A comparative study of zero-shot inference with large language models and supervised modeling in breast cancer pathology classification

Although supervised machine learning is popular for information extraction from clinical notes, creating large, annotated datasets requires extensive domain expertise and is time-consuming. Meanwhile, large language models (LLMs) have demonstrated promising transfer learning capability. In this study, we explored whether recent LLMs can reduce the need for large-scale data annotations. We curated a manually labeled dataset of 769 breast cancer pathology reports, labeled with 13 categories, to compare zero-shot classification capability of the GPT-4 model and the GPT-3.5 model with supervised classification performance of three model architectures: random forests classifier, long short-term memory networks with attention (LSTM-Att), and the UCSF-BERT model. Across all 13 tasks, the GPT-4 model performed either significantly better than or as well as the best supervised model, the LSTM-Att model (average macro F1 score of 0.83 vs. 0.75). On tasks with a high imbalance between labels, the differences were more prominent. Frequent sources of GPT-4 errors included inferences from multiple samples and complex task design. On complex tasks where large annotated datasets cannot be easily collected, LLMs can reduce the burden of large-scale data labeling. However, if the use of LLMs is prohibitive, the use of simpler supervised models with large annotated datasets can provide comparable results. LLMs demonstrated the potential to speed up the execution of clinical NLP studies by reducing the need for curating large annotated datasets. This may increase the utilization of NLP-based variables and outcomes in observational clinical studies.

[Evaluation of differences in quality of life in patients with chronic graft-versus-host disease]

Objective: To evaluate the status of, differences in, and factors influencing quality of life (QoL) in patients with chronic graft-versus-host disease (GVHD). Methods: From September 2021 to February 2023, a cross-sectional study of 140 patients with chronic GVHD was conducted at our center. Symptom burden was assessed by the Lee Symptomatology Scale (LSS), and QoL was assessed by the Medical Outcome Study 36-Item Short-Form Health Survey (SF-36) (version 1) and five-level EuroQoL five-dimensional questionnaire (EQ-5D-5L). Results: Data from 140 respondents, including 32 (22.9%) with mild chronic GVHD, 87 (62.1%) with moderate chronic GVHD, and 21 (15.0%) with severe chronic GVHD, were analyzed. Of the respondents, 61.4% were male, and the median transplantation age was 34 (15-68) years. The primary diagnoses were acute myeloid leukemia (50.0%), acute lymphoblastic leukemia (20.0%), and myelodysplastic syndrome (15.0%). The common chronic GVHD-affected organs included the skin in 74 patients (52.9%), the eyes in 57 patients (40.7%), and the liver in 50 patients (35.7%). Among the whole cohort, the eye (20.48±23.75), psychological (16.13±17.00), and oral (13.66±20.55) scores were highest in the LSS group. The physiological function (36.07±11.13), social function (36.10±10.68), and role-emotional functioning (38.36±11.88) scores were lowest in the SF-36 group. The EQ-5D index was 0.764. The total LSS scores for mild, moderate, and severe chronic GVHD were 6.51±6.15, 10.07±5.61, and 20.90±10.09, respectively. The SF-36 physical component scores (PCSs) were 43.12±6.38, 40.73±7.14, and 36.97±6.97, respectively, and the mental component scores (MCSs) were 43.00±8.47, 38.90±9.52, and 28.96±9.63, respectively. The EQ-5D values were 0.810±0.124, 0.762±0.179, and 0.702±0.198, respectively. The multivariate analysis showed that the overall symptom burden (β=-0.517), oral symptom burden (β=-0.456), National Institute of Health (NIH) criteria for the eyes (β=-0.376), and nutrition-related symptom burden (β=-0.211) were significantly negatively correlated with the PCS. The NIH score (β=-0.260) was negatively correlated with the MCS score. Oral symptom burden (β=-0.400), joint/fascia NIH criteria (β=-0.332), number of involved systems (β=-0.253), overall NIH criteria (β=-0.205), and number of immunosuppressants taken (β=-0.171) were significantly negatively correlated with the EQ-5D score (all P<0.05). Medium to strong correlations were found between the EQ-5D score and the SF-36 score (|r|=0.384-0.571, P<0.001). Conclusions: The QoL of patients with chronic GVHD is impaired, and the more severe the disease, the poorer the QoL. Overall symptom burden, severity of eyes, and oral symptom burden were the most important factors affecting QoL.

[Treatment response to Conbercept of different types of diabetic macular edema classified based on optical coherence tomography]

OBJECTIVE

To compare different types of diabetic macular edema (DME) classified based on optical coherence tomography (OCT) for their responses to Conbercept injection and analyze the factors that affect the treatment responses.

METHODS

We retrospectively analyzed the clinical data of 65 patients (76 eyes) with DME diagnosed and treated with intravitreal injection of Conbercept (1+PRN) in our hospital from February, 2019 to February, 2021. According to OCT findings, DME in these patients was classified into cystic macular edema (CME; 28 eyes), serous retinal detachment (SRD; 33 eyes), and diffuse retinal thickening (DRT; 15 eyes). The best corrected visual acuity (BCVA) and central retinal thickness (CRT) were measured before and at 3 months after the first treatment. The baseline OCT characteristics of different types of DME were compared, and the correlation of these OCT characteristics with the treatment response to Conbercept was analyzed.

RESULTS

All the patients showed significant improvement of the BCVA 3 months after the treatment (P < 0.05). For all the 3 types of DME, the CRT at 3 months after the first treatment was significantly reduced as compared to the baseline (P < 0.05). The number of hyperreflective foci (HF) in the outer retina and the proportion of ellipsoid zone (EZ) interruption were the greatest in SRD group (P < 0.05). The baseline outer retinal HF was significantly correlated with the baseline CRT, CRT changes and CRT after treatment (all P < 0.05). The patients with baseline outer limiting membrane (ELM)/ EZ disruption had poorer baseline BCVA, greater baseline CRT, greater variation of CRT and poorer BCVA at 3 months after treatment (all P < 0.05).

CONCLUSION

For all the 3 types of DME, treatment with intravitreal injection of Conbercept can significantly improve the BCVA and CRT of the patients. DME of the SRD type has the best morphological response to Conbercept, while the DRT type has a relatively poor response. A greater number of HF at baseline may indicate a better morphological response to Conbercept treatment, and baseline ELM/EZ disruption may suggest a poor visual prognosis at 3 months after treatment.

Primary intrasellar schwannoma with intratumoral hemorrhage mimicking pituitary apoplexy: A case report

Tumours growing in the sella turcica are mostly pituitary adenomas. We describe a rare case of primary intrasellar schwannoma with intratumoral bleeding. A 38-year-old man presented with headache in association with bilateral supratemporal quadrantopsia. MRI showed an intrasellar mixed signal mass lesion with suprasellar extension. The majority of the pituitary hormones were normal. He was diagnosed as non-functional pituitary adenoma with pituitary apoplexy. Subtotal resection was achieved eventually via an endoscopic transnasal trans-sphenoidal approach. The histopathologic diagnosis was schwannoma. It is the first intrasellar schwannoma with intratumoral hemorrhage in literature to date. It implied that the primary intrasellar schwannoma has potential risk of intratumoral bleeding, which should be considered in the differential diagnoses of sellar lesions.

[The clinical observation of sirolimus combined with calcineurin inhibitors for steroid-resistant/steroid-dependent extensive cGVHD]

Objective: To observe the efficacy and safety of sirolimus combined with calcineurin inhibitor (CNI) in the treatment of glucocorticoid resistant/dependent extensive chronic graft-versus-host disease (cGVHD) . Methods: A total of 27 patients with steroid-resistant/steroid-dependent extensive cGVHD from November 2015 to January 2019 were enrolled and given sirolimus capsules combined with cyclosporine or tacrolimus to observe the clinical efficacy and adverse events. Results: The median duration of medication was 14.2 months and the mean duration was 16.7 months. The median follow-up time was 20.1 months (12.9-46.1 months) . Following the 6-month follow-up, 3 cases achieved complete response (CR) and 12 cases partial response (PR) . The overall response rate (ORR) was 55.6% ; for progression-free survival (PFS) , PFS-6 reached 88.9% (24/27) , and for overall survival (OS) , OS-6 was 100% . At the 1-year follow-up, there were 5 cases of CR and 11 cases of PR, ORR was 59.3% , PFS-12 reached 62.9% (17/27) , and OS-12 was 100% . The subgroup analysis found that the program was more effective for cGVHD in male donors and the target organ analysis had an advantage in the treatment of oral cavity, skin, and liver rejection. Adverse events were observed: hyperlipidemia 11.1% , oral ulcer 7.4% , fungal infection 11.1% , liver injury 3.7% , renal insufficiency 0, and no new CMV and EB viremia. Conclusion: Sirolimus combined with calcineurin inhibitors is effective in treating steroid-resistant/steroid-dependent extensive cGVHD, especially because adverse reactions (renal toxicity, CMV, EBV infection) are low in number, which is suitable for long-term treatment of cGVHD.

Phosphorylation of nucleopolyhedrovirus 39K is essential for the regulation of viral gene transcription in silkworm cells

39K protein was proven to be the most notable hyperphosphorylated protein of Bombyx mori nucleopolyhedrovirus (BmNPV), since its amino acid 136 has the highest phosphorylation ratio (16.683) among all of BmNPV phosphorylated proteins (Shobahah et al., 2017). Therefore, we inserted positive (mimicking phosphorylation) and negative (mimicking dephosphorylation) mutants of the highest phosphorylated site of 39K and the wild type 39k into the 39k-ko-Bacmid using the Bac-to-Bac system. These three kinds of recombinant Bacmids along with wild type and knocked-out Bacmid were then transfected into the Bombyx mori cells (BmN) and further investigated by qPCR analysis. The results of the qPCR showed that 39K phosphorylation had no significant effect on viral genome replication, unlike the positive mutation that reduced the viral gene transcription drastically compared to the wild type. Thus, phosphorylation of BmNPV 39K protein does not appear to be the essential mechanism for viral genome replication, even though it has an important role in the viral gene transcription. Keywords: BmNPV; 39K; phosphorylation; virus replication; virus transcription.

Correction to 'Resveratrol-loaded PLGA nanoparticles: enhanced stability, solubility and bioactivity of resveratrol for non-alcoholic fatty liver disease therapy'

[This corrects the article DOI: 10.1098/rsos.181457.].

Long-term Rescue of Photoreceptors in a Rodent Model of Retinitis Pigmentosa Associated with MERTK Mutation

MERTK mutation reduces the ability of retinal pigment epithelial (RPE) cells to phagocytize the photoreceptor outer segments, which leads to accumulation of debris separating photoreceptors from RPE cells, resulting in their degeneration and loss of vision. In a rat model of Retinitis Pigmentosa due to MERTK mutation, we demonstrate that surgical removal of debris performed when about half of photoreceptors are lost (P38), allows the remaining photoreceptor cells to renew their outer segments and survive for at least 6 months - 3 times longer than in untreated eyes. In another set of experiments, patterned laser photocoagulation was performed before the debris formation (P19-25) to destroy a fraction of photoreceptors and thereby reduce the phagocytic load of shed outer segment fragments. This treatment also delayed the degeneration of the remaining photoreceptors. Both approaches were assessed functionally and morphologically, using electroretinography, optical coherence tomography, and histology. The long-term preservation of photoreceptors we observed indicates that MERTK-related form of inherited retinal degeneration, which has currently no cure, could be amenable to laser therapy or subretinal surgery, to extend the visual function, potentially for life.

Single Nodal Loop of Accidental Degeneracies in Minimal Symmetry: Triclinic CaAs_{3}

The existence of closed loops of degeneracies in crystals has been intimately connected with associated crystal symmetries, raising the following question: What is the minimum symmetry required for topological character, and can one find an example? Triclinic CaAs_{3}, in the space group P1[over ¯] with only a center of inversion, has been found to display, without need for tuning, a nodal loop of accidental degeneracies with topological character, centered on one face of the Brillouin zone that is otherwise fully gapped. The small loop is very flat in energy, yet is cut four times by the Fermi energy, a condition that results in an intricate repeated touching of inversion related pairs of Fermi surfaces at Weyl points. Spin-orbit coupling lifts the fourfold degeneracy along the loop, leaving trivial Kramers pairs. With its single nodal loop that emerges without protection from any point group symmetry, CaAs_{3} represents the primal "hydrogen atom" of nodal loop systems.

Functional characterization of Bombyx mori nucleopolyhedrovirus mutant lacking late expression factor 9

Baculoviridae is a family of invertebrate viruses with large double-stranded DNA genomes. Proteins encoded by some late expression factor (lef ) genes are involved in the regulation of viral gene expression. Lef-9 is one of four transcription-specific Lefs, which are components of the virus-encoded RNA polymerase, and can initiate and transcribe late and very late genes. As a multifunctional protein encoded by the Bombyx mori nucleopolyhedrovirus (BmNPV), Lef-9 may be involved in the regulation of viral propagation. However, the underlying mechanism remains unclear. To determine the role of lef-9 in baculovirus infection, lef-9-knockout virus (lef-9-KO-Bacmid virus) was constructed using the Red recombination system, and the Bac-to-Bac system was used to prepare lef-9-repaired virus (lef-9-Re-Bacmid virus). The lef-9-KO virus did not produce infectious viruses or show infection activity, while the lef-9-repaired virus recovered both. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis of the transcription levels in wild-type-Bacmid, lef-9-KO-Bacmid, and lef-9-Re-Bacmid viruses showed that the lef-9-KO bacmid had little effect on viral genome replication. However, the transcription levels of the early and late viral genes, lef-3, ie-1, vp39, and p10, were significantly lower in BmN cells transfected with lef-9-KO-Bacmids than in the controls. Electron microscopy showed no visible enveloped virions in cells transfected with lef-9-KO-Bacmids, while many mature virions in cells transfected with lef-9-Re-Bacmid and wt-Bacmid were present. Thus, lef-9 was not essential for viral genome replication, but significantly affected viral gene transcription and expression in all periods of cell life cycle.

Coexistence of intracranial aneurysm and hemangioblastoma: A case report and literature review

The association of intracranial aneurysm and hemangioblastoma is extremely rare. This report regards a patient affected by Von Hippel-Lindau syndrome with multiple hemangioblastoma and two intracranial aneurysms, of which one was on a hemangioblastoma feeder vessel and the other on an unrelated vessel. Review of the literature revealed 13 other previously reported cases. Possible mechanisms to explain the association are discussed.

Association between genetic variants of EGF-containing fibulin-like extracellular matrix protein1 gene and sporadic breast cancer in a Chinese Han population

PURPOSE OF INVESTIGATION

Genetic susceptibility of breast cancer has been shown to be modulated by inheritance of polymorphic genes. EGF-containing fibulin-like extracellular matrix protein 1 (EFEMP1) gene played an important role in many tumors, including lung cancer, hepatic carcinoma, and prostate cancer. In addition, it was importantly downexpressed in breast cancer. The present research aimed to assess the association between genetic variations of EFEMP1 and breast cancer risk.

MATERIALS AND METHODS

The authors genotyped 11 common tagging SNPs with an array platform including 960 cases and 972 cancer-free controls of Chinese women, according to the HapMap database based on the pairwise linkage disequilibrium (LD) r² threshold of 0.8, minor allele frequency of 0.05.

RESULTS

Three SNPs were significant associated with breast cancer (rs3791679, p = 0.016, OR = 1.21, 95% CI = 1.04-1.41; rs1346786, p = 0.005, OR = 1.31, 95% CI = 1.08 -1.59; rs727878, p = 0.002, OR = 1.29, 95%CI = 1.10-1.51). Multivariate logistic regression analysis revealed that, compared with wild-type carriers in a dominant model, a significantly increased breast cancer risk was associated with the three identified risk SNPs. Among the selected tagging SNPs, three haplotype blocks were identified, and the results of haplotype analysis were consistent with the single-locus analysis. The haplotype 'GG' in block 1 and haplotype 'AG' in block 2 were significantly associated with breast cancer, and had a 54% and 28% increased breast cancer risk respectively, compared with their corresponding noncarriers.

CONCLUSIONS

The present results suggested that the polymorphisms of EFEMP1 gene were associated with breast cancer and might contribute to the susceptibility of the progression of breast cancer in Chinese Han women. Individuals with the risk alleles might increase the risk of breast cancer.

The effect of BM67 gene deletion on Bombyx mori nuclear polyhedrosis virus replication

Homologs of Bombyx mori nuclear polyhedrosis virus (BmNPV) Bm67 gene ORF67 have been found in the genome of all lepidopteran nuclear polyhedrosis viruses, but their function is still not very clear. In order to analyze it we employed a  bacmid harboring the complete BmNPV genome including the Bm67 gene and expressing infectious virus (wtBacmid) for the construction of its Bm67-deficient variant (Bm67-KO-Bacmid) using the Red recombination system and the Bm67-repaired variant (Bm67-Re-Bacmid) using the Bac-to-Bac system. By transfecting BmN cells with these bacmids we demonstrated that the Bm67-deficient virus did not generate infectious virus, while the repaired virus restored its infectivity, indicating that the Bm67 gene is essential for the formation of infectious budding virus (BV). Electron microscopy of BmN cells transfected with the abovementioned bacmids showed many mature rodshaped virus particles in both wtBacmid- and Bm67-Re-Bacmid-transfected cells but none in Bm67-KO-Bacmid-transfected ones. Moreover, the real-time RT-PCR showed that the deletion of Bm67 from wtBacmid significantly reduced the levels of viral genomic DNA and transcripts of viral early genes dnapol, ie-1 and lef-3 but not those of transcripts of late gene vp39 and very late gene p10. The finding that the Bm67-deficient virus generated reduced levels of infectious virus and transcripts of early dnapol gene but not those of late genes indicates that the Bm67 gene is essential for BmNPV replication.

Role of extrinsic arbuscular mycorrhizal fungi in heavy metal-contaminated wetlands with various soil moisture levels

This study presents an efficient heavy metal (HM) control method in HM-contaminated wetlands with varied soil moisture levels through the introduction of extrinsic arbuscular mycorrhizal fungi (AMF) into natural wetland soil containing indigenous AMF species. A pot culture experiment was designed to determine the effect of two soil water contents (5-8% and 25-30%), five extrinsic AMF inoculants (Glomus mosseae, G. clarum, G. claroideum, G. etunicatum, and G. intraradices), and HM contamination on root colonization, plant growth, and element uptake of common reed (Phragmites australis (Cav.) Trin. ex Steudel) plantlets in wetland soils. This study showed the prevalence of mycorrhizae in the roots of all P. australis plantlets, regardless of extrinsic AMF inoculations, varied soil moisture or HM levels. It seems that different extrinsic AMF inoculations effectively lowered HM concentrations in the aboveground tissues of P. australis at two soil moisture levels. However, metal species, metal concentrations, and soil moisture should also be very important factors influencing the elemental uptake performance of plants in wetland ecosystems. Besides, the soil moisture level significantly influenced plant growth (including height, and shoot and root dry weight (DW)), and extrinsic AMF inoculations differently affected shoot DW.

Expression profiling based on graph-clustering approach to determine osteoarthritis related pathway

BACKGROUND

Osteoarthritis (OA) is the most common disease of joints in adults around the world. Current available drugs to treat osteoarthritis are predominantly directed towards the symptomatic relief of pain and inflammation but they do little to reduce joint destruction. Effective prevention of the structural damage must be a key objective of new therapeutic approaches. Therefore, it is worthwhile to search for important molecular markers that hold great promise for further treatment of patients with osteoarthritis.

AIM

In this study, we used a graph-clustering approach to identify gene expression profiles that distinguish OA patients from normal samples.

MATERIALS AND METHODS

We performed a comprehensive gene level assessment of osteoarthritis using five osteoarthritis samples and five normal samples graph-clustering approach.

RESULTS

The results showed that TNFAIP3, ATF3, PPARG, etc, have related with osteoarthritis. Besides, we further mined the underlying molecular mechanism within these differently genes.

CONCLUSIONS

The results indicated tyrosine metabolism pathway and cell cycle pathway were two significant pathways, and there was evident to demonstrate them based on previous reports. We hope to provide insights into the development of novel therapeutic targets and pathways.

MTSS1, a novel target of DNA methyltransferase 3B, functions as a tumor suppressor in hepatocellular carcinoma

DNA methyltransferase 3B (DNMT3B) mediates gene silencing via epigenetic mechanisms during hepatocellular carcinoma (HCC) progression. We aimed to identify novel targets of DNMT3B and their potential regulatory mechanisms in HCC. Metastasis suppressor 1 (MTSS1) was one of the DNMT3B targets and selected for further study. DNMT3B overexpression was detected in 81.25% of clinical HCC specimens and was negatively associated with MTSS1 in HCC cells and clinical samples. The underlying mechanism by which DNMT3B silences MTSS1 was studied using a combination of methylation-specific polymerase chain reaction (PCR) and bisulfite genome sequencing, chromatin immunoprecipitation-PCR and luciferase reporter assays. We found that the MTSS1 promoter region was sparsely methylated, and the methylation inhibitors failed to abolish DNMT3B-mediated MTSS1 silencing. DNMT3B protein bound directly to the 5'-flanking region (-865/-645) of the MTSS1 gene to inhibit its transcription. The functional role of MTSS1 was investigated using in vitro and in vivo tumorigenicity assays. As a result, MTSS1 exerted tumor suppressor effects and arrested cells in the G2/M phase, but not the G1/S phase of the cell cycle when it was depleted or overexpressed in HCC cells. Taken together, MTSS1, a novel target of DNMT3B, is repressed by DNMT3B via a DNA methylation-independent mechanism. MTSS1 was further characterized as a novel tumor suppressor gene in HCC. These findings highlight how DNMT3B regulates MTSS1, and such data may be useful for the development of new treatment options for HCC.

Selection and characterization of HIV-1 variants resistant to the (+) and (-) enantiomers of 2'-deoxy-3'-oxa-4'-thiocytidine (dOTC)

Human immunodeficiency virus type 1 (HIV-1) variants were selected for resistance against the (+) and (-) enantiomers of a novel nucleoside analogue, 2'-deoxy-3'-oxa-4'-thiocytidine (dOTC), using the infectious molecular clone HXB2D grown in the MT-4 line of human T cells. The variants selected with (+) dOTC were approximately 6-7-fold less sensitive than wild-type virus to this drug. Cloning and sequencing of the complete reverse transcriptase (RT) coding region of these variants identified the M1841 mutation and further selection with virus containing the M1841 substitution led to the appearance of an M184V mutation. In contrast, selection experiments performed with (-) dOTC yielded variants capable of growing in drug concentrations as high as 100 microM, but phenotypic analysis of these viruses revealed near wild-type 50% inhibitory concentration (IC50) values for this compound. Site-directed mutagenesis experiments in which the M1841 and M184V mutations were introduced into HXB2D confirmed the importance of these mutations when viruses were grown in MT4 cells. However, wild-type IC50 values in regard to both (-) and (+) dOTC were obtained when these recombinant viruses were grown in cord blood mononuclear cells (CBMC). Clinical isolates of HIV-1 resistant to lamivudine and containing the M184V substitution also displayed low-level resistance to both (-) and (+) dOTC when grown in CBMC. Finally, cell-free RT assays were performed in the presence of either (-) dOTC triphosphate, (+) dOTC triphosphate, or the triphosphate of a racemic mixture of (+) and (-) dOTC with wild-type and mutated M184V-containing recombinant RT. The data demonstrate chain termination effects of these compounds with regard to both wild-type and mutated enzyme and that the latter was approximately twofold less sensitive than the former to these drugs.

Sensitivity and resistance to (+)-calanolide A of wild-type and mutated forms of HIV-1 reverse transcriptase

We have tested both wild-type and drug-resistant mutated, recombinant human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) molecules for sensitivity to each of two non-nucleoside RT inhibitors (NNRTI), (+)-calanolide A and nevirapine, in primer extension assays. We found that RT containing either the V106A or Y181C substitutions, associated with NNRTI resistance, displayed approximately 90-fold resistance to nevirapine but remained fully sensitive to (+)-calanolide A and that the Y181C mutation marginally enhanced susceptibility to the latter drug. In contrast, the Y188H substitution in RT resulted in about 30-fold resistance to (+)-calanolide A in these assays but did not result in diminished sensitivity to nevirapine. Tissue culture results indicated that the combination of (+)-calanolide A and nevirapine possessed an additive to weakly synergistic effect in blocking replication of HIV-1 in tissue culture. These results suggest that (+)-calanolide A and nevirapine might have rationale as a combination therapy for HIV disease.

Identification and characterization of two G protein-coupled receptors for neuropeptide FF

The central nervous system octapeptide, neuropeptide FF (NPFF), is believed to play a role in pain modulation and opiate tolerance. Two G protein-coupled receptors, NPFF1 and NPFF2, were isolated from human and rat central nervous system tissues. NPFF specifically bound to NPFF1 (K(d) = 1.13 nm) and NPFF2 (K(d) = 0.37 nm), and both receptors were activated by NPFF in a variety of heterologous expression systems. The localization of mRNA and binding sites of these receptors in the dorsal horn of the spinal cord, the lateral hypothalamus, the spinal trigeminal nuclei, and the thalamic nuclei supports a role for NPFF in pain modulation. Among the receptors with the highest amino acid sequence homology to NPFF1 and NPFF2 are members of the orexin, NPY, and cholecystokinin families, which have been implicated in feeding. These similarities together with the finding that BIBP3226, an anorexigenic Y1 receptor ligand, also binds to NPFF1 suggest a potential role for NPFF1 in feeding. The identification of NPFF1 and NPFF2 will help delineate their roles in these and other physiological functions.

In vitro selection and characterization of HIV-1 with reduced susceptibility to PMPA

9-(2-phosphonomethoxypropyl)adenine (PMPA) has demonstrated remarkable anti-simian immunodeficiency virus (SIV) activity in macaque models of SIV infection and transmission prevention. Recently, PMPA and its oral prodrug, bis-POC PMPA, have also shown potent anti-human immunodeficiency virus type 1 (HIV-1) activity in Phase I clinical studies. In vitro experiments were performed to address the resistance properties of PMPA. After eight passages in increasing concentrations of PMPA, HIV-1IIIB was able to grow in the presence of 2 microM PMPA, fivefold above the IC50 of PMPA for wild-type parental virus. Sequence analysis of the reverse transcriptase (RT) genes from four of 15 RT clones demonstrated the presence of a K65R substitution in RT and recombinant HIV expressing the K65R RT mutation showed a threefold to fourfold increase in IC50 value for PMPA as compared to wild-type. Additional experiments demonstrated that viruses expressing other nucleoside-associated RT resistance mutations all showed wild-type or < threefold reduced susceptibility to PMPA in vitro. Interestingly, lamivudine-resistant viruses expressing the M184V RT mutation showed wild-type to slightly increased susceptibility to PMPA in vitro and addition of the M184V mutation to HIV with the K65R mutation resulted in reversion to wild-type susceptibility for PMPA. In agreement with the cell culture findings, Escherichia coli-expressed K65R RT showed fivefold reduced susceptibility to PMPA diphosphate, the active moiety of PMPA. Furthermore, in combination experiments, PMPA with hydroxyurea showed synergistic inhibition of HIV replication in vitro. The potent antiretroviral activity and favourable resistance profile of PMPA and bis-POC PMPA are being further investigated in ongoing clinical trials.

[Anterior segment reconstruction and secondary posterior chamber intraocular lens implantation supported by fibromembrane]

OBJECTIVE

To evaluate the methods and effects of anterior segment reconstruction and secondary posterior chamber intraocular lens (IOL) implantation supported by fibromembrane in pupillary area.

METHODS

Anterior segment was reconstructed in 86 eyes with different anterior segment disorders. Anterior segment reconstruction includes: partial penetrating keratoplasty, loosing front adhesion, suturing detached peripheral iris, loosing rear adhesion, reshaping pupil, perforating fibromembrane in the pupillary area. The IOL was secondarily implanted into the posterior chamber, and the patients were followed up in 3 - 32 months.

RESULTS

The surgery was successful in all patients. The postoperative visual acuities in 71 eyes were >or= 0.5 (82.6%), including >or= 0.9 (39.5%) in 34 eyes and <or= 0.2 in 15 eyes (17.4%). After IOL implantation, the IOL correctly centered was in 68 eyes (79.1%), and deviated in 18 eyes (20.9%). Anterior chamber hemorrhage occurred in 5 eyes, 4 of them were recovered by conservative treatment and the blood membrane in another eye was sucked out through its primary incision. All patients had slight postoperative inflammation and without severe long term complications.

CONCLUSION

With the support of enough fibromembrane in pupillary area, anterior segment reconstruction and secondary posterior chamber IOL implantation can be performed, thus IOL suture fixation is not necessary, and its associated complications can be avoided.

Prevalence of HIV-1 resistant to antiretroviral drugs in 81 individuals newly infected by sexual contact or injecting drug use. Investigators of the Quebec Primary Infection Study

OBJECTIVE

Prolonged treatment with antiretroviral drugs results in the selection of HIV-1 variants with mutations conferring resistance to nucleoside and non-nucleoside reverse transcriptase inhibitors (NRTI and NNRTI) or to protease inhibitors (PI). There is serious concern about transmission of resistant viruses to newly infected persons. This study monitored the prevalence of resistant viruses in individuals undergoing primary HIV infection.

DESIGN

Resistance testing was performed on 81 individuals infected between 1997 and 1999 by injecting drug use (n =21), sexual (n = 56), or unknown (n = 4) transmission.

METHODS

Automated sequencing was used to genotype the reverse transcriptase (RT) and protease regions of virus isolated from patients' plasma. The phenotypic susceptibility of stimulated peripheral blood mononuclear cells to antiretroviral drugs was assayed. Line probe assays detected quasispecies variations in wild-type and mutated RT codons.

RESULTS

A high prevalence of PI and RT genotypic variants, associated with high-level resistance to antiretroviral drugs, was observed in individuals newly infected by injecting drug use (PI = 24%, RT = 24%) or sexual transmission (PI = 12%, RT = 22%). The PI mutations, L101, V82A, and L90M, were found in 10.5, 3 and 4% of cases, respectively; whereas for RT, primary mutations at positions T215Y (zidovudine), M184V (lamivudine), T69D/A (zalcitabine), and K103N (multi-NNRTI) were present in 8, 5, 4, and 4% of subjects, respectively. Resistance to NRTI was demonstrated by phenotypic, genotypic, and line probe analyses. Transmission of multidrug (NRTI/NNRTI/PI) resistance in eight subjects (9.9%) was confirmed by showing that source partners possessed viruses of similar genotype.

CONCLUSIONS

The transmission of drug-resistant HIV is a serious problem that merits further attention by public health officials as well as virologists and clinicians.

Reverse transcriptase inhibitors can selectively block the synthesis of differently sized viral DNA transcripts in cells acutely infected with human immunodeficiency virus type 1

We have recently reported that the in vitro inhibition of human immunodeficiency virus type 1 (HIV-1) reverse transcription by inhibitors of reverse transcriptase (RT) occurred most efficiently when the expected DNA products of RT reactions were long (Quan et al. , Nucleic Acids Res. 26:5692-5698, 1998). Here, we have used a quantitative PCR to analyze HIV-1 reverse transcription within acutely infected cells treated with RT inhibitors. We found that levels of minus-strand strong-stop DNA [(-)ssDNA] formed in acutely infected MT2 cells were only slightly reduced if cells were infected with viruses that had been generated in the presence of either azidothymidine or nevirapine (5 microM) and maintained in the presence of this drug throughout the viral adsorption period and thereafter. Control experiments in which virus inoculation of cells was performed at 4 degrees C, followed directly by cell extraction, showed that less than 1% of total (-)ssDNA within acutely infected cells was attributable to its presence within adsorbed virions. In contrast, synthesis of intermediate-length reverse-transcribed DNA products decreased gradually as viral DNA strand elongation took place in the presence of either of these inhibitors. This establishes that nucleoside and nonnucleoside RT inhibitors can exert similar temporal impacts in regard to inhibition of viral DNA synthesis. Generation of full-length viral DNA, as expected, was almost completely blocked in the presence of these antiviral drugs. These results provide insight into the fact that high concentrations of drugs are often needed to yield inhibitory effects in cell-free RT assays performed with short templates, whereas relatively low drug concentrations are often strongly inhibitory in cellular systems.

Mutations within four distinct gag proteins are required to restore replication of human immunodeficiency virus type 1 after deletion mutagenesis within the dimerization initiation site

Human immunodeficiency virus type 1 (HIV-1) genomic RNA segments at nucleotide (nt) positions +240 to +274 are thought to form a stem-loop secondary structure, termed SL1, that serves as a dimerization initiation site for viral genomic RNA. We have generated two distinct deletion mutations within this region, termed BH10-LD3 and BH10-LD4, involving nt positions +238 to +253 and +261 to +274, respectively, and have shown that each of these resulted in significant diminutions in levels of viral infectiousness. However, long-term culture of each of these viruses in MT-2 cells resulted in a restoration of infectiousness, due to a series of compensatory point mutations within four distinct proteins that are normally cleaved from the Gag precursor. In the case of BH10-LD3, these four mutations were MA1, CA1, MP2, and MNC, and they involved changes of amino acid Val-35 to Ile within the matrix protein (MA), Ile-91 to Thr within the capsid (CA), Thr-12 to Ile within p2, and Thr-24 to Ile within the nucleocapsid (NC). The order in which these mutations were acquired by the mutated BH10-LD3 was MNC > CA1 > MP2 > MA1. The results of site-directed mutagenesis studies confirmed that each of these four substitutions contributed to the increased viability of the mutated BH10-LD3 viruses and that the MNC substitution, which was acquired first, played the most important role in this regard. Three point mutations, MP2, MNC, and MA2, were also shown to be sequentially acquired by viruses that had emerged in culture from the BH10-LD4 deletion. The first two of these were identical to those described above, while the last involved a change of Val-35 to Leu. All three of these substitutions were necessary to restore the infectiousness of mutated BH10-LD4 viruses to wild-type levels, although the MP2 mutation alone, but neither of the other two substitutions, was able to confer some viability on BH10-LD4 viruses. Studies of viral RNA packaging showed that the BH10-LD4 deletion only marginally impaired encapsidation while the BH10-LD3 deletion caused a severe deficit in this regard.

Enhanced impairment of chain elongation by inhibitors of HIV reverse transcriptase in cell-free reactions yielding longer DNA products

We have studied the relationship between the length of HIV-1 reverse transcriptase (RT)-mediated nucleotide polymerization and inhibitors of these reactions in cell-free RT assays performed in the presence of either of two dideoxynucleoside triphosphates (ddNTPs), i.e. AZTTP or 3TCTP, or nevirapine, a non-nucleoside RT inhibitor. These reactions employed a heterologous RNA template and three DNA oligonucleotide primers, i.e. pAR, dPR and PA, that yielded distinct full-length products of 65, 192 and 376 nt, respectively, in the absence of inhibitor. We now show that the extent of inhibition of RT activity was greatest with use of the PA primer, which normally yielded the longest reaction product, and that lesser degrees of inhibition were noted in the reactions that generated shorter products. For example, at a concentration of 5 microM AZTTP, the extent of inhibition was 75% with the PA primer but only 40% and <10% when reactions were primed by the dPR and pAR primers, respectively. Similar results were obtained when either a mutated form of HIV RT (i.e. M184V), associated with resistance to 3TC, was tested in the presence of 3TCTP or when RT derived from Moloney murine leukemia virus (M-MuLV) was tested in the presence of AZTTP.

Characterization of human immunodeficiency virus type-1 (HIV-1) particles that express protease-reverse transcriptase fusion proteins

We have selectively mutagenized specific residues at the junction between the protease (PR) and reverse transcriptase (RT) genes of human immunodeficiency virus type 1 (HIV-1) to study the effects of PR-RT fusion proteins in the context of a full-length, infectious proviral construct. Mutant viruses derived from COS-7 cells transfected with this construct were analyzed in regard to each of viral replication, maturation, and infectivity. Immunoblot analysis revealed that the mutation prevented cleavage between the PR and RT proteins and that both existed as a PR-RT fusion protein in each of cellular and viral lysates. Interestingly, intracellular PR that existed within the PR-RT fusion protein remained functionally active, whereby HIV-1 precursor proteins were processed efficiently. Furthermore, the RT component of the fusion protein also retained its enzymatic activity as shown in RT assays. Electron microscopy revealed that the mutant viruses containing the PR-RT fusion protein possessed wild-type morphology. These viruses also displayed wild-type sensitivities to inhibitors of each of the HIV-1 PR and RT activities. However, viruses containing the PR-RT fusion protein were 20 times less infectious than wild-type viruses. This defect was further pronounced when mutated Gag-Pol proteins were overexpressed as a consequence of an additional mutation that interfered with frameshifting. Thus, unlike cleavage site mutations at the N terminus of PR, a cleavage site mutation between PR and RT did not affect the enzymatic activities of either PR or RT and viruses containing PR-RT fusion proteins were viable.

Permeability characteristics of tetragastrins across intestinal membranes using the Caco-2 monolayer system: comparison between acylation and application of protease inhibitors

PURPOSE

Three types of acyl tetragastrin (TG), acetyl-TG (C2-TG), butyryl-TG (C4-TG) and caproyl-TG (C6-TG) were synthesized and their in vitro intestinal permeability characteristics were examined using Caco-2 monolayers.

METHODS

The disappearance of acyl-TGs from the apical side of Caco-2 monolayers was estimated by analyzing degradation and permeation processes in terms of clearance.

RESULTS

The amount of native TG transported to the basolateral side was very low due to its large degradation clearance (CLd) on the apical side. Degradation of TG was reduced by chemical modification with fatty acids, which resulted in an increase in the transport of TG across Caco-2 monolayers. In addition, the permeation clearance (CLp) value of carboxyfluorescein (CF), a paracellular transport and undegradable marker, was increased in the presence of acyl-TGs. Furthermore, we investigated the effects of the protease inhibitors bacitracin and gabexate on the transport of TG across Caco-2 monolayers. In the presence of a low concentration (0.1 mM) of protease inhibitor, the CLd value of TG was reduced, but they did not affect its CLp value. However, a higher concentration (1.0 mM) of bacitracin significantly reduced TG degradation on the apical side, and further increased its CLp value.

CONCLUSIONS

We demonstrated that acylation of TG made it resistant to intestinal proteases and caused it to enhance absorption of drugs, including itself, across Caco-2 monolayers. Further, bacitracin acted as both a protease inhibitor and an absorption enhancer.

Dominance of the E89G substitution in HIV-1 reverse transcriptase in regard to increased polymerase processivity and patterns of pausing

The substitution of a glycine for glutamic acid at position 89 in human immunodeficiency virus-1 (HIV-1) reverse transcriptase (RT) (E89G) confers resistance to several nucleoside and non-nucleoside inhibitors of RT. As residue 89 contacts the template strand, it has been suggested that this mutation may modulate the conformation of the RT.template/primer complex. In addition, certain mutations in RT that confer resistance to nucleoside analogs, such as M184V, are located near the polymerase active site. To characterize further these substitutions, we performed processivity assays alongside an analysis of pausing profiles with wild-type (wt) RT and recombinant RTs containing substitutions at E89G, M184V, or both. We now show that E89G RT has higher processivity than wt enzyme as well as a different pattern of pausing sites. Similar findings were obtained with the doubly mutated RT, although enzyme containing only the M184V mutation had lower processivity than wt. Consistent with these observations, and from a mechanistic standpoint, both E89G-containing as well as doubly mutated RT had decreased dissociation constants from a complex consisting of RT and template-primer, in comparison with either wt RT or M184V-containing RT. No significant differences were observed among the various enzymes in regard to Km values for the heteropolymeric RNA template used in these studies. Viruses containing the E89G mutation synthesized longer strand DNA products than either wt viruses or viruses containing only the M184V mutation in endogenous RT assays. Thus, the E89G substitution is a dominant determinant in regard to each of the koff values from an RT.template/primer complex, RT processivity, and specific patterns of pausing during DNA polymerization.

Mechanistic studies of early pausing events during initiation of HIV-1 reverse transcription

We have investigated the role of sequences that surround the primer binding site (PBS) in the reverse transcriptase-mediated initiation of (-) strand DNA synthesis in human immunodeficiency virus type 1. In comparisons of reverse transcription initiated from either the cognate primer tRNALys.3 or a DNA primer D-Lys.3, bound to PBS sequences, we observed that a +3 pausing site occurred in both circumstances. However, the initiation reaction with tRNALys.3 was also characterized by a pausing event after incorporation of the first nucleotide. Alteration of sequences at the 5'-end instead of the 3'-end of the PBS resulted in elimination of the +3 pausing site, suggesting that this site was template sequence-dependent. In contrast, the pausing event at the +1 nucleotide position was still present in experiments that employed either of these mutated RNA templates. The mutations at the 5'-end of the PBS also caused a severely diminished rate of initiation and the strong arrest of reactions at the +1 stage when tRNALys.3 was used as primer. Therefore, we propose that the +1 pausing event is an initiation-specific event in regard to reactions primed by tRNALys.3 and that sequences at the 5'-end of the PBS may facilitate the release of reverse transcription from initiation to elongation.

Endogenous reverse transcriptase assays reveal synergy between combinations of the M184V and other drug resistance-conferring mutations in interactions with nucleoside analog triphosphates

Resistance of HIV-1 reverse transcriptase (RT) to nucleoside analogs (e.g. AZT, ddC and 3TC) is conferred by various amino acid substitutions or combinations thereof on the RT molecule. The M184V mutation, that confers high and low-level resistance to 3TC and ddC, respectively, can restore sensitivity to AZT when introduced into RT against a background of AZT-resistance. The K65R mutation, that confers low level resistance to both 3TC and ddC, can also restore sensitivity to AZT. This information is of potential utility in choosing combinations of anti-viral drugs for clinical use. To explore this subject further, we have used an endogenous RT reaction to study mutated viruses containing M184V alone or M184V combined with each of the K65R, E89G or both the M41L and T215Y substitutions. Endogenous assays possess the advantage of utilizing genomic RNA as template in a reaction mixture that includes each of tRNALys.3 and viral nucleocapsid protein, necessary for specific initiation of reverse transcription, as well as all other viral proteins that might impact on this process. We now show that viruses containing both M184V and K65R displayed synergistic resistance to 3TC triphosphate (3TCTP), while the same combination yielded the same level of resistance to ddC triphosphate (ddCTP) as that manifested by K65R alone. The combination of M184V and E89G displayed synergistic resistance against ddCTP but not 3TCTP, while viruses containing only E89G were highly resistant to 3TCTP and displayed low-level resistance to ddCTP. The results show that endogenous RT assays can reveal variable synergistic, antagonistic, or neutral effects in regard to drug sensitivity, depending on the presence of specific amino acid substitutions in RT itself.

Sequence elements downstream of the human immunodeficiency virus type 1 long terminal repeat are required for efficient viral gene transcription

We investigated the role of a 54-nucleotide region (+200 to +253) located downstream of the HIV-1 long terminal repeat (LTR) on virus gene expression and found, using RT-PCR and p24 CA analysis, that deletion of this region inhibited synthesis of both viral RNA and protein. CAT assays showed that these results were attributable to decreased transcription efficiency of the HIV-1 LTR and not to the stability of the RNA transcripts produced. Further deletional analysis and transfection studies showed that the most important sequences with regard to proviral DNA expression were located between nucleotide positions +218 and +237. Furthermore, substitutional mutational analysis showed that a CTCTCTC sequence at positions +227 to +233, homologous to the pyrimidine-rich initiator (Inr) region found in several promoters, was required for efficient production of both viral RNA and protein. Deletion of the sequence +200 to +217, homologous to the interferon-stimulated response element (ISRE), resulted in impaired LTR promoter activity and decreased synthesis of viral RNA and protein. However, when the latter region was replaced by homologous ISRE sequences from an interferon-stimulated gene (ISG-54), an even more severe effect on HIV gene expression and replication was observed, suggesting that ISRE-like sequences in HIV act differently from homologous sequences in interferon-responsive cellular genes.

The alpha chain of laminin-1 is independently secreted and drives secretion of its beta- and gamma-chain partners

A mammalian recombinant strategy was established to dissect rules of basement membrane laminin assembly and secretion. The alpha-, beta-, and gamma-chain subunits of laminin-1 were expressed in all combinations, transiently and/or stably, in a near-null background. In the absence of its normal partners, the alpha chain was secreted as intact protein and protein that had been cleaved in the coiled-coil domain. In contrast, the beta and gamma chains, expressed separately or together, remained intracellular with formation of betabeta or betagamma, but not gammagamma, disulfide-linked dimers. Secretion of the beta and gamma chains required simultaneous expression of all three chains and their assembly into alphabetagamma heterotrimers. Epitope-tagged recombinant alpha subunit and recombinant laminin were affinity-purified from the conditioned medium of alphagamma and alphabetagamma clones. Rotary-shadow electron microscopy revealed that the free alpha subunit is a linear structure containing N-terminal and included globules with a foreshortened long arm, while the trimeric species has the typical four-arm morphology of native laminin. We conclude that the alpha chain can be delivered to the extracellular environment as a single subunit, whereas the beta and gamma chains cannot, and that the alpha chain drives the secretion of the trimeric molecule. Such an alpha-chain-dependent mechanism could allow for the regulation of laminin export into a nascent basement membrane, and might serve an important role in controlling basement membrane formation.

Identification of sequences downstream of the primer binding site that are important for efficient replication of human immunodeficiency virus type 1

Reverse transcription of retroviruses is initiated from an 18-nucleotide (nt) primer binding site (PBS), located within the 5' region of viral genomic RNA, to which the host cell-derived tRNA primer is annealed and also involves viral genomic sequences outside the PBS. We constructed proviral DNA clones of human immunodeficiency virus (HIV) that had selective deletions of either a 7-nt segment found immediately downstream of the PBS or an extended nontranslated 54-nt stretch located immediately downstream of the PBS and containing the aforementioned 7-nt segment. Synthesis of minus-strand strong-stop DNA was assessed with MT-4 cells infected with viruses derived from COS-7 cells that had been transfected with these various constructs. We found that similar levels of minus-strand strong-stop DNA as well as DNA produced after template switching were expressed in MT-4 cells infected with COS-7-derived wild-type viruses or with viruses that had the 7-nt segment deleted. In contrast, significantly lower levels of viral DNA were detected in MT-4 cells after infection with viruses that had deletions of the 54-nt stretch. Furthermore, the molecular clone containing the 7-nt deletion was able to replicate with wild-type kinetics, while that containing the 54-nt deletion displayed a significantly diminished capacity in this regard. Further deletion analysis showed that a 16-nt segment at the 3' end of this 54-nt segment was largely responsible for these effects. We also conducted studies to determine levels of viral mRNA in COS-7 cells that had been transfected with equivalent amounts of DNA derived from either a wild-type HIV construct or our various deletion mutants. In the case of transfections performed with the 7-nt deletion mutant and wild-type HIV DNA, high levels of viral mRNA transcripts were detected, which was not the case for the 54 nt-deletion mutant. However, these various mRNAs possessed similar stabilities, as shown through studies in which transcript formation was arrested by treatment of cells with actinomycin D. Thus, the 54-nt segment of 5' nontranslated RNA, located downstream of the PBS, is involved in efficient expression of each of viral DNA, mRNA, and infectious virus.

The importance of the A-rich loop in human immunodeficiency virus type 1 reverse transcription and infectivity

Nucleotide segment (+169)AAAA(+172) constitutes an A-rich loop within human immunodeficiency virus type 1 (HIV-1) (HXB2D) RNA and is able to interact with the anticodon loop (33)/USUU(36) of primer tRNA3(Lys). We have shown that the deletion of this A-rich loop resulted in diminished levels of infectivity and reduced synthesis of viral DNA in MT-2 cells and cord blood mononuclear cells. Endogenous reverse transcriptase (RT) assays revealed that the mutated viruses, termed HIV/del-A, generated fewer cDNA products than did wild-type virus, designated HIV/WT. We also employed in vitro RT assays with in vitro-synthesized viral RNA templates, recombinant HIV-1 RT(p66/51), and natural tRNA3(Lys) as primers to show that the mutated RNA templates, designated PBS/del-A, generated less minus-strand strong-stop DNA product than did the wild-type RNA template, designated PBS/WT. The initiation efficiency of reverse transcription from the mutated RNA template was significantly impaired compared with that from the wild-type RNA template when a single-base extension assay from the tRNA3(Lys) primer was employed. However, RT reactions performed with DNA oligonucleotides complementary to the primer binding site (PBS) as primers did not yield differences between the mutated PBS/del-A and wild-type RNA templates. Long-term culture of HIV/del-A in MT-2 cells resulted in the replacement of two G's at nucleotide positions 167 and 168 by two A's that possessed the same relationship to the 5' end of the PBS as did the wild-type A's at positions 171 and 172. In vitro RT assays performed with recombinant enzyme with tRNA3(Lys) as the primer showed that the RNA template thus generated, termed PBS/A2, yielded levels of minus-strand strong-stop DNA product similar to those yielded by the wild-type RNA template. Coincidentally, viruses containing A's at positions 167 and 168 were able to replicate with efficiencies similar to those of the wild-type viruses. Thus, the (+169)AAAA(+172) A-rich loop plays a key role in the synthesis of viral DNA.

Controlling elements in replication of the human immunodeficiency virus type 1

We have reviewed the genetic structure of HIV-1 from the perspective of understanding viral and cellular regulatory factors that affect viral replication. Comparisons are drawn, as appropriate, with other human retroviruses, such as HIV-2, in regard to our understanding of pathogenesis. The synthesis of viral protein and the manner in which viral assembly takes place is also discussed.

Endogenous reverse transcription assays reveal high-level resistance to the triphosphate of (-)2'-dideoxy-3'-thiacytidine by mutated M184V human immunodeficiency virus type 1

Kinetic analysis showed that the Ki values and the Ki/Km ratios for mutated, recombinant M184V human immunodeficiency virus type 1 reverse transcriptase (RT) for (-)2'-dideoxy-3'-thiacytidine triphosphate (3TCTP) were 35-fold higher than the equivalent values for wild-type RT but only about twice as high as the equivalent values for each of the triphosphates of ddC (ddCTP) and ddA (ddATP). Fully endogenous RT assays showed that viruses containing the M184V substitution were highly resistant to 3TCTP, with an increase in the 50% inhibitory concentration of 250-fold in comparison with wild-type recombinant virus.

Human immunodeficiency virus Type 1 nucleocapsid protein (NCp7) directs specific initiation of minus-strand DNA synthesis primed by human tRNA(Lys3) in vitro: studies of viral RNA molecules mutated in regions that flank the primer binding site

Retroviral reverse transcription starts near the 5' end of unspliced viral RNA at a sequence called the primer binding site (PBS), where the tRNA primer anneals to the RNA template for initiation of DNA synthesis. We have investigated the roles of NCp7 in annealing of primer tRNA(Lys3) to the PBS and in reverse transcriptase (RT) activity, using a cell-free reverse transcription reaction mixture consisting of various 5' viral RNA templates, natural primer tRNA(Lys3) or synthetic primer, human immunodeficiency virus type I (HIV-1) nucleocapsid protein (NCp7), and HIV-1 RT. In the presence of tRNA(Lys3), NCp7 was found to stimulate synthesis of minus-strand strong-stop DNA [(-)ssDNA], consistent with previous reports. However, specific DNA synthesis was observed only at a NCp7/RNA ratio similar to that predicted to be present in virions. Moreover, at these concentrations, NCp7 inhibited the synthesis of nonspecific reverse-transcribed DNA products, which are initiated because of self-priming by RNA templates. In contrast to results obtained with tRNA(Lys3) as primer, NCp7 inhibited the synthesis of (-)ssDNA products primed by an 18-nucleotide (nt) ribonucleotide (rPR), complementary to the PBS, even though rPR can initiate synthesis of such material in the absence of preannealing with NCp7. Primer placement band shift assays showed that NCp7 was necessary for efficient formation of the tRNA-RNA complex. In contrast, NCp7 was found to prevent formation of the rPR-RNA complex. Since NCp7 appears to exert opposite effects (annealing versus dissociation) on tRNA(Lys3) and rPR substrates, the non-PBS binding regions of the tRNA(Lys3) molecule may play a role in the annealing of tRNA to the template. We also investigated the roles of an A-rich loop upstream of the PBS, a 7-nt region immediately downstream of the PBS, and a 54-nt deletion further downstream of the PBS in interactions with tRNA(Lys3). We found that deletions in the 54-nt region that may prevent formation of the U5-leader stem prevented tRNA(Lys3) placement and priming, while deletions in the A-rich loop or the 7-nt sequence had relatively minor effects in this regard.

Studies of neutralizing monoclonal antibody to human immunodeficiency virus type 1 reverse transcriptase: antagonistic and synergistic effects in reactions performed in the presence of nucleoside and nonnucleoside inhibitors, respectively

We have assessed interactions between the reverse transcriptase (RT) of human immunodeficiency virus type 1 (HIV-1) and a neutralizing monoclonal antibody (1E8) that hinders binding of deoxynucleoside triphosphate (dNTP) substrates. Steady-state reactions with homopolymeric template-primers revealed that 1E8 antagonized inhibition of RT activity mediated by 3'-azido-3'-deoxythymidine triphosphate and 2',3'-dideoxycytidine triphosphate. However, an additive or synergistic inhibition of RT polymerase activity was noted when 1E8 and the nonnucleoside RT inhibitors nevirapine and delavirdine were studied. Chain elongation and dNTP incorporation studies using an HIV-1 genome-derived heteropolymeric template and either oligodeoxynucleotide or tRNA3(Lys) as the primer yielded results consistent with the above observations. 1E8 also increased pausing at certain sites during synthesis of negative-strand, strong-stop DNA, whether or not ddNTP and nonnucleoside RT inhibitors were present.