A case of septic arthritis of the hip in Central Plains, China, during the Western Han Dynasty (3rd century BCE-1st century CE)

OBJECTIVE

Septic arthritis is not commonly reported in paleopathology. This study aims to provide a differential diagnosis of septic arthritis by looking at a case from ancient China. We also aim to add to the current literature on septic arthritis in paleopathology.

MATERIALS

One adult male skeleton recovered from the Dapuzi Cemetery, Shaanxi, dating to the Western Han Dynasty (3rd century BCE-1st century CE).

METHODS

Macroscopic observations were conducted.

RESULTS

The lytic appearance and massive new bone formation on the left acetabulum of M142 are compatible with septic arthritis. The hip pathology greatly influenced his stature. The two femur shafts present different degrees of robusticity. He also showed severe osteoarthritis.

CONCLUSIONS

The individual suffered from septic arthritis of the hip, of unknown cause, for a long period, which greatly influenced his daily life. Complications included osteoarthritis, shortened stature, and difficulties in walking.

SIGNIFICANCE

This study offers a new case of septic arthritis and provides insight into the people who guarded the royal tombs in the West Han Dynasty.

LIMITATIONS

The skeleton is not well-preserved, limiting observations of bony changes to other areas of the body.

Genetic admixture history and forensic characteristics of Tibeto-Burman-speaking Qiang people explored via the newly developed Y-STR panel and genome-wide SNP data

Fine-scale patterns of population genetic structure and diversity of ethnolinguistically diverse populations are important for biogeographical ancestry inference, kinship testing, and development and validation of new kits focused on forensic personal identification. Analyses focused on forensic markers and genome-wide single nucleotide polymorphism (SNP) data can provide new insights into the origin, admixture processes, and forensic characteristics of targeted populations. Qiang people had a large sample size among Tibeto-Burmanspeaking populations, which widely resided in the middle latitude of the Tibetan Plateau. However, their genetic structure and forensic features have remained uncharacterized because of the paucity of comprehensive genetic analyses. Here, we first developed and validated the forensic performance of the AGCU-Y30 Y-short tandem repeats (STR) panel, which contains slowly and moderately mutating Y-STRs, and then we conducted comprehensive population genetic analyses based on Y-STRs and genome-wide SNPs to explore the admixture history of Qiang people and their neighbors. The validated results of this panel showed that the new Y-STR kit was sensitive and robust enough for forensic applications. Haplotype diversity (HD) ranging from 0.9932 to 0.9996 and allelic frequencies ranging from 0.001946 to 0.8326 in 514 Qiang people demonstrated that all included markers were highly polymorphic in Tibeto-Burman people. Population genetic analyses based on Y-STRs [RST, FST, multidimensional scaling (MDS) analysis, neighboring-joining (NJ) tree, principal component analysis (PCA), and median-joining network (MJN)] revealed that the Qiang people harbored a paternally close relationship with lowland Tibetan-Yi corridor populations. Furthermore, we conducted a comprehensive population admixture analysis among modern and ancient Eurasian populations based on genome-wide shared SNPs. We found that the Qiang people were a genetically admixed population and showed closest relationship with Tibetan and Neolithic Yellow River farmers. Admixture modeling showed that Qiang people shared the primary ancestry related to Tibetan, supporting the hypothesis of common origin between Tibetan and Qiang people from North China.

Genomic Insights Into the Population History and Biological Adaptation of Southwestern Chinese Hmong-Mien People

Hmong-Mien (HM) -speaking populations, widely distributed in South China, the north of Thailand, Laos, and Vietnam, have experienced different settlement environments, dietary habits, and pathogenic exposure. However, their specific biological adaptation remained largely uncharacterized, which is important in the population evolutionary genetics and Trans-Omics for regional Precision Medicine. Besides, the origin and genetic diversity of HM people and their phylogenetic relationship with surrounding modern and ancient populations are also unknown. Here, we reported genome-wide SNPs in 52 representative Miao people and combined them with 144 HM people from 13 geographically representative populations to characterize the full genetic admixture and adaptive landscape of HM speakers. We found that obvious genetic substructures existed in geographically different HM populations; one localized in the HM clines, and others possessed affinity with Han Chinese. We also identified one new ancestral lineage specifically existed in HM people, which spatially distributed from Sichuan and Guizhou in the north to Thailand in the south. The sharing patterns of the newly identified homogenous ancestry component combined the estimated admixture times via the decay of linkage disequilibrium and haplotype sharing in GLOBETROTTER suggested that the modern HM-speaking populations originated from Southwest China and migrated southward in the historic period, which is consistent with the reconstructed phenomena of linguistic and archeological documents. Additionally, we identified specific adaptive signatures associated with several important human nervous system biological functions. Our pilot work emphasized the importance of anthropologically informed sampling and deeply genetic structure reconstruction via whole-genome sequencing in the next step in the deep Chinese Population Genomic Diversity Project (CPGDP), especially in the regions with rich ethnolinguistic diversity.

Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs

Sherpa people, one of the high-altitude hypoxic adaptive populations, mainly reside in Nepal and the southern Tibet Autonomous Region. The genetic origin and detailed evolutionary profiles of Sherpas remain to be further explored and comprehensively characterized. Here we analyzed the newly-generated InDel genotype data from 628 Dingjie Sherpas by merging with 4222 worldwide InDel profiles and collected genome-wide SNP data (approximately 600K SNPs) from 1612 individuals in 191 modern and ancient populations to explore and reconstruct the fine-scale genetic structure of Sherpas and their relationships with nearby modern and ancient East Asians based on the shared alleles and haplotypes. The forensic parameters of 57 autosomal InDels (A-InDels) included in our used new-generation InDel amplification system showed that this focused InDel panel is informative and polymorphic in Dingjie Sherpas, suggesting that it can be used as the supplementary tool for forensic personal identification and parentage testing in Dingjie Sherpas. Descriptive findings from the PCA, ADMIXTURE, and TreeMix-based phylogenies suggested that studied Nepal Sherpas showed excess allele sharing with neighboring Tibeto-Burman Tibetans. Furthermore, patterns of allele sharing in f-statistics demonstrated that Nepal Sherpas had a different evolutionary history compared with their neighbors from Nepal (Newar and Gurung) but showed genetic similarity with 2700-year-old Chokhopani and modern Tibet Tibetans. QpAdm/qpGraph-based admixture sources and models further showed that Sherpas, core Tibetans, and Chokhopani formed one clade, which could be fitted as having the main ancestry from late Neolithic Qijia millet farmers and other deep ancestries from early Asians. Chromosome painting profiles and shared IBD fragments inferred from fineSTRUCTURE and ChromoPainter not only confirmed the abovementioned genomic affinity patterns but also revealed the fine-scale genetic microstructures among Sino-Tibetan speakers. Finally, natural-selection signals revealed via iHS, nSL and iHH12 showed natural selection signatures associated with disease susceptibility in Sherpas. Generally, we provided the comprehensive landscape of admixture and evolutionary history of Sherpa people based on the shared alleles and haplotypes from the InDel-based genotype data and high-density genome-wide SNP data. The more detailed genetic landscape of Sherpa people should be further confirmed and characterized via ancient genomes or single-molecule real-time sequencing technology.

Improved Prediction Model of Protein Lysine Crotonylation Sites Using Bidirectional Recurrent Neural Networks

Histone lysine crotonylation (Kcr) is a post-translational modification of histone proteins that is involved in the regulation of gene transcription, acute and chronic kidney injury, spermatogenesis, depression, cancer, and so forth. The identification of Kcr sites in proteins is important for characterizing and regulating primary biological mechanisms. The use of computational approaches such as machine learning and deep learning algorithms have emerged in recent years as the traditional wet-lab experiments are time-consuming and costly. We propose as part of this study a deep learning model based on a recurrent neural network (RNN) termed as Sohoko-Kcr for the prediction of Kcr sites. Through the embedded encoding of the peptide sequences, we investigate the efficiency of RNN-based models such as long short-term memory (LSTM), bidirectional LSTM (BiLSTM), and bidirectional gated recurrent unit (BiGRU) networks using cross-validation and independent tests. We also established the comparison between Sohoko-Kcr and other published tools to verify the efficiency of our model based on 3-fold, 5-fold, and 10-fold cross-validations using independent set tests. The results then show that the BiGRU model has consistently displayed outstanding performance and computational efficiency. Based on the proposed model, a webserver called Sohoko-Kcr was deployed for free use and is accessible at https://sohoko-research-9uu23.ondigitalocean.app.

Fine-Scale Genetic Structure and Natural Selection Signatures of Southwestern Hans Inferred From Patterns of Genome-Wide Allele, Haplotype, and Haplogroup Lineages

The evolutionary and admixture history of Han Chinese have been widely discussed via traditional autosomal and uniparental genetic markers [e.g., short tandem repeats, low-density single nucleotide polymorphisms). However, their fine-scale genetic landscapes (admixture scenarios and natural selection signatures) based on the high-density allele/haplotype sharing patterns have not been deeply characterized. Here, we collected and generated genome-wide data of 50 Han Chinese individuals from four populations in Guizhou Province, one of the most ethnolinguistically diverse regions, and merged it with over 3,000 publicly available modern and ancient Eurasians to describe the genetic origin and population admixture history of Guizhou Hans and their neighbors. PCA and ADMIXTURE results showed that the studied four populations were homogeneous and grouped closely to central East Asians. Genetic homogeneity within Guizhou populations was further confirmed via the observed strong genetic affinity with inland Hmong-Mien people through the observed genetic clade in Fst and outgroup f₃/f₄-statistics. qpGraph-based phylogenies and f₄-based demographic models illuminated that Guizhou Hans were well fitted via the admixture of ancient Yellow River Millet farmers related to Lajia people and southern Yangtze River farmers related to Hanben people. Further ChromoPainter-based chromosome painting profiles and GLOBETROTTER-based admixture signatures confirmed the two best source matches for southwestern Hans, respectively, from northern Shaanxi Hans and southern indigenes with variable mixture proportions in the historical period. Further three-way admixture models revealed larger genetic contributions from coastal southern East Asians into Guizhou Hans compared with the proposed inland ancient source from mainland Southeast Asia. We also identified candidate loci (e.g., MTUS2, NOTCH4, EDAR, ADH1B, and ABCG2) with strong natural selection signatures in Guizhou Hans via iHS, nSL, and ihh, which were associated with the susceptibility of the multiple complex diseases, morphology formation, alcohol and lipid metabolism. Generally, we provided a case and ideal strategy to reconstruct the detailed demographic evolutionary history of Guizhou Hans, which provided new insights into the fine-scale genomic formation of one ethnolinguistically specific targeted population from the comprehensive perspectives of the shared unlinked alleles, linked haplotypes, and paternal and maternal lineages.

Peopling History of the Tibetan Plateau and Multiple Waves of Admixture of Tibetans Inferred From Both Ancient and Modern Genome-Wide Data

Archeologically attested human occupation on the Tibetan Plateau (TP) can be traced back to 160 thousand years ago (kya) via the archaic Xiahe people and 30∼40 kya via the Nwya Devu anatomically modern human. However, the history of the Tibetan populations and their migration inferred from the ancient and modern DNA remains unclear. Here, we performed the first ancient and modern genomic meta-analysis among 3,017 Paleolithic to present-day Eastern Eurasian genomes (2,444 modern individuals from 183 populations and 573 ancient individuals). We identified a close genetic connection between the ancient-modern highland Tibetans and lowland island/coastal Neolithic Northern East Asians (NEA). This observed genetic affinity reflected the primary ancestry of high-altitude Tibeto-Burman speakers originated from the Neolithic farming populations in the Yellow River Basin. The identified pattern was consistent with the proposed common north-China origin hypothesis of the Sino-Tibetan languages and dispersal patterns of the northern millet farmers. We also observed the genetic differentiation between the highlanders and lowland NEAs. The former harbored more deeply diverged Hoabinhian/Onge-related ancestry and the latter possessed more Neolithic southern East Asian (SEA) or Siberian-related ancestry. Our reconstructed qpAdm and qpGraph models suggested the co-existence of Paleolithic and Neolithic ancestries in the Neolithic to modern East Asian highlanders. Additionally, we found that Tibetans from Ü-Tsang/Ando/Kham regions showed a strong population stratification consistent with their cultural background and geographic terrain. Ü-Tsang Tibetans possessed a stronger Chokhopani-affinity, Ando Tibetans had more Western Eurasian related ancestry and Kham Tibetans harbored greater Neolithic southern EA ancestry. Generally, ancient and modern genomes documented multiple waves of human migrations in the TP's past. The first layer of local hunter-gatherers mixed with incoming millet farmers and arose the Chokhopani-associated Proto-Tibetan-Burman highlanders, which further respectively mixed with additional genetic contributors from the western Eurasian Steppe, Yellow River and Yangtze River and finally gave rise to the modern Ando, Ü-Tsang and Kham Tibetans.

Genomic insights into the formation of human populations in East Asia

The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people1,2. Here we report genome-wide data from 166 East Asian individuals dating to between 6000 BC and AD 1000 and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan Plateau are linked by a deeply splitting lineage that probably reflects a coastal migration during the Late Pleistocene epoch. We also follow expansions during the subsequent Holocene epoch from four regions. First, hunter-gatherers from Mongolia and the Amur River Basin have ancestry shared by individuals who speak Mongolic and Tungusic languages, but do not carry ancestry characteristic of farmers from the West Liao River region (around 3000 BC), which contradicts theories that the expansion of these farmers spread the Mongolic and Tungusic proto-languages. Second, farmers from the Yellow River Basin (around 3000 BC) probably spread Sino-Tibetan languages, as their ancestry dispersed both to Tibet-where it forms approximately 84% of the gene pool in some groups-and to the Central Plain, where it has contributed around 59-84% to modern Han Chinese groups. Third, people from Taiwan from around 1300 BC to AD 800 derived approximately 75% of their ancestry from a lineage that is widespread in modern individuals who speak Austronesian, Tai-Kadai and Austroasiatic languages, and that we hypothesize derives from farmers of the Yangtze River Valley. Ancient people from Taiwan also derived about 25% of their ancestry from a northern lineage that is related to, but different from, farmers of the Yellow River Basin, which suggests an additional north-to-south expansion. Fourth, ancestry from Yamnaya Steppe pastoralists arrived in western Mongolia after around 3000 BC but was displaced by previously established lineages even while it persisted in western China, as would be expected if this ancestry was associated with the spread of proto-Tocharian Indo-European languages. Two later gene flows affected western Mongolia: migrants after around 2000 BC with Yamnaya and European farmer ancestry, and episodic influences of later groups with ancestry from Turan.

New insights into the fine-scale history of western-eastern admixture of the northwestern Chinese population in the Hexi Corridor via genome-wide genetic legacy

Trans-Eurasian cultural and genetic exchanges have significantly influenced the demographic dynamics of Eurasian populations. The Hexi Corridor, located along the southeastern edge of the Eurasian steppe, served as an important passage of the ancient Silk Road in Northwest China and intensified the transcontinental exchange and interaction between populations on the Central Plain and in Western Eurasia. Historical and archeological records indicate that the Western Eurasian cultural elements were largely brought into North China via this geographical corridor, but there is debate on the extent to which the spread of barley/wheat agriculture into North China and subsequent Bronze Age cultural and technological mixture/shifts were achieved by the movement of people or dissemination of ideas. Here, we presented higher-resolution genome-wide autosomal and uniparental Y/mtDNA SNP or STR data for 599 northwestern Han Chinese individuals and conducted 2 different comprehensive genetic studies among Neolithic-to-present-day Eurasians. Genetic studies based on lower-resolution STR markers via PCA, STRUCTURE, and phylogenetic trees showed that northwestern Han Chinese individuals had increased genetic homogeneity relative to northern Mongolic/Turkic/Tungusic speakers and Tibeto-Burman groups. The genomic signature constructed based on modern/ancient DNA further illustrated that the primary ancestry of the northwestern Han was derived from northern millet farmer ancestors, which was consistent with the hypothesis of Han origin in North China and more recent northwestward population expansion. This was subsequently confirmed via excess shared derived alleles in f₃/f₄ statistical analyses and by more northern East Asian-related ancestry in the qpAdm/qpGraph models. Interestingly, we identified one western Eurasian admixture signature that was present in northwestern Han but absent from southern Han, with an admixture time dated to approximately 1000 CE (Tang and Song dynasties). Generally, we provided supporting evidence that historic Trans-Eurasian communication was primarily maintained through population movement, not simply cultural diffusion. The observed population dynamics in northwestern Han Chinese not only support the North China origin hypothesis but also reflect the multiple sources of the genetic diversity observed in this population.

A probable case of multiple myeloma from Bronze Age China

OBJECTIVE

Paleopathological evidence of cancer from past populations is rare, especially outside of Europe and North Africa. This study expands upon the current temporal and spatial distribution of cancer by presenting a probable case of multiple myeloma from Bronze Age China.

MATERIAL

The human skeletal remains of an adult male from the Qijia culture horizon (1750-1400 BCE) of the Bronze Age cemetery of Mogou (), located in Gansu Province, Northwest China.

METHODS

The human skeletal remains were assessed macroscopically and radiographically using plain x-rays.

RESULTS

Multiple ovoid-shaped osteolytic lesions with sharply demarcated margins were observed. The axial skeletal had the greatest involvement, specifically the vertebrae, ribs, and sternum. Radiographic imaging revealed more extensive destruction of cancellous than cortical bone, indicating that the marrow was the focal point of the disease.

CONCLUSION

Based on the nature, distribution, and radiographic appearance of the lesions, the most likely diagnosis is multiple myeloma.

SIGNIFICANCE

This is one of the only cases of cancer identified in archaeological human skeletal remains from East Asia and is the first published case of a hematopoietic malignancy from mainland China. The analysis and publication of examples of neoplasia from areas that expand upon the current known temporal and spatial distribution is necessary in order to better reconstruct the history and evolution of cancer.

LIMITATIONS

Poor skeletal preservation prevented the full extent of osteolytic lesions to be observed.

SUGGESTIONS FOR FUTURE RESEARCH

By placing case studies such as this into a temporal and spatial framework, it is possible for future research to begin to interrogate possible underlying causes of cancer in ancient populations within the context of changing environmental conditions and subsistence strategies.

Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities

Ancient latrine sediments, which contain the concentrated collective biological waste of past whole human communities, have the potential to be excellent proxies for human gastrointestinal health on the population level. A rich body of literature explores their use to detect the presence of gut-associated eukaryotic parasites through microscopy, immunoassays and genetics. Despite this interest, a lack of studies have explored the whole genetic content of ancient latrine sediments through consideration not only of gut-associated parasites, but also of core community gut microbiome signals that remain from the group that used the latrine. Here, we present a metagenomic analysis of bulk sediment from medieval latrines in Riga (Latvia) and Jerusalem. Our analyses reveal survival of microbial DNA representative of intestinal flora as well as numerous parasites. These data are compared against parasite taxon identifications obtained via microscopy and ELISA techniques. Together, these findings provide a first glimpse into the rich prokaryotic and eukaryotic intestinal flora of pre-industrial agricultural populations, which may give a better context for interpreting the health of modern microbiomes.

This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

XGBoost Improves Classification of MGMT Promoter Methylation Status in IDH1 Wildtype Glioblastoma

Approximately 96% of patients with glioblastomas (GBM) have IDH1 wildtype GBMs, characterized by extremely poor prognosis, partly due to resistance to standard temozolomide treatment. O6-Methylguanine-DNA methyltransferase (MGMT) promoter methylation status is a crucial prognostic biomarker for alkylating chemotherapy resistance in patients with GBM. However, MGMT methylation status identification methods, where the tumor tissue is often undersampled, are time consuming and expensive. Currently, presurgical noninvasive imaging methods are used to identify biomarkers to predict MGMT methylation status. We evaluated a novel radiomics-based eXtreme Gradient Boosting (XGBoost) model to identify MGMT promoter methylation status in patients with IDH1 wildtype GBM. This retrospective study enrolled 53 patients with pathologically proven GBM and tested MGMT methylation and IDH1 status. Radiomics features were extracted from multimodality MRI and tested by F-score analysis to identify important features to improve our model. We identified nine radiomics features that reached an area under the curve of 0.896, which outperformed other classifiers reported previously. These features could be important biomarkers for identifying MGMT methylation status in IDH1 wildtype GBM. The combination of radiomics feature extraction and F-core feature selection significantly improved the performance of the XGBoost model, which may have implications for patient stratification and therapeutic strategy in GBM.

Investigation into the origins of an ancient BRCA1 founder mutation identified among Chinese families in Singapore

Identification of ancestry-specific pathogenic variants is imperative for diagnostic, treatment, management and prevention strategies, and to understand penetrance/modifiers on risk. Our study aimed to determine the clinical significance of a recurrent BRCA1 c.442-22_442-13del variant of unknown significance identified among 13 carriers from six Chinese families, all with a significant history of breast and/or ovarian cancer. We further aimed to establish whether this was due to a founder effect and explore its origins. Haplotype analysis, using nine microsatellite markers encompassing 2.5 megabase pairs around the BRCA1 locus, identified a common haploblock specific to the variant carriers, confirming a founder effect. Variant age was estimated to date back 77.9 generations to 69 bc using the Gamma approach. On principal component analysis using single nucleotide polymorphisms merged with 1000 Genomes dataset, variant carriers were observed to overlap predominantly with the southern Han Chinese population. To determine pathogenicity of the variant, we assessed the functional effect on RAD51 foci formation as well as replication fork stability upon induction of DNA damage and observed an impaired DNA repair response associated with the variant. In summary, we identified an ancient Chinese founder mutation dating back 77.9 generations, possibly common among individuals of southern Han Chinese descent. Using evidence from phenotypic/family history studies, segregation analysis and functional characterization, the BRCA1 variant was reclassified from uncertain significance to pathogenic.

Discovery of Eurytrema Eggs in Sediment from a Colonial Period Latrine in Taiwan

In this study we take a closer look at the diseases that afflicted Japanese police officers who were stationed in a remote mountainous region of Taiwan from 1921 to 1944. Samples were taken from the latrine at the Huabanuo police outpost, and analyzed for the eggs of intestinal parasites, using microscopy and ELISA. The eggs of Eurytrema sp., (possibly E. pancreaticum), whipworm and roundworm were shown to be present. True infection with Eurytrema would indicate that the policemen ate uncooked grasshoppers and crickets infected with the parasite. However, false parasitism might also occur if the policemen ate the uncooked intestines of infected cattle, and the Eurytrema eggs passed through the human intestines. These findings provide an insight into the diet and health of the Japanese colonists in Taiwan nearly a century ago.

Differential Change in the Prevalence of the Ascaris, Trichuris and Clonorchis infection Among Past East Asian Populations

As we learn more about parasites in ancient civilizations, data becomes available that can be used to see how infection may change over time. The aim of this study is to assess how common certain intestinal parasites were in China and Korea in the past 2000 years, and make comparisons with prevalence data from the 20th century. This allows us to go on to investigate how and why changes in parasite prevalence may have occurred at different times. Here we show that Chinese liver fluke (Clonorchis sinensis) dropped markedly in prevalence in both Korea and China earlier than did roundworm (Ascaris lumbricoides) and whipworm (Trichuris trichiura). We use historical evidence to determine why this was the case, exploring the role of developing sanitation infrastructure, changing use of human feces as crop fertilizer, development of chemical fertilizers, snail control programs, changing dietary preferences, and governmental public health campaigns during the 20th century.

Skeletal evidence for violent trauma from the bronze age Qijia culture (2,300-1,500 BCE), Gansu Province, China

This research explores how social and environmental factors may have contributed to conflict during the early Bronze Age in Northwest China by analyzing violent trauma on human skeletal remains from a cemetery of the Qijia culture (2300-1500 BCE). The Qijia culture existed during a period of dramatic social, technological, and environmental change, though minimal research has been conducted on how these factors may have contributed to violence within the area of the Qijia and other contemporaneous material cultures. An osteological assessment was conducted on 361 individuals (n = 241 adults, n = 120 non-adults) that were excavated from the Mogou site, Lintan County, Gansu, China. Injuries indicative of violence, including sharp- and blunt-force trauma that was sustained ante- or peri-mortem, were identified, and the patterns of trauma were analysed. Violent injuries were found on 8.58% (n = 31/361) of individuals, primarily adult males. No evidence of trauma was found on infants or children. Cranial trauma was found on 11.8% (n = 23/195) of the adult individuals examined. Of these, 43.5% (n = 10/23) presented with severe peri-mortem craniofacial trauma. The high rate of perimortem injuries and their locations indicate lethal intent. This lethality, in addition to the fact that individuals with trauma were predominantly male, suggest intergroup violence such as raiding, warfare, or feuding. Both social and environmental factors may have contributed to this conflict in the TaoRiver Valley, though future systematic archaeological and paleoenvironmental data will be needed to disentangle the many potential causal factors.

Classifying Promoters by Interpreting the Hidden Information of DNA Sequences via Deep Learning and Combination of Continuous FastText N-Grams

A promoter is a short region of DNA (100-1,000 bp) where transcription of a gene by RNA polymerase begins. It is typically located directly upstream or at the 5' end of the transcription initiation site. DNA promoter has been proven to be the primary cause of many human diseases, especially diabetes, cancer, or Huntington's disease. Therefore, classifying promoters has become an interesting problem and it has attracted the attention of a lot of researchers in the bioinformatics field. There were a variety of studies conducted to resolve this problem, however, their performance results still require further improvement. In this study, we will present an innovative approach by interpreting DNA sequences as a combination of continuous FastText N-grams, which are then fed into a deep neural network in order to classify them. Our approach is able to attain a cross-validation accuracy of 85.41 and 73.1% in the two layers, respectively. Our results outperformed the state-of-the-art methods on the same dataset, especially in the second layer (strength classification). Throughout this study, promoter regions could be identified with high accuracy and it provides analysis for further biological research as well as precision medicine. In addition, this study opens new paths for the natural language processing application in omics data in general and DNA sequences in particular.

Computational identification of vesicular transport proteins from sequences using deep gated recurrent units architecture

Protein function prediction is one of the most well-studied topics, attracting attention from countless researchers in the field of computational biology. Implementing deep neural networks that help improve the prediction of protein function, however, is still a major challenge. In this research, we suggested a new strategy that includes gated recurrent units and position-specific scoring matrix profiles to predict vesicular transportation proteins, a biological function of great importance. Although it is difficult to discover its function, our model is able to achieve accuracies of 82.3% and 85.8% in the cross-validation and independent dataset, respectively. We also solve the problem of imbalance in the dataset via tuning class weight in the deep learning model. The results generated showed sensitivity, specificity, MCC, and AUC to have values of 79.2%, 82.9%, 0.52, and 0.861, respectively. Our strategy shows superiority in results on the same dataset against all other state-of-the-art algorithms. In our suggested research, we have suggested a technique for the discovery of more proteins, particularly proteins connected with vesicular transport. In addition, our accomplishment could encourage the use of gated recurrent units architecture in protein function prediction.

Divided zygoma in Holocene human populations from Northern China

Objectives

Divided zygoma (DZ) occurs in contemporaneous human populations, with the highest incidences in people from East Asia and Southern Africa. The present study examines the prevalence and variation of this condition in the Holocene populations of Northern China for the first time.

Methods

In this study, 1145 skulls from various human populations living in Northern China from the Neolithic Age to recent dynasties (5000‐300 years BP) were examined. Specifically, cranial measurements and a CT scan were conducted to quantify craniofacial morphology.

Results

Fifteen skulls were identified with DZ, revealing an overall prevalence of 1.3% in the collection, while it was determined to be higher in North Asian and Northeast Asian regional groups. In skulls with unilateral DZ, the superior division of the zygoma was generally slender, while the inferior division of the zygoma was more robust. In skulls with bilateral DZ, the maxillae were generally more laterally extended. Moreover, unilateral DZ skulls displayed differences in cortical bone thickness between two sides of the facial skeleton.

Discussion

In context, the distribution pattern within these data points toward a greater prevalence of the DZ phenotype in North and Northeast Asian regional groups, suggesting a hypothesis that the DZ trait is more frequent in populations characterized by flat and broad faces. Accordingly, further studies into the DZ condition will deepen our understanding of developments in plasticity, variation, and recent evolution of the human cranium.

Identification of clathrin proteins by incorporating hyperparameter optimization in deep learning and PSSM profiles

BACKGROUND AND OBJECTIVES

Clathrin is an adaptor protein that serves as the principal element of the vesicle-coating complex and is important for the membrane cleavage to dispense the invaginated vesicle from the plasma membrane. The functional loss of clathrins has been tied to a lot of human diseases, i.e., neurodegenerative disorders, cancer, Alzheimer's diseases, and so on. Therefore, creating a precise model to identify its functions is a crucial step towards understanding human diseases and designing drug targets.

METHODS

We present a deep learning model using a two-dimensional convolutional neural network (CNN) and position-specific scoring matrix (PSSM) profiles to identify clathrin proteins from high throughput sequences. Traditionally, the 2D CNNs take images as an input so we treated the PSSM profile with a 20 × 20 matrix as an image of 20 × 20 pixels. The input PSSM profile was then connected to our 2D CNN in which we set a variety of parameters to improve the performance of the model. Based on the 10-fold cross-validation results, hyper-parameter optimization process was employed to find the best model for our dataset. Finally, an independent dataset was used to assess the predictive ability of the current model.

RESULTS

Our model could identify clathrin proteins with sensitivity of 92.2%, specificity of 91.2%, accuracy of 91.8%, and MCC of 0.83 in the independent dataset. Compared to state-of-the-art traditional neural networks, our method achieved a significant improvement in all typical measurement metrics.

CONCLUSIONS

Throughout the proposed study, we provide an effective tool for investigating clathrin proteins and our achievement could promote the use of deep learning in biomedical research. We also provide source codes and dataset freely at https://www.github.com/khanhlee/deep-clathrin/.

Ensemble of Deep Recurrent Neural Networks for Identifying Enhancers via Dinucleotide Physicochemical Properties

Enhancers are short deoxyribonucleic acid fragments that assume an important part in the genetic process of gene expression. Due to their possibly distant location relative to the gene that is acted upon, the identification of enhancers is difficult. There are many published works focused on identifying enhancers based on their sequence information, however, the resulting performance still requires improvements. Using deep learning methods, this study proposes a model ensemble of classifiers for predicting enhancers based on deep recurrent neural networks. The input features of deep ensemble networks were generated from six types of dinucleotide physicochemical properties, which had outperformed the other features. In summary, our model which used this ensemble approach could identify enhancers with achieved sensitivity of 75.5%, specificity of 76%, accuracy of 75.5%, and MCC of 0.51. For classifying enhancers into strong or weak sequences, our model reached sensitivity of 83.15%, specificity of 45.61%, accuracy of 68.49%, and MCC of 0.312. Compared to the benchmark result, our results had higher performance in term of most measurement metrics. The results showed that deep model ensembles hold the potential for improving on the best results achieved to date using shallow machine learning methods.

ET-GRU: using multi-layer gated recurrent units to identify electron transport proteins

BACKGROUND

Electron transport chain is a series of protein complexes embedded in the process of cellular respiration, which is an important process to transfer electrons and other macromolecules throughout the cell. It is also the major process to extract energy via redox reactions in the case of oxidation of sugars. Many studies have determined that the electron transport protein has been implicated in a variety of human diseases, i.e. diabetes, Parkinson, Alzheimer's disease and so on. Few bioinformatics studies have been conducted to identify the electron transport proteins with high accuracy, however, their performance results require a lot of improvements. Here, we present a novel deep neural network architecture to address this problem.

RESULTS

Most of the previous studies could not use the original position specific scoring matrix (PSSM) profiles to feed into neural networks, leading to a lack of information and the neural networks consequently could not achieve the best results. In this paper, we present a novel approach by using deep gated recurrent units (GRU) on full PSSMs to resolve this problem. Our approach can precisely predict the electron transporters with the cross-validation and independent test accuracy of 93.5 and 92.3%, respectively. Our approach demonstrates superior performance to all of the state-of-the-art predictors on electron transport proteins.

CONCLUSIONS

Through the proposed study, we provide ET-GRU, a web server for discriminating electron transport proteins in particular and other protein functions in general. Also, our achievement could promote the use of GRU in computational biology, especially in protein function prediction.

Intentional cranial modification from the Houtaomuga Site in Jilin, China: Earliest evidence and longest in situ practice during the Neolithic Age

OBJECTIVES

Intentional cranial modification (ICM) was a long-established tradition used to reshape the head. Unfortunately, motivation of the act is unclear. It has been found in recent and contemporary human populations throughout the Old and New Worlds, yet the drawback of the quest into the origin, diffusion, and meanings of ICM is the lack of early materials for scientific examination. This study reports the discovery of ICM from the Neolithic Houtaomuga Site in Northeast China and the importance in deepening our knowledge of this intriguing tradition.

MATERIALS AND METHODS

Twenty-five skeletons unearthed from the Neolithic cultural Phases 1-4 in the Houtaomuga Site were visually screened for ICM features. Cranial measurements were conducted to quantify the degree of variation in the modified skulls and typical ones were computer tomography (CT) scanned to obtain a diploë structure and 3D model.

RESULTS

Eleven skulls carrying signs of ICM from both sexes varying in age from juveniles to full adults were identified ranging from 12,000 BP to 5,000 BP. Three types of modification patterns were observed and most of them were of typical fronto-occipital modification pattern. In particular, there were remarkable variations in the curvature of the crania along the sagittal direction.

DISCUSSION

Overall, the antiquity as well as the cultural and genetic continuity of the population in Houtaomuga Site demonstrated the earliest confirmed ICM cases from the easternmost Old World, and the longest in situ duration of ICM practice at one single Neolithic site. This circumstance largely contributes to our understanding of the origins and distribution of ICM in Eurasia and the American continent.

Prioritization of SNPs in y+LAT-1 culpable of Lysinuric protein intolerance and their mutational impacts using protein-protein docking and molecular dynamics simulation studies

Lysinuric protein intolerance (LPI) is a rare, yet inimical, genetic disorder characterized by the paucity of essential dibasic amino acids in the cells. Amino acid transporter y+LAT-1 interacts with 4F2 cell-surface antigen heavy chain to transport the required dibasic amino acids. Mutation in y+LAT-1 is rumored to cause LPI. However, the underlying pathological mechanism is unknown, and, in this analysis, we investigate the impact of point mutation in y+LAT-1's interaction with 4F2 cell-surface antigen heavy chain in causing LPI. Using an efficient and extensive computational pipeline, we have isolated M50K and L334R single-nucleotide polymorphisms to be the most deleterious mutations in y+LAT-1s. Docking of mutant y+LAT-1 with 4F2 cell-surface antigen heavy chain showed decreased interaction compared with native y+LAT-1. Further, molecular dynamic simulation analysis reveals that the protein molecules increase in size, become more flexible, and alter their secondary structure upon mutation. We believe that these conformational changes because of mutation could be the reason for decreased interaction with 4F2 cell-surface antigen heavy chain causing LPI. Our analysis gives pathological insights about LPI and helps researchers to better understand the disease mechanism and develop an effective treatment strategy.

A comparison of ancient parasites as seen from archeological contexts and early medical texts in China

This paper integrates our knowledge from traditional Chinese medical texts and archeological findings to discuss parasitic loads in early China. Many studies have documented that several different species of eukaryotic endoparasites were present in early human populations throughout China. Nevertheless, comprehensive paleoparasitological records from China are patchy, largely due to taphonomic and environmental factors. An examination of early Chinese medical texts allows us to fill in some of the gaps and counteract apparent biases in the current archeoparasitological records. By integrating the findings of paleoparasitology with historic textual sources, we show that parasites have been affecting the lives of humans in China since ancient times. We discuss the presence and prevalence of three groups of parasites in ancient China: roundworm (Ascaris lumbricoides), Asian schistosoma (Schistosoma japonicum), and tapeworm (Taenia sp.). We also examine possible factors that favored the spread of these endoparasites among early humans. Therefore, this paper not only aims to reveal how humans have been affected by endoparasites, but also addresses how early medical knowledge developed to cope with the parasitic diseases.

In silico screening of sugar alcohol compounds to inhibit viral matrix protein VP40 of Ebola virus

Ebola virus is a virulent pathogen that causes highly lethal hemorrhagic fever in human and non-human species. The rapid growth of this virus infection has made the scenario increasingly complicated to control the disease. Receptor viral matrix protein (VP40) is highly responsible for the replication and budding of progeny virus. The binding of RNA to VP40 could be the crucial factor for the successful lifecycle of the Ebola virus. In this study, we aimed to identify the potential drug that could inhibit VP40. Sugar alcohols were enrich with antiviral properties used to inhibit VP40. Virtual screening analysis was perform for the 48 sugar alcohol compounds, of which the following three compounds show the best binding affinity: Sorbitol, Mannitol and Galactitol. To understand the perfect binding orientation and the strength of non-bonded interactions, individual molecular docking studies were perform for the best hits. Further molecular dynamics studies were conduct to analyze the efficacy between the protein-ligand complexes and it was identify that Sorbitol obtains the highest efficacy. The best-screened compounds obtained drug-like property and were less toxic, which could be use as a potential lead compound to develop anti-Ebola drugs.

iMotor-CNN: Identifying molecular functions of cytoskeleton motor proteins using 2D convolutional neural network via Chou's 5-step rule

Motor proteins are the driving force behind muscle contraction and are responsible for the active transportation of most proteins and vesicles in the cytoplasm. There are three superfamilies of cytoskeletal motor proteins with various molecular functions and structures: dynein, kinesin, and myosin. The functional loss of a specific motor protein molecular function has linked to a variety of human diseases, e.g., Charcot-Marie-Tooth disease, kidney disease. Therefore, creating a precise model to classify motor proteins is essential for helping biologists understand their molecular functions and design drug targets according to their impact on human diseases. Here we attempt to classify cytoskeleton motor proteins using deep learning, which has been increasingly and widely used to address numerous problems in a variety of fields resulting in state-of-the-art results. Our effective deep convolutional neural network is able to achieve an independent test accuracy of 97.5%, 96.4%, and 96.1% for each superfamily, respectively. Compared to other state-of-the-art methods, our approach showed a significant improvement in performance across a range of evaluation metrics. Through the proposed study, we provide an effective model for classifying motor proteins and a basis for further research that can enhance the performance of protein function classification using deep learning.

iEnhancer-5Step: Identifying enhancers using hidden information of DNA sequences via Chou's 5-step rule and word embedding

An enhancer is a short (50-1500bp) region of DNA that plays an important role in gene expression and the production of RNA and proteins. Genetic variation in enhancers has been linked to many human diseases, such as cancer, disorder or inflammatory bowel disease. Due to the importance of enhancers in genomics, the classification of enhancers has become a popular area of research in computational biology. Despite the few computational tools employed to address this problem, their resulting performance still requires improvements. In this study, we treat enhancers by the word embeddings, including sub-word information of its biological words, which then serve as features to be fed into a support vector machine algorithm to classify them. We present iEnhancer-5Step, a web server containing two-layer classifiers to identify enhancers and their strength. We are able to attain an independent test accuracy of 79% and 63.5% in the two layers, respectively. Compared to current predictors on the same dataset, our proposed method is able to yield superior performance as compared to the other methods. Moreover, this study provides a basis for further research that can enrich the field of applying natural language processing techniques in biological sequences. iEnhancer-5Step is freely accessible via http://biologydeep.com/fastenc/.

Extra-Alveolar Bone Screws for Conservative Correction of Severe Malocclusion Without Extractions or Orthognathic Surgery

PURPOSE OF REVIEW

Evaluate management of challenging malocclusions conservatively (no extractions or orthognathic surgery).

RECENT FINDINGS

Most malocclusions have a predominately environmental etiology. Optimal esthetics and function are restored by aligning the dentition over the apical base of bone at the appropriate vertical dimension of occlusion (VDO). Extra-alveolar (E-A) anchorage is achieved at three intraoral sites: mandibular buccal shelf (MBS), infrazygomatic crest (IZC), and anterior ramus. MBS and IZC bone screws effectively anchor the conservative correction of severe dental and skeletal malocclusions. All bone screw sites are effective for anchoring lever arms to recover impacted teeth. Rather than extracting teeth, E-A anchorage corrects crowding by retracting the posterior segments to increase arch length. Skeletal malocclusion is corrected by aligning teeth over the apical base of bone and restoring the VDO by retracting and posteriorly rotating the dental arches as segments. Challenging dental and skeletal malocclusions can be treated routinely via determinate mechanics anchored with E-A bone screws.

Intestinal parasites from the 2nd-5th century AD latrine in the Roman Baths at Sagalassos (Turkey)

The aim of this research was to determine the species of intestinal parasite present in a Roman Imperial period population in Asia Minor, and to use this information to improve our understanding of health in the eastern Mediterranean region in Roman times. We analyzed five samples from the latrines of the Roman bath complex at Sagalassos, Turkey. Fecal biomarker analysis using 5β-stanols has indicated the feces were of human origin. The eggs of roundworm (Ascaris) were identified in all five samples using microscopy, and the cysts of the protozoan Giardia duodenalis (which causes dysentery) were identified multiple times in one sample using ELISA. The positive G. duodenalis result at Sagalassos is particularly important as it represents the earliest reliable evidence for this parasite in the Old World (i.e. outside the Americas). As both these species of parasite are spread through the contamination of food and water by fecal material, their presence implies that Roman sanitation technologies such as latrines and public baths did not break the cycle of reinfection in this population. We then discuss the evidence for roundworm in the writings of the Roman physician Galen, who came from Pergamon, another town in western Asia Minor.

Ancient Human Parasites in Ethnic Chinese Populations

Whilst archaeological evidence for many aspects of life in ancient China is well studied, there has been much less interest in ancient infectious diseases, such as intestinal parasites in past Chinese populations. Here, we bring together evidence from mummies, ancient latrines, and pelvic soil from burials, dating from the Neolithic Period to the Qing Dynasty, in order to better understand the health of the past inhabitants of China and the diseases endemic in the region. Seven species of intestinal parasite have been identified, namely roundworm, whipworm, Chinese liver fluke, oriental schistosome, pinworm, Taenia sp. tapeworm, and the intestinal fluke Fasciolopsis buski. It was found that in the past, roundworm, whipworm, and Chinese liver fluke appear to have been much more common than the other species. While roundworm and whipworm remained common into the late 20th century, Chinese liver fluke seems to have undergone a marked decline in its prevalence over time. The iconic transport route known as the Silk Road has been shown to have acted as a vector for the transmission of ancient diseases, highlighted by the discovery of Chinese liver fluke in a 2,000 year-old relay station in northwest China, 1,500 km outside its endemic range.

Field trial in commercial broilers with a multivalent in ovo vaccine comprising a mixture of live viral vaccines against Marek's disease, infectious bursal disease, Newcastle disease, and fowl pox

A multivalent in ovo vaccine (MIV) was tested for safety and efficacy in a commercial broiler complex. The MIV comprised five replicating live viruses including serotypes 1, 2, and 3 of Marek's disease virus (MDV), an intermediate infectious bursal disease virus (IBDV) and a recombinant fowl poxvirus (FPV) vector vaccine containing HN and F genes of Newcastle disease virus (NDV). The performance of MIV-vaccinated broilers was compared with that of hatchmates that received turkey herpesvirus (HVT) alone (routinely used in ovo vaccine in the broiler complex). The chickens that hatched from the MIV-injected and HVT-injected eggs were raised under commercial conditions in six barns. Barn 1 housed 17,853 MIV-vaccinated chickens and each of the barns 2-6 housed 18,472-22,798 HVT-vaccinated chickens. The HVT-vaccinated chickens were given infectious bronchitis virus (IBV) and NDV vaccines at hatch and at 2 wk of age. The MIV-vaccinated chickens received IBV vaccine at hatch and IBV + NDV at 2 wk of age. The relative values of hatchability of eggs, livability and weight gain of chickens, and condemnation rates at processing were comparable between the MIV and the HVT groups (P > 0.05). Chickens from the MIV- and the HVT-vaccinated groups were challenged with virulent viruses under laboratory conditions. The resistance of vaccinated chickens against Marek's disease could not be assessed because of high natural resistance of unvaccinated commercial broilers to virulent MDV. The relative resistances of the MIV- and the HVT-vaccinated groups, respectively, against other virulent viruses were as follows: IBDV, 100% for both groups; NDV, 81% vs. 19%; FPV, 86% vs. 0%. The successful use of MIV under field conditions expands the usefulness of the in ovo technology for poultry.

Comparative immunopathogenesis of mild, intermediate, and virulent strains of classic infectious bursal disease virus

Differences in the immunopathogenesis of several strains of infectious bursal disease virus (IBDV) were compared. The strains included a virulent virus (IBDV-IM) and three vaccine viruses that included an intermediate vaccine virus (IBDV-B2) and two mild vaccine viruses (IBDV-Lukert and IBDV-BVM). The most significant differences were found in the systemic effects of these strains. In comparison with other strains, IBDV-IM antigen was detectable for up to 8 days postinfection (PI) in lymphoid tissues that included spleen and cecal tonsils, whereas only a few IBDV-B2- and IBDV-Lukert- and no IBDV-BVM-inoculated birds had detectable IBDV antigen in these tissues. IBDV-IM induced systemic circulating nitrite levels in over 86% of the birds at days 2 and 3 PI. IBDV-IM suppressed most vigorously the splenic mitogenic response on days 3-8 PI. Among the three vaccine strains, IBDV-B2 was the most virulent of the three, inducing a significant suppression of the mitogenic response (P < 0.05) and the most vigorous lesions in the bursa of Fabricius with the highest possible lesion score of 4 at 3 days PI (P < 0.05). IBDV-BVM was the mildest strain, not inducing any detectable lesions in lymphoid tissue at the tested time points. Whereas all IBDV-BVM-inoculated and 67% and 33% of the IBDV-Lukert- and IBDV-B2-inoculated birds, respectively, had detectable IBDV antigen in the bursa at 4 days postchallenge, none of the IBDV-IM-inoculated birds was positive for IBDV by immunohistochemistry. IBDV-IM induced the highest enzyme-linked immunosorbent assay (ELISA) antibody levels detected at days 8-29 PI (P < 0.05) and the best protection against challenge virus replication in comparison with IBDV-B2 and IBDV-Lukert. Only one of five IBDV-BVM-inoculated birds developed anti-IBDV ELISA antibodies at 29 days PI, and none of the birds was protected against IBDV challenge. We speculate that better protection with more virulent strains was due to more systemic antigenic stimulation on the basis of higher replication of IBDV in extrabursal lymphoid tissues. Interestingly, IBDV-IM did not differ from IBDV-B2 and IBDV-Lukert in its ability to induce T cell accumulation in the bursa at 8 days PI and local interferon-gamma induction from days 2 to 5 PI. These results suggested that the local T cell events in the bursa alone may not be indicative of a rapid and protective immune response.

Studies of a novel human thrombomodulin immobilized substrate: surface characterization and anticoagulation activity evaluation

Immobilization of the anticoagulative or antithrombogenic biomolecule has been considered as one of the important methods to improve the blood compatibility of artificial biomaterials. In this study, a novel immobilization reaction scheme was utilized to incorporate the human thrombomodulin, an endothelial cell associated glycoprotein, onto the cover glass surface with an aim to develop an anticoagulative substrate. Trichlorotriazine and amino-terminated silane were employed as the coupling agents, while the polyethylene glycol with a molecular weight of 1500 was used as the spacer in this reaction scheme. Protein C activation assay indicated the immobilized human thrombomodulin still has this coenzymatic activity but is lower, possibly due to the conformation variation by the coupling agents. In vitro platelet adhesion assay has demonstrated the surface with immobilized human thrombomodulin is much less platelet-activating than others. Therefore, the novel reaction scheme proposed here is very promising for future development of an anticoagulative silicon or cover glass substrate (e.g. implantable sensor or biochip) by the immobilization of antithrombogenic protein, such as the human thrombomodulin in this study.

Role of intrabursal T cells in infectious bursal disease virus (IBDV) infection: T cells promote viral clearance but delay follicular recovery

Infectious bursal disease virus (IBDV) induces an acute, highly contagious immunosuppressive disease in young chickens. We examined the role of T cells in IBDV-induced immunopathogenesis and tissue recovery. T cell-intact chickens and birds compromised in their T cell function by a combination of surgical thymectomy and Cyclosporin A treatment (Tx-CsA) were infected with an intermediate vaccine strain of IBDV (Bursine 2, Fort Dodge). Our data revealed that functional T cells were needed to control the IBDV-antigen load in the acute phase of infection at 5 days post infection. The target organ of IBDV, the bursa of Fabricius, of Tx-CsA-birds had a significantly higher antigen load than the one of T cell-intact birds (P < 0.05). Tx-CsA-treatment abrogated the IBDV-induced inflammatory response and significantly (P < 0.05) reduced the incidence of apoptotic bursa cells and the expression of cytokines such as interleukin 2 (IL-2) and interferon-gamma (IFN-gamma) in comparison to T cell-intact birds. T cell-released IL-2 and IFN-gamma may have mediated the induction of inflammation and cell death in T cell-intact birds. The IBDV-induced upregulation of tumor necrosis like-factor (TNF) expression was comparable between T cell-intact and Tx-CsA-birds. Tx-CsA-birds showed a significantly faster resolution of IBDV-induced bursa lesions than T cell-intact birds (P < 0.05). This study suggests that T cells modulate IBDV pathogenesis in two ways: a) they limit viral replication in the bursa in the early phase of the disease at 5 days post infection, and b) intrabursal T cells promote bursal tissue damage and delay tissue recovery possibly through the release of cytokines and cytotoxic effects.

Characteristics of bursal T lymphocytes induced by infectious bursal disease virus

Infectious bursal disease virus (IBDV) is an avian lymphotropic virus that causes immunosuppression. When specific-pathogen-free chickens were exposed to a pathogenic strain of IBDV (IM), the virus rapidly destroyed B cells in the bursa of Fabricius. Extensive viral replication was accompanied by an infiltration of T cells in the bursa. We studied the characteristics of intrabursal T lymphocytes in IBDV-infected chickens and examined whether T cells were involved in virus clearance. Flow cytometric analysis of single-cell suspensions of the bursal tissue revealed that T cells were first detectable at 4 days postinoculation (p.i.). At 7 days p.i., 65% of bursal cells were T cells and 7% were B cells. After virus infection, the numbers of bursal T cells expressing activation markers Ia and CD25 were significantly increased (P<0.03). In addition, IBDV-induced bursal T cells produced elevated levels of interleukin-6-like factor and nitric oxide-inducing factor in vitro. Spleen and bursal cells of IBDV-infected chickens had upregulated gamma interferon gene expression in comparison with virus-free chickens. In IBDV-infected chickens, bursal T cells proliferated in vitro upon stimulation with purified IBDV in a dose-dependent manner (P<0.02), whereas virus-specific T-cell expansion was not detected in the spleen. Cyclosporin A treatment, which reduced the number of circulating T cells and compromised T-cell mitogenesis, increased viral burden in the bursae of IBDV-infected chickens. The results suggest that intrabursal T cells and T-cell-mediated responses may be important in viral clearance and promoting recovery from infection.

Arsanilic acid-Sepharose chromatography of pyruvate kinase from KB cells

In the present study, arsanical-based affinity chromatography for pyruvate kinase (PK) isolation was explored. p-Arsanilic acid (4-aminophenyl arsonic acid), which contains an arsonic acid moiety structurally similar to inorganic pentavalent arsenate, was conjugated to Sepharose 4B via its para-amino group to form an As(V)-Sepharose matrix. The cellular proteins from KB cells bound to arsonic acid moieties were eluted by 50 mM sodium arsenate in Tris-HCl buffer (50 mM, pH 7.6). A single protein band with a molecular mass of 58 kDa was shown on a sodium dodecyl sulfate-polyacrylamide gel. By immunoblotting, amino acid sequencing and enzymatic analysis, the sodium arsenate-eluted 58-kDa protein was demonstrated to be a human PK (type M2). By using this one-step As(V)-Sepharose chromatography, PK from KB cells was purified 35.4-fold with a specific activity of 153.15 U/mg protein in the presence of 6 mM fructose-1,6-biphosphate. Although PK was eluted from an As(V)-Sepharose column with sodium arsenate, PK activity was apparently inhibited by the used eluent system, but not by p-arsanilic acid, indicating a specific interaction of As(V) to PK. In summary, our results indicate that As(V)-Sepharose can serve as a simple and efficient chromatographic support for PK purification from KB cells.

Short-term treatment with interferon-alpha/beta promotes remyelination, whereas long-term treatment aggravates demyelination in a murine model of multiple sclerosis

The mechanisms by which type I interferons (IFN) reduce the rate and severity of exacerbations in multiple sclerosis are unknown. We utilized a model of multiple sclerosis to determine the extent of demyelination and remyelination in Theiler's murine encephalomyelitis virus (TMEV)-infected SJL/J mice treated with mouse IFN-alpha/beta for a short (5 weeks) or a long (16 weeks) period. All mice were chronically infected with TMEV to simulate the clinical situation in multiple sclerosis. Short-term IFN-alpha/beta treatment increased the percent of remyelinated spinal cord white matter by threefold when compared with phosphate-buffered saline (PBS) treatment (P < 0.02), but it did not affect the extent of demyelination. In contrast, long-term IFN-alpha/beta treatment increased the extent of demyelination by twofold (P < 0.03). Long-term treatment increased the absolute area of remyelination, but the percent remyelination as a function of area of demyelination was not changed because of increased demyelination. An immunomodulatory mechanism may have contributed to the effect of IFN-alpha/beta on white matter pathology because treated mice had higher anti-TMEV IgGs in serum and demonstrated decreased numbers of B and T lymphocytes infiltrating the central nervous system (CNS). There was no correlation between the level of anti- IFN-alpha/beta antibodies and the extent of demyelination or remyelination. These results indicate that the length of type I IFN treatment may have paradoxical effects on demyelination and remyelination.

Infectious bursal disease virus of chickens: pathogenesis and immunosuppression

Infectious bursal disease virus (IBDV) is an important immunosuppressive virus of chickens. The virus is ubiquitous and, under natural conditions, chickens acquire infection by the oral route. IgM+ cells serve as targets for the virus. The most extensive virus replication takes place in the bursa of Fabricius. The acute phase of the disease lasts for about 7-10 days. Within this phase, bursal follicles are depleted of B cells and the bursa becomes atrophic. Abundant viral antigen can be detected in the bursal follicles and other peripheral lymphoid organs such as the cecal tonsils and spleen. CD4(+) and CD8(+) T cells accumulate at and near the site of virus replication. The virus-induced bursal T cells are activated, exhibit upregulation of cytokine genes, proliferate in response to in vitro stimulation with IBDV and have suppressive properties. Chickens may die during the acute phase of the disease although IBDV induced mortality is highly variable and depends, among other factors, upon the virulence of the virus strain. Chickens that survive the acute disease clear the virus and recover from its pathologic effects. Bursal follicles are repopulated with IgM(+) B cells. Clinical and subclinical infection with IBDV may cause immunosuppression. Both humoral and cellular immune responses are compromised. Inhibition of the humoral immunity is attributed to the destruction of immunoglobulin-producing cells by the virus. Other mechanisms such as altered antigen-presenting and helper T cell functions may also be involved. Infection with IBDV causes a transient inhibition of the in vitro proliferative response of T cells to mitogens. This inhibition is mediated by macrophages which are activated in virus-exposed chickens and exhibit a marked enhancement of expression of a number of cytokine genes. We speculate that T cell cytokines such as interferon (IFN)-gamma may stimulate macrophages to produce nitric oxide (NO) and other cytokines with anti-proliferative activity. Additional studies are needed to identify the possible direct immunosuppressive effect of IBDV on T cells and their functions. Studies are also needed to examine effects of the virus on innate immunity. Earlier data indicate that the virus did not affect normal natural killer (NK) cell levels in chickens.

In vitro effects of recombinant chicken interferon-gamma on immune cells

We used the recombinant chicken interferon-gamma (ChIFN-gamma) to determine its in vitro effects on chicken immune cells. We found that ChIFN-gamma induced nitric oxide (NO) production, upregulated Ia expression on the cell surface, and inhibited the replication of Newcastle disease virus in NCSU and HD11 cells (chicken macrophage cell lines). In addition, ChIFN-gamma had an antiproliferative effect on RP9 cells, a chicken B cell line. Finally, ChIFN-gamma inhibited mitogenic proliferation of normal chicken spleen cells and induced the cells to generate NO. Inhibition of viral replication and mitogenic proliferation of normal cells were correlated with NO production. We conclude that recombinant chicken ChIFN-gamma modulates chicken immune cells.

Genetic organization, size, and complete sequence of early region 3 genes of human adenovirus type 41

The complete nucleotide and predicted amino acid sequences for open reading frames (ORFs) of the human adenovirus type 41 (Ad41) early region 3 (E3) gene have been determined. The sequence of the Ad41 E3 gene (map units 74 to 83.9) consists of 3,373 nucleotides and has one TATA box and two polyadenylation signals (AATAAA). Analysis of the nucleotide sequence reveals that the E3 gene can encode six ORFs, designated RL1 to RL6. These are all expressed at the mRNA level, as determined by reverse transcription-PCR analysis of AD41-infected cell RNA. When compared with known E3 sequences of most other human adenoviruses deposited in GenBank, the sequences of RL1 to RL3 were found to be unique to subgroup F adenoviruses (Ad40 and Ad41). They encode putative proteins of 173 amino acids (19.4 kDa) and 276 amino acids (31.6 kDa) in one reading frame as well as a 59- amino-acid (6.7 kDa) protein in an overlapping reading frame. RL4 encodes a 90-amino-acid protein (10.1 kDa) with 40% homology to the Ad2 E3 10.4-kDa protein, which induces degradation of the epidermal growth factor receptor and functions together with the Ad2 E3 14.5-kDa protein to protect mouse cell lines against lysis. RL5 encodes a protein of 107 amino acid residues (12.3 kDa) and is analogous to the Ad E3 14.5-kDa protein. RL6 codes for a protein of 122 amino acids (14.7 kDa) that is analogous to the Ad2 14.7-kDa protein, which functions to protect Ad-infected cells from tumor necrosis factor-induced cytolysis. This finding of three unique (RL1 to RL3) E3 gene ORFs may explain why subgroup F adenoviruses differ substantially from other human adenoviruses in their host range; i.e., they replicate predominantly in the host's gastrointestinal rather than respiratory tract. A recent phylogenetic study that compared subgroup F Ad40 DNA sequences with representatives of subgroups B (Ad3), C (Ad2), and E (Ad4) reached a similar conclusion about the uniqueness of RL1 and RL2.

[A liveborn infant with triploidy (69, XXX): report of one case]

Triploidy is not rare and present in about 1% of all recognized human pregnancies, although most of these pregnancies end in spontaneous abortion during the first trimester. Survival of the fetus up to 20 weeks or beyond is rare. Therefore, liveborn infants with triploidy are very rare. Here is a report on a female liveborn infant with triploidy (69,XXX), who was born to a 27-year-old healthy mother. The clinical features are growth retardation, head-to-body disproportion, wide posterior fontanelle, hypertelorism, micrognathia, bilateral pre-auricular polyps, syndactyly of left 3rd and 4th fingers, syndactyly of right 2nd and 3rd fingers and talipes equinovarus. The infant died 4 hours after birth. The autopsy revealed transposition of great vessels, ventricular septal defect, one lobe of left lung and 2 lobes of right lung and duodenal atresia.