in aquatic environments: A first report for Argentina and environmental risk assessment.

The global surge in pharmaceutical consumption, driven by increasing population and the demand for animal proteins, leads to the discharge of diverse pollutants, including antibiotic residues, into water bodies. Sulfonamides, being water-soluble compounds, can readily enter surface run-off, posing potential risks to non-target species despite their low environmental concentrations. Latin America has implemented intensive production systems highly dependent on antimicrobials for productivity and animal health, yet there is a paucity of information regarding their concentration in the region. The objective of this study was to evaluate the presence of sulfonamides in water and sediment samples and assess their potential ecological risks through an environmental risk assessment. The Río de la Plata basin collects the waters of the Paraguay, Paraná, and Uruguay rivers, together with their tributaries and various wetlands, passing through the provinces in Argentina known for their significant animal husbandry production. Two sampling campaigns were carried out for sediment, while only one campaign was conducted for surface waters. The samples were analyzed by high performance liquid chromatography tandem mass-spectrometry (HPLC-MS/MS). None of the examined sulfonamide antibiotics were detected in the sediment samples from both sampling campaigns. In contrast, sulfadiazine (95 %), sulfamethoxazole (91 %), and sulfathiazole (73 %) were detected in the water samples. Sulfadiazine was found in the concentration range of 8 to 128 ng/L, while sulfamethoxazole and sulfathiazole were observed at concentrations ranging from 3.0 to 32.5 ng/L and 2.9 to 8.1 ng/L, respectively. Based on the environmental risk assessment conducted using the sulfonamide concentrations, most samples indicated a medium risk for aquatic biota, with only one sample surpassing the high-risk threshold. This study represents the first report presenting data on the presence of sulfonamide antibiotics in the aquatic environment of Argentina.

Higher-order combinatorial chromatin perturbations by engineered CRISPR-Cas12a for functional genomics.

Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting 1-3 genomic sites per cell. To develop a tool for higher-order ( > 3) combinatorial targeting of genomic sites with CRISPRi in functional genomics screens, we engineered an Acidaminococcus Cas12a variant -- referred to as mul tiplexed transcriptional interference AsCas12a (multiAsCas12a). multiAsCas12a incorporates a key mutation, R1226A, motivated by the hypothesis of nicking-induced stabilization of the ribonucleoprotein:DNA complex for improving CRISPRi activity. multiAsCas12a significantly outperforms prior state-of-the-art Cas12a variants in combinatorial CRISPRi targeting using high-order multiplexed arrays of lentivirally transduced CRISPR RNAs (crRNA), including in high-throughput pooled screens using 6-plex crRNA array libraries. Using multiAsCas12a CRISPRi, we discover new enhancer elements and dissect the combinatorial function of cis-regulatory elements. These results instantiate a group testing framework for efficiently surveying potentially numerous combinations of chromatin perturbations for biological discovery and engineering.

First evidence of environmental bioaccumulation of pharmaceuticals on adult native anurans (Rhinella arenarum) from Argentina.

The presence of pharmaceutically active compounds (PhACs) in surface water is well known, whereas their natural occurrence in biota is much less explored. The aim of this work was to evaluate the bioaccumulation of PhACs in adult toads of the neotropical species Rhinella arenarum. Three sites were selected in Buenos Aires (Argentina): a reference site (Site 1), a site with direct discharge from a secondary wastewater treatment plant (WWTP) (Site 2) and a site 300 m downstream of the WWTP discharge (Site 3). Surface water samples, as well as muscle, liver and fat bodies of toads were collected, extracted and analyzed by LC-MS/MS. Highly significant differences in total PhACs concentration in surface water (p < 0.005) were detected between Site 2 and the other sites. These concentrations ranged from 0.37 to 52.46 ng/L at Site 1, 0.71-6950.37 ng/L at Site 2, and 0.12-75.45 ng/L at Site 3. In general, bioaccumulation of PhACs in toad tissues was similar between sites and tissues of each site. The highest concentrations were detected in the muscle of toads from Site 3 (1.06-87.24 ng/g dw), followed by liver (1.77-38.10 ng/g dw) and fat bodies (0.68-20.59 ng/g dw) from Site 1. Ibuprofen (6950 ng/L), acetaminophen (3277 ng/L) and valsartan (2504 ng/L) were the compounds with the highest concentrations in surface water from Site 2, whereas acetaminophen (87.2 ng/g dw, muscle from Site 3), desloratadine (38.1 ng/g dw, liver from Site 1), and phenazone (25.9 ng/g dw, liver from Site 1) were the ones that showed the highest concentrations in biota. This is the first time a field study has examined the environmental bioaccumulation of PhACs in anurans, demonstrating their potential for monitoring the status of natural ecosystems.

Deep genetic subdivision within a continuously distributed and highly vagile marine mammal, the Steller's sea lion (Eumetopias jubatus).

The Steller's sea lion Eumetopias jubatus is an endangered marine mammal that has experienced dramatic population declines over much of its range during the past five decades. Studies using mitochondrial DNA (mtDNA) have shown that an apparently continuous population includes a strong division, yielding two discrete stocks, western and eastern. Based on a weaker split within the western stock, a third Asian stock has also been defined. While these findings indicate strong female philopatry, a recent study using nuclear microsatellite markers found little evidence of any genetic structure, implying extensive paternal gene flow. However, this result was at odds with mark-recapture data, and both sample sizes and genetic resolution were limited. To address these concerns, we increased analytical power by genotyping over 700 individuals from across the species' range at 13 highly polymorphic microsatellite loci. We found a clear phylogenetic break between populations of the eastern stock and those of the western and Asian stocks. However, our data provide little support for the classification of a separate Asian stock. Our findings show that mtDNA structuring is not due simply to female philopatry, but instead reflects a genuine discontinuity within the range, with implications for both the phylogeography and conservation of this important marine mammal.

Glacial refugia and the phylogeography of Steller's sea lion (Eumatopias jubatus) in the North Pacific.

Mitochondrial DNA sequence data were used to examine the phylogeographic history of Steller's sea lions (Eumetopias jubatus) in relation to the presence of Plio-Pleistocene insular refugia. Cytochrome b and control region sequences from 336 Steller's sea lions reveal phylogenetic lineages associated with continental refugia south of the ice sheets in North America and Eurasia. Phylogenetic analysis suggests the genetic structure of E. jubatus is the result of Pleistocene glacial geology, which caused the elimination and subsequent reappearance of suitable rookery habitat during glacial and interglacial periods. The cyclic nature of geological change produced a series of independent population expansions, contractions and isolations that had analogous results on Steller's sea lions and other marine and terrestrial species. Our data show evidence of four glacial refugia in which populations of Steller's sea lions diverged. These events occurred from approximately 60,000 to 180,000 years BP and thus preceded the last glacial maximum.

Lipoprotein lipase in lactating and neonatal northern fur seals: exploring physiological management of energetic conflicts.

Otariid lactation and neonatal growth are cyclical processes tied to maternal foraging and nursing patterns (i.e. at sea and on land). Both mother and pup undergo repeated shifts from a positive to a negative energy balance, the physiological mechanisms of which are unclear. We measured plasma and tissue lipoprotein lipase (LPL) in free-ranging northern fur seal mother-pup pairs throughout the first month of lactation. Plasma LPL levels were similar in lactating females (11.3-15.9 U) and growing neonates (8.2-15.2 U). Mammary LPL activity was variable, but highest during the attendance period (3.1 U), while maternal blubber LPL was consistently low (<0.5 U). Neonatal blubber LPL activity was also low (0.2-0.4 U) in accordance with their low growth rates and relatively limited blubber deposition.

Accumulation of silver in the liver of three species of pinnipeds.

Silver in the three species of pinnipeds [northern fur seal (Callorhinus ursinus), Steller sea lion (Eumetopias jubatus), and harbor seal (Phoca vitulina)] caught in the North Pacific Ocean were analyzed using inductively coupled plasma-mass spectrometry, in order to understand accumulation and distribution of silver in pinnipeds. In northern fur seals, relatively high concentrations of silver were observed in the liver and body hair. Some 70% of the silver burden was concentrated in the liver. Hepatic silver concentrations were significantly correlated to age in northern fur seals (r = 0.766, P < 0.001, n = 49) and Steller sea lions (r = 0.496, P < 0.01, n = 28). Levels of silver concentrations per wet weight (microgram g-1) in the three pinnipeds ranged from 0.04 to 0.55 for northern fur seals, from 0.1 to 1.04 for Steller sea lions and from 0.03 to 0.83 for harbor seals. Silver concentrations in liver for all pinnipeds were significantly correlated with mercury, and selenium (P < 0.001). Molar ratios between silver to selenium approximated 1:180 in northern fur seals, 1:120 in Steller sea lions, and 1:60 in harbor seals. The silver-mercury molar ratios were approximately 1:170 in northern fur seals, and 1:80 both in the other species. Increase in silver accumulation in the liver was caused by the retention in nuclei and mitochondria fraction together with mercury and selenium in the cells of northern fur seals.

Crystallization and preliminary X-ray diffraction analysis of MspI restriction endonuclease in complex with its cognate DNA.

The MspI restriction endonuclease is a type II restriction enzyme. Unlike all other restriction enzymes with known structures, MspI recognizes the palindromic tetranucleotide sequence 5'-C/CGG and cleaves it as indicated by the '/' to produce DNA products with 5' two-base overhangs. Owing to the nature of its cleavage pattern, it is likely that MspI would represent a new structural class of restriction endonucleases. Crystals of the dimeric MspI restriction enzyme bound to a duplex DNA molecule containing the specific recognition sequence have been obtained by vapor-diffusion techniques in the presence of polyethylene glycol as precipitant. The crystals belong to the monoclinic space group P2(1), with unit-cell parameters a = 50.2, b = 131.6, c = 59.3 A, beta = 109.7 degrees. The crystals contain one dimeric complex in the asymmetric unit. A complete native data set has been collected to a resolution of 2.05 A by cryo-crystallographic methods, with an R(merge) of 4.0%.

Enantiomeric separation of enzymatic hydrolysis products of dihydropyrimidinone methyl ester with cationic cyclodextrin by capillary electrophoresis.

The achiral separation of dihydropyrimidinone (DHP) methyl ester and its corresponding carboxylic acid and the chiral separation of their respective enantiomers were achieved in a single analysis using capillary electrophoresis (CE) with quaternary ammonium-beta-cyclodextrin (QA-beta-CD) as a chiral buffer additive. Separation of the DHP methyl ester from the corresponding carboxylic acid was achieved because the acid was negatively charged at pH 8.3 of the running buffer and the ester is neutral. Upon the addition of QA-beta-CD, the enantiomers of the acid and ester were well resolved before and after the electroosmotic flow, respectively. In addition, the minor DHP methyl ester enantiomer (R isomer) was well separated from several impurities. This CE system was used to monitor the progress of a bioresolution reaction that utilizes an enzyme to convert the R isomer of the ester to its corresponding acid. The quantities of all four enantiomers can be determined using a single set of CE conditions. In addition, it is demonstrated that samples can be directly injected into the capillary without sample pretreatment due to the fact that the coating of the cationic CD on the capillary surface prevents adsorption of the positively charged enzyme. The effects of other experimental parameters such as type of CDs, concentration of CDs, pH, temperature, and the preconditioning of capillary were also studied.

Identification of a CD4 domain required for interleukin-16 binding and lymphocyte activation.

Interleukin-16 (IL-16) activates CD4(+) cells, possibly by direct interaction with CD4. IL-16 structure and function are highly conserved across species, suggesting similar conservation of a putative IL-16 binding site on CD4. Comparison of the human CD4 amino acid sequence with that of several different species revealed that immunoglobulin-like domain 4 is the most conserved extracellular region. Potential interaction of this domain with IL-16 was studied by testing murine D4 sequence-based oligopeptides for inhibition of IL-16 chemoattractant activity and inhibition of IL-16 binding to CD4 in vitro. Three contiguous 12-residue D4 region peptides (designated A, B, and C) blocked IL-16 chemoattractant activity, with peptide B the most potent. Peptides A and B were synergistic for inhibition, but peptide C was not. Peptides A and B also blocked IL-16 binding to CD4 in vitro, whereas peptide C did not. CD4, in addition to its known function as a receptor for major histocompatibility complex class II, contains a binding site for IL-16 in the D4 domain. The D4 residues required for IL-16 binding overlap those previously shown to participate in CD4-CD4 dimerization following class II major histocompatibility complex binding, providing a mechanistic explanation for the known function of IL-16 to inhibit the mixed lymphocyte reaction.

Vanadium accumulation in pinnipeds.

Vanadium in four species of pinnipeds (northern fur seals [Callorhinus ursinus], Steller sea lions [Eumetopias jubatus], harbor seals [Phoca vitulina], and ribbon seals [Phoca fasciata]) caught in the Northern Pacific was analyzed using ICP-MS to understand its accumulation and distribution. In northern fur seals, relatively high concentrations of vanadium were observed in the liver, hair, and bone. Ninety percent of the vanadium burden in the body was concentrated in these three tissues, which comprise <20% of total body weight. Hepatic vanadium concentrations in the four pinniped species were significantly correlated to age, although the levels varied with species. An increase in vanadium accumulation in the liver of northern fur seals was caused by an increase of retention in nuclei and mitochondria fraction in the cells. Vanadium concentrations in liver were significantly correlated with mercury, silver, and selenium concentrations in northern fur seals, Steller sea lions, and harbor seals.

Health status of young Alaska Steller sea lion pups (Eumetopias jubatus) as indicated by blood chemistry and hematology.

Blood chemistry and hematology were examined in 238 Steller sea lion pups (Eumetopias jubatus) to assess the health status of pups <1 month of age. Failure of juvenile recruitment (possibly due to nutritionally or physiologically compromised pups) into breeding populations has been proposed as a cause of recent declines of this endangered species in Alaska. To identify potential correlations with areas of high population decline, blood chemistry data were considered for three areas: eastern Aleutian Islands (low rates of population decline to stable populations), Gulf of Alaska (high rates of decline), and Southeast Alaska (stable to increasing population). Southeast Alaska pups showed elevated ketone body concentrations (beta-hydroxybutyrate,(beta-HBA)) and depressed glucose levels than pups in the Gulf of Alaska. Over 40% of the pups from Southeast Alaska had elevated beta-HBA concentrations suggesting they underwent longer periods of fasting than seen in pups from other areas. Hematocrit (Hct), hemoglobin concentration (Hb) and water content of the blood exhibited typical mammalian relationships. In summary, blood chemistry and hematology data showed no indication that Steller sea lion pups <1 month old from areas of population decline were nutritionally compromised.

Drug substance manufacture process control: application of flow injection analysis and HPLC for monitoring an enantiospecific synthesis.

Effective process control can only be achieved through an understanding of the operating issues of the reaction. The development and use of effective and rugged analytical methods is necessary to monitor these parameters. The intent of this paper is to present some key analytical issues encountered in the synthesis of MK-0679, an LTD4 antagonist. In a key step of the compound's synthesis, a prochiral diester intermediate undergoes an enantioselective enzymatic hydrolysis (in the presence of Triton X-100) leading to the (S)-ester acid. Subsequent processing transforms the ester acid into the final product. The residual amount of the detergent in the final product, the rapid determination of the enzymatic activity and the optical purity of the final product emerged as key issues in the control of the reaction. As a solution, two techniques were utilized and are presented: flow injection analysis and HPLC.

Distribution of heavy metals in muscle, liver and kidney of northern fur seal (Callorhinus ursinus) caught off Sanriku, Japan and from the Pribilof Islands, Alaska.

The concentrations of iron, manganese, zinc, copper, cadmium, and mercury were determined in muscle, liver and kidney of 67 northern fur seals (Callorhinus ursinus) collected off Sanriku, Japan, and from the Pribilof Islands, Alaska. Almost all the elements except cadmium were highest in liver. Cadmium levels in kidney were higher than those in liver and muscle for all animals analyzed. Concentrations of mercury increased significantly with age in muscle, liver and kidney, as did iron levels in muscle and liver and cadmium levels in muscle, while manganese concentrations decreased with age in muscle and kidney. The kidney also showed decreased copper concentration with age. Cadmium concentrations of the northern fur seals in this study were higher than the other otariids, reflecting a predominantly squid diet. Concentrations of manganese and mercury were found to be higher in the fur seals caught off Sanriku than in animals from the Pribilof Islands, while those of zinc and cadmium were found to be lower. Variable concentrations of cadmium might have been attributed to those in seawaters. Discriminant analysis of heavy metal concentrations was used to identify habitat. Sixty-three of 67 animals (94%) were correctly classified using this technique. Heavy-metal concentrations in tissues may provide a useful method to elucidate the primary feeding grounds of fur seals.

Daily cortisol production rate in man determined by stable isotope dilution/mass spectrometry.

Growth retardation as well as the development of Cushingoid features in adrenally insufficient patients treated with the currently accepted replacement dose of cortisol (33-41 mumol/day.m2; 12-15 mg/m2.day) prompted us to reevaluate the cortisol production rate (FPR) in normal subjects and patients with Cushing's syndrome, using a recently developed thermospray liquid chromatography-mass spectrometry method. The stable isotope [9,12,12-2H3]cortisol was infused continuously for 31 h at about 5% of the anticipated FPR. Blood samples were obtained at 20-min intervals for 24 h, spun, and pooled in 4-h groups. Tracer dilution in plasma was determined by liquid chromatography/mass spectrometry. The method was validated with controlled infusions in 6 patients with adrenal insufficiency. Results from 12 normal volunteers revealed a FPR of 27.3 +/- 7.5 mumol/day (9.9 +/- 2.7 mg/day) or 15.7 mumol/day.m2; 5.7 mg/m2. day). A previously unreported circadian variation in FPR was observed. Patients with Cushing's syndrome demonstrated unequivocal elevation of FPR and cortisol concentration correlated during each sample period in normal volunteers, indicating that cortisol secretion, rather than metabolism, is mainly responsible for changes in plasma cortisol. Our data suggest that the FPR in normal subjects may be lower than previously believed.

Use of Telazol to immobilize female northern sea lions (Eumetopias jubatus) in Alaska.

Twenty-nine female northern sea lions (Eumetopias jubatus) were immobilized using Telazol in dosages ranging from 1.8 to 8.1 mg/kg. Best results were achieved with Telazol dosages ranging between 1.8 and 2.5 mg/kg which resulted in smooth induction and recovery. Optimal injection location was in the muscle mass of the lower back and hip. Dosages greater than 3.5 mg/kg resulted in a tendency toward hypothermia. Six mortalities occurred which were partially caused by the location of drug injection and perhaps the high dosage.

The effect of pulsatile human corticotropin-releasing hormone administration on the adrenal insufficiency that follows cure of Cushing's disease.

Successful transsphenoidal surgery for Cushing's disease leads to secondary adrenal insufficiency in most patients. This form of transient adrenal insufficiency is thought to result from hypothalamic and pituitary suppression due to the preceding hypercortisolism. Whether the rate-limiting step in the recovery of adrenal function in this setting is the hypothalamic CRH neuron or the pituitary corticotroph cell, however, is not known. We studied this question by examining the response to ovine CRH (oCRH) before, during, and after prolonged pulsatile administration of human CRH (hCRH) beginning 1-2 weeks after curative microadenomectomy for Cushing's disease. Five patients cured of Cushing's disease received eight hCRH injections (1 microgram/kg) daily for 7 days. This CRH regimen was found previously to normalize plasma ACTH and cortisol patterns in patients with secondary adrenal insufficiency who had normal ACTH responses to a single injection of oCRH (hypothalamic adrenal insufficiency). The plasma ACTH and cortisol responses to oCRH (1 microgram/kg at 2000 h) were assessed immediately before, 2.5 h after, and 7 days after the end of pulsatile hCRH administration. To control for time-related improvement in the hormonal response to ovine CRH, an additional five patients cured of Cushing's disease underwent oCRH tests 1-2 and 3-4 weeks after transsphenoidal surgery, but did not receive hCRH. There was no significant difference in basal or oCRH-stimulated plasma ACTH and cortisol levels among any of the three oCRH tests in the patients who received hCRH. The baseline and oCRH-stimulated plasma ACTH and cortisol levels 1-2 and 3-4 weeks after surgery in the patients who did not receive pulsatile hCRH were similar to the values at those times in the patients who received pulsatile hCRH. Compared to normal subjects, however, both the hCRH-treated and non-hCRH-treated patients had significantly decreased peak and time-integrated plasma ACTH and cortisol responses to oCRH. We conclude that an impaired pituitary response to CRH contributes to the postoperative hypocortisolism of patients recently cured of Cushing's disease, and that this impaired pituitary response to CRH is not reversible by 1 week of pulsatile hCRH administration.