Lichen-based critical loads for deposition of nitrogen and sulfur in US forests

Critical loads are thresholds of atmospheric deposition below which harmful ecological effects do not occur. Because lichens are sensitive to atmospheric deposition, lichen-based critical loads can foreshadow changes of other forest processes. Here, we derive critical loads of nitrogen (N) and sulfur (S) deposition for continental US and coastal Alaskan forests, based on nationally consistent lichen community surveys at 8855 sites. Across the eastern and western US ranges of 459 lichen species, each species' realized optimum was the N or S atmospheric deposition value at which it most frequently occurred. The mean of optima for all species at a site, weighted by their abundances, was defined as a community "airscore" indicative of species' collective responses to atmospheric deposition. To determine critical loads for adverse community compositional shifts, we then modeled changes in airscores as a function of deposition, climate and forest habitat predictors in nonparametric multiplicative regression. Critical loads, indicative of initial shifts from pollution-sensitive toward pollution-tolerant species, occurred at 1.5 kg N ha^-1 y^-1 and 2.7 kg S ha^-1 y^-1. Importantly, these critical loads remain constant under any climate regime nationwide, suggesting both simplicity and nationwide applicability. Our models predict that preventing excess N deposition of just 0.2-2.0 kg ha^-1 y^-1 in the next century could offset the detrimental effects of predicted climate warming on lichen communities. Because excess deposition and climate warming both harm the most ecologically influential species, keeping conditions below critical loads would sustain both forest ecosystem functioning and climate resilience.

Sex disparities and neutralizing antibody durability to SARS-CoV-2 infection in convalescent individuals

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) has now caused over 2 million deaths worldwide and continues to expand. Currently, much is unknown about functionally neutralizing human antibody responses and durability to SARS-CoV-2. Using convalescent sera collected from 101 COVID-19 recovered individuals 21-212 days after symptom onset with forty-eight additional longitudinal samples, we measured functionality and durability of serum antibodies. We also evaluated associations between individual demographic and clinical parameters with functional neutralizing antibody responses to COVID-19. We found robust antibody durability out to six months, as well as significant positive associations with the magnitude of the neutralizing antibody response and male sex. We also show that SARS-CoV-2 convalescent neutralizing antibodies are higher in individuals with cardio-metabolic comorbidities.

Sulfonamides without trimethoprim in the treatment of Nocardia infections: A case report and literature review

Sulfonamides are recommended as part of first-line therapy for most Nocardia infections, with trimethoprim-sulfamethoxazole (TMP-SMX) considered the drug of choice for susceptible isolates. However, in the case of central nervous system, disseminated disease, and other serious Nocardia infections, TMP-SMX should not be used as monotherapy. The preferred treatment for a patient unable to take TMP-SMX because of allergy or intolerance remains uncertain. Prior to the availability of TMP-SMX in 1973, other sulfonamides were mainstays of treatment. We describe a Nocardia infection successfully treated with sulfadiazine in a lung transplant recipient who could not tolerate TMP-SMX. A review of similar cases reported in the literature provides insight into the successful treatment of Nocardia infections with sulfonamide regimens not containing trimethoprim in transplant recipients and other immunocompromised hosts.

Visualization and quantitative analysis of extrachromosomal telomere-repeat DNA in individual human cells by Halo-FISH

Current methods for characterizing extrachromosomal nuclear DNA in mammalian cells do not permit single-cell analysis, are often semi-quantitative and frequently biased toward the detection of circular species. To overcome these limitations, we developed Halo-FISH to visualize and quantitatively analyze extrachromosomal DNA in single cells. We demonstrate Halo-FISH by using it to analyze extrachromosomal telomere-repeat (ECTR) in human cells that use the Alternative Lengthening of Telomeres (ALT) pathway(s) to maintain telomere lengths. We find that GM847 and VA13 ALT cells average ∼80 detectable G/C-strand ECTR DNA molecules/nucleus, while U2OS ALT cells average ∼18 molecules/nucleus. In comparison, human primary and telomerase-positive cells contain <5 ECTR DNA molecules/nucleus. ECTR DNA in ALT cells exhibit striking cell-to-cell variations in number (<20 to >300), range widely in length (<1 to >200 kb) and are composed of primarily G- or C-strand telomere-repeat DNA. Halo-FISH enables, for the first time, the simultaneous analysis of ECTR DNA and chromosomal telomeres in a single cell. We find that ECTR DNA comprises ∼15% of telomere-repeat DNA in GM847 and VA13 cells, but <4% in U2OS cells. In addition to its use in ALT cell analysis, Halo-FISH can facilitate the study of a wide variety of extrachromosomal DNA in mammalian cells.

Abnormal nasal nitric oxide production, ciliary beat frequency, and Toll-like receptor response in pulmonary nontuberculous mycobacterial disease epithelium

RATIONALE

Pulmonary nontuberculous mycobacterial (PNTM) disease has increased over the past several decades, especially in older women. Despite extensive investigation, no consistent immunological abnormalities have been found. Using evidence from diseases such as cystic fibrosis and primary ciliary dyskinesia, in which mucociliary dysfunction predisposes subjects to high rates of nontuberculous mycobacterial disease that increase with age, we investigated correlates of mucociliary function in subjects with PNTM infections and healthy control subjects.

OBJECTIVES

To define ex vivo characteristics of PNTM disease.

METHODS

From 2009 to 2012, 58 subjects with PNTM infections and 40 control subjects were recruited. Nasal nitric oxide (nNO) was determined at the time of respiratory epithelial collection. Ciliary beat frequency at rest and in response to Toll-like receptor (TLR) and other agonists was determined using high-speed video microscopy.

MEASUREMENTS AND MAIN RESULTS

We found decreased nNO production, abnormally low resting ciliary beat frequency, and abnormal responses to agonists of TLR2, -3, -5, -7/8, and -9 in subjects with PNTM compared with healthy control subjects. The low ciliary beat frequency in subjects with PNTM was normalized ex vivo by augmentation of the NO-cyclic guanosine monophosphate pathway without normalization of their TLR agonist responses.

CONCLUSIONS

Impaired nNO, ciliary beat frequency, and TLR responses in PNTM disease epithelium identify possible underlying susceptibility mechanisms as well as possible avenues for directed investigation and therapy.

Focal adhesion kinase protein regulates Wnt3a gene expression to control cell fate specification in the developing neural plate

FAK is linked to aggressive tumors, but its normal function is not clear. FAK knockdown early in Xenopus development anteriorizes the embryo via a loss of Wnt signaling. Wnt3a expression is FAK dependent in both embryos and human breast cancer cells, suggesting that a FAK–Wnt linkage is highly conserved.

Focal adhesion kinase (FAK) is a cytoplasmic tyrosine kinase protein localized to regions called focal adhesions, which are contact points between cells and the extracellular matrix. FAK protein acts as a scaffold to transfer adhesion-dependent and growth factor signals into the cell. Increased FAK expression is linked to aggressive metastatic and invasive tumors. However, little is known about its normal embryonic function. FAK protein knockdown during early Xenopus laevis development anteriorizes the embryo. Morphant embryos express increased levels of anterior neural markers, with reciprocally reduced posterior neural marker expression. Posterior neural plate folding and convergence-extension is also inhibited. This anteriorized phenotype resembles that of embryos knocked down zygotically for canonical Wnt signaling. FAK and Wnt3a genes are both expressed in the neural plate, and Wnt3a expression is FAK dependent. Ectopic Wnt expression rescues this FAK morphant anteriorized phenotype. Wnt3a thus acts downstream of FAK to balance anterior–posterior cell fate specification in the developing neural plate. Wnt3a gene expression is also FAK dependent in human breast cancer cells, suggesting that this FAK–Wnt linkage is highly conserved. This unique observation connects the FAK- and Wnt-signaling pathways, both of which act to promote cancer when aberrantly activated in mammalian cells.

Mesodermal Wnt signaling organizes the neural plate via Meis3

In vertebrates, canonical Wnt signaling controls posterior neural cell lineage specification. Although Wnt signaling to the neural plate is sufficient for posterior identity, the source and timing of this activity remain uncertain. Furthermore, crucial molecular targets of this activity have not been defined. Here, we identify the endogenous Wnt activity and its role in controlling an essential downstream transcription factor, Meis3. Wnt3a is expressed in a specialized mesodermal domain, the paraxial dorsolateral mesoderm, which signals to overlying neuroectoderm. Loss of zygotic Wnt3a in this region does not alter mesoderm cell fates, but blocks Meis3 expression in the neuroectoderm, triggering the loss of posterior neural fates. Ectopic Meis3 protein expression is sufficient to rescue this phenotype. Moreover, Wnt3a induction of the posterior nervous system requires functional Meis3 in the neural plate. Using ChIP and promoter analysis, we show that Meis3 is a direct target of Wnt/beta-catenin signaling. This suggests a new model for neural anteroposterior patterning, in which Wnt3a from the paraxial mesoderm induces posterior cell fates via direct activation of a crucial transcription factor in the overlying neural plate.

A phase I study of nelfinavir, an FDA approved HIV protease inhibitor, in adults with refractory solid tumors

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Background: Preclinical studies show that HIV protease inhibitors such as nelfinavir (N) have dose- dependent, pleiotropic anti-cancer activities. However, the maximum tolerated dose (MTD) of N has not been established in humans. Methods: Pts were treated on a modified Fibonacci dose-escalation scheme with a twice daily oral dose of N starting at the FDA approved dose of 1250 mg bid on a 21-day cycle. Patients with refractory solid tumors, ECOG PS < 2, and adequate organ function were eligible. Therapy continued until MTD or disease progression. PBMCs as well as optional tumor biopsies were collected for Akt inhibition and expression of markers of ER stress (ERS). Results: 14 patients have been enrolled. Of the 11 evaluable for toxicity, there were 10 men, 10 Caucasians, and 1 African American (median age 63 years (range 24 - 77)). Tumor types included NSCLC (3), SCLC (2), thyroid (3), pancreatic (1), colorectal (1), and renal cell (1). Median number of prior systemic therapies was 2 (range, 1 - 6). There have been no grade 4 or 5 toxicities. We observed 12 grade 3 toxicities that were asymptomatic laboratory abnormalities. The most prevalent toxicities were ALT transaminitis (5 events in 8 subjects in dose level ((DL) 2, 3, 4), AST transaminitis (4 events in 8 subjects in DL 2, 4), diarrhea (8 events in 5 subjects in DL 2, 3, 4), and hyperglycemia (5 events in 5 subjects in DL 1, 2, 3). Enrollment continues at DL 4 (3125 mg twice daily). There have been no responses. Two subjects with lung cancer had stable disease for 9 weeks. Pharmacokinetic data revealed median Cmax of 2,461.5 ng/ml (DL1), 11,809 ng/ml (DL2), 11,576 ng/ml (DL3), and 11,986 ng/ml (DL4), occurring 4 hours after an oral dose. There was no relationship between the drug levels and albumin levels. Akt inhibition and increased expression of markers of ERS and apoptosis have been observed in PBMCs from week 1 in the majority of patients at every dose level, but there was no correlation with clinical response. Conclusions: N appears to be well tolerated in subjects with advanced solid tumors at 2.5 times the FDA approved dose. AUC data suggest that there may be only minimal increases in plasma drug concentrations with doses above 1875 mg twice daily.

No significant financial relationships to disclose.

A novel putative low-affinity insulin-like growth factor-binding protein, LIBC (lost in inflammatory breast cancer), and RhoC GTPase correlate with the inflammatory breast cancer phenotype

Inflammatory breast cancer is a rapidly growing, distinct form of locally advanced breast cancer that carries a guarded prognosis. To identify the genes that contribute to this aggressive phenotype, we compared under- and overexpressed sequences in an inflammatory breast tumor cell line with those of actively replicating normal human mammary epithelial cell lines using differential display. Of the 17 transcripts isolated and characterized from these experiments, overexpression of RhoC GTPase and loss of expression of a novel gene on 6q22, LIBC (lost in inflammatory breast cancer), were highly correlated (P<0.0095 and P<0.0013, respectively) with the inflammatory phenotype when a panel of archival inflammatory breast cancers was compared with noninflammatory stage III breast cancers by in situ hybridization. This study suggests two new molecular markers specific for inflammatory breast cancer.

Contig map of the Parkinson's disease region on 4q21-q23

We have constructed a yeast artificial chromosome contig (YAC) map of human chromosome 4q21-q23 across the Parkinson's disease region by combining molecular and fluorescence in situ hybridization techniques. This map contains 55 YACs and 51 molecular markers, including 23 polymorphic markers. We have also isolated one P1 and 33 bacterial artificial chromosomes located within this contig. Plasmid libraries were generated from 11 of these BAC and P1 clones, and 614 random plasmid clones were sequenced for a total of about 200 kb. This contig allowed us to precisely determine the location of 18 transcripts within the D4S2460-D4S2986 interval, including the alpha-synuclein gene found to be mutated in some families with Parkinson's disease.

A stingray spine in the scapula of a bottlenose dolphin

A stingray spine was found lodged in the scapula of a deceased 272 cm, male bottlenose dolphin (Tursiops truncatus) from South Carolina (USA) following skeletal preparation, nearly 6 mo after necropsy. No external puncture wound, internal bruising, or laceration of muscle tissue surrounding the scapula was evident during necropsy of the animal. Implantation of the spine did not appear to be related to the death of the dolphin, but probably occurred at an early age. Abnormal development of bone surrounding the spine resulted in the formation of a cavity at the wound site. Two mechanisms were considered as contributors for the cavity formation. These were the mechanical action of the spine stimulating the body's defense system for managing foreign objects, and the release of potent toxins from the spine sheath.

Mutation in the alpha-synuclein gene identified in families with Parkinson's disease

Parkinson's disease (PD) is a common neurodegenerative disorder with a lifetime incidence of approximately 2 percent. A pattern of familial aggregation has been documented for the disorder, and it was recently reported that a PD susceptibility gene in a large Italian kindred is located on the long arm of human chromosome 4. A mutation was identified in the alpha-synuclein gene, which codes for a presynaptic protein thought to be involved in neuronal plasticity, in the Italian kindred and in three unrelated families of Greek origin with autosomal dominant inheritance for the PD phenotype. This finding of a specific molecular alteration associated with PD will facilitate the detailed understanding of the pathophysiology of the disorder.

Mutation in the alpha-synuclein gene identified in families with Parkinson's disease

Parkinson's disease (PD) is a common neurodegenerative disorder with a lifetime incidence of approximately 2 percent. A pattern of familial aggregation has been documented for the disorder, and it was recently reported that a PD susceptibility gene in a large Italian kindred is located on the long arm of human chromosome 4. A mutation was identified in the alpha-synuclein gene, which codes for a presynaptic protein thought to be involved in neuronal plasticity, in the Italian kindred and in three unrelated families of Greek origin with autosomal dominant inheritance for the PD phenotype. This finding of a specific molecular alteration associated with PD will facilitate the detailed understanding of the pathophysiology of the disorder.